def test_Part1Ruler(self,
enableScreenshotsFlag=0,
screenshotScaleFactor=1):
""" Test using rulers
"""
self.enableScreenshots = enableScreenshotsFlag
self.screenshotScaleFactor = screenshotScaleFactor
self.delayDisplay("Starting the test")
#
# first, get some data
#
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
tumor = sampleDataLogic.downloadMRBrainTumor1()
try:
# four up view
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
# annotations module
m = slicer.util.mainWindow()
m.moduleSelector().selectModule('Annotations')
# add ruler 1
rulerNode1 = slicer.vtkMRMLAnnotationRulerNode()
rulerNode1.SetName("d1")
rulerNode1.SetPosition1(-7.59519, 43.544, 28.6)
rulerNode1.SetPosition2(-5.56987, 14.177, 28.6)
rulerNode1.Initialize(slicer.mrmlScene)
self.delayDisplay("Ruler 1")
# add ruler 2
rulerNode2 = slicer.vtkMRMLAnnotationRulerNode()
rulerNode2.SetName("d2")
rulerNode2.SetPosition1(-3.54455, 27.656, 13.1646)
rulerNode2.SetPosition2(-2.5319, 27.656, 47.5949)
rulerNode2.Initialize(slicer.mrmlScene)
self.delayDisplay("Ruler 2")
# scroll
annotLogic = slicer.modules.annotations.logic()
annotLogic.JumpSlicesToAnnotationCoordinate(rulerNode1.GetID())
# show slices
redWidget = layoutManager.sliceWidget('Red')
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True)
self.takeScreenshot('Ruler',
'Ruler used to measure tumor diameter', -1)
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
def test_Part1Ruler(self,enableScreenshotsFlag=0,screenshotScaleFactor=1):
""" Test using rulers
"""
self.enableScreenshots = enableScreenshotsFlag
self.screenshotScaleFactor = screenshotScaleFactor
self.delayDisplay("Starting the test")
#
# first, get some data
#
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
tumor = sampleDataLogic.downloadMRBrainTumor1()
try:
# four up view
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
# annotations module
m = slicer.util.mainWindow()
m.moduleSelector().selectModule('Annotations')
# add ruler 1
rulerNode1 = slicer.vtkMRMLAnnotationRulerNode()
rulerNode1.SetName("d1")
rulerNode1.SetPosition1(-7.59519,43.544,28.6)
rulerNode1.SetPosition2(-5.56987,14.177,28.6)
rulerNode1.Initialize(slicer.mrmlScene)
self.delayDisplay("Ruler 1")
# add ruler 2
rulerNode2 = slicer.vtkMRMLAnnotationRulerNode()
rulerNode2.SetName("d2")
rulerNode2.SetPosition1(-3.54455,27.656,13.1646)
rulerNode2.SetPosition2(-2.5319,27.656,47.5949)
rulerNode2.Initialize(slicer.mrmlScene)
self.delayDisplay("Ruler 2")
# scroll
annotLogic = slicer.modules.annotations.logic()
annotLogic.JumpSlicesToAnnotationCoordinate(rulerNode1.GetID())
# show slices
redWidget = layoutManager.sliceWidget('Red')
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True);
self.takeScreenshot('Ruler','Ruler used to measure tumor diameter',-1)
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
def populateRulers(self, annotationHierarchy, verterbraeNames):
completeVerterbraeNames = []
for verterbraeName in verterbraeNames:
completeVerterbraeNames.append(verterbraeName + "-s")
completeVerterbraeNames.append(verterbraeName + "-i")
if annotationHierarchy != None:
rulerNodes = vtk.vtkCollection()
