diff --git a/configs/aggregator/span.yaml b/configs/aggregator/span.yaml index 5c3ce6af..98e14485 100644 --- a/configs/aggregator/span.yaml +++ b/configs/aggregator/span.yaml @@ -1,4 +1,4 @@ -_target_: prostate_cancer.aggregators.span.SpanAggregator +_target_: ml.aggregators.span.SpanAggregator extent_tile: ??? stride_tile: ??? k: ??? diff --git a/configs/callbacks/aggregator.yaml b/configs/callbacks/aggregator.yaml index fac8a1da..199f526d 100644 --- a/configs/callbacks/aggregator.yaml +++ b/configs/callbacks/aggregator.yaml @@ -1,3 +1,3 @@ aggregator_callback: - _target_: prostate_cancer.callbacks.AggregatorCallback + _target_: ml.callbacks.AggregatorCallback aggregator: ${aggregator} diff --git a/configs/callbacks/aggregator_estimation.yaml b/configs/callbacks/aggregator_estimation.yaml index 422dd49a..7fa01400 100644 --- a/configs/callbacks/aggregator_estimation.yaml +++ b/configs/callbacks/aggregator_estimation.yaml @@ -1,5 +1,5 @@ estimation_callback: - _target_: prostate_cancer.callbacks.EstimationCallback + _target_: ml.callbacks.EstimationCallback aggregator_cls_path: ??? to_estimate: ??? static: ??? diff --git a/configs/callbacks/cam.yaml b/configs/callbacks/cam.yaml index 0d2cb4d0..eeadd5a2 100644 --- a/configs/callbacks/cam.yaml +++ b/configs/callbacks/cam.yaml @@ -1,3 +1,3 @@ cam_callback: - _target_: prostate_cancer.callbacks.CAMExplainer + _target_: ml.callbacks.CAMExplainer resize_shape: [512, 512] diff --git a/configs/callbacks/carcinoma_prediction_table.yaml b/configs/callbacks/carcinoma_prediction_table.yaml index 0a4284a0..bd2483ed 100644 --- a/configs/callbacks/carcinoma_prediction_table.yaml +++ b/configs/callbacks/carcinoma_prediction_table.yaml @@ -1,3 +1,3 @@ carcinoma_table_callback: - _target_: prostate_cancer.callbacks.CarcinomaPredictionTableCallback + _target_: ml.callbacks.CarcinomaPredictionTableCallback threshold: ??? diff --git a/configs/callbacks/curves.yaml b/configs/callbacks/curves.yaml index 7cd9d2dc..501fe0fc 100644 --- a/configs/callbacks/curves.yaml +++ b/configs/callbacks/curves.yaml @@ -1,4 +1,4 @@ curves_callback: - _target_: prostate_cancer.callbacks.CurvesCallbackTile + _target_: ml.callbacks.CurvesCallbackTile threshold: ${tile_threshold} optimal_seek: false diff --git a/configs/callbacks/curves_mil.yaml b/configs/callbacks/curves_mil.yaml index ee55fe20..db0e28f7 100644 --- a/configs/callbacks/curves_mil.yaml +++ b/configs/callbacks/curves_mil.yaml @@ -1,4 +1,4 @@ curves_callback: - _target_: prostate_cancer.callbacks.CurvesCallbackMIL + _target_: ml.callbacks.CurvesCallbackMIL threshold: ${tile_threshold} optimal_seek: false diff --git a/configs/callbacks/curves_sl.yaml b/configs/callbacks/curves_sl.yaml index 4604407f..0b3a47c2 100644 --- a/configs/callbacks/curves_sl.yaml +++ b/configs/callbacks/curves_sl.yaml @@ -1,4 +1,4 @@ curves_callback: - _target_: prostate_cancer.callbacks.CurvesCallbackSL + _target_: ml.callbacks.CurvesCallbackSL threshold: ${slide_threshold} optimal_seek: false diff --git a/configs/callbacks/heatmap.yaml b/configs/callbacks/heatmap.yaml index 9c43ae0f..eac3d106 100644 --- a/configs/callbacks/heatmap.yaml +++ b/configs/callbacks/heatmap.yaml @@ -1,2 +1,2 @@ heatmap_callback: - _target_: prostate_cancer.callbacks.HeatmapCallback + _target_: ml.callbacks.HeatmapCallback diff --git a/configs/callbacks/mil_prediction_callback.yaml b/configs/callbacks/mil_prediction_callback.yaml index 9651a8a1..c3a09dd1 100644 --- a/configs/callbacks/mil_prediction_callback.yaml +++ b/configs/callbacks/mil_prediction_callback.yaml @@ -1,2 +1,2 @@ mil_prediction_callback: - _target_: prostate_cancer.callbacks.MILPredictionCallback \ No newline at end of file + _target_: ml.callbacks.MILPredictionCallback \ No newline at end of file diff --git a/configs/callbacks/multi_aggregator_eval.yaml b/configs/callbacks/multi_aggregator_eval.yaml index 3ea0cf37..12bb9cc0 100644 --- a/configs/callbacks/multi_aggregator_eval.yaml +++ b/configs/callbacks/multi_aggregator_eval.yaml @@ -1,5 +1,5 @@ multi_aggregator_eval_callback: - _target_: prostate_cancer.callbacks.MultiAggregatorEvalCallback + _target_: ml.callbacks.MultiAggregatorEvalCallback max_aggregator: ${max_aggregator} mean_pool_max_aggregator: ${mean_pool_max_aggregator} top_k_aggregator: ${top_k_aggregator} diff --git a/configs/callbacks/nested_metrics.yaml b/configs/callbacks/nested_metrics.yaml index 4e8981d8..2e7ebbec 100644 --- a/configs/callbacks/nested_metrics.yaml +++ b/configs/callbacks/nested_metrics.yaml @@ -1,3 +1,3 @@ nested_metrics_callback: - _target_: prostate_cancer.callbacks.NestedMetricsCallback + _target_: ml.callbacks.NestedMetricsCallback threshold: ${tile_threshold} diff --git a/configs/callbacks/nested_metrics_mil.yaml b/configs/callbacks/nested_metrics_mil.yaml index a340547c..912ac806 100644 --- a/configs/callbacks/nested_metrics_mil.yaml +++ b/configs/callbacks/nested_metrics_mil.yaml @@ -1,3 +1,3 @@ nested_metrics_callback: - _target_: prostate_cancer.callbacks.NestedMetricsCallbackMIL + _target_: ml.callbacks.NestedMetricsCallbackMIL threshold: ${tile_threshold} diff --git a/configs/callbacks/slide_histograms_mil.yaml b/configs/callbacks/slide_histograms_mil.yaml index 6730cd43..a1852bf4 100644 --- a/configs/callbacks/slide_histograms_mil.yaml +++ b/configs/callbacks/slide_histograms_mil.yaml @@ -1,2 +1,2 @@ slide_histograms_callback: - _target_: prostate_cancer.callbacks.SlideHistogramsCallbackMIL + _target_: ml.callbacks.SlideHistogramsCallbackMIL diff --git a/configs/callbacks/tile_histograms.yaml b/configs/callbacks/tile_histograms.yaml index 8f1e765b..dae3ee39 100644 --- a/configs/callbacks/tile_histograms.yaml +++ b/configs/callbacks/tile_histograms.yaml @@ -1,2 +1,2 @@ tile_histograms_callback: - _target_: prostate_cancer.callbacks.TileHistogramsCallbackTile + _target_: ml.callbacks.TileHistogramsCallbackTile diff --git a/configs/callbacks/tile_histograms_mil.yaml b/configs/callbacks/tile_histograms_mil.yaml index 87f8a110..4ab67859 100644 --- a/configs/callbacks/tile_histograms_mil.yaml +++ b/configs/callbacks/tile_histograms_mil.yaml @@ -1,2 +1,2 @@ tile_histograms_callback: - _target_: prostate_cancer.callbacks.TileHistogramsCallbackMIL + _target_: ml.callbacks.TileHistogramsCallbackMIL diff --git a/configs/data/prostate/base.yaml b/configs/data/prostate/base.yaml new file mode 100644 index 00000000..1a600ab0 --- /dev/null +++ b/configs/data/prostate/base.yaml @@ -0,0 +1,6 @@ +# @package _global_ + +carcinoma_artifacts: /mnt/projects/prostate_cancer/cancer + +metadata: + experiment_name: Prostate diff --git a/configs/data/comenius/base.yaml b/configs/data/prostate/comenius/base.yaml similarity index 60% rename from configs/data/comenius/base.yaml rename to configs/data/prostate/comenius/base.yaml index 1a5246e9..bcd04fdc 100644 --- a/configs/data/comenius/base.yaml +++ b/configs/data/prostate/comenius/base.yaml @@ -1,3 +1,7 @@ +defaults: + - /data/prostate/base@_global_ + - _self_ + thresholds: tissue_roi_t: 0.5 residual_t: 0.25 diff --git a/configs/data/comenius/comenius_3_sample.yaml b/configs/data/prostate/comenius/comenius_3_sample.yaml similarity index 100% rename from configs/data/comenius/comenius_3_sample.yaml rename to configs/data/prostate/comenius/comenius_3_sample.yaml diff --git a/configs/data/fn_brno/base.yaml b/configs/data/prostate/fn_brno/base.yaml similarity index 60% rename from configs/data/fn_brno/base.yaml rename to configs/data/prostate/fn_brno/base.yaml index 1a5246e9..bcd04fdc 100644 --- a/configs/data/fn_brno/base.yaml +++ b/configs/data/prostate/fn_brno/base.yaml @@ -1,3 +1,7 @@ +defaults: + - /data/prostate/base@_global_ + - _self_ + thresholds: tissue_roi_t: 0.5 residual_t: 0.25 diff --git a/configs/data/fn_brno/full.yaml b/configs/data/prostate/fn_brno/full.yaml similarity index 100% rename from configs/data/fn_brno/full.yaml rename to configs/data/prostate/fn_brno/full.yaml diff --git a/configs/data/karolinska/base.yaml b/configs/data/prostate/karolinska/base.yaml similarity index 66% rename from configs/data/karolinska/base.yaml rename to configs/data/prostate/karolinska/base.yaml index 3ed49df4..36515759 100644 --- a/configs/data/karolinska/base.yaml +++ b/configs/data/prostate/karolinska/base.yaml @@ -1,3 +1,7 @@ +defaults: + - /data/prostate/base@_global_ + - _self_ + thresholds: tissue_roi_t: 0.5 residual_t: 0.25 diff --git a/configs/data/karolinska/full.yaml b/configs/data/prostate/karolinska/full.yaml similarity index 100% rename from configs/data/karolinska/full.yaml rename to configs/data/prostate/karolinska/full.yaml diff --git a/configs/data/mmci/base.yaml b/configs/data/prostate/mmci/base.yaml similarity index 90% rename from configs/data/mmci/base.yaml rename to configs/data/prostate/mmci/base.yaml index 1f02ade6..8a8361b0 100644 --- a/configs/data/mmci/base.yaml +++ b/configs/data/prostate/mmci/base.yaml @@ -1,5 +1,6 @@ defaults: - stats + - /data/prostate/base@_global_ - _self_ thresholds: diff --git a/configs/data/mmci/endoresection.yaml b/configs/data/prostate/mmci/endoresection.yaml similarity index 100% rename from configs/data/mmci/endoresection.yaml rename to configs/data/prostate/mmci/endoresection.yaml diff --git a/configs/data/mmci/sl.yaml b/configs/data/prostate/mmci/sl.yaml similarity index 100% rename from configs/data/mmci/sl.yaml rename to configs/data/prostate/mmci/sl.yaml diff --git a/configs/data/mmci/sl_group_1.yaml b/configs/data/prostate/mmci/sl_group_1.yaml similarity index 100% rename from configs/data/mmci/sl_group_1.yaml rename to configs/data/prostate/mmci/sl_group_1.yaml diff --git a/configs/data/mmci/sl_group_2.yaml b/configs/data/prostate/mmci/sl_group_2.yaml similarity index 100% rename from configs/data/mmci/sl_group_2.yaml rename to configs/data/prostate/mmci/sl_group_2.yaml diff --git a/configs/data/mmci/stats.yaml b/configs/data/prostate/mmci/stats.yaml similarity index 100% rename from configs/data/mmci/stats.yaml rename to configs/data/prostate/mmci/stats.yaml diff --git a/configs/data/mmci/tl.yaml b/configs/data/prostate/mmci/tl.yaml similarity index 100% rename from configs/data/mmci/tl.yaml rename to configs/data/prostate/mmci/tl.yaml diff --git a/configs/data/mmci/tl_test.yaml b/configs/data/prostate/mmci/tl_test.yaml similarity index 100% rename from configs/data/mmci/tl_test.yaml rename to configs/data/prostate/mmci/tl_test.yaml diff --git a/configs/data/mmci/tl_train.yaml b/configs/data/prostate/mmci/tl_train.yaml similarity index 100% rename from configs/data/mmci/tl_train.yaml rename to configs/data/prostate/mmci/tl_train.yaml diff --git a/configs/data/mmci/tl_val.yaml b/configs/data/prostate/mmci/tl_val.yaml similarity index 100% rename from configs/data/mmci/tl_val.yaml rename to configs/data/prostate/mmci/tl_val.yaml diff --git a/configs/data/mug/base.yaml b/configs/data/prostate/mug/base.yaml similarity index 60% rename from configs/data/mug/base.yaml rename to configs/data/prostate/mug/base.yaml index 1a5246e9..bcd04fdc 100644 --- a/configs/data/mug/base.yaml +++ b/configs/data/prostate/mug/base.yaml @@ -1,3 +1,7 @@ +defaults: + - /data/prostate/base@_global_ + - _self_ + thresholds: tissue_roi_t: 0.5 residual_t: 0.25 diff --git a/configs/data/mug/mug_400.yaml b/configs/data/prostate/mug/mug_400.yaml similarity index 100% rename from configs/data/mug/mug_400.yaml rename to configs/data/prostate/mug/mug_400.yaml diff --git a/configs/data/radboud/base.yaml b/configs/data/prostate/radboud/base.yaml similarity index 94% rename from configs/data/radboud/base.yaml rename to configs/data/prostate/radboud/base.yaml index 67ddf89c..883b49cd 100644 --- a/configs/data/radboud/base.yaml +++ b/configs/data/prostate/radboud/base.yaml @@ -1,5 +1,6 @@ defaults: - stats + - /data/prostate/base@_global_ - _self_ # point to public mlflow diff --git a/configs/data/radboud/base_val.yaml b/configs/data/prostate/radboud/base_val.yaml similarity index 100% rename from configs/data/radboud/base_val.yaml rename to configs/data/prostate/radboud/base_val.yaml diff --git a/configs/data/radboud/full.yaml b/configs/data/prostate/radboud/full.yaml similarity index 100% rename from configs/data/radboud/full.yaml rename to configs/data/prostate/radboud/full.yaml diff --git a/configs/data/radboud/stats.yaml b/configs/data/prostate/radboud/stats.yaml similarity index 100% rename from configs/data/radboud/stats.yaml rename to configs/data/prostate/radboud/stats.yaml diff --git a/configs/data/radboud/test.yaml b/configs/data/prostate/radboud/test.yaml similarity index 100% rename from configs/data/radboud/test.yaml rename to configs/data/prostate/radboud/test.yaml diff --git a/configs/data/radboud/train.yaml b/configs/data/prostate/radboud/train.yaml similarity index 100% rename from configs/data/radboud/train.yaml rename to configs/data/prostate/radboud/train.yaml diff --git a/configs/data/radboud/train_val.yaml b/configs/data/prostate/radboud/train_val.yaml similarity index 100% rename from configs/data/radboud/train_val.yaml rename to configs/data/prostate/radboud/train_val.yaml diff --git a/configs/data/radboud/val.yaml b/configs/data/prostate/radboud/val.yaml similarity index 100% rename from configs/data/radboud/val.yaml rename to configs/data/prostate/radboud/val.yaml diff --git a/configs/data/radboud/val_heuristic_normalized.yaml b/configs/data/prostate/radboud/val_heuristic_normalized.yaml similarity index 100% rename from configs/data/radboud/val_heuristic_normalized.yaml rename to configs/data/prostate/radboud/val_heuristic_normalized.yaml diff --git a/configs/data/radboud/val_ml_normalized.yaml b/configs/data/prostate/radboud/val_ml_normalized.yaml similarity index 100% rename from configs/data/radboud/val_ml_normalized.yaml rename to configs/data/prostate/radboud/val_ml_normalized.yaml diff --git a/configs/datamodule/bag_of_embeddings_datamodule.yaml b/configs/datamodule/bag_of_embeddings_datamodule.yaml index 8dd59464..65ac504d 100644 --- a/configs/datamodule/bag_of_embeddings_datamodule.yaml +++ b/configs/datamodule/bag_of_embeddings_datamodule.yaml @@ -6,7 +6,7 @@ defaults: - samplers@sampler: bag_of_tiles_stratified_weighted_random -_target_: prostate_cancer.datamodule.BagOfTilesDataModule +_target_: ml.datamodule.BagOfTilesDataModule batch_size: ??? num_workers: ??? diff --git a/configs/datamodule/classic_bag_of_embeddings_datamodule.yaml b/configs/datamodule/classic_bag_of_embeddings_datamodule.yaml index 3a23d90c..6cb21156 100644 --- a/configs/datamodule/classic_bag_of_embeddings_datamodule.yaml +++ b/configs/datamodule/classic_bag_of_embeddings_datamodule.yaml @@ -6,7 +6,7 @@ defaults: - samplers@sampler: bag_of_tiles_stratified_weighted_random -_target_: prostate_cancer.datamodule.ClassicBagOfTilesDataModule +_target_: ml.datamodule.ClassicBagOfTilesDataModule batch_size: ??? num_workers: ??? diff --git a/configs/datamodule/datasets/embeddings/bag_of_embeddings_labeled.yaml b/configs/datamodule/datasets/embeddings/bag_of_embeddings_labeled.yaml index b66012d8..1a64ef0d 100644 --- a/configs/datamodule/datasets/embeddings/bag_of_embeddings_labeled.yaml +++ b/configs/datamodule/datasets/embeddings/bag_of_embeddings_labeled.yaml @@ -1,3 +1,3 @@ -_target_: prostate_cancer.datamodule.datasets.LabeledBagOfEmbeddingsDataset +_target_: ml.datamodule.datasets.LabeledBagOfEmbeddingsDataset uris: ??? carcinoma_roi_t: ${carcinoma_roi_t} diff --git a/configs/datamodule/datasets/embeddings/bag_of_embeddings_sl_labeled.yaml b/configs/datamodule/datasets/embeddings/bag_of_embeddings_sl_labeled.yaml index ed8ade57..70727661 100644 --- a/configs/datamodule/datasets/embeddings/bag_of_embeddings_sl_labeled.yaml +++ b/configs/datamodule/datasets/embeddings/bag_of_embeddings_sl_labeled.yaml @@ -1,2 +1,2 @@ -_target_: prostate_cancer.datamodule.datasets.SLLabeledBagOfEmbeddingsDataset +_target_: ml.datamodule.datasets.SLLabeledBagOfEmbeddingsDataset uris: ??? diff --git a/configs/datamodule/datasets/embeddings/bag_of_embeddings_unlabeled.yaml b/configs/datamodule/datasets/embeddings/bag_of_embeddings_unlabeled.yaml index d43e87d9..0c520ea6 100644 --- a/configs/datamodule/datasets/embeddings/bag_of_embeddings_unlabeled.yaml +++ b/configs/datamodule/datasets/embeddings/bag_of_embeddings_unlabeled.yaml @@ -1,2 +1,2 @@ -_target_: prostate_cancer.datamodule.datasets.UnlabeledBagOfEmbeddingsDataset +_target_: ml.datamodule.datasets.UnlabeledBagOfEmbeddingsDataset uris: ??? diff --git a/configs/datamodule/datasets/embeddings/embeddings_labeled.yaml b/configs/datamodule/datasets/embeddings/embeddings_labeled.yaml index 80e6898f..16ed34b2 100644 --- a/configs/datamodule/datasets/embeddings/embeddings_labeled.yaml +++ b/configs/datamodule/datasets/embeddings/embeddings_labeled.yaml @@ -1,4 +1,4 @@ -_target_: prostate_cancer.datamodule.datasets.LabeledEmbeddingsDataset +_target_: ml.datamodule.datasets.LabeledEmbeddingsDataset uris: ??? stratified_filter: ??? carcinoma_roi_t: ${carcinoma_roi_t} diff --git a/configs/datamodule/datasets/embeddings/embeddings_unlabeled.yaml b/configs/datamodule/datasets/embeddings/embeddings_unlabeled.yaml index d4daf517..885f76a7 100644 --- a/configs/datamodule/datasets/embeddings/embeddings_unlabeled.yaml +++ b/configs/datamodule/datasets/embeddings/embeddings_unlabeled.yaml @@ -1,2 +1,2 @@ -_target_: prostate_cancer.datamodule.datasets.UnlabeledEmbeddingsDataset +_target_: ml.datamodule.datasets.UnlabeledEmbeddingsDataset uris: ??? diff --git a/configs/datamodule/datasets/images/labeled.yaml b/configs/datamodule/datasets/images/labeled.yaml index ce8f4854..c51f099a 100644 --- a/configs/datamodule/datasets/images/labeled.yaml +++ b/configs/datamodule/datasets/images/labeled.yaml @@ -1,4 +1,4 @@ -_target_: prostate_cancer.datamodule.datasets.LabeledTilesDataset +_target_: ml.datamodule.datasets.LabeledTilesDataset uris: ??? transforms: ??? carcinoma_roi_t: ${carcinoma_roi_t} diff --git a/configs/datamodule/datasets/images/unlabeled.yaml b/configs/datamodule/datasets/images/unlabeled.yaml index 8278ab13..21a29b73 100644 --- a/configs/datamodule/datasets/images/unlabeled.yaml +++ b/configs/datamodule/datasets/images/unlabeled.yaml @@ -1,3 +1,3 @@ -_target_: prostate_cancer.datamodule.datasets.UnlabeledTilesDataset +_target_: ml.datamodule.datasets.UnlabeledTilesDataset uris: ??? transforms: ??? diff --git a/configs/datamodule/embeddings_datamodule.yaml b/configs/datamodule/embeddings_datamodule.yaml index 3cb01190..0ce3f868 100644 --- a/configs/datamodule/embeddings_datamodule.yaml +++ b/configs/datamodule/embeddings_datamodule.yaml @@ -6,7 +6,7 @@ defaults: - samplers@sampler: tile_stratified_weighted_random -_target_: prostate_cancer.datamodule.TileDataModule +_target_: ml.datamodule.TileDataModule train: stratified_filter: true diff --git a/configs/datamodule/images_datamodule.yaml b/configs/datamodule/images_datamodule.yaml index 5794da3e..9b3c38df 100644 --- a/configs/datamodule/images_datamodule.yaml +++ b/configs/datamodule/images_datamodule.yaml @@ -7,7 +7,7 @@ defaults: - transforms@default_transform: normalize - samplers@sampler: tile_stratified_weighted_random -_target_: prostate_cancer.datamodule.TileDataModule +_target_: ml.datamodule.TileDataModule train: transforms: ??? # specified during the training (stain / non-stain augmentations) diff --git a/configs/datamodule/samplers/bag_of_tiles_stratified_weighted_random.yaml b/configs/datamodule/samplers/bag_of_tiles_stratified_weighted_random.yaml index 0dd20a5d..acd20feb 100644 --- a/configs/datamodule/samplers/bag_of_tiles_stratified_weighted_random.yaml +++ b/configs/datamodule/samplers/bag_of_tiles_stratified_weighted_random.yaml @@ -1,3 +1,3 @@ _partial_: true -_target_: prostate_cancer.datamodule.samplers.BagOfTilesStratifiedWeightedRandomSampler +_target_: ml.datamodule.samplers.BagOfTilesStratifiedWeightedRandomSampler replacement: true \ No newline at end of file diff --git a/configs/datamodule/samplers/tile_stratified_weighted_random.yaml b/configs/datamodule/samplers/tile_stratified_weighted_random.yaml index 13427598..28aa12cf 100644 --- a/configs/datamodule/samplers/tile_stratified_weighted_random.yaml +++ b/configs/datamodule/samplers/tile_stratified_weighted_random.yaml @@ -1,3 +1,3 @@ _partial_: true -_target_: prostate_cancer.datamodule.samplers.TileStratifiedWeightedRandomSampler +_target_: ml.datamodule.samplers.TileStratifiedWeightedRandomSampler replacement: true \ No newline at end of file diff --git a/configs/default.yaml b/configs/default.yaml index 2cfb07a7..5d4d700d 100644 --- a/configs/default.yaml +++ b/configs/default.yaml @@ -4,9 +4,6 @@ defaults: - _self_ -prostate_cancer_artifacts: /mnt/projects/prostate_cancer/cancer - metadata: - experiment_name: Prostate run_name: ??? description: ??? diff --git a/configs/experiment/correction/correct_metadata/mmci_sl_group_1.yaml b/configs/experiment/correction/correct_metadata/mmci_sl_group_1.yaml index 0ac4e917..6de52d1b 100644 --- a/configs/experiment/correction/correct_metadata/mmci_sl_group_1.yaml +++ b/configs/experiment/correction/correct_metadata/mmci_sl_group_1.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ source_of_truth: ${data.metadata_table} diff --git a/configs/experiment/correction/correct_metadata/mmci_sl_group_2.yaml b/configs/experiment/correction/correct_metadata/mmci_sl_group_2.yaml index a769e889..3615a196 100644 --- a/configs/experiment/correction/correct_metadata/mmci_sl_group_2.yaml +++ b/configs/experiment/correction/correct_metadata/mmci_sl_group_2.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl_group_2@data + - /data/prostate/mmci/sl_group_2@data - _self_ source_of_truth: ${data.metadata_table} diff --git a/configs/experiment/correction/correct_tiles/mmci_sl_group_1_224.yaml b/configs/experiment/correction/correct_tiles/mmci_sl_group_1_224.yaml index 29923d11..fa6f746f 100644 --- a/configs/experiment/correction/correct_tiles/mmci_sl_group_1_224.yaml +++ b/configs/experiment/correction/correct_tiles/mmci_sl_group_1_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ source_of_truth: ${data.metadata_table} diff --git a/configs/experiment/correction/correct_tiles/mmci_sl_group_1_512.yaml b/configs/experiment/correction/correct_tiles/mmci_sl_group_1_512.yaml index 32672a27..1ae0f735 100644 --- a/configs/experiment/correction/correct_tiles/mmci_sl_group_1_512.yaml +++ b/configs/experiment/correction/correct_tiles/mmci_sl_group_1_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ source_of_truth: ${data.metadata_table} diff --git a/configs/experiment/correction/correct_tiles/mmci_sl_group_2_224.yaml b/configs/experiment/correction/correct_tiles/mmci_sl_group_2_224.yaml index acac4cf2..8c82d733 100644 --- a/configs/experiment/correction/correct_tiles/mmci_sl_group_2_224.yaml +++ b/configs/experiment/correction/correct_tiles/mmci_sl_group_2_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl_group_2@data + - /data/prostate/mmci/sl_group_2@data - _self_ source_of_truth: ${data.metadata_table} diff --git a/configs/experiment/correction/correct_tiles/mmci_sl_group_2_512.yaml b/configs/experiment/correction/correct_tiles/mmci_sl_group_2_512.yaml index 3e7c181d..e189a2a4 100644 --- a/configs/experiment/correction/correct_tiles/mmci_sl_group_2_512.yaml +++ b/configs/experiment/correction/correct_tiles/mmci_sl_group_2_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl_group_2@data + - /data/prostate/mmci/sl_group_2@data - _self_ source_of_truth: ${data.metadata_table} diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/google_vit.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/google_vit.yaml index fa4e3cae..3678314d 100644 --- a/configs/experiment/postprocessing/eval_estimation/mpm/google_vit.yaml +++ b/configs/experiment/postprocessing/eval_estimation/mpm/google_vit.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/mpm/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/google_vit@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/google_vit@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/google_vit_stain.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/google_vit_stain.yaml index b494804b..2b3effd9 100644 --- a/configs/experiment/postprocessing/eval_estimation/mpm/google_vit_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/mpm/google_vit_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/mpm/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/google_vit_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/google_vit_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/pgp.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/pgp.yaml index 3d4217d7..0d1de758 100644 --- a/configs/experiment/postprocessing/eval_estimation/mpm/pgp.yaml +++ b/configs/experiment/postprocessing/eval_estimation/mpm/pgp.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/mpm/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/pgp@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/pgp@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/pgp_stain.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/pgp_stain.yaml index 18f5507a..2e391f14 100644 --- a/configs/experiment/postprocessing/eval_estimation/mpm/pgp_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/mpm/pgp_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/mpm/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/pgp_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/pgp_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/resnet50.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/resnet50.yaml index 11896171..1ad77ac1 100644 --- a/configs/experiment/postprocessing/eval_estimation/mpm/resnet50.yaml +++ b/configs/experiment/postprocessing/eval_estimation/mpm/resnet50.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/mpm/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/resnet50@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/resnet50@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_224.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_224.yaml index 2f29c2e2..1d10b4d5 100644 --- a/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_224.yaml +++ b/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/mpm/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/resnet50_224@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/resnet50_224@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_stain.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_stain.yaml index df78a0ea..4d135034 100644 --- a/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/mpm/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/resnet50_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/resnet50_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_stain_224.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_stain_224.yaml index ba6195a9..92d95b09 100644 --- a/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_stain_224.yaml +++ b/configs/experiment/postprocessing/eval_estimation/mpm/resnet50_stain_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/mpm/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/resnet50_stain_224@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/vgg16.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/vgg16.yaml index 45b9aecd..b3ec6c0e 100644 --- a/configs/experiment/postprocessing/eval_estimation/mpm/vgg16.yaml +++ b/configs/experiment/postprocessing/eval_estimation/mpm/vgg16.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/mpm/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/vgg16@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/vgg16@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_224.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_224.yaml index 2513d5b3..03cc738a 100644 --- a/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_224.yaml +++ b/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/mpm/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/vgg16_224@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/vgg16_224@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_stain.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_stain.yaml index 390b56d0..774f8f82 100644 --- a/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/mpm/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/vgg16_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/vgg16_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_stain_224.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_stain_224.yaml index 4db31a7b..bfaaeb83 100644 --- a/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_stain_224.yaml +++ b/configs/experiment/postprocessing/eval_estimation/mpm/vgg16_stain_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/mpm/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/vgg16_stain_224@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/virchow2.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/virchow2.yaml index 442811e4..d26c25ee 100644 --- a/configs/experiment/postprocessing/eval_estimation/mpm/virchow2.yaml +++ b/configs/experiment/postprocessing/eval_estimation/mpm/virchow2.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/mpm/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/virchow2@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/virchow2@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/mpm/virchow2_stain.yaml b/configs/experiment/postprocessing/eval_estimation/mpm/virchow2_stain.yaml index e1c27082..fcd72db6 100644 --- a/configs/experiment/postprocessing/eval_estimation/mpm/virchow2_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/mpm/virchow2_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/mpm/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/virchow2_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/virchow2_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/google_vit.yaml b/configs/experiment/postprocessing/eval_estimation/span/google_vit.yaml index 7c04e52d..eb39e93b 100644 --- a/configs/experiment/postprocessing/eval_estimation/span/google_vit.yaml +++ b/configs/experiment/postprocessing/eval_estimation/span/google_vit.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/span/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/google_vit@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/google_vit@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/google_vit_stain.yaml b/configs/experiment/postprocessing/eval_estimation/span/google_vit_stain.yaml index 744752fe..e35cb663 100644 --- a/configs/experiment/postprocessing/eval_estimation/span/google_vit_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/span/google_vit_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/span/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/google_vit_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/google_vit_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/pgp.yaml b/configs/experiment/postprocessing/eval_estimation/span/pgp.yaml index d5c4e945..cf93620d 100644 --- a/configs/experiment/postprocessing/eval_estimation/span/pgp.yaml +++ b/configs/experiment/postprocessing/eval_estimation/span/pgp.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/span/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/pgp@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/pgp@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/pgp_stain.yaml b/configs/experiment/postprocessing/eval_estimation/span/pgp_stain.yaml index 89635dee..4f29c648 100644 --- a/configs/experiment/postprocessing/eval_estimation/span/pgp_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/span/pgp_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/span/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/pgp_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/pgp_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/resnet50.yaml b/configs/experiment/postprocessing/eval_estimation/span/resnet50.yaml index fcd2a60f..7bc14d58 100644 --- a/configs/experiment/postprocessing/eval_estimation/span/resnet50.yaml +++ b/configs/experiment/postprocessing/eval_estimation/span/resnet50.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/span/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/resnet50@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/resnet50@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/resnet50_224.yaml b/configs/experiment/postprocessing/eval_estimation/span/resnet50_224.yaml index 473915aa..9de586c0 100644 --- a/configs/experiment/postprocessing/eval_estimation/span/resnet50_224.yaml +++ b/configs/experiment/postprocessing/eval_estimation/span/resnet50_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/span/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/resnet50_224@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/resnet50_224@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/resnet50_stain.yaml b/configs/experiment/postprocessing/eval_estimation/span/resnet50_stain.yaml index 6b933863..dc861046 100644 --- a/configs/experiment/postprocessing/eval_estimation/span/resnet50_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/span/resnet50_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/span/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/resnet50_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/resnet50_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/resnet50_stain_224.yaml b/configs/experiment/postprocessing/eval_estimation/span/resnet50_stain_224.yaml index 8b4fc22d..1a156785 100644 --- a/configs/experiment/postprocessing/eval_estimation/span/resnet50_stain_224.yaml +++ b/configs/experiment/postprocessing/eval_estimation/span/resnet50_stain_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/span/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/resnet50_stain_224@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/vgg16.yaml b/configs/experiment/postprocessing/eval_estimation/span/vgg16.yaml index a26c1349..a1880c8c 100644 --- a/configs/experiment/postprocessing/eval_estimation/span/vgg16.yaml +++ b/configs/experiment/postprocessing/eval_estimation/span/vgg16.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/span/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/vgg16@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/vgg16@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/vgg16_224.yaml b/configs/experiment/postprocessing/eval_estimation/span/vgg16_224.yaml index 904d2a9a..623c38f7 100644 --- a/configs/experiment/postprocessing/eval_estimation/span/vgg16_224.yaml +++ b/configs/experiment/postprocessing/eval_estimation/span/vgg16_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/span/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/vgg16_224@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/vgg16_224@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/vgg16_stain.yaml b/configs/experiment/postprocessing/eval_estimation/span/vgg16_stain.yaml index bce8a591..4db74d5c 100644 --- a/configs/experiment/postprocessing/eval_estimation/span/vgg16_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/span/vgg16_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/span/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/vgg16_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/vgg16_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/vgg16_stain_224.yaml b/configs/experiment/postprocessing/eval_estimation/span/vgg16_stain_224.yaml index e4d00a26..e98b6e0a 100644 --- a/configs/experiment/postprocessing/eval_estimation/span/vgg16_stain_224.yaml +++ b/configs/experiment/postprocessing/eval_estimation/span/vgg16_stain_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/span/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/vgg16_stain_224@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/virchow2.yaml b/configs/experiment/postprocessing/eval_estimation/span/virchow2.yaml index e08686f7..62ed5bfc 100644 --- a/configs/experiment/postprocessing/eval_estimation/span/virchow2.yaml +++ b/configs/experiment/postprocessing/eval_estimation/span/virchow2.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/span/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/virchow2@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/virchow2@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/span/virchow2_stain.yaml b/configs/experiment/postprocessing/eval_estimation/span/virchow2_stain.yaml index a53a403e..1c57e65b 100644 --- a/configs/experiment/postprocessing/eval_estimation/span/virchow2_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/span/virchow2_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/span/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/virchow2_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/virchow2_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/google_vit.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/google_vit.yaml index 3100b65d..858de6ca 100644 --- a/configs/experiment/postprocessing/eval_estimation/top_k/google_vit.yaml +++ b/configs/experiment/postprocessing/eval_estimation/top_k/google_vit.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/top_k/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/google_vit@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/google_vit@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/google_vit_stain.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/google_vit_stain.yaml index 13018fdc..7314a053 100644 --- a/configs/experiment/postprocessing/eval_estimation/top_k/google_vit_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/top_k/google_vit_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/top_k/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/google_vit_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/google_vit_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/pgp.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/pgp.yaml index ca2dd641..86919b28 100644 --- a/configs/experiment/postprocessing/eval_estimation/top_k/pgp.yaml +++ b/configs/experiment/postprocessing/eval_estimation/top_k/pgp.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/top_k/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/pgp@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/pgp@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/pgp_stain.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/pgp_stain.yaml index de61b65f..362537d6 100644 --- a/configs/experiment/postprocessing/eval_estimation/top_k/pgp_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/top_k/pgp_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/top_k/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/pgp_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/pgp_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/resnet50.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/resnet50.yaml index 52525871..c64c5677 100644 --- a/configs/experiment/postprocessing/eval_estimation/top_k/resnet50.yaml +++ b/configs/experiment/postprocessing/eval_estimation/top_k/resnet50.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/top_k/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/resnet50@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/resnet50@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_224.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_224.yaml index 8386fc40..e3c52edf 100644 --- a/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_224.yaml +++ b/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/top_k/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/resnet50_224@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/resnet50_224@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_stain.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_stain.yaml index 6f5ea73b..44dfd8b1 100644 --- a/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/top_k/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/resnet50_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/resnet50_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_stain_224.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_stain_224.yaml index bd540de0..beaac3d0 100644 --- a/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_stain_224.yaml +++ b/configs/experiment/postprocessing/eval_estimation/top_k/resnet50_stain_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/top_k/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/resnet50_stain_224@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/vgg16.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/vgg16.yaml index 68d302ef..edab2c0b 100644 --- a/configs/experiment/postprocessing/eval_estimation/top_k/vgg16.yaml +++ b/configs/experiment/postprocessing/eval_estimation/top_k/vgg16.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/top_k/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/vgg16@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/vgg16@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_224.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_224.yaml index a02c4080..c8d0ca3d 100644 --- a/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_224.yaml +++ b/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/top_k/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/vgg16_224@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/vgg16_224@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_stain.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_stain.yaml index 700921ba..9b834e4d 100644 --- a/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/top_k/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/vgg16_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/vgg16_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_stain_224.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_stain_224.yaml index f8c4e5f8..84bfeaf6 100644 --- a/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_stain_224.yaml +++ b/configs/experiment/postprocessing/eval_estimation/top_k/vgg16_stain_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/top_k/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/vgg16_stain_224@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/virchow2.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/virchow2.yaml index 091d2260..052c6865 100644 --- a/configs/experiment/postprocessing/eval_estimation/top_k/virchow2.yaml +++ b/configs/experiment/postprocessing/eval_estimation/top_k/virchow2.