def __init__(self, dbpath):
maxthread = 1
self.pool_sema = BoundedSemaphore(maxthread)
self.resample_sema = BoundedSemaphore(1)
self.dbpath = dbpath
# Status
self.StatusModifiedEvent = slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent
self.CLINode = slicer.vtkMRMLCommandLineModuleNode()
self.CLINode.SetStatus(self.CLINode.Idle)
# VTK Signals variables
self.Observations = []
def __init__(self):
# VTK Signals variables
self.Observations = []
self.StatusModifiedEvent = slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent
# Parameters dictionnaries
self.ChangeLabelParameters = {}
self.GenerateModelParameters = {}
self.DecimateParameters = {}
# Status
self.CLINode = slicer.vtkMRMLCommandLineModuleNode()
self.CLINode.SetStatus(self.CLINode.Idle)
def _testCLIStatusEventOnErrorTest(self, wait_for_completion):
self.delayDisplay('Testing status events for a bad execution of a CLI')
tempFile = qt.QTemporaryFile("CLIEventTest-outputFile-XXXXXX");
self.assertTrue(tempFile.open())
logic = CLIEventTestLogic()
parameters = {}
parameters["InputValue1"] = 1
parameters["InputValue2"] = 2
parameters["OperationType"] = 'Fail'
parameters["OutputFile"] = tempFile.fileName()
cliModule = slicer.modules.cli4test
cli = slicer.cli.createNode(cliModule)
self.assertEqual(cli.GetStatus(), cli.Idle)
logic.runCLI(cliModule, cli, parameters, wait_for_completion)
while not logic.ExecutionFinished:
self.delayDisplay('Waiting for module to complete...')
cli = slicer.vtkMRMLCommandLineModuleNode()
expectedEvents = []
if not wait_for_completion:
expectedEvents.append(cli.Scheduled)
expectedEvents.append(cli.CompletedWithErrors)
# Ignore cli.Running event (it may or may not be fired)
if cli.Running in logic.StatusEvents:
logic.StatusEvents.remove(cli.Running)
self.assertEqual(logic.StatusEvents, expectedEvents)
self.delayDisplay('Testing bad execution Passed')
def __init__(self):
VTKObservationMixin.__init__(self)
cli = slicer.vtkMRMLCommandLineModuleNode()
self.StatusModifiedEvent = cli.StatusModifiedEvent
self.StatusEvents = []
self.ExecutionFinished = False
self.StatusEventCallback = None
def runRegistration( self, run ):
if run:
cliNode = self.WorkflowStep.getCLINode(slicer.modules.expertautomatedregistration)
parameters = self.registerImageWorkflowParameters()
self.get('RegisterApplyPushButton').setChecked(True)
self.WorkflowStep.observeCLINode(cliNode, self.onRegistrationCLIModified)
cliNode = slicer.cli.run(slicer.modules.expertautomatedregistration, cliNode, parameters, wait_for_completion = False)
else:
cliNode = self.WorkflowStep.observer(
slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent,
self.onRegistrationCLIModified)
self.get('RegisterApplyPushButton').enabled = False
cliNode.Cancel()
def runVesselEnhancement( self, run ):
if run:
cliNode = self.getCLINode(slicer.modules.enhancetubesusingdiscriminantanalysis)
parameters = self.vesselEnhancementParameters()
self.get('VesselEnhancementApplyPushButton').setChecked(True)
self.observeCLINode(cliNode, self.onVesselEnhancementCLIModified)
cliNode = slicer.cli.run(slicer.modules.enhancetubesusingdiscriminantanalysis, cliNode, parameters, wait_for_completion = False)
else:
cliNode = self.observer(
slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent,
self.onVesselEnhancementCLIModified)
self.get('VesselEnhancementApplyPushButton').enabled = False
cliNode.Cancel()
def runMergeAll( self, run, currentMerge = 0 ):
if run:
# Add observer on the PDF segmenter CLI
cliNode = self.getCLINode(slicer.modules.imagelabelcombine)
parameters = self.imageLabelCombineParameters()
self.observeCLINode(cliNode, self.onImageLabelCombineModified)
self.get('MergeAllApplyButton').setChecked(True)
cliNode = slicer.cli.run(slicer.modules.imagelabelcombine, cliNode, parameters, wait_for_completion = False)
else:
cliNode = self.observer(
slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent,
self.onImageLabelCombineModified)
