def onUsePrecomputedFeaturesButtonClicked(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
filename = QFileDialog.getOpenFileName(self, 'Open Feature List', '.', options=options)
#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()
def initAppletDrawerUi(self):
# Load the ui file (find it in our own directory)
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir + "/drawer.ui")
self._drawer.selectFeaturesButton.pressed.connect(
self._selectFeaturesButtonPressed)
if not ilastik_config.getboolean("ilastik", "debug"):
self._drawer.exportButton.setVisible(False)
self._drawer.exportButton.pressed.connect(
self._exportFeaturesButtonPressed)
slot = self.topLevelOperatorView.Features
if slot.ready():
selectedFeatures = self.topLevelOperatorView.Features([]).wait()
else:
selectedFeatures = None
nfeatures = 0
if selectedFeatures is not None:
for plugin_features in selectedFeatures.values():
nfeatures += len(plugin_features)
self._drawer.featuresSelected.setText(
"{} features computed, \nsome may have multiple channels".format(
nfeatures))
# get the applet reference from the workflow (needed for the progressSignal)
self.applet = self.topLevelOperatorView.parent.parent.objectExtractionApplet
def getImageFileNamesToOpen(self, defaultDirectory):
"""
Launch an "Open File" dialog to ask the user for one or more image files.
"""
file_dialog = QFileDialog(self, "Select Images")
extensions = OpDataSelection.SupportedExtensions
filter_strs = ["*." + x for x in extensions]
filters = ["{filt} ({filt})".format(filt=x) for x in filter_strs]
filt_all_str = "Image files (" + ' '.join(filter_strs) + ')'
file_dialog.setFilters([filt_all_str] + filters)
# do not display file types associated with a filter
# the line for "Image files" is too long otherwise
file_dialog.setNameFilterDetailsVisible(False)
# select multiple files
file_dialog.setFileMode(QFileDialog.ExistingFiles)
if ilastik_config.getboolean("ilastik", "debug"):
file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
if file_dialog.exec_():
fileNames = file_dialog.selectedFiles()
# Convert from QtString to python str
fileNames = map(encode_from_qstring, fileNames)
return fileNames
return []
def initAppletDrawerUi(self):
# Load the ui file (find it in our own directory)
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir+"/drawer.ui")
self._drawer.selectFeaturesButton.pressed.connect(self._selectFeaturesButtonPressed)
if not ilastik_config.getboolean("ilastik", "debug"):
self._drawer.exportButton.setVisible(False)
self._drawer.exportButton.pressed.connect(self._exportFeaturesButtonPressed)
slot = self.topLevelOperatorView.Features
if slot.ready():
selectedFeatures = self.topLevelOperatorView.Features([]).wait()
else:
selectedFeatures = None
nfeatures = 0
if selectedFeatures is not None:
for plugin_features in selectedFeatures.itervalues():
nfeatures += len(plugin_features)
self._drawer.featuresSelected.setText("{} features computed, \nsome may have multiple channels".format(nfeatures))
# get the applet reference from the workflow (needed for the progressSignal)
self.applet = self.topLevelOperatorView.parent.parent.objectExtractionApplet
def getImageFileNamesToOpen(cls, parent_window, defaultDirectory):
"""
Launch an "Open File" dialog to ask the user for one or more image files.
"""
extensions = OpDataSelection.SupportedExtensions
filter_strs = ["*." + x for x in extensions]
filters = ["{filt} ({filt})".format(filt=x) for x in filter_strs]
filt_all_str = "Image files (" + " ".join(filter_strs) + ")"
fileNames = []
if ilastik_config.getboolean("ilastik", "debug"):
# use Qt dialog in debug mode (more portable?)
file_dialog = QFileDialog(parent_window, "Select Images")
file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
# do not display file types associated with a filter
# the line for "Image files" is too long otherwise
file_dialog.setFilters([filt_all_str] + filters)
file_dialog.setNameFilterDetailsVisible(False)
# select multiple files
file_dialog.setFileMode(QFileDialog.ExistingFiles)
file_dialog.setDirectory(defaultDirectory)
if file_dialog.exec_():
fileNames = file_dialog.selectedFiles()
else:
# otherwise, use native dialog of the present platform
fileNames = QFileDialog.getOpenFileNames(parent_window, "Select Images", defaultDirectory, filt_all_str)
# Convert from QtString to python str
fileNames = map(encode_from_qstring, fileNames)
return fileNames
def chooseNewExportDirectory(self):
"""
The user wants to choose a new export directory.
"""
# Launch the "Open File" dialog
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
defaultpath = self.topLevelOperator.WorkingDirectory.value
directoryName = QFileDialog.getExistingDirectory(self,
"Export Directory",
defaultpath,
options=options)
# Stop now if the user canceled
if directoryName.isNull():
return
self.chosenExportDirectory = str(directoryName)
self.drawer.outputDirEdit.setText(directoryName)
# Auto-check the radio button for this option if necessary
if not self.drawer.saveToDirButton.isChecked():
self.drawer.saveToDirButton.setChecked(True)
else:
self.handleExportLocationOptionChanged()
def _update_debug_mode(parsed_args):
# Force debug mode if any of these flags are active.
if parsed_args.debug or ilastik_config.getboolean("ilastik", "debug"):
# There are two places that debug mode can be checked.
# Make sure both are set.
ilastik_config.set("ilastik", "debug", "true")
parsed_args.debug = True
def handleAddStackButtonClicked(self):
"""
The user clicked the "Import Stack Directory" button.
