def core_helper(plate,
settings_dict,
imagecontainer,
position,
version,
redirect=True,
debug=False):
"""Embeds analysis of a positon in a single function"""
# see http://stackoverflow.com/questions/3288595/
# multiprocessing-using-pool-map-on-a-function-defined-in-a-class
logger = logging.getLogger(str(os.getpid()))
import numpy
reload(numpy.core._dotblas)
try:
settings = ConfigSettings()
settings.from_dict(settings_dict)
settings.set('General', 'constrain_positions', True)
settings.set('General', 'positions', position)
environ = CecogEnvironment(version, redirect=redirect, debug=debug)
if debug:
environ.pprint()
analyzer = AnalyzerCore(plate, settings, imagecontainer)
post_hdf5_link_list = analyzer.processPositions()
return plate, position, copy.deepcopy(post_hdf5_link_list)
except Exception as e:
errortxt = "plate: %s, position: %s\n" % (plate, position)
errortxt = "".join([errortxt] + \
traceback.format_exception(*sys.exc_info()))
logger.error(errortxt)
raise e.__class__(errortxt)
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
def core_helper(plate_id, settings_str, imagecontainer, position):
settings = ConfigSettings(SECTION_REGISTRY)
settings.from_string(settings_str)
settings.set(SECTION_NAME_GENERAL, 'constrain_positions', True)
settings.set(SECTION_NAME_GENERAL, 'positions', position)
try:
analyzer = AnalyzerCore(plate_id, settings, imagecontainer)
result = analyzer.processPositions()
except Exception:
traceback.print_exc()
raise
return plate_id, position, copy.deepcopy(result['post_hdf5_link_list'])
def core_helper(plate,
settings_dict,
imagecontainer,
position,
version,
mode="r+",
redirect=True):
"""Embedds analysis of a positon in a single function"""
# see http://stackoverflow.com/questions/3288595/
# multiprocessing-using-pool-map-on-a-function-defined-in-a-class
logger = logging.getLogger(str(os.getpid()))
try:
# FIXME numpy 1.11 does not have ._dotblas
import numpy.core._dotblas
reload(numpy.core._dotblas)
except ImportError as e:
pass
try:
settings = ConfigSettings()
settings.from_dict(settings_dict)
settings.set('General', 'constrain_positions', True)
settings.set('General', 'positions', position)
environ = CecogEnvironment(version, redirect=redirect)
analyzer = PlateAnalyzer(plate, settings, imagecontainer, mode=mode)
analyzer()
return plate, position
except Exception as e:
errortxt = "Plate: %s, Site: %s\n" % (plate, position)
errortxt = "".join([errortxt] + \
traceback.format_exception(*sys.exc_info()))
logger.error(errortxt)
raise type(e)(errortxt)
logger.info("*************************************************" + '*'*len(version))
logger.info("*** CellCognition - Batch Analyzer - Version %s ***" %version)
logger.info("*************************************************" + '*'*len(version))
logger.info('argv: %s' % sys.argv)
environ = CecogEnvironment(version)
if options.settings is None:
parser.error('Settings filename required.')
environ = CecogEnvironment(version, redirect=False, debug=False)
filename_settings = os.path.abspath(options.settings)
# 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)
def __init__(self, configfile):
self.img_height = None
self.img_width = None
self.settings = ConfigSettings()
self.settings.read(configfile)
logger.info("*************************************************" +
'*' * len(VERSION))
logger.info("*** CellCognition - Batch Analyzer - Version %s ***" %
VERSION)
logger.info("*************************************************" +
'*' * len(VERSION))
logger.info('argv: %s' % sys.argv)
if options.settings is None:
parser.error('Settings filename required.')
filename_settings = os.path.abspath(options.settings)
# 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)