def test_CLIStatusEventTestCancel(self):
self.delayDisplay(
'Testing status events when cancelling the 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"] = 'Addition'
parameters["OutputFile"] = tempFile.fileName()
cliModule = slicer.modules.cli4test
cli = slicer.cli.createNode(cliModule)
self.assertEqual(cli.GetStatus(), cli.Idle)
logic.runCLI(cliModule, cli, parameters, False)
cli.Cancel()
while not logic.ExecutionFinished:
self.delayDisplay('Waiting for module to complete...')
expectedEvents = [
cli.Scheduled,
cli.Cancelling,
cli.Cancelled,
]
self.assertEqual(logic.StatusEvents, expectedEvents)
self.delayDisplay('Testing cancelled execution Passed')
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)
self.assertEqual(logic.StatusEvents, expectedEvents)
self.delayDisplay('Testing bad execution Passed')
def test_TwoCLIsInARowTest(self):
self.delayDisplay('Running two CLIs in a row Test')
tempFile = qt.QTemporaryFile("TwoCLIsInARowTest-outputFile-XXXXXX")
self.assertTrue(tempFile.open())
logic = TwoCLIsInARowTestLogic()
logic.parameters = {}
logic.parameters["InputValue1"] = 1
logic.parameters["InputValue2"] = 2
logic.parameters["OperationType"] = 'Addition'
logic.parameters["OutputFile"] = tempFile.fileName()
logic.runTest()
while not logic.success:
self.delayDisplay('Waiting for module 2 to complete...')
self.assertTrue(logic.success)
self.delayDisplay('Two CLIs in a row test passed !')
def test_TwoCLIsInParallelTest(self):
self.delayDisplay('Running two CLIs in a row Test')
tempFile = qt.QTemporaryFile("TwoCLIsInParallelTest-outputFile-XXXXXX")
self.assertTrue(tempFile.open())
logic = TwoCLIsInParallelTestLogic()
logic.parameters = {}
logic.parameters["InputValue1"] = 1
logic.parameters["InputValue2"] = 2
logic.parameters["OperationType"] = 'Addition'
logic.parameters["OutputFile"] = tempFile.fileName()
logic.runModule1()
self.delayDisplay('... Waiting to start module 2 ...')
logic.runModule2()
self.assertTrue(logic.success)
self.delayDisplay('Two CLIs in parallel test passed !')
def run(self,inputVolume,atlasVolume, convexHullVolume, numIterations, boneThreshold, outVolume):
"""
Run the actual algorithm
"""
print('In Run method')
"""
Generate Atlas convex Hull
"""
#convexHullVolume = "~/TestConvexHull.vtk"
#cliparameters = {
#"leftAtlasFileName" : leftAtlasVolume.GetID(),
#"rightAtlasFileName" : rightAtlasVolume.GetID(),
#"downsampleFactor" : 4,
#"outputFileName" : outModel.GetID(), #"~/TestConvexHull.vtk", *** should be a vtk file
#}
#GenerateAtlasConvexHull = slicer.modules.generateatlasconvexhull
#slicer.cli.run(GenerateAtlasConvexHull,None, cliparameters, wait_for_completion=True)
#C:\ChestImagingPlatformPrivate\Build\bin\Debug>RegisterLungAtlas -i 200 -m D:/Po
# stdoc/Data/LungAtlases/atlasConvexHull.vtk -c D:/Postdoc/Data/10360K/10360Kinsp
# .nhdr -o d:/Postdoc/Data/10360K/AtlasTo10360Kinsp.tfm
#"""
#Call RegisterLungAtlas cli, tfm intermediate file ?
#"""
#Define temporary .tfm file
f = qt.QTemporaryFile( slicer.app.temporaryPath+ "/RegisterLungAtlas-XXXXXX.tfm") #slicer.app.temporaryPath
f.open() # Create the file
# Get model node by ID
modelNode = slicer.mrmlScene.GetNodeByID(convexHullVolume.GetID())
polyData = modelNode.GetPolyData()
cliparameters = {}
cliparameters['convexHullMeshFileName'] = convexHullVolume.GetID() #modelNode.GetID() #""/Users/rolaharmouche/Documents/Data/LungAtlases/atlasConvexHull.vtk" #
cliparameters['numberOfIterations'] = numIterations.value
cliparameters['boneThreshold'] = boneThreshold.value
cliparameters['outputTransformFileName'] = f.fileName()#"/Users/rolaharmouche/Documents/Data/tempdata/Test6.tfm" #outputTransform, slicer.app.temporarypath
cliparameters['ctFileName'] = inputVolume.GetID()
#cliparameters['ctFileName'] = "/Users/rolaharmouche/Documents/Data/COPDGene/14988Y/14988Y_INSP_STD_UAB_COPD/14988Y_INSP_STD_UAB_COPD_downsampled.nrrd"
#destructor delete stuff
RegisterLungAtlas = slicer.modules.registerlungatlas
cliNode = slicer.cli.run(RegisterLungAtlas,None, cliparameters, wait_for_completion=True)
#"""
#Call ResampleLabelMap cli, save the output volume directly
#"""
##ResampleLabelMap.exe -d D:/Postdoc/Data/10360K/10360Kinsp.nhdr -r D:/Postdoc/Data/10360K/10360KleftAtlas.nrrd -t
##D:/Postdoc/Data/10360K/AtlasTo10360Kinsp.tfm -l D:/Postdoc/Data/LungAtlases/leftLungAtlas.nhdr
#
cliparameters = {}
cliparameters['labelMapFileName'] = atlasVolume.GetID() # "/Users/rolaharmouche/Documents/Data/LungAtlases/leftLungAtlas.nhdr"
cliparameters['transformFileName'] = f.fileName()#"/Users/rolaharmouche/Documents/Data/tempdata/Test6.tfm"
cliparameters['resampledFileName'] = outVolume.GetID() #"~/Test.nrrd" #
cliparameters['destinationFileName'] = inputVolume.GetID() #"/Users/rolaharmouche/Documents/Data/COPDGene/14988Y/14988Y_INSP_STD_UAB_COPD/14988Y_INSP_STD_UAB_COPD_downsampled.nrrd"
cliparameters['isInvertTransformation'] =True
ResampleLabelMap = slicer.modules.resamplelabelmap
cliNode = slicer.cli.run(ResampleLabelMap,None, cliparameters, wait_for_completion=True), #use qt assistant
return True
