def test_SEGExporterSelfTest1(self):
""" Test DICOM import, segmentation, export
"""
self.messageDelay = 50
import os
self.delayDisplay("Starting the DICOM SEG Export test")
#
# first, get the data - a zip file of dicom data
#
filePath = self.logic.downloadSampleData()
self.delayDisplay('Finished with download\n')
self.delayDisplay("Unzipping")
dicomFilesDirectory = self.logic.unzipSampleData(filePath)
try:
self.delayDisplay("Switching to temp database directory")
tempDatabaseDirectory = slicer.app.temporaryPath + '/tempDICOMDatabase'
import shutil
try:
shutil.rmtree(tempDatabaseDirectory)
except OSError:
pass
qt.QDir().mkpath(tempDatabaseDirectory)
if slicer.dicomDatabase:
originalDatabaseDirectory = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
else:
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')
self.logic.importIntoDICOMDatabase(dicomFilesDirectory)
dicomWidget.detailsPopup.open()
# load the data by series UID
mrHeadSeriesUID = "2.16.840.1.113662.4.4168496325.1025306170.548651188813145058"
dicomWidget.detailsPopup.offerLoadables(mrHeadSeriesUID, 'Series')
dicomWidget.detailsPopup.examineForLoading()
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
#
# create a label map and set it for editing
#
masterNode = slicer.util.getNode('2: SAG*')
volumesLogic = slicer.modules.volumes.logic()
mergeNode = volumesLogic.CreateAndAddLabelVolume( slicer.mrmlScene, masterNode, masterNode.GetName() + '-label' )
mergeNode.GetDisplayNode().SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID( masterNode.GetID() )
selectionNode.SetReferenceActiveLabelVolumeID( mergeNode.GetID() )
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# go to the editor and do some drawing
#
slicer.util.selectModule('Editor')
import EditorLib
from EditorLib.EditUtil import EditUtil
parameterNode = EditUtil.getParameterNode()
parameterNode.SetParameter("LabelEffect,paintThreshold", "1")
parameterNode.SetParameter("LabelEffect,paintThresholdMin", "70.0")
parameterNode.SetParameter("LabelEffect,paintThresholdMax", "279.75")
parameterNode.SetParameter("PaintEffect,radius", "40")
parameterNode.SetParameter("PaintEffect,sphere", "1")
self.delayDisplay("Paint some things")
parameterNode = EditUtil.getParameterNode()
lm = slicer.app.layoutManager()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
paintTool = EditorLib.PaintEffectTool(sliceWidget)
EditUtil.setLabel(1)
paintTool.paintAddPoint(100,100)
paintTool.paintApply()
EditUtil.setLabel(2)
paintTool.paintAddPoint(200,200)
paintTool.paintApply()
paintTool.cleanup()
paintTool = None
# save these to compare with the one we read back
originalSegmentationArray = slicer.util.array(mergeNode.GetID())
originalSegmentationNodeCopy = slicer.vtkMRMLLabelMapVolumeNode()
originalSegmentationNodeCopy.CopyOrientation(mergeNode)
# export the volumes into a SEG
tempSEGDirectory = slicer.app.temporaryPath + '/tempDICOMSEG'
qt.QDir().mkpath(tempSEGDirectory)
segFilePath = os.path.join(tempSEGDirectory, "test.SEG.dcm")
self.delayDisplay('spliting...', 200)
EditUtil.splitPerStructureVolumes(masterNode, mergeNode)
self.delayDisplay('exporting...', 200)
EditUtil.exportAsDICOMSEG(masterNode)
# close scene re-load the input data and SEG
slicer.mrmlScene.Clear(0)
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, tempSEGDirectory, None)
indexer.waitForImportFinished()
mrHeadStudyUID = "2.16.840.1.113662.4.4168496325.1025305873.7118351817185979330"
dicomWidget.detailsPopup.offerLoadables(mrHeadStudyUID, 'Study')
dicomWidget.detailsPopup.examineForLoading()
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
# confirm that segmentations are correctly reloaded
headLabelName = '2: SAG/RF-FAST/VOL/FLIP 30-label'
reloadedLabel = slicer.util.getNode(headLabelName)
reloadedSegmentationArray = slicer.util.array(reloadedLabel.GetID())
import numpy
self.assertTrue(numpy.alltrue(originalSegmentationArray == reloadedSegmentationArray))
geometryWarnings = volumesLogic.CompareVolumeGeometry(mergeNode, reloadedLabel)
print(geometryWarnings)
self.assertTrue(geometryWarnings == '')
# re-export
# close scene re-load the input data and SEG
# confirm that segmentations are available again as per-structure volumes
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
def test_SEGExporterSelfTest1(self):
""" Test DICOM import, segmentation, export
"""
self.messageDelay = 50
