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
def load_image_container_from_settings(settings):
imagecontainer = ImageContainer()
infos = imagecontainer.iter_check_plates(settings)
scan_plates = dict((info[0], False) for info in infos)
import_iter = imagecontainer.iter_import_from_settings(
settings, scan_plates)
for idx, info in enumerate(import_iter):
pass
if len(imagecontainer.plates) > 0:
plate = imagecontainer.plates[0]
imagecontainer.set_plate(plate)
return imagecontainer
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.")
else:
path_input = settings.get2('pathin')
if path_output is not None:
settings.set2('pathout', path_output)
logger.info('Overwrite output path by %s' % path_output)
else:
path_output = settings.get2('pathout')
if multiple_plates is None:
multiple_plates = settings.get(SECTION_NAME_GENERAL, 'has_multiple_plates')
else:
logger.info('Overwrite has_multiple_plates by %s' % multiple_plates)
imagecontainer = ImageContainer()
imagecontainer.import_from_settings(settings)
# FIXME: Could be more generally specified. SGE is setting the job item index via an environment variable
if index is None:
pass
elif index.isdigit():
index = int(index)
else:
if index == ENV_INDEX_SGE:
logger.info("Using SGE job item index: environment variable '%s'" % index)
if index not in os.environ:
parser.error("SGE environment variable '%s' not defined.")
index = int(os.environ[index])
# decrement index (index is in range of 1..n for SGE)
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."))