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/top_k/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/virchow2@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/virchow2@model_data - _self_ diff --git a/configs/experiment/postprocessing/eval_estimation/top_k/virchow2_stain.yaml b/configs/experiment/postprocessing/eval_estimation/top_k/virchow2_stain.yaml index b98c0794..5179eb35 100644 --- a/configs/experiment/postprocessing/eval_estimation/top_k/virchow2_stain.yaml +++ b/configs/experiment/postprocessing/eval_estimation/top_k/virchow2_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/eval_estimation/top_k/base - - /data/mmci/sl_group_1@data - - /model/checkpoints/mmci_tl/virchow2_stain@model_data + - /data/prostate/mmci/sl_group_1@data + - /model/checkpoints/prostate/virchow2_stain@model_data - _self_ diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/base.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/base.yaml index ebc6c878..6f004bed 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/base.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/base - - /model/checkpoints/mmci_tl/google_vit@model_data + - /model/checkpoints/prostate/google_vit@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/base_stain.yaml index ae575de2..bf54cd18 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/base_stain.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/base - - /model/checkpoints/mmci_tl/google_vit_stain@model_data + - /model/checkpoints/prostate/google_vit_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/mmci_sl_group_1.yaml index ffeb81d4..b160e14f 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/stain_mmci_sl_group_1.yaml index aa034ce5..adcf1b0c 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/google_vit/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/base.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/base.yaml index 61e47a08..7e5a4b5b 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/base.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/base - - /model/checkpoints/mmci_tl/pgp@model_data + - /model/checkpoints/prostate/pgp@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/base_stain.yaml index e7204676..db430cde 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/base_stain.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/base - - /model/checkpoints/mmci_tl/pgp_stain@model_data + - /model/checkpoints/prostate/pgp_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/mmci_sl_group_1.yaml index 25971221..e3e657eb 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/pgp/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/stain_mmci_sl_group_1.yaml index c1d7d116..cdcad274 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/pgp/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/pgp/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} \ No newline at end of file diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base.yaml index 4d7ea04f..5d35514c 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/base - - /model/checkpoints/mmci_tl/resnet50@model_data + - /model/checkpoints/prostate/resnet50@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_224.yaml index 8ac87a27..9d43824c 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_224.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/base - - /model/checkpoints/mmci_tl/resnet50_224@model_data + - /model/checkpoints/prostate/resnet50_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_stain.yaml index cdd10a22..721f4d89 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_stain.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/base - - /model/checkpoints/mmci_tl/resnet50_stain@model_data + - /model/checkpoints/prostate/resnet50_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_stain_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_stain_224.yaml index e54c70e1..ab8b5c05 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_stain_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_stain_224.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/base - - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data + - /model/checkpoints/prostate/resnet50_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/mmci_sl_group_1.yaml index bec14e15..9e242f54 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/mmci_sl_group_1_224.yaml index de9a5f39..717c2526 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/mmci_sl_group_1_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/mmci_sl_group_1_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_224 - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/stain_mmci_sl_group_1.yaml index d95f2465..07a8fb2b 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml index b6081695..f49a5349 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/resnet50/base_stain_224 - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base.yaml index b12187c1..c18bb53f 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/base - - /model/checkpoints/mmci_tl/vgg16@model_data + - /model/checkpoints/prostate/vgg16@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_224.yaml index 3b571bda..ce3b9c90 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_224.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/base - - /model/checkpoints/mmci_tl/vgg16_224@model_data + - /model/checkpoints/prostate/vgg16_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_stain.yaml index 4c25674d..2bbca311 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_stain.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/base - - /model/checkpoints/mmci_tl/vgg16_stain@model_data + - /model/checkpoints/prostate/vgg16_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_stain_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_stain_224.yaml index c460f2c8..b987e702 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_stain_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_stain_224.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/base - - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data + - /model/checkpoints/prostate/vgg16_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/mmci_sl_group_1.yaml index f2d15c3b..64a58032 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/mmci_sl_group_1_224.yaml index 850a4f58..7735fdc0 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/mmci_sl_group_1_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/mmci_sl_group_1_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_224 - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/stain_mmci_sl_group_1.yaml index 51a67c1f..c19faa23 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml index 9f1aede5..5343798c 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/vgg16/base_stain_224 - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/base.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/base.yaml index 1bd529fe..15f329c1 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/base.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/base - - /model/checkpoints/mmci_tl/virchow2@model_data + - /model/checkpoints/prostate/virchow2@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/base_stain.yaml index bec85f2e..1e70b7d2 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/base_stain.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/base - - /model/checkpoints/mmci_tl/virchow2_stain@model_data + - /model/checkpoints/prostate/virchow2_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/mmci_sl_group_1.yaml index 4c5b18e7..6e174acf 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/stain_mmci_sl_group_1.yaml index cf0f0721..0814d35f 100644 --- a/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/max_aggregations/virchow2/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/base.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/base.yaml index d145c1d1..b8463b7c 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/google_vit@model_data + - /model/checkpoints/prostate/google_vit@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/base_stain.yaml index 92f1f21f..55e2fdd9 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/base_stain.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/google_vit_stain@model_data + - /model/checkpoints/prostate/google_vit_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/mmci_sl_group_1.yaml index 30a05142..28e97e69 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/stain_mmci_sl_group_1.yaml index dcbce075..8200690f 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/google_vit/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/base.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/base.yaml index 7c45f58c..39592981 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/pgp@model_data + - /model/checkpoints/prostate/pgp@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/base_stain.yaml index c2e341ee..03c250f3 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/base_stain.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/pgp_stain@model_data + - /model/checkpoints/prostate/pgp_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/mmci_sl_group_1.yaml index 6beefe97..064dcee1 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/stain_mmci_sl_group_1.yaml index dcc9b88e..131e718d 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/pgp/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base.yaml index d9845314..c926c626 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/resnet50@model_data + - /model/checkpoints/prostate/resnet50@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_224.yaml index d388eac1..46034236 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_224.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/resnet50_224@model_data + - /model/checkpoints/prostate/resnet50_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_stain.yaml index 88025f74..6f6e1497 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_stain.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/resnet50_stain@model_data + - /model/checkpoints/prostate/resnet50_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_stain_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_stain_224.yaml index d9d95385..5a369a09 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_stain_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_stain_224.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data + - /model/checkpoints/prostate/resnet50_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/mmci_sl_group_1.yaml index 9c769bcf..f383dbfa 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/mmci_sl_group_1_224.yaml index 89996763..02bd058c 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/mmci_sl_group_1_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/mmci_sl_group_1_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_224 - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/stain_mmci_sl_group_1.yaml index 7b7bcb33..660d007b 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml index b405fece..a98ab59f 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/resnet50/base_stain_224 - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base.yaml index 558fb3ca..2c7ba7db 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/vgg16@model_data + - /model/checkpoints/prostate/vgg16@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_224.yaml index dabfe82f..09be2d07 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_224.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/vgg16_224@model_data + - /model/checkpoints/prostate/vgg16_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_stain.yaml index 77b72c87..9b95adff 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_stain.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/vgg16_stain@model_data + - /model/checkpoints/prostate/vgg16_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_stain_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_stain_224.yaml index fe5e2fa9..9927a97a 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_stain_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_stain_224.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data + - /model/checkpoints/prostate/vgg16_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/mmci_sl_group_1.yaml index 7ef811eb..0b0e6485 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/mmci_sl_group_1_224.yaml index 3959a107..d9f7227d 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/mmci_sl_group_1_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/mmci_sl_group_1_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_224 - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/stain_mmci_sl_group_1.yaml index fc0ae87a..30e492c0 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml index 1c9e7e1f..de1295e3 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/vgg16/base_stain_224 - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/base.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/base.yaml index 8bc3386a..8cdc050d 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/virchow2@model_data + - /model/checkpoints/prostate/virchow2@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/base_stain.yaml index b454e354..cc3a557a 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/base_stain.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/virchow2_stain@model_data + - /model/checkpoints/prostate/virchow2_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/mmci_sl_group_1.yaml index c7f2b47f..3e0d06a6 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/stain_mmci_sl_group_1.yaml index 4a0f4577..315835a7 100644 --- a/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/mean_pool_max_aggregations/virchow2/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/base.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/base.yaml index d145c1d1..b8463b7c 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/google_vit@model_data + - /model/checkpoints/prostate/google_vit@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/base_stain.yaml index 92f1f21f..55e2fdd9 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/base_stain.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/google_vit_stain@model_data + - /model/checkpoints/prostate/google_vit_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/mmci_sl_group_1.yaml index 9c2fdbe1..0f52b884 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/stain_mmci_sl_group_1.yaml index d7f0f974..6945fcd6 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/top_k_aggregations/google_vit/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/base.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/base.yaml index 7c45f58c..39592981 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/pgp@model_data + - /model/checkpoints/prostate/pgp@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/base_stain.yaml index c2e341ee..03c250f3 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/base_stain.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/pgp_stain@model_data + - /model/checkpoints/prostate/pgp_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/mmci_sl_group_1.yaml index b8ae4f2b..d707b377 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/stain_mmci_sl_group_1.yaml index 628cc0a0..311ce3ec 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/top_k_aggregations/pgp/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base.yaml index d9845314..c926c626 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/resnet50@model_data + - /model/checkpoints/prostate/resnet50@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_224.yaml index d388eac1..46034236 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_224.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/resnet50_224@model_data + - /model/checkpoints/prostate/resnet50_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_stain.yaml index 88025f74..6f6e1497 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_stain.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/resnet50_stain@model_data + - /model/checkpoints/prostate/resnet50_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_stain_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_stain_224.yaml index d9d95385..5a369a09 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_stain_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_stain_224.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data + - /model/checkpoints/prostate/resnet50_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/mmci_sl_group_1.yaml index 6efb1aee..3e087abe 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/mmci_sl_group_1_224.yaml index 4450314f..976fedbf 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/mmci_sl_group_1_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/mmci_sl_group_1_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_224 - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/stain_mmci_sl_group_1.yaml index 39fc5b26..e1387d41 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml index 0519fb41..aadadc87 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/stain_mmci_sl_group_1_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/top_k_aggregations/resnet50/base_stain_224 - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base.yaml index 558fb3ca..2c7ba7db 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/vgg16@model_data + - /model/checkpoints/prostate/vgg16@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_224.yaml index dabfe82f..09be2d07 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_224.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/vgg16_224@model_data + - /model/checkpoints/prostate/vgg16_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_stain.yaml index 77b72c87..9b95adff 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_stain.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/vgg16_stain@model_data + - /model/checkpoints/prostate/vgg16_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_stain_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_stain_224.yaml index fe5e2fa9..9927a97a 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_stain_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_stain_224.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data + - /model/checkpoints/prostate/vgg16_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/mmci_sl_group_1.yaml index dc61d3ff..4faa7478 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/mmci_sl_group_1_224.yaml index 71f48a99..ae81f4bd 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/mmci_sl_group_1_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/mmci_sl_group_1_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_224 - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/stain_mmci_sl_group_1.yaml index 612a59fc..60dd423b 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml index 472be9d3..cb502ef9 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/stain_mmci_sl_group_1_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/top_k_aggregations/vgg16/base_stain_224 - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/base.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/base.yaml index 8bc3386a..8cdc050d 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/base.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/virchow2@model_data + - /model/checkpoints/prostate/virchow2@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/base_stain.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/base_stain.yaml index b454e354..cc3a557a 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/base_stain.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/virchow2_stain@model_data + - /model/checkpoints/prostate/virchow2_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/mmci_sl_group_1.yaml index 544c6f9a..5ca5b1e4 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/stain_mmci_sl_group_1.yaml index e2e6e918..97f611c7 100644 --- a/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_level_curves/top_k_aggregations/virchow2/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/google_vit/base.yaml b/configs/experiment/postprocessing/slide_level_eval/google_vit/base.yaml index d145c1d1..b8463b7c 100644 --- a/configs/experiment/postprocessing/slide_level_eval/google_vit/base.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/google_vit/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/google_vit@model_data + - /model/checkpoints/prostate/google_vit@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/google_vit/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/google_vit/max_aggregations/mmci_sl_group_1.yaml index d67004e6..c55a50de 100644 --- a/configs/experiment/postprocessing/slide_level_eval/google_vit/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/google_vit/max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/google_vit/max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/google_vit/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/google_vit/max_aggregations/mmci_tl_test.yaml index 31371868..c3807d61 100644 --- a/configs/experiment/postprocessing/slide_level_eval/google_vit/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/google_vit/max_aggregations/mmci_tl_test.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/google_vit/max_aggregations/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data preds_uri: "mlflow-artifacts:/65/c5ff83e1fcf8496fb2cf9381c62123a8/artifacts/tables/aggregated_predictions.json" diff --git a/configs/experiment/postprocessing/slide_level_eval/google_vit/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/google_vit/mean_pool_max_aggregations/mmci_sl_group_1.yaml index 664bf7a7..7cab2a63 100644 --- a/configs/experiment/postprocessing/slide_level_eval/google_vit/mean_pool_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/google_vit/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/google_vit/mean_pool_max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/google_vit/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/google_vit/span_aggregations/mmci_sl_group_1.yaml index 3f314eca..be134ee7 100644 --- a/configs/experiment/postprocessing/slide_level_eval/google_vit/span_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/google_vit/span_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/google_vit/span_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/google_vit/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/google_vit/top_k_aggregations/mmci_sl_group_1.yaml index 7cb46dec..d0c393cc 100644 --- a/configs/experiment/postprocessing/slide_level_eval/google_vit/top_k_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/google_vit/top_k_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/google_vit/top_k_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/base.yaml b/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/base.yaml index 92f1f21f..55e2fdd9 100644 --- a/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/base.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/google_vit_stain@model_data + - /model/checkpoints/prostate/google_vit_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/max_aggregations/mmci_sl_group_1.yaml index 3258c8c5..5813a883 100644 --- a/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/google_vit_stain/max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/max_aggregations/mmci_tl_test.yaml index 7a8883f6..3551a0ff 100644 --- a/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/max_aggregations/mmci_tl_test.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/google_vit_stain/max_aggregations/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data preds_uri: "mlflow-artifacts:/65/03bee8e193094f40a0c7dc859900f5e2/artifacts/tables/aggregated_predictions.json" diff --git a/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml index 5853a692..e1571a5a 100644 --- a/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/google_vit_stain/mean_pool_max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/span_aggregations/mmci_sl_group_1.yaml index b48aa7f8..6a93596f 100644 --- a/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/span_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/span_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/google_vit_stain/span_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/top_k_aggregations/mmci_sl_group_1.yaml index 1f9227e2..21b8cb37 100644 --- a/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/top_k_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/google_vit_stain/top_k_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/google_vit_stain/top_k_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/pgp/base.yaml b/configs/experiment/postprocessing/slide_level_eval/pgp/base.yaml index 7c45f58c..39592981 100644 --- a/configs/experiment/postprocessing/slide_level_eval/pgp/base.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/pgp/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/pgp@model_data + - /model/checkpoints/prostate/pgp@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/pgp/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/pgp/max_aggregations/mmci_sl_group_1.yaml index 41348649..53e1b0a9 100644 --- a/configs/experiment/postprocessing/slide_level_eval/pgp/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/pgp/max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/pgp/max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/pgp/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/pgp/max_aggregations/mmci_tl_test.yaml index 60dd5fff..2fb12440 100644 --- a/configs/experiment/postprocessing/slide_level_eval/pgp/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/pgp/max_aggregations/mmci_tl_test.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/pgp/max_aggregations/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data preds_uri: "mlflow-artifacts:/65/001dd3914dc04fa48f9eb98784709c4d/artifacts/tables/aggregated_predictions.json" diff --git a/configs/experiment/postprocessing/slide_level_eval/pgp/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/pgp/mean_pool_max_aggregations/mmci_sl_group_1.yaml index f18d1183..f160eb50 100644 --- a/configs/experiment/postprocessing/slide_level_eval/pgp/mean_pool_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/pgp/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/pgp/mean_pool_max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/pgp/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/pgp/span_aggregations/mmci_sl_group_1.yaml index a3ce167a..f86281b5 100644 --- a/configs/experiment/postprocessing/slide_level_eval/pgp/span_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/pgp/span_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/pgp/span_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/pgp/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/pgp/top_k_aggregations/mmci_sl_group_1.yaml index 15d67b74..814529e5 100644 --- a/configs/experiment/postprocessing/slide_level_eval/pgp/top_k_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/pgp/top_k_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/pgp/top_k_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/pgp_stain/base.yaml b/configs/experiment/postprocessing/slide_level_eval/pgp_stain/base.yaml index c2e341ee..03c250f3 100644 --- a/configs/experiment/postprocessing/slide_level_eval/pgp_stain/base.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/pgp_stain/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/pgp_stain@model_data + - /model/checkpoints/prostate/pgp_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/pgp_stain/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/pgp_stain/max_aggregations/mmci_sl_group_1.yaml index 8fbef951..7c3b4d7b 100644 --- a/configs/experiment/postprocessing/slide_level_eval/pgp_stain/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/pgp_stain/max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/pgp_stain/max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/pgp_stain/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/pgp_stain/max_aggregations/mmci_tl_test.yaml index cdc7843e..f809f9b0 100644 --- a/configs/experiment/postprocessing/slide_level_eval/pgp_stain/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/pgp_stain/max_aggregations/mmci_tl_test.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/pgp_stain/max_aggregations/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data preds_uri: "mlflow-artifacts:/65/fd46c62186c44f599d6021bb7e394b23/artifacts/tables/aggregated_predictions.json" diff --git a/configs/experiment/postprocessing/slide_level_eval/pgp_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/pgp_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml index 7da43f6a..5d5d4684 100644 --- a/configs/experiment/postprocessing/slide_level_eval/pgp_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/pgp_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/pgp_stain/mean_pool_max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/pgp_stain/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/pgp_stain/span_aggregations/mmci_sl_group_1.yaml index 0bcda981..e6a93d09 100644 --- a/configs/experiment/postprocessing/slide_level_eval/pgp_stain/span_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/pgp_stain/span_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/pgp_stain/span_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/pgp_stain/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/pgp_stain/top_k_aggregations/mmci_sl_group_1.yaml index 9efd12ec..cce70a7a 100644 --- a/configs/experiment/postprocessing/slide_level_eval/pgp_stain/top_k_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/pgp_stain/top_k_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/pgp_stain/top_k_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50/base.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50/base.yaml index d9845314..c926c626 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50/base.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/resnet50@model_data + - /model/checkpoints/prostate/resnet50@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50/max_aggregations/mmci_sl_group_1.yaml index b0032c3e..f401465c 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50/max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50/max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50/max_aggregations/mmci_tl_test.yaml index 8bd584b9..86437f82 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50/max_aggregations/mmci_tl_test.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50/max_aggregations/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data preds_uri: "mlflow-artifacts:/65/1edeef1da08745a8b8f754f17810f61c/artifacts/tables/aggregated_predictions.json" diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50/mean_pool_max_aggregations/mmci_sl_group_1.yaml index ec832b66..eb61c6bb 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50/mean_pool_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50/mean_pool_max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50/span_aggregations/mmci_sl_group_1.yaml index bf1ff9aa..79cfd398 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50/span_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50/span_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50/span_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50/top_k_aggregations/mmci_sl_group_1.yaml index bf05e0f8..7aa03848 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50/top_k_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50/top_k_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50/top_k_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/base.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/base.yaml index d388eac1..46034236 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/base.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/resnet50_224@model_data + - /model/checkpoints/prostate/resnet50_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/mmci_sl_group_1.yaml index 07285114..3c93f33d 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/mmci_tl_test.yaml index 84c33573..22bf2b65 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/mmci_tl_test.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_224/max_aggregations/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data preds_uri: null diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml index 36f5c1cf..c7185636 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_224/mean_pool_max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/span_aggregations/mmci_sl_group_1.yaml index d337beba..c890ba70 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/span_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/span_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_224/span_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/top_k_aggregations/mmci_sl_group_1.yaml index b36ad3bc..2006327d 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_224/top_k_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_224/top_k_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_224/top_k_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/base.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/base.yaml index 88025f74..6f6e1497 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/base.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/resnet50_stain@model_data + - /model/checkpoints/prostate/resnet50_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/max_aggregations/mmci_sl_group_1.yaml index 89de3e0a..c8882ec7 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_stain/max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/max_aggregations/mmci_tl_test.yaml index 6ad59337..7f94170e 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/max_aggregations/mmci_tl_test.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_stain/max_aggregations/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data preds_uri: "mlflow-artifacts:/65/d37931f5a1b943c6888d2b61202df549/artifacts/tables/aggregated_predictions.json" diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml index 2a404392..302eab52 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_stain/mean_pool_max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/span_aggregations/mmci_sl_group_1.yaml index 13adef54..09d1fa70 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/span_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/span_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_stain/span_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/top_k_aggregations/mmci_sl_group_1.yaml index 7e24d355..105ad9d2 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/top_k_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain/top_k_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_stain/top_k_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/base.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/base.yaml index d9d95385..5a369a09 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/base.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data + - /model/checkpoints/prostate/resnet50_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/mmci_sl_group_1.yaml index 050de748..3cf605c0 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/mmci_tl_test.yaml index 13dbd0db..338a4654 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/mmci_tl_test.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_stain_224/max_aggregations/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data preds_uri: null diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml index a2008124..b57167b2 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_stain_224/mean_pool_max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/span_aggregations/mmci_sl_group_1.yaml index b923102d..ba6dc532 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/span_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/span_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_stain_224/span_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/top_k_aggregations/mmci_sl_group_1.yaml index 37ce1b31..b0bc58f6 100644 --- a/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/top_k_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/resnet50_stain_224/top_k_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/resnet50_stain_224/top_k_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16/base.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16/base.yaml index 558fb3ca..2c7ba7db 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16/base.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/vgg16@model_data + - /model/checkpoints/prostate/vgg16@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16/max_aggregations/mmci_sl_group_1.yaml index e58c2f17..544def69 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16/max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16/max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16/max_aggregations/mmci_tl_test.yaml index a1a8271b..1dde314d 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16/max_aggregations/mmci_tl_test.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16/max_aggregations/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data preds_uri: "mlflow-artifacts:/65/cd257b7683094f0fa2ab3e03c7639e79/artifacts/tables/aggregated_predictions.json" diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16/mean_pool_max_aggregations/mmci_sl_group_1.yaml index 9b3fc305..9955e249 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16/mean_pool_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16/mean_pool_max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16/span_aggregations/mmci_sl_group_1.yaml index b4f5f93c..6afb8620 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16/span_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16/span_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16/span_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16/top_k_aggregations/mmci_sl_group_1.yaml index 3c98eed9..6b0fe74a 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16/top_k_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16/top_k_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16/top_k_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/base.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/base.yaml index dabfe82f..09be2d07 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/base.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/vgg16_224@model_data + - /model/checkpoints/prostate/vgg16_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/mmci_sl_group_1.yaml index b7152834..c311c8c8 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/mmci_tl_test.yaml index 827208a6..8e189035 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/mmci_tl_test.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_224/max_aggregations/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data preds_uri: null diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml index 4dc48cbf..13445811 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_224/mean_pool_max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/span_aggregations/mmci_sl_group_1.yaml index a7d6ab62..37ba727c 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/span_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/span_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_224/span_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/top_k_aggregations/mmci_sl_group_1.yaml index c0a75c58..ddce03b6 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_224/top_k_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_224/top_k_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_224/top_k_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/base.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/base.yaml index 77b72c87..9b95adff 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/base.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/vgg16_stain@model_data + - /model/checkpoints/prostate/vgg16_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/max_aggregations/mmci_sl_group_1.yaml index d03d11e3..3385f6ca 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_stain/max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/max_aggregations/mmci_tl_test.yaml index 9838f3a5..f2b08318 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/max_aggregations/mmci_tl_test.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_stain/max_aggregations/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data preds_uri: "mlflow-artifacts:/65/50bb0b6a6f234b149ad04ef82a24e45c/artifacts/tables/aggregated_predictions.json" diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml index 6374af50..cda036f7 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_stain/mean_pool_max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/span_aggregations/mmci_sl_group_1.yaml index da0a94b4..a44d8985 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/span_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/span_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_stain/span_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/top_k_aggregations/mmci_sl_group_1.yaml index 547d0fc0..e05b0e26 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/top_k_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain/top_k_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_stain/top_k_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/base.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/base.yaml index fe5e2fa9..9927a97a 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/base.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data + - /model/checkpoints/prostate/vgg16_stain_224@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/mmci_sl_group_1.yaml index 68507789..c20a7cb4 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/mmci_tl_test.yaml index ea6f6f28..d3a8e8de 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/mmci_tl_test.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_stain_224/max_aggregations/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data preds_uri: null diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml index 0ab876d8..d5a3ab6c 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_stain_224/mean_pool_max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/span_aggregations/mmci_sl_group_1.yaml index 58b0e796..9d0e8bab 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/span_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/span_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_stain_224/span_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/top_k_aggregations/mmci_sl_group_1.yaml index 4b22c9b2..c1a1e8e6 100644 --- a/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/top_k_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/vgg16_stain_224/top_k_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/vgg16_stain_224/top_k_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/virchow2/base.yaml b/configs/experiment/postprocessing/slide_level_eval/virchow2/base.yaml index 8bc3386a..8cdc050d 100644 --- a/configs/experiment/postprocessing/slide_level_eval/virchow2/base.