def _load_data(self, mappings, channel):
dtable = HmmDataTable()
# XXX read region names from hdf not from settings
chreg = "%s__%s" %(channel, self.ecopts.regionnames[channel])
progress = ProgressMsg(max=len(self.files))
for file_ in self.files:
position = splitext(basename(file_))[0]
progress.meta = meta=("loading plate: %s, file: %s"
%(self.plate, file_))
progress.increment_progress()
QThread.currentThread().interruption_point()
self.parent().progressUpdate.emit(progress)
QtCore.QCoreApplication.processEvents()
try:
ch5 = cellh5.CH5File(file_, "r", cached=True)
for pos in ch5.iter_positions():
# only segmentation
if not pos.has_classification(chreg):
continue
# make dtable aware of all positions, sometime they contain
# no tracks and I don't want to ignore them
dtable.add_position(position, mappings[position])
if not pos.has_events():
continue
objidx = np.array( \
pos.get_events(not self.ecopts.ignore_tracking_branches),
dtype=int)
tracks = pos.get_class_label(objidx, chreg)
try:
probs = pos.get_prediction_probabilities(objidx, chreg)
except KeyError as e:
probs = None
grp_coord = cellh5.CH5GroupCoordinate( \
chreg, pos.pos, pos.well, pos.plate)
dtable.add_tracks(tracks, position, mappings[position],
objidx, grp_coord, probs)
finally:
ch5.close()
if dtable.is_empty():
raise RuntimeError(
"No data found for plate '%s' and channel '%s' "
%(self.plate, channel))
return dtable, self._load_classdef(chreg)
def _load_data(self, mappings, channel):
dtable = HmmDataTable()
# XXX read region names from hdf not from settings
chreg = "%s__%s" % (channel, self.ecopts.regionnames[channel])
progress = ProgressMsg(max=len(self.files))
for file_ in self.files:
position = splitext(basename(file_))[0]
progress.meta = meta = ("loading plate: %s, file: %s" %
(self.plate, file_))
progress.increment_progress()
QThread.currentThread().interruption_point()
self.parent().progressUpdate.emit(progress)
QtCore.QCoreApplication.processEvents()
try:
ch5 = cellh5.CH5File(file_, "r", cached=True)
for pos in ch5.iter_positions():
# only segmentation
if not pos.has_classification(chreg):
continue
# make dtable aware of all positions, sometime they contain
# no tracks and I don't want to ignore them
dtable.add_position(position, mappings[position])
if not pos.has_events():
continue
objidx = np.array( \
pos.get_events(not self.ecopts.ignore_tracking_branches),
dtype=int)
tracks = pos.get_class_label(objidx, chreg)
try:
probs = pos.get_prediction_probabilities(objidx, chreg)
except KeyError as e:
probs = None
grp_coord = cellh5.CH5GroupCoordinate( \
chreg, pos.pos, pos.well, pos.plate)
dtable.add_tracks(tracks, position, mappings[position],
objidx, grp_coord, probs)
finally:
ch5.close()
if dtable.is_empty():
raise RuntimeError(
"No data found for plate '%s' and channel '%s' " %
(self.plate, channel))
return dtable, self._load_classdef(chreg)
def __call__(self):
if self.params_ec.position_labels:
self._check_mapping_files()
progress = ProgressMsg(max=len(self.plates), meta="Error correction...")
for i, plate in enumerate(self.plates):
QThread.currentThread().interruption_point()
progress.text = ("Plate: '%s' (%d / %d)"
%(plate, i+1, len(self.plates)))
self.progressUpdate.emit(progress)
ch5file = join(self._outdirs[plate], 'hdf5', "_all_positions.ch5")
runner = PositionRunner(plate, self._outdirs[plate],
self.params_ec, parent=self,
ch5file=ch5file)
runner()
self.progressUpdate.emit(progress)
def __init__(self, parent, job_count, ncpu):
self.parent = parent
self.ncpu = ncpu
self._timer = StopWatch(start=True)
self.progress = ProgressMsg(
max=job_count,
meta=('Parallel processing %d / %d positions '
'(%d cores)' % (0, job_count, self.ncpu)))
self.parent.stage_info.emit(self.progress)
def __call__(self):
if self.params_ec.position_labels:
self._check_mapping_files()
progress = ProgressMsg(max=len(self.plates),
meta="Error correction...")
for i, plate in enumerate(self.plates):
QThread.currentThread().interruption_point()
progress.text = ("Plate: '%s' (%d / %d)" %
(plate, i + 1, len(self.plates)))
self.progressUpdate.emit(progress)
ch5file = join(self._outdirs[plate], 'hdf5', "_all_positions.ch5")
runner = PositionRunner(plate,
self._outdirs[plate],
self.params_ec,
parent=self,
ch5file=ch5file)
runner()
self.progressUpdate.emit(progress)
def interruption_point(self, message=None):
if message is not None:
prgs = ProgressMsg(meta=message)
self.parent().progressUpdate.emit(prgs)
QThread.currentThread().interruption_point()
