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
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_())
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."))