"""
# 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.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
# Launch the "Open File" dialog
directoryName = QFileDialog.getExistingDirectory(self,
"Image Stack Directory",
defaultDirectory,
options=options)
# If the user didn't cancel
if not directoryName.isNull():
PreferencesManager().set('DataSelection', 'recent stack directory', str(directoryName))
globString = self.getGlobString( str(directoryName).replace("\\","/" ) )
if globString is not None:
self.importStackFromGlobString( globString )
def getImageFileNamesToOpen(self, defaultDirectory):
"""
Launch an "Open File" dialog to ask the user for one or more image files.
"""
extensions = OpDataSelection.SupportedExtensions
filt = "Image files (" + ' '.join('*.' + x for x in extensions) + ')'
dlg = QFileDialog( self, "Select Images", defaultDirectory, filt )
dlg.setOption( QFileDialog.HideNameFilterDetails, False )
if ilastik_config.getboolean("ilastik", "debug"):
dlg.setOption( QFileDialog.DontUseNativeDialog, True )
dlg.setViewMode( QFileDialog.Detail )
dlg.setFileMode( QFileDialog.ExistingFiles )
if True: # FIXME: Test scripts can't allow modal dialogs
dlg.show()
if dlg.result() == QDialog.Accepted:
fileNames = dlg.selectedFiles()
else:
fileNames = []
if dlg.exec_():
fileNames = dlg.selectedFiles()
else:
fileNames = []
# Convert from QtString to python str
fileNames = [str(s) for s in fileNames]
return fileNames
def _update_debug_mode(parsed_args):
# Force debug mode if any of these flags are active.
if parsed_args.debug or ilastik_config.getboolean('ilastik', 'debug'):
# There are two places that debug mode can be checked.
# Make sure both are set.
ilastik_config.set('ilastik', 'debug', 'true')
parsed_args.debug = True
def connectLane(self, laneIndex):
# Get a handle to each operator
opData = self.dataSelectionApplet.topLevelOperator.getLane(laneIndex)
opTrainingFeatures = self.featureSelectionApplet.topLevelOperator.getLane(laneIndex)
opClassify = self.pcApplet.topLevelOperator.getLane(laneIndex)
opDataExport = self.dataExportApplet.topLevelOperator.getLane(laneIndex)
# Input Image -> Feature Op
# and -> Classification Op (for display)
opTrainingFeatures.InputImage.connect( opData.Image )
opClassify.InputImages.connect( opData.Image )
if ilastik_config.getboolean('ilastik', 'debug'):
opClassify.PredictionMasks.connect( opData.ImageGroup[self.DATA_ROLE_PREDICTION_MASK] )
# Feature Images -> Classification Op (for training, prediction)
opClassify.FeatureImages.connect( opTrainingFeatures.OutputImage )
opClassify.CachedFeatureImages.connect( opTrainingFeatures.CachedOutputImage )
# Training flags -> Classification Op (for GUI restrictions)
opClassify.LabelsAllowedFlags.connect( opData.AllowLabels )
# Data Export connections
opDataExport.RawData.connect( opData.ImageGroup[self.DATA_ROLE_RAW] )
opDataExport.RawDatasetInfo.connect( opData.DatasetGroup[self.DATA_ROLE_RAW] )
opDataExport.ConstraintDataset.connect( opData.ImageGroup[self.DATA_ROLE_RAW] )
opDataExport.Inputs.resize( len(self.EXPORT_NAMES) )
opDataExport.Inputs[0].connect( opClassify.HeadlessPredictionProbabilities )
opDataExport.Inputs[1].connect( opClassify.SimpleSegmentation )
opDataExport.Inputs[2].connect( opClassify.HeadlessUncertaintyEstimate )
opDataExport.Inputs[3].connect( opClassify.FeatureImages )
for slot in opDataExport.Inputs:
assert slot.partner is not None
def _onExportTifButtonPressed(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
directory = QFileDialog.getExistingDirectory(self, 'Select Directory',os.getenv('HOME'), options=options)
if directory is None:
print "cancelled."
return
print 'Saving results as tiffs...'
label2color = self.mainOperator.label2color
lshape = list(self.mainOperator.LabelImage.meta.shape)
for t, label2color_at in enumerate(label2color):
if len(label2color_at) == 0:
continue
print '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)
print 'Tiffs exported.'
def connectLane(self, laneIndex):
# Get a handle to each operator
opData = self.dataSelectionApplet.topLevelOperator.getLane(laneIndex)
opTrainingFeatures = self.featureSelectionApplet.topLevelOperator.getLane(laneIndex)
opClassify = self.pcApplet.topLevelOperator.getLane(laneIndex)
opDataExport = self.dataExportApplet.topLevelOperator.getLane(laneIndex)
# Input Image -> Feature Op
# and -> Classification Op (for display)
opTrainingFeatures.InputImage.connect( opData.Image )
opClassify.InputImages.connect( opData.Image )
if ilastik_config.getboolean('ilastik', 'debug'):
opClassify.PredictionMasks.connect( opData.ImageGroup[self.DATA_ROLE_PREDICTION_MASK] )
# Feature Images -> Classification Op (for training, prediction)
opClassify.FeatureImages.connect( opTrainingFeatures.OutputImage )
opClassify.CachedFeatureImages.connect( opTrainingFeatures.CachedOutputImage )
# Training flags -> Classification Op (for GUI restrictions)
opClassify.LabelsAllowedFlags.connect( opData.AllowLabels )
# Data Export connections
opDataExport.RawData.connect( opData.ImageGroup[self.DATA_ROLE_RAW] )
opDataExport.RawDatasetInfo.connect( opData.DatasetGroup[self.DATA_ROLE_RAW] )
opDataExport.ConstraintDataset.connect( opData.ImageGroup[self.DATA_ROLE_RAW] )
opDataExport.Inputs.resize( len(self.EXPORT_NAMES) )
