def exportRelabeling(self):
# Ask for the export path
exportPath = QFileDialog.getSaveFileName(
self,
"Save supervoxel relabeling",
"",
"Hdf5 Files (*.h5 *.hdf5)",
options=QFileDialog.Options(QFileDialog.DontUseNativeDialog))
if exportPath.isNull():
return
def handleProgress(progress):
# TODO: Hook this up to the progress bar
logger.info("Export progress: {}%".format(progress))
op = self.topLevelOperatorView
req = op.exportFinalSupervoxels(encode_from_qstring(exportPath), "zyx",
handleProgress)
self._drawer.exportButton.setEnabled(False)
def handleFinish(*args):
self._drawer.exportButton.setEnabled(True)
req.notify_finished(handleFinish)
req.notify_failed(handleFinish)
def _chooseDirectory(self):
# Find the directory of the most recently opened image file
mostRecentStackDirectory = PreferencesManager().get(
'DataSelection', 'recent stack directory')
if mostRecentStackDirectory is not None:
defaultDirectory = os.path.split(mostRecentStackDirectory)[0]
else:
defaultDirectory = os.path.expanduser('~')
options = QFileDialog.Options(QFileDialog.ShowDirsOnly)
if ilastik.config.cfg.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
# Launch the "Open File" dialog
directory = QFileDialog.getExistingDirectory(self,
"Image Stack Directory",
defaultDirectory,
options=options)
if directory.isNull():
# User cancelled
return
directory = encode_from_qstring(directory)
PreferencesManager().set('DataSelection', 'recent stack directory',
directory)
self.directoryEdit.setText(decode_to_qstring(directory))
try:
globstring = self._getGlobString(directory)
except StackFileSelectionWidget.DetermineStackError, e:
QMessageBox.warning(self, "Invalid selection", str(e))
def repairFile(self, path, filt=None):
"""get new path to lost file"""
from PyQt4.QtGui import QFileDialog, QMessageBox
from volumina.utility import encode_from_qstring
text = "The file at {} could not be found any more. Do you want to search for it at another directory?".format(
path)
logger.info(text)
c = QMessageBox.critical(None, "update external data", text,
QMessageBox.Ok | QMessageBox.Cancel)
if c == QMessageBox.Cancel:
raise RuntimeError("Could not find external data: " + path)
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
fileName = QFileDialog.getOpenFileName(None,
"repair files",
path,
filt,
options=options)
if fileName.isEmpty():
raise RuntimeError("Could not find external data: " + path)
else:
return encode_from_qstring(fileName)
def _chooseDirectory(self):
# Find the directory of the most recently opened image file
mostRecentStackDirectory = PreferencesManager().get(
'DataSelection', 'recent stack directory')
if mostRecentStackDirectory is not None:
defaultDirectory = os.path.split(mostRecentStackDirectory)[0]
else:
defaultDirectory = os.path.expanduser('~')
options = QFileDialog.Options(QFileDialog.ShowDirsOnly)
if ilastik.config.cfg.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
# Launch the "Open File" dialog
directory = QFileDialog.getExistingDirectory(self,
"Image Stack Directory",
defaultDirectory,
options=options)
if directory.isNull():
# User cancelled
return
directory = encode_from_qstring(directory)
PreferencesManager().set('DataSelection', 'recent stack directory',
directory)
self.directoryEdit.setText(decode_to_qstring(directory))
globstring = self._getGlobString(directory)
if globstring:
filenames = OpStackLoader.expandGlobStrings(globstring)
self._updateFileList(sorted(filenames))
# As a convenience, also show the glob string in the pattern field
self.patternEdit.setText(decode_to_qstring(globstring))
def _printToLog(self, *args, **kwargs):
parts = []
for s in (self.text(), self.informativeText(), self.detailedText()):
if len(s) > 0:
parts.append(encode_from_qstring(s))
msg = "\n".join(parts)
logger.warn(msg)
def _printToLog(self, *args, **kwargs):
parts = []
for s in (self.text(), self.informativeText(), self.detailedText()):
if len(s) > 0:
parts.append(encode_from_qstring(s))
msg = "\n".join(parts)
logger.warn(msg)
def _chooseDirectory(self):
