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
else:
parser.error("Only SGE supported at the moment (environment variable '%s')." % ENV_INDEX_SGE)
# if no position list was specified via the program options get it from the settings file
if position_list is None:
if settings.get(SECTION_NAME_GENERAL, 'constrain_positions'):
position_list = settings.get(SECTION_NAME_GENERAL, 'positions') or None
# construct a dummy string containing all plates and positions known to imagecontainer
if position_list is None:
positions = []
for plate_id in imagecontainer.plates:
imagecontainer.set_plate(plate_id)
meta_data = imagecontainer.get_meta_data()
positions += ['%s___%s' % (plate_id, pos) for pos in meta_data.positions]
else:
positions = position_list.split(',')
if index is not None and (index < 0 or index >= len(positions)):
parser.error("Cluster index %s does not match number of positions %d." % (index, len(positions)))
# batch size was specified
if batch_size is not None:
if index is None:
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
def _load_image_container(self, plate_infos, scan_plates=None, show_dlg=True):
self._clear_browser()
imagecontainer = ImageContainer()
self._imagecontainer = imagecontainer
if scan_plates is None:
scan_plates = dict((info[0], False) for info in plate_infos)
def load(dlg):
iter = imagecontainer.iter_import_from_settings(self._settings, scan_plates)
for idx, info in enumerate(iter):
dlg.targetSetValue.emit(idx + 1)
if len(imagecontainer.plates) > 0:
plate = imagecontainer.plates[0]
imagecontainer.set_plate(plate)
self.dlg = waitingProgressDialog('Please wait until the input structure is scanned\n'
'or the structure data loaded...', self, load, (0, len(scan_plates)))
self.dlg.exec_(passDialog=True)
if len(imagecontainer.plates) > 0:
imagecontainer.check_dimensions()
channels = imagecontainer.channels
# do not report value changes to the main window
self._settings.set_notify_change(False)
self.set_image_crop_size()
problems = []
for prefix in ['primary', 'secondary', 'tertiary']:
trait = self._settings.get_trait(SECTION_NAME_OBJECTDETECTION,
'%s_channelid' % prefix)
if trait.set_list_data(channels) is None:
problems.append(prefix)
self._tabs[1].get_widget('%s_channelid' % prefix).update()
# report problems about a mismatch between channel IDs found in the data and specified by the user
if len(problems) > 0:
critical(self, "Selected channel IDs not valid",
"The selected channel IDs for %s are not valid.\nValid IDs are %s." %
(", ".join(["'%s Channel'" % s.capitalize() for s in problems]),
", ".join(["'%s'" % s for s in channels])))
# a mismatch between settings and data will cause changed settings
self.settings_changed(True)
trait = self._settings.get_trait(SECTION_NAME_TRACKING,
'tracking_duration_unit')
# allow time-base tracking durations only if time-stamp
# information is present
meta_data = imagecontainer.get_meta_data()
if meta_data.has_timestamp_info:
result = trait.set_list_data(TRACKING_DURATION_UNITS_TIMELAPSE)
else:
result = trait.set_list_data(TRACKING_DURATION_UNITS_DEFAULT)
if result is None:
critical(self, "Could not set tracking duration units",
"The tracking duration units selected to match the load data. Please check your settings.")
# a mismatch between settings and data will cause changed settings
self.settings_changed(True)
# activate change notification again
self._settings.set_notify_change(True)
self.set_modules_active(state=True)
if show_dlg:
information(self, "Plate(s) successfully loaded",
"%d plates loaded successfully." % len(imagecontainer.plates))
else:
critical(self, "No valid image data found",
"The naming schema provided might not fit your image data"
"or the coordinate file is not correct.\n\nPlease modify "
"the values and scan the structure again.")
def _load_image_container(self, plate_infos=None, scan_plates=None,
show_dialog=True):
self._clear_browser()
if plate_infos is None:
plate_infos = list(ImageContainer.iter_check_plates(self._settings))
imagecontainer = ImageContainer()
self._imagecontainer = imagecontainer
if scan_plates is None:
scan_plates = dict((info[0], False) for info in plate_infos)
def load(emitter, icontainer, settings, splates):
iter_ = icontainer.iter_import_from_settings(settings, scan_plates=splates)
for idx, info in enumerate(iter_):
emitter.setValue.emit(idx)
emitter.setLabelText.emit("checking dimensions...")
emitter.setRange.emit(0, 0)
QtCore.QCoreApplication.processEvents()
if len(icontainer.plates) > 0:
icontainer.set_plate(icontainer.plates[0])
icontainer.check_dimensions()
label = ('Please wait until the input structure is scanned\n'
'or the structure data loaded...')
self._dlg = ProgressDialog(label, None, 0, len(scan_plates), self)
emitter = ProgressObject()
emitter.setRange.connect(self._dlg.setRange)
emitter.setValue.connect(self._dlg.setValue)
emitter.setLabelText.connect(self._dlg.setLabelText)
try:
func = lambda: load(emitter, imagecontainer,
self._settings, scan_plates)
self._dlg.exec_(func, (emitter, ))
except ImportError as e:
# structure file from versions older than 1.3 contain pdk which is
# removed
if 'pdk' in str(e):
QMessageBox.critical(self, "Error",
("Your structure file format is outdated.\n"
"You have to rescan the plate(s)"))
else:
QMessageBox.critical(self, "Error", traceback.format_exc())
return
except Exception as e:
QMessageBox.critical(self, "Error", str(e))
try: # I hate lookup tables!
