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 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 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)
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)