AutoMorph-Batch/build_taskfile.py at master · HullLab/AutoMorph-Batch · GitHub

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#!/usr/env/python
import argparse
import sys
import os

function_list = ['segment', 'focus', '2dmorph', '3dmorph']


def build_taskfile(function, directory_list=None):

    if directory_list is None:
        directory_list = 'dirs_segmented.txt'

    if function not in function_list:
        print 'Error: unknown function specified. Choose from: %s' % ', '.join(function_list)
        sys.exit(1)

    # output filename for tasklist
    f = open('taskfile_'+function+'.txt', 'w')
    # input list of directories
    l = open(directory_list, 'r')

    for line in l:
        if directory_list.endswith('.csv'):
            directory = line.strip('\n').split(',')[0]
        else:
            directory = line.strip('\n')
        task = []
        task.append('source ~/.bashrc')
        task.append('cd '+directory)

        if function == 'segment':
            if os.path.exists(directory+'/segment_settings.txt'):
                task.append('segment segment_settings.txt')
            else:
                print 'Settings file not found in %s. Double check your directory list: %s' % (directory, directory_list)
                continue
        elif function == 'focus':
            task.append('focus final')

        elif function == '2dmorph':
            if os.path.exists(directory+'/2dmorph_settings.txt'):
                task.append('run2dmorph 2dmorph_settings.txt')
            else:
                print 'Settings file not found in %s. Double check your directory list: %s' % (directory, directory_list)
                continue

        elif function == '3dmorph':
            if os.path.exists(directory+'/3dmorph_settings.txt'):
                task.append('run3dmorph 3dmorph_settings.txt')
            else:
                print 'Settings file not found in %s. Double check your directory list: %s' % (directory, directory_list)
                continue

        else:
            sys.exit(1)

        task_string = "; ".join(task)
        f.write(task_string+'\n')

    f.close()


if __name__ == "__main__":

    parser = argparse.ArgumentParser(description='')

    parser.add_argument('function', help='specify AutoMorph function', choices=function_list)
    parser.add_argument('-d', '--dirs', help="directory list file (required for 2d and 3d morph)")
    args = parser.parse_args()

    if args.function in ['2dmorph', '3dmorph']:
        if args.dirs is None:
            sys.exit('directory list is required for 2d and 3dmorph. Specify with -d <dir_list>.')
        else:
            if os.path.exists(args.dirs):
                build_taskfile(args.function, args.dirs)
            else:
                sys.exit('directory list file not found %s.' % args.dirs)
    else:
        if args.dirs is not None:
            build_taskfile(args.function, args.dirs)
        else:
            build_taskfile(args.function)