# Find the directory of the most recently opened image file
mostRecentStackDirectory = PreferencesManager().get( 'DataSelection', 'recent stack directory' )
if mostRecentStackDirectory is not None:
defaultDirectory = os.path.split(mostRecentStackDirectory)[0]
else:
defaultDirectory = os.path.expanduser('~')
options = QFileDialog.Options(QFileDialog.ShowDirsOnly)
if ilastik.config.cfg.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
# Launch the "Open File" dialog
directory = QFileDialog.getExistingDirectory(
self, "Image Stack Directory", defaultDirectory, options=options )
if directory.isNull():
# User cancelled
return
directory = encode_from_qstring( directory )
PreferencesManager().set('DataSelection', 'recent stack directory', directory)
self.directoryEdit.setText( decode_to_qstring(directory) )
globstring = self._getGlobString(directory)
if globstring is not None:
filenames = [k.replace('\\', '/') for k in glob.glob(globstring)]
self._updateFileList( sorted(filenames) )
# As a convenience, also show the glob string in the pattern field
self.patternEdit.setText( decode_to_qstring(globstring) )
def _updateFromGui(self):
export_dir = encode_from_qstring( self.directoryEdit.text() )
filename_pattern = encode_from_qstring( self.filePatternEdit.text() )
export_path = os.path.join( export_dir, filename_pattern )
self._filepathSlot.setValue( export_path )
old_valid_state = self.settings_are_valid
if re.search("{slice_index(:.*)?}", export_path):
self.settings_are_valid = True
self.filePatternEdit.setStyleSheet("QLineEdit {background-color: white}" )
else:
self.settings_are_valid = False
self.filePatternEdit.setStyleSheet("QLineEdit {background-color: red}" )
if old_valid_state != self.settings_are_valid:
self.pathValidityChange.emit( self.settings_are_valid )
def name( self, n ):
if isinstance(n, str):
n = decode_to_qstring(n, 'utf-8')
assert isinstance(n, QString)
pystr = encode_from_qstring(n, 'utf-8')
if self._name != n:
self._name = n
self.nameChanged.emit(pystr)
def _updateFromGui(self):
export_dir = encode_from_qstring(self.directoryEdit.text())
filename_pattern = encode_from_qstring(self.filePatternEdit.text())
export_path = os.path.join(export_dir, filename_pattern)
self._filepathSlot.setValue(export_path)
old_valid_state = self.settings_are_valid
if re.search("{slice_index(:.*)?}", export_path):
self.settings_are_valid = True
self.filePatternEdit.setStyleSheet(
"QLineEdit {background-color: white}")
else:
self.settings_are_valid = False
self.filePatternEdit.setStyleSheet(
"QLineEdit {background-color: red}")
if old_valid_state != self.settings_are_valid:
self.pathValidityChange.emit(self.settings_are_valid)
def eventFilter(self, watched, event):
# Apply the new path if the user presses
# 'enter' or clicks outside the filepathe editbox
if watched == self.filepathEdit:
if event.type() == QEvent.FocusOut or \
( event.type() == QEvent.KeyPress and \
( event.key() == Qt.Key_Enter or event.key() == Qt.Key_Return) ):
newpath = self.filepathEdit.text()
newpath = encode_from_qstring(newpath)
self._filepathSlot.setValue( newpath )
return False
def _onExportTifButtonPressed(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
directory = encode_from_qstring(QFileDialog.getExistingDirectory(self, 'Select Directory',os.path.expanduser("~"), options=options))
if directory is None or len(str(directory)) == 0:
logger.info( "cancelled." )
return
logger.info( 'Saving results as tiffs...' )
label2color = self.mainOperator.label2color
lshape = list(self.mainOperator.LabelImage.meta.shape)
def _handle_progress(x):
self.applet.progressSignal.emit(x)
def _export():
num_files = float(len(label2color))
for t, label2color_at in enumerate(label2color):
if len(label2color_at) == 0:
continue
logger.info( 'exporting tiffs for t = ' + str(t) )
roi = SubRegion(self.mainOperator.LabelImage, start=[t,] + 4*[0,], stop=[t+1,] + list(lshape[1:]))
labelImage = self.mainOperator.LabelImage.get(roi).wait()
relabeled = relabel(labelImage[0,...,0],label2color_at)
for i in range(relabeled.shape[2]):
out_im = relabeled[:,:,i]
