object_file_postfixes.append(object_file_postfix) pdc = import_cp2_csv_results(cp2_csv_path, image_file_postfix, object_file_postfixes, csv_delimiter, csv_extension) Importer().set_pdc(pdc) utils.update_state(importer.__name__, 'imported') print 'Finished importing data from CellProfiler' return 'Finished importing data from CellProfiler' __dict__ = sys.modules[__name__].__dict__ utils.register_module(__name__, 'CellProfiler import', __dict__, utils.DEFAULT_STATE) utils.register_parameter(__name__, 'image_cp2_file', utils.PARAM_INPUT_FILE, 'Image CSV file from CellProfiler 2', optional=True) utils.set_parameter_hook(__name__, 'image_cp2_file', importer.filename_hook) utils.register_parameter(__name__, 'object_cp2_csv_files', utils.PARAM_INPUT_FILES, 'Object CSV files from CellProfiler 2', optional=True) utils.set_parameter_hook(__name__, 'object_cp2_csv_files', importer.filename_hook) utils.register_parameter(__name__, 'cp2_csv_path', utils.PARAM_PATH, 'Path to CellProfiler 2 CSV files', optional=True) utils.set_parameter_hook(__name__, 'cp2_csv_path', importer.filename_hook) utils.register_parameter(__name__, 'csv_delimiter', utils.PARAM_STR, 'Delimiter for the CSV files', ',') utils.register_parameter(__name__, 'csv_extension', utils.PARAM_STR, 'Extension for the CSV files', '.csv') utils.register_action(__name__, 'import_cp', 'Import data from CellProfiler CSV files', import_data_from_cp)
else: values = param_value for i, value in enumerate(values): if not os.path.isabs(value): values[i] = os.path.join(os.path.dirname(yaml_filename), value) if type(param_value) == str: return values[0] else: return values __dict__ = sys.modules[__name__].__dict__ utils.register_module(__name__, 'Data import', __dict__, utils.DEFAULT_STATE) utils.register_parameter(__name__, 'hdf5_input_file', utils.PARAM_INPUT_FILE, 'YACA HDF5 input file', optional=True) utils.set_parameter_hook(__name__, 'hdf5_input_file', filename_hook) utils.register_parameter(__name__, 'optional_hdf5_input_files', utils.PARAM_INPUT_FILES, 'Further YACA HDF5 input files', optional=True) utils.set_parameter_hook(__name__, 'optional_hdf5_input_files', filename_hook) utils.register_parameter(__name__, 'hdf5_output_file', utils.PARAM_OUTPUT_FILE, 'YACA HDF5 output file', optional=True) utils.set_parameter_hook(__name__, 'hdf5_output_file', filename_hook) utils.register_action(__name__, 'load_hdf5', 'Load data from a YACA HDF5 file', load_hdf5) utils.register_action(__name__, 'save_hdf5', 'Save data as YACA HDF5 file', save_hdf5) utils.register_action(__name__, 'normalize_intensities', 'Normalize intensity features to mean control cell intensity', normalize_intensities) utils.set_module_state_callback(__name__, set_state)