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/virchow2/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/virchow2@model_data + - /model/checkpoints/prostate/virchow2@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/virchow2/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/virchow2/max_aggregations/mmci_sl_group_1.yaml index 44414643..187388ae 100644 --- a/configs/experiment/postprocessing/slide_level_eval/virchow2/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/virchow2/max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/virchow2/max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/virchow2/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/virchow2/max_aggregations/mmci_tl_test.yaml index 6aee044e..f236f8c4 100644 --- a/configs/experiment/postprocessing/slide_level_eval/virchow2/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/virchow2/max_aggregations/mmci_tl_test.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/virchow2/max_aggregations/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data preds_uri: "mlflow-artifacts:/65/9f48b149031743529ba456c236e4aee5/artifacts/tables/aggregated_predictions.json" diff --git a/configs/experiment/postprocessing/slide_level_eval/virchow2/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/virchow2/mean_pool_max_aggregations/mmci_sl_group_1.yaml index 710036b0..d55a63d7 100644 --- a/configs/experiment/postprocessing/slide_level_eval/virchow2/mean_pool_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/virchow2/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/virchow2/mean_pool_max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/virchow2/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/virchow2/span_aggregations/mmci_sl_group_1.yaml index ef9b6878..62698fd8 100644 --- a/configs/experiment/postprocessing/slide_level_eval/virchow2/span_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/virchow2/span_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/virchow2/span_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/virchow2/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/virchow2/top_k_aggregations/mmci_sl_group_1.yaml index 9191e55a..e2812669 100644 --- a/configs/experiment/postprocessing/slide_level_eval/virchow2/top_k_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/virchow2/top_k_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/virchow2/top_k_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/base.yaml b/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/base.yaml index b454e354..cc3a557a 100644 --- a/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/base.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/base.yaml @@ -1,4 +1,4 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/virchow2_stain@model_data + - /model/checkpoints/prostate/virchow2_stain@model_data diff --git a/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/max_aggregations/mmci_sl_group_1.yaml index c661649f..3164ba5d 100644 --- a/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/virchow2_stain/max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/max_aggregations/mmci_tl_test.yaml b/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/max_aggregations/mmci_tl_test.yaml index a0f325a2..b93cf3c0 100644 --- a/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/max_aggregations/mmci_tl_test.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/virchow2_stain/max_aggregations/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data preds_uri: "mlflow-artifacts:/65/ab793fef8da2486aa443f6da26188561/artifacts/tables/aggregated_predictions.json" diff --git a/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml index 50ab94e1..3d523fec 100644 --- a/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/mean_pool_max_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/virchow2_stain/mean_pool_max_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.mean_pool_max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/span_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/span_aggregations/mmci_sl_group_1.yaml index 3c7a76d7..640895b6 100644 --- a/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/span_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/span_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/virchow2_stain/span_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.span.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/top_k_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/top_k_aggregations/mmci_sl_group_1.yaml index d978d978..38f3672c 100644 --- a/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/top_k_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_level_eval/virchow2_stain/top_k_aggregations/mmci_sl_group_1.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/postprocessing/slide_level_eval/virchow2_stain/top_k_aggregations/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data preds_uri: ${model_data.slide_level_prediction_uris.top_k.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/pgp/base.yaml b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/pgp/base.yaml index 7913f488..6badf17f 100644 --- a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/pgp/base.yaml +++ b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/pgp/base.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_prediction_table/max_aggregations/base - - /model/checkpoints/mmci_tl/pgp@model_data + - /model/checkpoints/prostate/pgp@model_data diff --git a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/pgp/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/pgp/mmci_sl_group_1.yaml index 854eb875..2a635f6a 100644 --- a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/pgp/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/pgp/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_prediction_table/max_aggregations/pgp/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} \ No newline at end of file diff --git a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/base.yaml b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/base.yaml index 5a4f6f9a..7cb00012 100644 --- a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/base.yaml +++ b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/base.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_prediction_table/max_aggregations/base - - /model/checkpoints/mmci_tl/resnet50@model_data + - /model/checkpoints/prostate/resnet50@model_data diff --git a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/base_stain.yaml b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/base_stain.yaml index 6cb8560e..cb6ad51d 100644 --- a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/base_stain.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_prediction_table/max_aggregations/base - - /model/checkpoints/mmci_tl/resnet50_stain@model_data + - /model/checkpoints/prostate/resnet50_stain@model_data diff --git a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/mmci_sl_group_1.yaml index 992eef4d..372188a3 100644 --- a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/stain_mmci_sl_group_1.yaml index bd082e71..b50af878 100644 --- a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_prediction_table/max_aggregations/resnet50/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/base.yaml b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/base.yaml index 34aed9fa..c0f67c45 100644 --- a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/base.yaml +++ b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/base.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_prediction_table/max_aggregations/base - - /model/checkpoints/mmci_tl/vgg16@model_data + - /model/checkpoints/prostate/vgg16@model_data diff --git a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/base_stain.yaml b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/base_stain.yaml index 626feb0d..6f847555 100644 --- a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/base_stain.yaml +++ b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/base_stain.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_prediction_table/max_aggregations/base - - /model/checkpoints/mmci_tl/vgg16_stain@model_data + - /model/checkpoints/prostate/vgg16_stain@model_data diff --git a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/mmci_sl_group_1.yaml index c19171d7..a66985e2 100644 --- a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/stain_mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/stain_mmci_sl_group_1.yaml index 132631d8..0fb1362f 100644 --- a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/stain_mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_prediction_table/max_aggregations/vgg16/base_stain - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/virchow2/base.yaml b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/virchow2/base.yaml index 9c7716ad..a6ccb68f 100644 --- a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/virchow2/base.yaml +++ b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/virchow2/base.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/postprocessing/slide_prediction_table/max_aggregations/base - - /model/checkpoints/mmci_tl/virchow2@model_data + - /model/checkpoints/prostate/virchow2@model_data diff --git a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/virchow2/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/virchow2/mmci_sl_group_1.yaml index e40f86ac..997cb292 100644 --- a/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/virchow2/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_prediction_table/max_aggregations/virchow2/mmci_sl_group_1.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/postprocessing/slide_prediction_table/max_aggregations/virchow2/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ preds_uri: ${model_data.slide_level_prediction_uris.max.mmci_sl_group_1} diff --git a/configs/experiment/postprocessing/slide_prediction_table_merge/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/postprocessing/slide_prediction_table_merge/max_aggregations/mmci_sl_group_1.yaml index 0d975fc8..81490d93 100644 --- a/configs/experiment/postprocessing/slide_prediction_table_merge/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/postprocessing/slide_prediction_table_merge/max_aggregations/mmci_sl_group_1.yaml @@ -1,12 +1,12 @@ # @package _global_ defaults: - - /model/checkpoints/mmci_tl/pgp@pgp_data - - /model/checkpoints/mmci_tl/resnet50@resnet50_data - - /model/checkpoints/mmci_tl/resnet50_stain@resnet50_stain_data - - /model/checkpoints/mmci_tl/vgg16@vgg16_data - - /model/checkpoints/mmci_tl/vgg16_stain@vgg16_stain_data - - /model/checkpoints/mmci_tl/virchow2@virchow2_data + - /model/checkpoints/prostate/pgp@pgp_data + - /model/checkpoints/prostate/resnet50@resnet50_data + - /model/checkpoints/prostate/resnet50_stain@resnet50_stain_data + - /model/checkpoints/prostate/vgg16@vgg16_data + - /model/checkpoints/prostate/vgg16_stain@vgg16_stain_data + - /model/checkpoints/prostate/virchow2@virchow2_data - _self_ pred_column: "prediction" diff --git a/configs/experiment/predict/bag_of_embeddings/pgp/classic_base.yaml b/configs/experiment/predict/bag_of_embeddings/pgp/classic_base.yaml index 1dbaf40d..012b92e1 100644 --- a/configs/experiment/predict/bag_of_embeddings/pgp/classic_base.yaml +++ b/configs/experiment/predict/bag_of_embeddings/pgp/classic_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/bag_of_embeddings/classic_base - /model/pgp_classic_mil_model@model - - /model/checkpoints/mmci_tl/pgp_classic_mil@model_data + - /model/checkpoints/prostate/pgp_classic_mil@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/bag_of_embeddings/pgp/classic_slide_threshold.yaml b/configs/experiment/predict/bag_of_embeddings/pgp/classic_slide_threshold.yaml index eb302c57..56e864dc 100644 --- a/configs/experiment/predict/bag_of_embeddings/pgp/classic_slide_threshold.yaml +++ b/configs/experiment/predict/bag_of_embeddings/pgp/classic_slide_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/slide_threshold_mil@callbacks - /experiment/predict/bag_of_embeddings/pgp/classic_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ slide_threshold: 0.99 # My estimate for other models diff --git a/configs/experiment/predict/bag_of_embeddings/pgp/hybrid_base.yaml b/configs/experiment/predict/bag_of_embeddings/pgp/hybrid_base.yaml index f701af45..a11d9405 100644 --- a/configs/experiment/predict/bag_of_embeddings/pgp/hybrid_base.yaml +++ b/configs/experiment/predict/bag_of_embeddings/pgp/hybrid_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/bag_of_embeddings/hybrid_base - /model/pgp_hybrid_mil_model@model - - /model/checkpoints/mmci_tl/pgp_hybrid_mil@model_data + - /model/checkpoints/prostate/pgp_hybrid_mil@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/bag_of_embeddings/pgp/hybrid_slide_threshold.yaml b/configs/experiment/predict/bag_of_embeddings/pgp/hybrid_slide_threshold.yaml index dad11f6c..38a656ac 100644 --- a/configs/experiment/predict/bag_of_embeddings/pgp/hybrid_slide_threshold.yaml +++ b/configs/experiment/predict/bag_of_embeddings/pgp/hybrid_slide_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/slide_threshold_mil@callbacks - /experiment/predict/bag_of_embeddings/pgp/hybrid_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ slide_threshold: 0.99 # My estimate for other models diff --git a/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_mmci_sl_group_1.yaml b/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_mmci_sl_group_1.yaml index a46d9ed6..9b8b1af4 100644 --- a/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_mmci_sl_group_1.yaml +++ b/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_mmci_tl_val.yaml b/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_mmci_tl_val.yaml index 26fbb884..4c2bd842 100644 --- a/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_mmci_tl_val.yaml +++ b/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/bag_of_embeddings/pgp/mil_predictions/classic_base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/hybrid_mci_tl_val.yaml b/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/hybrid_mci_tl_val.yaml index 2f622a9a..85234b28 100644 --- a/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/hybrid_mci_tl_val.yaml +++ b/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/hybrid_mci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/bag_of_embeddings/pgp/mil_predictions/hybrid_base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/hybrid_mmci_sl_group_1.yaml b/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/hybrid_mmci_sl_group_1.yaml index 5112fa0a..668c8e50 100644 --- a/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/hybrid_mmci_sl_group_1.yaml +++ b/configs/experiment/predict/bag_of_embeddings/pgp/mil_predictions/hybrid_mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/bag_of_embeddings/pgp/mil_predictions/hybrid_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/bag_of_embeddings/virchow2/classic_base.yaml b/configs/experiment/predict/bag_of_embeddings/virchow2/classic_base.yaml index 3b22a5a4..6ada83f1 100644 --- a/configs/experiment/predict/bag_of_embeddings/virchow2/classic_base.yaml +++ b/configs/experiment/predict/bag_of_embeddings/virchow2/classic_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/bag_of_embeddings/classic_base - /model/virchow2_classic_mil_model@model - - /model/checkpoints/mmci_tl/virchow2_classic_mil@model_data + - /model/checkpoints/prostate/virchow2_classic_mil@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/bag_of_embeddings/virchow2/classic_slide_threshold.yaml b/configs/experiment/predict/bag_of_embeddings/virchow2/classic_slide_threshold.yaml index 4d58bfd2..c710f51b 100644 --- a/configs/experiment/predict/bag_of_embeddings/virchow2/classic_slide_threshold.yaml +++ b/configs/experiment/predict/bag_of_embeddings/virchow2/classic_slide_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/slide_threshold_mil@callbacks - /experiment/predict/bag_of_embeddings/virchow2/classic_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ slide_threshold: 0.99 # My estimate for other models diff --git a/configs/experiment/predict/bag_of_embeddings/virchow2/hybrid_base.yaml b/configs/experiment/predict/bag_of_embeddings/virchow2/hybrid_base.yaml index 37be6954..a680b3fe 100644 --- a/configs/experiment/predict/bag_of_embeddings/virchow2/hybrid_base.yaml +++ b/configs/experiment/predict/bag_of_embeddings/virchow2/hybrid_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/bag_of_embeddings/hybrid_base - /model/virchow2_hybrid_mil_model@model - - /model/checkpoints/mmci_tl/virchow2_hybrid_mil@model_data + - /model/checkpoints/prostate/virchow2_hybrid_mil@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/bag_of_embeddings/virchow2/hybrid_slide_threshold.yaml b/configs/experiment/predict/bag_of_embeddings/virchow2/hybrid_slide_threshold.yaml index b59bc3dc..34e0e4d4 100644 --- a/configs/experiment/predict/bag_of_embeddings/virchow2/hybrid_slide_threshold.yaml +++ b/configs/experiment/predict/bag_of_embeddings/virchow2/hybrid_slide_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/slide_threshold_mil@callbacks - /experiment/predict/bag_of_embeddings/virchow2/hybrid_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ slide_threshold: 0.99 # My estimate for other models diff --git a/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_mmci_sl_group_1.yaml b/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_mmci_sl_group_1.yaml index a59daeaa..516fa3a6 100644 --- a/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_mmci_sl_group_1.yaml +++ b/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_mmci_tl_val.yaml b/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_mmci_tl_val.yaml index b7d6c054..5b982c12 100644 --- a/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_mmci_tl_val.yaml +++ b/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/bag_of_embeddings/virchow2/mil_predictions/classic_base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/hybrid_mmci_sl_group_1.yaml b/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/hybrid_mmci_sl_group_1.yaml index b6383a10..cd4a7f28 100644 --- a/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/hybrid_mmci_sl_group_1.yaml +++ b/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/hybrid_mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/bag_of_embeddings/virchow2/mil_predictions/hybrid_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/hybrid_mmci_tl_val.yaml b/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/hybrid_mmci_tl_val.yaml index e72a3f3c..2bf17fa1 100644 --- a/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/hybrid_mmci_tl_val.yaml +++ b/configs/experiment/predict/bag_of_embeddings/virchow2/mil_predictions/hybrid_mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/bag_of_embeddings/virchow2/mil_predictions/hybrid_base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/pgp/base.yaml b/configs/experiment/predict/embeddings/pgp/base.yaml index 4d1c91ba..f6d4a83e 100644 --- a/configs/experiment/predict/embeddings/pgp/base.yaml +++ b/configs/experiment/predict/embeddings/pgp/base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/embeddings/base - /model/pgp_model@model - - /model/checkpoints/mmci_tl/pgp@model_data + - /model/checkpoints/prostate/pgp@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/embeddings/pgp/estimations/mpm_estimation.yaml b/configs/experiment/predict/embeddings/pgp/estimations/mpm_estimation.yaml index e313ae22..8fa15a88 100644 --- a/configs/experiment/predict/embeddings/pgp/estimations/mpm_estimation.yaml +++ b/configs/experiment/predict/embeddings/pgp/estimations/mpm_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/embeddings/pgp/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/embeddings/pgp/estimations/span_estimation.yaml b/configs/experiment/predict/embeddings/pgp/estimations/span_estimation.yaml index 24eb8ab6..d247fa61 100644 --- a/configs/experiment/predict/embeddings/pgp/estimations/span_estimation.yaml +++ b/configs/experiment/predict/embeddings/pgp/estimations/span_estimation.yaml @@ -3,12 +3,12 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/embeddings/pgp/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: estimation_callback: - aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + aggregator_cls_path: ml.aggregators.span.SpanAggregator static: extent_tile: 224 stride_tile: 112 diff --git a/configs/experiment/predict/embeddings/pgp/estimations/stain_mpm_estimation.yaml b/configs/experiment/predict/embeddings/pgp/estimations/stain_mpm_estimation.yaml index 0d70a8c8..0d67ab72 100644 --- a/configs/experiment/predict/embeddings/pgp/estimations/stain_mpm_estimation.yaml +++ b/configs/experiment/predict/embeddings/pgp/estimations/stain_mpm_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/embeddings/pgp/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/embeddings/pgp/estimations/stain_span_estimation.yaml b/configs/experiment/predict/embeddings/pgp/estimations/stain_span_estimation.yaml index 781fbfa7..3a6d2cb7 100644 --- a/configs/experiment/predict/embeddings/pgp/estimations/stain_span_estimation.yaml +++ b/configs/experiment/predict/embeddings/pgp/estimations/stain_span_estimation.yaml @@ -3,12 +3,12 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/embeddings/pgp/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: estimation_callback: - aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + aggregator_cls_path: ml.aggregators.span.SpanAggregator static: extent_tile: 224 stride_tile: 112 diff --git a/configs/experiment/predict/embeddings/pgp/estimations/stain_top_k_estimation.yaml b/configs/experiment/predict/embeddings/pgp/estimations/stain_top_k_estimation.yaml index ecc34900..fdc7cdf7 100644 --- a/configs/experiment/predict/embeddings/pgp/estimations/stain_top_k_estimation.yaml +++ b/configs/experiment/predict/embeddings/pgp/estimations/stain_top_k_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/embeddings/pgp/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/embeddings/pgp/estimations/top_k_estimation.yaml b/configs/experiment/predict/embeddings/pgp/estimations/top_k_estimation.yaml index 5b92a0f9..c148038a 100644 --- a/configs/experiment/predict/embeddings/pgp/estimations/top_k_estimation.yaml +++ b/configs/experiment/predict/embeddings/pgp/estimations/top_k_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/embeddings/pgp/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/embeddings/pgp/heatmaps/stain_mmci_tl_val.yaml b/configs/experiment/predict/embeddings/pgp/heatmaps/stain_mmci_tl_val.yaml index 5cc5e63a..bdb67dce 100644 --- a/configs/experiment/predict/embeddings/pgp/heatmaps/stain_mmci_tl_val.yaml +++ b/configs/experiment/predict/embeddings/pgp/heatmaps/stain_mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/pgp/heatmaps/stain_base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml index d54344e0..7dc129fa 100644 --- a/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml b/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml index e483a43f..e2b4ea9c 100644 --- a/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml +++ b/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/base - - /data/mmci/sl_group_2@predict_data + - /data/prostate/mmci/sl_group_2@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_tl_test.yaml b/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_tl_test.yaml index f04f1312..9a01c9fb 100644 --- a/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_tl_train.yaml b/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_tl_train.yaml index 286bf6ba..79e9be79 100644 --- a/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_tl_train.yaml +++ b/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_tl_train.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/base - - /data/mmci/tl_train@predict_data + - /data/prostate/mmci/tl_train@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_tl_val.yaml b/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_tl_val.yaml index 3f7b4239..2472adad 100644 --- a/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_tl_val.yaml +++ b/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml b/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml index c1a71e2c..216884f3 100644 --- a/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/stain_mmci_tl_val.yaml b/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/stain_mmci_tl_val.yaml index 0728ab9b..ba6bdc5c 100644 --- a/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/stain_mmci_tl_val.yaml +++ b/configs/experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/stain_mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/pgp/heatmaps_and_max_aggregations/stain_base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/pgp/max_aggregations/mmci_tl_test.yaml b/configs/experiment/predict/embeddings/pgp/max_aggregations/mmci_tl_test.yaml index 863dfdaf..ea7bba93 100644 --- a/configs/experiment/predict/embeddings/pgp/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/predict/embeddings/pgp/max_aggregations/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/pgp/max_aggregations/base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/pgp/max_aggregations/stain_mmci_tl_test.yaml b/configs/experiment/predict/embeddings/pgp/max_aggregations/stain_mmci_tl_test.yaml index 34ae09d3..01426f68 100644 --- a/configs/experiment/predict/embeddings/pgp/max_aggregations/stain_mmci_tl_test.yaml +++ b/configs/experiment/predict/embeddings/pgp/max_aggregations/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/pgp/max_aggregations/stain_base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/mmci_tl_test.yaml b/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/mmci_tl_test.yaml index 6b3172c5..183e2f83 100644 --- a/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/mmci_tl_test.yaml +++ b/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/pgp/multi_aggregator_eval/base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/radboud_test.yaml b/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/radboud_test.yaml index bd7323c9..90c61833 100644 --- a/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/radboud_test.yaml +++ b/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/predict/embeddings/pgp/multi_aggregator_eval/base - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_mmci_tl_test.yaml b/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_mmci_tl_test.yaml index 2c9cc2e2..ec591371 100644 --- a/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_mmci_tl_test.yaml +++ b/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_radboud_test.yaml b/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_radboud_test.yaml index dcbcc96d..8d9342e3 100644 --- a/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_radboud_test.yaml +++ b/configs/experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/predict/embeddings/pgp/multi_aggregator_eval/stain_base - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/predict/embeddings/pgp/stain_base.yaml b/configs/experiment/predict/embeddings/pgp/stain_base.yaml index d8f75112..07394764 100644 --- a/configs/experiment/predict/embeddings/pgp/stain_base.yaml +++ b/configs/experiment/predict/embeddings/pgp/stain_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/embeddings/base - /model/pgp_model@model - - /model/checkpoints/mmci_tl/pgp_stain@model_data + - /model/checkpoints/prostate/pgp_stain@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/embeddings/virchow2/base.yaml b/configs/experiment/predict/embeddings/virchow2/base.yaml index 816ffcc8..a17e278f 100644 --- a/configs/experiment/predict/embeddings/virchow2/base.yaml +++ b/configs/experiment/predict/embeddings/virchow2/base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/embeddings/base - /model/virchow2_model@model - - /model/checkpoints/mmci_tl/virchow2@model_data + - /model/checkpoints/prostate/virchow2@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/embeddings/virchow2/carcinoma_prediction_tables/mmci_sl.yaml b/configs/experiment/predict/embeddings/virchow2/carcinoma_prediction_tables/mmci_sl.yaml index b6607c00..6a3158b2 100644 --- a/configs/experiment/predict/embeddings/virchow2/carcinoma_prediction_tables/mmci_sl.yaml +++ b/configs/experiment/predict/embeddings/virchow2/carcinoma_prediction_tables/mmci_sl.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/virchow2/carcinoma_prediction_tables/base - - /data/mmci/sl@predict_data + - /data/prostate/mmci/sl@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/virchow2/estimations/mpm_estimation.yaml b/configs/experiment/predict/embeddings/virchow2/estimations/mpm_estimation.yaml index b6ca5fb6..59f8acc2 100644 --- a/configs/experiment/predict/embeddings/virchow2/estimations/mpm_estimation.yaml +++ b/configs/experiment/predict/embeddings/virchow2/estimations/mpm_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/embeddings/virchow2/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/embeddings/virchow2/estimations/span_estimation.yaml b/configs/experiment/predict/embeddings/virchow2/estimations/span_estimation.yaml index 135abb3f..b7c9bf26 100644 --- a/configs/experiment/predict/embeddings/virchow2/estimations/span_estimation.yaml +++ b/configs/experiment/predict/embeddings/virchow2/estimations/span_estimation.yaml @@ -3,12 +3,12 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/embeddings/virchow2/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: estimation_callback: - aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + aggregator_cls_path: ml.aggregators.span.SpanAggregator static: extent_tile: 224 stride_tile: 112 diff --git a/configs/experiment/predict/embeddings/virchow2/estimations/stain_mpm_estimation.yaml b/configs/experiment/predict/embeddings/virchow2/estimations/stain_mpm_estimation.yaml index 13ffc0b6..43345a91 100644 --- a/configs/experiment/predict/embeddings/virchow2/estimations/stain_mpm_estimation.yaml +++ b/configs/experiment/predict/embeddings/virchow2/estimations/stain_mpm_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/embeddings/virchow2/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/embeddings/virchow2/estimations/stain_span_estimation.yaml b/configs/experiment/predict/embeddings/virchow2/estimations/stain_span_estimation.yaml index 1cd269bc..030b705b 100644 --- a/configs/experiment/predict/embeddings/virchow2/estimations/stain_span_estimation.yaml +++ b/configs/experiment/predict/embeddings/virchow2/estimations/stain_span_estimation.yaml @@ -3,12 +3,12 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/embeddings/virchow2/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: estimation_callback: - aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + aggregator_cls_path: ml.aggregators.span.SpanAggregator static: extent_tile: 224 stride_tile: 112 diff --git a/configs/experiment/predict/embeddings/virchow2/estimations/stain_top_k_estimation.yaml b/configs/experiment/predict/embeddings/virchow2/estimations/stain_top_k_estimation.yaml index e7ee4722..7efdcc8e 100644 --- a/configs/experiment/predict/embeddings/virchow2/estimations/stain_top_k_estimation.yaml +++ b/configs/experiment/predict/embeddings/virchow2/estimations/stain_top_k_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/embeddings/virchow2/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/embeddings/virchow2/estimations/top_k_estimation.yaml b/configs/experiment/predict/embeddings/virchow2/estimations/top_k_estimation.yaml index 46b90640..05f3c456 100644 --- a/configs/experiment/predict/embeddings/virchow2/estimations/top_k_estimation.yaml +++ b/configs/experiment/predict/embeddings/virchow2/estimations/top_k_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/embeddings/virchow2/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/embeddings/virchow2/heatmaps/stain_mmci_tl_val.yaml b/configs/experiment/predict/embeddings/virchow2/heatmaps/stain_mmci_tl_val.yaml index 39a892a1..25ff4572 100644 --- a/configs/experiment/predict/embeddings/virchow2/heatmaps/stain_mmci_tl_val.yaml +++ b/configs/experiment/predict/embeddings/virchow2/heatmaps/stain_mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/virchow2/heatmaps/stain_base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/comenius_3_sample.yaml b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/comenius_3_sample.yaml index 4fab06aa..e9a4fa8c 100644 --- a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/comenius_3_sample.yaml +++ b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/comenius_3_sample.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/base - - /data/comenius/comenius_3_sample@predict_data + - /data/prostate/comenius/comenius_3_sample@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_endoresection.yaml b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_endoresection.yaml index 7d31ce70..65bfb8df 100644 --- a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_endoresection.yaml +++ b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_endoresection.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/base - - /data/mmci/endoresection@predict_data + - /data/prostate/mmci/endoresection@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml index 5402f8c5..3443748d 100644 --- a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml index 6b19da9b..efb69b69 100644 --- a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml +++ b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/base - - /data/mmci/sl_group_2@predict_data + - /data/prostate/mmci/sl_group_2@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_tl_test.yaml b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_tl_test.yaml index c63cb025..15d0ebab 100644 --- a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_tl_train.yaml b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_tl_train.yaml index 6cdf5318..9690d35a 100644 --- a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_tl_train.yaml +++ b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_tl_train.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/base - - /data/mmci/tl_train@predict_data + - /data/prostate/mmci/tl_train@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_tl_val.yaml b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_tl_val.yaml index 12ef136c..67cda08b 100644 --- a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_tl_val.yaml +++ b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml index 7eec4b1c..57a4cf24 100644 --- a/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/virchow2/heatmaps_and_max_aggregations/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/virchow2/max_aggregations/mmci_tl_test.yaml b/configs/experiment/predict/embeddings/virchow2/max_aggregations/mmci_tl_test.yaml index 859a86c7..80228967 100644 --- a/configs/experiment/predict/embeddings/virchow2/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/predict/embeddings/virchow2/max_aggregations/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/virchow2/max_aggregations/base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/virchow2/max_aggregations/stain_mmci_tl_test.yaml b/configs/experiment/predict/embeddings/virchow2/max_aggregations/stain_mmci_tl_test.yaml index 90035b77..618a17ca 100644 --- a/configs/experiment/predict/embeddings/virchow2/max_aggregations/stain_mmci_tl_test.yaml +++ b/configs/experiment/predict/embeddings/virchow2/max_aggregations/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/virchow2/max_aggregations/stain_base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/mmci_tl_test.yaml b/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/mmci_tl_test.yaml index adf49986..48fb31ff 100644 --- a/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/mmci_tl_test.yaml +++ b/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/virchow2/multi_aggregator_eval/base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/radboud_test.yaml b/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/radboud_test.yaml index 02478538..79a03056 100644 --- a/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/radboud_test.yaml +++ b/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/predict/embeddings/virchow2/multi_aggregator_eval/base - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_mmci_tl_test.yaml b/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_mmci_tl_test.yaml index 4856694a..848a0ccc 100644 --- a/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_mmci_tl_test.yaml +++ b/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_radboud_test.yaml b/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_radboud_test.yaml index d994a82a..6c768152 100644 --- a/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_radboud_test.yaml +++ b/configs/experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/predict/embeddings/virchow2/multi_aggregator_eval/stain_base - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/predict/embeddings/virchow2/stain_base.yaml b/configs/experiment/predict/embeddings/virchow2/stain_base.yaml index a12dd7ef..3e271f75 100644 --- a/configs/experiment/predict/embeddings/virchow2/stain_base.yaml +++ b/configs/experiment/predict/embeddings/virchow2/stain_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/embeddings/base - /model/virchow2_model@model - - /model/checkpoints/mmci_tl/virchow2_stain@model_data + - /model/checkpoints/prostate/virchow2_stain@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/images/google_vit/base.yaml b/configs/experiment/predict/images/google_vit/base.yaml index 929753ca..b8e079ed 100644 --- a/configs/experiment/predict/images/google_vit/base.yaml +++ b/configs/experiment/predict/images/google_vit/base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/images/base - /model/google_vit_model@model - - /model/checkpoints/mmci_tl/google_vit@model_data + - /model/checkpoints/prostate/google_vit@model_data - _self_ diff --git a/configs/experiment/predict/images/google_vit/estimations/mpm_estimation.yaml b/configs/experiment/predict/images/google_vit/estimations/mpm_estimation.yaml index df39c5ec..952cb2bf 100644 --- a/configs/experiment/predict/images/google_vit/estimations/mpm_estimation.yaml +++ b/configs/experiment/predict/images/google_vit/estimations/mpm_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/google_vit/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/google_vit/estimations/span_estimation.yaml b/configs/experiment/predict/images/google_vit/estimations/span_estimation.yaml index dfb7b22b..74192403 100644 --- a/configs/experiment/predict/images/google_vit/estimations/span_estimation.yaml +++ b/configs/experiment/predict/images/google_vit/estimations/span_estimation.yaml @@ -3,12 +3,12 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/google_vit/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: estimation_callback: - aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + aggregator_cls_path: ml.aggregators.span.SpanAggregator static: extent_tile: 224 stride_tile: 112 diff --git a/configs/experiment/predict/images/google_vit/estimations/stain_mpm_estimation.yaml b/configs/experiment/predict/images/google_vit/estimations/stain_mpm_estimation.yaml index 50858f75..51521449 100644 --- a/configs/experiment/predict/images/google_vit/estimations/stain_mpm_estimation.yaml +++ b/configs/experiment/predict/images/google_vit/estimations/stain_mpm_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/google_vit/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/google_vit/estimations/stain_span_estimation.yaml b/configs/experiment/predict/images/google_vit/estimations/stain_span_estimation.yaml index 471c1c1a..16ae39d4 100644 --- a/configs/experiment/predict/images/google_vit/estimations/stain_span_estimation.yaml +++ b/configs/experiment/predict/images/google_vit/estimations/stain_span_estimation.yaml @@ -3,12 +3,12 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/google_vit/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: estimation_callback: - aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + aggregator_cls_path: ml.aggregators.span.SpanAggregator static: extent_tile: 224 stride_tile: 112 diff --git a/configs/experiment/predict/images/google_vit/estimations/stain_top_k_estimation.yaml b/configs/experiment/predict/images/google_vit/estimations/stain_top_k_estimation.yaml index cb479b51..b0a63a6a 100644 --- a/configs/experiment/predict/images/google_vit/estimations/stain_top_k_estimation.yaml +++ b/configs/experiment/predict/images/google_vit/estimations/stain_top_k_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/google_vit/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/google_vit/estimations/top_k_estimation.yaml b/configs/experiment/predict/images/google_vit/estimations/top_k_estimation.yaml index 8c98c09c..4beed19f 100644 --- a/configs/experiment/predict/images/google_vit/estimations/top_k_estimation.yaml +++ b/configs/experiment/predict/images/google_vit/estimations/top_k_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/google_vit/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/google_vit/heatmaps/mmci_sl_group_1.yaml b/configs/experiment/predict/images/google_vit/heatmaps/mmci_sl_group_1.yaml index c80d8861..763d2214 100644 --- a/configs/experiment/predict/images/google_vit/heatmaps/mmci_sl_group_1.yaml +++ b/configs/experiment/predict/images/google_vit/heatmaps/mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/google_vit/heatmaps/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/images/google_vit/heatmaps/mmci_tl_val.yaml b/configs/experiment/predict/images/google_vit/heatmaps/mmci_tl_val.yaml index b55399d8..19634cff 100644 --- a/configs/experiment/predict/images/google_vit/heatmaps/mmci_tl_val.yaml +++ b/configs/experiment/predict/images/google_vit/heatmaps/mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/google_vit/heatmaps/base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/images/google_vit/heatmaps/stain_mmci_sl_group_1.yaml b/configs/experiment/predict/images/google_vit/heatmaps/stain_mmci_sl_group_1.yaml index 8d2ba7ab..a7f61c82 100644 --- a/configs/experiment/predict/images/google_vit/heatmaps/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/predict/images/google_vit/heatmaps/stain_mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/google_vit/heatmaps/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/images/google_vit/heatmaps/stain_mmci_tl_val.yaml b/configs/experiment/predict/images/google_vit/heatmaps/stain_mmci_tl_val.yaml index 6892d233..11e07ee9 100644 --- a/configs/experiment/predict/images/google_vit/heatmaps/stain_mmci_tl_val.yaml +++ b/configs/experiment/predict/images/google_vit/heatmaps/stain_mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/google_vit/heatmaps/stain_base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/images/google_vit/max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/predict/images/google_vit/max_aggregations/mmci_sl_group_1.yaml index 97fbb684..c756ce22 100644 --- a/configs/experiment/predict/images/google_vit/max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/predict/images/google_vit/max_aggregations/mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/google_vit/max_aggregations/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/images/google_vit/max_aggregations/mmci_tl_test.yaml b/configs/experiment/predict/images/google_vit/max_aggregations/mmci_tl_test.yaml index cf3c9238..4fe22555 100644 --- a/configs/experiment/predict/images/google_vit/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/predict/images/google_vit/max_aggregations/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/google_vit/max_aggregations/base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/google_vit/max_aggregations/stain_mmci_tl_test.yaml b/configs/experiment/predict/images/google_vit/max_aggregations/stain_mmci_tl_test.yaml index 757db470..87059507 100644 --- a/configs/experiment/predict/images/google_vit/max_aggregations/stain_mmci_tl_test.yaml +++ b/configs/experiment/predict/images/google_vit/max_aggregations/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/google_vit/max_aggregations/stain_base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/google_vit/multi_aggregator_eval/mmci_tl_test.yaml b/configs/experiment/predict/images/google_vit/multi_aggregator_eval/mmci_tl_test.yaml index 7b9e66d0..cb6728eb 100644 --- a/configs/experiment/predict/images/google_vit/multi_aggregator_eval/mmci_tl_test.yaml +++ b/configs/experiment/predict/images/google_vit/multi_aggregator_eval/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/google_vit/multi_aggregator_eval/base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/google_vit/multi_aggregator_eval/radboud_test.yaml b/configs/experiment/predict/images/google_vit/multi_aggregator_eval/radboud_test.yaml index a6875770..7dbc8fbc 100644 --- a/configs/experiment/predict/images/google_vit/multi_aggregator_eval/radboud_test.yaml +++ b/configs/experiment/predict/images/google_vit/multi_aggregator_eval/radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/predict/images/google_vit/multi_aggregator_eval/base - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/predict/images/google_vit/multi_aggregator_eval/stain_mmci_tl_test.yaml b/configs/experiment/predict/images/google_vit/multi_aggregator_eval/stain_mmci_tl_test.yaml index 8b0c1cc2..a27c1270 100644 --- a/configs/experiment/predict/images/google_vit/multi_aggregator_eval/stain_mmci_tl_test.yaml +++ b/configs/experiment/predict/images/google_vit/multi_aggregator_eval/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/google_vit/multi_aggregator_eval/stain_base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/google_vit/multi_aggregator_eval/stain_radboud_test.yaml b/configs/experiment/predict/images/google_vit/multi_aggregator_eval/stain_radboud_test.yaml index 08800bdc..92ba2dbb 100644 --- a/configs/experiment/predict/images/google_vit/multi_aggregator_eval/stain_radboud_test.yaml +++ b/configs/experiment/predict/images/google_vit/multi_aggregator_eval/stain_radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/predict/images/google_vit/multi_aggregator_eval/stain_base - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/predict/images/google_vit/stain_base.yaml b/configs/experiment/predict/images/google_vit/stain_base.yaml index 5096ee0a..a83b8e3d 100644 --- a/configs/experiment/predict/images/google_vit/stain_base.yaml +++ b/configs/experiment/predict/images/google_vit/stain_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/images/base - /model/google_vit_model@model - - /model/checkpoints/mmci_tl/google_vit_stain@model_data + - /model/checkpoints/prostate/google_vit_stain@model_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/base.yaml b/configs/experiment/predict/images/resnet50/base.yaml index e61a8d50..0f58032a 100644 --- a/configs/experiment/predict/images/resnet50/base.yaml +++ b/configs/experiment/predict/images/resnet50/base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/images/base - /model/resnet50_model@model - - /model/checkpoints/mmci_tl/resnet50@model_data + - /model/checkpoints/prostate/resnet50@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/images/resnet50/base_224.yaml b/configs/experiment/predict/images/resnet50/base_224.yaml index 57d18cf7..a630b008 100644 --- a/configs/experiment/predict/images/resnet50/base_224.yaml +++ b/configs/experiment/predict/images/resnet50/base_224.