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
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)
imagecontainer = ImageContainer()
imagecontainer.import_from_settings(settings)
# FIXME: Could be more generally specified. SGE is setting the job item index via an environment variable
if index is None:
pass
elif index.isdigit():
index = int(index)
else:
if index == ENV_INDEX_SGE:
logger.info("Using SGE job item index: environment variable '%s'" % index)
if index not in os.environ:
parser.error("SGE environment variable '%s' not defined.")
index = int(os.environ[index])
# decrement index (index is in range of 1..n for SGE)
index -= 1
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)
imagecontainer = ImageContainer()
imagecontainer.import_from_settings(settings)
# FIXME: Could be more generally specified. SGE is setting the job item index via an environment variable
if index is None:
pass
elif index.isdigit():
index = int(index)
else:
if index == ENV_INDEX_SGE:
logger.info("Using SGE job item index: environment variable '%s'" % index)
if index not in os.environ:
parser.error("SGE environment variable '%s' not defined.")
index = int(os.environ[index])
# decrement index (index is in range of 1..n for SGE)
index -= 1
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)
imagecontainer = ImageContainer()
if position_list is not None:
positions = position_list.split(',')
plates = set(np.array([el.split('___') for el in positions])[:,0])
else:
plates=None
imagecontainer.import_from_settings(settings, plates_restriction=plates)
# FIXME: Could be more generally specified. SGE is setting the job item index via an environment variable
if index is None:
pass
elif index.isdigit():
index = int(index)
else:
if index == ENV_INDEX_SGE:
logger.info("Using SGE job item index: environment variable '%s'" % index)
if index not in os.environ:
parser.error("SGE environment variable '%s' not defined.")
index = int(os.environ[index])
# decrement index (index is in range of 1..n for SGE)
index -= 1
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)
imagecontainer = ImageContainer()
if position_list is not None:
positions = position_list.split(',')
plates = set(np.array([el.split('___') for el in positions])[:, 0])
else:
plates = None
imagecontainer.import_from_settings(settings, plates_restriction=plates)
# FIXME: Could be more generally specified. SGE is setting the job item index via an environment variable
if index is None:
pass
elif index.isdigit():
index = int(index)
else:
if index == ENV_INDEX_SGE:
logger.info("Using SGE job item index: environment variable '%s'" %
index)
if index not in os.environ:
parser.error("SGE environment variable '%s' not defined.")
index = int(os.environ[index])
# decrement index (index is in range of 1..n for SGE)
