class ConservationTrackingGui(TrackingBaseGui, ExportingGui):
withMergers = True
@threadRouted
def _setMergerLegend(self, labels, selection):
param = self.topLevelOperatorView.Parameters.value
if 'withMergerResolution' in list(param.keys()):
if param['withMergerResolution']:
selection = 1
elif self._drawer.mergerResolutionBox.isChecked():
selection = 1
for i in range(2, len(labels) + 1):
if i <= selection:
labels[i - 1].setVisible(True)
else:
labels[i - 1].setVisible(False)
# hide merger legend if selection < 2
self._drawer.label_4.setVisible(selection > 1)
labels[0].setVisible(selection > 1)
def _loadUiFile(self):
# Load the ui file (find it in our own directory)
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir + "/drawer.ui")
parameters = self.topLevelOperatorView.Parameters.value
if 'maxDist' in list(parameters.keys()):
self._drawer.maxDistBox.setValue(parameters['maxDist'])
if 'maxObj' in list(parameters.keys()):
self._drawer.maxObjectsBox.setValue(parameters['maxObj'])
if 'divThreshold' in list(parameters.keys()):
self._drawer.divThreshBox.setValue(parameters['divThreshold'])
if 'avgSize' in list(parameters.keys()):
self._drawer.avgSizeBox.setValue(parameters['avgSize'][0])
if 'withTracklets' in list(parameters.keys()):
self._drawer.trackletsBox.setChecked(parameters['withTracklets'])
if 'sizeDependent' in list(parameters.keys()):
self._drawer.sizeDepBox.setChecked(parameters['sizeDependent'])
if 'divWeight' in list(parameters.keys()):
self._drawer.divWeightBox.setValue(parameters['divWeight'])
if 'transWeight' in list(parameters.keys()):
self._drawer.transWeightBox.setValue(parameters['transWeight'])
if 'withDivisions' in list(parameters.keys()):
self._drawer.divisionsBox.setChecked(parameters['withDivisions'])
if 'withOpticalCorrection' in list(parameters.keys()):
self._drawer.opticalBox.setChecked(
parameters['withOpticalCorrection'])
if 'withClassifierPrior' in list(parameters.keys()):
self._drawer.classifierPriorBox.setChecked(
parameters['withClassifierPrior'])
if 'withMergerResolution' in list(parameters.keys()):
self._drawer.mergerResolutionBox.setChecked(
parameters['withMergerResolution'])
if 'borderAwareWidth' in list(parameters.keys()):
self._drawer.bordWidthBox.setValue(parameters['borderAwareWidth'])
if 'cplex_timeout' in list(parameters.keys()):
self._drawer.timeoutBox.setText(str(parameters['cplex_timeout']))
if 'appearanceCost' in list(parameters.keys()):
self._drawer.appearanceBox.setValue(parameters['appearanceCost'])
if 'disappearanceCost' in list(parameters.keys()):
self._drawer.disappearanceBox.setValue(
parameters['disappearanceCost'])
if 'max_nearest_neighbors' in list(parameters.keys()):
self._drawer.maxNearestNeighborsSpinBox.setValue(
parameters['max_nearest_neighbors'])
if 'numFramesPerSplit' in list(parameters.keys()):
self._drawer.numFramesPerSplitSpinBox.setValue(
parameters['numFramesPerSplit'])
# solver: use stored value only if that solver is available
self._drawer.solverComboBox.clear()
availableSolvers = self.getAvailableTrackingSolverTypes()
self._drawer.solverComboBox.addItems(availableSolvers)
if 'solver' in list(parameters.keys()
) and parameters['solver'] in availableSolvers:
self._drawer.solverComboBox.setCurrentIndex(
availableSolvers.index(parameters['solver']))
# listen on the main operator's NumLabels slot for changes, and adjust the max value of the "maxNumObjects" box
self.topLevelOperatorView.NumLabels.notifyDirty(
self._updateMaxObjectsBoxMaxValue)
self._updateMaxObjectsBoxMaxValue()
# Hide division GUI widgets
if 'withAnimalTracking' in list(parameters.keys(
)) and parameters['withAnimalTracking'] == True:
self._drawer.label_5.hide()
self._drawer.divThreshBox.hide()
self._drawer.divisionsBox.hide()
self._drawer.divWeightBox.hide()
self._drawer.label_6.hide()
return self._drawer
@threadRouted
def _updateMaxObjectsBoxMaxValue(self, *args, **kwargs):
if self.topLevelOperatorView.NumLabels.ready():
if self.topLevelOperatorView.NumLabels.value > 1:
self._drawer.maxObjectsBox.setMaximum(
self.topLevelOperatorView.NumLabels.value - 1)
self._drawer.maxObjectsBox.setValue(
self.topLevelOperatorView.NumLabels.value - 1)
self._drawer.TrackButton.setEnabled(True)
else:
self._drawer.maxObjectsBox.setMaximum(0)
self._drawer.maxObjectsBox.setValue(0)
self._drawer.TrackButton.setEnabled(False)
@staticmethod
def getAvailableTrackingSolverTypes():
solvers = []
try:
if dpct:
solvers.append('Flow-based')
except Exception as e:
logger.info(str(e))
try:
if mht:
solvers.append('ILP')
except Exception as e:
logger.info(str(e))
return solvers
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()
@threadRouted
def _onTimeoutBoxChanged(self, *args):
inString = str(self._drawer.timeoutBox.text())
if self._allowedTimeoutInputRegEx.match(inString) is None:
self._drawer.timeoutBox.setText(inString[:-1])
def _setRanges(self, *args):
super(ConservationTrackingGui, self)._setRanges()
maxx = self.topLevelOperatorView.LabelImage.meta.shape[1] - 1
maxy = self.topLevelOperatorView.LabelImage.meta.shape[2] - 1
maxz = self.topLevelOperatorView.LabelImage.meta.shape[3] - 1
maxBorder = min(maxx, maxy)
if maxz != 0:
maxBorder = min(maxBorder, maxz)
self._drawer.bordWidthBox.setRange(0, old_div(maxBorder, 2))
def _onMaxObjectsBoxChanged(self):
self._setMergerLegend(self.mergerLabels,
self._drawer.maxObjectsBox.value())
def _onTrackButtonPressed(self):
if not self.mainOperator.ObjectFeatures.ready():
self._criticalMessage("You have to compute object features first.")
return
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
numStages = 8
# object features
# detection probabilities
# creating traxel store
# generating probabilities
# insert energies
# convexify costs
# solver
# compute lineages
if self._drawer.divisionsBox.isChecked():
# division probabilities
numStages += 1
if withMergerResolution:
numStages += 1 # merger resolution
withTracklets = self._drawer.trackletsBox.isChecked()
if withTracklets:
numStages += 3 # initializing tracklet graph, finding tracklets, contracting edges in tracklet graph
self.progressWindow = TrackProgressDialog(parent=self,
numStages=numStages)
self.progressWindow.run()
self.progressWindow.show()
self.progressVisitor = GuiProgressVisitor(
progressWindow=self.progressWindow)
def _track():
self.applet.busy = True
self.applet.appletStateUpdateRequested()
maxDist = self._drawer.maxDistBox.value()
maxObj = self._drawer.maxObjectsBox.value()
divThreshold = self._drawer.divThreshBox.value()
from_t = self._drawer.from_time.value()
to_t = self._drawer.to_time.value()
from_x = self._drawer.from_x.value()
to_x = self._drawer.to_x.value()
from_y = self._drawer.from_y.value()
to_y = self._drawer.to_y.value()
from_z = self._drawer.from_z.value()
to_z = self._drawer.to_z.value()
from_size = self._drawer.from_size.value()
to_size = self._drawer.to_size.value()
self.time_range = list(range(from_t, to_t + 1))
avgSize = [self._drawer.avgSizeBox.value()]
cplex_timeout = None
if len(str(self._drawer.timeoutBox.text())):
cplex_timeout = int(self._drawer.timeoutBox.text())
withTracklets = self._drawer.trackletsBox.isChecked()
sizeDependent = self._drawer.sizeDepBox.isChecked()
hardPrior = self._drawer.hardPriorBox.isChecked()
classifierPrior = self._drawer.classifierPriorBox.isChecked()
divWeight = self._drawer.divWeightBox.value()
transWeight = self._drawer.transWeightBox.value()
withDivisions = self._drawer.divisionsBox.isChecked()
withOpticalCorrection = self._drawer.opticalBox.isChecked()
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
borderAwareWidth = self._drawer.bordWidthBox.value()
withArmaCoordinates = True
appearanceCost = self._drawer.appearanceBox.value()
disappearanceCost = self._drawer.disappearanceBox.value()
motionModelWeight = self._drawer.motionModelWeightBox.value()
solver = self._drawer.solverComboBox.currentText()
ndim = 3
if (to_z - from_z == 0):
ndim = 2
try:
self.mainOperator.track(
time_range=self.time_range,
x_range=(from_x, to_x + 1),
y_range=(from_y, to_y + 1),
z_range=(from_z, to_z + 1),
size_range=(from_size, to_size + 1),
x_scale=self._drawer.x_scale.value(),
y_scale=self._drawer.y_scale.value(),
z_scale=self._drawer.z_scale.value(),
maxDist=maxDist,
maxObj=maxObj,
divThreshold=divThreshold,
avgSize=avgSize,
withTracklets=withTracklets,
sizeDependent=sizeDependent,
detWeight=10.0,
divWeight=divWeight,
transWeight=transWeight,
withDivisions=withDivisions,
withOpticalCorrection=withOpticalCorrection,
withClassifierPrior=classifierPrior,
ndim=ndim,
withMergerResolution=withMergerResolution,
borderAwareWidth=borderAwareWidth,
withArmaCoordinates=withArmaCoordinates,
cplex_timeout=cplex_timeout,
appearance_cost=appearanceCost,
disappearance_cost=disappearanceCost,
motionModelWeight=motionModelWeight,
force_build_hypotheses_graph=False,
max_nearest_neighbors=self._drawer.
maxNearestNeighborsSpinBox.value(),
numFramesPerSplit=self._drawer.numFramesPerSplitSpinBox.
value(),
solverName=solver,
progressWindow=self.progressWindow,
progressVisitor=self.progressVisitor)
except Exception as ex:
self.progressWindow.onTrackDone()
log_exception(
logger,
"Error during tracking. See above error traceback.")
self._criticalMessage(
"Error during tracking. See error log.\n\n"
"Exception was:\n\n{})".format(ex))
return
def _handle_finished(*args):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
self._drawer.TrackButton.setEnabled(True)
self._drawer.exportButton.setEnabled(True)
self._drawer.exportTifButton.setEnabled(True)
self._setLayerVisible("Objects", False)
# update showing the merger legend,
# as it might be (no longer) needed if merger resolving
# is disabled(enabled)
self._setMergerLegend(self.mergerLabels,
self._drawer.maxObjectsBox.value())
def _handle_failure(exc, exc_info):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
traceback.print_exception(*exc_info)
sys.stderr.write(
"Exception raised during tracking. See traceback above.\n")
self._drawer.TrackButton.setEnabled(True)
req = Request(_track)
req.notify_failed(_handle_failure)
req.notify_finished(_handle_finished)
req.submit()
def get_raw_shape(self):
return self.topLevelOperatorView.RawImage.meta.shape
def get_feature_names(self):
params = self.topLevelOperatorView.Parameters
if params.ready() and params.value["withDivisions"]:
return self.topLevelOperatorView.ComputedFeatureNamesWithDivFeatures(
[]).wait()
return self.topLevelOperatorView.ComputedFeatureNames([]).wait()
def get_color(self, pos5d):
slicing = tuple(slice(i, i + 1) for i in pos5d)
color = self.mainOperator.CachedOutput(slicing).wait()
return color.flat[0]
def get_object(self, pos5d):
slicing = tuple(slice(i, i + 1) for i in pos5d)
label = self.mainOperator.RelabeledImage(slicing).wait()
return label.flat[0], pos5d[0]
@property
def gui_applet(self):
return self.applet
def get_export_dialog_title(self):
return "Export Tracking Information"
def handleEditorRightClick(self, position5d, win_coord):
debug = ilastik_config.getboolean("ilastik", "debug")
obj, time = self.get_object(position5d)
if obj == 0:
menu = TitledMenu(["Background"])
if debug:
menu.addAction("Clear Hilite",
IPCFacade().broadcast(Protocol.cmd("clear")))
menu.exec_(win_coord)
return
# Get color and track from hypotheses graph (which is a slot in the new operator)
hypothesesGraph = self.mainOperator.HypothesesGraph.value
if hypothesesGraph == None:
color = None
track = None
else:
color = hypothesesGraph.getLineageId(time, obj)
track = hypothesesGraph.getTrackId(time, obj)
tracks = None
children = None
parents = None
menu = TitledMenu([
"Object {} of lineage id {}".format(obj, color),
"Track id: " + (str(track) or "None"),
])
if not debug:
menu.exec_(win_coord)
return
if any(IPCFacade().sending):
obj_sub_menu = menu.addMenu("Hilite Object")
for mode in Protocol.ValidHiliteModes:
where = Protocol.simple("and", ilastik_id=obj, time=time)
cmd = Protocol.cmd(mode, where)
obj_sub_menu.addAction(mode.capitalize(),
IPCFacade().broadcast(cmd))
sub_menus = [("Tracks", Protocol.simple_in, tracks),
("Parents", Protocol.simple_in, parents),
("Children", Protocol.simple_in, children)]
for name, protocol, args in sub_menus:
if args:
sub = menu.addMenu("Hilite {}".format(name))
for mode in Protocol.ValidHiliteModes[:-1]:
mode = mode.capitalize()
where = protocol("track_id*", args)
cmd = Protocol.cmd(mode, where)
sub.addAction(mode, IPCFacade().broadcast(cmd))
else:
sub = menu.addAction("Hilite {}".format(name))
sub.setEnabled(False)
menu.addAction("Clear Hilite",
IPCFacade().broadcast(Protocol.cmd("clear")))
else:
menu.addAction("Open IPC Server Window", IPCFacade().show_info)
menu.addAction("Start IPC Server", IPCFacade().start)
menu.exec_(win_coord)
def _onTrackButtonPressed(self):
if not self.mainOperator.ObjectFeatures.ready():
self._criticalMessage("You have to compute object features first.")