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/images/base - /model/resnet50_model@model - - /model/checkpoints/mmci_tl/resnet50_224@model_data + - /model/checkpoints/prostate/resnet50_224@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/images/resnet50/estimations/mpm_estimation.yaml b/configs/experiment/predict/images/resnet50/estimations/mpm_estimation.yaml index edc6fce5..85d45ac1 100644 --- a/configs/experiment/predict/images/resnet50/estimations/mpm_estimation.yaml +++ b/configs/experiment/predict/images/resnet50/estimations/mpm_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/resnet50/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/resnet50/estimations/mpm_estimation_224.yaml b/configs/experiment/predict/images/resnet50/estimations/mpm_estimation_224.yaml index 7becb63b..81dab58e 100644 --- a/configs/experiment/predict/images/resnet50/estimations/mpm_estimation_224.yaml +++ b/configs/experiment/predict/images/resnet50/estimations/mpm_estimation_224.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/resnet50/base_224 - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/resnet50/estimations/span_estimation.yaml b/configs/experiment/predict/images/resnet50/estimations/span_estimation.yaml index 769f8347..0d8c9ddd 100644 --- a/configs/experiment/predict/images/resnet50/estimations/span_estimation.yaml +++ b/configs/experiment/predict/images/resnet50/estimations/span_estimation.yaml @@ -3,12 +3,12 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/resnet50/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: estimation_callback: - aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + aggregator_cls_path: ml.aggregators.span.SpanAggregator static: extent_tile: 512 stride_tile: 256 diff --git a/configs/experiment/predict/images/resnet50/estimations/span_estimation_224.yaml b/configs/experiment/predict/images/resnet50/estimations/span_estimation_224.yaml index 8aa88a5e..c8e0c732 100644 --- a/configs/experiment/predict/images/resnet50/estimations/span_estimation_224.yaml +++ b/configs/experiment/predict/images/resnet50/estimations/span_estimation_224.yaml @@ -3,12 +3,12 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/resnet50/base_224 - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: estimation_callback: - aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + aggregator_cls_path: ml.aggregators.span.SpanAggregator static: extent_tile: 224 stride_tile: 112 diff --git a/configs/experiment/predict/images/resnet50/estimations/stain_mpm_estimation.yaml b/configs/experiment/predict/images/resnet50/estimations/stain_mpm_estimation.yaml index 4b2500f0..7b004664 100644 --- a/configs/experiment/predict/images/resnet50/estimations/stain_mpm_estimation.yaml +++ b/configs/experiment/predict/images/resnet50/estimations/stain_mpm_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/resnet50/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/resnet50/estimations/stain_mpm_estimation_224.yaml b/configs/experiment/predict/images/resnet50/estimations/stain_mpm_estimation_224.yaml index c7a53eb4..36788f45 100644 --- a/configs/experiment/predict/images/resnet50/estimations/stain_mpm_estimation_224.yaml +++ b/configs/experiment/predict/images/resnet50/estimations/stain_mpm_estimation_224.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/resnet50/stain_base_224 - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/resnet50/estimations/stain_span_estimation.yaml b/configs/experiment/predict/images/resnet50/estimations/stain_span_estimation.yaml index e492e813..bc03a006 100644 --- a/configs/experiment/predict/images/resnet50/estimations/stain_span_estimation.yaml +++ b/configs/experiment/predict/images/resnet50/estimations/stain_span_estimation.yaml @@ -3,12 +3,12 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/resnet50/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: estimation_callback: - aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + aggregator_cls_path: ml.aggregators.span.SpanAggregator static: extent_tile: 512 stride_tile: 256 diff --git a/configs/experiment/predict/images/resnet50/estimations/stain_span_estimation_224.yaml b/configs/experiment/predict/images/resnet50/estimations/stain_span_estimation_224.yaml index e532684a..410902d7 100644 --- a/configs/experiment/predict/images/resnet50/estimations/stain_span_estimation_224.yaml +++ b/configs/experiment/predict/images/resnet50/estimations/stain_span_estimation_224.yaml @@ -3,12 +3,12 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/resnet50/stain_base_224 - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: estimation_callback: - aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + aggregator_cls_path: ml.aggregators.span.SpanAggregator static: extent_tile: 224 stride_tile: 112 diff --git a/configs/experiment/predict/images/resnet50/estimations/stain_top_k_estimation.yaml b/configs/experiment/predict/images/resnet50/estimations/stain_top_k_estimation.yaml index c4c54b97..7d684497 100644 --- a/configs/experiment/predict/images/resnet50/estimations/stain_top_k_estimation.yaml +++ b/configs/experiment/predict/images/resnet50/estimations/stain_top_k_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/resnet50/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/resnet50/estimations/stain_top_k_estimation_224.yaml b/configs/experiment/predict/images/resnet50/estimations/stain_top_k_estimation_224.yaml index f057b7f1..70efd94d 100644 --- a/configs/experiment/predict/images/resnet50/estimations/stain_top_k_estimation_224.yaml +++ b/configs/experiment/predict/images/resnet50/estimations/stain_top_k_estimation_224.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/resnet50/stain_base_224 - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/resnet50/estimations/top_k_estimation.yaml b/configs/experiment/predict/images/resnet50/estimations/top_k_estimation.yaml index 71dedc59..5ddb0e56 100644 --- a/configs/experiment/predict/images/resnet50/estimations/top_k_estimation.yaml +++ b/configs/experiment/predict/images/resnet50/estimations/top_k_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/resnet50/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/resnet50/estimations/top_k_estimation_224.yaml b/configs/experiment/predict/images/resnet50/estimations/top_k_estimation_224.yaml index 4c406a33..5b94fa37 100644 --- a/configs/experiment/predict/images/resnet50/estimations/top_k_estimation_224.yaml +++ b/configs/experiment/predict/images/resnet50/estimations/top_k_estimation_224.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/resnet50/base_224 - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/resnet50/heatmaps/mmci_tl_val_224.yaml b/configs/experiment/predict/images/resnet50/heatmaps/mmci_tl_val_224.yaml index 236de55a..fcab7af4 100644 --- a/configs/experiment/predict/images/resnet50/heatmaps/mmci_tl_val_224.yaml +++ b/configs/experiment/predict/images/resnet50/heatmaps/mmci_tl_val_224.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/heatmaps/base_224 - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/heatmaps/stain_mmci_tl_val_224.yaml b/configs/experiment/predict/images/resnet50/heatmaps/stain_mmci_tl_val_224.yaml index 3f925e49..18201a57 100644 --- a/configs/experiment/predict/images/resnet50/heatmaps/stain_mmci_tl_val_224.yaml +++ b/configs/experiment/predict/images/resnet50/heatmaps/stain_mmci_tl_val_224.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/heatmaps/stain_base_224 - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml index 9350f56b..213179c6 100644 --- a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/heatmaps_and_max_aggregations/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml index 1828ba43..24af87ba 100644 --- a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml +++ b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/heatmaps_and_max_aggregations/base - - /data/mmci/sl_group_2@predict_data + - /data/prostate/mmci/sl_group_2@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_tl_test.yaml b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_tl_test.yaml index cba09c7e..b62de8ef 100644 --- a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/heatmaps_and_max_aggregations/base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_tl_train.yaml b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_tl_train.yaml index 0247b0eb..be1d2b85 100644 --- a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_tl_train.yaml +++ b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_tl_train.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/heatmaps_and_max_aggregations/base - - /data/mmci/tl_train@predict_data + - /data/prostate/mmci/tl_train@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_tl_val.yaml b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_tl_val.yaml index 48fc94f8..5fba57a9 100644 --- a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_tl_val.yaml +++ b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/heatmaps_and_max_aggregations/base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/radboud_test.yaml b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/radboud_test.yaml index 35ee7dbb..d9f42e9a 100644 --- a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/radboud_test.yaml +++ b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/radboud_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/heatmaps_and_max_aggregations/base - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_endoresection.yaml b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_endoresection.yaml index ff4da2c5..55efaf73 100644 --- a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_endoresection.yaml +++ b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_endoresection.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_base - - /data/mmci/endoresection@predict_data + - /data/prostate/mmci/endoresection@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml index 854aee0b..734615e0 100644 --- a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_sl_group_2.yaml b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_sl_group_2.yaml index e77ed1f9..72ab59ab 100644 --- a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_sl_group_2.yaml +++ b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_sl_group_2.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_base - - /data/mmci/sl_group_2@predict_data + - /data/prostate/mmci/sl_group_2@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_tl_test.yaml b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_tl_test.yaml index 2f1ed85f..7ea68053 100644 --- a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_tl_test.yaml +++ b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_tl_train.yaml b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_tl_train.yaml index 45e35ac5..ff7e74db 100644 --- a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_tl_train.yaml +++ b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_tl_train.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_base - - /data/mmci/tl_train@predict_data + - /data/prostate/mmci/tl_train@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_tl_val.yaml b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_tl_val.yaml index 5ce35c6b..c8373f30 100644 --- a/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_tl_val.yaml +++ b/configs/experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/heatmaps_and_max_aggregations/stain_base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/max_aggregations/mmci_tl_test.yaml b/configs/experiment/predict/images/resnet50/max_aggregations/mmci_tl_test.yaml index eb32a0a9..6fa0e571 100644 --- a/configs/experiment/predict/images/resnet50/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/predict/images/resnet50/max_aggregations/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/max_aggregations/base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/max_aggregations/stain_mmci_tl_test.yaml b/configs/experiment/predict/images/resnet50/max_aggregations/stain_mmci_tl_test.yaml index 04f8856a..49640f1a 100644 --- a/configs/experiment/predict/images/resnet50/max_aggregations/stain_mmci_tl_test.yaml +++ b/configs/experiment/predict/images/resnet50/max_aggregations/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/max_aggregations/stain_base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/mmci_tl_test.yaml b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/mmci_tl_test.yaml index 10b5f0dc..3bed74b5 100644 --- a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/mmci_tl_test.yaml +++ b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/multi_aggregator_eval/base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/mmci_tl_test_224.yaml b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/mmci_tl_test_224.yaml index 764577b3..579cd192 100644 --- a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/mmci_tl_test_224.yaml +++ b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/mmci_tl_test_224.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/multi_aggregator_eval/base_224 - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/radboud_test.yaml b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/radboud_test.yaml index b76dbcc4..b39f54f2 100644 --- a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/radboud_test.yaml +++ b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/predict/images/resnet50/multi_aggregator_eval/base - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/radboud_test_224.yaml b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/radboud_test_224.yaml index 55ffa8cd..88d14744 100644 --- a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/radboud_test_224.yaml +++ b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/radboud_test_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/predict/images/resnet50/multi_aggregator_eval/base_224 - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_mmci_tl_test.yaml b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_mmci_tl_test.yaml index 8f78a41e..7f577c81 100644 --- a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_mmci_tl_test.yaml +++ b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/multi_aggregator_eval/stain_base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_mmci_tl_test_224.yaml b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_mmci_tl_test_224.yaml index 83cfd6b6..adb95235 100644 --- a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_mmci_tl_test_224.yaml +++ b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_mmci_tl_test_224.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/resnet50/multi_aggregator_eval/stain_base_224 - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_radboud_test.yaml b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_radboud_test.yaml index f8eb8f19..a7e1fb3c 100644 --- a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_radboud_test.yaml +++ b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/predict/images/resnet50/multi_aggregator_eval/stain_base - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_radboud_test_224.yaml b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_radboud_test_224.yaml index e9346f2a..779cd687 100644 --- a/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_radboud_test_224.yaml +++ b/configs/experiment/predict/images/resnet50/multi_aggregator_eval/stain_radboud_test_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/predict/images/resnet50/multi_aggregator_eval/stain_base_224 - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/predict/images/resnet50/stain_base.yaml b/configs/experiment/predict/images/resnet50/stain_base.yaml index c700662b..d1ad6d74 100644 --- a/configs/experiment/predict/images/resnet50/stain_base.yaml +++ b/configs/experiment/predict/images/resnet50/stain_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/images/base - /model/resnet50_model@model - - /model/checkpoints/mmci_tl/resnet50_stain@model_data + - /model/checkpoints/prostate/resnet50_stain@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/images/resnet50/stain_base_224.yaml b/configs/experiment/predict/images/resnet50/stain_base_224.yaml index 214cb1b3..2da31dee 100644 --- a/configs/experiment/predict/images/resnet50/stain_base_224.yaml +++ b/configs/experiment/predict/images/resnet50/stain_base_224.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/images/base - /model/resnet50_model@model - - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data + - /model/checkpoints/prostate/resnet50_stain_224@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/images/vgg16/base.yaml b/configs/experiment/predict/images/vgg16/base.yaml index 7e2c7086..3ed3067c 100644 --- a/configs/experiment/predict/images/vgg16/base.yaml +++ b/configs/experiment/predict/images/vgg16/base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/images/base - /model/vgg16_model@model - - /model/checkpoints/mmci_tl/vgg16@model_data + - /model/checkpoints/prostate/vgg16@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/images/vgg16/base_224.yaml b/configs/experiment/predict/images/vgg16/base_224.yaml index 2262e324..915f91d9 100644 --- a/configs/experiment/predict/images/vgg16/base_224.yaml +++ b/configs/experiment/predict/images/vgg16/base_224.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/images/base - /model/vgg16_model@model - - /model/checkpoints/mmci_tl/vgg16_224@model_data + - /model/checkpoints/prostate/vgg16_224@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/images/vgg16/estimations/mpm_estimation.yaml b/configs/experiment/predict/images/vgg16/estimations/mpm_estimation.yaml index bce6e294..abfff46d 100644 --- a/configs/experiment/predict/images/vgg16/estimations/mpm_estimation.yaml +++ b/configs/experiment/predict/images/vgg16/estimations/mpm_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/vgg16/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/vgg16/estimations/mpm_estimation_224.yaml b/configs/experiment/predict/images/vgg16/estimations/mpm_estimation_224.yaml index 3ec1b3e4..b144726b 100644 --- a/configs/experiment/predict/images/vgg16/estimations/mpm_estimation_224.yaml +++ b/configs/experiment/predict/images/vgg16/estimations/mpm_estimation_224.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/vgg16/base_224 - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/vgg16/estimations/span_estimation.yaml b/configs/experiment/predict/images/vgg16/estimations/span_estimation.yaml index d24a26d8..f53e49a5 100644 --- a/configs/experiment/predict/images/vgg16/estimations/span_estimation.yaml +++ b/configs/experiment/predict/images/vgg16/estimations/span_estimation.yaml @@ -3,12 +3,12 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/vgg16/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: estimation_callback: - aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + aggregator_cls_path: ml.aggregators.span.SpanAggregator static: extent_tile: 512 stride_tile: 256 diff --git a/configs/experiment/predict/images/vgg16/estimations/span_estimation_224.yaml b/configs/experiment/predict/images/vgg16/estimations/span_estimation_224.yaml index 99a8ddf8..ad2e1f12 100644 --- a/configs/experiment/predict/images/vgg16/estimations/span_estimation_224.yaml +++ b/configs/experiment/predict/images/vgg16/estimations/span_estimation_224.yaml @@ -3,12 +3,12 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/vgg16/base_224 - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: estimation_callback: - aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + aggregator_cls_path: ml.aggregators.span.SpanAggregator static: extent_tile: 224 stride_tile: 112 diff --git a/configs/experiment/predict/images/vgg16/estimations/stain_mpm_estimation.yaml b/configs/experiment/predict/images/vgg16/estimations/stain_mpm_estimation.yaml index aaea610d..6a776076 100644 --- a/configs/experiment/predict/images/vgg16/estimations/stain_mpm_estimation.yaml +++ b/configs/experiment/predict/images/vgg16/estimations/stain_mpm_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/vgg16/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/vgg16/estimations/stain_mpm_estimation_224.yaml b/configs/experiment/predict/images/vgg16/estimations/stain_mpm_estimation_224.yaml index f3e7d01d..5c0653b1 100644 --- a/configs/experiment/predict/images/vgg16/estimations/stain_mpm_estimation_224.yaml +++ b/configs/experiment/predict/images/vgg16/estimations/stain_mpm_estimation_224.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/vgg16/stain_base_224 - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/vgg16/estimations/stain_span_estimation.yaml b/configs/experiment/predict/images/vgg16/estimations/stain_span_estimation.yaml index 69b13b48..39289eb0 100644 --- a/configs/experiment/predict/images/vgg16/estimations/stain_span_estimation.yaml +++ b/configs/experiment/predict/images/vgg16/estimations/stain_span_estimation.yaml @@ -3,12 +3,12 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/vgg16/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: estimation_callback: - aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + aggregator_cls_path: ml.aggregators.span.SpanAggregator static: extent_tile: 512 stride_tile: 256 diff --git a/configs/experiment/predict/images/vgg16/estimations/stain_span_estimation_224.yaml b/configs/experiment/predict/images/vgg16/estimations/stain_span_estimation_224.yaml index 0c7db32d..7eb8dbe7 100644 --- a/configs/experiment/predict/images/vgg16/estimations/stain_span_estimation_224.yaml +++ b/configs/experiment/predict/images/vgg16/estimations/stain_span_estimation_224.yaml @@ -3,12 +3,12 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/vgg16/stain_base_224 - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: estimation_callback: - aggregator_cls_path: prostate_cancer.aggregators.span.SpanAggregator + aggregator_cls_path: ml.aggregators.span.SpanAggregator static: extent_tile: 224 stride_tile: 112 diff --git a/configs/experiment/predict/images/vgg16/estimations/stain_top_k_estimation.yaml b/configs/experiment/predict/images/vgg16/estimations/stain_top_k_estimation.yaml index 94e64b97..d5ab9192 100644 --- a/configs/experiment/predict/images/vgg16/estimations/stain_top_k_estimation.yaml +++ b/configs/experiment/predict/images/vgg16/estimations/stain_top_k_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/vgg16/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/vgg16/estimations/stain_top_k_estimation_224.yaml b/configs/experiment/predict/images/vgg16/estimations/stain_top_k_estimation_224.yaml index eae21493..3b2e2f2d 100644 --- a/configs/experiment/predict/images/vgg16/estimations/stain_top_k_estimation_224.yaml +++ b/configs/experiment/predict/images/vgg16/estimations/stain_top_k_estimation_224.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/vgg16/stain_base_224 - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/vgg16/estimations/top_k_estimation.yaml b/configs/experiment/predict/images/vgg16/estimations/top_k_estimation.yaml index ed8d9a40..089a327a 100644 --- a/configs/experiment/predict/images/vgg16/estimations/top_k_estimation.yaml +++ b/configs/experiment/predict/images/vgg16/estimations/top_k_estimation.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/vgg16/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/vgg16/estimations/top_k_estimation_224.yaml b/configs/experiment/predict/images/vgg16/estimations/top_k_estimation_224.yaml index 97217c4b..ae71803f 100644 --- a/configs/experiment/predict/images/vgg16/estimations/top_k_estimation_224.yaml +++ b/configs/experiment/predict/images/vgg16/estimations/top_k_estimation_224.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/aggregator_estimation@callbacks - /experiment/predict/images/vgg16/base_224 - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ callbacks: diff --git a/configs/experiment/predict/images/vgg16/heatmaps/mmci_tl_val_224.yaml b/configs/experiment/predict/images/vgg16/heatmaps/mmci_tl_val_224.yaml index 40109d33..68f114e6 100644 --- a/configs/experiment/predict/images/vgg16/heatmaps/mmci_tl_val_224.yaml +++ b/configs/experiment/predict/images/vgg16/heatmaps/mmci_tl_val_224.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/heatmaps/base_224 - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/heatmaps/stain_mmci_tl_val_224.yaml b/configs/experiment/predict/images/vgg16/heatmaps/stain_mmci_tl_val_224.yaml index 07257527..c69d9ee6 100644 --- a/configs/experiment/predict/images/vgg16/heatmaps/stain_mmci_tl_val_224.yaml +++ b/configs/experiment/predict/images/vgg16/heatmaps/stain_mmci_tl_val_224.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/heatmaps/stain_base_224 - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml index a136e4fe..9564ac15 100644 --- a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml +++ b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/heatmaps_and_max_aggregations/base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml index d205552c..c04fa00e 100644 --- a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml +++ b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_sl_group_2.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/heatmaps_and_max_aggregations/base - - /data/mmci/sl_group_2@predict_data + - /data/prostate/mmci/sl_group_2@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_tl_test.yaml b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_tl_test.yaml index 9adce09b..1f7d7d25 100644 --- a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/heatmaps_and_max_aggregations/base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_tl_train.yaml b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_tl_train.yaml index 022568ec..44d9eb1a 100644 --- a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_tl_train.yaml +++ b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_tl_train.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/heatmaps_and_max_aggregations/base - - /data/mmci/tl_train@predict_data + - /data/prostate/mmci/tl_train@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_tl_val.yaml b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_tl_val.yaml index 7c3cfa43..142af5e7 100644 --- a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_tl_val.yaml +++ b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/heatmaps_and_max_aggregations/base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml index d74aa3b6..256cf800 100644 --- a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml +++ b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_base - - /data/mmci/sl_group_1@predict_data + - /data/prostate/mmci/sl_group_1@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_sl_group_2.yaml b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_sl_group_2.yaml index 15a9f5a8..6d411a84 100644 --- a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_sl_group_2.yaml +++ b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_sl_group_2.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_base - - /data/mmci/sl_group_2@predict_data + - /data/prostate/mmci/sl_group_2@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_tl_test.yaml b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_tl_test.yaml index ae9fb9fb..4c412c60 100644 --- a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_tl_test.yaml +++ b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_tl_train.yaml b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_tl_train.yaml index d6c670a2..8d9e4e68 100644 --- a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_tl_train.yaml +++ b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_tl_train.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_base - - /data/mmci/tl_train@predict_data + - /data/prostate/mmci/tl_train@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_tl_val.yaml b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_tl_val.yaml index 13366855..57e556b8 100644 --- a/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_tl_val.yaml +++ b/configs/experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/heatmaps_and_max_aggregations/stain_base - - /data/mmci/tl_val@predict_data + - /data/prostate/mmci/tl_val@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/max_aggregations/mmci_tl_test.yaml b/configs/experiment/predict/images/vgg16/max_aggregations/mmci_tl_test.yaml index 05ca212d..abc0350c 100644 --- a/configs/experiment/predict/images/vgg16/max_aggregations/mmci_tl_test.yaml +++ b/configs/experiment/predict/images/vgg16/max_aggregations/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/max_aggregations/base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/max_aggregations/stain_mmci_tl_test.yaml b/configs/experiment/predict/images/vgg16/max_aggregations/stain_mmci_tl_test.yaml index 771e365c..d33c0d3d 100644 --- a/configs/experiment/predict/images/vgg16/max_aggregations/stain_mmci_tl_test.yaml +++ b/configs/experiment/predict/images/vgg16/max_aggregations/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/max_aggregations/stain_base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/mmci_tl_test.yaml b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/mmci_tl_test.yaml index 0e585312..8f6e3596 100644 --- a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/mmci_tl_test.yaml +++ b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/multi_aggregator_eval/base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/mmci_tl_test_224.yaml b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/mmci_tl_test_224.yaml index 33168aef..6c5a30db 100644 --- a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/mmci_tl_test_224.yaml +++ b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/mmci_tl_test_224.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/multi_aggregator_eval/base_224 - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/radboud_test.yaml b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/radboud_test.yaml index 93ad0bac..627fe468 100644 --- a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/radboud_test.yaml +++ b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/predict/images/vgg16/multi_aggregator_eval/base - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/radboud_test_224.yaml b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/radboud_test_224.yaml index 47512064..4fc029b8 100644 --- a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/radboud_test_224.yaml +++ b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/radboud_test_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/predict/images/vgg16/multi_aggregator_eval/base_224 - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_mmci_tl_test.yaml b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_mmci_tl_test.yaml index f4c042ec..31bbafd2 100644 --- a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_mmci_tl_test.yaml +++ b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/multi_aggregator_eval/stain_base - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_mmci_tl_test_224.yaml b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_mmci_tl_test_224.yaml index ac6bfa41..6d24d287 100644 --- a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_mmci_tl_test_224.yaml +++ b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_mmci_tl_test_224.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/predict/images/vgg16/multi_aggregator_eval/stain_base_224 - - /data/mmci/tl_test@predict_data + - /data/prostate/mmci/tl_test@predict_data - _self_ diff --git a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_radboud_test.yaml b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_radboud_test.yaml index 95828140..2bc1a534 100644 --- a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_radboud_test.yaml +++ b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/predict/images/vgg16/multi_aggregator_eval/stain_base - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_radboud_test_224.yaml b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_radboud_test_224.yaml index 722914ec..1631b3a1 100644 --- a/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_radboud_test_224.yaml +++ b/configs/experiment/predict/images/vgg16/multi_aggregator_eval/stain_radboud_test_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/predict/images/vgg16/multi_aggregator_eval/stain_base_224 - - /data/radboud/test@predict_data + - /data/prostate/radboud/test@predict_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/predict/images/vgg16/stain_base.yaml b/configs/experiment/predict/images/vgg16/stain_base.yaml index 20782b52..d584a0e3 100644 --- a/configs/experiment/predict/images/vgg16/stain_base.yaml +++ b/configs/experiment/predict/images/vgg16/stain_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/images/base - /model/vgg16_model@model - - /model/checkpoints/mmci_tl/vgg16_stain@model_data + - /model/checkpoints/prostate/vgg16_stain@model_data - _self_ datamodule: diff --git a/configs/experiment/predict/images/vgg16/stain_base_224.yaml b/configs/experiment/predict/images/vgg16/stain_base_224.yaml index 792aca11..56c01ca0 100644 --- a/configs/experiment/predict/images/vgg16/stain_base_224.yaml +++ b/configs/experiment/predict/images/vgg16/stain_base_224.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/predict/images/base - /model/vgg16_model@model - - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data + - /model/checkpoints/prostate/vgg16_stain_224@model_data - _self_ datamodule: diff --git a/configs/experiment/preprocessing/annot_masks/mmci_tl_test.yaml b/configs/experiment/preprocessing/annot_masks/mmci_tl_test.yaml index b72b6113..0548bdb6 100644 --- a/configs/experiment/preprocessing/annot_masks/mmci_tl_test.yaml +++ b/configs/experiment/preprocessing/annot_masks/mmci_tl_test.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data - _self_ diff --git a/configs/experiment/preprocessing/annot_masks/mmci_tl_train.yaml b/configs/experiment/preprocessing/annot_masks/mmci_tl_train.yaml index 6fd82935..09d568ce 100644 --- a/configs/experiment/preprocessing/annot_masks/mmci_tl_train.yaml +++ b/configs/experiment/preprocessing/annot_masks/mmci_tl_train.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_train@data + - /data/prostate/mmci/tl_train@data - _self_ diff --git a/configs/experiment/preprocessing/annot_masks/mmci_tl_val.yaml b/configs/experiment/preprocessing/annot_masks/mmci_tl_val.yaml index a9502109..a833874b 100644 --- a/configs/experiment/preprocessing/annot_masks/mmci_tl_val.yaml +++ b/configs/experiment/preprocessing/annot_masks/mmci_tl_val.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_val@data + - /data/prostate/mmci/tl_val@data - _self_ diff --git a/configs/experiment/preprocessing/filter_embeddings/mmci_sl_group_1.yaml b/configs/experiment/preprocessing/filter_embeddings/mmci_sl_group_1.yaml index f711bfba..2bc42847 100644 --- a/configs/experiment/preprocessing/filter_embeddings/mmci_sl_group_1.yaml +++ b/configs/experiment/preprocessing/filter_embeddings/mmci_sl_group_1.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ diff --git a/configs/experiment/preprocessing/filter_embeddings/mmci_sl_group_2.yaml b/configs/experiment/preprocessing/filter_embeddings/mmci_sl_group_2.yaml index ddc7face..1592f65c 100644 --- a/configs/experiment/preprocessing/filter_embeddings/mmci_sl_group_2.yaml +++ b/configs/experiment/preprocessing/filter_embeddings/mmci_sl_group_2.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/sl_group_2@data + - /data/prostate/mmci/sl_group_2@data - _self_ diff --git a/configs/experiment/preprocessing/filter_embeddings/mmci_tl_test.yaml b/configs/experiment/preprocessing/filter_embeddings/mmci_tl_test.yaml index b72b6113..0548bdb6 100644 --- a/configs/experiment/preprocessing/filter_embeddings/mmci_tl_test.yaml +++ b/configs/experiment/preprocessing/filter_embeddings/mmci_tl_test.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data - _self_ diff --git a/configs/experiment/preprocessing/filter_embeddings/mmci_tl_train.yaml b/configs/experiment/preprocessing/filter_embeddings/mmci_tl_train.yaml index 6fd82935..09d568ce 100644 --- a/configs/experiment/preprocessing/filter_embeddings/mmci_tl_train.yaml +++ b/configs/experiment/preprocessing/filter_embeddings/mmci_tl_train.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_train@data + - /data/prostate/mmci/tl_train@data - _self_ diff --git a/configs/experiment/preprocessing/filter_embeddings/mmci_tl_val.yaml b/configs/experiment/preprocessing/filter_embeddings/mmci_tl_val.yaml index a9502109..a833874b 100644 --- a/configs/experiment/preprocessing/filter_embeddings/mmci_tl_val.yaml +++ b/configs/experiment/preprocessing/filter_embeddings/mmci_tl_val.