fix: convert em_rates to backend array in Identity.render (#124)

DEV_NOTES.md

@@ -0,0 +1,39 @@
+# Development Notes
+
+Setup friction encountered on this fork during GPU development — kept
+here separately so the main README stays clean. Not universal microsim
+guidance, just what was hit on this machine.
+
+## GPU backend (cupy) setup
+
+1. **numpy version conflict** — microsim's metadata pins `numpy<2.0`, but
+   `cupy-cuda12x` requires `numpy>=2.0`. In practice, numpy 2.4.6 worked
+   fine at runtime with this version of microsim despite the metadata
+   warning — if `pip` flags the conflict, it's likely safe to ignore,
+   but verify by running a real simulation before trusting it.
+
+2. **CUDA headers not found** (`RuntimeError: Failed to find CUDA headers`)
+   — if your system has multiple CUDA toolkit installs (common after
+   driver updates over time), cupy's JIT compiler may not find headers
+   even with `CUDA_PATH` set correctly. Installing the toolkit extra
+   directly into the venv sidesteps the problem:
+```bash
+   pip install "cupy-cuda12x[ctk]"
+```
+
+3. **zarr / numcodecs mismatch** (`ImportError: cannot import name
+   'cbuffer_sizes' from 'numcodecs.blosc'`) — zarr 2.17.x expects an
+   older numcodecs API:
+```bash
+   pip install "numcodecs<0.13"
+```
+
+4. **COSEM data fetching** — loading real segmentation data (e.g. the
+   `cosem` example) requires the optional extra:
+```bash
+   pip install "microsim[cosem]"
+```
+
+None of these are bugs in microsim itself, except where already filed
+as upstream PRs (#140, #141) — mostly environment/dependency friction
+from multiple existing CUDA/Python installs on a dev machine.

README.md

@@ -64,6 +64,9 @@ These are not installed by default, see the
 or [cupy](https://docs.cupy.dev/en/stable/install.html) installation instructions,
 paying attention to your GPU requirements.  Support for torch is planned.
 
+See [DEV_NOTES.md](DEV_NOTES.md) for real setup issues hit on this fork
+(numpy/cupy version conflicts, CUDA header errors, zarr/numcodecs mismatch).
+
 ## Usage
 
 Construct and run a

src/microsim/schema/modality/_simple_psf.py

@@ -208,16 +208,19 @@ def render(
         self,
         truth: xrDataArray,  # (F, Z, Y, X)
         em_rates: xrDataArray,  # (C, F, W)
-        *args: Any,
-        **kwargs: Any,
+        objective_lens: ObjectiveLens,
+        settings: Settings,
+        xp: NumpyAPI,
     ) -> xrDataArray:
         """Render a 3D image of the truth for F fluorophores, in C channels.
 
         In this case we don't apply the PSF convolution, as the truth is assumed to be
         already convolved with the PSF. Therefore, we simply compute the emission flux
         for each fluorophore and each channel.
         """
-        em_image = em_rates.sum(Axis.W) * truth
+        em_rates = em_rates.sum(Axis.W)
+        em_rates = em_rates.copy(data=xp.asarray(em_rates.data))
+        em_image = em_rates * truth
         return DataArray(
             em_image,
             dims=[Axis.C, Axis.F, Axis.Z, Axis.Y, Axis.X],

tests/test_simulation.py

@@ -166,3 +166,17 @@ def test_simulation_write_from_ground_truth(tmp_path: Path) -> None:
     )
     sim.run()
     assert (tmp_path / "output.zarr").exists()
+
+
+def test_identity_modality_backend_conversion(np_backend: ms.BackendName) -> None:
+    """Regression test for #124: em_rates must be converted to the active
+    backend before use in Identity.render(), same as truth already is."""
+    sim = ms.Simulation(
+        truth_space=ms.ShapeScaleSpace(shape=(8, 32, 32), scale=(0.2, 0.1, 0.1)),
+        output_space={"downscale": 1},
+        sample=ms.Sample(labels=[MATSLINES]),
+        modality=ms.Identity(),
+        settings=ms.Settings(np_backend=np_backend),
+    )
+    result = sim.optical_image()
+    assert result.shape[1:] == sim.truth_space.shape