opDataExport.Inputs[0].connect( opClassify.HeadlessPredictionProbabilities )
opDataExport.Inputs[1].connect( opClassify.SimpleSegmentation )
opDataExport.Inputs[2].connect( opClassify.HeadlessUncertaintyEstimate )
opDataExport.Inputs[3].connect( opClassify.FeatureImages )
for slot in opDataExport.Inputs:
assert slot.partner is not None
def initAppletDrawerUi(self):
super(ConservationTrackingGui, self).initAppletDrawerUi()
self._allowedTimeoutInputRegEx = re.compile('^[0-9]*$')
self._drawer.timeoutBox.textChanged.connect(self._onTimeoutBoxChanged)
if not ilastik_config.getboolean("ilastik", "debug"):
assert self._drawer.trackletsBox.isChecked()
self._drawer.trackletsBox.hide()
assert not self._drawer.hardPriorBox.isChecked()
self._drawer.hardPriorBox.hide()
assert not self._drawer.opticalBox.isChecked()
self._drawer.opticalBox.hide()
self._drawer.maxDistBox.hide() # hide the maximal distance box
self._drawer.label_2.hide() # hie the maximal distance label
self._drawer.label_5.hide() # hide division threshold label
self._drawer.divThreshBox.hide()
self._drawer.label_25.hide() # hide avg. obj size label
self._drawer.avgSizeBox.hide()
self.mergerLabels = [self._drawer.merg1,
self._drawer.merg2,
self._drawer.merg3,
self._drawer.merg4,
self._drawer.merg5,
self._drawer.merg6,
self._drawer.merg7]
for i in range(len(self.mergerLabels)):
self._labelSetStyleSheet(self.mergerLabels[i], self.mergerColors[i+1])
self._onMaxObjectsBoxChanged()
self._drawer.maxObjectsBox.valueChanged.connect(self._onMaxObjectsBoxChanged)
def menus(self):
m = QMenu("&Export", self.volumeEditorWidget)
#m.addAction("Export Object Information").triggered.connect(self.show_export_dialog)
if ilastik_config.getboolean("ilastik", "debug"):
m.addAction("Export All Label Info").triggered.connect( self.exportLabelInfo )
m.addAction("Import New Label Info").triggered.connect( self.importLabelInfo )
return [m]
def chooseNewExportDirectory(self):
"""
The user wants to choose a new export directory.
"""
with Tracer(traceLogger):
# Launch the "Open File" dialog
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
defaultpath = self.topLevelOperator.WorkingDirectory.value
directoryName = QFileDialog.getExistingDirectory(
self, "Export Directory", defaultpath, options=options)
# Stop now if the user canceled
if directoryName.isNull():
return
self.chosenExportDirectory = str(directoryName)
self.drawer.outputDirEdit.setText(directoryName)
# Auto-check the radio button for this option if necessary
if not self.drawer.saveToDirButton.isChecked():
self.drawer.saveToDirButton.setChecked(True)
else:
self.handleExportLocationOptionChanged()
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 str(fileName)
def _init_logging( parsed_args ):
from ilastik.ilastik_logging import default_config, startUpdateInterval
if ilastik_config.getboolean('ilastik', 'debug') or parsed_args.headless:
default_config.init(output_mode=default_config.OutputMode.BOTH)
else:
default_config.init(output_mode=default_config.OutputMode.LOGFILE_WITH_CONSOLE_ERRORS)
startUpdateInterval(10) # 10 second periodic refresh
def initAppletDrawerUi(self):
super(ConservationTrackingGui, self).initAppletDrawerUi()
self._allowedTimeoutInputRegEx = re.compile('^[0-9]*$')
self._drawer.timeoutBox.textChanged.connect(self._onTimeoutBoxChanged)
if not ilastik_config.getboolean("ilastik", "debug"):
assert self._drawer.trackletsBox.isChecked()
self._drawer.trackletsBox.hide()
assert not self._drawer.hardPriorBox.isChecked()
self._drawer.hardPriorBox.hide()
assert not self._drawer.opticalBox.isChecked()
self._drawer.opticalBox.hide()
self._drawer.maxDistBox.hide() # hide the maximal distance box
self._drawer.label_2.hide() # hie the maximal distance label
self._drawer.label_5.hide() # hide division threshold label
self._drawer.divThreshBox.hide()
self._drawer.label_25.hide() # hide avg. obj size label
self._drawer.avgSizeBox.hide()
self.mergerLabels = [
self._drawer.merg1, self._drawer.merg2, self._drawer.merg3,
self._drawer.merg4, self._drawer.merg5, self._drawer.merg6,
self._drawer.merg7
]
for i in range(len(self.mergerLabels)):
self._labelSetStyleSheet(self.mergerLabels[i],
self.mergerColors[i + 1])
self._onMaxObjectsBoxChanged()
self._drawer.maxObjectsBox.valueChanged.connect(
self._onMaxObjectsBoxChanged)
def menus(self):
m = QMenu("&Export", self.volumeEditorWidget)
#m.addAction("Export Object Information").triggered.connect(self.show_export_dialog)
if ilastik_config.getboolean("ilastik", "debug"):
m.addAction("Export All Label Info").triggered.connect( self.exportLabelInfo )
m.addAction("Import New Label Info").triggered.connect( self.importLabelInfo )
return [m]
def testBasic(self):
# NOTE: In this test, cmd-line args to nosetests will also end up getting "parsed" by ilastik.
# That shouldn't be an issue, since the pixel classification workflow ignores unrecognized options.
# See if __name__ == __main__ section, below.
args = "--project=" + self.PROJECT_FILE
args += " --headless"
#args += " --sys_tmp_dir=/tmp"
# Batch export options
args += " --output_format=hdf5"
args += " --output_filename_format={dataset_dir}/{nickname}_prediction.h5"
args += " --output_internal_path=volume/pred_volume"
args += " --raw_data" # (Specifying the role name like this is optional for pixel classification, unless we are also using a mask...)
