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)