return
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
withTracklets = True
numStages = 6
# creating traxel store
# generating probabilities
# insert energies
# convexify costs
# solver
# compute lineages
if withMergerResolution:
numStages += 1 # merger resolution
if withTracklets:
numStages += 3 # initializing tracklet graph, finding tracklets, contracting edges in tracklet graph
if WITH_HYTRA:
self.progressWindow = TrackProgressDialog(parent=self,
numStages=numStages)
self.progressWindow.run()
self.progressWindow.show()
self.progressVisitor = GuiProgressVisitor(
progressWindow=self.progressWindow)
else:
self.progressWindow = None
self.progressVisitor = DefaultProgressVisitor()
def _track():
self.applet.busy = True
self.applet.appletStateUpdateRequested.emit()
maxDist = self._drawer.maxDistBox.value()
maxObj = self._drawer.maxObjectsBox.value()
divThreshold = self._drawer.divThreshBox.value()
from_t = self._drawer.from_time.value()
to_t = self._drawer.to_time.value()
from_x = self._drawer.from_x.value()
to_x = self._drawer.to_x.value()
from_y = self._drawer.from_y.value()
to_y = self._drawer.to_y.value()
from_z = self._drawer.from_z.value()
to_z = self._drawer.to_z.value()
from_size = self._drawer.from_size.value()
to_size = self._drawer.to_size.value()
self.time_range = range(from_t, to_t + 1)
avgSize = [self._drawer.avgSizeBox.value()]
cplex_timeout = None
if len(str(self._drawer.timeoutBox.text())):
cplex_timeout = int(self._drawer.timeoutBox.text())
withTracklets = True
sizeDependent = self._drawer.sizeDepBox.isChecked()
hardPrior = self._drawer.hardPriorBox.isChecked()
classifierPrior = self._drawer.classifierPriorBox.isChecked()
detWeight = self._drawer.detWeightBox.value()
divWeight = self._drawer.divWeightBox.value()
transWeight = self._drawer.transWeightBox.value()
withDivisions = self._drawer.divisionsBox.isChecked()
withOpticalCorrection = self._drawer.opticalBox.isChecked()
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
borderAwareWidth = self._drawer.bordWidthBox.value()
withArmaCoordinates = True
appearanceCost = self._drawer.appearanceBox.value()
disappearanceCost = self._drawer.disappearanceBox.value()
solverName = self._drawer.solverComboBox.currentText()
ndim = 3
if (to_z - from_z == 0):
ndim = 2
try:
self.mainOperator.track(
time_range=self.time_range,
x_range=(from_x, to_x + 1),
y_range=(from_y, to_y + 1),
z_range=(from_z, to_z + 1),
size_range=(from_size, to_size + 1),
x_scale=self._drawer.x_scale.value(),
y_scale=self._drawer.y_scale.value(),
z_scale=self._drawer.z_scale.value(),
maxDist=maxDist,
maxObj=maxObj,
divThreshold=divThreshold,
avgSize=avgSize,
withTracklets=withTracklets,
sizeDependent=sizeDependent,
detWeight=detWeight,
divWeight=divWeight,
transWeight=transWeight,
withDivisions=withDivisions,
withOpticalCorrection=withOpticalCorrection,
withClassifierPrior=classifierPrior,
ndim=ndim,
withMergerResolution=withMergerResolution,
borderAwareWidth=borderAwareWidth,
withArmaCoordinates=withArmaCoordinates,
cplex_timeout=cplex_timeout,
appearance_cost=appearanceCost,
disappearance_cost=disappearanceCost,
#graph_building_parameter_changed = True,
#trainingToHardConstraints = self._drawer.trainingToHardConstraints.isChecked(),
max_nearest_neighbors=self._maxNearestNeighbors,
solverName=solverName,
progressWindow=self.progressWindow,
progressVisitor=self.progressVisitor)
except Exception:
ex_type, ex, tb = sys.exc_info()
traceback.print_tb(tb)
self._criticalMessage("Exception(" + str(ex_type) + "): " +
str(ex))
return
def _handle_finished(*args):
self.applet.busy = False
self.applet.appletStateUpdateRequested.emit()
self._drawer.TrackButton.setEnabled(True)
self._drawer.exportButton.setEnabled(True)
self._drawer.exportTifButton.setEnabled(True)
self._setLayerVisible("Objects", False)
def _handle_failure(exc, exc_info):
self.applet.busy = False
self.applet.appletStateUpdateRequested.emit()
traceback.print_exception(*exc_info)
sys.stderr.write(
"Exception raised during tracking. See traceback above.\n")
self._drawer.TrackButton.setEnabled(True)
if self.progressWindow is not None:
self.progressWindow.onTrackDone()
req = Request(_track)
req.notify_failed(_handle_failure)
req.notify_finished(_handle_finished)
req.submit()
def _onTrackButtonPressed(self):
if not self.mainOperator.ObjectFeatures.ready():
self._criticalMessage("You have to compute object features first.")
return
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
numStages = 8
# object features
# detection probabilities
# creating traxel store
# generating probabilities
# insert energies
# convexify costs
# solver
# compute lineages
if self._drawer.divisionsBox.isChecked():
# division probabilities
numStages += 1
if withMergerResolution:
numStages += 1 # merger resolution
withTracklets = self._drawer.trackletsBox.isChecked()
if withTracklets:
numStages += 3 # initializing tracklet graph, finding tracklets, contracting edges in tracklet graph
self.progressWindow = TrackProgressDialog(parent=self,
numStages=numStages)
self.progressWindow.run()
self.progressWindow.show()
self.progressVisitor = GuiProgressVisitor(
progressWindow=self.progressWindow)
def _track():
self.applet.busy = True
self.applet.appletStateUpdateRequested()
maxDist = self._drawer.maxDistBox.value()
maxObj = self._drawer.maxObjectsBox.value()
divThreshold = self._drawer.divThreshBox.value()
from_t = self._drawer.from_time.value()
to_t = self._drawer.to_time.value()
from_x = self._drawer.from_x.value()
to_x = self._drawer.to_x.value()
from_y = self._drawer.from_y.value()
to_y = self._drawer.to_y.value()
from_z = self._drawer.from_z.value()
to_z = self._drawer.to_z.value()
from_size = self._drawer.from_size.value()
to_size = self._drawer.to_size.value()
self.time_range = list(range(from_t, to_t + 1))
avgSize = [self._drawer.avgSizeBox.value()]
cplex_timeout = None
if len(str(self._drawer.timeoutBox.text())):
cplex_timeout = int(self._drawer.timeoutBox.text())
withTracklets = self._drawer.trackletsBox.isChecked()
sizeDependent = self._drawer.sizeDepBox.isChecked()
hardPrior = self._drawer.hardPriorBox.isChecked()
classifierPrior = self._drawer.classifierPriorBox.isChecked()
divWeight = self._drawer.divWeightBox.value()
transWeight = self._drawer.transWeightBox.value()
withDivisions = self._drawer.divisionsBox.isChecked()
withOpticalCorrection = self._drawer.opticalBox.isChecked()
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
borderAwareWidth = self._drawer.bordWidthBox.value()
withArmaCoordinates = True
appearanceCost = self._drawer.appearanceBox.value()
disappearanceCost = self._drawer.disappearanceBox.value()
motionModelWeight = self._drawer.motionModelWeightBox.value()
solver = self._drawer.solverComboBox.currentText()
ndim = 3
if (to_z - from_z == 0):
ndim = 2
try:
self.mainOperator.track(
time_range=self.time_range,
x_range=(from_x, to_x + 1),
y_range=(from_y, to_y + 1),
z_range=(from_z, to_z + 1),
size_range=(from_size, to_size + 1),
x_scale=self._drawer.x_scale.value(),
y_scale=self._drawer.y_scale.value(),
z_scale=self._drawer.z_scale.value(),
maxDist=maxDist,
maxObj=maxObj,
divThreshold=divThreshold,
avgSize=avgSize,
withTracklets=withTracklets,
sizeDependent=sizeDependent,
detWeight=10.0,
divWeight=divWeight,
transWeight=transWeight,
withDivisions=withDivisions,
withOpticalCorrection=withOpticalCorrection,
withClassifierPrior=classifierPrior,
ndim=ndim,
withMergerResolution=withMergerResolution,
borderAwareWidth=borderAwareWidth,
withArmaCoordinates=withArmaCoordinates,
cplex_timeout=cplex_timeout,
appearance_cost=appearanceCost,
disappearance_cost=disappearanceCost,
motionModelWeight=motionModelWeight,
force_build_hypotheses_graph=False,
max_nearest_neighbors=self._drawer.
maxNearestNeighborsSpinBox.value(),
numFramesPerSplit=self._drawer.numFramesPerSplitSpinBox.
value(),
solverName=solver,
progressWindow=self.progressWindow,
progressVisitor=self.progressVisitor)
except Exception as ex:
self.progressWindow.onTrackDone()
log_exception(
logger,
"Error during tracking. See above error traceback.")
self._criticalMessage(
"Error during tracking. See error log.\n\n"
"Exception was:\n\n{})".format(ex))
return
def _handle_finished(*args):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
self._drawer.TrackButton.setEnabled(True)
self._drawer.exportButton.setEnabled(True)
self._drawer.exportTifButton.setEnabled(True)
self._setLayerVisible("Objects", False)
# update showing the merger legend,
# as it might be (no longer) needed if merger resolving
# is disabled(enabled)
self._setMergerLegend(self.mergerLabels,
self._drawer.maxObjectsBox.value())
def _handle_failure(exc, exc_info):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
traceback.print_exception(*exc_info)
sys.stderr.write(
"Exception raised during tracking. See traceback above.\n")
self._drawer.TrackButton.setEnabled(True)
req = Request(_track)
req.notify_failed(_handle_failure)
req.notify_finished(_handle_finished)
req.submit()
def _onRunStructuredLearningButtonPressed(self, withBatchProcessing=False):
numStages = 4
# creating traxel store
# generating probabilities
# insert energies
# structured learning
if WITH_HYTRA:
self.progressWindow = TrackProgressDialog(parent=self,
numStages=numStages)
self.progressWindow.run()
self.progressWindow.show()
self.progressVisitor = GuiProgressVisitor(
progressWindow=self.progressWindow)
else:
self.progressWindow = None
self.progressVisitor = DefaultProgressVisitor()
def _learn():
self.applet.busy = True
self.applet.appletStateUpdateRequested.emit()
try:
self.topLevelOperatorView._runStructuredLearning(
(self._drawer.from_z.value(), self._drawer.to_z.value()),
self._maxNumObj,
self._maxNearestNeighbors,
self._drawer.maxDistBox.value(),
self._drawer.divThreshBox.value(),
(self._drawer.x_scale.value(),
self._drawer.y_scale.value(),
self._drawer.z_scale.value()),
(self._drawer.from_size.value(),
self._drawer.to_size.value()),
self._drawer.divisionsBox.isChecked(),
self._drawer.bordWidthBox.value(),
self._drawer.classifierPriorBox.isChecked(),
withBatchProcessing,
progressWindow=self.progressWindow,
progressVisitor=self.progressVisitor)
except Exception:
ex_type, ex, tb = sys.exc_info()
traceback.print_tb(tb)
self._criticalMessage("Exception(" + str(ex_type) + "): " +
str(ex))
return
def _handle_finished(*args):
self.applet.busy = False
self.applet.appletStateUpdateRequested.emit()
def _handle_failure(exc, exc_info):
self.applet.busy = False
self.applet.appletStateUpdateRequested.emit()
traceback.print_exception(*exc_info)
sys.stderr.write(
"Exception raised during learning. See traceback above.\n")
if self.progressWindow is not None:
self.progressWindow.onTrackDone()
req = Request(_learn)
req.notify_failed(_handle_failure)
req.notify_finished(_handle_finished)
req.submit()
class StructuredTrackingGui(TrackingBaseGui, ExportingGui):
withMergers = True
@threadRouted
def _setMergerLegend(self, labels, selection):
param = self.topLevelOperatorView.Parameters.value
if 'withMergerResolution' in param.keys():
if param['withMergerResolution']:
selection = 1
elif self._drawer.mergerResolutionBox.isChecked():
selection = 1
for i in range(2, len(labels) + 1):
if i <= selection:
labels[i - 1].setVisible(True)
else:
labels[i - 1].setVisible(False)
# hide merger legend if selection < 2
self._drawer.label_4.setVisible(selection > 1)
labels[0].setVisible(selection > 1)
def __init__(self, parentApplet, topLevelOperatorView):
"""
"""
self._initColors()
self.topLevelOperatorView = topLevelOperatorView
self.progressWindow = None
super(TrackingBaseGui, self).__init__(parentApplet,
topLevelOperatorView)
self.mainOperator = topLevelOperatorView
if self.mainOperator.LabelImage.meta.shape:
self.editor.dataShape = self.mainOperator.LabelImage.meta.shape
self.applet = self.mainOperator.parent.parent.trackingApplet
self._drawer.mergerResolutionBox.setChecked(True)
self.connect(self, QtCore.SIGNAL('postInformationMessage(QString)'),
self.postInformationMessage)
self.parentApplet = parentApplet
self._headless = False
def _loadUiFile(self):
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir + "/drawer.ui")
parameters = self.topLevelOperatorView.Parameters.value
if 'maxDist' in parameters.keys():
self._drawer.maxDistBox.setValue(parameters['maxDist'])
if 'maxObj' in parameters.keys():
self._drawer.maxObjectsBox.setValue(parameters['maxObj'])
if 'maxNearestNeighbors' in parameters.keys():
self._drawer.maxObjectsBox.setValue(
parameters['maxNearestNeighbors'])
if 'divThreshold' in parameters.keys():
self._drawer.divThreshBox.setValue(parameters['divThreshold'])
if 'avgSize' in parameters.keys():
self._drawer.avgSizeBox.setValue(parameters['avgSize'][0])
if 'withTracklets' in parameters.keys():
self._drawer.trackletsBox.setChecked(parameters['withTracklets'])
if 'sizeDependent' in parameters.keys():
self._drawer.sizeDepBox.setChecked(parameters['sizeDependent'])
if 'detWeight' in parameters.keys():
self._drawer.detWeightBox.setValue(parameters['detWeight'])
if 'divWeight' in parameters.keys():
self._drawer.divWeightBox.setValue(parameters['divWeight'])
if 'transWeight' in parameters.keys():
self._drawer.transWeightBox.setValue(parameters['transWeight'])
if 'withDivisions' in parameters.keys():