args += " " + self.SAMPLE_DATA
if ilastik_config.getboolean('ilastik', 'debug'):
args += " --prediction_mask" # (Specifying the role name like this is optional for pixel classification)
args += " " + self.SAMPLE_MASK
sys.argv = ['ilastik.py'] # Clear the existing commandline args so it looks like we're starting fresh.
sys.argv += args.split()
# Start up the ilastik.py entry script as if we had launched it from the command line
self.ilastik_startup.main()
# Examine the output for basic attributes
output_path = self.SAMPLE_DATA[:-4] + "_prediction.h5"
with h5py.File(output_path, 'r') as f:
assert "/volume/pred_volume" in f
pred_shape = f["/volume/pred_volume"].shape
# Assume channel is last axis
assert pred_shape[:-1] == self.data.shape[:-1], "Prediction volume has wrong shape: {}".format( pred_shape )
assert pred_shape[-1] == 2, "Prediction volume has wrong shape: {}".format( pred_shape )
def getImageFileNamesToOpen(cls, parent_window, defaultDirectory):
"""
opens a QFileDialog for importing files
"""
extensions = ['nn']
filter_strs = ["*." + x for x in extensions]
filters = ["{filt} ({filt})".format(filt=x) for x in filter_strs]
filt_all_str = "Image files (" + ' '.join(filter_strs) + ')'
fileNames = []
if ilastik_config.getboolean("ilastik", "debug"):
# use Qt dialog in debug mode (more portable?)
file_dialog = QFileDialog(parent_window, "Select Model")
file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
# do not display file types associated with a filter
# the line for "Image files" is too long otherwise
file_dialog.setNameFilters([filt_all_str] + filters)
#file_dialog.setNameFilterDetailsVisible(False)
# select multiple files
file_dialog.setFileMode(QFileDialog.ExistingFiles)
file_dialog.setDirectory(defaultDirectory)
if file_dialog.exec_():
fileNames = file_dialog.selectedFiles()
else:
# otherwise, use native dialog of the present platform
fileNames, _ = QFileDialog.getOpenFileNames(parent_window, "Select Model", defaultDirectory, filt_all_str)
return fileNames
def getModelFileNameToOpen(cls, parent_window, defaultDirectory):
"""
opens a QFileDialog for importing files
"""
extensions = ["pytorch"]
filter_strs = ["*." + x for x in extensions]
filters = ["{filt} ({filt})".format(filt=x) for x in filter_strs]
filt_all_str = "Neural nets (" + " ".join(filter_strs) + ")"
fileName = None
if ilastik_config.getboolean("ilastik", "debug"):
# use Qt dialog in debug mode (more portable?)
file_dialog = QFileDialog(parent_window, "Select Model")
file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
# do not display file types associated with a filter
# the line for "Image files" is too long otherwise
file_dialog.setNameFilters([filt_all_str] + filters)
# file_dialog.setNameFilterDetailsVisible(False)
file_dialog.setFileMode(QFileDialog.ExistingFile)
file_dialog.setDirectory(defaultDirectory)
if file_dialog.exec_():
fileName = file_dialog.selectedFiles()[0]
else:
# otherwise, use native dialog of the present platform
fileName, _ = QFileDialog.getOpenFileName(parent_window,
"Select Model",
defaultDirectory,
filt_all_str)
return fileName
def getImageFileNamesToOpen(cls, parent_window, defaultDirectory):
"""
Launch an "Open File" dialog to ask the user for one or more image files.
"""
extensions = OpDataSelection.SupportedExtensions
filter_strs = ["*." + x for x in extensions]
filters = ["{filt} ({filt})".format(filt=x) for x in filter_strs]
filt_all_str = "Image files (" + ' '.join(filter_strs) + ')'
fileNames = []
if ilastik_config.getboolean("ilastik", "debug"):
# use Qt dialog in debug mode (more portable?)
file_dialog = QFileDialog(parent_window, "Select Images")
file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
# do not display file types associated with a filter
# the line for "Image files" is too long otherwise
file_dialog.setNameFilters([filt_all_str] + filters)
#file_dialog.setNameFilterDetailsVisible(False)
# select multiple files
file_dialog.setFileMode(QFileDialog.ExistingFiles)
file_dialog.setDirectory( defaultDirectory )
if file_dialog.exec_():
fileNames = file_dialog.selectedFiles()
else:
# otherwise, use native dialog of the present platform
fileNames, _filter = QFileDialog.getOpenFileNames(parent_window, "Select Images", defaultDirectory, filt_all_str)
return fileNames
def menus(self):
if ilastik_config.getboolean('ilastik', 'debug'):
m = QMenu("Special Stuff", self.volumeEditorWidget)
m.addAction( "Export to Knime" ).triggered.connect(self.exportObjectInfo)
mlist = [m]
else:
mlist = []
return mlist
def initAppletDrawerUi(self):
super(ConservationTrackingGui, self).initAppletDrawerUi()
self._allowedTimeoutInputRegEx = re.compile("^[0-9]*$")
self._drawer.timeoutBox.textChanged.connect(self._onTimeoutBoxChanged)
if not ilastik_config.getboolean("ilastik", "debug"):
def checkboxAssertHandler(checkbox, assertEnabled=True):
if checkbox.isChecked() == assertEnabled:
checkbox.hide()
else:
checkbox.setEnabled(False)
checkboxAssertHandler(self._drawer.trackletsBox, True)
if self._drawer.classifierPriorBox.isChecked():
self._drawer.hardPriorBox.hide()
self._drawer.classifierPriorBox.hide()
self._drawer.sizeDepBox.hide()
else:
self._drawer.hardPriorBox.setEnabled(False)
self._drawer.classifierPriorBox.setEnabled(False)
self._drawer.sizeDepBox.setEnabled(False)
checkboxAssertHandler(self._drawer.opticalBox, False)
checkboxAssertHandler(self._drawer.mergerResolutionBox, True)
self._drawer.maxDistBox.hide() # hide the maximal distance box
self._drawer.label_2.hide() # hie the maximal distance label
self._drawer.label_5.hide() # hide division threshold label
self._drawer.divThreshBox.hide()
self._drawer.label_25.hide() # hide avg. obj size label
self._drawer.avgSizeBox.hide()
self._drawer.label_24.hide() # hide motion model weight label
self._drawer.motionModelWeightBox.hide()
self.mergerLabels = [
self._drawer.merg1,
self._drawer.merg2,
self._drawer.merg3,
self._drawer.merg4,
self._drawer.merg5,
