def onReportImport(self):
print('onReportImport here!!!')
# TODO
# -- popup file open dialog to choose the .xml AIM file
# -- warn the user if the selected report node is not empty
# -- populate the selected report node, initializing annotation template,
# content, markup hierarchy and content
if not self.__importAIMFile:
Helper.Debug('onReportImport: import file name not specified')
return
Helper.Debug('onReportImport')
# For now, always create a new report node
newReport = slicer.modulemrml.vtkMRMLReportingReportNode()
# always use the default color map
newReport.SetColorNodeID(self.__defaultColorNode.GetID())
slicer.mrmlScene.AddNode(newReport)
self.__reportSelector.setCurrentNode(newReport)
self.onReportNodeChanged()
# initialize the report hierarchy
# -- assume that report node has been created and is in the selector
Helper.LoadAIMFile(newReport.GetID(), self.__importAIMFile)
# update the GUI
Helper.Debug('onReportImport --> calling onReportNodeChanged()')
self.onReportNodeChanged()
def test_RoundTrip(self):
"""
Test fiducial round trip to and from AIM XML file on disk
"""
print("ctest, please don't truncate my output: CTEST_FULL_OUTPUT")
# enter the module
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('Reporting')
# l = slicer.modulelogic.vtkSlicerReportingModuleLogic()
l = slicer.modules.reporting.logic()
l.GUIHiddenOff()
# testDataPath = os.path.normpath(os.path.join(os.path.realpath(__file__), "..", "..", "Prototype/TestData/DICOM.CT/")
print("Reporting round trip test, current working directory = " +
os.getcwd())
testDataPath = os.path.join(os.getcwd(),
"../../Testing/Temporary/DICOM.CT")
# testDataPath = "/projects/birn/nicole/Slicer4/Reporting/Prototype/TestData/DICOM.CT"
print("test data path = " + testDataPath)
# set up a new DICOM database
print("Creating a dicomDatabase!")
ddb = ctk.ctkDICOMDatabase()
if not ddb:
print("ERROR: failed to create a new dicom database!")
return
dbpath = slicer.app.slicerHome + '/Testing/Temporary/TestingDCMDB/ctkDICOM.sql'
print('database path set to ' + dbpath)
if not os.path.exists(os.path.dirname(dbpath)):
print('Creating dir ' + os.path.dirname(dbpath))
os.makedirs(os.path.dirname(dbpath))
ddb.openDatabase(dbpath, "ReportingTesting")
if not ddb.isOpen:
print("ERROR: failed to open a new dicom database at path " +
dbpath)
return
retval = ddb.initializeDatabase()
if not retval:
print("ERROR: failed to init database")
return
l.InitializeDICOMDatabase(dbpath)
testFileNames = []
for n in [487, 488, 489]:
filename = os.path.join(testDataPath,
"instance_" + str(n) + ".dcm")
print("Adding file " + filename)
testFileNames.append(filename)
# check to see if the test data is already in it
patients = ddb.patients()
if len(patients) == 0:
# add the files
for filename in testFileNames:
print("Inserting file " + filename)
retval = ddb.insert(filename)
patients = ddb.patients()
if len(patients) == 0:
print("ERROR: unable to add test files to database!")
print(str(testFileNames))
return
# get the UID for the series
study = ddb.studiesForPatient(patients[0])
series = ddb.seriesForStudy(study[0])
seriesUID = series[0]
# seriesUID = "1.2.392.200103.20080913.113635.2.2009.6.22.21.43.10.23432.1"
# seriesUID = "2.16.840.1.114362.1.759508.1251415878280.192"
# seriesUID = "1.3.12.2.1107.5.1.4.53031.30000011032906120157800000219"
print("For test, using the AIM sample volume with series UID of " +
seriesUID)
fileList = ddb.filesForSeries(seriesUID)
print("fileList = " + str(fileList))
if not fileList:
print("ERROR: sample series with id " + seriesUID +
" not found in database!")