self._drawer.divisionsBox.setChecked(parameters['withDivisions'])
if 'withOpticalCorrection' in parameters.keys():
self._drawer.opticalBox.setChecked(
parameters['withOpticalCorrection'])
if 'withClassifierPrior' in parameters.keys():
self._drawer.classifierPriorBox.setChecked(
parameters['withClassifierPrior'])
if 'withMergerResolution' in parameters.keys():
self._drawer.mergerResolutionBox.setChecked(
parameters['withMergerResolution'])
if 'borderAwareWidth' in parameters.keys():
self._drawer.bordWidthBox.setValue(parameters['borderAwareWidth'])
if 'cplex_timeout' in parameters.keys():
self._drawer.timeoutBox.setText(str(parameters['cplex_timeout']))
if 'appearanceCost' in parameters.keys():
self._drawer.appearanceBox.setValue(parameters['appearanceCost'])
if 'disappearanceCost' in parameters.keys():
self._drawer.disappearanceBox.setValue(
parameters['disappearanceCost'])
solverName = self.topLevelOperatorView._solver
if solverName == "Flow-based":
self._drawer.StructuredLearningButton.setEnabled(False)
self._drawer.RandomButton.setEnabled(False)
self._drawer.OnesButton.setEnabled(False)
self._drawer.ZerosButton.setEnabled(False)
return self._drawer
def initAppletDrawerUi(self):
self._previousCrop = -1
self._currentCrop = -1
self._currentCropName = ""
self._maxNearestNeighbors = 1
super(StructuredTrackingGui, self).initAppletDrawerUi()
self.realOperator = self.topLevelOperatorView.Labels.getRealOperator()
for i, op in enumerate(self.realOperator.innerOperators):
self.operator = op
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.label_5.hide()
self._drawer.divThreshBox.hide()
self._drawer.label_25.hide()
self._drawer.avgSizeBox.hide()
self._drawer.InitialWeightsLabel.hide()
self._drawer.ZerosButton.hide()
self._drawer.OnesButton.hide()
self._drawer.RandomButton.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._drawer.maxObjectsBox.valueChanged.connect(
self._onMaxObjectsBoxChanged)
self._drawer.mergerResolutionBox.stateChanged.connect(
self._onMaxObjectsBoxChanged)
self._drawer.StructuredLearningButton.clicked.connect(
self._onRunStructuredLearningButtonPressed)
self._drawer.divWeightBox.valueChanged.connect(
self._onDivisionWeightBoxChanged)
self._drawer.detWeightBox.valueChanged.connect(
self._onDetectionWeightBoxChanged)
self._drawer.transWeightBox.valueChanged.connect(
self._onTransitionWeightBoxChanged)
self._drawer.appearanceBox.valueChanged.connect(
self._onAppearanceWeightBoxChanged)
self._drawer.disappearanceBox.valueChanged.connect(
self._onDisappearanceWeightBoxChanged)
self._drawer.maxNearestNeighborsSpinBox.valueChanged.connect(
self._onMaxNearestNeighborsSpinBoxChanged)
self._drawer.OnesButton.clicked.connect(self._onOnesButtonPressed)
self._drawer.ZerosButton.clicked.connect(self._onZerosButtonPressed)
self._drawer.RandomButton.clicked.connect(self._onRandomButtonPressed)
self._divisionWeight = self.topLevelOperatorView.DivisionWeight.value
self._detectionWeight = self.topLevelOperatorView.DetectionWeight.value
self._transitionWeight = self.topLevelOperatorView.TransitionWeight.value
self._appearanceWeight = self.topLevelOperatorView.AppearanceWeight.value
self._disappearanceWeight = self.topLevelOperatorView.DisappearanceWeight.value
self._drawer.detWeightBox.setValue(self._detectionWeight)
self._drawer.divWeightBox.setValue(self._divisionWeight)
self._drawer.transWeightBox.setValue(self._transitionWeight)
self._drawer.appearanceBox.setValue(self._appearanceWeight)
self._drawer.disappearanceBox.setValue(self._disappearanceWeight)
self._maxNumObj = self.topLevelOperatorView.MaxNumObj.value
self._drawer.maxObjectsBox.setValue(
self.topLevelOperatorView.MaxNumObj.value)
self._onMaxObjectsBoxChanged()
self._drawer.maxObjectsBox.setReadOnly(True)
self.topLevelOperatorView.Labels.notifyReady(
bind(self._updateLabelsFromOperator))
self.topLevelOperatorView.Divisions.notifyReady(
bind(self._updateDivisionsFromOperator))
self.operator.labels = self.operator.Labels.value
self.topLevelOperatorView._updateCropsFromOperator()
self._drawer.exportButton.setVisible(True)
self._drawer.exportTifButton.setVisible(False)
self.topLevelOperatorView._detectionWeight = self._detectionWeight
self.topLevelOperatorView._divisionWeight = self._divisionWeight
self.topLevelOperatorView._transitionWeight = self._transitionWeight
self.topLevelOperatorView._appearanceWeight = self._appearanceWeight
self.topLevelOperatorView._disappearanceWeight = self._disappearanceWeight
self._drawer.solverComboBox.clear()
availableSolvers = self.getAvailableTrackingSolverTypes()
self._drawer.solverComboBox.addItems(availableSolvers)
parameters = self.topLevelOperatorView.Parameters.value
if 'solver' in parameters.keys(
) and parameters['solver'] in availableSolvers:
self._drawer.solverComboBox.setCurrentIndex(
availableSolvers.index(parameters['solver']))
return self._drawer
@staticmethod
def getAvailableTrackingSolverTypes():
solvers = []
if WITH_HYTRA:
try:
if dpct:
solvers.append('Flow-based')
except Exception as e:
logger.info(str(e))
try:
if mht:
solvers.append('ILP')
except Exception as e:
logger.info(str(e))
else:
if hasattr(pgmlink.ConsTrackingSolverType, "CplexSolver"):
solvers.append("ILP")
if hasattr(pgmlink.ConsTrackingSolverType, "DynProgSolver"):
solvers.append("Magnusson")
if hasattr(pgmlink.ConsTrackingSolverType, "FlowSolver"):
solvers.append("Flow-based")
return solvers
def _onOnesButtonPressed(self):
val = math.sqrt(1.0 / 5)
self.topLevelOperatorView.DivisionWeight.setValue(val)
self.topLevelOperatorView.DetectionWeight.setValue(val)
self.topLevelOperatorView.TransitionWeight.setValue(val)
self.topLevelOperatorView.AppearanceWeight.setValue(val)
self.topLevelOperatorView.DisappearanceWeight.setValue(val)
self._divisionWeight = self.topLevelOperatorView.DivisionWeight.value
self._detectionWeight = self.topLevelOperatorView.DetectionWeight.value
self._transitionWeight = self.topLevelOperatorView.TransitionWeight.value
self._appearanceWeight = self.topLevelOperatorView.AppearanceWeight.value
self._disappearanceWeight = self.topLevelOperatorView.DisappearanceWeight.value
self._drawer.detWeightBox.setValue(self._detectionWeight)
self._drawer.divWeightBox.setValue(self._divisionWeight)
self._drawer.transWeightBox.setValue(self._transitionWeight)
self._drawer.appearanceBox.setValue(self._appearanceWeight)
self._drawer.disappearanceBox.setValue(self._disappearanceWeight)
def _onRandomButtonPressed(self):
weights = []
for i in range(5):
weights.append(random.random())
sltWeightNorm = 0
for i in range(5):
sltWeightNorm += weights[i] * weights[i]
sltWeightNorm = math.sqrt(sltWeightNorm)
self.topLevelOperatorView.DivisionWeight.setValue(weights[0] /
sltWeightNorm)
self.topLevelOperatorView.DetectionWeight.setValue(weights[1] /
sltWeightNorm)
self.topLevelOperatorView.TransitionWeight.setValue(weights[2] /
sltWeightNorm)
self.topLevelOperatorView.AppearanceWeight.setValue(weights[3] /
sltWeightNorm)
self.topLevelOperatorView.DisappearanceWeight.setValue(weights[4] /
sltWeightNorm)
self._divisionWeight = self.topLevelOperatorView.DivisionWeight.value
self._detectionWeight = self.topLevelOperatorView.DetectionWeight.value
self._transitionWeight = self.topLevelOperatorView.TransitionWeight.value
self._appearanceWeight = self.topLevelOperatorView.AppearanceWeight.value
self._disappearanceWeight = self.topLevelOperatorView.DisappearanceWeight.value
self._drawer.detWeightBox.setValue(self._detectionWeight)
self._drawer.divWeightBox.setValue(self._divisionWeight)
self._drawer.transWeightBox.setValue(self._transitionWeight)
self._drawer.appearanceBox.setValue(self._appearanceWeight)
self._drawer.disappearanceBox.setValue(self._disappearanceWeight)
def _onZerosButtonPressed(self):
self.topLevelOperatorView.DivisionWeight.setValue(0)
self.topLevelOperatorView.DetectionWeight.setValue(0)
self.topLevelOperatorView.TransitionWeight.setValue(0)
self.topLevelOperatorView.AppearanceWeight.setValue(0)
self.topLevelOperatorView.DisappearanceWeight.setValue(0)
self._divisionWeight = self.topLevelOperatorView.DivisionWeight.value
self._detectionWeight = self.topLevelOperatorView.DetectionWeight.value
self._transitionWeight = self.topLevelOperatorView.TransitionWeight.value
self._appearanceWeight = self.topLevelOperatorView.AppearanceWeight.value
self._disappearanceWeight = self.topLevelOperatorView.DisappearanceWeight.value
self._drawer.detWeightBox.setValue(self._detectionWeight)
self._drawer.divWeightBox.setValue(self._divisionWeight)
self._drawer.transWeightBox.setValue(self._transitionWeight)
self._drawer.appearanceBox.setValue(self._appearanceWeight)
self._drawer.disappearanceBox.setValue(self._disappearanceWeight)
@threadRouted
def _onTimeoutBoxChanged(self, *args):
inString = str(self._drawer.timeoutBox.text())
if self._allowedTimeoutInputRegEx.match(inString) is None:
self._drawer.timeoutBox.setText(
inString.decode("utf8").encode("ascii", "replace")[:-1])
def _onMaxNumObjChanged(self):
self._maxNumObj = self.topLevelOperatorView.MaxNumObj.value
self._setMergerLegend(self.mergerLabels, self._maxNumObj)
self._drawer.maxObjectsBox.setValue(self._maxNumObj)
@threadRouted
def _onDivisionWeightBoxChanged(self, *args):
self._divisionWeight = self._drawer.divWeightBox.value()
self.topLevelOperatorView.DivisionWeight.setValue(self._divisionWeight)
@threadRouted
def _onDetectionWeightBoxChanged(self, *args):
self._detectionWeight = self._drawer.detWeightBox.value()
self.topLevelOperatorView.DetectionWeight.setValue(
self._detectionWeight)
@threadRouted
def _onTransitionWeightBoxChanged(self, *args):
self._transitionWeight = self._drawer.transWeightBox.value()
self.topLevelOperatorView.TransitionWeight.setValue(
self._transitionWeight)
@threadRouted
def _onAppearanceWeightBoxChanged(self, *args):
self._appearanceWeight = self._drawer.appearanceBox.value()
self.topLevelOperatorView.AppearanceWeight.setValue(
self._appearanceWeight)
@threadRouted
def _onDisappearanceWeightBoxChanged(self, *args):
self._disappearanceWeight = self._drawer.disappearanceBox.value()
self.topLevelOperatorView.DisappearanceWeight.setValue(
self._disappearanceWeight)
@threadRouted
def _onMaxNearestNeighborsSpinBoxChanged(self, *args):
self._maxNearestNeighbors = self._drawer.maxNearestNeighborsSpinBox.value(
)
def _setRanges(self, *args):
super(StructuredTrackingGui, self)._setRanges()
maxx = self.topLevelOperatorView.LabelImage.meta.shape[1] - 1
maxy = self.topLevelOperatorView.LabelImage.meta.shape[2] - 1
maxz = self.topLevelOperatorView.LabelImage.meta.shape[3] - 1
maxBorder = min(maxx, maxy)
if maxz != 0:
maxBorder = min(maxBorder, maxz)
self._drawer.bordWidthBox.setRange(0, maxBorder / 2)
def _onMaxObjectsBoxChanged(self):
self._setMergerLegend(self.mergerLabels,
self._drawer.maxObjectsBox.value())
self._maxNumObj = self._drawer.maxObjectsBox.value()
self.topLevelOperatorView.MaxNumObjOut.setValue(self._maxNumObj)
@threadRouted
def _updateLabelsFromOperator(self):
self.operator.labels = self.topLevelOperatorView.Labels.wait()
@threadRouted
def _updateDivisionsFromOperator(self):
self.operator.divisions = self.topLevelOperatorView.Divisions.wait()
def getLabel(self, time, track):
for label in self.operator.labels[time].keys():
if self.operator.labels[time][label] == set([track]):
return label
return False
def _onRunStructuredLearningButtonPressed(self, withBatchProcessing=False):
numStages = 4
# creating traxel store
# generating probabilities
# insert energies
# structured learning
if WITH_HYTRA:
self.progressWindow = TrackProgressDialog(parent=self,
numStages=numStages)
self.progressWindow.run()
self.progressWindow.show()
self.progressVisitor = GuiProgressVisitor(
progressWindow=self.progressWindow)
else:
self.progressWindow = None
self.progressVisitor = DefaultProgressVisitor()
def _learn():
self.applet.busy = True
self.applet.appletStateUpdateRequested.emit()
try:
self.topLevelOperatorView._runStructuredLearning(
(self._drawer.from_z.value(), self._drawer.to_z.value()),
self._maxNumObj,
self._maxNearestNeighbors,
self._drawer.maxDistBox.value(),
self._drawer.divThreshBox.value(),
(self._drawer.x_scale.value(),
self._drawer.y_scale.value(),
self._drawer.z_scale.value()),
(self._drawer.from_size.value(),
self._drawer.to_size.value()),
self._drawer.divisionsBox.isChecked(),
self._drawer.bordWidthBox.value(),
self._drawer.classifierPriorBox.isChecked(),
withBatchProcessing,
progressWindow=self.progressWindow,
progressVisitor=self.progressVisitor)
except Exception:
ex_type, ex, tb = sys.exc_info()
traceback.print_tb(tb)
self._criticalMessage("Exception(" + str(ex_type) + "): " +
str(ex))
return
def _handle_finished(*args):
self.applet.busy = False
self.applet.appletStateUpdateRequested.emit()
def _handle_failure(exc, exc_info):
self.applet.busy = False
self.applet.appletStateUpdateRequested.emit()
traceback.print_exception(*exc_info)
sys.stderr.write(
"Exception raised during learning. See traceback above.\n")
if self.progressWindow is not None:
self.progressWindow.onTrackDone()
req = Request(_learn)
req.notify_failed(_handle_failure)
req.notify_finished(_handle_finished)
req.submit()
def _onTrackButtonPressed(self):
if not self.mainOperator.ObjectFeatures.ready():
self._criticalMessage("You have to compute object features first.")
