def captureSpatialsPositions(self,fidName ):
saml = slicer.modules.annotations.logic()
listNode = slicer.util.getNode("Tracker Points List")
saml.SetActiveHierarchyNodeID(listNode.GetID())
StylusTipToReferenceNode = slicer.util.getNode("StylusTipToProbe")
validTransformation = self.isValidTransformation("StylusTipToProbe")
if validTransformation == True:
#cfl = slicer.modules.collectfiducials.logic()
#cfl.SetProbeTransformNode(StylusTipToReferenceNode)
#cfl.AddFiducial()
transformation = StylusTipToReferenceNode.GetMatrixTransformToParent()
fidPos=[transformation.GetElement(0,3),transformation.GetElement(1,3),transformation.GetElement(2,3)]
trackerNode=slicer.vtkMRMLAnnotationFiducialNode()
trackerNode.SetFiducialWorldCoordinates(fidPos)
trackerNode.SetName(fidName + '-Tracker')
self.setActiveAnnotationsList("Tracker Points List")
slicer.mrmlScene.AddNode(trackerNode)
self.setActiveAnnotationsList("Fiducials List")
fidPos=[0,0,0]
fidNode=slicer.vtkMRMLAnnotationFiducialNode()
fidNode.SetFiducialWorldCoordinates(fidPos)
fidNode.SetName(fidName + '-Tracker')
self.takeUSSnapshot2(fidName + '-Snapshot')
snapshotNode=slicer.util.getNode(fidName + '-Snapshot')
snapshotNode.SetDisplayVisibility(False)
print("Tracker position recorded")
else:
print("Tracker position is invalid")
return validTransformation
def readStylusTipPosition(self):
tempFiducialsNode = self.stylusTrackerSelector.currentNode()
xCoordinate = tempFiducialsNode.GetMatrixTransformToParent().GetElement(0,3)
yCoordinate = tempFiducialsNode.GetMatrixTransformToParent().GetElement(1,3)
zCoordinate = tempFiducialsNode.GetMatrixTransformToParent().GetElement(2,3)
self.Coordinate = ([xCoordinate, yCoordinate, zCoordinate])
transformPositions = self.Coordinate
self.fiducial = slicer.vtkMRMLAnnotationFiducialNode()
if (self.iterationNo==0):
self.pointCollectedButton01.setChecked(1)
elif (self.iterationNo==1):
self.pointCollectedButton02.setChecked(1)
elif (self.iterationNo==2):
self.pointCollectedButton03.setChecked(1)
elif (self.iterationNo==3):
self.pointCollectedButton04.setChecked(1)
elif (self.iterationNo==4):
self.pointCollectedButton05.setChecked(1)
elif (self.iterationNo==5):
self.pointCollectedButton06.setChecked(1)
#print transformPositions
return self.Coordinate
def __init__(self, slicerVersion):
self.volume = slicer.vtkMRMLScalarVolumeNode()
self.display = slicer.vtkMRMLScalarVolumeDisplayNode()
if slicerVersion == 4:
self.fiducialList = slicer.vtkMRMLAnnotationHierarchyNode()
self.newFiducial = slicer.vtkMRMLAnnotationFiducialNode()
else:
self.fiducialList = slicer.vtkMRMLFiducialListNode()
self.newFiducial = slicer.vtkMRMLFiducial()
def __init__(self, slicerVersion):
self.volume = slicer.vtkMRMLScalarVolumeNode()
self.display = slicer.vtkMRMLScalarVolumeDisplayNode()
if slicerVersion == 4:
self.fiducialList = slicer.vtkMRMLAnnotationHierarchyNode()
self.newFiducial = slicer.vtkMRMLAnnotationFiducialNode()
else:
self.fiducialList = slicer.vtkMRMLFiducialListNode()
self.newFiducial = slicer.vtkMRMLFiducial()
def collect(self): fiducialsNode = self.readStylusTipPosition() #print "Getting the point..." fiducial = slicer.vtkMRMLAnnotationFiducialNode() fiducialName = "T" + str(self.iterationNo) fiducial.SetName(fiducialName) fiducial.SetFiducialCoordinates(fiducialsNode) fiducial.Initialize(slicer.mrmlScene) #fiducial.SetHideFromEditors() return fiducialsNode
def addFiducialsToTrackerList(self):
saml = slicer.modules.annotations.logic()
fnode=slicer.util.getNode("Tracker Points List")
saml.SetActiveHierarchyNodeID(fnode.GetID())
f1=slicer.vtkMRMLAnnotationFiducialNode()
f1.SetFiducialWorldCoordinates((10,0,5))
f1.SetName('Stylus Tip 1')
slicer.mrmlScene.AddNode(f1)
