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_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
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, 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 _on_load_input(self):
txt = "Error scanning image structure"
path_in = self._settings.get(SECTION_NAME_GENERAL, 'pathin')
if path_in == '':
critical(self, txt, "Image path must be defined.")
elif not os.path.isdir(path_in) and \
not os.path.isdir(os.path.join(self.environ.package_dir, path_in)):
critical(self, txt, "Image path '%s' not found." % path_in)
else:
try:
infos = list(ImageContainer.iter_check_plates(self._settings))
except:
exception(self, txt)
else:
found_any = numpy.any([not info[3] is None for info in infos])
cancel = False
if found_any:
found_plates = [info[0] for info in infos
if not info[3] is None]
missing_plates = [info[0] for info in infos
if info[3] is None]
has_missing = len(missing_plates) > 0
txt = '%s plates were already scanned.\nDo you want ' \
'to rescan the file structure(s)? ' \
'This can take several minutes.' % \
('Some' if has_missing else 'All')
title = 'Rescan input structure?'
box = QMessageBox(QMessageBox.Question, title, title,
QMessageBox.Cancel, self, Qt.Sheet)
box.setWindowModality(Qt.WindowModal)
box.setInformativeText(txt)
box.setDetailedText('Plates with scanned structure: \n%s\n'
'\nPlates without scanned structure: '
'\n%s' %
('\n'.join(found_plates),
'\n'.join(missing_plates)))
if not has_missing:
btn1 = QtGui.QPushButton('No', box)
box.addButton(btn1, QMessageBox.NoRole)
box.setDefaultButton(btn1)
elif len(found_plates) > 0:
btn1 = QtGui.QPushButton('Rescan missing', box)
box.addButton(btn1, QMessageBox.YesRole)
box.setDefaultButton(btn1)
else:
btn1 = None
btn2 = QtGui.QPushButton('Rescan all', box)
box.addButton(btn2, QMessageBox.YesRole)
if box.exec_() == QMessageBox.Cancel:
cancel = True
else:
btn = box.clickedButton()
if btn == btn1:
if has_missing:
scan_plates = dict([(info[0], info[0] in missing_plates) for info in infos])
else:
scan_plates = dict((info[0], False) for info in infos)
else:
scan_plates = dict((info[0], True) for info in infos)
else:
has_multiple = self._settings.get(SECTION_NAME_GENERAL,
"has_multiple_plates")
if not question(self, "No structure data found",
"Are you sure to scan %s?\n\nThis can take "
"several minutes depending on the number of"
" images." %
("%d plates" % len(infos) if has_multiple
else "one plate")):
cancel = True
scan_plates = dict((info[0], True) for info in infos)
if not cancel:
self._load_image_container(infos, scan_plates)
help='Run applicaton in debug mode')
args, _ = parser.parse_known_args()
freeze_support()
app = QtGui.QApplication(sys.argv)
app.setWindowIcon(QtGui.QIcon(':cecog_analyzer_icon'))
app.setApplicationName(cecog.APPNAME)
splash = QtGui.QSplashScreen(QtGui.QPixmap(':cecog_splash'))
splash.show()
is_app = hasattr(sys, 'frozen')
if is_app:
redirect = (sys.frozen == "windows_exe")
else:
redirect = False
main = CecogAnalyzer(cecog.APPNAME, cecog.VERSION, redirect, args.debug)
main._read_settings(join(main.environ.user_config_dir, args.configfile))
try:
if (args.load and os.path.isfile(args.configfile)) or is_app:
infos = list(ImageContainer.iter_check_plates(main._settings))
main._load_image_container(infos, show_dlg=False)
except Exception, e:
msg = "Could not load images\n%s" %e.message
QMessageBox.critical(None, "Error", msg)
main.show()
splash.finish(main)
sys.exit(app.exec_())
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)
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()
if position_list is not None:
positions = position_list.split(',')
plates = set(np.array([el.split('___') for el in positions])[:,0])
else:
plates=None
imagecontainer.import_from_settings(settings, plates_restriction=plates)
# 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:
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."))
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."))
logger.setLevel(logging.ERROR)
print "*"*(len(version) + 53)
print "*** CellCognition - Batch Script - Version %s ***" %version
print "*"*(len(version) + 53)
print "SGE job item index: environment variable '%s'" %str(index)
print 'cmd: %s' %" ".join(sys.argv)
environ = CecogEnvironment(version, redirect=False, debug=False)
settingsfile = os.path.abspath(args.settings)
# read the settings data from file
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]
logger.info('Overwrite input path by %s' % path_input)
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()
if position_list is not None:
positions = position_list.split(',')
plates = set(np.array([el.split('___') for el in positions])[:, 0])
else:
plates = None
imagecontainer.import_from_settings(settings, plates_restriction=plates)
# 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:
