def _run(self):
for plate_id in self._imagecontainer.plates:
analyzer = AnalyzerCore(plate_id, self._settings,
copy.deepcopy(self._imagecontainer))
h5_links = analyzer.processPositions(self)
if h5_links:
link_hdf5_files(h5_links)
def finish(self):
self.log_receiver.shutdown()
self.log_receiver.server_close()
self.log_receiver_thread.join()
if len(self.post_hdf5_link_list) > 0:
post_hdf5_link_list = reduce(lambda x,y: x + y,
self.post_hdf5_link_list)
link_hdf5_files(sorted(post_hdf5_link_list))
def finish(self):
self.log_receiver.shutdown()
self.log_receiver.server_close()
self.log_receiver_thread.join()
if len(self.post_hdf5_link_list) > 0:
post_hdf5_link_list = reduce(lambda x, y: x + y,
self.post_hdf5_link_list)
link_hdf5_files(sorted(post_hdf5_link_list))
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)
if not plate_id in plates:
plates[plate_id] = []
plates[plate_id].append(pos)
# start one analyzer per plate with the corresponding positions
post_hdf5_link_list = []
for plate_id in plates:
# redefine the positions
settings.set(SECTION_NAME_GENERAL, 'constrain_positions', True)
settings.set(SECTION_NAME_GENERAL, 'positions', ','.join(plates[plate_id]))
logger.info("Launching analyzer for plate '%s' with positions %s" % (plate_id, plates[plate_id]))
# initialize and run the analyzer
analyzer = AnalyzerCore(plate_id, settings, imagecontainer)
hdf_links = analyzer.processPositions()
post_hdf5_link_list.append(hdf_links)
if settings.get('Output', 'hdf5_create_file') and settings.get('Output', 'hdf5_merge_positions'):
if len(post_hdf5_link_list) > 0:
post_hdf5_link_list = reduce(lambda x,y: x + y, post_hdf5_link_list)
link_hdf5_files(sorted(post_hdf5_link_list))
print 'BATCHPROCESSING DONE!'
try:
plate, pos, hdf_files = r.get()
if len(hdf_files) > 0:
hdf5_link_list.append(hdf_files)
except Exception, e:
exceptions.append(e)
if len(exceptions) > 0:
sep = 79*'-'+'\n'
msg = sep.join([traceback.format_exc(e) for e in exceptions])
raise MultiProcessingError(msg)
finally:
self.close_logreceiver()
if len(hdf5_link_list) > 0:
hdf5_link_list = reduce(lambda x, y: x + y, hdf5_link_list)
link_hdf5_files(sorted(hdf5_link_list))
def abort(self, wait=False):
self._mutex.lock()
try:
self._abort = True
finally:
self._mutex.unlock()
# timing is essential, flag must be set before terminate is called
self.pool.terminate()
if wait:
self.wait()
self.aborted.emit()
def _run(self):
self._abort = False
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)
if not plate_id in plates:
plates[plate_id] = []
plates[plate_id].append(pos)
# start one analyzer per plate with the corresponding positions
post_hdf5_link_list = []
for plate_id in plates:
# redefine the positions
settings.set(SECTION_NAME_GENERAL, 'constrain_positions', True)
settings.set(SECTION_NAME_GENERAL, 'positions', ','.join(plates[plate_id]))
logger.info("Launching analyzer for plate '%s' with positions %s" % (plate_id, plates[plate_id]))
# initialize and run the analyzer
analyzer = AnalyzerCore(plate_id, settings, imagecontainer)
hdf_links = analyzer.processPositions()
post_hdf5_link_list.append(hdf_links)
if settings.get('Output', 'hdf5_create_file') and settings.get('Output', 'hdf5_merge_positions'):
if len(post_hdf5_link_list) > 0:
post_hdf5_link_list = reduce(lambda x,y: x + y, post_hdf5_link_list)
link_hdf5_files(sorted(post_hdf5_link_list))
print 'BATCHPROCESSING DONE!'
try:
plate, pos, hdf_files = r.get()
if len(hdf_files) > 0:
hdf5_link_list.append(hdf_files)
except Exception, e:
exceptions.append(e)
if len(exceptions) > 0:
sep = 79 * '-' + '\n'
msg = sep.join([traceback.format_exc(e) for e in exceptions])
raise MultiProcessingError(msg)
finally:
self.close_logreceiver()
if len(hdf5_link_list) > 0:
hdf5_link_list = reduce(lambda x, y: x + y, hdf5_link_list)
link_hdf5_files(sorted(hdf5_link_list))
def abort(self, wait=False):
self._mutex.lock()
try:
self._abort = True
finally:
self._mutex.unlock()
# timing is essential, flag must be set before terminate is called
self.pool.terminate()
if wait:
self.wait()
self.aborted.emit()
def _run(self):
self._abort = False