annotationHierarchy.GetDirectChildren(rulerNodes)
rulerNodeNames = []
for nodeIndex in range(rulerNodes.GetNumberOfItems()):
if rulerNodes.GetItemAsObject(nodeIndex).GetClassName(
) == "vtkMRMLAnnotationRulerNode":
rulerNodeNames.append(
rulerNodes.GetItemAsObject(nodeIndex).GetName())
addedRulerNodesList = []
addedVerterbrae = 200
for completeVerterbraeName in completeVerterbraeNames:
if completeVerterbraeName not in rulerNodeNames:
newRulerNode = slicer.vtkMRMLAnnotationRulerNode()
newRulerNode.SetName(completeVerterbraeName)
newRulerNode.SetPosition1(0, addedVerterbrae, 0)
newRulerNode.SetPosition2(-300, addedVerterbrae, 0)
newRulerNode.SetPointColour([0, 0, 1])
newRulerNode.Initialize(slicer.mrmlScene)
annotationHierarchy.SetAndObserveDisplayNodeID(
newRulerNode.GetDisplayNodeID())
addedVerterbrae -= 50
addedRulerNodesList.append(newRulerNode)
else:
addedVerterbrae = 200
for completeVerterbraeName in completeVerterbraeNames:
newRulerNode = slicer.vtkMRMLAnnotationRulerNode()
newRulerNode.SetName(completeVerterbraeName)
newRulerNode.SetPosition1(0, addedVerterbrae, 0)
newRulerNode.SetPosition2(-300, addedVerterbrae, 0)
newRulerNode.Initialize(slicer.mrmlScene)
annotationHierarchy.SetAndObserveDisplayNodeID(
newRulerNode.GetDisplayNodeID())
addedVerterbrae -= 50
return addedRulerNodesList
def test_LineIntensityProfile1(self):
""" Ideally you should have several levels of tests. At the lowest level
tests sould exercise the functionality of the logic with different inputs
(both valid and invalid). At higher levels your tests should emulate the
way the user would interact with your code and confirm that it still works
the way you intended.
One of the most important features of the tests is that it should alert other
developers when their changes will have an impact on the behavior of your
module. For example, if a developer removes a feature that you depend on,
your test should break so they know that the feature is needed.
"""
self.delayDisplay("Starting the test")
#
# first, get some data
#
import urllib
downloads = (
('http://slicer.kitware.com/midas3/download?items=5767', 'FA.nrrd', slicer.util.loadVolume),
)
for url,name,loader in downloads:
filePath = slicer.app.temporaryPath + '/' + name
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
print('Requesting download %s from %s...\n' % (name, url))
urllib.urlretrieve(url, filePath)
if loader:
print('Loading %s...\n' % (name,))
loader(filePath)
self.delayDisplay('Finished with download and loading\n')
volumeNode = slicer.util.getNode(pattern="FA")
logic = LineIntensityProfileLogic()
self.assertTrue( logic.hasImageData(volumeNode) )
# add ruler node
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
slicer.mrmlScene.AddNode(rulerNode)
rulerNode.SetPosition1(-65,110,60)
rulerNode.SetPosition2(-15,60,60)
rulerNode.SetName('Test')
# initialize selectors
moduleWidget = slicer.modules.LineIntensityProfileWidget
moduleWidget.rulerSelector.setCurrentNode(rulerNode)
moduleWidget.inputSelector.setCurrentNode(volumeNode)
self.delayDisplay('Inputs initialized!')
# run the test
moduleWidget.onApplyButton()
self.delayDisplay('If you see a ruler and a plot - test passed!')