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_val@data + - /data/prostate/mmci/tl_val@data - _self_ diff --git a/configs/experiment/preprocessing/filter_tiles/mmci_sl_group_1.yaml b/configs/experiment/preprocessing/filter_tiles/mmci_sl_group_1.yaml index f711bfba..2bc42847 100644 --- a/configs/experiment/preprocessing/filter_tiles/mmci_sl_group_1.yaml +++ b/configs/experiment/preprocessing/filter_tiles/mmci_sl_group_1.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ diff --git a/configs/experiment/preprocessing/filter_tiles/mmci_sl_group_2.yaml b/configs/experiment/preprocessing/filter_tiles/mmci_sl_group_2.yaml index ddc7face..1592f65c 100644 --- a/configs/experiment/preprocessing/filter_tiles/mmci_sl_group_2.yaml +++ b/configs/experiment/preprocessing/filter_tiles/mmci_sl_group_2.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/sl_group_2@data + - /data/prostate/mmci/sl_group_2@data - _self_ diff --git a/configs/experiment/preprocessing/filter_tiles/mmci_tl_test.yaml b/configs/experiment/preprocessing/filter_tiles/mmci_tl_test.yaml index b72b6113..0548bdb6 100644 --- a/configs/experiment/preprocessing/filter_tiles/mmci_tl_test.yaml +++ b/configs/experiment/preprocessing/filter_tiles/mmci_tl_test.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data - _self_ diff --git a/configs/experiment/preprocessing/filter_tiles/mmci_tl_train.yaml b/configs/experiment/preprocessing/filter_tiles/mmci_tl_train.yaml index 6fd82935..09d568ce 100644 --- a/configs/experiment/preprocessing/filter_tiles/mmci_tl_train.yaml +++ b/configs/experiment/preprocessing/filter_tiles/mmci_tl_train.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_train@data + - /data/prostate/mmci/tl_train@data - _self_ diff --git a/configs/experiment/preprocessing/filter_tiles/mmci_tl_val.yaml b/configs/experiment/preprocessing/filter_tiles/mmci_tl_val.yaml index a9502109..a833874b 100644 --- a/configs/experiment/preprocessing/filter_tiles/mmci_tl_val.yaml +++ b/configs/experiment/preprocessing/filter_tiles/mmci_tl_val.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_val@data + - /data/prostate/mmci/tl_val@data - _self_ diff --git a/configs/experiment/preprocessing/filter_tiles/radboud_test.yaml b/configs/experiment/preprocessing/filter_tiles/radboud_test.yaml index 23100058..510c4cc2 100644 --- a/configs/experiment/preprocessing/filter_tiles/radboud_test.yaml +++ b/configs/experiment/preprocessing/filter_tiles/radboud_test.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/radboud/test@data + - /data/prostate/radboud/test@data - _self_ diff --git a/configs/experiment/preprocessing/filter_tiles/radboud_train.yaml b/configs/experiment/preprocessing/filter_tiles/radboud_train.yaml index c6d87616..176f71d5 100644 --- a/configs/experiment/preprocessing/filter_tiles/radboud_train.yaml +++ b/configs/experiment/preprocessing/filter_tiles/radboud_train.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/radboud/train@data + - /data/prostate/radboud/train@data - _self_ diff --git a/configs/experiment/preprocessing/filter_tiles/radboud_val.yaml b/configs/experiment/preprocessing/filter_tiles/radboud_val.yaml index 8ead8fb8..c0abc974 100644 --- a/configs/experiment/preprocessing/filter_tiles/radboud_val.yaml +++ b/configs/experiment/preprocessing/filter_tiles/radboud_val.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/radboud/val@data + - /data/prostate/radboud/val@data - _self_ diff --git a/configs/experiment/preprocessing/group_split/mmci_sl.yaml b/configs/experiment/preprocessing/group_split/mmci_sl.yaml index f67768e0..3bf89993 100644 --- a/configs/experiment/preprocessing/group_split/mmci_sl.yaml +++ b/configs/experiment/preprocessing/group_split/mmci_sl.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl@data + - /data/prostate/mmci/sl@data - _self_ test_size: 0.2 diff --git a/configs/experiment/preprocessing/group_split/mmci_tl.yaml b/configs/experiment/preprocessing/group_split/mmci_tl.yaml index 75b339e6..4d928268 100644 --- a/configs/experiment/preprocessing/group_split/mmci_tl.yaml +++ b/configs/experiment/preprocessing/group_split/mmci_tl.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/tl@data + - /data/prostate/mmci/tl@data - _self_ test_size: 0.1 diff --git a/configs/experiment/preprocessing/k_fold/mmci_sl_group_2.yaml b/configs/experiment/preprocessing/k_fold/mmci_sl_group_2.yaml deleted file mode 100644 index 2f2cc25d..00000000 --- a/configs/experiment/preprocessing/k_fold/mmci_sl_group_2.yaml +++ /dev/null @@ -1,7 +0,0 @@ -# @package _global_ - -defaults: - - /data/mmci/sl_group_2@data - - _self_ - -k: 5 diff --git a/configs/experiment/preprocessing/mean_and_std/mmci_tl_train_512.yaml b/configs/experiment/preprocessing/mean_and_std/mmci_tl_train_512.yaml index 1fce7292..c8c4cf6e 100644 --- a/configs/experiment/preprocessing/mean_and_std/mmci_tl_train_512.yaml +++ b/configs/experiment/preprocessing/mean_and_std/mmci_tl_train_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/tl_train@data + - /data/prostate/mmci/tl_train@data - _self_ uris: diff --git a/configs/experiment/preprocessing/mean_and_std/radboud_train_512.yaml b/configs/experiment/preprocessing/mean_and_std/radboud_train_512.yaml index 9b475f37..52c1a9b4 100644 --- a/configs/experiment/preprocessing/mean_and_std/radboud_train_512.yaml +++ b/configs/experiment/preprocessing/mean_and_std/radboud_train_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/train@data + - /data/prostate/radboud/train@data - _self_ uris: diff --git a/configs/experiment/preprocessing/mean_and_std/radboud_val_heuristic_512.yaml b/configs/experiment/preprocessing/mean_and_std/radboud_val_heuristic_512.yaml index 9122e3cc..433084ec 100644 --- a/configs/experiment/preprocessing/mean_and_std/radboud_val_heuristic_512.yaml +++ b/configs/experiment/preprocessing/mean_and_std/radboud_val_heuristic_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/val_heuristic_normalized@data + - /data/prostate/radboud/val_heuristic_normalized@data - _self_ uris: diff --git a/configs/experiment/preprocessing/mean_and_std/radboud_val_ml_512.yaml b/configs/experiment/preprocessing/mean_and_std/radboud_val_ml_512.yaml index 759cd851..3e164fd6 100644 --- a/configs/experiment/preprocessing/mean_and_std/radboud_val_ml_512.yaml +++ b/configs/experiment/preprocessing/mean_and_std/radboud_val_ml_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/val_ml_normalized@data + - /data/prostate/radboud/val_ml_normalized@data - _self_ uris: diff --git a/configs/experiment/preprocessing/mean_and_std/radboud_val_raw_512.yaml b/configs/experiment/preprocessing/mean_and_std/radboud_val_raw_512.yaml index 1ea78b0c..ef37fbce 100644 --- a/configs/experiment/preprocessing/mean_and_std/radboud_val_raw_512.yaml +++ b/configs/experiment/preprocessing/mean_and_std/radboud_val_raw_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/val@data + - /data/prostate/radboud/val@data - _self_ uris: diff --git a/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_sl_group_1.yaml b/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_sl_group_1.yaml index c1d30f90..f885c11f 100644 --- a/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_sl_group_1.yaml +++ b/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/preprocessing/merge_embeddings/pgp/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ diff --git a/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_sl_group_2.yaml b/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_sl_group_2.yaml index a217b6c6..614b9be0 100644 --- a/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_sl_group_2.yaml +++ b/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_sl_group_2.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/preprocessing/merge_embeddings/pgp/base - - /data/mmci/sl_group_2@data + - /data/prostate/mmci/sl_group_2@data - _self_ diff --git a/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_tl_test.yaml b/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_tl_test.yaml index 9bb9467e..8cc93cef 100644 --- a/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_tl_test.yaml +++ b/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/preprocessing/merge_embeddings/pgp/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data - _self_ diff --git a/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_tl_train.yaml b/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_tl_train.yaml index 048d1318..598df299 100644 --- a/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_tl_train.yaml +++ b/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_tl_train.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/preprocessing/merge_embeddings/pgp/base - - /data/mmci/tl_train@data + - /data/prostate/mmci/tl_train@data - _self_ diff --git a/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_tl_val.yaml b/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_tl_val.yaml index 1e36f0be..bdf134b7 100644 --- a/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_tl_val.yaml +++ b/configs/experiment/preprocessing/merge_embeddings/pgp/mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/preprocessing/merge_embeddings/pgp/base - - /data/mmci/tl_val@data + - /data/prostate/mmci/tl_val@data - _self_ diff --git a/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_sl_group_1.yaml b/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_sl_group_1.yaml index 4cc06fec..92dfaa24 100644 --- a/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_sl_group_1.yaml +++ b/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_sl_group_1.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/preprocessing/merge_embeddings/virchow2/base - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ diff --git a/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_sl_group_2.yaml b/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_sl_group_2.yaml index 631683fc..13de5ea6 100644 --- a/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_sl_group_2.yaml +++ b/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_sl_group_2.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/preprocessing/merge_embeddings/virchow2/base - - /data/mmci/sl_group_2@data + - /data/prostate/mmci/sl_group_2@data - _self_ diff --git a/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_tl_test.yaml b/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_tl_test.yaml index dc0776f4..04789929 100644 --- a/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_tl_test.yaml +++ b/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/preprocessing/merge_embeddings/virchow2/base - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data - _self_ diff --git a/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_tl_train.yaml b/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_tl_train.yaml index 2f726a91..572bcae1 100644 --- a/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_tl_train.yaml +++ b/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_tl_train.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/preprocessing/merge_embeddings/virchow2/base - - /data/mmci/tl_train@data + - /data/prostate/mmci/tl_train@data - _self_ diff --git a/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_tl_val.yaml b/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_tl_val.yaml index 9a907eef..03b7f5e2 100644 --- a/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_tl_val.yaml +++ b/configs/experiment/preprocessing/merge_embeddings/virchow2/mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/preprocessing/merge_embeddings/virchow2/base - - /data/mmci/tl_val@data + - /data/prostate/mmci/tl_val@data - _self_ diff --git a/configs/experiment/preprocessing/qc_masks/comenius_3_sample.yaml b/configs/experiment/preprocessing/qc_masks/comenius_3_sample.yaml index fc9903bf..b01d15f1 100644 --- a/configs/experiment/preprocessing/qc_masks/comenius_3_sample.yaml +++ b/configs/experiment/preprocessing/qc_masks/comenius_3_sample.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/comenius/comenius_3_sample@data + - /data/prostate/comenius/comenius_3_sample@data - _self_ diff --git a/configs/experiment/preprocessing/qc_masks/mmci_endoresection.yaml b/configs/experiment/preprocessing/qc_masks/mmci_endoresection.yaml index 1d339791..fca01877 100644 --- a/configs/experiment/preprocessing/qc_masks/mmci_endoresection.yaml +++ b/configs/experiment/preprocessing/qc_masks/mmci_endoresection.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/endoresection@data + - /data/prostate/mmci/endoresection@data - _self_ diff --git a/configs/experiment/preprocessing/qc_masks/mmci_sl_group_1.yaml b/configs/experiment/preprocessing/qc_masks/mmci_sl_group_1.yaml index f711bfba..2bc42847 100644 --- a/configs/experiment/preprocessing/qc_masks/mmci_sl_group_1.yaml +++ b/configs/experiment/preprocessing/qc_masks/mmci_sl_group_1.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ diff --git a/configs/experiment/preprocessing/qc_masks/mmci_sl_group_2.yaml b/configs/experiment/preprocessing/qc_masks/mmci_sl_group_2.yaml index ddc7face..1592f65c 100644 --- a/configs/experiment/preprocessing/qc_masks/mmci_sl_group_2.yaml +++ b/configs/experiment/preprocessing/qc_masks/mmci_sl_group_2.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/sl_group_2@data + - /data/prostate/mmci/sl_group_2@data - _self_ diff --git a/configs/experiment/preprocessing/qc_masks/mmci_tl_test.yaml b/configs/experiment/preprocessing/qc_masks/mmci_tl_test.yaml index b72b6113..0548bdb6 100644 --- a/configs/experiment/preprocessing/qc_masks/mmci_tl_test.yaml +++ b/configs/experiment/preprocessing/qc_masks/mmci_tl_test.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data - _self_ diff --git a/configs/experiment/preprocessing/qc_masks/mmci_tl_train.yaml b/configs/experiment/preprocessing/qc_masks/mmci_tl_train.yaml index 6fd82935..09d568ce 100644 --- a/configs/experiment/preprocessing/qc_masks/mmci_tl_train.yaml +++ b/configs/experiment/preprocessing/qc_masks/mmci_tl_train.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_train@data + - /data/prostate/mmci/tl_train@data - _self_ diff --git a/configs/experiment/preprocessing/qc_masks/mmci_tl_val.yaml b/configs/experiment/preprocessing/qc_masks/mmci_tl_val.yaml index a9502109..a833874b 100644 --- a/configs/experiment/preprocessing/qc_masks/mmci_tl_val.yaml +++ b/configs/experiment/preprocessing/qc_masks/mmci_tl_val.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_val@data + - /data/prostate/mmci/tl_val@data - _self_ diff --git a/configs/experiment/preprocessing/qc_masks/radboud.yaml b/configs/experiment/preprocessing/qc_masks/radboud.yaml index 5624dd5e..63bbfb69 100644 --- a/configs/experiment/preprocessing/qc_masks/radboud.yaml +++ b/configs/experiment/preprocessing/qc_masks/radboud.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/full@data + - /data/prostate/radboud/full@data - _self_ sample_level: 0 diff --git a/configs/experiment/preprocessing/quality_control_v2/fn_brno.yaml b/configs/experiment/preprocessing/quality_control_v2/fn_brno.yaml index 48f60971..a9f09a86 100644 --- a/configs/experiment/preprocessing/quality_control_v2/fn_brno.yaml +++ b/configs/experiment/preprocessing/quality_control_v2/fn_brno.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/fn_brno/full@data + - /data/prostate/fn_brno/full@data - _self_ diff --git a/configs/experiment/preprocessing/quality_control_v2/karolinska.yaml b/configs/experiment/preprocessing/quality_control_v2/karolinska.yaml index 5e996cd1..e95001e7 100644 --- a/configs/experiment/preprocessing/quality_control_v2/karolinska.yaml +++ b/configs/experiment/preprocessing/quality_control_v2/karolinska.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/karolinska/full@data + - /data/prostate/karolinska/full@data - _self_ diff --git a/configs/experiment/preprocessing/quality_control_v2/radboud.yaml b/configs/experiment/preprocessing/quality_control_v2/radboud.yaml index 1dd2cda5..38687177 100644 --- a/configs/experiment/preprocessing/quality_control_v2/radboud.yaml +++ b/configs/experiment/preprocessing/quality_control_v2/radboud.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/radboud/full@data + - /data/prostate/radboud/full@data - _self_ diff --git a/configs/experiment/preprocessing/repath_normalization/radboud_val_heuristic.yaml b/configs/experiment/preprocessing/repath_normalization/radboud_val_heuristic.yaml index 34423087..f944a007 100644 --- a/configs/experiment/preprocessing/repath_normalization/radboud_val_heuristic.yaml +++ b/configs/experiment/preprocessing/repath_normalization/radboud_val_heuristic.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/val@data + - /data/prostate/radboud/val@data - _self_ normalized_data_dir: /mnt/projects/prostate_cancer/cancer/PANDA/normalized_images_percentile_25 diff --git a/configs/experiment/preprocessing/repath_normalization/radboud_val_ml.yaml b/configs/experiment/preprocessing/repath_normalization/radboud_val_ml.yaml index e3c667e1..e6f6783c 100644 --- a/configs/experiment/preprocessing/repath_normalization/radboud_val_ml.yaml +++ b/configs/experiment/preprocessing/repath_normalization/radboud_val_ml.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/val@data + - /data/prostate/radboud/val@data - _self_ normalized_data_dir: /mnt/projects/prostate_cancer/cancer/Radboud_val_test diff --git a/configs/experiment/preprocessing/simple_split/karolinska.yaml b/configs/experiment/preprocessing/simple_split/karolinska.yaml index 658ef696..caa41d33 100644 --- a/configs/experiment/preprocessing/simple_split/karolinska.yaml +++ b/configs/experiment/preprocessing/simple_split/karolinska.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/karolinska/full@data + - /data/prostate/karolinska/full@data - _self_ target_column: gleason_score diff --git a/configs/experiment/preprocessing/simple_split/radboud.yaml b/configs/experiment/preprocessing/simple_split/radboud.yaml index d9d4d23f..7c4f1c4e 100644 --- a/configs/experiment/preprocessing/simple_split/radboud.yaml +++ b/configs/experiment/preprocessing/simple_split/radboud.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/full@data + - /data/prostate/radboud/full@data - _self_ target_column: gleason_score diff --git a/configs/experiment/preprocessing/simple_split/radboud_train_val.yaml b/configs/experiment/preprocessing/simple_split/radboud_train_val.yaml index 8725858f..5769b158 100644 --- a/configs/experiment/preprocessing/simple_split/radboud_train_val.yaml +++ b/configs/experiment/preprocessing/simple_split/radboud_train_val.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/train_val@data + - /data/prostate/radboud/train_val@data - _self_ target_column: gleason_score diff --git a/configs/experiment/preprocessing/tile_embeddings/pgp/base.yaml b/configs/experiment/preprocessing/tile_embeddings/pgp/base.yaml index 7ee4520c..4bc1c615 100644 --- a/configs/experiment/preprocessing/tile_embeddings/pgp/base.yaml +++ b/configs/experiment/preprocessing/tile_embeddings/pgp/base.yaml @@ -1,4 +1,4 @@ # @package _global_ tile_encoder: - _target_: prostate_cancer.modeling.backbone.pgp.ProvGigaPath + _target_: ml.modeling.backbone.pgp.ProvGigaPath diff --git a/configs/experiment/preprocessing/tile_embeddings/pgp/mmci_sl.yaml b/configs/experiment/preprocessing/tile_embeddings/pgp/mmci_sl.yaml index 1d535b13..785352b1 100644 --- a/configs/experiment/preprocessing/tile_embeddings/pgp/mmci_sl.yaml +++ b/configs/experiment/preprocessing/tile_embeddings/pgp/mmci_sl.yaml @@ -2,8 +2,8 @@ defaults: - /experiment/preprocessing/tile_embeddings/pgp/base - - /data/mmci/sl_group_1@data_group_1 - - /data/mmci/sl_group_2@data_group_2 + - /data/prostate/mmci/sl_group_1@data_group_1 + - /data/prostate/mmci/sl_group_2@data_group_2 - _self_ uris: diff --git a/configs/experiment/preprocessing/tile_embeddings/pgp/mmci_tl.yaml b/configs/experiment/preprocessing/tile_embeddings/pgp/mmci_tl.yaml index 5fef87e0..e296e6a8 100644 --- a/configs/experiment/preprocessing/tile_embeddings/pgp/mmci_tl.yaml +++ b/configs/experiment/preprocessing/tile_embeddings/pgp/mmci_tl.yaml @@ -2,9 +2,9 @@ defaults: - /experiment/preprocessing/tile_embeddings/pgp/base - - /data/mmci/tl_train@data_train - - /data/mmci/tl_val@data_val - - /data/mmci/tl_test@data_test + - /data/prostate/mmci/tl_train@data_train + - /data/prostate/mmci/tl_val@data_val + - /data/prostate/mmci/tl_test@data_test - _self_ uris: diff --git a/configs/experiment/preprocessing/tile_embeddings/virchow2/base.yaml b/configs/experiment/preprocessing/tile_embeddings/virchow2/base.yaml index 3c1be55a..173e39ac 100644 --- a/configs/experiment/preprocessing/tile_embeddings/virchow2/base.yaml +++ b/configs/experiment/preprocessing/tile_embeddings/virchow2/base.yaml @@ -1,4 +1,4 @@ # @package _global_ tile_encoder: - _target_: prostate_cancer.modeling.backbone.virchow2.Virchow2 + _target_: ml.modeling.backbone.virchow2.Virchow2 diff --git a/configs/experiment/preprocessing/tile_embeddings/virchow2/comenius_3_sample.yaml b/configs/experiment/preprocessing/tile_embeddings/virchow2/comenius_3_sample.yaml index 13f0e6c2..51414a1d 100644 --- a/configs/experiment/preprocessing/tile_embeddings/virchow2/comenius_3_sample.yaml +++ b/configs/experiment/preprocessing/tile_embeddings/virchow2/comenius_3_sample.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/preprocessing/tile_embeddings/virchow2/base - - /data/comenius/comenius_3_sample@data + - /data/prostate/comenius/comenius_3_sample@data - _self_ uris: diff --git a/configs/experiment/preprocessing/tile_embeddings/virchow2/mmci_endoresection.yaml b/configs/experiment/preprocessing/tile_embeddings/virchow2/mmci_endoresection.yaml index 05ba5e88..7786187f 100644 --- a/configs/experiment/preprocessing/tile_embeddings/virchow2/mmci_endoresection.yaml +++ b/configs/experiment/preprocessing/tile_embeddings/virchow2/mmci_endoresection.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/preprocessing/tile_embeddings/virchow2/base - - /data/mmci/endoresection@data + - /data/prostate/mmci/endoresection@data - _self_ uris: diff --git a/configs/experiment/preprocessing/tile_embeddings/virchow2/mmci_sl.yaml b/configs/experiment/preprocessing/tile_embeddings/virchow2/mmci_sl.yaml index 7ecc14aa..84c68894 100644 --- a/configs/experiment/preprocessing/tile_embeddings/virchow2/mmci_sl.yaml +++ b/configs/experiment/preprocessing/tile_embeddings/virchow2/mmci_sl.yaml @@ -2,8 +2,8 @@ defaults: - /experiment/preprocessing/tile_embeddings/virchow2/base - - /data/mmci/sl_group_1@data_group_1 - - /data/mmci/sl_group_2@data_group_2 + - /data/prostate/mmci/sl_group_1@data_group_1 + - /data/prostate/mmci/sl_group_2@data_group_2 - _self_ uris: diff --git a/configs/experiment/preprocessing/tile_embeddings/virchow2/mmci_tl.yaml b/configs/experiment/preprocessing/tile_embeddings/virchow2/mmci_tl.yaml index 0365a00b..a470dc2e 100644 --- a/configs/experiment/preprocessing/tile_embeddings/virchow2/mmci_tl.yaml +++ b/configs/experiment/preprocessing/tile_embeddings/virchow2/mmci_tl.yaml @@ -2,9 +2,9 @@ defaults: - /experiment/preprocessing/tile_embeddings/virchow2/base - - /data/mmci/tl_train@data_train - - /data/mmci/tl_val@data_val - - /data/mmci/tl_test@data_test + - /data/prostate/mmci/tl_train@data_train + - /data/prostate/mmci/tl_val@data_val + - /data/prostate/mmci/tl_test@data_test - _self_ uris: diff --git a/configs/experiment/preprocessing/tile_embeddings_v2/pgp/radboud_test.yaml b/configs/experiment/preprocessing/tile_embeddings_v2/pgp/radboud_test.yaml index 4f0f5548..e8e68e14 100644 --- a/configs/experiment/preprocessing/tile_embeddings_v2/pgp/radboud_test.yaml +++ b/configs/experiment/preprocessing/tile_embeddings_v2/pgp/radboud_test.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/preprocessing/tile_embeddings_v2/pgp/base - - /data/radboud/test@data + - /data/prostate/radboud/test@data diff --git a/configs/experiment/preprocessing/tile_embeddings_v2/pgp/radboud_val.yaml b/configs/experiment/preprocessing/tile_embeddings_v2/pgp/radboud_val.yaml index 6d312f4d..a8dc6ec0 100644 --- a/configs/experiment/preprocessing/tile_embeddings_v2/pgp/radboud_val.yaml +++ b/configs/experiment/preprocessing/tile_embeddings_v2/pgp/radboud_val.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/preprocessing/tile_embeddings_v2/pgp/base - - /data/radboud/val@data + - /data/prostate/radboud/val@data diff --git a/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/mmci_tl_val.yaml b/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/mmci_tl_val.yaml index 9e86ccb4..36b3587a 100644 --- a/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/mmci_tl_val.yaml +++ b/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/mmci_tl_val.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/preprocessing/tile_embeddings_v2/virchow2/base - - /data/mmci/tl_val@data + - /data/prostate/mmci/tl_val@data diff --git a/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/radboud_test.yaml b/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/radboud_test.yaml index ce19ac71..5081ba8a 100644 --- a/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/radboud_test.yaml +++ b/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/radboud_test.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/preprocessing/tile_embeddings_v2/virchow2/base - - /data/radboud/test@data + - /data/prostate/radboud/test@data diff --git a/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/radboud_val.yaml b/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/radboud_val.yaml index 38e710a1..129fb764 100644 --- a/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/radboud_val.yaml +++ b/configs/experiment/preprocessing/tile_embeddings_v2/virchow2/radboud_val.yaml @@ -2,4 +2,4 @@ defaults: - /experiment/preprocessing/tile_embeddings_v2/virchow2/base - - /data/radboud/val@data + - /data/prostate/radboud/val@data diff --git a/configs/experiment/preprocessing/tile_masks/mmci_sl_group_1_224.yaml b/configs/experiment/preprocessing/tile_masks/mmci_sl_group_1_224.yaml index 39221a34..daf1582e 100644 --- a/configs/experiment/preprocessing/tile_masks/mmci_sl_group_1_224.yaml +++ b/configs/experiment/preprocessing/tile_masks/mmci_sl_group_1_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/mmci_sl_group_1_512.yaml b/configs/experiment/preprocessing/tile_masks/mmci_sl_group_1_512.yaml index 1b9339d7..60532bc0 100644 --- a/configs/experiment/preprocessing/tile_masks/mmci_sl_group_1_512.yaml +++ b/configs/experiment/preprocessing/tile_masks/mmci_sl_group_1_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/mmci_sl_group_2_224.yaml b/configs/experiment/preprocessing/tile_masks/mmci_sl_group_2_224.yaml index a0ef0631..0c27f6d8 100644 --- a/configs/experiment/preprocessing/tile_masks/mmci_sl_group_2_224.yaml +++ b/configs/experiment/preprocessing/tile_masks/mmci_sl_group_2_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl_group_2@data + - /data/prostate/mmci/sl_group_2@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/mmci_sl_group_2_512.yaml b/configs/experiment/preprocessing/tile_masks/mmci_sl_group_2_512.yaml index 04ee150e..567d9e00 100644 --- a/configs/experiment/preprocessing/tile_masks/mmci_sl_group_2_512.yaml +++ b/configs/experiment/preprocessing/tile_masks/mmci_sl_group_2_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl_group_2@data + - /data/prostate/mmci/sl_group_2@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/mmci_tl_test_224.yaml b/configs/experiment/preprocessing/tile_masks/mmci_tl_test_224.yaml index 1dcf9100..b8296ff9 100644 --- a/configs/experiment/preprocessing/tile_masks/mmci_tl_test_224.yaml +++ b/configs/experiment/preprocessing/tile_masks/mmci_tl_test_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/mmci_tl_test_512.yaml b/configs/experiment/preprocessing/tile_masks/mmci_tl_test_512.yaml index bbe000ba..39688ebf 100644 --- a/configs/experiment/preprocessing/tile_masks/mmci_tl_test_512.yaml +++ b/configs/experiment/preprocessing/tile_masks/mmci_tl_test_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/mmci_tl_train_224.yaml b/configs/experiment/preprocessing/tile_masks/mmci_tl_train_224.yaml index fae085aa..5cccb770 100644 --- a/configs/experiment/preprocessing/tile_masks/mmci_tl_train_224.yaml +++ b/configs/experiment/preprocessing/tile_masks/mmci_tl_train_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/tl_train@data + - /data/prostate/mmci/tl_train@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/mmci_tl_train_512.yaml b/configs/experiment/preprocessing/tile_masks/mmci_tl_train_512.yaml index 9c4fd355..25ccb292 100644 --- a/configs/experiment/preprocessing/tile_masks/mmci_tl_train_512.yaml +++ b/configs/experiment/preprocessing/tile_masks/mmci_tl_train_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/tl_train@data + - /data/prostate/mmci/tl_train@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/mmci_tl_val_224.yaml b/configs/experiment/preprocessing/tile_masks/mmci_tl_val_224.yaml index 8bbc5487..cc634dc8 100644 --- a/configs/experiment/preprocessing/tile_masks/mmci_tl_val_224.yaml +++ b/configs/experiment/preprocessing/tile_masks/mmci_tl_val_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/tl_val@data + - /data/prostate/mmci/tl_val@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/mmci_tl_val_512.yaml b/configs/experiment/preprocessing/tile_masks/mmci_tl_val_512.yaml index 3df30d20..2ce87088 100644 --- a/configs/experiment/preprocessing/tile_masks/mmci_tl_val_512.yaml +++ b/configs/experiment/preprocessing/tile_masks/mmci_tl_val_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/tl_val@data + - /data/prostate/mmci/tl_val@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/radboud_test_224.yaml b/configs/experiment/preprocessing/tile_masks/radboud_test_224.yaml index ca9819ee..42c389b2 100644 --- a/configs/experiment/preprocessing/tile_masks/radboud_test_224.yaml +++ b/configs/experiment/preprocessing/tile_masks/radboud_test_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/test@data + - /data/prostate/radboud/test@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/radboud_test_512.yaml b/configs/experiment/preprocessing/tile_masks/radboud_test_512.yaml index 4ff4d6ed..f4b07211 100644 --- a/configs/experiment/preprocessing/tile_masks/radboud_test_512.yaml +++ b/configs/experiment/preprocessing/tile_masks/radboud_test_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/test@data + - /data/prostate/radboud/test@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/radboud_train_224.yaml b/configs/experiment/preprocessing/tile_masks/radboud_train_224.yaml index bef43107..43cf14e1 100644 --- a/configs/experiment/preprocessing/tile_masks/radboud_train_224.yaml +++ b/configs/experiment/preprocessing/tile_masks/radboud_train_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/train@data + - /data/prostate/radboud/train@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/radboud_train_512.yaml b/configs/experiment/preprocessing/tile_masks/radboud_train_512.yaml index ecd8700f..995c603a 100644 --- a/configs/experiment/preprocessing/tile_masks/radboud_train_512.yaml +++ b/configs/experiment/preprocessing/tile_masks/radboud_train_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/train@data + - /data/prostate/radboud/train@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/radboud_val_224.yaml b/configs/experiment/preprocessing/tile_masks/radboud_val_224.yaml index cd3f0fa9..ed30ed52 100644 --- a/configs/experiment/preprocessing/tile_masks/radboud_val_224.yaml +++ b/configs/experiment/preprocessing/tile_masks/radboud_val_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/val@data + - /data/prostate/radboud/val@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tile_masks/radboud_val_512.yaml b/configs/experiment/preprocessing/tile_masks/radboud_val_512.yaml index 82c5458c..f3a25677 100644 --- a/configs/experiment/preprocessing/tile_masks/radboud_val_512.yaml +++ b/configs/experiment/preprocessing/tile_masks/radboud_val_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/val@data + - /data/prostate/radboud/val@data - _self_ tile_uris: diff --git a/configs/experiment/preprocessing/tiling/comenius_3_sample_224.yaml b/configs/experiment/preprocessing/tiling/comenius_3_sample_224.yaml index fe1a41dd..b37f1849 100644 --- a/configs/experiment/preprocessing/tiling/comenius_3_sample_224.yaml +++ b/configs/experiment/preprocessing/tiling/comenius_3_sample_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/comenius/comenius_3_sample@data + - /data/prostate/comenius/comenius_3_sample@data - _self_ tile_extent: 224 diff --git a/configs/experiment/preprocessing/tiling/mmci_endoresection_224.yaml b/configs/experiment/preprocessing/tiling/mmci_endoresection_224.yaml index e5f4d88d..4c8a6f89 100644 --- a/configs/experiment/preprocessing/tiling/mmci_endoresection_224.yaml +++ b/configs/experiment/preprocessing/tiling/mmci_endoresection_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/endoresection@data + - /data/prostate/mmci/endoresection@data - _self_ tile_extent: 224 diff --git a/configs/experiment/preprocessing/tiling/mmci_endoresection_512.yaml b/configs/experiment/preprocessing/tiling/mmci_endoresection_512.yaml index f87997ff..9c2a37db 100644 --- a/configs/experiment/preprocessing/tiling/mmci_endoresection_512.yaml +++ b/configs/experiment/preprocessing/tiling/mmci_endoresection_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/endoresection@data + - /data/prostate/mmci/endoresection@data - _self_ tile_extent: 512 diff --git a/configs/experiment/preprocessing/tiling/mmci_sl_group_1_224.yaml b/configs/experiment/preprocessing/tiling/mmci_sl_group_1_224.yaml index 05ad3e29..39db755a 100644 --- a/configs/experiment/preprocessing/tiling/mmci_sl_group_1_224.yaml +++ b/configs/experiment/preprocessing/tiling/mmci_sl_group_1_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ tile_extent: 224 diff --git a/configs/experiment/preprocessing/tiling/mmci_sl_group_1_512.yaml b/configs/experiment/preprocessing/tiling/mmci_sl_group_1_512.yaml index 117c3e82..5728fff7 100644 --- a/configs/experiment/preprocessing/tiling/mmci_sl_group_1_512.yaml +++ b/configs/experiment/preprocessing/tiling/mmci_sl_group_1_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ tile_extent: 512 diff --git a/configs/experiment/preprocessing/tiling/mmci_sl_group_2_224.yaml b/configs/experiment/preprocessing/tiling/mmci_sl_group_2_224.yaml index 62913459..7796558a 100644 --- a/configs/experiment/preprocessing/tiling/mmci_sl_group_2_224.yaml +++ b/configs/experiment/preprocessing/tiling/mmci_sl_group_2_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl_group_2@data + - /data/prostate/mmci/sl_group_2@data - _self_ tile_extent: 224 diff --git a/configs/experiment/preprocessing/tiling/mmci_sl_group_2_512.yaml b/configs/experiment/preprocessing/tiling/mmci_sl_group_2_512.yaml index 15452d67..c56523fb 100644 --- a/configs/experiment/preprocessing/tiling/mmci_sl_group_2_512.yaml +++ b/configs/experiment/preprocessing/tiling/mmci_sl_group_2_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/sl_group_2@data + - /data/prostate/mmci/sl_group_2@data - _self_ tile_extent: 512 diff --git a/configs/experiment/preprocessing/tiling/mmci_tl_test_224.yaml b/configs/experiment/preprocessing/tiling/mmci_tl_test_224.yaml index 0a6ebc4c..089a7893 100644 --- a/configs/experiment/preprocessing/tiling/mmci_tl_test_224.yaml +++ b/configs/experiment/preprocessing/tiling/mmci_tl_test_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data - _self_ tile_extent: 224 diff --git a/configs/experiment/preprocessing/tiling/mmci_tl_test_512.yaml b/configs/experiment/preprocessing/tiling/mmci_tl_test_512.yaml index 0b0db0c2..0ffd9103 100644 --- a/configs/experiment/preprocessing/tiling/mmci_tl_test_512.yaml +++ b/configs/experiment/preprocessing/tiling/mmci_tl_test_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data - _self_ tile_extent: 512 diff --git a/configs/experiment/preprocessing/tiling/mmci_tl_train_224.yaml b/configs/experiment/preprocessing/tiling/mmci_tl_train_224.yaml index bd32d4f0..972e3ef4 100644 --- a/configs/experiment/preprocessing/tiling/mmci_tl_train_224.yaml +++ b/configs/experiment/preprocessing/tiling/mmci_tl_train_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/tl_train@data + - /data/prostate/mmci/tl_train@data - _self_ tile_extent: 224 diff --git a/configs/experiment/preprocessing/tiling/mmci_tl_train_512.yaml b/configs/experiment/preprocessing/tiling/mmci_tl_train_512.yaml index aa345978..77f75bd3 100644 --- a/configs/experiment/preprocessing/tiling/mmci_tl_train_512.yaml +++ b/configs/experiment/preprocessing/tiling/mmci_tl_train_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/tl_train@data + - /data/prostate/mmci/tl_train@data - _self_ tile_extent: 512 diff --git a/configs/experiment/preprocessing/tiling/mmci_tl_val_224.yaml b/configs/experiment/preprocessing/tiling/mmci_tl_val_224.yaml index e04642d8..adfd41ef 100644 --- a/configs/experiment/preprocessing/tiling/mmci_tl_val_224.yaml +++ b/configs/experiment/preprocessing/tiling/mmci_tl_val_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/tl_val@data + - /data/prostate/mmci/tl_val@data - _self_ tile_extent: 224 diff --git a/configs/experiment/preprocessing/tiling/mmci_tl_val_512.yaml b/configs/experiment/preprocessing/tiling/mmci_tl_val_512.yaml index 3f1cfefd..d12eb84c 100644 --- a/configs/experiment/preprocessing/tiling/mmci_tl_val_512.yaml +++ b/configs/experiment/preprocessing/tiling/mmci_tl_val_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mmci/tl_val@data + - /data/prostate/mmci/tl_val@data - _self_ tile_extent: 512 diff --git a/configs/experiment/preprocessing/tiling/radboud_val_512.yaml b/configs/experiment/preprocessing/tiling/radboud_val_512.yaml index 83e23acc..d93bc4af 100644 --- a/configs/experiment/preprocessing/tiling/radboud_val_512.yaml +++ b/configs/experiment/preprocessing/tiling/radboud_val_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/val@data + - /data/prostate/radboud/val@data - _self_ tile_extent: 512 diff --git a/configs/experiment/preprocessing/tiling_v2/radboud_test_224.yaml b/configs/experiment/preprocessing/tiling_v2/radboud_test_224.yaml index a48b679f..ccc973f2 100644 --- a/configs/experiment/preprocessing/tiling_v2/radboud_test_224.yaml +++ b/configs/experiment/preprocessing/tiling_v2/radboud_test_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/test@data + - /data/prostate/radboud/test@data - /overlappers/classic_overlappers@overlappers - /experiment/preprocessing/tiling_v2/base_224 - _self_ diff --git a/configs/experiment/preprocessing/tiling_v2/radboud_test_512.yaml b/configs/experiment/preprocessing/tiling_v2/radboud_test_512.yaml index 1e2d9c30..00757e63 100644 --- a/configs/experiment/preprocessing/tiling_v2/radboud_test_512.yaml +++ b/configs/experiment/preprocessing/tiling_v2/radboud_test_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/test@data + - /data/prostate/radboud/test@data - /overlappers/classic_overlappers@overlappers - /experiment/preprocessing/tiling_v2/base_512 - _self_ diff --git a/configs/experiment/preprocessing/tiling_v2/radboud_train_224.yaml b/configs/experiment/preprocessing/tiling_v2/radboud_train_224.yaml index b4afb44e..89c2d20c 100644 --- a/configs/experiment/preprocessing/tiling_v2/radboud_train_224.yaml +++ b/configs/experiment/preprocessing/tiling_v2/radboud_train_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/train@data + - /data/prostate/radboud/train@data - /overlappers/classic_overlappers@overlappers - /experiment/preprocessing/tiling_v2/base_224 - _self_ diff --git a/configs/experiment/preprocessing/tiling_v2/radboud_train_512.yaml b/configs/experiment/preprocessing/tiling_v2/radboud_train_512.yaml index eb030bcf..e5931ff6 100644 --- a/configs/experiment/preprocessing/tiling_v2/radboud_train_512.yaml +++ b/configs/experiment/preprocessing/tiling_v2/radboud_train_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/train@data + - /data/prostate/radboud/train@data - /overlappers/classic_overlappers@overlappers - /experiment/preprocessing/tiling_v2/base_512 - _self_ diff --git a/configs/experiment/preprocessing/tiling_v2/radboud_val_224.yaml b/configs/experiment/preprocessing/tiling_v2/radboud_val_224.yaml index 1dd166d2..1538bc0a 100644 --- a/configs/experiment/preprocessing/tiling_v2/radboud_val_224.yaml +++ b/configs/experiment/preprocessing/tiling_v2/radboud_val_224.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/val@data + - /data/prostate/radboud/val@data - /overlappers/classic_overlappers@overlappers - /experiment/preprocessing/tiling_v2/base_224 - _self_ diff --git a/configs/experiment/preprocessing/tiling_v2/radboud_val_512.yaml b/configs/experiment/preprocessing/tiling_v2/radboud_val_512.yaml index e18c0099..2bfddb77 100644 --- a/configs/experiment/preprocessing/tiling_v2/radboud_val_512.yaml +++ b/configs/experiment/preprocessing/tiling_v2/radboud_val_512.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/val@data + - /data/prostate/radboud/val@data - /overlappers/classic_overlappers@overlappers - /experiment/preprocessing/tiling_v2/base_512 - _self_ diff --git a/configs/experiment/preprocessing/tissue_masks/comenius_3_sample.yaml b/configs/experiment/preprocessing/tissue_masks/comenius_3_sample.yaml index fc9903bf..b01d15f1 100644 --- a/configs/experiment/preprocessing/tissue_masks/comenius_3_sample.yaml +++ b/configs/experiment/preprocessing/tissue_masks/comenius_3_sample.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/comenius/comenius_3_sample@data + - /data/prostate/comenius/comenius_3_sample@data - _self_ diff --git a/configs/experiment/preprocessing/tissue_masks/fn_brno.yaml b/configs/experiment/preprocessing/tissue_masks/fn_brno.yaml index 63592216..e7ef9378 100644 --- a/configs/experiment/preprocessing/tissue_masks/fn_brno.yaml +++ b/configs/experiment/preprocessing/tissue_masks/fn_brno.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/fn_brno/full@data + - /data/prostate/fn_brno/full@data - _self_ level: 3 \ No newline at end of file diff --git a/configs/experiment/preprocessing/tissue_masks/mmci_endoresection.yaml b/configs/experiment/preprocessing/tissue_masks/mmci_endoresection.yaml index 1d339791..fca01877 100644 --- a/configs/experiment/preprocessing/tissue_masks/mmci_endoresection.yaml +++ b/configs/experiment/preprocessing/tissue_masks/mmci_endoresection.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/endoresection@data + - /data/prostate/mmci/endoresection@data - _self_ diff --git a/configs/experiment/preprocessing/tissue_masks/mmci_sl_group_1.yaml b/configs/experiment/preprocessing/tissue_masks/mmci_sl_group_1.yaml index f711bfba..2bc42847 100644 --- a/configs/experiment/preprocessing/tissue_masks/mmci_sl_group_1.yaml +++ b/configs/experiment/preprocessing/tissue_masks/mmci_sl_group_1.