self._drawer.merg6,
self._drawer.merg7,
]
for i in range(len(self.mergerLabels)):
self._labelSetStyleSheet(self.mergerLabels[i],
QColor(self.mergerColors[i + 1]))
self._onMaxObjectsBoxChanged()
self._drawer.maxObjectsBox.valueChanged.connect(
self._onMaxObjectsBoxChanged)
self._drawer.mergerResolutionBox.stateChanged.connect(
self._onMaxObjectsBoxChanged)
self._drawer.exportButton.hide()
def handleDirectoryButtonClicked(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
directoryName = QFileDialog.getExistingDirectory(self,
"Base Directory",
self.defaultDirectory,
options=options)
self.ui.directoryInput.setText(directoryName)
def handleDirectoryButtonClicked(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
directoryName = QFileDialog.getExistingDirectory(self,
"Base Directory",
self.defaultDirectory,
options=options)
self.ui.directoryInput.setText(directoryName)
def _onLineageFileNameButton(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
fn = QFileDialog.getSaveFileName(self, 'Save Lineage Trees', os.getenv('HOME'), options=options)
if fn is None:
logger.info( "cancelled." )
return
self._drawer.lineageFileNameEdit.setText(str(fn))
def _onLineageFileNameButton(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
fn = QFileDialog.getSaveFileName(self, 'Save Lineage Trees', os.getenv('HOME'), options=options)
if fn is None:
logger.info( "cancelled." )
return
self._drawer.lineageFileNameEdit.setText(str(fn))
def menus(self):
if ilastik_config.getboolean('ilastik', 'debug'):
m = QMenu("Special Stuff", self.volumeEditorWidget)
m.addAction("Export to Knime").triggered.connect(
self.exportObjectInfo)
mlist = [m]
else:
mlist = []
return mlist
def _update_debug_mode( parsed_args ):
# Force debug mode if any of these flags are active.
if parsed_args.debug \
or parsed_args.start_recording \
or parsed_args.playback_script \
or ilastik_config.getboolean('ilastik', 'debug'):
# There are two places that debug mode can be checked.
# Make sure both are set.
ilastik_config.set('ilastik', 'debug', 'true')
parsed_args.debug = True
def _init_logging( parsed_args ):
from ilastik.ilastik_logging import default_config, startUpdateInterval
if ilastik_config.getboolean('ilastik', 'debug') or parsed_args.headless:
default_config.init(output_mode=default_config.OutputMode.BOTH)
else:
default_config.init(output_mode=default_config.OutputMode.LOGFILE_WITH_CONSOLE_ERRORS)
startUpdateInterval(10) # 10 second periodic refresh
if parsed_args.redirect_output:
logger.info( "All console output is being redirected to: {}"
.format( parsed_args.redirect_output ) )
def _onExportTifButtonPressed(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
directory = QFileDialog.getExistingDirectory(self, 'Select Directory',os.getenv('HOME'), options=options)
if directory is None or len(str(directory)) == 0:
print "cancelled."
return
print '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
print '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)
print '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 main( parsed_args, workflow_cmdline_args=[] ):
this_path = os.path.dirname(__file__)
ilastik_dir = os.path.abspath(os.path.join(this_path, "..%s.." % os.path.sep))
# If necessary, redirect stdout BEFORE logging is initialized
_redirect_output( parsed_args )
_init_logging( parsed_args ) # Initialize logging before anything else
_init_configfile( parsed_args )
_clean_paths( parsed_args, ilastik_dir )
_update_debug_mode( parsed_args )
_init_threading_monkeypatch()
_validate_arg_compatibility( parsed_args )
# Extra initialization functions.
# Called during app startup.
init_funcs = []
lazyflow_config_fn = _prepare_lazyflow_config( parsed_args )
if lazyflow_config_fn:
init_funcs.append( lazyflow_config_fn )
load_fn = _prepare_auto_open_project( parsed_args )
if load_fn:
init_funcs.append( load_fn )
create_fn = _prepare_auto_create_new_project( parsed_args )
if create_fn:
init_funcs.append( create_fn )
_enable_faulthandler()
_init_excepthooks( parsed_args )
eventcapture_mode, playback_args = _prepare_test_recording_and_playback( parsed_args )
if ilastik_config.getboolean("ilastik", "debug"):
message = 'Starting ilastik in debug mode from "%s".' % ilastik_dir
logger.info(message)
print message # always print the startup message
else:
message = 'Starting ilastik from "%s".' % ilastik_dir
logger.info(message)
print message # always print the startup message
# Headless launch
if parsed_args.headless:
from ilastik.shell.headless.headlessShell import HeadlessShell
shell = HeadlessShell( workflow_cmdline_args )
for f in init_funcs:
f(shell)
return shell
# Normal launch
else:
from ilastik.shell.gui.startShellGui import startShellGui
sys.exit(startShellGui(workflow_cmdline_args, eventcapture_mode, playback_args, *init_funcs))
def _init_excepthooks( parsed_args ):
# Initialize global exception handling behavior
import ilastik.excepthooks
if parsed_args.exit_on_failure:
# Auto-exit on uncaught exceptions (useful for testing)
ilastik.excepthooks.init_early_exit_excepthook()
elif not ilastik_config.getboolean('ilastik', 'debug') and not parsed_args.headless:
# Show most uncaught exceptions to the user (default behavior)
ilastik.excepthooks.init_user_mode_excepthook()
else:
# Log all exceptions as errors
ilastik.excepthooks.init_developer_mode_excepthook()
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 _init_excepthooks( parsed_args ):
# Initialize global exception handling behavior
import ilastik.excepthooks
if parsed_args.exit_on_failure:
# Auto-exit on uncaught exceptions (useful for testing)
ilastik.excepthooks.init_early_exit_excepthook()
elif not ilastik_config.getboolean('ilastik', 'debug') and not parsed_args.headless:
# Show most uncaught exceptions to the user (default behavior)
ilastik.excepthooks.init_user_mode_excepthook()
else:
# Log all exceptions as errors
ilastik.excepthooks.init_developer_mode_excepthook()
def _update_debug_mode(parsed_args):