def __init__(self, markupNode):
self.info={}
#put the first fiducial coordinates into startPtCoords
startPtCoords = [0.0, 0.0, 0.0]
markupNode.GetNthFiducialPosition(0,startPtCoords)
endPtCoords = [0.0, 0.0, 0.0]
#create rulers node in a ruler List the calculate the distances between fiducials
#in this way it's easy to manage the distance data in other future modules
for fidIndex in xrange(markupNode.GetNumberOfFiducials()):
ruler = slicer.mrmlScene.AddNode(slicer.vtkMRMLAnnotationRulerNode())
markupNode.GetNthFiducialPosition(fidIndex,endPtCoords)
ruler.SetPosition1(startPtCoords[0],startPtCoords[1],startPtCoords[2])
ruler.SetPosition2(endPtCoords[0],endPtCoords[1],endPtCoords[2])
def test_ReportingAIMRoundTrip(self):
print("CTEST_FULL_OUTPUT")
""" Load the data using DICOM module
"""
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import urllib
downloads = (
('http://slicer.kitware.com/midas3/download?items=10881', 'JANCT-CT.zip'),
)
self.delayDisplay("Downloading")
for url,name in downloads:
filePath = slicer.app.temporaryPath + '/' + name
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
self.delayDisplay('Requesting download %s from %s...\n' % (name, url))
urllib.urlretrieve(url, filePath)
self.delayDisplay('Finished with download\n')
reportingTempDir = slicer.app.temporaryPath+'/Reporting'
print('Temporary directory location: '+reportingTempDir)
qt.QDir().mkpath(reportingTempDir)
dicomFilesDirectory = reportingTempDir + '/dicomFiles'
self.cleanupDir(dicomFilesDirectory)
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
try:
self.delayDisplay("Switching to temp database directory")
tempDatabaseDirectory = reportingTempDir + '/tempDICOMDatbase'
qt.QDir().mkpath(tempDatabaseDirectory)
self.cleanupDir(tempDatabaseDirectory)
if slicer.dicomDatabase:
self.originalDatabaseDirectory = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
else:
self.originalDatabaseDirectory = None
settings = qt.QSettings()
settings.setValue('DatabaseDirectory', tempDatabaseDirectory)
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(tempDatabaseDirectory)
self.delayDisplay('Importing DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
#dicomWidget.dicomApp.suspendModel()
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory, None)
indexer.waitForImportFinished()
patient = slicer.dicomDatabase.patients()[0]
studies = slicer.dicomDatabase.studiesForPatient(patient)
series = [slicer.dicomDatabase.seriesForStudy(study) for study in studies]
seriesUIDs = [uid for uidList in series for uid in uidList]
dicomWidget.detailsPopup.offerLoadables(seriesUIDs, 'SeriesUIDList')
dicomWidget.detailsPopup.examineForLoading()
loadablesByPlugin = dicomWidget.detailsPopup.loadablesByPlugin
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
# initialize the module with the report and volume
volumes = slicer.util.getNodes('vtkMRMLScalarVolumeNode*')
self.assertTrue(len(volumes) == 1)
(name,volume) = volumes.items()[0]
self.delayDisplay('Loaded volume name %s' % volume.GetName())
self.delayDisplay('Configure Module')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('Reporting')
reporting = slicer.modules.reporting.widgetRepresentation().self()
report = slicer.mrmlScene.CreateNodeByClass('vtkMRMLReportingReportNode')
report.SetReferenceCount(report.GetReferenceCount()-1)
slicer.mrmlScene.AddNode(report)
report.SetFindingLabel(7)
reporting.reportSelector.setCurrentNode(report)
self.delayDisplay('Setting volume to %s' % volume.GetName())
reporting.volumeSelector.setCurrentNode(volume)
slicer.app.processEvents()
# place some markups and add a segmentation label
# add fiducial
fidNode = slicer.vtkMRMLAnnotationFiducialNode()
fidName = "AIM Round Trip Test Fiducial"
fidNode.SetName(fidName)
fidNode.SetSelected(1)
fidNode.SetDisplayVisibility(1)
fidNode.SetLocked(0)
# TODO: ask Nicole where this is assigned in the regular workflow
fidNode.SetAttribute('AssociatedNodeID',volume.GetID())
print("Calling set fid coords")
startCoords = [15.8, 70.8, -126.7]
fidNode.SetFiducialCoordinates(startCoords[0],startCoords[1],startCoords[2])
print("Starting fiducial coordinates: "+str(startCoords))
slicer.mrmlScene.AddNode(fidNode)
# add ruler
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
rulerNode.SetName('Test Ruler')
m = vtk.vtkMatrix4x4()
volume.GetIJKToRASMatrix(m)
ijk0 = [0,0,1,1]
ijk1 = [50,50,1,1]
ras0 = m.MultiplyPoint(ijk0)
