def load_image_container_from_settings(settings):
imagecontainer = ImageContainer()
infos = imagecontainer.iter_check_plates(settings)
scan_plates = dict((info[0], False) for info in infos)
import_iter = imagecontainer.iter_import_from_settings(settings, scan_plates)
for idx, info in enumerate(import_iter):
pass
if len(imagecontainer.plates) > 0:
plate = imagecontainer.plates[0]
imagecontainer.set_plate(plate)
return imagecontainer
def load_image_container_from_settings(settings):
imagecontainer = ImageContainer()
infos = imagecontainer.iter_check_plates(settings)
scan_plates = dict((info[0], False) for info in infos)
import_iter = imagecontainer.iter_import_from_settings(
settings, scan_plates)
for idx, info in enumerate(import_iter):
pass
if len(imagecontainer.plates) > 0:
plate = imagecontainer.plates[0]
imagecontainer.set_plate(plate)
return imagecontainer
index -= 1
else:
parser.error("Only SGE supported at the moment (environment variable '%s')." % ENV_INDEX_SGE)
# if no position list was specified via the program options get it from the settings file
if position_list is None:
if settings.get(SECTION_NAME_GENERAL, 'constrain_positions'):
position_list = settings.get(SECTION_NAME_GENERAL, 'positions') or None
# construct a dummy string containing all plates and positions known to imagecontainer
if position_list is None:
positions = []
for plate_id in imagecontainer.plates:
imagecontainer.set_plate(plate_id)
meta_data = imagecontainer.get_meta_data()
positions += ['%s___%s' % (plate_id, pos) for pos in meta_data.positions]
else:
positions = position_list.split(',')
if index is not None and (index < 0 or index >= len(positions)):
parser.error("Cluster index %s does not match number of positions %d." % (index, len(positions)))
# batch size was specified
if batch_size is not None:
if index is None:
parser.error("Batch size requires a cluster index.")
# select slice of positions according to index and batch size
positions = positions[(index*batch_size) : ((index+1)*batch_size)]
index -= 1
else:
parser.error("Only SGE supported at the moment (environment variable '%s')." % ENV_INDEX_SGE)
# if no position list was specified via the program options get it from the settings file
if position_list is None:
if settings.get(SECTION_NAME_GENERAL, 'constrain_positions'):
position_list = settings.get(SECTION_NAME_GENERAL, 'positions') or None
# construct a dummy string containing all plates and positions known to imagecontainer
if position_list is None:
positions = []
for plate_id in imagecontainer.plates:
imagecontainer.set_plate(plate_id)
meta_data = imagecontainer.get_meta_data()
positions += ['%s___%s' % (plate_id, pos) for pos in meta_data.positions]
else:
positions = position_list.split(',')
if index is not None and (index < 0 or index >= len(positions)):
parser.error("Cluster index %s does not match number of positions %d." % (index, len(positions)))
# batch size was specified
if batch_size is not None:
if index is None:
parser.error("Batch size requires a cluster index.")
# select slice of positions according to index and batch size
positions = positions[(index*batch_size) : ((index+1)*batch_size)]
# read the settings data from file
settings = ConfigSettings()
settings.read(settingsfile)
imagecontainer = ImageContainer()
imagecontainer.import_from_settings(settings)
if settings('General', 'constrain_positions'):
positions = settings('General', 'positions').split(POSSEP)
if not settings('General', 'has_multiple_plates'):
plate = os.path.split(settings("General", "pathin"))[1]
positions = ['%s%s%s' % (plate, PLATESEP, p) for p in positions]
else:
positions = list()
for plate in imagecontainer.plates:
imagecontainer.set_plate(plate)
meta_data = imagecontainer.get_meta_data()
positions += \
['%s%s%s' % (plate, PLATESEP, pos) for pos in meta_data.positions]
n_positions = len(positions)
if index is not None and (index < 0 or index >= len(positions)):
raise RuntimeError(
"Cluster index %s does not match number of positions %d."
%(index, len(positions)))
# batch size was specified
if batch_size is not None:
if index is None:
raise RuntimeError("Batch size requires a cluster index.")