# Force debug mode if any of these flags are active.
if (
parsed_args.debug
or parsed_args.start_recording
or parsed_args.playback_script
or ilastik_config.getboolean("ilastik", "debug")
):
# There are two places that debug mode can be checked.
# Make sure both are set.
ilastik_config.set("ilastik", "debug", "true")
parsed_args.debug = True
def initAppletDrawerUi(self):
"""
Load the ui file for the applet drawer, which we own.
"""
localDir = os.path.split(__file__)[0]
# (We don't pass self here because we keep the drawer ui in a separate object.)
self.drawer = uic.loadUi(localDir + "/featureSelectionDrawer.ui")
self.drawer.SelectFeaturesButton.clicked.connect(self.onFeatureButtonClicked)
self.drawer.UsePrecomputedFeaturesButton.clicked.connect(self.onUsePrecomputedFeaturesButtonClicked)
dbg = ilastik_config.getboolean("ilastik", "debug")
if not dbg:
self.drawer.UsePrecomputedFeaturesButton.setHidden(True)
def init(format_prefix="",
output_mode=OutputMode.LOGFILE_WITH_CONSOLE_ERRORS,
logfile_path=DEFAULT_LOGFILE_PATH):
if logfile_path == "/dev/null":
assert output_mode != OutputMode.LOGFILE, "Must enable a logging mode."
output_mode = OutputMode.CONSOLE
# Preserve pre-existing handlers
original_root_handlers = list(logging.getLogger().handlers)
# Start with the default
default_config = get_default_config(format_prefix, output_mode,
logfile_path)
logging.config.dictConfig(default_config)
# Preserve pre-existing handlers
for handler in original_root_handlers:
logging.getLogger().addHandler(handler)
# Update from the user's customizations
loggingHelpers.updateFromConfigFile()
# Capture warnings from the warnings module
logging.captureWarnings(True)
# Warnings module warnings are shown only once
warnings.filterwarnings("once")
# Don't warn about pending deprecations (PyQt generates some of these)
warnings.filterwarnings("ignore", category=PendingDeprecationWarning)
# Don't warn about duplicate python bindings for opengm
# (We import opengm twice, as 'opengm' 'opengm_with_cplex'.)
warnings.filterwarnings("ignore",
message='.*to-Python converter for .*opengm.*',
category=RuntimeWarning)
# Hide all other python converter warnings unless we're in debug mode.
if not ilastik_config.getboolean("ilastik", "debug"):
warnings.filterwarnings(
"ignore",
message=
'.*to-Python converter for .*second conversion method ignored.*',
category=RuntimeWarning)
# Custom format for warnings
def simple_warning_format(message, category, filename, lineno, line=None):
filename = os.path.split(filename)[1]
return filename + "(" + str(
lineno) + "): " + category.__name__ + ": " + message[0]
warnings.formatwarning = simple_warning_format
def getImageFileNamesToOpen(self, defaultDirectory):
"""
Launch an "Open File" dialog to ask the user for one or more image files.
"""
extensions = OpDataSelection.SupportedExtensions
filt = "Image files (" + " ".join("*." + x for x in extensions) + ")"
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
fileNames = QFileDialog.getOpenFileNames(self, "Select Images", defaultDirectory, filt, options=options)
# Convert from QtString to python str
fileNames = [str(s) for s in fileNames]
return fileNames
def initAppletDrawerUi(self):
super(ConservationTrackingGui, self).initAppletDrawerUi()
self._allowedTimeoutInputRegEx = re.compile('^[0-9]*$')
self._drawer.timeoutBox.textChanged.connect(self._onTimeoutBoxChanged)
if not ilastik_config.getboolean("ilastik", "debug"):
def checkboxAssertHandler(checkbox, assertEnabled=True):
if checkbox.isChecked() == assertEnabled:
checkbox.hide()
else:
checkbox.setEnabled(False)
checkboxAssertHandler(self._drawer.trackletsBox, True)
if self._drawer.classifierPriorBox.isChecked():
self._drawer.hardPriorBox.hide()
self._drawer.classifierPriorBox.hide()
self._drawer.sizeDepBox.hide()
else:
self._drawer.hardPriorBox.setEnabled(False)
self._drawer.classifierPriorBox.setEnabled(False)
self._drawer.sizeDepBox.setEnabled(False)
checkboxAssertHandler(self._drawer.opticalBox, False)
checkboxAssertHandler(self._drawer.mergerResolutionBox, True)
self._drawer.maxDistBox.hide() # hide the maximal distance box
self._drawer.label_2.hide() # hie the maximal distance label
self._drawer.label_5.hide() # hide division threshold label
self._drawer.divThreshBox.hide()
self._drawer.label_25.hide() # hide avg. obj size label
self._drawer.avgSizeBox.hide()
self._drawer.label_24.hide() # hide motion model weight label
self._drawer.motionModelWeightBox.hide()
self._drawer.maxNearestNeighborsSpinBox.hide()
self._drawer.MaxNearestNeighbourLabel.hide()
self.mergerLabels = [self._drawer.merg1,
self._drawer.merg2,
self._drawer.merg3,
self._drawer.merg4,
self._drawer.merg5,
self._drawer.merg6,
self._drawer.merg7]
for i in range(len(self.mergerLabels)):
self._labelSetStyleSheet(self.mergerLabels[i], self.mergerColors[i+1])
self._onMaxObjectsBoxChanged()
self._drawer.maxObjectsBox.valueChanged.connect(self._onMaxObjectsBoxChanged)
self._drawer.mergerResolutionBox.stateChanged.connect(self._onMaxObjectsBoxChanged)
def add_peer(self, name, address):
host, port = address
key = (host, name)
if key not in self.peers:
self.peers[key] = {
"enabled": ilastik_config.getboolean("ipc raw tcp", "autoaccept"),
"address": [host, port]
}
elif self.peers[key]["address"][1] != port:
self.peers[key]["address"][1] = port
else:
return
self.info.update_connections(self.peers)
def initAppletDrawerUi(self):
"""
Load the ui file for the applet drawer, which we own.