return
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
withTracklets = True
numStages = 6
# creating traxel store
# generating probabilities
# insert energies
# convexify costs
# solver
# compute lineages
if withMergerResolution:
numStages += 1 # merger resolution
if withTracklets:
numStages += 3 # initializing tracklet graph, finding tracklets, contracting edges in tracklet graph
if WITH_HYTRA:
self.progressWindow = TrackProgressDialog(parent=self,
numStages=numStages)
self.progressWindow.run()
self.progressWindow.show()
self.progressVisitor = GuiProgressVisitor(
progressWindow=self.progressWindow)
else:
self.progressWindow = None
self.progressVisitor = DefaultProgressVisitor()
def _track():
self.applet.busy = True
self.applet.appletStateUpdateRequested.emit()
maxDist = self._drawer.maxDistBox.value()
maxObj = self._drawer.maxObjectsBox.value()
divThreshold = self._drawer.divThreshBox.value()
from_t = self._drawer.from_time.value()
to_t = self._drawer.to_time.value()
from_x = self._drawer.from_x.value()
to_x = self._drawer.to_x.value()
from_y = self._drawer.from_y.value()
to_y = self._drawer.to_y.value()
from_z = self._drawer.from_z.value()
to_z = self._drawer.to_z.value()
from_size = self._drawer.from_size.value()
to_size = self._drawer.to_size.value()
self.time_range = range(from_t, to_t + 1)
avgSize = [self._drawer.avgSizeBox.value()]
cplex_timeout = None
if len(str(self._drawer.timeoutBox.text())):
cplex_timeout = int(self._drawer.timeoutBox.text())
withTracklets = True
sizeDependent = self._drawer.sizeDepBox.isChecked()
hardPrior = self._drawer.hardPriorBox.isChecked()
classifierPrior = self._drawer.classifierPriorBox.isChecked()
detWeight = self._drawer.detWeightBox.value()
divWeight = self._drawer.divWeightBox.value()
transWeight = self._drawer.transWeightBox.value()
withDivisions = self._drawer.divisionsBox.isChecked()
withOpticalCorrection = self._drawer.opticalBox.isChecked()
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
borderAwareWidth = self._drawer.bordWidthBox.value()
withArmaCoordinates = True
appearanceCost = self._drawer.appearanceBox.value()
disappearanceCost = self._drawer.disappearanceBox.value()
solverName = self._drawer.solverComboBox.currentText()
ndim = 3
if (to_z - from_z == 0):
ndim = 2
try:
self.mainOperator.track(
time_range=self.time_range,
x_range=(from_x, to_x + 1),
y_range=(from_y, to_y + 1),
z_range=(from_z, to_z + 1),
size_range=(from_size, to_size + 1),
x_scale=self._drawer.x_scale.value(),
y_scale=self._drawer.y_scale.value(),
z_scale=self._drawer.z_scale.value(),
maxDist=maxDist,
maxObj=maxObj,
divThreshold=divThreshold,
avgSize=avgSize,
withTracklets=withTracklets,
sizeDependent=sizeDependent,
detWeight=detWeight,
divWeight=divWeight,
transWeight=transWeight,
withDivisions=withDivisions,
withOpticalCorrection=withOpticalCorrection,
withClassifierPrior=classifierPrior,
ndim=ndim,
withMergerResolution=withMergerResolution,
borderAwareWidth=borderAwareWidth,
withArmaCoordinates=withArmaCoordinates,
cplex_timeout=cplex_timeout,
appearance_cost=appearanceCost,
disappearance_cost=disappearanceCost,
#graph_building_parameter_changed = True,
#trainingToHardConstraints = self._drawer.trainingToHardConstraints.isChecked(),
max_nearest_neighbors=self._maxNearestNeighbors,
solverName=solverName,
progressWindow=self.progressWindow,
progressVisitor=self.progressVisitor)
except Exception:
ex_type, ex, tb = sys.exc_info()
traceback.print_tb(tb)
self._criticalMessage("Exception(" + str(ex_type) + "): " +
str(ex))
return
def _handle_finished(*args):
self.applet.busy = False
self.applet.appletStateUpdateRequested.emit()
self._drawer.TrackButton.setEnabled(True)
self._drawer.exportButton.setEnabled(True)
self._drawer.exportTifButton.setEnabled(True)
self._setLayerVisible("Objects", False)
def _handle_failure(exc, exc_info):
self.applet.busy = False
self.applet.appletStateUpdateRequested.emit()
traceback.print_exception(*exc_info)
sys.stderr.write(
"Exception raised during tracking. See traceback above.\n")
self._drawer.TrackButton.setEnabled(True)
if self.progressWindow is not None:
self.progressWindow.onTrackDone()
req = Request(_track)
req.notify_failed(_handle_failure)
req.notify_finished(_handle_finished)
req.submit()
def menus(self):
m = QtGui.QMenu("&Export", self.volumeEditorWidget)
m.addAction("Export Tracking Information").triggered.connect(
self.show_export_dialog)
return [m]
def get_raw_shape(self):
return self.topLevelOperatorView.RawImage.meta.shape
def get_feature_names(self):
params = self.topLevelOperatorView.Parameters
if params.ready() and params.value["withDivisions"]:
return self.topLevelOperatorView.ComputedFeatureNamesWithDivFeatures(
[]).wait()
return self.topLevelOperatorView.ComputedFeatureNames([]).wait()
def get_color(self, pos5d):
slicing = tuple(slice(i, i + 1) for i in pos5d)
color = self.mainOperator.CachedOutput(slicing).wait()
return color.flat[0]
def get_object(self, pos5d):
slicing = tuple(slice(i, i + 1) for i in pos5d)
label = self.mainOperator.RelabeledImage(slicing).wait()
return label.flat[0], pos5d[0]
@property
def gui_applet(self):
return self.applet
def get_export_dialog_title(self):
return "Export Tracking Information"
# def handleEditorRightClick(self, position5d, win_coord):
# debug = ilastik_config.getboolean("ilastik", "debug")
#
# obj, time = self.get_object(position5d)
# if obj == 0:
# menu = TitledMenu(["Background"])
# if debug:
# menu.addAction("Clear Hilite", IPCFacade().broadcast(Protocol.cmd("clear")))
# menu.exec_(win_coord)
# return
#
# try:
# extra = self.mainOperator.extra_track_ids
# except (IndexError, KeyError):
# extra = {}
#
# # if this is a resolved merger, find which of the merged IDs we actually clicked on
# if time in extra and obj in extra[time]:
# colors = [self.mainOperator.label2color[time][t] for t in extra[time][obj]]
# tracks = [self.mainOperator.track_id[time][t] for t in extra[time][obj]]
# selected_track = self.get_color(position5d)
# idx = colors.index(selected_track)
# color = colors[idx]
# track = tracks[idx]
# else:
# try:
# color = self.mainOperator.label2color[time][obj]
# track = [self.mainOperator.track_id[time][obj]][0]
# except (IndexError, KeyError):
# color = None
# track = []
#
# if track:
# children, parents = self.mainOperator.track_family(track)
# else:
# children, parents = None, None
#
# menu = TitledMenu([
# "Object {} of lineage id {}".format(obj, color),
# "Track id: " + (str(track) or "None"),
# ])
#
# if not debug:
# menu.exec_(win_coord)
# return
#
# if any(IPCFacade().sending):
#
# obj_sub_menu = menu.addMenu("Hilite Object")
# for mode in Protocol.ValidHiliteModes:
# where = Protocol.simple("and", ilastik_id=obj, time=time)
# cmd = Protocol.cmd(mode, where)
# obj_sub_menu.addAction(mode.capitalize(), IPCFacade().broadcast(cmd))
#
# sub_menus = [
# ("Tracks", Protocol.simple_in, tracks),
# ("Parents", Protocol.simple_in, parents),
# ("Children", Protocol.simple_in, children)
# ]
# for name, protocol, args in sub_menus:
# if args:
# sub = menu.addMenu("Hilite {}".format(name))
# for mode in Protocol.ValidHiliteModes[:-1]:
# mode = mode.capitalize()
# where = protocol("track_id*", args)
# cmd = Protocol.cmd(mode, where)
# sub.addAction(mode, IPCFacade().broadcast(cmd))
# else:
# sub = menu.addAction("Hilite {}".format(name))
# sub.setEnabled(False)
#
# menu.addAction("Clear Hilite", IPCFacade().broadcast(Protocol.cmd("clear")))
# else:
# menu.addAction("Open IPC Server Window", IPCFacade().show_info)
# menu.addAction("Start IPC Server", IPCFacade().start)
#
# menu.exec_(win_coord)
def handleEditorRightClick(self, position5d, win_coord):
debug = ilastik_config.getboolean("ilastik", "debug")
obj, time = self.get_object(position5d)
if obj == 0:
menu = TitledMenu(["Background"])
if debug:
menu.addAction("Clear Hilite",
IPCFacade().broadcast(Protocol.cmd("clear")))
menu.exec_(win_coord)
return
hypothesesGraph = self.mainOperator.HypothesesGraph.value
if hypothesesGraph == None:
color = None
track = None
else:
color = hypothesesGraph.getLineageId(time, obj)
track = hypothesesGraph.getTrackId(time, obj)
children = None
parents = None
menu = TitledMenu([
"Object {} of lineage id {}".format(obj, color),
"Track id: " + (str(track) or "None"),
])
if not debug:
menu.exec_(win_coord)
return
if any(IPCFacade().sending):
obj_sub_menu = menu.addMenu("Hilite Object")
for mode in Protocol.ValidHiliteModes:
where = Protocol.simple("and", ilastik_id=obj, time=time)
cmd = Protocol.cmd(mode, where)
obj_sub_menu.addAction(mode.capitalize(),
IPCFacade().broadcast(cmd))
sub_menus = [("Tracks", Protocol.simple_in, tracks),
("Parents", Protocol.simple_in, parents),
("Children", Protocol.simple_in, children)]
for name, protocol, args in sub_menus:
if args:
sub = menu.addMenu("Hilite {}".format(name))
for mode in Protocol.ValidHiliteModes[:-1]:
mode = mode.capitalize()
where = protocol("track_id*", args)
cmd = Protocol.cmd(mode, where)
sub.addAction(mode, IPCFacade().broadcast(cmd))
else:
sub = menu.addAction("Hilite {}".format(name))
sub.setEnabled(False)
menu.addAction("Clear Hilite",
IPCFacade().broadcast(Protocol.cmd("clear")))
else:
menu.addAction("Open IPC Server Window", IPCFacade().show_info)
menu.addAction("Start IPC Server", IPCFacade().start)
menu.exec_(win_coord)
@threadRouted
def _informationMessage(self, prompt):
self.emit(QtCore.SIGNAL('postInformationMessage(QString)'), prompt)
@threadRouted
def postInformationMessage(self, prompt):
QtGui.QMessageBox.information(self, "Info:", prompt,
QtGui.QMessageBox.Ok)
def _onTrackButtonPressed( self ):
if not self.mainOperator.ObjectFeatures.ready():
self._criticalMessage("You have to compute object features first.")