self._tab_lookup['Cluster'][1].set_imagecontainer(imagecontainer)
except KeyError:
pass
if len(imagecontainer.plates) > 0:
channels = imagecontainer.channels
# do not report value changes to the main window
self._settings.set_notify_change(False)
self.set_image_crop_size()
problems = []
for prefix in ['primary', 'secondary', 'tertiary']:
trait = self._settings.get_trait(SECTION_NAME_OBJECTDETECTION,
'%s_channelid' % prefix)
if trait.set_list_data(channels) is None:
problems.append(prefix)
self._tabs[1].get_widget('%s_channelid' % prefix).update()
# report problems about a mismatch between channel IDs found in the data
# and specified by the user
if len(problems) > 0:
# a mismatch between settings and data will cause changed settings
self.settings_changed(True)
trait = self._settings.get_trait(SECTION_NAME_EVENT_SELECTION,
'duration_unit')
# allow time-base tracking durations only if time-stamp
# information is present
meta_data = imagecontainer.get_meta_data()
if meta_data.has_timestamp_info:
result = trait.set_list_data(TimeConverter.units)
else:
result = trait.set_list_data([TimeConverter.FRAMES])
if result is None:
QMessageBox.critical(self, "Could not set tracking duration units",
("The tracking duration units selected to match the "
"load data. Please check your settings."))
# a mismatch between settings and data will cause changed settings
self.settings_changed(True)
# activate change notification again
self._settings.set_notify_change(True)
self.set_modules_active(state=True)
if show_dialog:
QMessageBox.information(
self, "Information",
"%d plate(s) successfully loaded." % len(imagecontainer.plates))
else:
QMessageBox.critical(self, "Error",
("No images found\n"
"Verifiy your nameing scheme and rescan the data."))
else:
parser.error("Only SGE supported at the moment (environment variable '%s')." % ENV_INDEX_SGE)
# if no position list was specified via the program options get it from the settings file
if position_list is None:
if settings.get(SECTION_NAME_GENERAL, 'constrain_positions'):
position_list = settings.get(SECTION_NAME_GENERAL, 'positions') or None
# construct a dummy string containing all plates and positions known to imagecontainer
if position_list is None:
positions = []
for plate_id in imagecontainer.plates:
imagecontainer.set_plate(plate_id)
meta_data = imagecontainer.get_meta_data()
positions += ['%s___%s' % (plate_id, pos) for pos in meta_data.positions]
# else:
# positions = position_list.split(',')
if index is not None and (index < 0 or index >= len(positions)):
parser.error("Cluster index %s does not match number of positions %d." % (index, len(positions)))
# batch size was specified
if batch_size is not None:
if index is None:
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
settings = ConfigSettings()
settings.read(settingsfile)
imagecontainer = ImageContainer()
imagecontainer.import_from_settings(settings)
if settings('General', 'constrain_positions'):
positions = settings('General', 'positions').split(POSSEP)
if not settings('General', 'has_multiple_plates'):
plate = os.path.split(settings("General", "pathin"))[1]
positions = ['%s%s%s' % (plate, PLATESEP, p) for p in positions]
else:
positions = list()
for plate in imagecontainer.plates:
imagecontainer.set_plate(plate)
meta_data = imagecontainer.get_meta_data()
positions += \
['%s%s%s' % (plate, PLATESEP, pos) for pos in meta_data.positions]
n_positions = len(positions)
if index is not None and (index < 0 or index >= len(positions)):
raise RuntimeError(
"Cluster index %s does not match number of positions %d."
%(index, len(positions)))
# batch size was specified
if batch_size is not None:
if index is None:
raise RuntimeError("Batch size requires a cluster index.")
# select slice of positions according to index and batch size
parser.error(
"Only SGE supported at the moment (environment variable '%s')."
% ENV_INDEX_SGE)
# if no position list was specified via the program options get it from the settings file
if position_list is None:
if settings.get(SECTION_NAME_GENERAL, 'constrain_positions'):
position_list = settings.get(SECTION_NAME_GENERAL,
'positions') or None
# construct a dummy string containing all plates and positions known to imagecontainer
if position_list is None:
positions = []
for plate_id in imagecontainer.plates:
imagecontainer.set_plate(plate_id)
meta_data = imagecontainer.get_meta_data()
positions += [
'%s___%s' % (plate_id, pos) for pos in meta_data.positions
]
# else:
# positions = position_list.split(',')
if index is not None and (index < 0 or index >= len(positions)):
parser.error(
"Cluster index %s does not match number of positions %d." %
(index, len(positions)))
# batch size was specified
if batch_size is not None:
if index is None:
parser.error("Batch size requires a cluster index.")