import os
self.delayDisplay("Starting the DICOM SEG Export test")
#
# first, get the data - a zip file of dicom data
#
import urllib
downloads = ((
'http://slicer.kitware.com/midas3/download/item/220834/PieperMRHead.zip',
'PieperMRHead.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')
self.delayDisplay("Unzipping")
dicomFilesDirectory = slicer.app.temporaryPath + '/dicomFiles'
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
try:
self.delayDisplay("Switching to temp database directory")
tempDatabaseDirectory = slicer.app.temporaryPath + '/tempDICOMDatabase'
import shutil
shutil.rmtree(tempDatabaseDirectory)
qt.QDir().mkpath(tempDatabaseDirectory)
if slicer.dicomDatabase:
originalDatabaseDirectory = os.path.split(
slicer.dicomDatabase.databaseFilename)[0]
else:
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')
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory,
None)
indexer.waitForImportFinished()
dicomWidget.detailsPopup.open()
# load the data by series UID
mrHeadSeriesUID = "2.16.840.1.113662.4.4168496325.1025306170.548651188813145058"
dicomWidget.detailsPopup.offerLoadables(mrHeadSeriesUID, 'Series')
dicomWidget.detailsPopup.examineForLoading()
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
#
# create a label map and set it for editing
#
masterNode = slicer.util.getNode('2: SAG*')
volumesLogic = slicer.modules.volumes.logic()
mergeNode = volumesLogic.CreateAndAddLabelVolume(
slicer.mrmlScene, masterNode,
masterNode.GetName() + '-label')
mergeNode.GetDisplayNode().SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(masterNode.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(mergeNode.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# go to the editor and do some drawing
#
slicer.util.selectModule('Editor')
import EditorLib
from EditorLib.EditUtil import EditUtil
parameterNode = EditUtil.getParameterNode()
parameterNode.SetParameter("LabelEffect,paintThreshold", "1")
parameterNode.SetParameter("LabelEffect,paintThresholdMin", "70.0")
parameterNode.SetParameter("LabelEffect,paintThresholdMax",
"279.75")
parameterNode.SetParameter("PaintEffect,radius", "40")
parameterNode.SetParameter("PaintEffect,sphere", "1")
self.delayDisplay("Paint some things")
parameterNode = EditUtil.getParameterNode()
lm = slicer.app.layoutManager()
paintEffect = EditorLib.PaintEffectOptions()
paintEffect.setMRMLDefaults()
paintEffect.__del__()
sliceWidget = lm.sliceWidget('Red')
paintTool = EditorLib.PaintEffectTool(sliceWidget)
EditUtil.setLabel(1)
paintTool.paintAddPoint(100, 100)
paintTool.paintApply()
EditUtil.setLabel(2)
paintTool.paintAddPoint(200, 200)
paintTool.paintApply()
paintTool.cleanup()
paintTool = None
# save these to compare with the one we read back
originalSegmentationArray = slicer.util.array(mergeNode.GetID())
originalSegmentationNodeCopy = slicer.vtkMRMLLabelMapVolumeNode()
originalSegmentationNodeCopy.CopyOrientation(mergeNode)
# export the volumes into a SEG
tempSEGDirectory = slicer.app.temporaryPath + '/tempDICOMSEG'
qt.QDir().mkpath(tempSEGDirectory)
segFilePath = os.path.join(tempSEGDirectory, "test.SEG.dcm")
self.delayDisplay('spliting...', 200)
EditUtil.splitPerStructureVolumes(masterNode, mergeNode)
self.delayDisplay('exporting...', 200)
EditUtil.exportAsDICOMSEG(masterNode)
# close scene re-load the input data and SEG
slicer.mrmlScene.Clear(0)
indexer.addDirectory(slicer.dicomDatabase, tempSEGDirectory, None)
indexer.waitForImportFinished()
mrHeadStudyUID = "2.16.840.1.113662.4.4168496325.1025305873.7118351817185979330"
dicomWidget.detailsPopup.offerLoadables(mrHeadStudyUID, 'Study')
dicomWidget.detailsPopup.examineForLoading()
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
# confirm that segmentations are correctly reloaded
headLabelName = '2: SAG/RF-FAST/VOL/FLIP 30-label'
reloadedLabel = slicer.util.getNode(headLabelName)
reloadedSegmentationArray = slicer.util.array(
reloadedLabel.GetID())
import numpy
self.assertTrue(
numpy.alltrue(
originalSegmentationArray == reloadedSegmentationArray))
geometryWarnings = volumesLogic.CompareVolumeGeometry(
mergeNode, reloadedLabel)
print(geometryWarnings)
self.assertTrue(geometryWarnings == '')
# re-export
# close scene re-load the input data and SEG
# confirm that segmentations are available again as per-structure volumes
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