self.get('SegmentApplyPDFPushButton').enabled = False
cliNode.Cancel()
def runPDFSegmenter( self, run ):
if run:
# Add observer on the PDF segmenter CLI
pdfSegmenterCLINode = self.WorkflowStep.getCLINode(slicer.modules.segmentconnectedcomponentsusingparzenpdfs, 'PDFSegmenterEditorEffect')
self.observeCLINode(pdfSegmenterCLINode, self.onPDFSegmenterCLIModified)
self.get('SegmentApplyPDFPushButton').setChecked(True)
self.UndoRedo.saveState()
self.updatePDFSegmenterParameters()
self.PDFSegmenter.logic(None).applyPDFSegmenter()
else:
cliNode = self.observer(
slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent,
self.onPDFSegmenterCLIModified)
self.get('SegmentApplyPDFPushButton').enabled = False
cliNode.Cancel()
def runVesselEnhancement(self, run):
if run:
cliNode = self.getCLINode(
slicer.modules.enhancetubesusingdiscriminantanalysis)
parameters = self.vesselEnhancementParameters()
self.get('VesselEnhancementApplyPushButton').setChecked(True)
self.observeCLINode(cliNode, self.onVesselEnhancementCLIModified)
cliNode = slicer.cli.run(
slicer.modules.enhancetubesusingdiscriminantanalysis,
cliNode,
parameters,
wait_for_completion=False)
else:
cliNode = self.observer(
slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent,
self.onVesselEnhancementCLIModified)
self.get('VesselEnhancementApplyPushButton').enabled = False
cliNode.Cancel()
def runPDFSegmenter(self, run):
if run:
# Add observer on the PDF segmenter CLI
pdfSegmenterCLINode = self.WorkflowStep.getCLINode(
slicer.modules.segmentconnectedcomponentsusingparzenpdfs,
'PDFSegmenterEditorEffect')
self.observeCLINode(pdfSegmenterCLINode,
self.onPDFSegmenterCLIModified)
self.get('SegmentApplyPDFPushButton').setChecked(True)
self.UndoRedo.saveState()
self.updatePDFSegmenterParameters()
self.PDFSegmenter.logic(None).applyPDFSegmenter()
else:
cliNode = self.observer(
slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent,
self.onPDFSegmenterCLIModified)
self.get('SegmentApplyPDFPushButton').enabled = False
cliNode.Cancel()
def onApply(self, run):
if run:
self.get('ApplyPushButton').setChecked(True)
parameters = {}
parameters["InputVolume"] = self.get('VolumeNodeComboBox').currentNode()
parameters["OutputGeometry"] = self.get('OutputSkinModelNodeComboBox').currentNode()
parameters['BackgroundLabel'] = self.get('BackgroundLabelSpinBox').value
parameters['SkinLabel'] = self.get('SkinLabelsLineEdit').text
parameters['Decimate'] = self.get('DecimateOutputSkinLabelCheckBox').isChecked()
parameters['Spacing'] = self.get('SpacingLineEdit').text
for i in parameters.keys():
if parameters[i] == None:
print 'Skin model maker not ran: Parameters incorrect'
self.get('ApplyPushButton').setChecked(False)
return
self.Logic.addObserver(self.Logic.GetCLINode(), slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent, self.onLogicModified)
self.Logic.CreateSkinModel(parameters, False)
else:
self.get('ApplyPushButton').setChecked(True) # Keep checked until actually cancelled
self.get('ApplyPushButton').setEnabled(False)
self.Logic.Cancel()
def observeCLINode(self, cliNode, onCLINodeModified = None):
if cliNode != None and onCLINodeModified != None:
self.WorkflowStep.addObserver(cliNode,
slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent,
onCLINodeModified)
self.WorkflowStep.Workflow.getProgressBar().setCommandLineModuleNode(cliNode)
def __init__(self):
self.Observations = []
self.StatusModifiedEvent = slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent
self.parameters = {}
self.success = False
def __init__(self):
self.Observations = []
self.StatusModifiedEvent = slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent
self.parameters = {}
self.success = False
def observeCLINode(self, cliNode, onCLINodeModified=None):
"""Utility function to observe the given cli StatusModifiedEvent.
"""
if cliNode != None and onCLINodeModified != None:
self.addObserver(cliNode, slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent, onCLINodeModified)