out_fn = str(directory) + '/vis_t' + str(t).zfill(4) + '_z' + str(i).zfill(4) + '.tif'
vigra.impex.writeImage(np.asarray(out_im,dtype=np.uint32), out_fn)
_handle_progress(t/num_files * 100)
logger.info( 'Tiffs exported.' )
def _handle_finished(*args):
self._drawer.exportTifButton.setEnabled(True)
self.applet.progressSignal.emit(100)
def _handle_failure( exc, exc_info ):
import traceback, sys
traceback.print_exception(*exc_info)
sys.stderr.write("Exception raised during export. See traceback above.\n")
self.applet.progressSignal.emit(100)
self._drawer.exportTifButton.setEnabled(True)
self._drawer.exportTifButton.setEnabled(False)
self.applet.progressSignal.emit(0)
req = Request( _export )
req.notify_failed( _handle_failure )
req.notify_finished( _handle_finished )
req.submit()
def eventFilter(self, watched, event):
# Apply the new path if the user presses
# 'enter' or clicks outside the filepathe editbox
if watched == self.filepathEdit:
if event.type() == QEvent.FocusOut or \
( event.type() == QEvent.KeyPress and \
( event.key() == Qt.Key_Enter or event.key() == Qt.Key_Return) ):
newpath = self.filepathEdit.text()
newpath = encode_from_qstring(newpath)
self._filepathSlot.setValue(newpath)
return False
def _onExportTifButtonPressed(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
directory = encode_from_qstring(QFileDialog.getExistingDirectory(self, 'Select Directory',os.path.expanduser("~"), options=options))
if directory is None or len(str(directory)) == 0:
logger.info( "cancelled." )
return
logger.info( 'Saving results as tiffs...' )
label2color = self.mainOperator.label2color
lshape = list(self.mainOperator.LabelImage.meta.shape)
def _handle_progress(x):
self.applet.progressSignal.emit(x)
def _export():
num_files = float(len(label2color))
for t, label2color_at in enumerate(label2color):
if len(label2color_at) == 0:
continue
logger.info( 'exporting tiffs for t = ' + str(t) )
roi = SubRegion(self.mainOperator.LabelImage, start=[t,] + 4*[0,], stop=[t+1,] + list(lshape[1:]))
labelImage = self.mainOperator.LabelImage.get(roi).wait()
relabeled = relabel(labelImage[0,...,0],label2color_at)
for i in range(relabeled.shape[2]):
out_im = relabeled[:,:,i]
out_fn = str(directory) + '/vis_t' + str(t).zfill(4) + '_z' + str(i).zfill(4) + '.tif'
vigra.impex.writeImage(np.asarray(out_im,dtype=np.uint32), out_fn)
_handle_progress(t/num_files * 100)
logger.info( 'Tiffs exported.' )
def _handle_finished(*args):
self._drawer.exportTifButton.setEnabled(True)
self.applet.progressSignal.emit(100)
def _handle_failure( exc, exc_info ):
msg = "Exception raised during export. See traceback above.\n"
log_exception( logger, msg, exc_info )
self.applet.progressSignal.emit(100)
self._drawer.exportTifButton.setEnabled(True)
self._drawer.exportTifButton.setEnabled(False)
self.applet.progressSignal.emit(0)
req = Request( _export )
req.notify_failed( _handle_failure )
req.notify_finished( _handle_finished )
req.submit()
def setData(self, index, value, role=Qt.EditRole):
'''
Reimplement, see labelListModel or boxListModel for concrete example
:param index:
'''
if role == Qt.EditRole and index.column() == self.ColumnID.Name:
row = index.row()
# value is a user provided QVariant, possibly with unicode
# characters in it. internally, we keep a str
self._elements[row].name = encode_from_qstring(value.toString(), 'utf-8')
self.dataChanged.emit(index, index)
return True
return False
def _browseForFilepath(self):
starting_dir = os.path.expanduser("~")
if self._filepathSlot.ready():
starting_dir = os.path.split(self._filepathSlot.value)[-1]
dlg = QFileDialog( self, "Export Location", starting_dir, self._file_filter )
dlg.setDefaultSuffix(self._extension)
dlg.setAcceptMode(QFileDialog.AcceptSave)
if not dlg.exec_():
return
exportPath = encode_from_qstring( dlg.selectedFiles()[0] )
self._filepathSlot.setValue( exportPath )
self.filepathEdit.setText( decode_to_qstring(exportPath) )
def _browseForFilepath(self):
starting_dir = os.path.expanduser("~")
if self._filepathSlot.ready():