return
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
withTracklets = True
numStages = 6
# creating traxel store
# generating probabilities
# insert energies
# convexify costs
# solver
# compute lineages
if withMergerResolution:
numStages += 1 # merger resolution
if withTracklets:
numStages += 3 # initializing tracklet graph, finding tracklets, contracting edges in tracklet graph
self.progressWindow = TrackProgressDialog(parent=self,numStages=numStages)
self.progressWindow.run()
self.progressWindow.show()
self.progressVisitor = GuiProgressVisitor(progressWindow=self.progressWindow)
def _track():
self.applet.busy = True
self.applet.appletStateUpdateRequested()
maxDist = self._drawer.maxDistBox.value()
maxObj = self._drawer.maxObjectsBox.value()
divThreshold = self._drawer.divThreshBox.value()
from_t = self._drawer.from_time.value()
to_t = self._drawer.to_time.value()
from_x = self._drawer.from_x.value()
to_x = self._drawer.to_x.value()
from_y = self._drawer.from_y.value()
to_y = self._drawer.to_y.value()
from_z = self._drawer.from_z.value()
to_z = self._drawer.to_z.value()
from_size = self._drawer.from_size.value()
to_size = self._drawer.to_size.value()
self.time_range = list(range(from_t, to_t + 1))
avgSize = [self._drawer.avgSizeBox.value()]
cplex_timeout = None
if len(str(self._drawer.timeoutBox.text())):
cplex_timeout = int(self._drawer.timeoutBox.text())
withTracklets = True
sizeDependent = self._drawer.sizeDepBox.isChecked()
hardPrior = self._drawer.hardPriorBox.isChecked()
classifierPrior = self._drawer.classifierPriorBox.isChecked()
detWeight = self._drawer.detWeightBox.value()
divWeight = self._drawer.divWeightBox.value()
transWeight = self._drawer.transWeightBox.value()
withDivisions = self._drawer.divisionsBox.isChecked()
withOpticalCorrection = self._drawer.opticalBox.isChecked()
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
borderAwareWidth = self._drawer.bordWidthBox.value()
withArmaCoordinates = True
appearanceCost = self._drawer.appearanceBox.value()
disappearanceCost = self._drawer.disappearanceBox.value()
solverName = self._drawer.solverComboBox.currentText()
ndim=3
if (to_z - from_z == 0):
ndim=2
try:
self.mainOperator.track(
time_range = self.time_range,
x_range = (from_x, to_x + 1),
y_range = (from_y, to_y + 1),
z_range = (from_z, to_z + 1),
size_range = (from_size, to_size + 1),
x_scale = self._drawer.x_scale.value(),
y_scale = self._drawer.y_scale.value(),
z_scale = self._drawer.z_scale.value(),
maxDist=maxDist,
maxObj = maxObj,
divThreshold=divThreshold,
avgSize=avgSize,
withTracklets=withTracklets,
sizeDependent=sizeDependent,
detWeight=detWeight,
divWeight=divWeight,
transWeight=transWeight,
withDivisions=withDivisions,
withOpticalCorrection=withOpticalCorrection,
withClassifierPrior=classifierPrior,
ndim=ndim,
withMergerResolution=withMergerResolution,
borderAwareWidth = borderAwareWidth,
withArmaCoordinates = withArmaCoordinates,
cplex_timeout = cplex_timeout,
appearance_cost = appearanceCost,
disappearance_cost = disappearanceCost,
#graph_building_parameter_changed = True,
#trainingToHardConstraints = self._drawer.trainingToHardConstraints.isChecked(),
max_nearest_neighbors = self._maxNearestNeighbors,
solverName=solverName,
progressWindow=self.progressWindow,
progressVisitor=self.progressVisitor
)
except Exception:
self.progressWindow.onTrackDone()
ex_type, ex, tb = sys.exc_info()
traceback.print_tb(tb)
self._criticalMessage("Exception(" + str(ex_type) + "): " + str(ex))
return
def _handle_finished(*args):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
self._drawer.TrackButton.setEnabled(True)
self._drawer.exportButton.setEnabled(True)
self._drawer.exportTifButton.setEnabled(True)
self._setLayerVisible("Objects", False)
def _handle_failure( exc, exc_info ):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
traceback.print_exception(*exc_info)
sys.stderr.write("Exception raised during tracking. See traceback above.\n")
self._drawer.TrackButton.setEnabled(True)
if self.progressWindow is not None:
self.progressWindow.onTrackDone()
req = Request( _track )
req.notify_failed( _handle_failure )
req.notify_finished( _handle_finished )
req.submit()
class StructuredTrackingGui(TrackingBaseGui, ExportingGui):
withMergers = True
@threadRouted
def _setMergerLegend(self, labels, selection):
param = self.topLevelOperatorView.Parameters.value
if 'withMergerResolution' in list(param.keys()):
if param['withMergerResolution']:
selection = 1
elif self._drawer.mergerResolutionBox.isChecked():
selection = 1
for i in range(2,len(labels)+1):
if i <= selection:
labels[i-1].setVisible(True)
else:
labels[i-1].setVisible(False)
# hide merger legend if selection < 2
self._drawer.label_4.setVisible(selection > 1)
labels[0].setVisible(selection > 1)
def __init__(self, parentApplet, topLevelOperatorView):
"""
"""
self._initColors()
self.topLevelOperatorView = topLevelOperatorView
self.progressWindow = None
super(TrackingBaseGui, self).__init__(parentApplet, topLevelOperatorView)
self.mainOperator = topLevelOperatorView
if self.mainOperator.LabelImage.meta.shape:
self.editor.dataShape = self.mainOperator.LabelImage.meta.shape
self.applet = self.mainOperator.parent.parent.trackingApplet
self._drawer.mergerResolutionBox.setChecked(True)
self.parentApplet = parentApplet
self._headless = False
def _loadUiFile(self):
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir+"/drawer.ui")
parameters = self.topLevelOperatorView.Parameters.value
if 'maxDist' in list(parameters.keys()):
self._drawer.maxDistBox.setValue(parameters['maxDist'])
if 'maxObj' in list(parameters.keys()):
self._drawer.maxObjectsBox.setValue(parameters['maxObj'])
if 'maxNearestNeighbors' in list(parameters.keys()):
self._drawer.maxObjectsBox.setValue(parameters['maxNearestNeighbors'])
if 'divThreshold' in list(parameters.keys()):
self._drawer.divThreshBox.setValue(parameters['divThreshold'])
if 'avgSize' in list(parameters.keys()):
self._drawer.avgSizeBox.setValue(parameters['avgSize'][0])
if 'withTracklets' in list(parameters.keys()):
self._drawer.trackletsBox.setChecked(parameters['withTracklets'])
if 'sizeDependent' in list(parameters.keys()):
self._drawer.sizeDepBox.setChecked(parameters['sizeDependent'])
if 'detWeight' in list(parameters.keys()):
self._drawer.detWeightBox.setValue(parameters['detWeight'])
if 'divWeight' in list(parameters.keys()):
self._drawer.divWeightBox.setValue(parameters['divWeight'])
if 'transWeight' in list(parameters.keys()):
self._drawer.transWeightBox.setValue(parameters['transWeight'])
if 'withDivisions' in list(parameters.keys()):
self._drawer.divisionsBox.setChecked(parameters['withDivisions'])
if 'withOpticalCorrection' in list(parameters.keys()):
self._drawer.opticalBox.setChecked(parameters['withOpticalCorrection'])
if 'withClassifierPrior' in list(parameters.keys()):
self._drawer.classifierPriorBox.setChecked(parameters['withClassifierPrior'])
if 'withMergerResolution' in list(parameters.keys()):
self._drawer.mergerResolutionBox.setChecked(parameters['withMergerResolution'])
if 'borderAwareWidth' in list(parameters.keys()):
self._drawer.bordWidthBox.setValue(parameters['borderAwareWidth'])
if 'cplex_timeout' in list(parameters.keys()):
self._drawer.timeoutBox.setText(str(parameters['cplex_timeout']))
if 'appearanceCost' in list(parameters.keys()):
self._drawer.appearanceBox.setValue(parameters['appearanceCost'])
if 'disappearanceCost' in list(parameters.keys()):
self._drawer.disappearanceBox.setValue(parameters['disappearanceCost'])
solverName = self.topLevelOperatorView._solver
if solverName == "Flow-based":
self._drawer.StructuredLearningButton.setEnabled(False)
self._drawer.RandomButton.setEnabled(False)
self._drawer.OnesButton.setEnabled(False)
self._drawer.ZerosButton.setEnabled(False)
return self._drawer
def initAppletDrawerUi(self):
self._maxNearestNeighbors = 1
super(StructuredTrackingGui, self).initAppletDrawerUi()
self.realOperator = self.topLevelOperatorView.Labels.getRealOperator()
for i, op in enumerate(self.realOperator.innerOperators):
self.operator = op
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.label_5.hide()
self._drawer.divThreshBox.hide()
self._drawer.label_25.hide()
self._drawer.avgSizeBox.hide()
self._drawer.InitialWeightsLabel.hide()
self._drawer.ZerosButton.hide()
self._drawer.OnesButton.hide()
self._drawer.RandomButton.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._drawer.maxObjectsBox.valueChanged.connect(self._onMaxObjectsBoxChanged)
self._drawer.mergerResolutionBox.stateChanged.connect(self._onMaxObjectsBoxChanged)
self._drawer.StructuredLearningButton.clicked.connect(self._onRunStructuredLearningButtonPressed)
self._drawer.divWeightBox.valueChanged.connect(self._onDivisionWeightBoxChanged)
self._drawer.detWeightBox.valueChanged.connect(self._onDetectionWeightBoxChanged)
self._drawer.transWeightBox.valueChanged.connect(self._onTransitionWeightBoxChanged)
self._drawer.appearanceBox.valueChanged.connect(self._onAppearanceWeightBoxChanged)
self._drawer.disappearanceBox.valueChanged.connect(self._onDisappearanceWeightBoxChanged)
self._drawer.maxNearestNeighborsSpinBox.valueChanged.connect(self._onMaxNearestNeighborsSpinBoxChanged)
self._drawer.OnesButton.clicked.connect(self._onOnesButtonPressed)
self._drawer.ZerosButton.clicked.connect(self._onZerosButtonPressed)
self._drawer.RandomButton.clicked.connect(self._onRandomButtonPressed)
self._divisionWeight = self.topLevelOperatorView.DivisionWeight.value
self._detectionWeight = self.topLevelOperatorView.DetectionWeight.value
self._transitionWeight = self.topLevelOperatorView.TransitionWeight.value
self._appearanceWeight = self.topLevelOperatorView.AppearanceWeight.value
self._disappearanceWeight = self.topLevelOperatorView.DisappearanceWeight.value
self._drawer.detWeightBox.setValue(self._detectionWeight)
self._drawer.divWeightBox.setValue(self._divisionWeight)
self._drawer.transWeightBox.setValue(self._transitionWeight)
self._drawer.appearanceBox.setValue(self._appearanceWeight)
self._drawer.disappearanceBox.setValue(self._disappearanceWeight)
self._maxNumObj = self.topLevelOperatorView.MaxNumObj.value
self._drawer.maxObjectsBox.setValue(self.topLevelOperatorView.MaxNumObj.value)
self._onMaxObjectsBoxChanged()
self._drawer.maxObjectsBox.setReadOnly(False)
self.topLevelOperatorView.Labels.notifyReady( bind(self._updateLabelsFromOperator) )
self.topLevelOperatorView.Divisions.notifyReady( bind(self._updateDivisionsFromOperator) )
self.topLevelOperatorView.Appearances.notifyReady( bind(self._updateAppearancesFromOperator) )
self.topLevelOperatorView.Disappearances.notifyReady( bind(self._updateDisappearancesFromOperator) )
self.operator.labels = self.operator.Labels.value
self.operator.appearances = self.operator.Appearances.value
self.operator.disappearances = self.operator.Disappearances.value
self._drawer.exportButton.setVisible(False)
self._drawer.exportTifButton.setVisible(False)
self.topLevelOperatorView._detectionWeight = self._detectionWeight
self.topLevelOperatorView._divisionWeight = self._divisionWeight
self.topLevelOperatorView._transitionWeight = self._transitionWeight
self.topLevelOperatorView._appearanceWeight = self._appearanceWeight
self.topLevelOperatorView._disappearanceWeight = self._disappearanceWeight
self._drawer.solverComboBox.clear()
availableSolvers = self.getAvailableTrackingSolverTypes()
self._drawer.solverComboBox.addItems(availableSolvers)
parameters = self.topLevelOperatorView.Parameters.value
if 'solver' in parameters.keys() and parameters['solver'] in availableSolvers:
self._drawer.solverComboBox.setCurrentIndex(availableSolvers.index(parameters['solver']))
# listen on the main operator's NumLabels slot for changes, and adjust the max value of the "maxNumObjects" box
self.topLevelOperatorView.NumLabels.notifyDirty(self._updateMaxObjectsBoxMaxValue)
self._updateMaxObjectsBoxMaxValue()
return self._drawer
@threadRouted
def _updateMaxObjectsBoxMaxValue(self, *args, **kwargs):
if self.topLevelOperatorView.NumLabels.ready():
if self.topLevelOperatorView.NumLabels.value > 1:
self._drawer.maxObjectsBox.setMaximum(self.topLevelOperatorView.NumLabels.value - 1)
self._drawer.maxObjectsBox.setValue(self.topLevelOperatorView.NumLabels.value - 1)
self._drawer.TrackButton.setEnabled(True)
else:
self._drawer.maxObjectsBox.setMaximum(0)
self._drawer.maxObjectsBox.setValue(0)
self._drawer.TrackButton.setEnabled(False)
@staticmethod
def getAvailableTrackingSolverTypes():
solvers = []
try:
if dpct:
solvers.append('Flow-based')
except Exception as e:
logger.info(str(e))
try:
if mht:
solvers.append('ILP')
except Exception as e:
logger.info(str(e))
return solvers
def _onOnesButtonPressed(self):