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/sl_group_1@data + - /data/prostate/mmci/sl_group_1@data - _self_ diff --git a/configs/experiment/preprocessing/tissue_masks/mmci_sl_group_2.yaml b/configs/experiment/preprocessing/tissue_masks/mmci_sl_group_2.yaml index ddc7face..1592f65c 100644 --- a/configs/experiment/preprocessing/tissue_masks/mmci_sl_group_2.yaml +++ b/configs/experiment/preprocessing/tissue_masks/mmci_sl_group_2.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/sl_group_2@data + - /data/prostate/mmci/sl_group_2@data - _self_ diff --git a/configs/experiment/preprocessing/tissue_masks/mmci_tl_test.yaml b/configs/experiment/preprocessing/tissue_masks/mmci_tl_test.yaml index b72b6113..0548bdb6 100644 --- a/configs/experiment/preprocessing/tissue_masks/mmci_tl_test.yaml +++ b/configs/experiment/preprocessing/tissue_masks/mmci_tl_test.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_test@data + - /data/prostate/mmci/tl_test@data - _self_ diff --git a/configs/experiment/preprocessing/tissue_masks/mmci_tl_train.yaml b/configs/experiment/preprocessing/tissue_masks/mmci_tl_train.yaml index 6fd82935..09d568ce 100644 --- a/configs/experiment/preprocessing/tissue_masks/mmci_tl_train.yaml +++ b/configs/experiment/preprocessing/tissue_masks/mmci_tl_train.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_train@data + - /data/prostate/mmci/tl_train@data - _self_ diff --git a/configs/experiment/preprocessing/tissue_masks/mmci_tl_val.yaml b/configs/experiment/preprocessing/tissue_masks/mmci_tl_val.yaml index a9502109..a833874b 100644 --- a/configs/experiment/preprocessing/tissue_masks/mmci_tl_val.yaml +++ b/configs/experiment/preprocessing/tissue_masks/mmci_tl_val.yaml @@ -1,5 +1,5 @@ # @package _global_ defaults: - - /data/mmci/tl_val@data + - /data/prostate/mmci/tl_val@data - _self_ diff --git a/configs/experiment/preprocessing/tissue_masks/mug_400.yaml b/configs/experiment/preprocessing/tissue_masks/mug_400.yaml index 8bb686d4..167427f7 100644 --- a/configs/experiment/preprocessing/tissue_masks/mug_400.yaml +++ b/configs/experiment/preprocessing/tissue_masks/mug_400.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/mug/mug_400@data + - /data/prostate/mug/mug_400@data - _self_ level: 2 diff --git a/configs/experiment/preprocessing/untie_masks/karolinska.yaml b/configs/experiment/preprocessing/untie_masks/karolinska.yaml index 4a1c04ad..fe1940ba 100644 --- a/configs/experiment/preprocessing/untie_masks/karolinska.yaml +++ b/configs/experiment/preprocessing/untie_masks/karolinska.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/karolinska/full@data + - /data/prostate/karolinska/full@data - _self_ combined_masks_dir: /mnt/data/Public/Public/prostate/PANDA/train_label_masks diff --git a/configs/experiment/preprocessing/untie_masks/radboud.yaml b/configs/experiment/preprocessing/untie_masks/radboud.yaml index 41798a23..911f1bd5 100644 --- a/configs/experiment/preprocessing/untie_masks/radboud.yaml +++ b/configs/experiment/preprocessing/untie_masks/radboud.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /data/radboud/full@data + - /data/prostate/radboud/full@data - _self_ combined_masks_dir: /mnt/data/Public/Public/prostate/PANDA/train_label_masks diff --git a/configs/experiment/test/bag_of_embeddings/pgp/classic_base.yaml b/configs/experiment/test/bag_of_embeddings/pgp/classic_base.yaml index f7f44a44..6ff71ff6 100644 --- a/configs/experiment/test/bag_of_embeddings/pgp/classic_base.yaml +++ b/configs/experiment/test/bag_of_embeddings/pgp/classic_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/bag_of_embeddings/classic_base - /model/pgp_classic_mil_model@model - - /model/checkpoints/mmci_tl/pgp_classic_mil@model_data + - /model/checkpoints/prostate/pgp_classic_mil@model_data - _self_ datamodule: diff --git a/configs/experiment/test/bag_of_embeddings/pgp/classic_tile_threshold.yaml b/configs/experiment/test/bag_of_embeddings/pgp/classic_tile_threshold.yaml index ebe77aaf..8b4a9080 100644 --- a/configs/experiment/test/bag_of_embeddings/pgp/classic_tile_threshold.yaml +++ b/configs/experiment/test/bag_of_embeddings/pgp/classic_tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold_mil@callbacks - /experiment/test/bag_of_embeddings/pgp/classic_base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ tile_threshold: 0.9 # Pathologist's estimate for other models diff --git a/configs/experiment/test/bag_of_embeddings/pgp/hybrid_base.yaml b/configs/experiment/test/bag_of_embeddings/pgp/hybrid_base.yaml index 613f5477..3b349190 100644 --- a/configs/experiment/test/bag_of_embeddings/pgp/hybrid_base.yaml +++ b/configs/experiment/test/bag_of_embeddings/pgp/hybrid_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/bag_of_embeddings/hybrid_base - /model/pgp_hybrid_mil_model@model - - /model/checkpoints/mmci_tl/pgp_hybrid_mil@model_data + - /model/checkpoints/prostate/pgp_hybrid_mil@model_data - _self_ datamodule: diff --git a/configs/experiment/test/bag_of_embeddings/pgp/hybrid_tile_threshold.yaml b/configs/experiment/test/bag_of_embeddings/pgp/hybrid_tile_threshold.yaml index 9ee56695..307ed2f2 100644 --- a/configs/experiment/test/bag_of_embeddings/pgp/hybrid_tile_threshold.yaml +++ b/configs/experiment/test/bag_of_embeddings/pgp/hybrid_tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold_mil@callbacks - /experiment/test/bag_of_embeddings/pgp/hybrid_base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ tile_threshold: 0.9 # Pathologist's estimate for other models diff --git a/configs/experiment/test/bag_of_embeddings/pgp/test_suite/classic_mmci_tl_test.yaml b/configs/experiment/test/bag_of_embeddings/pgp/test_suite/classic_mmci_tl_test.yaml index 1fcab4ea..8ecf2831 100644 --- a/configs/experiment/test/bag_of_embeddings/pgp/test_suite/classic_mmci_tl_test.yaml +++ b/configs/experiment/test/bag_of_embeddings/pgp/test_suite/classic_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/bag_of_embeddings/pgp/test_suite/classic_base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/bag_of_embeddings/pgp/test_suite/classic_radboud_test.yaml b/configs/experiment/test/bag_of_embeddings/pgp/test_suite/classic_radboud_test.yaml index f05a3f29..a8720c7c 100644 --- a/configs/experiment/test/bag_of_embeddings/pgp/test_suite/classic_radboud_test.yaml +++ b/configs/experiment/test/bag_of_embeddings/pgp/test_suite/classic_radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/bag_of_embeddings/pgp/test_suite/classic_base - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/bag_of_embeddings/pgp/test_suite/hybrid_mmci_tl_test.yaml b/configs/experiment/test/bag_of_embeddings/pgp/test_suite/hybrid_mmci_tl_test.yaml index a478a197..e527d92e 100644 --- a/configs/experiment/test/bag_of_embeddings/pgp/test_suite/hybrid_mmci_tl_test.yaml +++ b/configs/experiment/test/bag_of_embeddings/pgp/test_suite/hybrid_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/bag_of_embeddings/pgp/test_suite/hybrid_base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/bag_of_embeddings/pgp/test_suite/hybrid_radboud_test.yaml b/configs/experiment/test/bag_of_embeddings/pgp/test_suite/hybrid_radboud_test.yaml index 5507086a..edd08d49 100644 --- a/configs/experiment/test/bag_of_embeddings/pgp/test_suite/hybrid_radboud_test.yaml +++ b/configs/experiment/test/bag_of_embeddings/pgp/test_suite/hybrid_radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/bag_of_embeddings/pgp/test_suite/hybrid_base - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/classic_base.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/classic_base.yaml index d53707ce..99fd1809 100644 --- a/configs/experiment/test/bag_of_embeddings/virchow2/classic_base.yaml +++ b/configs/experiment/test/bag_of_embeddings/virchow2/classic_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/bag_of_embeddings/classic_base - /model/virchow2_classic_mil_model@model - - /model/checkpoints/mmci_tl/virchow2_classic_mil@model_data + - /model/checkpoints/prostate/virchow2_classic_mil@model_data - _self_ datamodule: diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/classic_tile_threshold.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/classic_tile_threshold.yaml index c70913f6..553a768a 100644 --- a/configs/experiment/test/bag_of_embeddings/virchow2/classic_tile_threshold.yaml +++ b/configs/experiment/test/bag_of_embeddings/virchow2/classic_tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold_mil@callbacks - /experiment/test/bag_of_embeddings/virchow2/classic_base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ tile_threshold: 0.9 # Pathologist's estimate for other models diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/hybrid_base.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/hybrid_base.yaml index c226c019..4d24a1a2 100644 --- a/configs/experiment/test/bag_of_embeddings/virchow2/hybrid_base.yaml +++ b/configs/experiment/test/bag_of_embeddings/virchow2/hybrid_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/bag_of_embeddings/hybrid_base - /model/virchow2_hybrid_mil_model@model - - /model/checkpoints/mmci_tl/virchow2_hybrid_mil@model_data + - /model/checkpoints/prostate/virchow2_hybrid_mil@model_data - _self_ datamodule: diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/hybrid_tile_threshold.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/hybrid_tile_threshold.yaml index 6ca0cfc1..a66b317e 100644 --- a/configs/experiment/test/bag_of_embeddings/virchow2/hybrid_tile_threshold.yaml +++ b/configs/experiment/test/bag_of_embeddings/virchow2/hybrid_tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold_mil@callbacks - /experiment/test/bag_of_embeddings/virchow2/hybrid_base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ tile_threshold: 0.9 # Pathologist's estimate for other models diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/classic_mmci_tl_test.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/classic_mmci_tl_test.yaml index b9cf0792..eb7affeb 100644 --- a/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/classic_mmci_tl_test.yaml +++ b/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/classic_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/bag_of_embeddings/virchow2/test_suite/classic_base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/classic_radboud_test.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/classic_radboud_test.yaml index 0b9dc7fd..32ffcf26 100644 --- a/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/classic_radboud_test.yaml +++ b/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/classic_radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/bag_of_embeddings/virchow2/test_suite/classic_base - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_mmci_tl_test.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_mmci_tl_test.yaml index 157bdbac..27cb4aa2 100644 --- a/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_mmci_tl_test.yaml +++ b/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_radboud_test.yaml b/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_radboud_test.yaml index debfccc8..0bef4f84 100644 --- a/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_radboud_test.yaml +++ b/configs/experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/bag_of_embeddings/virchow2/test_suite/hybrid_base - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/embeddings/pgp/base.yaml b/configs/experiment/test/embeddings/pgp/base.yaml index e38576f9..63ff7674 100644 --- a/configs/experiment/test/embeddings/pgp/base.yaml +++ b/configs/experiment/test/embeddings/pgp/base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/embeddings/base - /model/pgp_model@model - - /model/checkpoints/mmci_tl/pgp@model_data + - /model/checkpoints/prostate/pgp@model_data - _self_ datamodule: diff --git a/configs/experiment/test/embeddings/pgp/stain_base.yaml b/configs/experiment/test/embeddings/pgp/stain_base.yaml index 383dd335..0a4bddf6 100644 --- a/configs/experiment/test/embeddings/pgp/stain_base.yaml +++ b/configs/experiment/test/embeddings/pgp/stain_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/embeddings/base - /model/pgp_model@model - - /model/checkpoints/mmci_tl/pgp_stain@model_data + - /model/checkpoints/prostate/pgp_stain@model_data - _self_ datamodule: diff --git a/configs/experiment/test/embeddings/pgp/stain_tile_threshold.yaml b/configs/experiment/test/embeddings/pgp/stain_tile_threshold.yaml index e657c584..1f5e645c 100644 --- a/configs/experiment/test/embeddings/pgp/stain_tile_threshold.yaml +++ b/configs/experiment/test/embeddings/pgp/stain_tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/embeddings/pgp/stain_base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ datamodule: diff --git a/configs/experiment/test/embeddings/pgp/test_suite/mmci_tl_test.yaml b/configs/experiment/test/embeddings/pgp/test_suite/mmci_tl_test.yaml index 6c2a1311..cd17e41f 100644 --- a/configs/experiment/test/embeddings/pgp/test_suite/mmci_tl_test.yaml +++ b/configs/experiment/test/embeddings/pgp/test_suite/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/embeddings/pgp/test_suite/base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/embeddings/pgp/test_suite/radboud_test.yaml b/configs/experiment/test/embeddings/pgp/test_suite/radboud_test.yaml index 24e1ab6b..ae6722d3 100644 --- a/configs/experiment/test/embeddings/pgp/test_suite/radboud_test.yaml +++ b/configs/experiment/test/embeddings/pgp/test_suite/radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/embeddings/pgp/test_suite/base - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/embeddings/pgp/test_suite/stain_mmci_tl_test.yaml b/configs/experiment/test/embeddings/pgp/test_suite/stain_mmci_tl_test.yaml index 1caa862b..7d2350b0 100644 --- a/configs/experiment/test/embeddings/pgp/test_suite/stain_mmci_tl_test.yaml +++ b/configs/experiment/test/embeddings/pgp/test_suite/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/embeddings/pgp/test_suite/stain_base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/embeddings/pgp/test_suite/stain_radboud_test.yaml b/configs/experiment/test/embeddings/pgp/test_suite/stain_radboud_test.yaml index b74ba07b..6c4a9f49 100644 --- a/configs/experiment/test/embeddings/pgp/test_suite/stain_radboud_test.yaml +++ b/configs/experiment/test/embeddings/pgp/test_suite/stain_radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/embeddings/pgp/test_suite/stain_base - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/embeddings/pgp/tile_threshold.yaml b/configs/experiment/test/embeddings/pgp/tile_threshold.yaml index 19b0518d..84471c26 100644 --- a/configs/experiment/test/embeddings/pgp/tile_threshold.yaml +++ b/configs/experiment/test/embeddings/pgp/tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/embeddings/pgp/base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ datamodule: diff --git a/configs/experiment/test/embeddings/virchow2/base.yaml b/configs/experiment/test/embeddings/virchow2/base.yaml index 31ba413a..7c915c04 100644 --- a/configs/experiment/test/embeddings/virchow2/base.yaml +++ b/configs/experiment/test/embeddings/virchow2/base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/embeddings/base - /model/virchow2_model@model - - /model/checkpoints/mmci_tl/virchow2@model_data + - /model/checkpoints/prostate/virchow2@model_data - _self_ datamodule: diff --git a/configs/experiment/test/embeddings/virchow2/stain_base.yaml b/configs/experiment/test/embeddings/virchow2/stain_base.yaml index 75bdaddb..72b74e9e 100644 --- a/configs/experiment/test/embeddings/virchow2/stain_base.yaml +++ b/configs/experiment/test/embeddings/virchow2/stain_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/embeddings/base - /model/virchow2_model@model - - /model/checkpoints/mmci_tl/virchow2_stain@model_data + - /model/checkpoints/prostate/virchow2_stain@model_data - _self_ datamodule: diff --git a/configs/experiment/test/embeddings/virchow2/stain_tile_threshold.yaml b/configs/experiment/test/embeddings/virchow2/stain_tile_threshold.yaml index e31dbabe..0be02ce2 100644 --- a/configs/experiment/test/embeddings/virchow2/stain_tile_threshold.yaml +++ b/configs/experiment/test/embeddings/virchow2/stain_tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/embeddings/virchow2/stain_base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ datamodule: diff --git a/configs/experiment/test/embeddings/virchow2/test_suite/mmci_tl_test.yaml b/configs/experiment/test/embeddings/virchow2/test_suite/mmci_tl_test.yaml index 7fb46798..7a2a34dc 100644 --- a/configs/experiment/test/embeddings/virchow2/test_suite/mmci_tl_test.yaml +++ b/configs/experiment/test/embeddings/virchow2/test_suite/mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/embeddings/virchow2/test_suite/base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/embeddings/virchow2/test_suite/radboud_test.yaml b/configs/experiment/test/embeddings/virchow2/test_suite/radboud_test.yaml index 03d7b8a7..c91a88cd 100644 --- a/configs/experiment/test/embeddings/virchow2/test_suite/radboud_test.yaml +++ b/configs/experiment/test/embeddings/virchow2/test_suite/radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/embeddings/virchow2/test_suite/base - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/embeddings/virchow2/test_suite/stain_mmci_tl_test.yaml b/configs/experiment/test/embeddings/virchow2/test_suite/stain_mmci_tl_test.yaml index 2a3ace81..47a44315 100644 --- a/configs/experiment/test/embeddings/virchow2/test_suite/stain_mmci_tl_test.yaml +++ b/configs/experiment/test/embeddings/virchow2/test_suite/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/embeddings/virchow2/test_suite/stain_base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/embeddings/virchow2/test_suite/stain_radboud_test.yaml b/configs/experiment/test/embeddings/virchow2/test_suite/stain_radboud_test.yaml index c103e074..6840bc9e 100644 --- a/configs/experiment/test/embeddings/virchow2/test_suite/stain_radboud_test.yaml +++ b/configs/experiment/test/embeddings/virchow2/test_suite/stain_radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/embeddings/virchow2/test_suite/stain_base - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/embeddings/virchow2/tile_threshold.yaml b/configs/experiment/test/embeddings/virchow2/tile_threshold.yaml index da9f57b6..687ffafc 100644 --- a/configs/experiment/test/embeddings/virchow2/tile_threshold.yaml +++ b/configs/experiment/test/embeddings/virchow2/tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/embeddings/virchow2/base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ datamodule: diff --git a/configs/experiment/test/images/google_vit/base.yaml b/configs/experiment/test/images/google_vit/base.yaml index 7e426a1a..f3dc28b4 100644 --- a/configs/experiment/test/images/google_vit/base.yaml +++ b/configs/experiment/test/images/google_vit/base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/images/base - /model/google_vit_model@model - - /model/checkpoints/mmci_tl/google_vit@model_data + - /model/checkpoints/prostate/google_vit@model_data - _self_ datamodule: diff --git a/configs/experiment/test/images/google_vit/stain_base.yaml b/configs/experiment/test/images/google_vit/stain_base.yaml index 0e415172..34fe8dd8 100644 --- a/configs/experiment/test/images/google_vit/stain_base.yaml +++ b/configs/experiment/test/images/google_vit/stain_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/images/base - /model/google_vit_model@model - - /model/checkpoints/mmci_tl/google_vit_stain@model_data + - /model/checkpoints/prostate/google_vit_stain@model_data - _self_ datamodule: diff --git a/configs/experiment/test/images/google_vit/stain_tile_threshold.yaml b/configs/experiment/test/images/google_vit/stain_tile_threshold.yaml index 1084134f..5bf4836e 100644 --- a/configs/experiment/test/images/google_vit/stain_tile_threshold.yaml +++ b/configs/experiment/test/images/google_vit/stain_tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/images/google_vit/stain_base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ datamodule: diff --git a/configs/experiment/test/images/google_vit/test_suite/mmci_tl.yaml b/configs/experiment/test/images/google_vit/test_suite/mmci_tl.yaml index f213fbac..61da51fc 100644 --- a/configs/experiment/test/images/google_vit/test_suite/mmci_tl.yaml +++ b/configs/experiment/test/images/google_vit/test_suite/mmci_tl.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/images/google_vit/test_suite/base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/images/google_vit/test_suite/radboud_test.yaml b/configs/experiment/test/images/google_vit/test_suite/radboud_test.yaml index d71bad18..ad23fd8c 100644 --- a/configs/experiment/test/images/google_vit/test_suite/radboud_test.yaml +++ b/configs/experiment/test/images/google_vit/test_suite/radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/google_vit/test_suite/base - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/google_vit/test_suite/stain_mmci_tl.yaml b/configs/experiment/test/images/google_vit/test_suite/stain_mmci_tl.yaml index 1b360a4a..2487113a 100644 --- a/configs/experiment/test/images/google_vit/test_suite/stain_mmci_tl.yaml +++ b/configs/experiment/test/images/google_vit/test_suite/stain_mmci_tl.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/images/google_vit/test_suite/stain_base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/images/google_vit/test_suite/stain_radboud_test.yaml b/configs/experiment/test/images/google_vit/test_suite/stain_radboud_test.yaml index fb049c19..96c8658d 100644 --- a/configs/experiment/test/images/google_vit/test_suite/stain_radboud_test.yaml +++ b/configs/experiment/test/images/google_vit/test_suite/stain_radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/google_vit/test_suite/stain_base - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/google_vit/tile_threshold.yaml b/configs/experiment/test/images/google_vit/tile_threshold.yaml index b1b87e08..373ca763 100644 --- a/configs/experiment/test/images/google_vit/tile_threshold.yaml +++ b/configs/experiment/test/images/google_vit/tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/images/google_vit/base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ datamodule: diff --git a/configs/experiment/test/images/resnet50/base.yaml b/configs/experiment/test/images/resnet50/base.yaml index 76e4816d..52262a9c 100644 --- a/configs/experiment/test/images/resnet50/base.yaml +++ b/configs/experiment/test/images/resnet50/base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/images/base - /model/resnet50_model@model - - /model/checkpoints/mmci_tl/resnet50@model_data + - /model/checkpoints/prostate/resnet50@model_data - _self_ datamodule: diff --git a/configs/experiment/test/images/resnet50/base_224.yaml b/configs/experiment/test/images/resnet50/base_224.yaml index f69ae438..35d4347c 100644 --- a/configs/experiment/test/images/resnet50/base_224.yaml +++ b/configs/experiment/test/images/resnet50/base_224.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/images/base - /model/resnet50_model@model - - /model/checkpoints/mmci_tl/resnet50_224@model_data + - /model/checkpoints/prostate/resnet50_224@model_data - _self_ datamodule: diff --git a/configs/experiment/test/images/resnet50/stain_base.yaml b/configs/experiment/test/images/resnet50/stain_base.yaml index d8a52f6d..c7affaec 100644 --- a/configs/experiment/test/images/resnet50/stain_base.yaml +++ b/configs/experiment/test/images/resnet50/stain_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/images/base - /model/resnet50_model@model - - /model/checkpoints/mmci_tl/resnet50_stain@model_data + - /model/checkpoints/prostate/resnet50_stain@model_data - _self_ datamodule: diff --git a/configs/experiment/test/images/resnet50/stain_base_224.yaml b/configs/experiment/test/images/resnet50/stain_base_224.yaml index 04d57f7c..74b373e3 100644 --- a/configs/experiment/test/images/resnet50/stain_base_224.yaml +++ b/configs/experiment/test/images/resnet50/stain_base_224.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/images/base - /model/resnet50_model@model - - /model/checkpoints/mmci_tl/resnet50_stain_224@model_data + - /model/checkpoints/prostate/resnet50_stain_224@model_data - _self_ datamodule: diff --git a/configs/experiment/test/images/resnet50/stain_tile_threshold.yaml b/configs/experiment/test/images/resnet50/stain_tile_threshold.yaml index a97000d1..675b531e 100644 --- a/configs/experiment/test/images/resnet50/stain_tile_threshold.yaml +++ b/configs/experiment/test/images/resnet50/stain_tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/images/resnet50/stain_base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ datamodule: diff --git a/configs/experiment/test/images/resnet50/stain_tile_threshold_224.yaml b/configs/experiment/test/images/resnet50/stain_tile_threshold_224.yaml index 5e8a0883..a51d7ef0 100644 --- a/configs/experiment/test/images/resnet50/stain_tile_threshold_224.yaml +++ b/configs/experiment/test/images/resnet50/stain_tile_threshold_224.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/images/resnet50/stain_base_224 - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ datamodule: diff --git a/configs/experiment/test/images/resnet50/test_suite/mmci_tl.yaml b/configs/experiment/test/images/resnet50/test_suite/mmci_tl.yaml index 1d0ff6cc..b03cdcdd 100644 --- a/configs/experiment/test/images/resnet50/test_suite/mmci_tl.yaml +++ b/configs/experiment/test/images/resnet50/test_suite/mmci_tl.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/images/resnet50/test_suite/base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/images/resnet50/test_suite/mmci_tl_224.yaml b/configs/experiment/test/images/resnet50/test_suite/mmci_tl_224.yaml index fe006f05..56e93972 100644 --- a/configs/experiment/test/images/resnet50/test_suite/mmci_tl_224.yaml +++ b/configs/experiment/test/images/resnet50/test_suite/mmci_tl_224.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/images/resnet50/test_suite/base_224 - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/images/resnet50/test_suite/radboud_test.yaml b/configs/experiment/test/images/resnet50/test_suite/radboud_test.yaml index dd61d2f0..03ba189d 100644 --- a/configs/experiment/test/images/resnet50/test_suite/radboud_test.yaml +++ b/configs/experiment/test/images/resnet50/test_suite/radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/resnet50/test_suite/base - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/resnet50/test_suite/radboud_test_224.yaml b/configs/experiment/test/images/resnet50/test_suite/radboud_test_224.yaml index 8ff63dea..f814fd49 100644 --- a/configs/experiment/test/images/resnet50/test_suite/radboud_test_224.yaml +++ b/configs/experiment/test/images/resnet50/test_suite/radboud_test_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/resnet50/test_suite/base_224 - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/resnet50/test_suite/radboud_val.yaml b/configs/experiment/test/images/resnet50/test_suite/radboud_val.yaml index 3b9b67b1..4758d11c 100644 --- a/configs/experiment/test/images/resnet50/test_suite/radboud_val.yaml +++ b/configs/experiment/test/images/resnet50/test_suite/radboud_val.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/resnet50/test_suite/base - - /data/radboud/val@test_data + - /data/prostate/radboud/val@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/resnet50/test_suite/radboud_val_heuristic_normalized.yaml b/configs/experiment/test/images/resnet50/test_suite/radboud_val_heuristic_normalized.yaml index 0043a41e..919c01db 100644 --- a/configs/experiment/test/images/resnet50/test_suite/radboud_val_heuristic_normalized.yaml +++ b/configs/experiment/test/images/resnet50/test_suite/radboud_val_heuristic_normalized.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/resnet50/test_suite/base - - /data/radboud/val_heuristic_normalized@test_data + - /data/prostate/radboud/val_heuristic_normalized@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/resnet50/test_suite/radboud_val_ml_normalized.yaml b/configs/experiment/test/images/resnet50/test_suite/radboud_val_ml_normalized.yaml index bfc513ac..baae5cec 100644 --- a/configs/experiment/test/images/resnet50/test_suite/radboud_val_ml_normalized.yaml +++ b/configs/experiment/test/images/resnet50/test_suite/radboud_val_ml_normalized.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/resnet50/test_suite/base - - /data/radboud/val_ml_normalized@test_data + - /data/prostate/radboud/val_ml_normalized@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/resnet50/test_suite/stain_mmci_tl.yaml b/configs/experiment/test/images/resnet50/test_suite/stain_mmci_tl.yaml index e24e123f..0f3d3901 100644 --- a/configs/experiment/test/images/resnet50/test_suite/stain_mmci_tl.yaml +++ b/configs/experiment/test/images/resnet50/test_suite/stain_mmci_tl.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/images/resnet50/test_suite/stain_base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/images/resnet50/test_suite/stain_mmci_tl_224.yaml b/configs/experiment/test/images/resnet50/test_suite/stain_mmci_tl_224.yaml index 92ebcecc..f1177e1c 100644 --- a/configs/experiment/test/images/resnet50/test_suite/stain_mmci_tl_224.yaml +++ b/configs/experiment/test/images/resnet50/test_suite/stain_mmci_tl_224.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/images/resnet50/test_suite/stain_base_224 - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/images/resnet50/test_suite/stain_radboud_test.yaml b/configs/experiment/test/images/resnet50/test_suite/stain_radboud_test.yaml index 6b7bd7e8..2a89ce14 100644 --- a/configs/experiment/test/images/resnet50/test_suite/stain_radboud_test.yaml +++ b/configs/experiment/test/images/resnet50/test_suite/stain_radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/resnet50/test_suite/stain_base - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/resnet50/test_suite/stain_radboud_test_224.yaml b/configs/experiment/test/images/resnet50/test_suite/stain_radboud_test_224.yaml index 4f2c2959..4d86f44b 100644 --- a/configs/experiment/test/images/resnet50/test_suite/stain_radboud_test_224.yaml +++ b/configs/experiment/test/images/resnet50/test_suite/stain_radboud_test_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/resnet50/test_suite/stain_base_224 - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/resnet50/test_suite/stain_radboud_val.yaml b/configs/experiment/test/images/resnet50/test_suite/stain_radboud_val.yaml index 3f806e8c..51bf28a7 100644 --- a/configs/experiment/test/images/resnet50/test_suite/stain_radboud_val.yaml +++ b/configs/experiment/test/images/resnet50/test_suite/stain_radboud_val.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/resnet50/test_suite/stain_base - - /data/radboud/val@test_data + - /data/prostate/radboud/val@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/resnet50/test_suite/stain_radboud_val_heuristic_normalized.yaml b/configs/experiment/test/images/resnet50/test_suite/stain_radboud_val_heuristic_normalized.yaml index d3b609cd..77e37c7d 100644 --- a/configs/experiment/test/images/resnet50/test_suite/stain_radboud_val_heuristic_normalized.yaml +++ b/configs/experiment/test/images/resnet50/test_suite/stain_radboud_val_heuristic_normalized.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/resnet50/test_suite/stain_base - - /data/radboud/val_heuristic_normalized@test_data + - /data/prostate/radboud/val_heuristic_normalized@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/resnet50/test_suite/stain_radboud_val_ml_normalized.yaml b/configs/experiment/test/images/resnet50/test_suite/stain_radboud_val_ml_normalized.yaml index 053772bf..1faac772 100644 --- a/configs/experiment/test/images/resnet50/test_suite/stain_radboud_val_ml_normalized.yaml +++ b/configs/experiment/test/images/resnet50/test_suite/stain_radboud_val_ml_normalized.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/resnet50/test_suite/stain_base - - /data/radboud/val_ml_normalized@test_data + - /data/prostate/radboud/val_ml_normalized@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/resnet50/tile_threshold.yaml b/configs/experiment/test/images/resnet50/tile_threshold.yaml index fe50783c..7a95029a 100644 --- a/configs/experiment/test/images/resnet50/tile_threshold.yaml +++ b/configs/experiment/test/images/resnet50/tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/images/resnet50/base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ datamodule: diff --git a/configs/experiment/test/images/resnet50/tile_threshold_224.yaml b/configs/experiment/test/images/resnet50/tile_threshold_224.yaml index 65a1482e..c7cd54e7 100644 --- a/configs/experiment/test/images/resnet50/tile_threshold_224.yaml +++ b/configs/experiment/test/images/resnet50/tile_threshold_224.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/images/resnet50/base_224 - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ datamodule: diff --git a/configs/experiment/test/images/vgg16/base.yaml b/configs/experiment/test/images/vgg16/base.yaml index 589951af..16c92bc9 100644 --- a/configs/experiment/test/images/vgg16/base.yaml +++ b/configs/experiment/test/images/vgg16/base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/images/base - /model/vgg16_model@model - - /model/checkpoints/mmci_tl/vgg16@model_data + - /model/checkpoints/prostate/vgg16@model_data - _self_ datamodule: diff --git a/configs/experiment/test/images/vgg16/base_224.yaml b/configs/experiment/test/images/vgg16/base_224.yaml index 0c243799..76b65fe6 100644 --- a/configs/experiment/test/images/vgg16/base_224.yaml +++ b/configs/experiment/test/images/vgg16/base_224.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/images/base - /model/vgg16_model@model - - /model/checkpoints/mmci_tl/vgg16_224@model_data + - /model/checkpoints/prostate/vgg16_224@model_data - _self_ datamodule: diff --git a/configs/experiment/test/images/vgg16/cam/stain_mmci_tl_test.yaml b/configs/experiment/test/images/vgg16/cam/stain_mmci_tl_test.yaml index 9577b374..509c5c48 100644 --- a/configs/experiment/test/images/vgg16/cam/stain_mmci_tl_test.yaml +++ b/configs/experiment/test/images/vgg16/cam/stain_mmci_tl_test.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/images/vgg16/cam/stain_base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/images/vgg16/cam/stain_mmci_tl_train.yaml b/configs/experiment/test/images/vgg16/cam/stain_mmci_tl_train.yaml index b6b69c20..e5199305 100644 --- a/configs/experiment/test/images/vgg16/cam/stain_mmci_tl_train.yaml +++ b/configs/experiment/test/images/vgg16/cam/stain_mmci_tl_train.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/images/vgg16/cam/stain_base - - /data/mmci/tl_train@test_data + - /data/prostate/mmci/tl_train@test_data - _self_ diff --git a/configs/experiment/test/images/vgg16/cam/stain_mmci_tl_val.yaml b/configs/experiment/test/images/vgg16/cam/stain_mmci_tl_val.yaml index 5f0c2b25..c662c7a0 100644 --- a/configs/experiment/test/images/vgg16/cam/stain_mmci_tl_val.yaml +++ b/configs/experiment/test/images/vgg16/cam/stain_mmci_tl_val.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/images/vgg16/cam/stain_base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ diff --git a/configs/experiment/test/images/vgg16/radboud_stain_tile_threshold.yaml b/configs/experiment/test/images/vgg16/radboud_stain_tile_threshold.yaml index b56abf15..3765f75f 100644 --- a/configs/experiment/test/images/vgg16/radboud_stain_tile_threshold.yaml +++ b/configs/experiment/test/images/vgg16/radboud_stain_tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/images/vgg16/radboud_stain_base - - /data/radboud/val@test_data + - /data/prostate/radboud/val@test_data - _self_ datamodule: diff --git a/configs/experiment/test/images/vgg16/stain_base.yaml b/configs/experiment/test/images/vgg16/stain_base.yaml index 5fa31c6b..391ccb6d 100644 --- a/configs/experiment/test/images/vgg16/stain_base.yaml +++ b/configs/experiment/test/images/vgg16/stain_base.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/images/base - /model/vgg16_model@model - - /model/checkpoints/mmci_tl/vgg16_stain@model_data + - /model/checkpoints/prostate/vgg16_stain@model_data - _self_ datamodule: diff --git a/configs/experiment/test/images/vgg16/stain_base_224.yaml b/configs/experiment/test/images/vgg16/stain_base_224.yaml index b0ccf0f1..a56459ae 100644 --- a/configs/experiment/test/images/vgg16/stain_base_224.yaml +++ b/configs/experiment/test/images/vgg16/stain_base_224.yaml @@ -3,7 +3,7 @@ defaults: - /experiment/test/images/base - /model/vgg16_model@model - - /model/checkpoints/mmci_tl/vgg16_stain_224@model_data + - /model/checkpoints/prostate/vgg16_stain_224@model_data - _self_ datamodule: diff --git a/configs/experiment/test/images/vgg16/stain_tile_threshold.yaml b/configs/experiment/test/images/vgg16/stain_tile_threshold.yaml index 2f1cfe9e..b6ab1f5b 100644 --- a/configs/experiment/test/images/vgg16/stain_tile_threshold.yaml +++ b/configs/experiment/test/images/vgg16/stain_tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/images/vgg16/stain_base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ datamodule: diff --git a/configs/experiment/test/images/vgg16/stain_tile_threshold_224.yaml b/configs/experiment/test/images/vgg16/stain_tile_threshold_224.yaml index 60a3fba5..fdd5d4ac 100644 --- a/configs/experiment/test/images/vgg16/stain_tile_threshold_224.yaml +++ b/configs/experiment/test/images/vgg16/stain_tile_threshold_224.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/images/vgg16/stain_base_224 - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ datamodule: diff --git a/configs/experiment/test/images/vgg16/test_suite/mmci_tl.yaml b/configs/experiment/test/images/vgg16/test_suite/mmci_tl.yaml index d5966719..747e957f 100644 --- a/configs/experiment/test/images/vgg16/test_suite/mmci_tl.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/mmci_tl.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/images/vgg16/test_suite/base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/images/vgg16/test_suite/mmci_tl_224.yaml b/configs/experiment/test/images/vgg16/test_suite/mmci_tl_224.yaml index 48860f1c..0e401fd4 100644 --- a/configs/experiment/test/images/vgg16/test_suite/mmci_tl_224.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/mmci_tl_224.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/images/vgg16/test_suite/base_224 - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/images/vgg16/test_suite/radboud_model/stain_radboud_val.yaml b/configs/experiment/test/images/vgg16/test_suite/radboud_model/stain_radboud_val.yaml index 389a09dd..87da38ab 100644 --- a/configs/experiment/test/images/vgg16/test_suite/radboud_model/stain_radboud_val.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/radboud_model/stain_radboud_val.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/vgg16/test_suite/radboud_model/stain_base - - /data/radboud/val@test_data + - /data/prostate/radboud/val@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/vgg16/test_suite/radboud_test.yaml b/configs/experiment/test/images/vgg16/test_suite/radboud_test.yaml index 80d26deb..e58fc25b 100644 --- a/configs/experiment/test/images/vgg16/test_suite/radboud_test.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/vgg16/test_suite/base - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/vgg16/test_suite/radboud_test_224.yaml b/configs/experiment/test/images/vgg16/test_suite/radboud_test_224.yaml index 0a5a9a6a..e6936d4f 100644 --- a/configs/experiment/test/images/vgg16/test_suite/radboud_test_224.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/radboud_test_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/vgg16/test_suite/base_224 - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/vgg16/test_suite/radboud_val.yaml b/configs/experiment/test/images/vgg16/test_suite/radboud_val.yaml index d38308a1..3dff6f8b 100644 --- a/configs/experiment/test/images/vgg16/test_suite/radboud_val.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/radboud_val.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/vgg16/test_suite/base - - /data/radboud/val@test_data + - /data/prostate/radboud/val@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/vgg16/test_suite/radboud_val_heuristic_normalized.yaml b/configs/experiment/test/images/vgg16/test_suite/radboud_val_heuristic_normalized.yaml index 170a40aa..1d7164f1 100644 --- a/configs/experiment/test/images/vgg16/test_suite/radboud_val_heuristic_normalized.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/radboud_val_heuristic_normalized.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/vgg16/test_suite/base - - /data/radboud/val_heuristic_normalized@test_data + - /data/prostate/radboud/val_heuristic_normalized@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/vgg16/test_suite/radboud_val_ml_normalized.yaml b/configs/experiment/test/images/vgg16/test_suite/radboud_val_ml_normalized.yaml index da6cee96..aacb32e9 100644 --- a/configs/experiment/test/images/vgg16/test_suite/radboud_val_ml_normalized.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/radboud_val_ml_normalized.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/vgg16/test_suite/base - - /data/radboud/val_ml_normalized@test_data + - /data/prostate/radboud/val_ml_normalized@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/vgg16/test_suite/stain_mmci_tl.yaml b/configs/experiment/test/images/vgg16/test_suite/stain_mmci_tl.yaml index 97c541c0..a83939fd 100644 --- a/configs/experiment/test/images/vgg16/test_suite/stain_mmci_tl.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/stain_mmci_tl.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/images/vgg16/test_suite/stain_base - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/images/vgg16/test_suite/stain_mmci_tl_224.yaml b/configs/experiment/test/images/vgg16/test_suite/stain_mmci_tl_224.yaml index 5b5c9ed7..dce21d9a 100644 --- a/configs/experiment/test/images/vgg16/test_suite/stain_mmci_tl_224.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/stain_mmci_tl_224.yaml @@ -2,5 +2,5 @@ defaults: - /experiment/test/images/vgg16/test_suite/stain_base_224 - - /data/mmci/tl_test@test_data + - /data/prostate/mmci/tl_test@test_data - _self_ diff --git a/configs/experiment/test/images/vgg16/test_suite/stain_radboud_test.yaml b/configs/experiment/test/images/vgg16/test_suite/stain_radboud_test.yaml index db1a9b4d..f877da09 100644 --- a/configs/experiment/test/images/vgg16/test_suite/stain_radboud_test.