starting_dir = os.path.split(self._filepathSlot.value)[-1]
dlg = QFileDialog(self, "Export Location", starting_dir,
self._file_filter)
dlg.setAcceptMode(QFileDialog.AcceptSave)
if not dlg.exec_():
return
exportPath = encode_from_qstring(dlg.selectedFiles()[0])
self._filepathSlot.setValue(exportPath)
self.filepathEdit.setText(decode_to_qstring(exportPath))
def setData(self, index, value, role=Qt.EditRole):
'''
Reimplement, see labelListModel or boxListModel for concrete example
:param index:
'''
if role == Qt.EditRole and index.column() == self.ColumnID.Name:
row = index.row()
# value is a user provided QVariant, possibly with unicode
# characters in it. internally, we keep a str
self._elements[row].name = encode_from_qstring(value.toString())
self.dataChanged.emit(index, index)
return True
return False
def onUsePrecomputedFeaturesButtonClicked(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
filename = QFileDialog.getOpenFileName(self,
'Open Feature List',
'.',
options=options)
filename = encode_from_qstring(filename)
#sanity checks on the given file
if not filename:
return
if not os.path.exists(filename):
QMessageBox.critical(self, "Open Feature List",
"File '%s' does not exist" % filename)
return
f = open(filename, 'r')
with f:
for line in f:
line = line.strip()
if len(line) == 0:
continue
if not os.path.exists(line):
QMessageBox.critical(
self, "Open Feature List",
"File '%s', referenced in '%s', does not exist" %
(line, filename))
return
try:
h = h5py.File(line, 'r')
with h:
assert len(h["data"].shape) == 3
except:
QMessageBox.critical(
self, "Open Feature List",
"File '%s', referenced in '%s', could not be opened as an HDF5 file or does not contain a 3D dataset called 'data'"
% (line, filename))
return
self.topLevelOperatorView.FeatureListFilename.setValue(filename)
self.topLevelOperatorView._setupOutputs()
self.onFeaturesSelectionsChanged()
# Notify the workflow that some applets may have changed state now.
# (For example, the downstream pixel classification applet can
# be used now that there are features selected)
self.parentApplet.appletStateUpdateRequested.emit()
def _browseForFilepath(self):
starting_dir = os.path.expanduser("~")
if self._filepathSlot.ready():
starting_dir = os.path.split(self._filepathSlot.value)[0]
dlg = QFileDialog( self, "Export Location", starting_dir, "HDF5 Files (*.h5 *.hdf5)" )
dlg.setDefaultSuffix("h5")
dlg.setAcceptMode(QFileDialog.AcceptSave)
if not dlg.exec_():
return
exportPath = dlg.selectedFiles()[0]
self.filepathEdit.setText( exportPath )
self._filepathSlot.setValue( encode_from_qstring(exportPath) )
def _browseForFilepath(self):
starting_dir = os.path.expanduser("~")
if self._filepathSlot.ready():
starting_dir = os.path.split(self._filepathSlot.value)[-1]
dlg = QFileDialog( self, "Export Location", starting_dir, "HDF5 Files (*.h5 *.hdf5)" )
dlg.setDefaultSuffix("h5")
dlg.setAcceptMode(QFileDialog.AcceptSave)
if not dlg.exec_():
return
exportPath = dlg.selectedFiles()[0]
self.filepathEdit.setText( exportPath )
self._filepathSlot.setValue( encode_from_qstring(exportPath) )
def _applyPattern(self):
globStrings = encode_from_qstring(self.patternEdit.text())
H5EXTS = OpStreamingHdf5SequenceReaderM.H5EXTS
filenames = []
# see if some glob strings include HDF5 files
globStrings = globStrings.split(os.path.pathsep)
pcs = [PathComponents(x) for x in globStrings]
ish5 = [x.extension in H5EXTS for x in pcs]
h5GlobStrings = os.path.pathsep.join(
[x for x, y in zip(globStrings, ish5) if y is True])
globStrings = os.path.pathsep.join(
[x for x, y in zip(globStrings, ish5) if y is False])
filenames.extend(OpStackLoader.expandGlobStrings(globStrings))
try:
OpStreamingHdf5SequenceReaderS.checkGlobString(h5GlobStrings)
# OK, if nothing raised there is a single h5 file in h5GlobStrings:
pathComponents = PathComponents(
h5GlobStrings.split(os.path.pathsep)[0])
h5file = h5py.File(pathComponents.externalPath, mode='r')
filenames.extend(
"{}/{}".format(pathComponents.externalPath, internal)
for internal in OpStreamingHdf5SequenceReaderS.