ras1 = m.MultiplyPoint(ijk1)
rulerNode.SetPosition1(19.386751174926758, 68.528785705566406, -127.69000244140625)
rulerNode.SetPosition2(132.72709655761719, -34.349384307861328, -127.69000244140625)
rulerNode.SetAttribute('AssociatedNodeID',volume.GetID())
slicer.mrmlScene.AddNode(rulerNode)
slicer.app.processEvents()
# add label node
volumesLogic = slicer.modules.volumes.logic()
labelNode = volumesLogic.CreateAndAddLabelVolume(slicer.mrmlScene, volume, "Segmentation")
labelDisplayNode = labelNode.GetDisplayNode()
labelDisplayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
image = volume.GetImageData()
thresh = vtk.vtkImageThreshold()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
thresh.SetInput(image)
else:
thresh.SetInputData(image)
thresh.ThresholdBetween(10,400)
thresh.SetInValue(report.GetFindingLabel())
thresh.SetOutValue(0)
thresh.Update()
labelNode.SetAndObserveImageData(thresh.GetOutput())
reporting.segmentationSelector.setCurrentNode(labelNode)
# Save the report
exportDir = reportingTempDir+'/Output'
qt.QDir().mkpath(exportDir)
self.cleanupDir(exportDir)
report.SetStorageDirectoryName(exportDir)
reportingLogic = slicer.modules.reporting.logic()
print("Before saving report")
reportingLogic.SaveReportToAIM(report)
self.delayDisplay('Report saved')
slicer.mrmlScene.Clear(0)
# parse on patient level, find segmentation object, load and make sure
# it matches the input
# close the scene and load the report, check consistency
# try to load back the saved AIM
import glob
print glob.glob(exportDir+'/*')
xmlFiles = glob.glob(exportDir+'/*xml')
print xmlFiles
self.assertTrue(len(xmlFiles) == 1)
reporting.importAIMFile = xmlFiles[0]
reporting.onReportImport()
self.delayDisplay('Report loaded from AIM! Test passed.')
self.delayDisplay("Restoring original database directory")
if self.originalDatabaseDirectory:
dicomWidget.onDatabaseDirectoryChanged(self.originalDatabaseDirectory)
except Exception, e:
if self.originalDatabaseDirectory:
dicomWidget.onDatabaseDirectoryChanged(self.originalDatabaseDirectory)
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.assertTrue(False)
def onCompute(self): slicer.app.processEvents() self.logic = CalculateDistanceLogic(self.markupSelector.currentNode()) self.DistanceList = slicer.vtkMRMLAnnotationRulerNode()
def test_LineIntensityProfile1(self):
""" Ideally you should have several levels of tests. At the lowest level
tests sould exercise the functionality of the logic with different inputs
(both valid and invalid). At higher levels your tests should emulate the
way the user would interact with your code and confirm that it still works
the way you intended.
One of the most important features of the tests is that it should alert other
developers when their changes will have an impact on the behavior of your
module. For example, if a developer removes a feature that you depend on,
your test should break so they know that the feature is needed.
"""
self.delayDisplay("Starting the test")
#
# first, get some data
#
import urllib
downloads = (
('http://slicer.kitware.com/midas3/download?items=5767', 'FA.nrrd', slicer.util.loadVolume),
)
for url,name,loader in downloads:
filePath = slicer.app.temporaryPath + '/' + name
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
print('Requesting download %s from %s...\n' % (name, url))
urllib.urlretrieve(url, filePath)
if loader:
print('Loading %s...\n' % (name,))
loader(filePath)
self.delayDisplay('Finished with download and loading\n')
volumeNode = slicer.util.getNode(pattern="FA")
logic = LineIntensityProfileLogic()
self.assertTrue( logic.hasImageData(volumeNode) )
# initialize ruler node in a known location
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
slicer.mrmlScene.AddNode(rulerNode)
rulerNode.SetPosition1(-65,110,60)
rulerNode.SetPosition2(-15,60,60)
rulerNode.SetName('Test')
numOfPointsField = qt.QSpinBox()
numOfPointsField.value = 100
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
# initialize input selectors
moduleWidget = slicer.modules.LineIntensityProfileWidget
moduleWidget.rulerSelector.setCurrentNode(rulerNode)
moduleWidget.inputSelector1.setCurrentNode(volumeNode)
moduleWidget.inputSelector2.setCurrentNode(volumeNode)
self.delayDisplay('Inputs initialized!')
# run the logic with the initialized inputs
moduleWidget.onApplyButton()
self.delayDisplay('If you see a ruler and a plot - test passed!')