return
# add a parameter node
parameterNode = slicer.vtkMRMLScriptedModuleNode()
parameterNode.SetModuleName('Reporting')
slicer.mrmlScene.AddNode(parameterNode)
# set it to be the active parameter node
l.SetActiveParameterNodeID(parameterNode.GetID())
#
# create a new report, make it the report in the parameter node, set up hierarchy
#
reportNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLReportingReportNode")
reportNode.SetReferenceCount(reportNode.GetReferenceCount() - 1)
# set the color id
colorID = 'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt'
reportNode.SetColorNodeID(colorID)
reportNode.SetDICOMDatabaseFileName(dbpath)
slicer.mrmlScene.AddNode(reportNode)
parameterNode.SetParameter("reportID", reportNode.GetID())
print(
"Init hierarchy for report node, set parameter node to report id of "
+ reportNode.GetID())
l.InitializeHierarchyForReport(reportNode)
#
# get some sample data from the database
#
volId = 1
volumeNode = None
volName = 'AIM volume ' + str(volId)
print("Dicom data base = " + ddb)
slicer.dicomDatabase = ddb
scalarVolumePlugin = slicer.modules.dicomPlugins[
'DICOMScalarVolumePlugin']()
scalarVolumeLoadables = scalarVolumePlugin.examine([filelist])
volumeNode = scalarVolumePlugin.load(scalarVolumeLoadables[0])
volumeNode.SetName(volName)
# print "volumeNode = ",volumeNode
print("Initialize Hierarchy For Volume with id " + volumeNode.GetID())
l.InitializeHierarchyForVolume(volumeNode)
print("---Now active mark up is " + l.GetActiveMarkupHierarchyID())
print("adding a fiducial")
#
# define a fiducial
#
fidNode = slicer.vtkMRMLAnnotationFiducialNode()
fidName = "AIM Round Trip Test Fiducial"
fidNode.SetName(fidName)
fidNode.SetSelected(1)
fidNode.SetVisible(1)
fidNode.SetLocked(0)
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))
# point it to the volume
fidNode.SetAttribute("AssociatedNodeID", volumeNode.GetID())
fidNode.SetScene(slicer.mrmlScene)
print("Adding text disp node")
fidNode.CreateAnnotationTextDisplayNode()
print("Adding point display node")
fidNode.CreateAnnotationPointDisplayNode()
print("add node:")
# slicer.mrmlScene.DebugOn()
# l.DebugOn()
slicer.mrmlScene.AddNode(fidNode)
print("getting slice uid")
uid = l.GetSliceUIDFromMarkUp(fidNode)
print("fidNode uid = " + uid)
#
# create a label volume
#
volumesLogic = slicer.modules.volumes.logic()
labelNode = volumesLogic.CreateLabelVolume(slicer.mrmlScene,
volumeNode, "Segmentation")
labelDisplayNode = labelNode.GetDisplayNode()
labelDisplayNode.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
l.AddNodeToReport(labelNode)
# initialize image content
labelImage = labelNode.GetImageData()
extent = labelImage.GetExtent()
pixelCounter = 0
for k in range(extent[5]):
for j in range(extent[3]):
for i in range(extent[1]):
if pixelCounter in initializedSegmentationVoxels:
labelImage.SetScalarComponentFromFloat(i, j, k, 0, 1)
else:
labelImage.SetScalarComponentFromFloat(i, j, k, 0, 0)
pixelCounter = pixelCounter + 1
# test save to mrml
# slicer.mrmlScene.SetURL('/spl/tmp/nicole/Testing/aim/RoundTripTest.mrml')
# slicer.mrmlScene.Commit()
#
# output AIM XML
#
dirName = slicer.app.slicerHome + '/Testing/Temporary/'
reportNode.SetStorageDirectoryName(dirName)
print("Saving report to " + dirName)
retval = l.SaveReportToAIM(reportNode)
if (retval != 0):
print("ERROR: unable to save report to aim file " + dirName +
", retval=" + retval)
else:
print("Saved report to " + dirName)
self.assertEqual(retval, 0)
print("\n\n\nReloading aim file...")
#
# now clear the scene so can read in
#
# TBD: this causes a crash
# slicer.mrmlScene.Clear(0)
#
# load in the aim file
#
newReport = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLReportingReportNode")
newReport.SetReferenceCount(newReport.GetReferenceCount() - 1)
# set the default color map
newReport.SetColorNodeID(colorID)
newReport.SetDICOMDatabaseFileName(dbpath)
slicer.mrmlScene.AddNode(newReport)
parameterNode.SetParameter("reportID", newReport.GetID())
Helper.LoadAIMFile(newReport.GetID(), aimFileName)
# check the fiducial
endCoords = [0, 0, 0]
col = slicer.mrmlScene.GetNodesByClass("vtkMRMLAnnotationFiducialNode")
col.SetReferenceCount(col.GetReferenceCount() - 1)
# if the scene is not cleared, we should have 2 fiducials
nFiducials = col.GetNumberOfItems()
if nFiducials != 2:
print("Failed to read fiducial form the saved report!")
self.assertTrue(False)
f = col.GetItemAsObject(1)
f.GetFiducialCoordinates(endCoords)
print("Start Coords = " + str(startCoords[0]) + "," +
str(startCoords[1]) + "," + str(startCoords[2]))
print("End Coords = " + str(endCoords))
xdiff = endCoords[0] - startCoords[0]
ydiff = endCoords[1] - startCoords[1]
zdiff = endCoords[2] - startCoords[2]
diffTotal = xdiff + ydiff + zdiff
print(
"Difference between coordinates after loaded the aim file and value from before stored the aim file: "
+ str(xdiff) + "," + str(ydiff) + "," + str(zdiff) +
". Total difference = " + str(diffTotal))
if diffTotal > 0.1:
print("Fiducial coordinates error exceeds the allowed bounds")
self.assertTrue(False)
# check the label node
sceneVolumes = slicer.mrmlScene.GetNodesByClass(
"vtkMRMLScalarVolumeNode")
sceneVolumes.SetReferenceCount(sceneVolumes.GetReferenceCount() - 1)
sceneLabels = []
for i in range(sceneVolumes.GetNumberOfItems()):
vol = sceneVolumes.GetItemAsObject(i)
if vol.GetLabelMap():
sceneLabels.append(vol)
if len(sceneLabels) != 2:
print(
"Scene does not have two label nodes after reloading from AIM!"
)
self.assertTrue(False)
newLabelNode = sceneLabels[1]
newLabelImage = newLabelNode.GetImageData()
extent = newLabelImage.GetExtent()
pixelCounter = 0
for k in range(extent[5]):
for j in range(extent[3]):
for i in range(extent[1]):
pixel = newLabelImage.GetScalarComponentAsFloat(i, j, k, 0)
if ((pixelCounter in initializedSegmentationVoxels)
and pixel != 1) or (not (
pixelCounter in initializedSegmentationVoxels)
and pixel != 0):
print("Segmentation content not recovered correctly!")
print("Pixel counter " + str(pixelCounter) +
" is set to " + str(pixel))
self.assertTrue(False)
pixelCounter = pixelCounter + 1
self.assertTrue(True)