expandGlobStrings(h5file, h5GlobStrings))
except (OpStreamingHdf5SequenceReaderS.WrongFileTypeError,
OpStreamingHdf5SequenceReaderS.NotTheSameFileError,
OpStreamingHdf5SequenceReaderS.NoInternalPlaceholderError,
OpStreamingHdf5SequenceReaderS.ExternalPlaceholderError):
pass
try:
OpStreamingHdf5SequenceReaderM.checkGlobString(h5GlobStrings)
filenames.extend(
"{}/{}".format(external, internal)
for external, internal in zip(
*OpStreamingHdf5SequenceReaderM.expandGlobStrings(
h5GlobStrings)))
except (OpStreamingHdf5SequenceReaderM.WrongFileTypeError,
OpStreamingHdf5SequenceReaderM.SameFileError,
OpStreamingHdf5SequenceReaderM.NoExternalPlaceholderError,
OpStreamingHdf5SequenceReaderM.InternalPlaceholderError):
pass
self._updateFileList(filenames)
def onUsePrecomputedFeaturesButtonClicked(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
filename = QFileDialog.getOpenFileName(self, "Open Feature List", ".", options=options)
filename = encode_from_qstring(filename)
# sanity checks on the given file
if not filename:
return
if not os.path.exists(filename):
QMessageBox.critical(self, "Open Feature List", "File '%s' does not exist" % filename)
return
f = open(filename, "r")
with f:
for line in f:
line = line.strip()
if len(line) == 0:
continue
if not os.path.exists(line):
QMessageBox.critical(
self, "Open Feature List", "File '%s', referenced in '%s', does not exist" % (line, filename)
)
return
try:
h = h5py.File(line, "r")
with h:
assert len(h["data"].shape) == 3
except:
QMessageBox.critical(
self,
"Open Feature List",
"File '%s', referenced in '%s', could not be opened as an HDF5 file or does not contain a 3D dataset called 'data'"
% (line, filename),
)
return
self.topLevelOperatorView.FeatureListFilename.setValue(filename)
self.topLevelOperatorView._setupOutputs()
self.onFeaturesSelectionsChanged()
# Notify the workflow that some applets may have changed state now.
# (For example, the downstream pixel classification applet can
# be used now that there are features selected)
self.parentApplet.appletStateUpdateRequested.emit()
def _loadNewAnnotationFile(self):
"""
Ask the user for a new annotation filepath, and then load it.
"""
navDir = ""
if self._annotationFilepath is not None:
navDir = os.path.split(self._annotationFilepath)[0]
selected_file = QFileDialog.getOpenFileName(
self, "Load Split Annotation File", navDir, "JSON files (*.json)", options=QFileDialog.DontUseNativeDialog
)
self.refreshButton.setEnabled(not selected_file.isNull())
if selected_file.isNull():
return
self._loadAnnotationFile(encode_from_qstring(selected_file))
def _exportFeaturesButtonPressed(self):
mainOperator = self.topLevelOperatorView
if not mainOperator.RegionFeatures.ready():
mexBox=QMessageBox()
mexBox.setText("No features have been computed yet. Nothing to save.")
mexBox.exec_()
return
fname = QFileDialog.getSaveFileName(self, caption='Export Computed Features',
filter="Pickled Objects (*.pkl);;All Files (*)")
fname = encode_from_qstring( fname )
if len(fname)>0: #not cancelled
with open(fname, 'w') as f:
pickle.dump(mainOperator.RegionFeatures(list()).wait(), f)
logger.debug("Exported object features to file '{}'".format(fname))
def _exportFeaturesButtonPressed(self):
mainOperator = self.topLevelOperatorView
if not mainOperator.RegionFeatures.ready():
mexBox=QMessageBox()
mexBox.setText("No features have been computed yet. Nothing to save.")