# here we check the sample is correct or not
GroundTruth = [0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0 \
,0.0499952547252 ,0.132161304355,0.157250195742,0.182541355491 ,0.224097684026,0.307691186666,0.421751081944,0.539702475071,0.566307783127,0.502181112766,0.466381758451 \
,0.454870164394 ,0.451874107122 ,0.45154094696,0.445982009172,0.434947699308,0.422306239605,0.413488268852,0.409934103489,0.414202958345,0.409307956696 \
,0.397122174501,0.397800117731,0.411369532347,0.429417848587,0.439514577389,0.423818171024,0.40110757947,0.386767745018,0.379366248846,0.370953738689,0.36441424489 \
,0.36140397191,0.367857933044,0.38929861784,0.418379157782,0.408268928528,0.379027366638,0.332919150591,0.297374159098,0.296240001917,0.311986237764,0.350458532572 \
,0.370930314064,0.357974469662,0.326200008392,0.316009640694,0.312490910292,0.32052642107,0.316521972418,0.279196560383,0.244257837534,0.238702788949,0.255041092634 \
,0.280225723982,0.320494830608,0.28876376152,0.277780592442,0.253679126501,0.247220918536,0.244660764933]
logic.run(volumeNode, volumeNode, rulerNode, numOfPointsField, chartNode)
sample = logic.getImageSamples()[0]
isTestValid = True
for i in range(numOfPointsField.value):
if abs(sample.GetTuple1(i)-float(GroundTruth[i])) > 0.000001:
isTestValid = False
if isTestValid:
self.delayDisplay('Sample point test passed!')
else:
self.delayDisplay('Sample point test failed!')
def test_ReportingAIMRoundTrip(self):
print ("CTEST_FULL_OUTPUT")
""" Load the data using DICOM module
"""
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import urllib
downloads = (("http://slicer.kitware.com/midas3/download?items=10881", "JANCT-CT.zip"),)
self.delayDisplay("Downloading")
for url, name in downloads:
filePath = slicer.app.temporaryPath + "/" + name
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
self.delayDisplay("Requesting download %s from %s...\n" % (name, url))
urllib.urlretrieve(url, filePath)
self.delayDisplay("Finished with download\n")
reportingTempDir = slicer.app.temporaryPath + "/Reporting"
print ("Temporary directory location: " + reportingTempDir)
qt.QDir().mkpath(reportingTempDir)
dicomFilesDirectory = reportingTempDir + "/dicomFiles"
self.cleanupDir(dicomFilesDirectory)
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
try:
self.delayDisplay("Switching to temp database directory")
tempDatabaseDirectory = reportingTempDir + "/tempDICOMDatbase"
qt.QDir().mkpath(tempDatabaseDirectory)
self.cleanupDir(tempDatabaseDirectory)
if slicer.dicomDatabase:
self.originalDatabaseDirectory = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
else:
self.originalDatabaseDirectory = None
settings = qt.QSettings()
settings.setValue("DatabaseDirectory", tempDatabaseDirectory)
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(tempDatabaseDirectory)
self.delayDisplay("Importing DICOM")
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule("DICOM")
# dicomWidget.dicomApp.suspendModel()
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory, None)
indexer.waitForImportFinished()
patient = slicer.dicomDatabase.patients()[0]
studies = slicer.dicomDatabase.studiesForPatient(patient)
series = [slicer.dicomDatabase.seriesForStudy(study) for study in studies]
seriesUIDs = [uid for uidList in series for uid in uidList]
dicomWidget.detailsPopup.offerLoadables(seriesUIDs, "SeriesUIDList")
dicomWidget.detailsPopup.examineForLoading()
loadablesByPlugin = dicomWidget.detailsPopup.loadablesByPlugin
self.delayDisplay("Loading Selection")
dicomWidget.detailsPopup.loadCheckedLoadables()
# initialize the module with the report and volume
volumes = slicer.util.getNodes("vtkMRMLScalarVolumeNode*")
self.assertTrue(len(volumes) == 1)
(name, volume) = volumes.items()[0]
self.delayDisplay("Loaded volume name %s" % volume.GetName())