f2=slicer.vtkMRMLAnnotationFiducialNode()
f2.SetFiducialWorldCoordinates((10,10,5))
f2.SetName('Stylus Tip 2')
slicer.mrmlScene.AddNode(f2)
f3=slicer.vtkMRMLAnnotationFiducialNode()
f3.SetFiducialWorldCoordinates((20,10,5))
f3.SetName('Stylus Tip 3')
slicer.mrmlScene.AddNode(f3)
f4=slicer.vtkMRMLAnnotationFiducialNode()
f4.SetFiducialWorldCoordinates((20,10,15))
f4.SetName('Stylus Tip 4')
slicer.mrmlScene.AddNode(f4)
print("Fiducials added to Tracker List")
def create_fiducials_list(seedList):
saml = slicer.modules.annotations.logic()
saml.SetActiveHierarchyNodeID(saml.GetTopLevelHierarchyNodeID())
saml.AddHierarchy()
currentList = saml.GetActiveHierarchyNode()
for seed in seedList:
seedFN = slicer.vtkMRMLAnnotationFiducialNode()
seedFN.SetFiducialWorldCoordinates(seed)
seedFN.Initialize(slicer.mrmlScene)
seedHN = slicer.vtkMRMLAnnotationHierarchyNode()
seedHN.SetParentNodeID(currentList.GetID())
seedHN.SetAssociatedNodeID(seedFN.GetID())
return currentList
def onDrawNeedleButtonClicked(self):
self.progress = qt.QProgressDialog(slicer.util.mainWindow())
self.progress.minimumDuration = 0
self.progress.show()
self.progress.setValue(0)
self.progress.setMaximum(0)
self.progress.setCancelButton(0)
self.progress.setWindowModality(2)
self.progress.setLabelText('Creating Fiducials')
slicer.app.processEvents(qt.QEventLoop.ExcludeUserInputEvents)
self.progress.repaint()
self.drawNeedleButton.enabled = False
print 'Please wait drawing fiducials...'
color = [random.randrange(50,100,1)/100,random.randrange(50,100,1)/100,random.randrange(50,100,1)/100]
#color = [0,1,0]
for i in xrange (len(self.trajectory)):
fiducial = slicer.vtkMRMLAnnotationFiducialNode()
fiducialName = self.status.text
fiducialName = fiducialName
fiducialLabel = self.status.text
fiducial.SetName(fiducialName)
fiducial.SetLocked(1)
fiducial.SetFiducialLabel(fiducialLabel)
fiducial.SetFiducialCoordinates(self.trajectory[i])
fiducial.Initialize(slicer.mrmlScene)
displayNode=fiducial.GetDisplayNode()
displayNode.SetGlyphScale(2)
displayNode.SetColor(color)
textNode=fiducial.GetAnnotationTextDisplayNode()
textNode.SetTextScale(1)
textNode.SetColor(color)
self.progress.setValue(2)
self.progress.repaint()
slicer.app.processEvents(qt.QEventLoop.ExcludeUserInputEvents)
self.progress.close()
self.progress = None
def addFiducial(self,name,position=(0,0,0),associatedNode=None):
"""Add an instance of a fiducial to the scene for a given
volume node"""
annoLogic = slicer.modules.annotations.logic()
originalActiveHierarchy = annoLogic.GetActiveHierarchyNodeID()
slicer.mrmlScene.StartState(slicer.mrmlScene.BatchProcessState)
# make the fiducial list if required
listName = associatedNode.GetName() + "-landmarks"
fidListHierarchyNode = slicer.util.getNode(listName)
if not fidListHierarchyNode:
fidListHierarchyNode = slicer.vtkMRMLAnnotationHierarchyNode()
fidListHierarchyNode.HideFromEditorsOff()
fidListHierarchyNode.SetName(listName)
slicer.mrmlScene.AddNode(fidListHierarchyNode)
# make it a child of the top level node
fidListHierarchyNode.SetParentNodeID(annoLogic.GetTopLevelHierarchyNodeID())
# make this active so that the fids will be added to it
annoLogic.SetActiveHierarchyNodeID(fidListHierarchyNode.GetID())
fiducialNode = slicer.vtkMRMLAnnotationFiducialNode()
if associatedNode:
fiducialNode.SetAttribute("AssociatedNodeID", associatedNode.GetID())
fiducialNode.SetName(name)
fiducialNode.AddControlPoint(position, True, True)
fiducialNode.SetSelected(False)
fiducialNode.SetLocked(False)
slicer.mrmlScene.AddNode(fiducialNode)
fiducialNode.CreateAnnotationTextDisplayNode()
fiducialNode.CreateAnnotationPointDisplayNode()
# TODO: pick appropriate defaults
# 135,135,84
fiducialNode.SetTextScale(3.)