mexBox.exec_()
return
fname = QFileDialog.getSaveFileName(self, caption='Export Computed Features',
filter="Pickled Objects (*.pkl);;All Files (*)")
fname = encode_from_qstring( fname )
if len(fname)>0: #not cancelled
with open(fname, 'w') as f:
pickle.dump(mainOperator.RegionFeatures(list()).wait(), f)
logger.debug("Exported object features to file '{}'".format(fname))
def repairFile(self,path,filt = None):
"""get new path to lost file"""
from PyQt4.QtGui import QFileDialog,QMessageBox
text = "The file at {} could not be found any more. Do you want to search for it at another directory?".format(path)
c = QMessageBox.critical(None, "update external data",text, QMessageBox.Ok | QMessageBox.Cancel)
if c == QMessageBox.Cancel:
raise RuntimeError("Could not find external data: " + path)
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
fileName = QFileDialog.getOpenFileName( None, "repair files", path, filt, options=options)
if fileName.isEmpty():
raise RuntimeError("Could not find external data: " + path)
else:
return encode_from_qstring(fileName)
def _browseForFilepath(self):
from lazyflow.utility import PathComponents
if self._fullPathOutputSlot.ready():
starting_dir = PathComponents(
self._fullPathOutputSlot.value).externalDirectory
else:
starting_dir = os.path.expanduser("~")
dlg = QFileDialog(self, "Export Location", starting_dir,
"HDF5 Files (*.h5 *.hdf5)")
dlg.setDefaultSuffix("h5")
dlg.setAcceptMode(QFileDialog.AcceptSave)
if not dlg.exec_():
return
exportPath = dlg.selectedFiles()[0]
self.filepathEdit.setText(exportPath)
self._filepathSlot.setValue(encode_from_qstring(exportPath))
def _loadNewAnnotationFile(self):
"""
Ask the user for a new annotation filepath, and then load it.
"""
navDir = ""
if self._annotation_filepath is not None:
navDir = os.path.split(self._annotation_filepath)[0]
selected_file = QFileDialog.getOpenFileName(
self,
"Load Split Annotation File",
navDir,
"JSON files (*.json)",
options=QFileDialog.DontUseNativeDialog)
self.refreshButton.setEnabled(not selected_file.isNull())
if selected_file.isNull():
return
self._loadAnnotationFile(encode_from_qstring(selected_file))
def exportFinalSegmentation(self):
# Ask for the export path
exportPath = QFileDialog.getSaveFileName( self,
"Save final segmentation",
"",
"Hdf5 Files (*.h5 *.hdf5)",
options=QFileDialog.Options(QFileDialog.DontUseNativeDialog) )
if exportPath.isNull():
return
def handleProgress(progress):
# TODO: Hook this up to the progress bar
logger.info( "Export progress: {}%".format( progress ) )
op = self.topLevelOperatorView
req = op.exportFinalSegmentation( encode_from_qstring( exportPath ),
"zyx",
handleProgress )
self._drawer.exportButton.setEnabled(False)
def handleFinish(*args):
self._drawer.exportButton.setEnabled(True)
req.notify_finished( handleFinish )
req.notify_failed( handleFinish )
def _applyNicknameToTempOps(self):
newNickname = encode_from_qstring(self.nicknameEdit.text(), 'utf-8')
if "<multiple>" in newNickname:
return
try:
# Remove the event filter while this function executes because we don't
# want to trigger additional calls to this very function.
self.nicknameEdit.removeEventFilter(self)
# Save a copy of our settings
oldInfos = {}
for laneIndex, op in self.tempOps.items():
oldInfos[laneIndex] = copy.copy( op.Dataset.value )
try:
for laneIndex, op in self.tempOps.items():
info = copy.copy( op.Dataset.value )
info.nickname = newNickname
op.Dataset.setValue( info )
self._error_fields.discard('Nickname')
return True
except Exception as e:
# Revert everything back to the previous state
for laneIndex, op in self.tempOps.items():
op.Dataset.setValue( oldInfos[laneIndex] )
msg = "Could not set new nickname due to an exception:\n"
msg += "{}".format( e )
QMessageBox.warning(self, "Error", msg)
log_exception( logger, msg )
self._error_fields += 'Nickname'
return False
finally:
self.nicknameEdit.installEventFilter(self)
self._updateNickname()
def _onExportButtonPressed(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
directory = encode_from_qstring(QFileDialog.getExistingDirectory(self, 'Select Directory',os.path.expanduser("~"), options=options))
if directory is None or len(str(directory)) == 0:
logger.info( "cancelled." )
return
def _handle_progress(x):
self.applet.progressSignal.emit(x)
def _export():
self.applet.busy = True
self.applet.appletStateUpdateRequested.emit()
if hasattr(self.mainOperator,"RelabeledImage"):
labelImageSlot = self.mainOperator.RelabeledImage
else:
labelImageSlot = self.mainOperator.LabelImage
logger.info( "Saving first label image..." )
key = []
for idx, flag in enumerate(axisTagsToString(labelImageSlot.meta.axistags)):
if flag is 't':
key.append(slice(0,labelImageSlot.meta.shape[idx]))#slice(t_from,t_from+1))
elif flag is 'c':
key.append(slice(0,1))
else:
key.append(slice(0,labelImageSlot.meta.shape[idx]))
try:
events = self.mainOperator.EventsVector.value
logger.info( "Saving events..." )
logger.info( "Length of events " + str(len(events)) )
num_files = float(len(events))
for i in sorted(events.keys()):
events_at = events[i]
i = int(i)
t = i
key[0] = slice(t,t+1)
roi = SubRegion(labelImageSlot, key)
labelImage = labelImageSlot.get(roi).wait()
labelImage = labelImage[0,...,0]
write_events(events_at, str(directory), t, labelImage)
_handle_progress(i/num_files * 100)
except IOError as e:
self._criticalMessage("Cannot export the tracking results. Maybe these files already exist. "\
"Please delete them or choose a different directory.")