val = math.sqrt(old_div(1.0,5))
self.topLevelOperatorView.DivisionWeight.setValue(val)
self.topLevelOperatorView.DetectionWeight.setValue(val)
self.topLevelOperatorView.TransitionWeight.setValue(val)
self.topLevelOperatorView.AppearanceWeight.setValue(val)
self.topLevelOperatorView.DisappearanceWeight.setValue(val)
self._divisionWeight = self.topLevelOperatorView.DivisionWeight.value
self._detectionWeight = self.topLevelOperatorView.DetectionWeight.value
self._transitionWeight = self.topLevelOperatorView.TransitionWeight.value
self._appearanceWeight = self.topLevelOperatorView.AppearanceWeight.value
self._disappearanceWeight = self.topLevelOperatorView.DisappearanceWeight.value
self._drawer.detWeightBox.setValue(self._detectionWeight)
self._drawer.divWeightBox.setValue(self._divisionWeight)
self._drawer.transWeightBox.setValue(self._transitionWeight)
self._drawer.appearanceBox.setValue(self._appearanceWeight)
self._drawer.disappearanceBox.setValue(self._disappearanceWeight)
def _onRandomButtonPressed(self):
weights = []
for i in range(5):
weights.append(random.random())
sltWeightNorm = 0
for i in range(5):
sltWeightNorm += weights[i] * weights[i]
sltWeightNorm = math.sqrt(sltWeightNorm)
self.topLevelOperatorView.DivisionWeight.setValue(old_div(weights[0],sltWeightNorm))
self.topLevelOperatorView.DetectionWeight.setValue(old_div(weights[1],sltWeightNorm))
self.topLevelOperatorView.TransitionWeight.setValue(old_div(weights[2],sltWeightNorm))
self.topLevelOperatorView.AppearanceWeight.setValue(old_div(weights[3],sltWeightNorm))
self.topLevelOperatorView.DisappearanceWeight.setValue(old_div(weights[4],sltWeightNorm))
self._divisionWeight = self.topLevelOperatorView.DivisionWeight.value
self._detectionWeight = self.topLevelOperatorView.DetectionWeight.value
self._transitionWeight = self.topLevelOperatorView.TransitionWeight.value
self._appearanceWeight = self.topLevelOperatorView.AppearanceWeight.value
self._disappearanceWeight = self.topLevelOperatorView.DisappearanceWeight.value
self._drawer.detWeightBox.setValue(self._detectionWeight)
self._drawer.divWeightBox.setValue(self._divisionWeight)
self._drawer.transWeightBox.setValue(self._transitionWeight)
self._drawer.appearanceBox.setValue(self._appearanceWeight)
self._drawer.disappearanceBox.setValue(self._disappearanceWeight)
def _onZerosButtonPressed(self):
self.topLevelOperatorView.DivisionWeight.setValue(0)
self.topLevelOperatorView.DetectionWeight.setValue(0)
self.topLevelOperatorView.TransitionWeight.setValue(0)
self.topLevelOperatorView.AppearanceWeight.setValue(0)
self.topLevelOperatorView.DisappearanceWeight.setValue(0)
self._divisionWeight = self.topLevelOperatorView.DivisionWeight.value
self._detectionWeight = self.topLevelOperatorView.DetectionWeight.value
self._transitionWeight = self.topLevelOperatorView.TransitionWeight.value
self._appearanceWeight = self.topLevelOperatorView.AppearanceWeight.value
self._disappearanceWeight = self.topLevelOperatorView.DisappearanceWeight.value
self._drawer.detWeightBox.setValue(self._detectionWeight)
self._drawer.divWeightBox.setValue(self._divisionWeight)
self._drawer.transWeightBox.setValue(self._transitionWeight)
self._drawer.appearanceBox.setValue(self._appearanceWeight)
self._drawer.disappearanceBox.setValue(self._disappearanceWeight)
@threadRouted
def _onTimeoutBoxChanged(self, *args):
inString = str(self._drawer.timeoutBox.text())
if self._allowedTimeoutInputRegEx.match(inString) is None:
self._drawer.timeoutBox.setText(inString[:-1])
def _onMaxNumObjChanged(self):
self._maxNumObj = self.topLevelOperatorView.MaxNumObj.value
self._setMergerLegend(self.mergerLabels, self._maxNumObj)
self._drawer.maxObjectsBox.setValue(self._maxNumObj)
@threadRouted
def _onDivisionWeightBoxChanged(self, *args):
self._divisionWeight = self._drawer.divWeightBox.value()
self.topLevelOperatorView.DivisionWeight.setValue(self._divisionWeight)
@threadRouted
def _onDetectionWeightBoxChanged(self, *args):
self._detectionWeight = self._drawer.detWeightBox.value()
self.topLevelOperatorView.DetectionWeight.setValue(self._detectionWeight)
@threadRouted
def _onTransitionWeightBoxChanged(self, *args):
self._transitionWeight = self._drawer.transWeightBox.value()
self.topLevelOperatorView.TransitionWeight.setValue(self._transitionWeight)
@threadRouted
def _onAppearanceWeightBoxChanged(self, *args):
self._appearanceWeight = self._drawer.appearanceBox.value()
self.topLevelOperatorView.AppearanceWeight.setValue(self._appearanceWeight)
@threadRouted
def _onDisappearanceWeightBoxChanged(self, *args):
self._disappearanceWeight = self._drawer.disappearanceBox.value()
self.topLevelOperatorView.DisappearanceWeight.setValue(self._disappearanceWeight)
@threadRouted
def _onMaxNearestNeighborsSpinBoxChanged(self, *args):
self._maxNearestNeighbors = self._drawer.maxNearestNeighborsSpinBox.value()
def _setRanges(self, *args):
super(StructuredTrackingGui, self)._setRanges()
maxx = self.topLevelOperatorView.LabelImage.meta.shape[1] - 1
maxy = self.topLevelOperatorView.LabelImage.meta.shape[2] - 1
maxz = self.topLevelOperatorView.LabelImage.meta.shape[3] - 1
maxBorder = min(maxx, maxy)
if maxz != 0:
maxBorder = min(maxBorder, maxz)
self._drawer.bordWidthBox.setRange(0, old_div(maxBorder,2))
def _onMaxObjectsBoxChanged(self):
self._setMergerLegend(self.mergerLabels, self._drawer.maxObjectsBox.value())
self._maxNumObj = self._drawer.maxObjectsBox.value()
self.topLevelOperatorView.MaxNumObjOut.setValue(self._maxNumObj)
@threadRouted
def _updateLabelsFromOperator(self):
self.operator.labels = self.topLevelOperatorView.Labels.wait()
@threadRouted
def _updateDivisionsFromOperator(self):
self.operator.divisions = self.topLevelOperatorView.Divisions.wait()
@threadRouted
def _updateAppearancesFromOperator(self):
self.operator.appearances = self.topLevelOperatorView.Appearances.wait()
@threadRouted
def _updateDisappearancesFromOperator(self):
self.operator.disappearances = self.topLevelOperatorView.Disappearances.wait()
def getLabel(self, time, track):
for label in list(self.operator.labels[time].keys()):
if self.operator.labels[time][label] == set([track]):
return label
return False
def _onRunStructuredLearningButtonPressed(self, withBatchProcessing=False):
if not self.mainOperator.ObjectFeatures.ready():
self._criticalMessage("You have to compute object features first.")
return
numStages = 6
# object features
# detection probabilities
# creating traxel store
# generating probabilities
# insert energies
# structured learning
if self._drawer.divisionsBox.isChecked():
# division probabilities
numStages +=1
self.progressWindow = TrackProgressDialog(parent=self,numStages=numStages)
self.progressWindow.run()
self.progressWindow.show()
self.progressVisitor = GuiProgressVisitor(progressWindow=self.progressWindow)
def _learn():
self.applet.busy = True
self.applet.appletStateUpdateRequested()
try:
self.topLevelOperatorView._runStructuredLearning(
(self._drawer.from_z.value(),self._drawer.to_z.value()),
self._maxNumObj,
self._maxNearestNeighbors,
self._drawer.maxDistBox.value(),
self._drawer.divThreshBox.value(),
(self._drawer.x_scale.value(), self._drawer.y_scale.value(), self._drawer.z_scale.value()),
(self._drawer.from_size.value(), self._drawer.to_size.value()),
self._drawer.divisionsBox.isChecked(),
self._drawer.bordWidthBox.value(),
self._drawer.classifierPriorBox.isChecked(),
withBatchProcessing,
progressWindow=self.progressWindow,
progressVisitor=self.progressVisitor
)
except Exception:
ex_type, ex, tb = sys.exc_info()
traceback.print_tb(tb)
self._criticalMessage("Exception(" + str(ex_type) + "): " + str(ex))
return
def _handle_finished(*args):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
def _handle_failure( exc, exc_info ):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
traceback.print_exception(*exc_info)
sys.stderr.write("Exception raised during learning. See traceback above.\n")
if self.progressWindow is not None:
self.progressWindow.onTrackDone()
req = Request( _learn )
req.notify_failed( _handle_failure )
req.notify_finished( _handle_finished )
req.submit()
def _onTrackButtonPressed( self ):
if not self.mainOperator.ObjectFeatures.ready():
self._criticalMessage("You have to compute object features first.")
return
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
withTracklets = True
numStages = 6
# creating traxel store
# generating probabilities
# insert energies
# convexify costs
# solver
# compute lineages
if withMergerResolution:
numStages += 1 # merger resolution
if withTracklets:
numStages += 3 # initializing tracklet graph, finding tracklets, contracting edges in tracklet graph
self.progressWindow = TrackProgressDialog(parent=self,numStages=numStages)
self.progressWindow.run()
self.progressWindow.show()
self.progressVisitor = GuiProgressVisitor(progressWindow=self.progressWindow)
def _track():
self.applet.busy = True
self.applet.appletStateUpdateRequested()
maxDist = self._drawer.maxDistBox.value()
maxObj = self._drawer.maxObjectsBox.value()
divThreshold = self._drawer.divThreshBox.value()
from_t = self._drawer.from_time.value()
to_t = self._drawer.to_time.value()
from_x = self._drawer.from_x.value()
to_x = self._drawer.to_x.value()
from_y = self._drawer.from_y.value()
to_y = self._drawer.to_y.value()
from_z = self._drawer.from_z.value()
to_z = self._drawer.to_z.value()
from_size = self._drawer.from_size.value()
to_size = self._drawer.to_size.value()
self.time_range = list(range(from_t, to_t + 1))
avgSize = [self._drawer.avgSizeBox.value()]
cplex_timeout = None
if len(str(self._drawer.timeoutBox.text())):
cplex_timeout = int(self._drawer.timeoutBox.text())
withTracklets = True
sizeDependent = self._drawer.sizeDepBox.isChecked()
hardPrior = self._drawer.hardPriorBox.isChecked()
classifierPrior = self._drawer.classifierPriorBox.isChecked()
detWeight = self._drawer.detWeightBox.value()
divWeight = self._drawer.divWeightBox.value()
transWeight = self._drawer.transWeightBox.value()
withDivisions = self._drawer.divisionsBox.isChecked()
withOpticalCorrection = self._drawer.opticalBox.isChecked()
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
borderAwareWidth = self._drawer.bordWidthBox.value()
withArmaCoordinates = True
appearanceCost = self._drawer.appearanceBox.value()
disappearanceCost = self._drawer.disappearanceBox.value()
solverName = self._drawer.solverComboBox.currentText()
ndim=3
if (to_z - from_z == 0):
ndim=2
try:
self.mainOperator.track(
time_range = self.time_range,
x_range = (from_x, to_x + 1),
y_range = (from_y, to_y + 1),
z_range = (from_z, to_z + 1),
size_range = (from_size, to_size + 1),
x_scale = self._drawer.x_scale.value(),
y_scale = self._drawer.y_scale.value(),
z_scale = self._drawer.z_scale.value(),
maxDist=maxDist,
maxObj = maxObj,
divThreshold=divThreshold,
avgSize=avgSize,
withTracklets=withTracklets,
sizeDependent=sizeDependent,
detWeight=detWeight,
divWeight=divWeight,
transWeight=transWeight,
withDivisions=withDivisions,
withOpticalCorrection=withOpticalCorrection,
withClassifierPrior=classifierPrior,
ndim=ndim,
withMergerResolution=withMergerResolution,
borderAwareWidth = borderAwareWidth,
withArmaCoordinates = withArmaCoordinates,
cplex_timeout = cplex_timeout,
appearance_cost = appearanceCost,
disappearance_cost = disappearanceCost,
#graph_building_parameter_changed = True,
#trainingToHardConstraints = self._drawer.trainingToHardConstraints.isChecked(),
max_nearest_neighbors = self._maxNearestNeighbors,
solverName=solverName,
progressWindow=self.progressWindow,
progressVisitor=self.progressVisitor
)
except Exception:
self.progressWindow.onTrackDone()
ex_type, ex, tb = sys.exc_info()
traceback.print_tb(tb)
self._criticalMessage("Exception(" + str(ex_type) + "): " + str(ex))
return
def _handle_finished(*args):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
self._drawer.TrackButton.setEnabled(True)
self._drawer.exportButton.setEnabled(True)
self._drawer.exportTifButton.setEnabled(True)
self._setLayerVisible("Objects", False)
def _handle_failure( exc, exc_info ):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
traceback.print_exception(*exc_info)
sys.stderr.write("Exception raised during tracking. See traceback above.\n")
self._drawer.TrackButton.setEnabled(True)
if self.progressWindow is not None:
self.progressWindow.onTrackDone()
req = Request( _track )
req.notify_failed( _handle_failure )
req.notify_finished( _handle_finished )
req.submit()
def get_raw_shape(self):
return self.topLevelOperatorView.RawImage.meta.shape
def get_feature_names(self):
params = self.topLevelOperatorView.Parameters
if params.ready() and params.value["withDivisions"]:
return self.topLevelOperatorView.ComputedFeatureNamesWithDivFeatures([]).wait()