fiducialNode.GetAnnotationPointDisplayNode().SetGlyphScale(3.)
fiducialNode.GetAnnotationPointDisplayNode().SetGlyphTypeFromString('StarBurst2D')
fiducialNode.GetAnnotationPointDisplayNode().SetColor((1,1,0))
fiducialNode.GetAnnotationTextDisplayNode().SetColor((1,1,0))
fiducialNode.SetDisplayVisibility(True)
annoLogic.SetActiveHierarchyNodeID(originalActiveHierarchy)
slicer.mrmlScene.EndState(slicer.mrmlScene.BatchProcessState)
def convertTransformToFiducial(self):
self.setUp
scene = slicer.mrmlScene
collection = scene.GetNodesByClass('vtkMRMLLinearTransformNode');
ntransforms = collection.GetNumberOfItems()
collection.InitTraversal()
n = 0
scene = slicer.mrmlScene
while n < ntransforms:
tnode = collection.GetNextItemAsObject()
n = n + 1
m = vtk.vtkMatrix4x4()
tnode.GetMatrixTransformToWorld(m)
fnode = slicer.vtkMRMLAnnotationFiducialNode()
pos = [m.GetElement(0,3), m.GetElement(1,3), m.GetElement(2,3)]
fnode.SetFiducialCoordinates(pos[0], pos[1], pos[2]);
scene.AddNode(fnode)
fnode.CreateAnnotationTextDisplayNode();
fnode.CreateAnnotationPointDisplayNode();
name = '%s_Fiducial' % tnode.GetName()
fnode.SetName(name)
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)
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())
#
# 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("Adding to Report: Volume with id "+volumeNode.GetID())
l.AddVolumeToReport(volumeNode)
# set it on the report
reportNode.SetVolumeNodeID(volumeNode.GetID())
print("adding a fiducial")
#
# define a fiducial
#
fidNode = slicer.vtkMRMLAnnotationFiducialNode()
fidName = "AIM Round Trip Test Fiducial"
fidNode.SetName(fidName)
fidNode.SetSelected(1)
fidNode.SetDisplayVisibility(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())
# point it to the report
fidNode.SetAttribute("ReportingReportNodeID", reportNode.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.CreateAndAddLabelVolume(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+" in file "+reportNode.GetAIMFileName())
self.assertEqual(retval, 0)
print("\n\n\nReloading aim file"+reportNode.GetAIMFileName())
#
# 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(),reportNode.GetAIMFileName())
# 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 a fiducial from the saved report! Expect 2 in the non cleared scene, have " + str(nFiducials))
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)
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 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 onRegistrationButtonClicked(self):
print "Hello Registration :) "
self.referenceAttachmentCollapsibleButton.enabled = True
linearTransformExistence = False
linearTransformNodes = slicer.util.getNodes('vtkMRMLlinearTransformNode*')
for linearTransformNode in linearTransformNodes.keys():
if linearTransformNode=='ModelToTemplateTransform':
linearTransformExistence = True
if linearTransformExistence == False:
followupTransform = slicer.vtkMRMLLinearTransformNode()
followupTransform.SetName('ModelToTemplateTransform')
followupTransform.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(followupTransform)
self.followupTransform = followupTransform
self.fiducialListNode = slicer.util.getNode('Template Fiducials')
movingLandmarksListID = self.fiducialListNode.GetID()
modelFiducials = self.modelFiducialSelector.currentNode()
# extracting the effects of transform parameters
transformNode1 = self.templateSelector.currentNode().GetParentTransformNode()
#print transformNode1
shiftTransform1 = [0 , 0, 0]
