def getListOfExperiments(self): settings = ConfigSettings(SECTION_REGISTRY) settings.read(self.oBatchSettings.settingsFilename) settings.set_section(SECTION_NAME_GENERAL) settings.set2('pathin', self.oBatchSettings.baseInDir) settings.set2('pathout', self.oBatchSettings.baseOutDir) imagecontainer = ImageContainer() imagecontainer.import_from_settings(settings) if self.oBatchSettings.plates is None: plates = imagecontainer.plates else: plates = self.oBatchSettings.plates lstExperiments = [] for plate in plates: meta_data = imagecontainer.get_meta_data(plate) positions = meta_data.positions if self.oBatchSettings.omit_processed_positions: finished_pos = [os.path.splitext(x)[0].split('__')[0] for x in os.listdir(os.path.join(self.oBatchSettings.baseOutDir, plate, 'log', '_finished'))] positions = filter(lambda x: x not in finished_pos, positions) lstExperiments.extend([(x,y) for x,y in zip([plate for i in positions], positions) ]) return lstExperiments
# read the settings data from file settings = ConfigSettings(SECTION_REGISTRY) settings.read(filename_settings) settings.set_section(SECTION_NAME_GENERAL) index = options.cluster_index batch_size = options.batch_size position_list = options.position_list create_images = options.create_images multiple_plates = options.multiple_plates path_input = options.input path_output = options.output if path_input is not None: settings.set2('pathin', path_input) logger.info('Overwrite input path by %s' % path_input) else: path_input = settings.get2('pathin') if path_output is not None: settings.set2('pathout', path_output) logger.info('Overwrite output path by %s' % path_output) else: path_output = settings.get2('pathout') if multiple_plates is None: multiple_plates = settings.get(SECTION_NAME_GENERAL, 'has_multiple_plates') else: logger.info('Overwrite has_multiple_plates by %s' % multiple_plates)
# read the settings data from file settings = ConfigSettings() settings.read(filename_settings) settings.set_section(SECTION_NAME_GENERAL) index = options.cluster_index batch_size = options.batch_size position_list = options.position_list create_images = options.create_images multiple_plates = options.multiple_plates path_input = options.input path_output = options.output if path_input is not None: settings.set2('pathin', path_input) logger.info('Overwrite input path by %s' % path_input) else: path_input = settings.get2('pathin') if path_output is not None: settings.set2('pathout', path_output) logger.info('Overwrite output path by %s' % path_output) else: path_output = settings.get2('pathout') if multiple_plates is None: multiple_plates = settings.get(SECTION_NAME_GENERAL, 'has_multiple_plates') else: logger.info('Overwrite has_multiple_plates by %s' % multiple_plates)