"""
localDir = os.path.split(__file__)[0]
# (We don't pass self here because we keep the drawer ui in a separate object.)
self.drawer = uic.loadUi(localDir + "/featureSelectionDrawer.ui")
self.drawer.SelectFeaturesButton.clicked.connect(
self.onFeatureButtonClicked)
self.drawer.UsePrecomputedFeaturesButton.clicked.connect(
self.onUsePrecomputedFeaturesButtonClicked)
dbg = ilastik_config.getboolean("ilastik", "debug")
if not dbg:
self.drawer.UsePrecomputedFeaturesButton.setHidden(True)
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 add_peer(self, name, address):
host, port = address
key = (host, name)
if key not in self.peers:
self.peers[key] = {
"enabled": ilastik_config.getboolean("ipc raw tcp",
"autoaccept"),
"address": [host, port],
}
elif self.peers[key]["address"][1] != port:
self.peers[key]["address"][1] = port
else:
return
self.info.update_connections(self.peers)
def menus( self ):
menus = super( PixelClassificationGui, self ).menus()
# For now classifier selection is only available in debug mode
if ilastik_config.getboolean('ilastik', 'debug'):
def handleClassifierAction():
dlg = ClassifierSelectionDlg(self.topLevelOperatorView, parent=self)
dlg.exec_()
advanced_menu = QMenu("Advanced", parent=self)
classifier_action = advanced_menu.addAction("Classifier...")
classifier_action.triggered.connect( handleClassifierAction )
menus += [advanced_menu]
return menus
def _onExportButtonPressed(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
directory = QFileDialog.getExistingDirectory(self, 'Select Directory',os.getenv('HOME'), options=options)
if directory is None:
print "cancelled."
return
# 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
print "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]
write_events([], str(directory), t_from, labelImage)
events = self.mainOperator.events
print "Saving events..."
print "Length of events " + str(len(events))
for i, events_at in enumerate(events):
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)
def populate(self):
self.ui.treeWidget.setColumnCount(1)
for pluginName, features in self.featureDict.iteritems():
if pluginName == "TestFeatures" and not ilastik_config.getboolean(
"ilastik", "debug"):
continue
parent = QTreeWidgetItem(self.ui.treeWidget)
parent.setText(0, pluginName)
parent.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
# hack to ensure checkboxes visible
parent.setCheckState(0, Qt.Checked)
parent.setCheckState(0, Qt.Unchecked)
parent.setExpanded(False)
self.countChecked[pluginName] = 0
self.countAll[pluginName] = len(self.featureDict[pluginName])
advanced_names = []
simple_names = []
for name in sorted(features.keys()):
parameters = features[name]
if 'advanced' in parameters:
advanced_names.append(name)
else:
simple_names.append(name)
for name in simple_names + advanced_names:
parameters = features[name]
item = QTreeWidgetItem(parent)
item.setText(0, name)
item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
if 'tooltip' in parameters:
item.setToolTip(0, parameters['tooltip'])
# hack to ensure checkboxes visible
item.setCheckState(0, Qt.Checked)
item.setCheckState(0, Qt.Unchecked)
if pluginName in self.selectedFeatures:
if name in self.selectedFeatures[pluginName]:
item.setCheckState(0, Qt.Checked)
self.countChecked[pluginName] += 1
if self.countChecked[pluginName] == 0:
parent.setCheckState(0, Qt.Unchecked)
elif self.countChecked[pluginName] == self.countAll[pluginName]:
parent.setCheckState(0, Qt.Checked)
else:
parent.setCheckState(0, Qt.PartiallyChecked)
self.updateToolTip(parent)
# facilitates switching of the CheckBox when clicking on the Text of a QTreeWidgetItem
self.ui.treeWidget.setCurrentItem(None)
def onUsePrecomputedFeaturesButtonClicked(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
filenames, _filter = QFileDialog.getOpenFileNames(self,
"Open Feature Files",
".",
options=options)
# Check if file exists
if not filenames:
return
for filename in filenames:
if not os.path.exists(filename):
QMessageBox.critical(self, "Open Feature List",
"File '%s' does not exist" % filename)
return
num_lanes = len(self.parentApplet.topLevelOperator.FeatureListFilename)
if num_lanes != len(filenames):
QMessageBox.critical(
self,
"Wrong number of feature files",
"You must select all pre-computed feature files at once (shift-click).\n"
"You selected {} file(s), but there are {} image(s) loaded".