rotationTransform1 = [[1, 0,0],[0,1,0],[0,0,1]]
#shiftTransform2 = [0, 0, 0]
#rotationTransform2 = [1, 0,0],[0,1,0],[0,0,1]]
if transformNode1 != None:
m = vtk.vtkMatrix4x4()
transformNode1.GetMatrixTransformToWorld(m)
shiftTransform1 = [ m.GetElement(0,3), m.GetElement(1,3), m.GetElement(2,3) ]
rotationTransform1 = [[m.GetElement(0,0), m.GetElement(0,1),m.GetElement(0,2)],[m.GetElement(1,0), m.GetElement(1,1),m.GetElement(1,2)],[m.GetElement(2,0), m.GetElement(2,1),m.GetElement(2,2)]]
#transformNode2 = transformNode1.GetParentTransformNode()
#if transformNode2 != None:
#transformNode2.GetMatrixTransformToWorld(m)
#shiftTransform2 = [ m.GetElement(0,3), m.GetElement(1,3), m.GetElement(2,3) ]
#rotationTransform2 = [[m.GetElement(0,0), m.GetElement(0,1),m.GetElement(0,2)],[m.GetElement(1,0), m.GetElement(1,1),m.GetElement(1,2)],[m.GetElement(2,0), m.GetElement(2,1),m.GetElement(2,2)]
#shiftTransform = numpy.add(shiftTransform1,shiftTransform2)
# Changing the fiducial coordinates according to the transform
if modelFiducials.GetClassName() == "vtkMRMLAnnotationHierarchyNode":
# slicer4 style hierarchy nodes
collection = vtk.vtkCollection()
modelFiducials.GetChildrenDisplayableNodes(collection)
n = collection.GetNumberOfItems()
if n != 6:
return
# output an error and ask user to select a fiducial with 6 points
listExitence = False
hierarchyNodes = slicer.util.getNodes('vtkMRMLAnnotationHierarchyNode*')
for hierarchyNode in hierarchyNodes.keys():
if hierarchyNode=='New Model Fiducials':
listExitence = True
self.newModelFiducialAnnotationList.RemoveAllChildrenNodes()
if listExitence == False:
newModelFiducialAnnotationList = slicer.vtkMRMLAnnotationHierarchyNode()
newModelFiducialAnnotationList.SetName('New Model Fiducials')
# hide the fiducial list from the scene
newModelFiducialAnnotationList.SetHideFromEditors(1)
newModelFiducialAnnotationList.SetScene(self.scene)
self.scene.AddNode(newModelFiducialAnnotationList)
self.newModelFiducialAnnotationList = newModelFiducialAnnotationList
self.logic.SetActiveHierarchyNodeID(self.newModelFiducialAnnotationList.GetID())
#self.logic.AddHierarchy
#a=self.logic.GetActiveHierarchyNode()
#a.SetName('New Model Fiducials')
p = numpy.zeros((n,3))
for i in xrange(n):
f = collection.GetItemAsObject(i)
coords = [0,0,0]
# Need to change to consider the transform that is applied to the points
f.GetFiducialCoordinates(coords)
newCoords = numpy.add(numpy.dot(rotationTransform1,coords),shiftTransform1)
newfid = slicer.vtkMRMLAnnotationFiducialNode()
newfid.SetFiducialCoordinates(newCoords)
newfid.SetHideFromEditors(0)
newfid.SetName(str(i))
self.scene.AddNode(newfid)
fixedLandmarksListID = self.newModelFiducialAnnotationList.GetID()
self.OutputMessage = ""
parameters = {}
parameters["fixedLandmarks"] = fixedLandmarksListID
parameters["movingLandmarks"] = movingLandmarksListID
parameters["saveTransform"] = self.followupTransform
parameters["transformType"] = "Rigid"
parameters["rms"] = self.RMS
parameters["outputMessage"] = self.OutputMessage
fidreg = slicer.modules.fiducialregistration
self.__cliNode = None
self.__cliNode = slicer.cli.run(fidreg, self.__cliNode, parameters)
print "RMS is", self.RMS
#self.__cliObserverTag = self.__cliNode.AddObserver('ModifiedEvent', self.processRegistrationCompletion)
#self.__registrationStatus.setText('Wait ...')
#self.firstRegButton.setEnabled(0)
stylusNode = self.stylusTrackerSelector.currentNode()
stylusNode.SetAndObserveTransformNodeID(self.followupTransform.GetID())