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/stain_radboud_test.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/vgg16/test_suite/stain_base - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/vgg16/test_suite/stain_radboud_test_224.yaml b/configs/experiment/test/images/vgg16/test_suite/stain_radboud_test_224.yaml index e7e6e754..32ffa60f 100644 --- a/configs/experiment/test/images/vgg16/test_suite/stain_radboud_test_224.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/stain_radboud_test_224.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/vgg16/test_suite/stain_base_224 - - /data/radboud/test@test_data + - /data/prostate/radboud/test@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/vgg16/test_suite/stain_radboud_val.yaml b/configs/experiment/test/images/vgg16/test_suite/stain_radboud_val.yaml index 751d0770..c172c44d 100644 --- a/configs/experiment/test/images/vgg16/test_suite/stain_radboud_val.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/stain_radboud_val.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/vgg16/test_suite/stain_base - - /data/radboud/val@test_data + - /data/prostate/radboud/val@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/vgg16/test_suite/stain_radboud_val_heuristic_normalized.yaml b/configs/experiment/test/images/vgg16/test_suite/stain_radboud_val_heuristic_normalized.yaml index f78450ed..cc85f6af 100644 --- a/configs/experiment/test/images/vgg16/test_suite/stain_radboud_val_heuristic_normalized.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/stain_radboud_val_heuristic_normalized.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/vgg16/test_suite/stain_base - - /data/radboud/val_heuristic_normalized@test_data + - /data/prostate/radboud/val_heuristic_normalized@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/vgg16/test_suite/stain_radboud_val_ml_normalized.yaml b/configs/experiment/test/images/vgg16/test_suite/stain_radboud_val_ml_normalized.yaml index 554b8c6c..8b0869ad 100644 --- a/configs/experiment/test/images/vgg16/test_suite/stain_radboud_val_ml_normalized.yaml +++ b/configs/experiment/test/images/vgg16/test_suite/stain_radboud_val_ml_normalized.yaml @@ -2,7 +2,7 @@ defaults: - /experiment/test/images/vgg16/test_suite/stain_base - - /data/radboud/val_ml_normalized@test_data + - /data/prostate/radboud/val_ml_normalized@test_data - _self_ checkpoint: ${model_data.public_checkpoint} diff --git a/configs/experiment/test/images/vgg16/tile_threshold.yaml b/configs/experiment/test/images/vgg16/tile_threshold.yaml index c6b91977..274c9caa 100644 --- a/configs/experiment/test/images/vgg16/tile_threshold.yaml +++ b/configs/experiment/test/images/vgg16/tile_threshold.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/images/vgg16/base - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ datamodule: diff --git a/configs/experiment/test/images/vgg16/tile_threshold_224.yaml b/configs/experiment/test/images/vgg16/tile_threshold_224.yaml index 45f714a9..a1265bff 100644 --- a/configs/experiment/test/images/vgg16/tile_threshold_224.yaml +++ b/configs/experiment/test/images/vgg16/tile_threshold_224.yaml @@ -3,7 +3,7 @@ defaults: - /callbacks/tile_threshold@callbacks - /experiment/test/images/vgg16/base_224 - - /data/mmci/tl_val@test_data + - /data/prostate/mmci/tl_val@test_data - _self_ datamodule: diff --git a/configs/experiment/train/bag_of_embeddings/base.yaml b/configs/experiment/train/bag_of_embeddings/base.yaml index 627f0db4..c88af9ad 100644 --- a/configs/experiment/train/bag_of_embeddings/base.yaml +++ b/configs/experiment/train/bag_of_embeddings/base.yaml @@ -2,8 +2,8 @@ defaults: - /experiment/train/base - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ model: diff --git a/configs/experiment/train/embeddings/pgp/mmci.yaml b/configs/experiment/train/embeddings/pgp/mmci.yaml index d843b226..2cd04660 100644 --- a/configs/experiment/train/embeddings/pgp/mmci.yaml +++ b/configs/experiment/train/embeddings/pgp/mmci.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/embeddings/pgp/base - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ diff --git a/configs/experiment/train/embeddings/virchow2/mmci.yaml b/configs/experiment/train/embeddings/virchow2/mmci.yaml index 983f7e09..8fafdebc 100644 --- a/configs/experiment/train/embeddings/virchow2/mmci.yaml +++ b/configs/experiment/train/embeddings/virchow2/mmci.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/embeddings/virchow2/base - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ diff --git a/configs/experiment/train/images/google_vit/mmci_tl.yaml b/configs/experiment/train/images/google_vit/mmci_tl.yaml index a05dc8be..05ad6c8b 100644 --- a/configs/experiment/train/images/google_vit/mmci_tl.yaml +++ b/configs/experiment/train/images/google_vit/mmci_tl.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/images/google_vit/base - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ diff --git a/configs/experiment/train/images/google_vit/mmci_tl_stain.yaml b/configs/experiment/train/images/google_vit/mmci_tl_stain.yaml index f16f0bb5..59e6762d 100644 --- a/configs/experiment/train/images/google_vit/mmci_tl_stain.yaml +++ b/configs/experiment/train/images/google_vit/mmci_tl_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/images/google_vit/base_stain - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ diff --git a/configs/experiment/train/images/google_vit/radboud_stain.yaml b/configs/experiment/train/images/google_vit/radboud_stain.yaml index 6e36f209..85a1bbd8 100644 --- a/configs/experiment/train/images/google_vit/radboud_stain.yaml +++ b/configs/experiment/train/images/google_vit/radboud_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/images/google_vit/base_stain - - /data/radboud/train@train_data - - /data/radboud/val@val_data + - /data/prostate/radboud/train@train_data + - /data/prostate/radboud/val@val_data - _self_ diff --git a/configs/experiment/train/images/pgp/mmci_tl_stain.yaml b/configs/experiment/train/images/pgp/mmci_tl_stain.yaml index 23b85019..3968ecf1 100644 --- a/configs/experiment/train/images/pgp/mmci_tl_stain.yaml +++ b/configs/experiment/train/images/pgp/mmci_tl_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/images/pgp/base_stain - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ diff --git a/configs/experiment/train/images/resnet50/mmci.yaml b/configs/experiment/train/images/resnet50/mmci.yaml index daaf46a5..9c676bc1 100644 --- a/configs/experiment/train/images/resnet50/mmci.yaml +++ b/configs/experiment/train/images/resnet50/mmci.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/images/resnet50/base - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ diff --git a/configs/experiment/train/images/resnet50/mmci_224.yaml b/configs/experiment/train/images/resnet50/mmci_224.yaml index f5c06567..17bb4ad5 100644 --- a/configs/experiment/train/images/resnet50/mmci_224.yaml +++ b/configs/experiment/train/images/resnet50/mmci_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/images/resnet50/base_224 - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ diff --git a/configs/experiment/train/images/resnet50/mmci_stain.yaml b/configs/experiment/train/images/resnet50/mmci_stain.yaml index 0fa12ce4..94ac3908 100644 --- a/configs/experiment/train/images/resnet50/mmci_stain.yaml +++ b/configs/experiment/train/images/resnet50/mmci_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/images/resnet50/base_stain - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ diff --git a/configs/experiment/train/images/resnet50/mmci_stain_224.yaml b/configs/experiment/train/images/resnet50/mmci_stain_224.yaml index 14a400c0..bb058ac6 100644 --- a/configs/experiment/train/images/resnet50/mmci_stain_224.yaml +++ b/configs/experiment/train/images/resnet50/mmci_stain_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/images/resnet50/base_stain_224 - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ diff --git a/configs/experiment/train/images/vgg16/mmci.yaml b/configs/experiment/train/images/vgg16/mmci.yaml index f37f6b3d..329e318e 100644 --- a/configs/experiment/train/images/vgg16/mmci.yaml +++ b/configs/experiment/train/images/vgg16/mmci.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/images/vgg16/base - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ diff --git a/configs/experiment/train/images/vgg16/mmci_224.yaml b/configs/experiment/train/images/vgg16/mmci_224.yaml index 95128f7b..a49fc8b7 100644 --- a/configs/experiment/train/images/vgg16/mmci_224.yaml +++ b/configs/experiment/train/images/vgg16/mmci_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/images/vgg16/base_224 - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ diff --git a/configs/experiment/train/images/vgg16/mmci_stain.yaml b/configs/experiment/train/images/vgg16/mmci_stain.yaml index 7765af21..10051f4f 100644 --- a/configs/experiment/train/images/vgg16/mmci_stain.yaml +++ b/configs/experiment/train/images/vgg16/mmci_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/images/vgg16/base_stain - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ diff --git a/configs/experiment/train/images/vgg16/mmci_stain_224.yaml b/configs/experiment/train/images/vgg16/mmci_stain_224.yaml index 86c9ad80..c7f2d78f 100644 --- a/configs/experiment/train/images/vgg16/mmci_stain_224.yaml +++ b/configs/experiment/train/images/vgg16/mmci_stain_224.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/images/vgg16/base_stain_224 - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ diff --git a/configs/experiment/train/images/vgg16/radboud_stain.yaml b/configs/experiment/train/images/vgg16/radboud_stain.yaml index cc5f83a1..8c1e9d52 100644 --- a/configs/experiment/train/images/vgg16/radboud_stain.yaml +++ b/configs/experiment/train/images/vgg16/radboud_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/images/vgg16/base_stain - - /data/radboud/train@train_data - - /data/radboud/val@val_data + - /data/prostate/radboud/train@train_data + - /data/prostate/radboud/val@val_data - _self_ diff --git a/configs/experiment/train/images/virchow2/mmci_tl_stain.yaml b/configs/experiment/train/images/virchow2/mmci_tl_stain.yaml index d57f2ea5..875e8658 100644 --- a/configs/experiment/train/images/virchow2/mmci_tl_stain.yaml +++ b/configs/experiment/train/images/virchow2/mmci_tl_stain.yaml @@ -2,6 +2,6 @@ defaults: - /experiment/train/images/virchow2/base_stain - - /data/mmci/tl_train@train_data - - /data/mmci/tl_val@val_data + - /data/prostate/mmci/tl_train@train_data + - /data/prostate/mmci/tl_val@val_data - _self_ diff --git a/configs/exploration/mmci_2k.yaml b/configs/exploration/mmci_2k.yaml deleted file mode 100644 index f5914132..00000000 --- a/configs/exploration/mmci_2k.yaml +++ /dev/null @@ -1,12 +0,0 @@ -# @package _global_ - -defaults: - - /default - - _self_ - -annot_table_path: "${prostate_data}/slide_level_annotations/Prostaty2023-tabulka-final-corrections.xlsx" -data_dir: "${prostate_data}/slide_level_annotations" - -metadata: - run_name: MMCI 2k data - description: MMCI 2k data diff --git a/configs/exploration/prostate/base.yaml b/configs/exploration/prostate/base.yaml new file mode 100644 index 00000000..161db1df --- /dev/null +++ b/configs/exploration/prostate/base.yaml @@ -0,0 +1,6 @@ +# @package _global_ + +defaults: + - /default + - /data/prostate/base@_global_ + - _self_ diff --git a/configs/exploration/comenius_3_sample.yaml b/configs/exploration/prostate/comenius_3_sample.yaml similarity index 84% rename from configs/exploration/comenius_3_sample.yaml rename to configs/exploration/prostate/comenius_3_sample.yaml index be5fd617..121c7c4f 100644 --- a/configs/exploration/comenius_3_sample.yaml +++ b/configs/exploration/prostate/comenius_3_sample.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /default + - /exploration/prostate/base - _self_ data_dir: "/mnt/data/LF_CU/prostate/prostate_test_v2" diff --git a/configs/exploration/fn_brno.yaml b/configs/exploration/prostate/fn_brno.yaml similarity index 91% rename from configs/exploration/fn_brno.yaml rename to configs/exploration/prostate/fn_brno.yaml index e8fb00a6..fc3c5cfa 100644 --- a/configs/exploration/fn_brno.yaml +++ b/configs/exploration/prostate/fn_brno.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /default + - /exploration/prostate/base - _self_ data_dir: "/mnt/data/FNBrno/prostate/AI-prostata" diff --git a/configs/exploration/prostate/mmci_2k.yaml b/configs/exploration/prostate/mmci_2k.yaml new file mode 100644 index 00000000..58788ab0 --- /dev/null +++ b/configs/exploration/prostate/mmci_2k.yaml @@ -0,0 +1,12 @@ +# @package _global_ + +defaults: + - /exploration/prostate/base + - _self_ + +annot_table_path: "/mnt/data/MOU/prostate/slide_level_annotations/Prostaty2023-tabulka-final-corrections.xlsx" +data_dir: "/mnt/data/MOU/prostate/slide_level_annotations/slide_level_annotations" + +metadata: + run_name: MMCI 2k data + description: MMCI 2k data diff --git a/configs/exploration/mug_400.yaml b/configs/exploration/prostate/mug_400.yaml similarity index 95% rename from configs/exploration/mug_400.yaml rename to configs/exploration/prostate/mug_400.yaml index f3a10e73..ebef4a81 100644 --- a/configs/exploration/mug_400.yaml +++ b/configs/exploration/prostate/mug_400.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /default + - /exploration/prostate/base - _self_ data_dir: "/mnt/projects/prostate_cancer/cancer/Graz 400_rescaled" diff --git a/configs/exploration/panda.yaml b/configs/exploration/prostate/panda.yaml similarity index 88% rename from configs/exploration/panda.yaml rename to configs/exploration/prostate/panda.yaml index e3516a57..f7c5590c 100644 --- a/configs/exploration/panda.yaml +++ b/configs/exploration/prostate/panda.yaml @@ -1,7 +1,7 @@ # @package _global_ defaults: - - /default + - /exploration/prostate/base - _self_ # Points to the public mlflow diff --git a/configs/model/backbone/google_vit.yaml b/configs/model/backbone/google_vit.yaml index 3e9b3e96..6f130eba 100644 --- a/configs/model/backbone/google_vit.yaml +++ b/configs/model/backbone/google_vit.yaml @@ -1 +1 @@ -_target_: prostate_cancer.modeling.backbone.google_vit \ No newline at end of file +_target_: ml.modeling.backbone.google_vit \ No newline at end of file diff --git a/configs/model/backbone/pgp.yaml b/configs/model/backbone/pgp.yaml index 5d69380c..f338abbf 100644 --- a/configs/model/backbone/pgp.yaml +++ b/configs/model/backbone/pgp.yaml @@ -1 +1 @@ -_target_: prostate_cancer.modeling.backbone.ProvGigaPath \ No newline at end of file +_target_: ml.modeling.backbone.ProvGigaPath \ No newline at end of file diff --git a/configs/model/backbone/resnet50.yaml b/configs/model/backbone/resnet50.yaml index a68e2297..3882538c 100644 --- a/configs/model/backbone/resnet50.yaml +++ b/configs/model/backbone/resnet50.yaml @@ -1,2 +1,2 @@ -_target_: prostate_cancer.modeling.backbone.resnet50 +_target_: ml.modeling.backbone.resnet50 weights: IMAGENET1K_V1 diff --git a/configs/model/backbone/vgg16.yaml b/configs/model/backbone/vgg16.yaml index 1c14d4cc..a0ba61d8 100644 --- a/configs/model/backbone/vgg16.yaml +++ b/configs/model/backbone/vgg16.yaml @@ -1,2 +1,2 @@ -_target_: prostate_cancer.modeling.backbone.vgg16 +_target_: ml.modeling.backbone.vgg16 weights: IMAGENET1K_V1 diff --git a/configs/model/backbone/virchow2.yaml b/configs/model/backbone/virchow2.yaml index 1b61c5e1..b6daeee2 100644 --- a/configs/model/backbone/virchow2.yaml +++ b/configs/model/backbone/virchow2.yaml @@ -1 +1 @@ -_target_: prostate_cancer.modeling.backbone.Virchow2 \ No newline at end of file +_target_: ml.modeling.backbone.Virchow2 \ No newline at end of file diff --git a/configs/model/checkpoints/mmci_tl/base.yaml b/configs/model/checkpoints/mmci_tl/base.yaml deleted file mode 100644 index a61bfca9..00000000 --- a/configs/model/checkpoints/mmci_tl/base.yaml +++ /dev/null @@ -1,2 +0,0 @@ -defaults: - - /data/mmci/stats@stats diff --git a/configs/model/checkpoints/prostate/base.yaml b/configs/model/checkpoints/prostate/base.yaml new file mode 100644 index 00000000..0041b55c --- /dev/null +++ b/configs/model/checkpoints/prostate/base.yaml @@ -0,0 +1,2 @@ +defaults: + - /data/prostate/mmci/stats@stats diff --git a/configs/model/checkpoints/mmci_tl/base_foundation.yaml b/configs/model/checkpoints/prostate/base_foundation.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/base_foundation.yaml rename to configs/model/checkpoints/prostate/base_foundation.yaml diff --git a/configs/model/checkpoints/mmci_tl/google_vit.yaml b/configs/model/checkpoints/prostate/google_vit.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/google_vit.yaml rename to configs/model/checkpoints/prostate/google_vit.yaml diff --git a/configs/model/checkpoints/mmci_tl/google_vit_stain.yaml b/configs/model/checkpoints/prostate/google_vit_stain.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/google_vit_stain.yaml rename to configs/model/checkpoints/prostate/google_vit_stain.yaml diff --git a/configs/model/checkpoints/mmci_tl/pgp.yaml b/configs/model/checkpoints/prostate/pgp.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/pgp.yaml rename to configs/model/checkpoints/prostate/pgp.yaml diff --git a/configs/model/checkpoints/mmci_tl/pgp_classic_mil.yaml b/configs/model/checkpoints/prostate/pgp_classic_mil.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/pgp_classic_mil.yaml rename to configs/model/checkpoints/prostate/pgp_classic_mil.yaml diff --git a/configs/model/checkpoints/mmci_tl/pgp_hybrid_mil.yaml b/configs/model/checkpoints/prostate/pgp_hybrid_mil.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/pgp_hybrid_mil.yaml rename to configs/model/checkpoints/prostate/pgp_hybrid_mil.yaml diff --git a/configs/model/checkpoints/mmci_tl/pgp_stain.yaml b/configs/model/checkpoints/prostate/pgp_stain.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/pgp_stain.yaml rename to configs/model/checkpoints/prostate/pgp_stain.yaml diff --git a/configs/model/checkpoints/mmci_tl/resnet50.yaml b/configs/model/checkpoints/prostate/resnet50.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/resnet50.yaml rename to configs/model/checkpoints/prostate/resnet50.yaml diff --git a/configs/model/checkpoints/mmci_tl/resnet50_224.yaml b/configs/model/checkpoints/prostate/resnet50_224.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/resnet50_224.yaml rename to configs/model/checkpoints/prostate/resnet50_224.yaml diff --git a/configs/model/checkpoints/mmci_tl/resnet50_stain.yaml b/configs/model/checkpoints/prostate/resnet50_stain.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/resnet50_stain.yaml rename to configs/model/checkpoints/prostate/resnet50_stain.yaml diff --git a/configs/model/checkpoints/mmci_tl/resnet50_stain_224.yaml b/configs/model/checkpoints/prostate/resnet50_stain_224.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/resnet50_stain_224.yaml rename to configs/model/checkpoints/prostate/resnet50_stain_224.yaml diff --git a/configs/model/checkpoints/mmci_tl/vgg16.yaml b/configs/model/checkpoints/prostate/vgg16.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/vgg16.yaml rename to configs/model/checkpoints/prostate/vgg16.yaml diff --git a/configs/model/checkpoints/mmci_tl/vgg16_224.yaml b/configs/model/checkpoints/prostate/vgg16_224.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/vgg16_224.yaml rename to configs/model/checkpoints/prostate/vgg16_224.yaml diff --git a/configs/model/checkpoints/mmci_tl/vgg16_stain.yaml b/configs/model/checkpoints/prostate/vgg16_stain.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/vgg16_stain.yaml rename to configs/model/checkpoints/prostate/vgg16_stain.yaml diff --git a/configs/model/checkpoints/mmci_tl/vgg16_stain_224.yaml b/configs/model/checkpoints/prostate/vgg16_stain_224.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/vgg16_stain_224.yaml rename to configs/model/checkpoints/prostate/vgg16_stain_224.yaml diff --git a/configs/model/checkpoints/mmci_tl/virchow2.yaml b/configs/model/checkpoints/prostate/virchow2.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/virchow2.yaml rename to configs/model/checkpoints/prostate/virchow2.yaml diff --git a/configs/model/checkpoints/mmci_tl/virchow2_classic_mil.yaml b/configs/model/checkpoints/prostate/virchow2_classic_mil.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/virchow2_classic_mil.yaml rename to configs/model/checkpoints/prostate/virchow2_classic_mil.yaml diff --git a/configs/model/checkpoints/mmci_tl/virchow2_hybrid_mil.yaml b/configs/model/checkpoints/prostate/virchow2_hybrid_mil.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/virchow2_hybrid_mil.yaml rename to configs/model/checkpoints/prostate/virchow2_hybrid_mil.yaml diff --git a/configs/model/checkpoints/mmci_tl/virchow2_stain.yaml b/configs/model/checkpoints/prostate/virchow2_stain.yaml similarity index 100% rename from configs/model/checkpoints/mmci_tl/virchow2_stain.yaml rename to configs/model/checkpoints/prostate/virchow2_stain.yaml diff --git a/configs/model/checkpoints/radboud/base.yaml b/configs/model/checkpoints/radboud/base.yaml deleted file mode 100644 index ce4b97b7..00000000 --- a/configs/model/checkpoints/radboud/base.yaml +++ /dev/null @@ -1,2 +0,0 @@ -defaults: - - /data/radboud/stats@stats diff --git a/configs/model/checkpoints/radboud/vgg16_stain.yaml b/configs/model/checkpoints/radboud/vgg16_stain.yaml deleted file mode 100644 index 0dbcd934..00000000 --- a/configs/model/checkpoints/radboud/vgg16_stain.yaml +++ /dev/null @@ -1,8 +0,0 @@ -defaults: - - base - - _self_ - -tile_threshold: 0.57 - -model_name: "VGG-16 Stain" -public_checkpoint: "mlflow-artifacts:/38/0607fa72ad8a4c298c781a130343808b/artifacts/checkpoints/epoch=4-step=70840/checkpoint.ckpt" diff --git a/configs/model/decode_head/cnn_classifier.yaml b/configs/model/decode_head/cnn_classifier.yaml index 7d66347d..3878dbfd 100644 --- a/configs/model/decode_head/cnn_classifier.yaml +++ b/configs/model/decode_head/cnn_classifier.yaml @@ -1,2 +1,2 @@ -_target_: prostate_cancer.modeling.decode_head.BinaryCNNClassifier +_target_: ml.modeling.decode_head.BinaryCNNClassifier in_features: ??? diff --git a/configs/model/decode_head/embedding_classifier.yaml b/configs/model/decode_head/embedding_classifier.yaml index 8af19f44..4c666a72 100644 --- a/configs/model/decode_head/embedding_classifier.yaml +++ b/configs/model/decode_head/embedding_classifier.yaml @@ -1,2 +1,2 @@ -_target_: prostate_cancer.modeling.decode_head.BinaryEmbeddingClassifier +_target_: ml.modeling.decode_head.BinaryEmbeddingClassifier in_features: ??? diff --git a/configs/model/decode_head/vit_classifier.yaml b/configs/model/decode_head/vit_classifier.yaml index 6c5b5180..80bdeada 100644 --- a/configs/model/decode_head/vit_classifier.yaml +++ b/configs/model/decode_head/vit_classifier.yaml @@ -1,2 +1,2 @@ -_target_: prostate_cancer.modeling.decode_head.BinaryViTClassifier +_target_: ml.modeling.decode_head.BinaryViTClassifier in_features: ??? diff --git a/configs/model/google_vit_model.yaml b/configs/model/google_vit_model.yaml index 82b101f2..287013e5 100644 --- a/configs/model/google_vit_model.yaml +++ b/configs/model/google_vit_model.yaml @@ -7,6 +7,6 @@ decode_head: in_features: 768 pooling: cls -_target_: prostate_cancer.vit_model.ViTProstateModel +_target_: ml.vit_model.ViTCarcinomaModel lr: ??? -tl_threshold: ??? \ No newline at end of file +tl_threshold: ??? diff --git a/configs/model/pgp_classic_mil_model.yaml b/configs/model/pgp_classic_mil_model.yaml index 42edbe12..e287e93d 100644 --- a/configs/model/pgp_classic_mil_model.yaml +++ b/configs/model/pgp_classic_mil_model.yaml @@ -1,4 +1,4 @@ -_target_: prostate_cancer.classic_mil_model.ProstateCancerClassicMIL +_target_: ml.classic_mil_model.CarcinomaClassicMIL foundation: "pgp" lr: ??? tl_threshold: ??? diff --git a/configs/model/pgp_full_model.yaml b/configs/model/pgp_full_model.yaml index 55948d52..ca8f9673 100644 --- a/configs/model/pgp_full_model.yaml +++ b/configs/model/pgp_full_model.yaml @@ -6,6 +6,6 @@ defaults: decode_head: in_features: 1536 -_target_: prostate_cancer.foundation_model.FoundationProstateModel +_target_: ml.foundation_model.FoundationCarcinomaModel lr: ??? tl_threshold: ??? diff --git a/configs/model/pgp_hybrid_mil_model.yaml b/configs/model/pgp_hybrid_mil_model.yaml index 180dedad..6e4739bd 100644 --- a/configs/model/pgp_hybrid_mil_model.yaml +++ b/configs/model/pgp_hybrid_mil_model.yaml @@ -1,4 +1,4 @@ -_target_: prostate_cancer.attention_mil_model.ProstateCancerAttentionMIL +_target_: ml.attention_mil_model.CarcinomaHybridMIL foundation: "pgp" lr: ??? tl_threshold: ??? diff --git a/configs/model/pgp_model.yaml b/configs/model/pgp_model.yaml index cfe50045..a6305ae2 100644 --- a/configs/model/pgp_model.yaml +++ b/configs/model/pgp_model.yaml @@ -1,6 +1,6 @@ -_target_: prostate_cancer.embedding_model.EmbeddingProstateModel +_target_: ml.embedding_model.EmbeddingCarcinomaModel decode_head: - _target_: prostate_cancer.modeling.decode_head.BinaryEmbeddingClassifier + _target_: ml.modeling.decode_head.BinaryEmbeddingClassifier in_features: 1536 lr: ??? -tl_threshold: ??? \ No newline at end of file +tl_threshold: ??? diff --git a/configs/model/resnet50_model.yaml b/configs/model/resnet50_model.yaml index a5e1473b..60807664 100644 --- a/configs/model/resnet50_model.yaml +++ b/configs/model/resnet50_model.yaml @@ -6,6 +6,6 @@ defaults: decode_head: in_features: 2048 -_target_: prostate_cancer.cnn_model.CNNProstateModel +_target_: ml.cnn_model.CNNCarcinomaModel lr: ??? -tl_threshold: ??? \ No newline at end of file +tl_threshold: ??? diff --git a/configs/model/vgg16_model.yaml b/configs/model/vgg16_model.yaml index ef24702b..ab5959ab 100644 --- a/configs/model/vgg16_model.yaml +++ b/configs/model/vgg16_model.yaml @@ -6,6 +6,6 @@ defaults: decode_head: in_features: 512 -_target_: prostate_cancer.cnn_model.CNNProstateModel +_target_: ml.cnn_model.CNNCarcinomaModel lr: ??? -tl_threshold: ??? \ No newline at end of file +tl_threshold: ??? diff --git a/configs/model/virchow2_classic_mil_model.yaml b/configs/model/virchow2_classic_mil_model.yaml index 621bca68..984724c7 100644 --- a/configs/model/virchow2_classic_mil_model.yaml +++ b/configs/model/virchow2_classic_mil_model.yaml @@ -1,4 +1,4 @@ -_target_: prostate_cancer.classic_mil_model.ProstateCancerClassicMIL +_target_: ml.classic_mil_model.CarcinomaClassicMIL foundation: "virchow2" lr: ??? tl_threshold: ??? diff --git a/configs/model/virchow2_full_model.yaml b/configs/model/virchow2_full_model.yaml index 967d50f4..95a8f91c 100644 --- a/configs/model/virchow2_full_model.yaml +++ b/configs/model/virchow2_full_model.yaml @@ -6,6 +6,6 @@ defaults: decode_head: in_features: 2560 -_target_: prostate_cancer.foundation_model.FoundationProstateModel +_target_: ml.foundation_model.FoundationCarcinomaModel lr: ??? tl_threshold: ??? diff --git a/configs/model/virchow2_hybrid_mil_model.yaml b/configs/model/virchow2_hybrid_mil_model.yaml index 29e9012f..58fa8755 100644 --- a/configs/model/virchow2_hybrid_mil_model.yaml +++ b/configs/model/virchow2_hybrid_mil_model.yaml @@ -1,4 +1,4 @@ -_target_: prostate_cancer.attention_mil_model.ProstateCancerAttentionMIL +_target_: ml.attention_mil_model.CarcinomaHybridMIL foundation: "virchow2" lr: ??? tl_threshold: ??? diff --git a/configs/model/virchow2_model.yaml b/configs/model/virchow2_model.yaml index 3bcbc193..643836d1 100644 --- a/configs/model/virchow2_model.yaml +++ b/configs/model/virchow2_model.yaml @@ -1,6 +1,6 @@ -_target_: prostate_cancer.embedding_model.EmbeddingProstateModel +_target_: ml.embedding_model.EmbeddingCarcinomaModel decode_head: - _target_: prostate_cancer.modeling.decode_head.BinaryEmbeddingClassifier + _target_: ml.modeling.decode_head.BinaryEmbeddingClassifier in_features: 2560 lr: ??? -tl_threshold: ??? \ No newline at end of file +tl_threshold: ??? diff --git a/configs/preprocessing/annot_masks.yaml b/configs/preprocessing/annot_masks.yaml index 0607bc62..cd77823c 100644 --- a/configs/preprocessing/annot_masks.yaml +++ b/configs/preprocessing/annot_masks.yaml @@ -2,7 +2,7 @@ level: 5 max_concurrent: 100 -output_path: ${prostate_cancer_artifacts}/annot_masks/${data.data_name} +output_path: ${carcinoma_artifacts}/annot_masks/${data.data_name} use_case: Annotation Masks metadata: diff --git a/configs/preprocessing/k_fold.yaml b/configs/preprocessing/k_fold.yaml deleted file mode 100644 index d04fd65f..00000000 --- a/configs/preprocessing/k_fold.yaml +++ /dev/null @@ -1,11 +0,0 @@ -# @package _global_ - -k: ??? - -target_column: "carcinoma" -group_column: "patient_id" -use_case: K-Fold - -metadata: - hyperparams: - k: ${k} diff --git a/configs/preprocessing/merge_embeddings.yaml b/configs/preprocessing/merge_embeddings.yaml index 9f26f21f..bd82a13d 100644 --- a/configs/preprocessing/merge_embeddings.yaml +++ b/configs/preprocessing/merge_embeddings.yaml @@ -3,7 +3,7 @@ data: ??? filtered_embeddings_uri: ??? encoder: ??? -output_dir: ${prostate_cancer_artifacts}/tiling_parquets_sharded/${data.data_name}/${encoder} +output_dir: ${carcinoma_artifacts}/tiling_parquets_sharded/${data.data_name}/${encoder} rows_per_file: 50000 use_case: Merge Embeddings ${encoder} diff --git a/configs/preprocessing/qc_masks.yaml b/configs/preprocessing/qc_masks.yaml index 3a86d22a..970c56eb 100644 --- a/configs/preprocessing/qc_masks.yaml +++ b/configs/preprocessing/qc_masks.yaml @@ -7,7 +7,7 @@ num_repeats: 10 url: "http://rayservice-qc-serve-svc.rationai-jobs-ns.svc.cluster.local:8000/" mask_level: 3 sample_level: 1 -output_path: ${prostate_cancer_artifacts}/qc_masks/${data.data_name} +output_path: ${carcinoma_artifacts}/qc_masks/${data.data_name} use_case: QC Masks metadata: diff --git a/configs/preprocessing/quality_control_v2.yaml b/configs/preprocessing/quality_control_v2.yaml index 756ee58e..d7c5ab05 100644 --- a/configs/preprocessing/quality_control_v2.yaml +++ b/configs/preprocessing/quality_control_v2.yaml @@ -11,7 +11,7 @@ qc_parameters: subsample_masks: False base_url: http://rayservice-qc-update-trial-serve-svc.rationai-jobs-ns.svc.cluster.local:8000/ -output_path: ${prostate_cancer_artifacts}/qc_masks/${data.data_name} +output_path: ${carcinoma_artifacts}/qc_masks/${data.data_name} use_case: QC Masks (v2) metadata: diff --git a/configs/preprocessing/resize_wsi.yaml b/configs/preprocessing/resize_wsi.yaml index a9aeb9a1..a95037d0 100644 --- a/configs/preprocessing/resize_wsi.yaml +++ b/configs/preprocessing/resize_wsi.yaml @@ -1,6 +1,6 @@ # @package _global_ -output_path: ${prostate_cancer_artifacts}/${data.data_name}_rescaled/${desired_mpp} +output_path: ${carcinoma_artifacts}/${data.data_name}_rescaled/${desired_mpp} desired_mpp: ??? max_concurrent: 5 use_case: WSI resize diff --git a/configs/preprocessing/tile_embeddings.yaml b/configs/preprocessing/tile_embeddings.yaml index d6154027..33b34f94 100644 --- a/configs/preprocessing/tile_embeddings.yaml +++ b/configs/preprocessing/tile_embeddings.yaml @@ -1,7 +1,7 @@ # @package _global_ batch_size: 1024 -output_path: ${prostate_cancer_artifacts}/tile_embeddings/${tile_encoder.name}/${data.data_name} +output_path: ${carcinoma_artifacts}/tile_embeddings/${tile_encoder.name}/${data.data_name} tile_encoder: _target_: ??? diff --git a/configs/preprocessing/tile_embeddings_v2.yaml b/configs/preprocessing/tile_embeddings_v2.yaml index b113c662..fd978d1f 100644 --- a/configs/preprocessing/tile_embeddings_v2.yaml +++ b/configs/preprocessing/tile_embeddings_v2.yaml @@ -2,7 +2,7 @@ encoder: ??? -output_path: ${prostate_cancer_artifacts}/tiles_with_embeddings/${encoder}/${data.data_name} +output_path: ${carcinoma_artifacts}/tiles_with_embeddings/${encoder}/${data.data_name} concurrency: 64 block_size: 128 rows_per_file: 50000 diff --git a/configs/preprocessing/tile_masks.yaml b/configs/preprocessing/tile_masks.yaml index ea26b259..1435e89d 100644 --- a/configs/preprocessing/tile_masks.yaml +++ b/configs/preprocessing/tile_masks.yaml @@ -1,6 +1,6 @@ # @package _global_ -output_path: ${prostate_cancer_artifacts}/tile_masks/${data.data_name} +output_path: ${carcinoma_artifacts}/tile_masks/${data.data_name} max_concurrent: 5 tile_uris: [] percentage_cols: [] diff --git a/configs/preprocessing/tissue_masks.yaml b/configs/preprocessing/tissue_masks.yaml index a5b707f9..4b0de583 100644 --- a/configs/preprocessing/tissue_masks.yaml +++ b/configs/preprocessing/tissue_masks.yaml @@ -2,7 +2,7 @@ level: 5 max_concurrent: 100 -output_path: ${prostate_cancer_artifacts}/tissue_masks/${data.data_name} +output_path: ${carcinoma_artifacts}/tissue_masks/${data.data_name} use_case: Tissue Masks metadata: diff --git a/exploration/comenius_3_sample.py b/exploration/comenius_3_sample.py index 29615c6a..7f9ce8d9 100644 --- a/exploration/comenius_3_sample.py +++ b/exploration/comenius_3_sample.py @@ -10,7 +10,7 @@ @hydra.main( config_path="../configs", - config_name="exploration/comenius_3_sample", + config_name="exploration/prostate/comenius_3_sample", version_base=None, ) @autolog diff --git a/exploration/fn_brno.py b/exploration/fn_brno.py index ecf98417..fa36d1a8 100644 --- a/exploration/fn_brno.py +++ b/exploration/fn_brno.py @@ -162,7 +162,9 @@ def create_df(slides: list[Path], annot_table: pd.DataFrame) -> pd.DataFrame: @hydra.main( - config_path="../configs", config_name="exploration/fn_brno", version_base=None + config_path="../configs", + config_name="exploration/prostate/fn_brno", + version_base=None, ) @autolog def main(config: DictConfig, logger: MLFlowLogger) -> None: diff --git a/exploration/mmci_2k.py b/exploration/mmci_2k.py index 6bf56e99..674c60de 100644 --- a/exploration/mmci_2k.py +++ b/exploration/mmci_2k.py @@ -91,7 +91,9 @@ def create_df(slides: list[Path], annot_table: pd.DataFrame) -> pd.DataFrame: @hydra.main( - config_path="../configs", config_name="exploration/mmci_2k", version_base=None + config_path="../configs", + config_name="exploration/prostate/mmci_2k", + version_base=None, ) @autolog def main(config: DictConfig, logger: MLFlowLogger) -> None: diff --git a/exploration/mug_400.py b/exploration/mug_400.py index 5c8dac9a..57857730 100644 --- a/exploration/mug_400.py +++ b/exploration/mug_400.py @@ -11,7 +11,7 @@ @hydra.main( config_path="../configs", - config_name="exploration/mug_400", + config_name="exploration/prostate/mug_400", version_base=None, ) @autolog diff --git a/exploration/panda.py b/exploration/panda.py index cbde5010..1a60ac6a 100644 --- a/exploration/panda.py +++ b/exploration/panda.py @@ -13,7 +13,7 @@ @hydra.main( config_path="../configs", - config_name="exploration/panda", + config_name="exploration/prostate/panda", version_base=None, ) @autolog diff --git a/prostate_cancer/__init__.py b/ml/__init__.py similarity index 100% rename from prostate_cancer/__init__.py rename to ml/__init__.py diff --git a/prostate_cancer/__main__.py b/ml/__main__.py similarity index 94% rename from prostate_cancer/__main__.py rename to ml/__main__.py index fb06feaf..c88a5881 100644 --- a/prostate_cancer/__main__.py +++ b/ml/__main__.py @@ -8,7 +8,7 @@ from rationai.mlkit import Trainer, autolog from rationai.mlkit.lightning.loggers.mlflow import MLFlowLogger -from prostate_cancer._mlflow_compat import apply_mlflow_compat_patch +from ml._mlflow_compat import apply_mlflow_compat_patch OmegaConf.register_new_resolver( diff --git a/prostate_cancer/_mlflow_compat.py b/ml/_mlflow_compat.py similarity index 100% rename from prostate_cancer/_mlflow_compat.py rename to ml/_mlflow_compat.py diff --git a/prostate_cancer/aggregators/__init__.py b/ml/aggregators/__init__.py similarity index 100% rename from prostate_cancer/aggregators/__init__.py rename to ml/aggregators/__init__.py diff --git a/prostate_cancer/aggregators/span.py b/ml/aggregators/span.py similarity index 100% rename from prostate_cancer/aggregators/span.py rename to ml/aggregators/span.py diff --git a/prostate_cancer/base_model.py b/ml/base_model.py similarity index 96% rename from prostate_cancer/base_model.py rename to ml/base_model.py index b56e1973..6cf58fc2 100644 --- a/prostate_cancer/base_model.py +++ b/ml/base_model.py @@ -16,10 +16,10 @@ Specificity, ) -from prostate_cancer.typing import LabeledTileSampleBatch, UnlabeledTileSampleBatch +from ml.typing import LabeledTileSampleBatch, UnlabeledTileSampleBatch -class ProstateCancerModel(LightningModule): +class CarcinomaTileModel(LightningModule): def __init__(self, lr: float, tl_threshold: float) -> None: super().