return
def _handle_finished(*args):
self.applet.busy = False
self.applet.appletStateUpdateRequested.emit()
self._drawer.exportButton.setEnabled(True)
self.applet.progressSignal.emit(100)
def _handle_failure( exc, exc_info ):
self.applet.busy = False
self.applet.appletStateUpdateRequested.emit()
msg = "Exception raised during export. See traceback above.\n"
log_exception( logger, msg, exc_info=exc_info )
self.applet.progressSignal.emit(100)
self._drawer.exportButton.setEnabled(True)
self._drawer.exportButton.setEnabled(False)
self.applet.progressSignal.emit(0)
req = Request( _export )
req.notify_failed( _handle_failure )
req.notify_finished( _handle_finished )
req.submit()
def handleProjectNameWidgetChanged(newText):
self._projectMetadata.projectName = encode_from_qstring(newText)
def handleLabelerWidgetChanged(newText):
self._projectMetadata.labeler = encode_from_qstring(newText)
def handleDescriptionWidgetChanged():
self._projectMetadata.description = encode_from_qstring(self.descriptionEdit.toPlainText())
def handleProjectNameWidgetChanged(newText):
self._projectMetadata.projectName = encode_from_qstring(
newText, 'utf-8')
def _applyPattern(self):
globStrings = encode_from_qstring(self.patternEdit.text())
filenames = OpStackLoader.expandGlobStrings(globStrings)
self._updateFileList(filenames)
def _applyFilepath(self):
filepath = self.filepathEdit.text()
self._filepathSlot.setValue( encode_from_qstring(filepath) )
def handleDescriptionWidgetChanged():
self._projectMetadata.description = encode_from_qstring(
self.descriptionEdit.toPlainText(), 'utf-8')
def _applyFilepath(self):
filepath = self.filepathEdit.text()
self._filepathSlot.setValue(encode_from_qstring(filepath))
def _onExportButtonPressed(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
directory = encode_from_qstring(
QFileDialog.getExistingDirectory(self,
'Select Directory',
os.path.expanduser("~"),
options=options))
if directory is None or len(str(directory)) == 0:
logger.info("cancelled.")
return
def _handle_progress(x):
self.applet.progressSignal.emit(x)
def _export():
self.applet.busy = True
self.applet.appletStateUpdateRequested.emit()
t_from = None
# determine from_time (it could has been changed in the GUI meanwhile)
for t_from, label2color_at in enumerate(
self.mainOperator.label2color):
if len(label2color_at) == 0:
continue
else:
break
if t_from is None:
self._criticalMessage("There is nothing to export.")
return
t_from = int(t_from)
logger.info("Saving first label image...")
key = []
for idx, flag in enumerate(
axisTagsToString(
self.mainOperator.LabelImage.meta.axistags)):
if flag is 't':
key.append(slice(t_from, t_from + 1))
elif flag is 'c':
key.append(slice(0, 1))
else:
key.append(
slice(0, self.mainOperator.LabelImage.meta.shape[idx]))
roi = SubRegion(self.mainOperator.LabelImage, key)
labelImage = self.mainOperator.LabelImage.get(roi).wait()
labelImage = labelImage[0, ..., 0]
try:
# write_events([], str(directory), t_from, labelImage)
events = self.mainOperator.EventsVector.value
logger.info("Saving events...")