self.delayDisplay("Configure Module")
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule("Reporting")
reporting = slicer.modules.reporting.widgetRepresentation().self()
report = slicer.mrmlScene.CreateNodeByClass("vtkMRMLReportingReportNode")
report.SetReferenceCount(report.GetReferenceCount() - 1)
slicer.mrmlScene.AddNode(report)
report.SetFindingLabel(7)
reporting.reportSelector.setCurrentNode(report)
self.delayDisplay("Setting volume to %s" % volume.GetName())
reporting.volumeSelector.setCurrentNode(volume)
slicer.app.processEvents()
# place some markups and add a segmentation label
# add fiducial
fidNode = slicer.vtkMRMLAnnotationFiducialNode()
fidName = "AIM Round Trip Test Fiducial"
fidNode.SetName(fidName)
fidNode.SetSelected(1)
fidNode.SetDisplayVisibility(1)
fidNode.SetLocked(0)
# TODO: ask Nicole where this is assigned in the regular workflow
fidNode.SetAttribute("AssociatedNodeID", volume.GetID())
print ("Calling set fid coords")
startCoords = [15.8, 70.8, -126.7]
fidNode.SetFiducialCoordinates(startCoords[0], startCoords[1], startCoords[2])
print ("Starting fiducial coordinates: " + str(startCoords))
slicer.mrmlScene.AddNode(fidNode)
# add ruler
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
rulerNode.SetName("Test Ruler")
m = vtk.vtkMatrix4x4()
volume.GetIJKToRASMatrix(m)
ijk0 = [0, 0, 1, 1]
ijk1 = [50, 50, 1, 1]
ras0 = m.MultiplyPoint(ijk0)
ras1 = m.MultiplyPoint(ijk1)
rulerNode.SetPosition1(19.386751174926758, 68.528785705566406, -127.69000244140625)
rulerNode.SetPosition2(132.72709655761719, -34.349384307861328, -127.69000244140625)
rulerNode.SetAttribute("AssociatedNodeID", volume.GetID())
slicer.mrmlScene.AddNode(rulerNode)
slicer.app.processEvents()
# add label node
volumesLogic = slicer.modules.volumes.logic()
labelNode = volumesLogic.CreateAndAddLabelVolume(slicer.mrmlScene, volume, "Segmentation")
labelDisplayNode = labelNode.GetDisplayNode()
labelDisplayNode.SetAndObserveColorNodeID("vtkMRMLColorTableNodeFileGenericAnatomyColors.txt")
image = volume.GetImageData()
thresh = vtk.vtkImageThreshold()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
thresh.SetInput(image)
else:
thresh.SetInputData(image)
thresh.ThresholdBetween(10, 400)
thresh.SetInValue(report.GetFindingLabel())
thresh.SetOutValue(0)
thresh.Update()
labelNode.SetAndObserveImageData(thresh.GetOutput())
reporting.segmentationSelector.setCurrentNode(labelNode)
# Save the report
exportDir = reportingTempDir + "/Output"
qt.QDir().mkpath(exportDir)
self.cleanupDir(exportDir)
report.SetStorageDirectoryName(exportDir)
reportingLogic = slicer.modules.reporting.logic()
print ("Before saving report")
reportingLogic.SaveReportToAIM(report)
self.delayDisplay("Report saved")
slicer.mrmlScene.Clear(0)
# parse on patient level, find segmentation object, load and make sure
# it matches the input
# close the scene and load the report, check consistency
# try to load back the saved AIM
import glob
print glob.glob(exportDir + "/*")
xmlFiles = glob.glob(exportDir + "/*xml")
print xmlFiles
self.assertTrue(len(xmlFiles) == 1)
reporting.importAIMFile = xmlFiles[0]
reporting.onReportImport()
self.delayDisplay("Report loaded from AIM! Test passed.")
self.delayDisplay("Restoring original database directory")
if self.originalDatabaseDirectory:
dicomWidget.onDatabaseDirectoryChanged(self.originalDatabaseDirectory)
except Exception, e:
if self.originalDatabaseDirectory:
dicomWidget.onDatabaseDirectoryChanged(self.originalDatabaseDirectory)
import traceback
traceback.print_exc()
self.delayDisplay("Test caused exception!\n" + str(e))
self.assertTrue(False)
def runCaliper(self):
inputVolume = self.inputSelector.currentNode()
if not (inputVolume):
qt.QMessageBox.critical(
slicer.util.mainWindow(),
'Deploy Caliper', 'Input volume is required for calculation.')