__init__() self.lr = lr diff --git a/ml/callbacks/__init__.py b/ml/callbacks/__init__.py new file mode 100644 index 00000000..d16d6238 --- /dev/null +++ b/ml/callbacks/__init__.py @@ -0,0 +1,50 @@ +from ml.callbacks.aggregator_callback import AggregatorCallback +from ml.callbacks.cam_callback import CAMExplainer +from ml.callbacks.carcinoma_prediction_table_callback import ( + CarcinomaPredictionTableCallback, +) +from ml.callbacks.curves_callback_mil import CurvesCallbackMIL +from ml.callbacks.curves_callback_sl import CurvesCallbackSL +from ml.callbacks.curves_callback_tl import CurvesCallbackTile +from ml.callbacks.estimation_callback import ( + EstimationCallback, +) +from ml.callbacks.heatmap_callback import HeatmapCallback +from ml.callbacks.mil_prediction_callback import MILPredictionCallback +from ml.callbacks.multi_aggregator_eval_callback import ( + MultiAggregatorEvalCallback, +) +from ml.callbacks.nested_metrics_callback import NestedMetricsCallback +from ml.callbacks.nested_metrics_callback_mil import ( + NestedMetricsCallbackMIL, +) +from ml.callbacks.num_positive_callback import NumPositiveCallback +from ml.callbacks.slide_histograms_callback_mil import ( + SlideHistogramsCallbackMIL, +) +from ml.callbacks.tile_histograms_callback_mil import ( + TileHistogramsCallbackMIL, +) +from ml.callbacks.tile_histograms_callback_tl import ( + TileHistogramsCallbackTile, +) + + +__all__ = [ + "AggregatorCallback", + "CAMExplainer", + "CarcinomaPredictionTableCallback", + "CurvesCallbackMIL", + "CurvesCallbackSL", + "CurvesCallbackTile", + "EstimationCallback", + "HeatmapCallback", + "MILPredictionCallback", + "MultiAggregatorEvalCallback", + "NestedMetricsCallback", + "NestedMetricsCallbackMIL", + "NumPositiveCallback", + "SlideHistogramsCallbackMIL", + "TileHistogramsCallbackMIL", + "TileHistogramsCallbackTile", +] diff --git a/prostate_cancer/callbacks/aggregator_callback.py b/ml/callbacks/aggregator_callback.py similarity index 95% rename from prostate_cancer/callbacks/aggregator_callback.py rename to ml/callbacks/aggregator_callback.py index 60575710..fb6c52d9 100644 --- a/prostate_cancer/callbacks/aggregator_callback.py +++ b/ml/callbacks/aggregator_callback.py @@ -9,11 +9,11 @@ from rationai.mlkit.lightning.callbacks import MultiloaderLifecycle from rationai.mlkit.metrics.aggregators import Aggregator -from prostate_cancer.typing import TilingSlideMetadata, UnlabeledTileSampleBatch +from ml.typing import TilingSlideMetadata, UnlabeledTileSampleBatch if TYPE_CHECKING: - from prostate_cancer.datamodule import TileDataModule + from ml.datamodule import TileDataModule class AggregatorCallback(MultiloaderLifecycle): diff --git a/prostate_cancer/callbacks/cam_callback.py b/ml/callbacks/cam_callback.py similarity index 88% rename from prostate_cancer/callbacks/cam_callback.py rename to ml/callbacks/cam_callback.py index e0e482f0..f3465b2e 100644 --- a/prostate_cancer/callbacks/cam_callback.py +++ b/ml/callbacks/cam_callback.py @@ -11,13 +11,13 @@ from rationai.mlkit.lightning.callbacks import MultiloaderLifecycle from torchvision.transforms import Resize -from prostate_cancer.cnn_model import CNNProstateModel -from prostate_cancer.typing import LabeledTileSampleBatch, TilingSlideMetadata +from ml.cnn_model import CNNCarcinomaModel +from ml.typing import LabeledTileSampleBatch, TilingSlideMetadata if TYPE_CHECKING: - from prostate_cancer.datamodule import TileDataModule - from prostate_cancer.modeling.decode_head import BinaryClassifier + from ml.datamodule import TileDataModule + from ml.modeling.decode_head import BinaryClassifier class CAMExplainer(MultiloaderLifecycle): @@ -28,8 +28,8 @@ def __init__(self, resize_shape: tuple[int, int]) -> None: def on_test_start( self, trainer: lightning.Trainer, pl_module: lightning.LightningModule ) -> None: - if not isinstance(pl_module, CNNProstateModel): - raise TypeError("Model must be a CNNProstateModel to generate CAMs.") + if not isinstance(pl_module, CNNCarcinomaModel): + raise TypeError("Model must be a CNNCarcinomaModel to generate CAMs.") self.model = pl_module self.decode_head = cast("BinaryClassifier", self.model.decode_head) diff --git a/prostate_cancer/callbacks/carcinoma_prediction_table_callback.py b/ml/callbacks/carcinoma_prediction_table_callback.py similarity index 94% rename from prostate_cancer/callbacks/carcinoma_prediction_table_callback.py rename to ml/callbacks/carcinoma_prediction_table_callback.py index c30b4877..4cc35735 100644 --- a/prostate_cancer/callbacks/carcinoma_prediction_table_callback.py +++ b/ml/callbacks/carcinoma_prediction_table_callback.py @@ -7,11 +7,11 @@ import torch from rationai.mlkit.lightning.callbacks import MultiloaderLifecycle -from prostate_cancer.typing import TilingSlideMetadata, UnlabeledTileSampleBatch +from ml.typing import TilingSlideMetadata, UnlabeledTileSampleBatch if TYPE_CHECKING: - from prostate_cancer.datamodule import TileDataModule + from ml.datamodule import TileDataModule class CarcinomaPredictionTableCallback(MultiloaderLifecycle): diff --git a/prostate_cancer/callbacks/curves_callback_base.py b/ml/callbacks/curves_callback_base.py similarity index 100% rename from prostate_cancer/callbacks/curves_callback_base.py rename to ml/callbacks/curves_callback_base.py diff --git a/prostate_cancer/callbacks/curves_callback_mil.py b/ml/callbacks/curves_callback_mil.py similarity index 83% rename from prostate_cancer/callbacks/curves_callback_mil.py rename to ml/callbacks/curves_callback_mil.py index ae3ad927..a40b3eb6 100644 --- a/prostate_cancer/callbacks/curves_callback_mil.py +++ b/ml/callbacks/curves_callback_mil.py @@ -1,7 +1,7 @@ from lightning import LightningModule, Trainer -from prostate_cancer.callbacks.curves_callback_base import CurvesCallbackBase -from prostate_cancer.typing import LabeledBagOfTilesSampleBatch, MILModelOutput +from ml.callbacks.curves_callback_base import CurvesCallbackBase +from ml.typing import LabeledBagOfTilesSampleBatch, MILModelOutput class CurvesCallbackMIL(CurvesCallbackBase): diff --git a/prostate_cancer/callbacks/curves_callback_sl.py b/ml/callbacks/curves_callback_sl.py similarity index 85% rename from prostate_cancer/callbacks/curves_callback_sl.py rename to ml/callbacks/curves_callback_sl.py index 9a2bca89..ec61da66 100644 --- a/prostate_cancer/callbacks/curves_callback_sl.py +++ b/ml/callbacks/curves_callback_sl.py @@ -3,12 +3,12 @@ import torch from lightning import LightningModule, Trainer -from prostate_cancer.callbacks.curves_callback_base import CurvesCallbackBase -from prostate_cancer.typing import MILModelOutput, UnlabeledBagOfTilesSampleBatch +from ml.callbacks.curves_callback_base import CurvesCallbackBase +from ml.typing import MILModelOutput, UnlabeledBagOfTilesSampleBatch if TYPE_CHECKING: - from prostate_cancer.datamodule import BagOfTilesDataModule + from ml.datamodule import BagOfTilesDataModule class CurvesCallbackSL(CurvesCallbackBase): diff --git a/prostate_cancer/callbacks/curves_callback_tl.py b/ml/callbacks/curves_callback_tl.py similarity index 82% rename from prostate_cancer/callbacks/curves_callback_tl.py rename to ml/callbacks/curves_callback_tl.py index 51b31bb3..66035afc 100644 --- a/prostate_cancer/callbacks/curves_callback_tl.py +++ b/ml/callbacks/curves_callback_tl.py @@ -2,8 +2,8 @@ from lightning import LightningModule, Trainer -from prostate_cancer.callbacks.curves_callback_base import CurvesCallbackBase -from prostate_cancer.typing import LabeledTileSampleBatch +from ml.callbacks.curves_callback_base import CurvesCallbackBase +from ml.typing import LabeledTileSampleBatch class CurvesCallbackTile(CurvesCallbackBase): diff --git a/prostate_cancer/callbacks/estimation_callback.py b/ml/callbacks/estimation_callback.py similarity index 96% rename from prostate_cancer/callbacks/estimation_callback.py rename to ml/callbacks/estimation_callback.py index 2c6dcbfa..64d0fda8 100644 --- a/prostate_cancer/callbacks/estimation_callback.py +++ b/ml/callbacks/estimation_callback.py @@ -10,11 +10,11 @@ from rationai.mlkit.lightning.callbacks import MultiloaderLifecycle from rationai.mlkit.metrics.aggregators import Aggregator -from prostate_cancer.typing import TilingSlideMetadata, UnlabeledTileSampleBatch +from ml.typing import TilingSlideMetadata, UnlabeledTileSampleBatch if TYPE_CHECKING: - from prostate_cancer.datamodule import TileDataModule + from ml.datamodule import TileDataModule class EstimationCallback(MultiloaderLifecycle): diff --git a/prostate_cancer/callbacks/heatmap_callback.py b/ml/callbacks/heatmap_callback.py similarity index 97% rename from prostate_cancer/callbacks/heatmap_callback.py rename to ml/callbacks/heatmap_callback.py index fa058ec7..a83ea5f8 100644 --- a/prostate_cancer/callbacks/heatmap_callback.py +++ b/ml/callbacks/heatmap_callback.py @@ -6,7 +6,7 @@ from rationai.masks.mask_builders import ScalarMaskBuilder from rationai.mlkit.lightning.callbacks import MultiloaderLifecycle -from prostate_cancer.typing import ( +from ml.typing import ( LabeledTileSampleBatch, TilingSlideMetadata, UnlabeledTileSampleBatch, @@ -14,7 +14,7 @@ if TYPE_CHECKING: - from prostate_cancer.datamodule import TileDataModule + from ml.datamodule import TileDataModule class HeatmapCallback(MultiloaderLifecycle): diff --git a/prostate_cancer/callbacks/mil_prediction_callback.py b/ml/callbacks/mil_prediction_callback.py similarity index 97% rename from prostate_cancer/callbacks/mil_prediction_callback.py rename to ml/callbacks/mil_prediction_callback.py index 9e847262..ee75c4fb 100644 --- a/prostate_cancer/callbacks/mil_prediction_callback.py +++ b/ml/callbacks/mil_prediction_callback.py @@ -9,7 +9,7 @@ from rationai.masks.mask_builders import ScalarMaskBuilder from rationai.mlkit.lightning.loggers.mlflow import MLFlowLogger -from prostate_cancer.typing import ( +from ml.typing import ( LabeledBagOfTilesSampleBatch, MILModelOutput, UnlabeledBagOfTilesSampleBatch, @@ -17,7 +17,7 @@ if TYPE_CHECKING: - from prostate_cancer.datamodule import BagOfTilesDataModule + from ml.datamodule import BagOfTilesDataModule def min_max_normalization(tensor: torch.Tensor) -> torch.Tensor: diff --git a/prostate_cancer/callbacks/multi_aggregator_eval_callback.py b/ml/callbacks/multi_aggregator_eval_callback.py similarity index 97% rename from prostate_cancer/callbacks/multi_aggregator_eval_callback.py rename to ml/callbacks/multi_aggregator_eval_callback.py index 4507b88f..fd75633b 100644 --- a/prostate_cancer/callbacks/multi_aggregator_eval_callback.py +++ b/ml/callbacks/multi_aggregator_eval_callback.py @@ -17,11 +17,11 @@ Specificity, ) -from prostate_cancer.typing import TilingSlideMetadata, UnlabeledTileSampleBatch +from ml.typing import TilingSlideMetadata, UnlabeledTileSampleBatch if TYPE_CHECKING: - from prostate_cancer.datamodule import TileDataModule + from ml.datamodule import TileDataModule class MultiAggregatorEvalCallback(MultiloaderLifecycle): diff --git a/prostate_cancer/callbacks/nested_metrics_callback.py b/ml/callbacks/nested_metrics_callback.py similarity index 81% rename from prostate_cancer/callbacks/nested_metrics_callback.py rename to ml/callbacks/nested_metrics_callback.py index 23fea58b..7515cea3 100644 --- a/prostate_cancer/callbacks/nested_metrics_callback.py +++ b/ml/callbacks/nested_metrics_callback.py @@ -2,10 +2,10 @@ from lightning import LightningModule, Trainer -from prostate_cancer.callbacks.nested_metrics_callback_base import ( +from ml.callbacks.nested_metrics_callback_base import ( NestedMetricsCallbackBase, ) -from prostate_cancer.typing import LabeledTileSampleBatch +from ml.typing import LabeledTileSampleBatch class NestedMetricsCallback(NestedMetricsCallbackBase): diff --git a/prostate_cancer/callbacks/nested_metrics_callback_base.py b/ml/callbacks/nested_metrics_callback_base.py similarity index 100% rename from prostate_cancer/callbacks/nested_metrics_callback_base.py rename to ml/callbacks/nested_metrics_callback_base.py diff --git a/prostate_cancer/callbacks/nested_metrics_callback_mil.py b/ml/callbacks/nested_metrics_callback_mil.py similarity index 86% rename from prostate_cancer/callbacks/nested_metrics_callback_mil.py rename to ml/callbacks/nested_metrics_callback_mil.py index 954b1374..bd1c9a38 100644 --- a/prostate_cancer/callbacks/nested_metrics_callback_mil.py +++ b/ml/callbacks/nested_metrics_callback_mil.py @@ -1,9 +1,9 @@ from lightning import LightningModule, Trainer -from prostate_cancer.callbacks.nested_metrics_callback_base import ( +from ml.callbacks.nested_metrics_callback_base import ( NestedMetricsCallbackBase, ) -from prostate_cancer.typing import LabeledBagOfTilesSampleBatch, MILModelOutput +from ml.typing import LabeledBagOfTilesSampleBatch, MILModelOutput class NestedMetricsCallbackMIL(NestedMetricsCallbackBase): diff --git a/prostate_cancer/callbacks/num_positive_callback.py b/ml/callbacks/num_positive_callback.py similarity index 90% rename from prostate_cancer/callbacks/num_positive_callback.py rename to ml/callbacks/num_positive_callback.py index d05843b5..2f92c4d4 100644 --- a/prostate_cancer/callbacks/num_positive_callback.py +++ b/ml/callbacks/num_positive_callback.py @@ -5,12 +5,12 @@ import pandas as pd from rationai.mlkit.lightning.callbacks import MultiloaderLifecycle -from prostate_cancer.datamodule.datasets.base import get_slide_name -from prostate_cancer.typing import TilingSlideMetadata, UnlabeledTileSampleBatch +from ml.datamodule.datasets.base import get_slide_name +from ml.typing import TilingSlideMetadata, UnlabeledTileSampleBatch if TYPE_CHECKING: - from prostate_cancer.datamodule import TileDataModule + from ml.datamodule import TileDataModule class NumPositiveCallback(MultiloaderLifecycle): diff --git a/prostate_cancer/callbacks/slide_histograms_callback_mil.py b/ml/callbacks/slide_histograms_callback_mil.py similarity index 85% rename from prostate_cancer/callbacks/slide_histograms_callback_mil.py rename to ml/callbacks/slide_histograms_callback_mil.py index 7f48386d..f8574e4f 100644 --- a/prostate_cancer/callbacks/slide_histograms_callback_mil.py +++ b/ml/callbacks/slide_histograms_callback_mil.py @@ -3,14 +3,14 @@ import numpy as np from lightning import LightningModule, Trainer -from prostate_cancer.callbacks.tile_histograms_callback_base import ( +from ml.callbacks.tile_histograms_callback_base import ( TileHistogramsCallbackBase, ) -from prostate_cancer.typing import MILModelOutput, UnlabeledBagOfTilesSampleBatch +from ml.typing import MILModelOutput, UnlabeledBagOfTilesSampleBatch if TYPE_CHECKING: - from prostate_cancer.datamodule import BagOfTilesDataModule + from ml.datamodule import BagOfTilesDataModule class SlideHistogramsCallbackMIL(TileHistogramsCallbackBase): diff --git a/prostate_cancer/callbacks/tile_histograms_callback_base.py b/ml/callbacks/tile_histograms_callback_base.py similarity index 100% rename from prostate_cancer/callbacks/tile_histograms_callback_base.py rename to ml/callbacks/tile_histograms_callback_base.py diff --git a/prostate_cancer/callbacks/tile_histograms_callback_mil.py b/ml/callbacks/tile_histograms_callback_mil.py similarity index 84% rename from prostate_cancer/callbacks/tile_histograms_callback_mil.py rename to ml/callbacks/tile_histograms_callback_mil.py index d61dbf6e..5f2177e6 100644 --- a/prostate_cancer/callbacks/tile_histograms_callback_mil.py +++ b/ml/callbacks/tile_histograms_callback_mil.py @@ -1,9 +1,9 @@ from lightning import LightningModule, Trainer -from prostate_cancer.callbacks.tile_histograms_callback_base import ( +from ml.callbacks.tile_histograms_callback_base import ( TileHistogramsCallbackBase, ) -from prostate_cancer.typing import LabeledBagOfTilesSampleBatch, MILModelOutput +from ml.typing import LabeledBagOfTilesSampleBatch, MILModelOutput class TileHistogramsCallbackMIL(TileHistogramsCallbackBase): diff --git a/prostate_cancer/callbacks/tile_histograms_callback_tl.py b/ml/callbacks/tile_histograms_callback_tl.py similarity index 82% rename from prostate_cancer/callbacks/tile_histograms_callback_tl.py rename to ml/callbacks/tile_histograms_callback_tl.py index be49aec8..326c3957 100644 --- a/prostate_cancer/callbacks/tile_histograms_callback_tl.py +++ b/ml/callbacks/tile_histograms_callback_tl.py @@ -2,10 +2,10 @@ from lightning import LightningModule, Trainer -from prostate_cancer.callbacks.tile_histograms_callback_base import ( +from ml.callbacks.tile_histograms_callback_base import ( TileHistogramsCallbackBase, ) -from prostate_cancer.typing import LabeledTileSampleBatch +from ml.typing import LabeledTileSampleBatch class TileHistogramsCallbackTile(TileHistogramsCallbackBase): diff --git a/prostate_cancer/classic_mil_model.py b/ml/classic_mil_model.py similarity index 83% rename from prostate_cancer/classic_mil_model.py rename to ml/classic_mil_model.py index de883170..eab2b098 100644 --- a/prostate_cancer/classic_mil_model.py +++ b/ml/classic_mil_model.py @@ -1,14 +1,14 @@ from torch import Tensor -from prostate_cancer.mil_model_base import ProstateCancerMILBase -from prostate_cancer.typing import SLLabeledBagOfTilesSampleBatch +from ml.mil_model_base import CarcinomaMILBase +from ml.typing import SLLabeledBagOfTilesSampleBatch -class ProstateCancerClassicMIL(ProstateCancerMILBase): +class CarcinomaClassicMIL(CarcinomaMILBase): """Classic MIL: trained only on slide-level (SL) labels, no TL supervision. `test_step` (SL + TL metrics) and the architecture are inherited unchanged - from `ProstateCancerMILBase` - TL ground truth is still used to evaluate + from `CarcinomaMILBase` - TL ground truth is still used to evaluate the (unsupervised) per-tile classifier at test time, it just never contributes to the training loss here. """ diff --git a/prostate_cancer/cnn_model.py b/ml/cnn_model.py similarity index 73% rename from prostate_cancer/cnn_model.py rename to ml/cnn_model.py index 79f1ed57..42ca171f 100644 --- a/prostate_cancer/cnn_model.py +++ b/ml/cnn_model.py @@ -1,10 +1,10 @@ from torch import Tensor, nn -from prostate_cancer.base_model import ProstateCancerModel -from prostate_cancer.modeling.decode_head import BinaryCNNClassifier +from ml.base_model import CarcinomaTileModel +from ml.modeling.decode_head import BinaryCNNClassifier -class CNNProstateModel(ProstateCancerModel): +class CNNCarcinomaModel(CarcinomaTileModel): def __init__( self, backbone: nn.Module, diff --git a/prostate_cancer/datamodule/__init__.py b/ml/datamodule/__init__.py similarity index 51% rename from prostate_cancer/datamodule/__init__.py rename to ml/datamodule/__init__.py index d733127a..38b3c6f1 100644 --- a/prostate_cancer/datamodule/__init__.py +++ b/ml/datamodule/__init__.py @@ -1,8 +1,8 @@ -from prostate_cancer.datamodule.bag_of_tiles_data_module import ( +from ml.datamodule.bag_of_tiles_data_module import ( BagOfTilesDataModule, ClassicBagOfTilesDataModule, ) -from prostate_cancer.datamodule.tile_data_module import TileDataModule +from ml.datamodule.tile_data_module import TileDataModule __all__ = ["BagOfTilesDataModule", "ClassicBagOfTilesDataModule", "TileDataModule"] diff --git a/prostate_cancer/datamodule/bag_of_tiles_data_module.py b/ml/datamodule/bag_of_tiles_data_module.py similarity index 98% rename from prostate_cancer/datamodule/bag_of_tiles_data_module.py rename to ml/datamodule/bag_of_tiles_data_module.py index df3a09d4..a816a4c0 100644 --- a/prostate_cancer/datamodule/bag_of_tiles_data_module.py +++ b/ml/datamodule/bag_of_tiles_data_module.py @@ -10,12 +10,12 @@ if TYPE_CHECKING: - from prostate_cancer.datamodule.datasets import ( + from ml.datamodule.datasets import ( BagOfEmbeddingsDataset, UnlabeledBagOfEmbeddingsDataset, ) -from prostate_cancer.typing import ( +from ml.typing import ( LabeledBagOfTilesSample, LabeledBagOfTilesSampleBatch, SLLabeledBagOfTilesSample, diff --git a/prostate_cancer/datamodule/datasets/__init__.py b/ml/datamodule/datasets/__init__.py similarity index 72% rename from prostate_cancer/datamodule/datasets/__init__.py rename to ml/datamodule/datasets/__init__.py index 4d63aae5..c27e2961 100644 --- a/prostate_cancer/datamodule/datasets/__init__.py +++ b/ml/datamodule/datasets/__init__.py @@ -1,14 +1,14 @@ -from prostate_cancer.datamodule.datasets.bag_of_embeddings_dataset import ( +from ml.datamodule.datasets.bag_of_embeddings_dataset import ( BagOfEmbeddingsDataset, LabeledBagOfEmbeddingsDataset, SLLabeledBagOfEmbeddingsDataset, UnlabeledBagOfEmbeddingsDataset, ) -from prostate_cancer.datamodule.datasets.embeddings_dataset import ( +from ml.datamodule.datasets.embeddings_dataset import ( LabeledEmbeddingsDataset, UnlabeledEmbeddingsDataset, ) -from prostate_cancer.datamodule.datasets.tile_dataset import ( +from ml.datamodule.datasets.tile_dataset import ( LabeledTilesDataset, UnlabeledTilesDataset, ) diff --git a/prostate_cancer/datamodule/datasets/bag_of_embeddings_dataset.py b/ml/datamodule/datasets/bag_of_embeddings_dataset.py similarity index 98% rename from prostate_cancer/datamodule/datasets/bag_of_embeddings_dataset.py rename to ml/datamodule/datasets/bag_of_embeddings_dataset.py index 02133ab9..b415f463 100644 --- a/prostate_cancer/datamodule/datasets/bag_of_embeddings_dataset.py +++ b/ml/datamodule/datasets/bag_of_embeddings_dataset.py @@ -12,7 +12,7 @@ from rationai.mlkit.data.datasets.slides_tiles_loader import SlidesTilesLoader from torch.utils.data import Dataset -from prostate_cancer.typing import ( +from ml.typing import ( LabeledBagOfTilesSample, SlideMetadata, SLLabeledBagOfTilesSample, @@ -29,7 +29,7 @@ ) -class BagOfEmbeddingsDataset(Dataset[T], Generic[T], ABC): +class BagOfEmbeddingsDataset(Dataset[T], ABC, Generic[T]): """Base for bag-of-embeddings (MIL) datasets: one item per slide. Handles loading slide/tile metadata, assembling the (padded) bag of tile diff --git a/prostate_cancer/datamodule/datasets/base.py b/ml/datamodule/datasets/base.py similarity index 98% rename from prostate_cancer/datamodule/datasets/base.py rename to ml/datamodule/datasets/base.py index 8939d598..90029e7c 100644 --- a/prostate_cancer/datamodule/datasets/base.py +++ b/ml/datamodule/datasets/base.py @@ -8,7 +8,7 @@ from rationai.mlkit.data.datasets import MetaTiledSlides from torch.utils.data import Dataset -from prostate_cancer.typing import ( +from ml.typing import ( LabeledTileSample, TilingSlideMetadata, UnlabeledTileSample, diff --git a/prostate_cancer/datamodule/datasets/embeddings_dataset.py b/ml/datamodule/datasets/embeddings_dataset.py similarity index 95% rename from prostate_cancer/datamodule/datasets/embeddings_dataset.py rename to ml/datamodule/datasets/embeddings_dataset.py index 88156cd0..17c878a7 100644 --- a/prostate_cancer/datamodule/datasets/embeddings_dataset.py +++ b/ml/datamodule/datasets/embeddings_dataset.py @@ -4,12 +4,12 @@ import torch from datasets import Dataset as HFDataset -from prostate_cancer.datamodule.datasets.base import ( +from ml.datamodule.datasets.base import ( BaseSingleSlideDataset, BaseTileDataset, get_slide_name, ) -from prostate_cancer.typing import ( +from ml.typing import ( LabeledTileSample, TileMetadata, TilingSlideMetadata, diff --git a/prostate_cancer/datamodule/datasets/tile_dataset.py b/ml/datamodule/datasets/tile_dataset.py similarity index 96% rename from prostate_cancer/datamodule/datasets/tile_dataset.py rename to ml/datamodule/datasets/tile_dataset.py index 69bc42ab..624725bb 100644 --- a/prostate_cancer/datamodule/datasets/tile_dataset.py +++ b/ml/datamodule/datasets/tile_dataset.py @@ -7,11 +7,11 @@ from datasets import Dataset as HFDataset from rationai.mlkit.data.datasets import OpenSlideTilesDataset -from prostate_cancer.datamodule.datasets.base import ( +from ml.datamodule.datasets.base import ( BaseSingleSlideDataset, BaseTileDataset, ) -from prostate_cancer.typing import ( +from ml.typing import ( LabeledTileSample, TileMetadata, TilingSlideMetadata, diff --git a/prostate_cancer/datamodule/samplers/__init__.py b/ml/datamodule/samplers/__init__.py similarity index 51% rename from prostate_cancer/datamodule/samplers/__init__.py rename to ml/datamodule/samplers/__init__.py index cc5d8754..d021878a 100644 --- a/prostate_cancer/datamodule/samplers/__init__.py +++ b/ml/datamodule/samplers/__init__.py @@ -1,7 +1,7 @@ -from prostate_cancer.datamodule.samplers.bag_of_tiles_stratified_weighted_random_sampler import ( +from ml.datamodule.samplers.bag_of_tiles_stratified_weighted_random_sampler import ( BagOfTilesStratifiedWeightedRandomSampler, ) -from prostate_cancer.datamodule.samplers.tile_stratified_weighted_random_sampler import ( +from ml.datamodule.samplers.tile_stratified_weighted_random_sampler import ( TileStratifiedWeightedRandomSampler, ) diff --git a/prostate_cancer/datamodule/samplers/bag_of_tiles_stratified_weighted_random_sampler.py b/ml/datamodule/samplers/bag_of_tiles_stratified_weighted_random_sampler.py similarity index 92% rename from prostate_cancer/datamodule/samplers/bag_of_tiles_stratified_weighted_random_sampler.py rename to ml/datamodule/samplers/bag_of_tiles_stratified_weighted_random_sampler.py index 1969e438..682451e4 100644 --- a/prostate_cancer/datamodule/samplers/bag_of_tiles_stratified_weighted_random_sampler.py +++ b/ml/datamodule/samplers/bag_of_tiles_stratified_weighted_random_sampler.py @@ -4,7 +4,7 @@ from datasets import Dataset as HFDataset from torch.utils.data import WeightedRandomSampler -from prostate_cancer.datamodule.datasets.bag_of_embeddings_dataset import ( +from ml.datamodule.datasets.bag_of_embeddings_dataset import ( BagOfEmbeddingsDataset, ) diff --git a/prostate_cancer/datamodule/samplers/tile_stratified_weighted_random_sampler.py b/ml/datamodule/samplers/tile_stratified_weighted_random_sampler.py similarity index 92% rename from prostate_cancer/datamodule/samplers/tile_stratified_weighted_random_sampler.py rename to ml/datamodule/samplers/tile_stratified_weighted_random_sampler.py index 344b78bb..9e8c772a 100644 --- a/prostate_cancer/datamodule/samplers/tile_stratified_weighted_random_sampler.py +++ b/ml/datamodule/samplers/tile_stratified_weighted_random_sampler.py @@ -3,7 +3,7 @@ from datasets import Dataset as HFDataset from torch.utils.data import WeightedRandomSampler -from prostate_cancer.datamodule.datasets import LabeledTilesDataset +from ml.datamodule.datasets import LabeledTilesDataset class TileStratifiedWeightedRandomSampler(WeightedRandomSampler): diff --git a/prostate_cancer/datamodule/tile_data_module.py b/ml/datamodule/tile_data_module.py similarity index 98% rename from prostate_cancer/datamodule/tile_data_module.py rename to ml/datamodule/tile_data_module.py index e34c88c6..69e45f8a 100644 --- a/prostate_cancer/datamodule/tile_data_module.py +++ b/ml/datamodule/tile_data_module.py @@ -7,7 +7,7 @@ from rationai.mlkit.data.datasets import MetaTiledSlides from torch.utils.data import DataLoader -from prostate_cancer.typing import ( +from ml.typing import ( LabeledTileSample, LabeledTileSampleBatch, UnlabeledTileSample, diff --git a/prostate_cancer/datamodule/transforms/__init__.py b/ml/datamodule/transforms/__init__.py similarity index 100% rename from prostate_cancer/datamodule/transforms/__init__.py rename to ml/datamodule/transforms/__init__.py diff --git a/ml/datamodule/transforms/stain_normalization.py b/ml/datamodule/transforms/stain_normalization.py new file mode 100644 index 00000000..8d1a075f --- /dev/null +++ b/ml/datamodule/transforms/stain_normalization.py @@ -0,0 +1,24 @@ +from typing import cast + +from rationai.staining import ColorConversion, NormalizeStainingTransform + + +def build_normalize_staining_transform( + stain1: tuple[float, float, float], + stain2: tuple[float, float, float], + stain3: tuple[float, float, float], + target_stain1: tuple[float, float, float], + target_stain2: tuple[float, float, float], + target_stain3: tuple[float, float, float], +) -> NormalizeStainingTransform: + conversion = ColorConversion.from_stain_vectors( + cast("tuple[float, float, float]", tuple(stain1)), + cast("tuple[float, float, float]", tuple(stain2)), + cast("tuple[float, float, float]", tuple(stain3)), + ) + return NormalizeStainingTransform( + rgb2stain=conversion.matrix, + target_stain1=cast("tuple[float, float, float]", tuple(target_stain1)), + target_stain2=cast("tuple[float, float, float]", tuple(target_stain2)), + target_stain3=cast("tuple[float, float, float]", tuple(target_stain3)), + ) diff --git a/prostate_cancer/embedding_model.py b/ml/embedding_model.py similarity index 65% rename from prostate_cancer/embedding_model.py rename to ml/embedding_model.py index 0ed0b0b6..609bcf98 100644 --- a/prostate_cancer/embedding_model.py +++ b/ml/embedding_model.py @@ -1,10 +1,10 @@ from torch import Tensor -from prostate_cancer.base_model import ProstateCancerModel -from prostate_cancer.modeling.decode_head import BinaryEmbeddingClassifier +from ml.base_model import CarcinomaTileModel +from ml.modeling.decode_head import BinaryEmbeddingClassifier -class EmbeddingProstateModel(ProstateCancerModel): +class EmbeddingCarcinomaModel(CarcinomaTileModel): def __init__( self, decode_head: BinaryEmbeddingClassifier, lr: float, tl_threshold: float ) -> None: diff --git a/prostate_cancer/foundation_model.py b/ml/foundation_model.py similarity index 84% rename from prostate_cancer/foundation_model.py rename to ml/foundation_model.py index af085e0c..a23ee9d7 100644 --- a/prostate_cancer/foundation_model.py +++ b/ml/foundation_model.py @@ -3,12 +3,12 @@ import torch -from prostate_cancer.base_model import ProstateCancerModel -from prostate_cancer.modeling.backbone.foundation_base import FoundationModel -from prostate_cancer.modeling.decode_head import BinaryEmbeddingClassifier +from ml.base_model import CarcinomaTileModel +from ml.modeling.backbone.foundation_base import FoundationModel +from ml.modeling.decode_head import BinaryEmbeddingClassifier -class FoundationProstateModel(ProstateCancerModel): +class FoundationCarcinomaModel(CarcinomaTileModel): def __init__( self, backbone: FoundationModel, diff --git a/prostate_cancer/attention_mil_model.py b/ml/hybrid_mil_model.py similarity index 94% rename from prostate_cancer/attention_mil_model.py rename to ml/hybrid_mil_model.py index ff6aa472..5d9d1a1a 100644 --- a/prostate_cancer/attention_mil_model.py +++ b/ml/hybrid_mil_model.py @@ -6,11 +6,11 @@ from torch import Tensor, nn from torchmetrics import MetricCollection -from prostate_cancer.mil_model_base import ProstateCancerMILBase, binary_metrics -from prostate_cancer.typing import LabeledBagOfTilesSampleBatch +from ml.mil_model_base import CarcinomaMILBase, binary_metrics +from ml.typing import LabeledBagOfTilesSampleBatch -class ProstateCancerAttentionMIL(ProstateCancerMILBase): +class CarcinomaHybridMIL(CarcinomaMILBase): """Hybrid MIL: trained on both slide-level (SL) and tile-level (TL) labels.""" def __init__( diff --git a/prostate_cancer/mil_model_base.py b/ml/mil_model_base.py similarity index 98% rename from prostate_cancer/mil_model_base.py rename to ml/mil_model_base.py index 8424bc02..c80f5ddd 100644 --- a/prostate_cancer/mil_model_base.py +++ b/ml/mil_model_base.py @@ -17,7 +17,7 @@ Specificity, ) -from prostate_cancer.typing import ( +from ml.typing import ( LabeledBagOfTilesSampleBatch, MILModelOutput, UnlabeledBagOfTilesSampleBatch, @@ -37,7 +37,7 @@ def binary_metrics(threshold: float) -> dict[str, Metric | MetricCollection]: } -class ProstateCancerMILBase(LightningModule): +class CarcinomaMILBase(LightningModule): """Attention-MIL architecture shared by hybrid (SL+TL) and classic (SL-only) models. The bag encoder/attention/classifier and the forward pass are identical diff --git a/ml/modeling/backbone/__init__.py b/ml/modeling/backbone/__init__.py new file mode 100644 index 00000000..b231616a --- /dev/null +++ b/ml/modeling/backbone/__init__.py @@ -0,0 +1,8 @@ +from ml.modeling.backbone.google_vit import google_vit +from ml.modeling.backbone.pgp import ProvGigaPath +from ml.modeling.backbone.resnet50 import resnet50 +from ml.modeling.backbone.vgg16 import vgg16 +from ml.modeling.backbone.virchow2 import Virchow2 + + +__all__ = ["ProvGigaPath", "Virchow2", "google_vit", "resnet50", "vgg16"] diff --git a/prostate_cancer/modeling/backbone/foundation_base.py b/ml/modeling/backbone/foundation_base.py similarity index 100% rename from prostate_cancer/modeling/backbone/foundation_base.py rename to ml/modeling/backbone/foundation_base.py diff --git a/prostate_cancer/modeling/backbone/google_vit.py b/ml/modeling/backbone/google_vit.py similarity index 100% rename from prostate_cancer/modeling/backbone/google_vit.py rename to ml/modeling/backbone/google_vit.py diff --git a/prostate_cancer/modeling/backbone/pgp.py b/ml/modeling/backbone/pgp.py similarity index 85% rename from prostate_cancer/modeling/backbone/pgp.py rename to ml/modeling/backbone/pgp.py index 5efbc9a7..212b942c 100644 --- a/prostate_cancer/modeling/backbone/pgp.py +++ b/ml/modeling/backbone/pgp.py @@ -1,7 +1,7 @@ import timm import torch -from prostate_cancer.modeling.backbone.foundation_base import FoundationModel +from ml.modeling.backbone.foundation_base import FoundationModel class ProvGigaPath(FoundationModel): diff --git a/prostate_cancer/modeling/backbone/resnet50.py b/ml/modeling/backbone/resnet50.py similarity index 100% rename from prostate_cancer/modeling/backbone/resnet50.py rename to ml/modeling/backbone/resnet50.py diff --git a/prostate_cancer/modeling/backbone/vgg16.py b/ml/modeling/backbone/vgg16.py similarity index 100% rename from prostate_cancer/modeling/backbone/vgg16.py rename to ml/modeling/backbone/vgg16.py diff --git a/prostate_cancer/modeling/backbone/virchow2.py b/ml/modeling/backbone/virchow2.py similarity index 92% rename from prostate_cancer/modeling/backbone/virchow2.py rename to ml/modeling/backbone/virchow2.py index 852c85af..3de26c8e 100644 --- a/prostate_cancer/modeling/backbone/virchow2.py +++ b/ml/modeling/backbone/virchow2.py @@ -2,7 +2,7 @@ import torch from timm.layers import SwiGLUPacked # type: ignore[attr-defined] -from prostate_cancer.modeling.backbone.foundation_base import FoundationModel +from ml.modeling.backbone.foundation_base import FoundationModel class Virchow2(FoundationModel): diff --git a/ml/modeling/decode_head/__init__.py b/ml/modeling/decode_head/__init__.py new file mode 100644 index 00000000..3a710473 --- /dev/null +++ b/ml/modeling/decode_head/__init__.py @@ -0,0 +1,14 @@ +from ml.modeling.decode_head.binary_classifier import BinaryClassifier +from ml.modeling.decode_head.cnn_classifier import BinaryCNNClassifier +from ml.modeling.decode_head.embedding_classifier import ( + BinaryEmbeddingClassifier, +) +from ml.modeling.decode_head.vit_classifier import BinaryViTClassifier + + +__all__ = [ + "BinaryCNNClassifier", + "BinaryClassifier", + "BinaryEmbeddingClassifier", + "BinaryViTClassifier", +] diff --git a/prostate_cancer/modeling/decode_head/binary_classifier.py b/ml/modeling/decode_head/binary_classifier.py similarity index 100% rename from prostate_cancer/modeling/decode_head/binary_classifier.py rename to ml/modeling/decode_head/binary_classifier.py diff --git a/prostate_cancer/modeling/decode_head/cnn_classifier.py b/ml/modeling/decode_head/cnn_classifier.py similarity index 86% rename from prostate_cancer/modeling/decode_head/cnn_classifier.py rename to ml/modeling/decode_head/cnn_classifier.py index e16048ea..aa08f76a 100644 --- a/prostate_cancer/modeling/decode_head/cnn_classifier.py +++ b/ml/modeling/decode_head/cnn_classifier.py @@ -1,6 +1,6 @@ from torch import Tensor, nn -from prostate_cancer.modeling.decode_head.binary_classifier import BinaryClassifier +from ml.modeling.decode_head.binary_classifier import BinaryClassifier class BinaryCNNClassifier(BinaryClassifier): diff --git a/prostate_cancer/modeling/decode_head/embedding_classifier.py b/ml/modeling/decode_head/embedding_classifier.py similarity index 77% rename from prostate_cancer/modeling/decode_head/embedding_classifier.py rename to ml/modeling/decode_head/embedding_classifier.py index d31821c1..7a566a5e 100644 --- a/prostate_cancer/modeling/decode_head/embedding_classifier.py +++ b/ml/modeling/decode_head/embedding_classifier.py @@ -1,6 +1,6 @@ from torch import Tensor -from prostate_cancer.modeling.decode_head.binary_classifier import BinaryClassifier +from ml.modeling.decode_head.binary_classifier import BinaryClassifier class BinaryEmbeddingClassifier(BinaryClassifier): diff --git a/prostate_cancer/modeling/decode_head/vit_classifier.py b/ml/modeling/decode_head/vit_classifier.py similarity index 88% rename from prostate_cancer/modeling/decode_head/vit_classifier.py rename to ml/modeling/decode_head/vit_classifier.py index 3b11889a..3c076dea 100644 --- a/prostate_cancer/modeling/decode_head/vit_classifier.py +++ b/ml/modeling/decode_head/vit_classifier.py @@ -1,6 +1,6 @@ from torch import Tensor -from prostate_cancer.modeling.decode_head.binary_classifier import BinaryClassifier +from ml.modeling.decode_head.binary_classifier import BinaryClassifier class BinaryViTClassifier(BinaryClassifier): diff --git a/prostate_cancer/typing.py b/ml/typing.py similarity index 100% rename from prostate_cancer/typing.py rename to ml/typing.py diff --git a/prostate_cancer/vit_model.py b/ml/vit_model.py similarity index 74% rename from prostate_cancer/vit_model.py rename to ml/vit_model.py index dac7c77a..20aedb17 100644 --- a/prostate_cancer/vit_model.py +++ b/ml/vit_model.py @@ -1,13 +1,10 @@ -from collections.abc import Mapping -from typing import Any - from torch import Tensor, nn from transformers import ViTModel -from prostate_cancer.base_model import ProstateCancerModel +from ml.base_model import CarcinomaTileModel -class ViTProstateModel(ProstateCancerModel): +class ViTCarcinomaModel(CarcinomaTileModel): def __init__( self, backbone: ViTModel, decode_head: nn.Module, lr: float, tl_threshold: float ) -> None: diff --git a/preprocessing/embeddings/tile_embeddings.py b/preprocessing/embeddings/tile_embeddings.py index b79dc315..8d5b5345 100644 --- a/preprocessing/embeddings/tile_embeddings.py +++ b/preprocessing/embeddings/tile_embeddings.py @@ -12,11 +12,11 @@ from torch.utils.data import DataLoader from tqdm import tqdm -from prostate_cancer.datamodule.datasets import UnlabeledTilesDataset +from ml.datamodule.datasets import UnlabeledTilesDataset if TYPE_CHECKING: - from prostate_cancer.modeling.backbone.foundation_base import FoundationModel + from ml.modeling.backbone.foundation_base import FoundationModel def save_embeddings( diff --git a/preprocessing/k_fold.py b/preprocessing/k_fold.py deleted file mode 100644 index a0e48eec..00000000 --- a/preprocessing/k_fold.py +++ /dev/null @@ -1,133 +0,0 @@ -import hydra -import mlflow -import numpy as np -import pandas as pd -from omegaconf import DictConfig -from rationai.mlkit import autolog, with_cli_args -from rationai.mlkit.lightning.loggers import MLFlowLogger -from rationai.tiling.writers import save_mlflow_dataset -from sklearn.model_selection import StratifiedGroupKFold - - -def stratified_group_k_fold_split( - slides_df: pd.DataFrame, - target_col: str, - group_col: str, - k: int, -) -> pd.DataFrame: - slides_df = slides_df.copy() - fold_mask = np.empty(len(slides_df), dtype=int) - - sgkf = StratifiedGroupKFold(n_splits=k, shuffle=True, random_state=42) - folds = sgkf.split( - slides_df, - slides_df[target_col], - slides_df[group_col], - ) - - for i, (_, fold_index) in enumerate(folds): - fold_mask[fold_index] = i - - slides_df["fold"] = fold_mask - return slides_df - - -def load_tiling_tables( - uri: str, -) -> tuple[pd.DataFrame, pd.DataFrame] | tuple[None, None]: - tiling_path = mlflow.artifacts.download_artifacts(uri) if uri else None - if tiling_path is None: - return None, None - - slides_df = pd.read_parquet(f"{tiling_path}/slides.parquet") - tiles_df = pd.read_parquet(f"{tiling_path}/tiles.parquet") - return slides_df, tiles_df - - -def attach_group( - base_slides_df: pd.DataFrame, annotations_source: pd.DataFrame, group_col: str -) -> pd.DataFrame: - base_slides_df = base_slides_df.join( - annotations_source.set_index("slide_path")[group_col], - on="path", - how="left", - validate="one_to_one", - ) - - if base_slides_df[group_col].isna().any(): - raise ValueError(f"Missing '{group_col}' after joining annotations source.") - - return base_slides_df - - -def compute_folds( - base_slides_df: pd.DataFrame, target_column: str, group_column: str, k: int -) -> pd.DataFrame: - slides_with_folds = stratified_group_k_fold_split( - base_slides_df, target_column, group_column, k - ) - fold_by_path = slides_with_folds.set_index("path")["fold"] - - group_to_folds = slides_with_folds.groupby(group_column)["fold"].nunique() - leaking_groups = group_to_folds[group_to_folds > 1] - if len(leaking_groups) != 0: - raise ValueError("Cross-fold patient leakage") - - return fold_by_path - - -def apply_folds( - slides_df: pd.DataFrame, - tiles_df: pd.DataFrame, - fold_by_path: pd.DataFrame, - name: str, -) -> None: - slides_df = slides_df.join( - fold_by_path, on="path", how="left", validate="one_to_one" - ) - if slides_df["fold"].isna().any(): - raise ValueError("Missing fold assignment for some slides") - - save_mlflow_dataset( - slides=slides_df, - tiles=tiles_df, - dataset_name=f"{name}_with_folds", - ) - - -@with_cli_args(["+preprocessing=k_fold"]) -@hydra.main(config_path="../configs", config_name="preprocessing", version_base=None) -@autolog -def main(config: DictConfig, logger: MLFlowLogger) -> None: - annotations_source = pd.read_csv( - mlflow.artifacts.download_artifacts(config.data.metadata_table) - ) - - slides_df_512, tiles_df_512 = load_tiling_tables(config.data.tiles_uri_512) - slides_df_224, tiles_df_224 = load_tiling_tables(config.data.tiles_uri_224) - - if slides_df_512 is None and slides_df_224 is None: - raise ValueError("At least one tiling must be present") - - base_slides_df = slides_df_512 if slides_df_512 is not None else slides_df_224 - - base_slides_df = attach_group( - base_slides_df, annotations_source, config.group_column - ) - fold_by_path = compute_folds( - base_slides_df, config.target_column, config.group_column, config.k - ) - - if slides_df_512 is not None: - apply_folds( - slides_df_512, tiles_df_512, fold_by_path, f"{config.data.data_name}_512" - ) - - if slides_df_224 is not None: - apply_folds( - slides_df_224, tiles_df_224, fold_by_path, f"{config.data.data_name}_224" - ) - - -if __name__ == "__main__": - main() diff --git a/preprocessing/masks/quality_control.py b/preprocessing/masks/quality_control.py index cf4ab3cb..94cf1d1c 100644 --- a/preprocessing/masks/quality_control.py +++ b/preprocessing/masks/quality_control.py @@ -165,7 +165,7 @@ async def qc_main( def main(config: DictConfig, logger: MLFlowLogger) -> None: output_path = Path(config.output_path) output_path.mkdir(exist_ok=True, parents=True) - prostate_cancer_path = config.prostate_cancer_artifacts + artifacts_path = config.carcinoma_artifacts df = pd.read_csv(mlflow.artifacts.download_artifacts(config.data.metadata_table)) slides = [Path(path) for path in df["slide_path"]] @@ -173,7 +173,7 @@ def main(config: DictConfig, logger: MLFlowLogger) -> None: semaphore = asyncio.Semaphore(config.request_limit) with tempfile.TemporaryDirectory( - prefix="qc_masks_report_", dir=Path(prostate_cancer_path).as_posix() + prefix="qc_masks_report_", dir=Path(artifacts_path).as_posix() ) as tmp_dir: # Create a temporary directory for the report report_path = Path(tmp_dir) / "report.html" diff --git a/preprocessing/stats.py b/preprocessing/stats.py index 21566daf..1676d3f5 100644 --- a/preprocessing/stats.py +++ b/preprocessing/stats.py @@ -8,8 +8,8 @@ from rationai.mlkit import autolog, with_cli_args from rationai.mlkit.lightning.loggers import MLFlowLogger -from prostate_cancer.datamodule.datasets import UnlabeledTilesDataset -from prostate_cancer.datamodule.datasets.tile_dataset import SlideTiles +from ml.datamodule.datasets import UnlabeledTilesDataset +from ml.datamodule.datasets.tile_dataset import SlideTiles @ray.remote diff --git a/preprocessing/tiling/tiling.py b/preprocessing/tiling/tiling.py index 8968d603..bc0133c9 100644 --- a/preprocessing/tiling/tiling.py +++ b/preprocessing/tiling/tiling.py @@ -1,4 +1,4 @@ -"""Script for creating slides and tiles datasets for prostate cancer binary prediction.""" +"""Script for creating slides and tiles datasets for carcinoma binary prediction.""" from dataclasses import asdict, dataclass from pathlib import Path diff --git a/prostate_cancer/callbacks/__init__.py b/prostate_cancer/callbacks/__init__.py deleted file mode 100644 index 875e6156..00000000 --- a/prostate_cancer/callbacks/__init__.py +++ /dev/null @@ -1,50 +0,0 @@ -from prostate_cancer.callbacks.aggregator_callback import AggregatorCallback -from prostate_cancer.callbacks.cam_callback import CAMExplainer -from prostate_cancer.callbacks.carcinoma_prediction_table_callback import ( - CarcinomaPredictionTableCallback, -) -from prostate_cancer.callbacks.curves_callback_mil import CurvesCallbackMIL -from prostate_cancer.callbacks.curves_callback_sl import CurvesCallbackSL -from prostate_cancer.callbacks.curves_callback_tl import CurvesCallbackTile -from prostate_cancer.callbacks.estimation_callback import ( - EstimationCallback, -) -from prostate_cancer.callbacks.heatmap_callback import HeatmapCallback -from prostate_cancer.callbacks.mil_prediction_callback import MILPredictionCallback -from prostate_cancer.callbacks.multi_aggregator_eval_callback import ( - MultiAggregatorEvalCallback, -) -from prostate_cancer.callbacks.nested_metrics_callback import NestedMetricsCallback -from prostate_cancer.callbacks.nested_metrics_callback_mil import ( - NestedMetricsCallbackMIL, -) -from prostate_cancer.callbacks.num_positive_callback import NumPositiveCallback -from prostate_cancer.callbacks.slide_histograms_callback_mil import ( - SlideHistogramsCallbackMIL, -) -from prostate_cancer.callbacks.tile_histograms_callback_mil import ( - TileHistogramsCallbackMIL, -) -from prostate_cancer.callbacks.tile_histograms_callback_tl import ( - TileHistogramsCallbackTile, -) - - -__all__ = [ - "AggregatorCallback", - "CAMExplainer", - "CarcinomaPredictionTableCallback", - "CurvesCallbackMIL", - "CurvesCallbackSL", - "CurvesCallbackTile", - "EstimationCallback", - "HeatmapCallback", - "MILPredictionCallback", - "MultiAggregatorEvalCallback", - "NestedMetricsCallback", - "NestedMetricsCallbackMIL", - "NumPositiveCallback", - "SlideHistogramsCallbackMIL", - "TileHistogramsCallbackMIL", - "TileHistogramsCallbackTile", -] diff --git a/prostate_cancer/datamodule/transforms/stain_normalization.py b/prostate_cancer/datamodule/transforms/stain_normalization.py deleted file mode 100644 index 4b3fd33d..00000000 --- a/prostate_cancer/datamodule/transforms/stain_normalization.py +++ /dev/null @@ -1,22 +0,0 @@ -from collections.abc import Sequence - -from rationai.staining import ColorConversion, NormalizeStainingTransform - - -def build_normalize_staining_transform( - stain1: Sequence[float], - stain2: Sequence[float], - stain3: Sequence[float], - target_stain1: Sequence[float], - target_stain2: Sequence[float], - target_stain3: Sequence[float], -) -> NormalizeStainingTransform: - conversion = ColorConversion.from_stain_vectors( - tuple(stain1), tuple(stain2), tuple(stain3) - ) - return NormalizeStainingTransform( - rgb2stain=conversion.matrix, - target_stain1=tuple(target_stain1), - target_stain2=tuple(target_stain2), - target_stain3=tuple(target_stain3), - ) diff --git a/prostate_cancer/modeling/backbone/__init__.py b/prostate_cancer/modeling/backbone/__init__.py deleted file mode 100644 index f6c3b814..00000000 --- a/prostate_cancer/modeling/backbone/__init__.py +++ /dev/null @@ -1,8 +0,0 @@ -from prostate_cancer.modeling.backbone.google_vit import google_vit -from prostate_cancer.modeling.backbone.pgp import ProvGigaPath -from prostate_cancer.modeling.backbone.resnet50 import resnet50 -from prostate_cancer.modeling.backbone.vgg16 import vgg16 -from prostate_cancer.modeling.backbone.virchow2 import Virchow2 - - -__all__ = ["ProvGigaPath", "Virchow2", "google_vit", "resnet50", "vgg16"] diff --git a/prostate_cancer/modeling/decode_head/__init__.py b/prostate_cancer/modeling/decode_head/__init__.py deleted file mode 100644 index a964ca41..00000000 --- a/prostate_cancer/modeling/decode_head/__init__.py +++ /dev/null @@ -1,14 +0,0 @@ -from prostate_cancer.modeling.decode_head.binary_classifier import BinaryClassifier -from prostate_cancer.modeling.decode_head.cnn_classifier import BinaryCNNClassifier -from prostate_cancer.modeling.decode_head.embedding_classifier import ( - BinaryEmbeddingClassifier, -) -from prostate_cancer.modeling.decode_head.vit_classifier import BinaryViTClassifier - - -__all__ = [ - "BinaryCNNClassifier", - "BinaryClassifier", - "BinaryEmbeddingClassifier", - "BinaryViTClassifier", -]