format(len(filenames), num_lanes),
)
return
for filename, slot in zip(
filenames,
self.parentApplet.topLevelOperator.FeatureListFilename):
slot.setValue(filename)
# Create a dummy SelectionMatrix, just so the operator knows it is configured
# This is a little hacky. We should really make SelectionMatrix optional,
# and then handle the choice correctly in setupOutputs, probably involving
# the Output.meta.NOTREADY flag
dummy_matrix = numpy.zeros((6, 7), dtype=bool)
dummy_matrix[0, 0] = True
self.parentApplet.topLevelOperator.SelectionMatrix.setValue(True)
# 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()
def _init_logging(parsed_args):
from ilastik.ilastik_logging import default_config, startUpdateInterval, DEFAULT_LOGFILE_PATH
logfile_path = parsed_args.logfile or DEFAULT_LOGFILE_PATH
process_name = ""
if parsed_args.process_name:
process_name = parsed_args.process_name + " "
if ilastik_config.getboolean("ilastik", "debug") or parsed_args.headless:
default_config.init(process_name, default_config.OutputMode.BOTH, logfile_path)
else:
default_config.init(process_name, default_config.OutputMode.LOGFILE_WITH_CONSOLE_ERRORS, logfile_path)
startUpdateInterval(10) # 10 second periodic refresh
if parsed_args.redirect_output:
logger.info("All console output is being redirected to: {}".format(parsed_args.redirect_output))
def menus(self):
menus = super(PixelClassificationGui, self).menus()
# For now classifier selection is only available in debug mode
if ilastik_config.getboolean('ilastik', 'debug'):
def handleClassifierAction():
dlg = ClassifierSelectionDlg(self.topLevelOperatorView,
parent=self)
dlg.exec_()
advanced_menu = QMenu("Advanced", parent=self)
classifier_action = advanced_menu.addAction("Classifier...")
classifier_action.triggered.connect(handleClassifierAction)
menus += [advanced_menu]
return menus
def getImageFileNamesToOpen(self, defaultDirectory):
"""
Launch an "Open File" dialog to ask the user for one or more image files.
"""
extensions = OpDataSelection.SupportedExtensions
filt = "Image files (" + ' '.join('*.' + x for x in extensions) + ')'
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
fileNames = QFileDialog.getOpenFileNames(self,
"Select Images",
defaultDirectory,
filt,
options=options)
# Convert from QtString to python str
fileNames = [str(s) for s in fileNames]
return fileNames
def _init_logging( parsed_args ):
from ilastik.ilastik_logging import default_config, startUpdateInterval, DEFAULT_LOGFILE_PATH
logfile_path = parsed_args.logfile or DEFAULT_LOGFILE_PATH
process_name = ""
if parsed_args.process_name:
process_name = parsed_args.process_name + " "
if ilastik_config.getboolean('ilastik', 'debug') or parsed_args.headless:
default_config.init(process_name, default_config.OutputMode.BOTH, logfile_path)
else:
default_config.init(process_name, default_config.OutputMode.LOGFILE_WITH_CONSOLE_ERRORS, logfile_path)
startUpdateInterval(10) # 10 second periodic refresh
if parsed_args.redirect_output:
logger.info( "All console output is being redirected to: {}"
.format( parsed_args.redirect_output ) )
def initAppletDrawerUi(self):
self._drawer = self._loadUiFile()
if not ilastik_config.getboolean("ilastik", "debug"):
self._drawer.exportLabel.hide()
self._drawer.exportTifButton.hide()
self._drawer.TrackButton.pressed.connect(self._onTrackButtonPressed)
self._drawer.exportButton.pressed.connect(self._onExportButtonPressed)
self._drawer.exportTifButton.pressed.connect(self._onExportTifButtonPressed)
self._drawer.from_time.valueChanged.connect(self._setRanges)
self._drawer.from_x.valueChanged.connect(self._setRanges)
self._drawer.from_y.valueChanged.connect(self._setRanges)
self._drawer.from_z.valueChanged.connect(self._setRanges)
self._drawer.to_time.valueChanged.connect(self._setRanges)
self._drawer.to_x.valueChanged.connect(self._setRanges)
self._drawer.to_y.valueChanged.connect(self._setRanges)
self._drawer.to_z.valueChanged.connect(self._setRanges)
def onUsePrecomputedFeaturesButtonClicked(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
filename = QFileDialog.getOpenFileName(self,
'Open Feature List',
'.',
options=options)
#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()
def populate(self):
self.ui.treeWidget.setColumnCount(1)
for pluginName, features in self.featureDict.iteritems():
if pluginName == "TestFeatures" and not ilastik_config.getboolean(
"ilastik", "debug"):
continue
parent = QTreeWidgetItem(self.ui.treeWidget)
if pluginName == "Standard Object Features":
parent.setText(0, pluginName)
parent.setToolTip(
0,
'http://hci.iwr.uni-heidelberg.de/vigra/doc/vigra/group__FeatureAccumulators.html'
)
else:
parent.setText(0, pluginName)
parent.setExpanded(True)
advanced_names = []
simple_names = []
for name in sorted(features.keys()):
parameters = features[name]
if 'advanced' in parameters:
advanced_names.append(name)
else:
simple_names.append(name)
for name in simple_names + advanced_names:
parameters = features[name]
item = QTreeWidgetItem(parent)
item.setText(0, name)
item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
if 'tooltip' in parameters:
item.setToolTip(0, parameters['tooltip'])
# hack to ensure checkboxes visible
item.setCheckState(0, Qt.Checked)
item.setCheckState(0, Qt.Unchecked)
if pluginName in self.selectedFeatures:
if name in self.selectedFeatures[pluginName]:
item.setCheckState(0, Qt.Checked)