logger.info("Length of events " + str(len(events)))
num_files = float(len(events))
for i in sorted(events.keys()):
events_at = events[i]
i = int(i)
t = t_from + i
key[0] = slice(t, t + 1)
roi = SubRegion(self.mainOperator.LabelImage, key)
labelImage = self.mainOperator.LabelImage.get(roi).wait()
labelImage = labelImage[0, ..., 0]
if self.withMergers:
write_events(events_at, str(directory), t, labelImage,
self.mainOperator.mergers)
else:
write_events(events_at, str(directory), t, labelImage)
_handle_progress(i / num_files * 100)
except IOError as e:
self._criticalMessage("Cannot export the tracking results. Maybe these files already exist. "\
"Please delete them or choose a different directory.")
return
def _handle_finished(*args):
self.applet.busy = False
self.applet.appletStateUpdateRequested.emit()
self._drawer.exportButton.setEnabled(True)
self.applet.progressSignal.emit(100)
def _handle_failure(exc, exc_info):
self.applet.busy = False
self.applet.appletStateUpdateRequested.emit()
msg = "Exception raised during export. See traceback above.\n"
log_exception(logger, msg, exc_info=exc_info)
self.applet.progressSignal.emit(100)
self._drawer.exportButton.setEnabled(True)
self._drawer.exportButton.setEnabled(False)
self.applet.progressSignal.emit(0)
req = Request(_export)
req.notify_failed(_handle_failure)
req.notify_finished(_handle_finished)
req.submit()
def _applyPattern(self):
globStrings = encode_from_qstring(self.patternEdit.text())
filenames = OpStackLoader.expandGlobStrings(globStrings)
self._updateFileList(filenames)
def _onExportButtonPressed(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
directory = encode_from_qstring(QFileDialog.getExistingDirectory(self, 'Select Directory',os.path.expanduser("~"), options=options))
if directory is None or len(str(directory)) == 0:
logger.info( "cancelled." )
return
def _handle_progress(x):
self.applet.progressSignal.emit(x)
def _export():
t_from = None
# determine from_time (it could has been changed in the GUI meanwhile)
for t_from, label2color_at in enumerate(self.mainOperator.label2color):
if len(label2color_at) == 0:
continue
else:
break
if t_from == None:
return
logger.info( "Saving first label image..." )
key = []
for idx, flag in enumerate(axisTagsToString(self.mainOperator.LabelImage.meta.axistags)):
if flag is 't':
key.append(slice(t_from,t_from+1))
elif flag is 'c':
key.append(slice(0,1))
else:
key.append(slice(0,self.mainOperator.LabelImage.meta.shape[idx]))
roi = SubRegion(self.mainOperator.LabelImage, key)
labelImage = self.mainOperator.LabelImage.get(roi).wait()
labelImage = labelImage[0,...,0]
try:
write_events([], str(directory), t_from, labelImage)
events = self.mainOperator.EventsVector.value
logger.info( "Saving events..." )
logger.info( "Length of events " + str(len(events)) )
num_files = float(len(events))
for i in events.keys():
events_at = events[i]
t = t_from + i
key[0] = slice(t+1,t+2)
roi = SubRegion(self.mainOperator.LabelImage, key)
labelImage = self.mainOperator.LabelImage.get(roi).wait()
labelImage = labelImage[0,...,0]
if self.withMergers:
write_events(events_at, str(directory), t+1, labelImage, self.mainOperator.mergers)
else:
write_events(events_at, str(directory), t+1, labelImage)
_handle_progress(i/num_files * 100)
except IOError as e:
self._criticalMessage("Cannot export the tracking results. Maybe these files already exist. "\
"Please delete them or choose a different directory.")
return
def _handle_finished(*args):
self._drawer.exportButton.setEnabled(True)
self.applet.progressSignal.emit(100)
def _handle_failure( exc, exc_info ):
msg = "Exception raised during export. See traceback above.\n"
log_exception( logger, msg, exc_info=exc_info )
self.applet.progressSignal.emit(100)
self._drawer.exportButton.setEnabled(True)
self._drawer.exportButton.setEnabled(False)
self.applet.progressSignal.emit(0)
req = Request( _export )
req.notify_failed( _handle_failure )
req.notify_finished( _handle_finished )
req.submit()
def handleLabelerWidgetChanged(newText):
self._projectMetadata.labeler = encode_from_qstring(
newText, 'utf-8')