return
# If coordinates modified, use for calculation
if self.coordinatesWidgetModified:
widgetPointsList = slicer.vtkMRMLMarkupsFiducialNode()
widgetPointsList.SetName('WPL')
# widgetNode = slicer.util.getNode('WPL')
slicer.mrmlScene.AddNode(widgetPointsList)
# Grab first widget coordinate and display
print "PointNum1 is: "
pointNum1Str = (str(self.c1Select.coordinates)).split(",")
pointNum1 = [float(i) for i in pointNum1Str]
print pointNum1
widgetPointsList.AddFiducial(pointNum1[0], pointNum1[1], pointNum1[2], 'WP-1')
# Grab second widget coordinate and display
print "PointNum2 is: "
pointNum2Str = (str(self.c2Select.coordinates)).split(",")
pointNum2 = [float(i) for i in pointNum2Str]
print pointNum2
widgetPointsList.AddFiducial(pointNum2[0], pointNum2[1], pointNum2[2], 'WP-2')
# Center the slices on Point 1
slicer.modules.markups.logic().JumpSlicesToLocation(pointNum1[0], pointNum1[1], pointNum1[2], True)
# Calculate distance in mm and print to console
distanceValue = math.sqrt( math.pow((pointNum1[0] - pointNum2[0]), 2) + math.pow((pointNum1[1] - pointNum2[1]), 2) + math.pow((pointNum1[2] - pointNum2[2]), 2))
self.distUpdate.setText("Distance: %.2f mm" % distanceValue)
# Add a ruler
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
rulerNode.SetDistanceAnnotationVisibility(1)
rulerNode.SetPosition1(pointNum1[0], pointNum1[1], pointNum1[2])
rulerNode.SetPosition2(pointNum2[0], pointNum2[1], pointNum2[2])
rulerNode.SetName('Distance 1')
rulerNode.SetDistanceAnnotationVisibility(False)
rulerNode.Initialize(slicer.mrmlScene)
self.coordinatesWidgetModified = False
else:
# Get interactive coordinates, if any
intNode1 = slicer.util.getNode('IP1')
intNode2 = slicer.util.getNode('IP2')
if ((intNode1.GetNumberOfFiducials() == 1) and (intNode2.GetNumberOfFiducials() == 1)):
z3point1 = [0.0, 0.0, 0.0]
z3point2 = [0.0, 0.0, 0.0]
intNode1.GetNthFiducialPosition(0, z3point1)
intNode2.GetNthFiducialPosition(0, z3point2)
print "Interactive Point 1:"
print z3point1
print "Interactive Point 2:"
print z3point2
interactiveDistance = math.sqrt( math.pow((z3point1[0] - z3point2[0]), 2) + math.pow((z3point1[1] - z3point2[1]), 2) + math.pow((z3point1[2] - z3point2[2]), 2))
self.intDistUpdate.setText("Distance: %.2f mm" % interactiveDistance)
intRulerNode = slicer.vtkMRMLAnnotationRulerNode()
intRulerNode.SetDistanceAnnotationVisibility(1)
intRulerNode.SetPosition1(z3point1[0], z3point1[1], z3point1[2])
intRulerNode.SetPosition2(z3point2[0], z3point2[1], z3point2[2])
intRulerNode.SetName('Distance 2')
intRulerNode.SetDistanceAnnotationVisibility(False)
intRulerNode.Initialize(slicer.mrmlScene)
# Blur if checkbox is checked
if self.blur.isChecked():
gauss = vtk.vtkImageGaussianSmooth()
gauss.SetInputData(inputVolume.GetImageData())
gauss.SetDimensionality(3)
fwhmValue = .01 * distanceValue
gauss.SetStandardDeviation(fwhmValue)
gauss.Update()
ijkToRAS = vtk.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(ijkToRAS)
inputVolume.SetAndObserveImageData(gauss.GetOutput())
