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,
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_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_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)
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 alone was specified
elif index is not None:
positions = [positions[index]]
logger.info('Final list of position: %s' % positions)
# redefine the image write to disc
if create_images is not None:
logger.info('Overwrite image creation from settings by %s' % create_images)
for rendering in ['rendering_labels_discwrite',
'rendering_class_discwrite',
'rendering_contours_discwrite']:
settings.set(SECTION_NAME_OUTPUT, rendering, create_images)
# group positions by plate
plates = {}
for item in positions:
compound = item.split('___')
if len(compound) == 2:
plate_id, pos = compound
elif len(compound) == 1:
if not multiple_plates:
plate_id = os.path.split(path_input)[1]
pos = compound[0]
else:
parser.error("Position must be of the form 'plateid___position'. Found '%s' instead." % item)
else:
parser.error("Position must be of the form 'position' or 'plateid___position'. Found '%s' instead." % item)
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 alone was specified
elif index is not None:
positions = [positions[index]]
logger.info('Final list of position: %s' % positions)
# redefine the image write to disc
if create_images is not None:
logger.info('Overwrite image creation from settings by %s' % create_images)
for rendering in ['rendering_labels_discwrite',
'rendering_class_discwrite',
'rendering_contours_discwrite']:
settings.set(SECTION_NAME_OUTPUT, rendering, create_images)
# group positions by plate
plates = {}
for item in positions:
compound = item.split('___')
if len(compound) == 2:
plate_id, pos = compound
elif len(compound) == 1:
if not multiple_plates:
plate_id = os.path.split(path_input)[1]
pos = compound[0]
else:
parser.error("Position must be of the form 'plateid___position'. Found '%s' instead." % item)
else:
parser.error("Position must be of the form 'position' or 'plateid___position'. Found '%s' instead." % item)
def set(self, section_name, trait_name, value):
ConfigSettings.set(self, section_name, trait_name, value)
if not self._parent is None and self._notify_change:
self._parent.settings_changed(True)
# group positions by plate
plates = defaultdict(list)
for p in positions:
plate, pos = p.split(PLATESEP)
plates[plate].append(pos)
# HDF file lock does not work on different cluster nodes (no shared memory)
# only storage is shared
time.sleep(random.random()*30)
for plate, positions in plates.iteritems():
# redefine output path in case of mulitplate analyis
if settings('General', 'has_multiple_plates'):
settings.set('General', 'pathout',
os.path.join(settings('General', 'pathout'), plate))
# redefine the positions
settings.set('General', 'constrain_positions', True)
settings.set('General', 'positions', ','.join(positions))
print "Processing site %s - %s" % (plate, ", ".join(positions))
analyzer = PlateAnalyzer(plate, settings, imagecontainer, mode="a")
analyzer()
ch5file = analyzer.h5f
n_sites = len(glob.glob(os.path.join(settings("General", "pathout"), "cellh5", "*.tmp")))
n_total = len(imagecontainer.get_meta_data().positions)
posflag = settings("General", "constrain_positions")
# compare the number of processed positions with the number