return self.topLevelOperatorView.ComputedFeatureNames([]).wait()
def get_color(self, pos5d):
slicing = tuple(slice(i, i+1) for i in pos5d)
color = self.mainOperator.CachedOutput(slicing).wait()
return color.flat[0]
def get_object(self, pos5d):
slicing = tuple(slice(i, i+1) for i in pos5d)
label = self.mainOperator.RelabeledImage(slicing).wait()
return label.flat[0], pos5d[0]
@property
def gui_applet(self):
return self.applet
def get_export_dialog_title(self):
return "Export Tracking Information"
# def handleEditorRightClick(self, position5d, win_coord):
# debug = ilastik_config.getboolean("ilastik", "debug")
#
# obj, time = self.get_object(position5d)
# if obj == 0:
# menu = TitledMenu(["Background"])
# if debug:
# menu.addAction("Clear Hilite", IPCFacade().broadcast(Protocol.cmd("clear")))
# menu.exec_(win_coord)
# return
#
# try:
# extra = self.mainOperator.extra_track_ids
# except (IndexError, KeyError):
# extra = {}
#
# # if this is a resolved merger, find which of the merged IDs we actually clicked on
# if time in extra and obj in extra[time]:
# colors = [self.mainOperator.label2color[time][t] for t in extra[time][obj]]
# tracks = [self.mainOperator.track_id[time][t] for t in extra[time][obj]]
# selected_track = self.get_color(position5d)
# idx = colors.index(selected_track)
# color = colors[idx]
# track = tracks[idx]
# else:
# try:
# color = self.mainOperator.label2color[time][obj]
# track = [self.mainOperator.track_id[time][obj]][0]
# except (IndexError, KeyError):
# color = None
# track = []
#
# if track:
# children, parents = self.mainOperator.track_family(track)
# else:
# children, parents = None, None
#
# menu = TitledMenu([
# "Object {} of lineage id {}".format(obj, color),
# "Track id: " + (str(track) or "None"),
# ])
#
# if not debug:
# menu.exec_(win_coord)
# return
#
# if any(IPCFacade().sending):
#
# obj_sub_menu = menu.addMenu("Hilite Object")
# for mode in Protocol.ValidHiliteModes:
# where = Protocol.simple("and", ilastik_id=obj, time=time)
# cmd = Protocol.cmd(mode, where)
# obj_sub_menu.addAction(mode.capitalize(), IPCFacade().broadcast(cmd))
#
# sub_menus = [
# ("Tracks", Protocol.simple_in, tracks),
# ("Parents", Protocol.simple_in, parents),
# ("Children", Protocol.simple_in, children)
# ]
# for name, protocol, args in sub_menus:
# if args:
# sub = menu.addMenu("Hilite {}".format(name))
# for mode in Protocol.ValidHiliteModes[:-1]:
# mode = mode.capitalize()
# where = protocol("track_id*", args)
# cmd = Protocol.cmd(mode, where)
# sub.addAction(mode, IPCFacade().broadcast(cmd))
# else:
# sub = menu.addAction("Hilite {}".format(name))
# sub.setEnabled(False)
#
# menu.addAction("Clear Hilite", IPCFacade().broadcast(Protocol.cmd("clear")))
# else:
# menu.addAction("Open IPC Server Window", IPCFacade().show_info)
# menu.addAction("Start IPC Server", IPCFacade().start)
#
# menu.exec_(win_coord)
def handleEditorRightClick(self, position5d, win_coord):
debug = ilastik_config.getboolean("ilastik", "debug")
obj, time = self.get_object(position5d)
if obj == 0:
menu = TitledMenu(["Background"])
if debug:
menu.addAction("Clear Hilite", IPCFacade().broadcast(Protocol.cmd("clear")))
menu.exec_(win_coord)
return
hypothesesGraph = self.mainOperator.HypothesesGraph.value
if hypothesesGraph == None:
color = None
track = None
else:
color = hypothesesGraph.getLineageId(time, obj)
track = hypothesesGraph.getTrackId(time, obj)
tracks = None
children = None
parents = None
menu = TitledMenu([
"Object {} of lineage id {}".format(obj, color),
"Track id: " + (str(track) or "None"),
])
if not debug:
menu.exec_(win_coord)
return
if any(IPCFacade().sending):
obj_sub_menu = menu.addMenu("Hilite Object")
for mode in Protocol.ValidHiliteModes:
where = Protocol.simple("and", ilastik_id=obj, time=time)
cmd = Protocol.cmd(mode, where)
obj_sub_menu.addAction(mode.capitalize(), IPCFacade().broadcast(cmd))
sub_menus = [
("Tracks", Protocol.simple_in, tracks),
("Parents", Protocol.simple_in, parents),
("Children", Protocol.simple_in, children)
]
for name, protocol, args in sub_menus:
if args:
sub = menu.addMenu("Hilite {}".format(name))
for mode in Protocol.ValidHiliteModes[:-1]:
mode = mode.capitalize()
where = protocol("track_id*", args)
cmd = Protocol.cmd(mode, where)
sub.addAction(mode, IPCFacade().broadcast(cmd))
else:
sub = menu.addAction("Hilite {}".format(name))
sub.setEnabled(False)
menu.addAction("Clear Hilite", IPCFacade().broadcast(Protocol.cmd("clear")))
else:
menu.addAction("Open IPC Server Window", IPCFacade().show_info)
menu.addAction("Start IPC Server", IPCFacade().start)
menu.exec_(win_coord)
@threadRouted
def _informationMessage(self, prompt):
#
# This function used to be pass-throughs to a signal,
# but I don't see why that's necessary.
# (It is always called from the main thread.)
# So now we just call the target function directly.
#
self.postInformationMessage(prompt)
@threadRouted
def postInformationMessage(self, prompt):
QtWidgets.QMessageBox.information(self, "Info:", prompt, QtWidgets.QMessageBox.Ok)
def _onRunStructuredLearningButtonPressed(self, withBatchProcessing=False):
if not self.mainOperator.ObjectFeatures.ready():
self._criticalMessage("You have to compute object features first.")
return
numStages = 6
# object features
# detection probabilities
# creating traxel store
# generating probabilities
# insert energies
# structured learning
if self._drawer.divisionsBox.isChecked():
# division probabilities
numStages +=1
self.progressWindow = TrackProgressDialog(parent=self,numStages=numStages)
self.progressWindow.run()
self.progressWindow.show()
self.progressVisitor = GuiProgressVisitor(progressWindow=self.progressWindow)
def _learn():
self.applet.busy = True
self.applet.appletStateUpdateRequested()
try:
self.topLevelOperatorView._runStructuredLearning(
(self._drawer.from_z.value(),self._drawer.to_z.value()),
self._maxNumObj,
self._maxNearestNeighbors,
self._drawer.maxDistBox.value(),
self._drawer.divThreshBox.value(),
(self._drawer.x_scale.value(), self._drawer.y_scale.value(), self._drawer.z_scale.value()),
(self._drawer.from_size.value(), self._drawer.to_size.value()),
self._drawer.divisionsBox.isChecked(),
self._drawer.bordWidthBox.value(),
self._drawer.classifierPriorBox.isChecked(),
withBatchProcessing,
progressWindow=self.progressWindow,
progressVisitor=self.progressVisitor
)
except Exception:
ex_type, ex, tb = sys.exc_info()
traceback.print_tb(tb)
self._criticalMessage("Exception(" + str(ex_type) + "): " + str(ex))
return
def _handle_finished(*args):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
def _handle_failure( exc, exc_info ):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
traceback.print_exception(*exc_info)
sys.stderr.write("Exception raised during learning. See traceback above.\n")
if self.progressWindow is not None:
self.progressWindow.onTrackDone()
req = Request( _learn )
req.notify_failed( _handle_failure )
req.notify_finished( _handle_finished )
req.submit()
class ConservationTrackingGui(TrackingBaseGui, ExportingGui):
withMergers = True
@threadRouted
def _setMergerLegend(self, labels, selection):
param = self.topLevelOperatorView.Parameters.value
if 'withMergerResolution' in list(param.keys()):
if param['withMergerResolution']:
selection = 1
elif self._drawer.mergerResolutionBox.isChecked():
selection = 1
for i in range(2,len(labels)+1):
if i <= selection:
labels[i-1].setVisible(True)
else:
labels[i-1].setVisible(False)
# hide merger legend if selection < 2
self._drawer.label_4.setVisible(selection > 1)
labels[0].setVisible(selection > 1)
def _loadUiFile(self):
# Load the ui file (find it in our own directory)
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir+"/drawer.ui")
parameters = self.topLevelOperatorView.Parameters.value
if 'maxDist' in list(parameters.keys()):
self._drawer.maxDistBox.setValue(parameters['maxDist'])
if 'maxObj' in list(parameters.keys()):
self._drawer.maxObjectsBox.setValue(parameters['maxObj'])
if 'divThreshold' in list(parameters.keys()):
self._drawer.divThreshBox.setValue(parameters['divThreshold'])
if 'avgSize' in list(parameters.keys()):
self._drawer.avgSizeBox.setValue(parameters['avgSize'][0])
if 'withTracklets' in list(parameters.keys()):
self._drawer.trackletsBox.setChecked(parameters['withTracklets'])
if 'sizeDependent' in list(parameters.keys()):
self._drawer.sizeDepBox.setChecked(parameters['sizeDependent'])
if 'divWeight' in list(parameters.keys()):
self._drawer.divWeightBox.setValue(parameters['divWeight'])
if 'transWeight' in list(parameters.keys()):
self._drawer.transWeightBox.setValue(parameters['transWeight'])
if 'withDivisions' in list(parameters.keys()):
self._drawer.divisionsBox.setChecked(parameters['withDivisions'])
if 'withOpticalCorrection' in list(parameters.keys()):
self._drawer.opticalBox.setChecked(parameters['withOpticalCorrection'])
if 'withClassifierPrior' in list(parameters.keys()):
self._drawer.classifierPriorBox.setChecked(parameters['withClassifierPrior'])
if 'withMergerResolution' in list(parameters.keys()):
self._drawer.mergerResolutionBox.setChecked(parameters['withMergerResolution'])
if 'borderAwareWidth' in list(parameters.keys()):
self._drawer.bordWidthBox.setValue(parameters['borderAwareWidth'])
if 'cplex_timeout' in list(parameters.keys()):
self._drawer.timeoutBox.setText(str(parameters['cplex_timeout']))
if 'appearanceCost' in list(parameters.keys()):
self._drawer.appearanceBox.setValue(parameters['appearanceCost'])
if 'disappearanceCost' in list(parameters.keys()):
self._drawer.disappearanceBox.setValue(parameters['disappearanceCost'])
if 'max_nearest_neighbors' in list(parameters.keys()):
self._drawer.maxNearestNeighborsSpinBox.setValue(parameters['max_nearest_neighbors'])
if 'numFramesPerSplit' in list(parameters.keys()):
self._drawer.numFramesPerSplitSpinBox.setValue(parameters['numFramesPerSplit'])
# solver: use stored value only if that solver is available
self._drawer.solverComboBox.clear()
availableSolvers = self.getAvailableTrackingSolverTypes()
self._drawer.solverComboBox.addItems(availableSolvers)
if 'solver' in list(parameters.keys()) and parameters['solver'] in availableSolvers:
self._drawer.solverComboBox.setCurrentIndex(availableSolvers.index(parameters['solver']))
# listen on the main operator's NumLabels slot for changes, and adjust the max value of the "maxNumObjects" box
self.topLevelOperatorView.NumLabels.notifyDirty(self._updateMaxObjectsBoxMaxValue)
self._updateMaxObjectsBoxMaxValue()
# Hide division GUI widgets
if 'withAnimalTracking' in list(parameters.keys()) and parameters['withAnimalTracking'] == True:
self._drawer.label_5.hide()
self._drawer.divThreshBox.hide()
self._drawer.divisionsBox.hide()
self._drawer.divWeightBox.hide()
self._drawer.label_6.hide()
return self._drawer
@threadRouted
def _updateMaxObjectsBoxMaxValue(self, *args, **kwargs):
if self.topLevelOperatorView.NumLabels.ready():
if self.topLevelOperatorView.NumLabels.value > 1:
self._drawer.maxObjectsBox.setMaximum(self.topLevelOperatorView.NumLabels.value - 1)
self._drawer.maxObjectsBox.setValue(self.topLevelOperatorView.NumLabels.value - 1)
self._drawer.TrackButton.setEnabled(True)
else:
self._drawer.maxObjectsBox.setMaximum(0)
self._drawer.maxObjectsBox.setValue(0)
self._drawer.TrackButton.setEnabled(False)
@staticmethod
def getAvailableTrackingSolverTypes():
solvers = []
try:
if dpct:
solvers.append('Flow-based')
except Exception as e:
logger.info(str(e))
try:
if mht:
solvers.append('ILP')
except Exception as e:
logger.info(str(e))
return solvers
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], self.mergerColors[i+1])
self._onMaxObjectsBoxChanged()
self._drawer.maxObjectsBox.valueChanged.connect(self._onMaxObjectsBoxChanged)
self._drawer.mergerResolutionBox.stateChanged.connect(self._onMaxObjectsBoxChanged)
self._drawer.exportButton.hide()
@threadRouted
def _onTimeoutBoxChanged(self, *args):
inString = str(self._drawer.timeoutBox.text())
if self._allowedTimeoutInputRegEx.match(inString) is None:
self._drawer.timeoutBox.setText(inString[:-1])
def _setRanges(self, *args):
super(ConservationTrackingGui, self)._setRanges()
maxx = self.topLevelOperatorView.LabelImage.meta.shape[1] - 1
maxy = self.topLevelOperatorView.LabelImage.meta.shape[2] - 1
maxz = self.topLevelOperatorView.LabelImage.meta.shape[3] - 1
maxBorder = min(maxx, maxy)
if maxz != 0:
maxBorder = min(maxBorder, maxz)
self._drawer.bordWidthBox.setRange(0, old_div(maxBorder,2))
def _onMaxObjectsBoxChanged(self):
self._setMergerLegend(self.mergerLabels, self._drawer.maxObjectsBox.value())
def _onTrackButtonPressed( self ):
if not self.mainOperator.ObjectFeatures.ready():
self._criticalMessage("You have to compute object features first.")
return
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
numStages = 8
# object features
# detection probabilities
# creating traxel store
# generating probabilities
# insert energies
# convexify costs
# solver
# compute lineages
if self._drawer.divisionsBox.isChecked():
# division probabilities
numStages +=1
if withMergerResolution:
numStages += 1 # merger resolution
withTracklets = self._drawer.trackletsBox.isChecked()
if withTracklets:
numStages += 3 # initializing tracklet graph, finding tracklets, contracting edges in tracklet graph
self.progressWindow = TrackProgressDialog(parent=self,numStages=numStages)
self.progressWindow.run()
self.progressWindow.show()
self.progressVisitor = GuiProgressVisitor(progressWindow=self.progressWindow)
def _track():
self.applet.busy = True
self.applet.appletStateUpdateRequested()
maxDist = self._drawer.maxDistBox.value()
maxObj = self._drawer.maxObjectsBox.value()
divThreshold = self._drawer.divThreshBox.value()
from_t = self._drawer.from_time.value()
to_t = self._drawer.to_time.value()
from_x = self._drawer.from_x.value()
to_x = self._drawer.to_x.value()
from_y = self._drawer.from_y.value()
to_y = self._drawer.to_y.value()
from_z = self._drawer.from_z.value()
to_z = self._drawer.to_z.value()
from_size = self._drawer.from_size.value()
to_size = self._drawer.to_size.value()
self.time_range = list(range(from_t, to_t + 1))
avgSize = [self._drawer.avgSizeBox.value()]
cplex_timeout = None
if len(str(self._drawer.timeoutBox.text())):
cplex_timeout = int(self._drawer.timeoutBox.text())
withTracklets = self._drawer.trackletsBox.isChecked()
sizeDependent = self._drawer.sizeDepBox.isChecked()
hardPrior = self._drawer.hardPriorBox.isChecked()
classifierPrior = self._drawer.classifierPriorBox.isChecked()
divWeight = self._drawer.divWeightBox.value()
transWeight = self._drawer.transWeightBox.value()
withDivisions = self._drawer.divisionsBox.isChecked()
withOpticalCorrection = self._drawer.opticalBox.isChecked()
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
borderAwareWidth = self._drawer.bordWidthBox.value()
withArmaCoordinates = True
appearanceCost = self._drawer.appearanceBox.value()
disappearanceCost = self._drawer.disappearanceBox.value()
motionModelWeight = self._drawer.motionModelWeightBox.value()
solver = self._drawer.solverComboBox.currentText()
ndim=3
if (to_z - from_z == 0):
ndim=2
try:
self.mainOperator.track(
time_range = self.time_range,
x_range = (from_x, to_x + 1),
y_range = (from_y, to_y + 1),
z_range = (from_z, to_z + 1),
size_range = (from_size, to_size + 1),
x_scale = self._drawer.x_scale.value(),
y_scale = self._drawer.y_scale.value(),
z_scale = self._drawer.z_scale.value(),
maxDist=maxDist,
maxObj = maxObj,
divThreshold=divThreshold,
avgSize=avgSize,
withTracklets=withTracklets,
sizeDependent=sizeDependent,
detWeight=10.0,
divWeight=divWeight,
transWeight=transWeight,
withDivisions=withDivisions,
withOpticalCorrection=withOpticalCorrection,
withClassifierPrior=classifierPrior,
ndim=ndim,
withMergerResolution=withMergerResolution,
borderAwareWidth =borderAwareWidth,
withArmaCoordinates =withArmaCoordinates,
cplex_timeout =cplex_timeout,
appearance_cost =appearanceCost,
disappearance_cost =disappearanceCost,
motionModelWeight=motionModelWeight,
force_build_hypotheses_graph =False,
max_nearest_neighbors=self._drawer.maxNearestNeighborsSpinBox.value(),
numFramesPerSplit=self._drawer.numFramesPerSplitSpinBox.value(),
solverName=solver,
progressWindow=self.progressWindow,
progressVisitor=self.progressVisitor
)
except Exception as ex:
self.progressWindow.onTrackDone()
log_exception(logger, "Error during tracking. See above error traceback.")
self._criticalMessage("Error during tracking. See error log.\n\n"
"Exception was:\n\n{})".format( ex ))
return
def _handle_finished(*args):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
self._drawer.TrackButton.setEnabled(True)
self._drawer.exportButton.setEnabled(True)
self._drawer.exportTifButton.setEnabled(True)
self._setLayerVisible("Objects", False)
# update showing the merger legend,
# as it might be (no longer) needed if merger resolving
# is disabled(enabled)
self._setMergerLegend(self.mergerLabels, self._drawer.maxObjectsBox.value())
def _handle_failure( exc, exc_info ):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
traceback.print_exception(*exc_info)
sys.stderr.write("Exception raised during tracking. See traceback above.\n")
self._drawer.TrackButton.setEnabled(True)
req = Request( _track )
req.notify_failed( _handle_failure )
req.notify_finished( _handle_finished )
req.submit()
def get_raw_shape(self):
return self.topLevelOperatorView.RawImage.meta.shape
def get_feature_names(self):
params = self.topLevelOperatorView.Parameters
if params.ready() and params.value["withDivisions"]:
return self.topLevelOperatorView.ComputedFeatureNamesWithDivFeatures([]).wait()
return self.topLevelOperatorView.ComputedFeatureNames([]).wait()
def get_color(self, pos5d):
slicing = tuple(slice(i, i+1) for i in pos5d)
color = self.mainOperator.CachedOutput(slicing).wait()
return color.flat[0]
def get_object(self, pos5d):
slicing = tuple(slice(i, i+1) for i in pos5d)
label = self.mainOperator.RelabeledImage(slicing).wait()
return label.flat[0], pos5d[0]
@property
def gui_applet(self):
return self.applet
def get_export_dialog_title(self):
return "Export Tracking Information"
def handleEditorRightClick(self, position5d, win_coord):
debug = ilastik_config.getboolean("ilastik", "debug")
obj, time = self.get_object(position5d)
if obj == 0:
menu = TitledMenu(["Background"])
if debug:
menu.addAction("Clear Hilite", IPCFacade().broadcast(Protocol.cmd("clear")))
menu.exec_(win_coord)
return
# Get color and track from hypotheses graph (which is a slot in the new operator)
hypothesesGraph = self.mainOperator.HypothesesGraph.value
if hypothesesGraph == None:
color = None
track = None
else:
color = hypothesesGraph.getLineageId(time, obj)
track = hypothesesGraph.getTrackId(time, obj)
tracks = None
children = None
parents = None
menu = TitledMenu([
"Object {} of lineage id {}".format(obj, color),
"Track id: " + (str(track) or "None"),
])
if not debug:
menu.exec_(win_coord)
return
if any(IPCFacade().sending):
obj_sub_menu = menu.addMenu("Hilite Object")
for mode in Protocol.ValidHiliteModes:
where = Protocol.simple("and", ilastik_id=obj, time=time)
cmd = Protocol.cmd(mode, where)
obj_sub_menu.addAction(mode.capitalize(), IPCFacade().broadcast(cmd))
sub_menus = [
("Tracks", Protocol.simple_in, tracks),
("Parents", Protocol.simple_in, parents),
("Children", Protocol.simple_in, children)
]
for name, protocol, args in sub_menus:
if args:
sub = menu.addMenu("Hilite {}".format(name))
for mode in Protocol.ValidHiliteModes[:-1]:
mode = mode.capitalize()
where = protocol("track_id*", args)
cmd = Protocol.cmd(mode, where)
sub.addAction(mode, IPCFacade().broadcast(cmd))
else:
sub = menu.addAction("Hilite {}".format(name))
sub.setEnabled(False)
menu.addAction("Clear Hilite", IPCFacade().broadcast(Protocol.cmd("clear")))
else:
menu.addAction("Open IPC Server Window", IPCFacade().show_info)
menu.addAction("Start IPC Server", IPCFacade().start)
menu.exec_(win_coord)
def _onTrackButtonPressed( self ):
if not self.mainOperator.ObjectFeatures.ready():
self._criticalMessage("You have to compute object features first.")
return
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
numStages = 8
# object features
# detection probabilities
# creating traxel store
# generating probabilities
# insert energies
# convexify costs
# solver
# compute lineages
if self._drawer.divisionsBox.isChecked():
# division probabilities
numStages +=1
if withMergerResolution:
numStages += 1 # merger resolution
withTracklets = self._drawer.trackletsBox.isChecked()
if withTracklets:
numStages += 3 # initializing tracklet graph, finding tracklets, contracting edges in tracklet graph
self.progressWindow = TrackProgressDialog(parent=self,numStages=numStages)
self.progressWindow.run()
self.progressWindow.show()
self.progressVisitor = GuiProgressVisitor(progressWindow=self.progressWindow)
def _track():
self.applet.busy = True
self.applet.appletStateUpdateRequested()
maxDist = self._drawer.maxDistBox.value()
maxObj = self._drawer.maxObjectsBox.value()
divThreshold = self._drawer.divThreshBox.value()
from_t = self._drawer.from_time.value()
to_t = self._drawer.to_time.value()
from_x = self._drawer.from_x.value()
to_x = self._drawer.to_x.value()
from_y = self._drawer.from_y.value()
to_y = self._drawer.to_y.value()
from_z = self._drawer.from_z.value()
to_z = self._drawer.to_z.value()
from_size = self._drawer.from_size.value()
to_size = self._drawer.to_size.value()
self.time_range = list(range(from_t, to_t + 1))
avgSize = [self._drawer.avgSizeBox.value()]
cplex_timeout = None
if len(str(self._drawer.timeoutBox.text())):
cplex_timeout = int(self._drawer.timeoutBox.text())
withTracklets = self._drawer.trackletsBox.isChecked()
sizeDependent = self._drawer.sizeDepBox.isChecked()
hardPrior = self._drawer.hardPriorBox.isChecked()
classifierPrior = self._drawer.classifierPriorBox.isChecked()
divWeight = self._drawer.divWeightBox.value()
transWeight = self._drawer.transWeightBox.value()
withDivisions = self._drawer.divisionsBox.isChecked()
withOpticalCorrection = self._drawer.opticalBox.isChecked()
withMergerResolution = self._drawer.mergerResolutionBox.isChecked()
borderAwareWidth = self._drawer.bordWidthBox.value()
withArmaCoordinates = True
appearanceCost = self._drawer.appearanceBox.value()
disappearanceCost = self._drawer.disappearanceBox.value()
motionModelWeight = self._drawer.motionModelWeightBox.value()
solver = self._drawer.solverComboBox.currentText()
ndim=3
if (to_z - from_z == 0):
ndim=2
try:
self.mainOperator.track(
time_range = self.time_range,
x_range = (from_x, to_x + 1),
y_range = (from_y, to_y + 1),
z_range = (from_z, to_z + 1),
size_range = (from_size, to_size + 1),
x_scale = self._drawer.x_scale.value(),
y_scale = self._drawer.y_scale.value(),
z_scale = self._drawer.z_scale.value(),
maxDist=maxDist,
maxObj = maxObj,
divThreshold=divThreshold,
avgSize=avgSize,
withTracklets=withTracklets,
sizeDependent=sizeDependent,
detWeight=10.0,
divWeight=divWeight,
transWeight=transWeight,
withDivisions=withDivisions,
withOpticalCorrection=withOpticalCorrection,
withClassifierPrior=classifierPrior,
ndim=ndim,
withMergerResolution=withMergerResolution,
borderAwareWidth =borderAwareWidth,
withArmaCoordinates =withArmaCoordinates,
cplex_timeout =cplex_timeout,
appearance_cost =appearanceCost,
disappearance_cost =disappearanceCost,
motionModelWeight=motionModelWeight,
force_build_hypotheses_graph =False,
max_nearest_neighbors=self._drawer.maxNearestNeighborsSpinBox.value(),
numFramesPerSplit=self._drawer.numFramesPerSplitSpinBox.value(),
solverName=solver,
progressWindow=self.progressWindow,
progressVisitor=self.progressVisitor
)
except Exception as ex:
self.progressWindow.onTrackDone()
log_exception(logger, "Error during tracking. See above error traceback.")
self._criticalMessage("Error during tracking. See error log.\n\n"
"Exception was:\n\n{})".format( ex ))
return
def _handle_finished(*args):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
self._drawer.TrackButton.setEnabled(True)
self._drawer.exportButton.setEnabled(True)
self._drawer.exportTifButton.setEnabled(True)
self._setLayerVisible("Objects", False)
# update showing the merger legend,
# as it might be (no longer) needed if merger resolving
# is disabled(enabled)
self._setMergerLegend(self.mergerLabels, self._drawer.maxObjectsBox.value())
def _handle_failure( exc, exc_info ):
self.applet.busy = False
self.applet.appletStateUpdateRequested()
traceback.print_exception(*exc_info)
sys.stderr.write("Exception raised during tracking. See traceback above.\n")
self._drawer.TrackButton.setEnabled(True)
req = Request( _track )
req.notify_failed( _handle_failure )
req.notify_finished( _handle_finished )
req.submit()
