Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

BUG: fix failing tests (issue #221) #222

Merged
merged 2 commits into from
Feb 7, 2018
Merged

BUG: fix failing tests (issue #221) #222

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
e15c8f0
BUG: fix failing tests (issue #221)
che85 Feb 7, 2018
890b5ba
ENH: adding QuantitativeReportingTests back as a macro (issue #334)
che85 Feb 7, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 3 additions & 9 deletions CMakeLists.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,21 +22,15 @@ find_package(SlicerDevelopmentToolbox REQUIRED)
find_package(DCMQI REQUIRED)
find_package(PETDICOMExtension REQUIRED)

set(DEPENDENCY_BUILD_DIRS
set(DEPENDENCIES_ADDITIONAL_MODULE_PATHS
${SlicerDevelopmentToolbox_DIR}/${Slicer_QTSCRIPTEDMODULES_LIB_DIR}
${SlicerDevelopmentToolbox_DIR}/${Slicer_QTLOADABLEMODULES_LIB_DIR}
${SlicerDevelopmentToolbox_DIR}/${Slicer_CLIMODULES_LIB_DIR}
${PETDICOMExtension_DIR}/${Slicer_QTLOADABLEMODULES_LIB_DIR}
${PETDICOMExtension_DIR}/${Slicer_QTSCRIPTEDMODULES_LIB_DIR}
${PETDICOMExtension_DIR}/${Slicer_CLIMODULES_LIB_DIR}
${DCMQI_DIR}/dcmqi-build/bin
)

message("DEPENDENCY_BUILD_DIRS: ${DEPENDENCY_BUILD_DIRS}")

set(DEPENDENCIES_ADDITIONAL_MODULE_PATHS
${DEPENDENCY_BUILD_DIRS}
${SlicerDevelopmentToolbox_DIR}/${Slicer_QTSCRIPTEDMODULES_LIB_DIR}
)

add_subdirectory(DICOMPlugins)
add_subdirectory(QuantitativeReporting)

Expand Down
6 changes: 2 additions & 4 deletions QuantitativeReporting/QuantitativeReporting.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -211,10 +211,8 @@ def loadSeriesByFileName(self, filename):
self.loadSeries(seriesUID)

def loadSeries(self, seriesUID):
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.detailsPopup.offerLoadables(seriesUID, 'Series')
dicomWidget.detailsPopup.examineForLoading()
dicomWidget.detailsPopup.loadCheckedLoadables()
from DICOMLib.DICOMUtils import loadSeriesByUID
loadSeriesByUID([seriesUID])

def setupSelectionArea(self):
self.segmentEditorWidget.editor.masterVolumeNodeSelectorAddAttribute("vtkMRMLScalarVolumeNode",
Expand Down
7 changes: 6 additions & 1 deletion Testing/CMakeLists.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,9 @@ slicer_add_python_unittest(
SLICER_ARGS --additional-module-paths
${CMAKE_BINARY_DIR}/${Slicer_QTSCRIPTEDMODULES_LIB_DIR}
${DEPENDENCIES_ADDITIONAL_MODULE_PATHS}
)
)

slicerMacroBuildScriptedModule(
NAME ${MODULE_NAME}SelfTests
SCRIPTS QuantitativeReportingTests.py
)
214 changes: 107 additions & 107 deletions Testing/QuantitativeReportingTests.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
import vtk
import slicer
import inspect
from DICOMLib import DICOMUtils

import vtkSegmentationCorePython as vtkSegmentationCore

Expand Down Expand Up @@ -36,7 +37,6 @@ def __init__(self, parent):
except AttributeError:
slicer.selfTests = {}
slicer.selfTests['QuantitativeReporting'] = self.runTest
slicer.selfTests['QuantitativeReportingTests'] = self.runTest

def runTest(self):
tester = QuantitativeReportingTest()
Expand Down Expand Up @@ -102,6 +102,8 @@ def layoutManager(self):

def setUp(self):
self.delayDisplay("Closing the scene")
self.dicomDatabaseDir = os.path.join(slicer.app.temporaryPath, 'QuantitativeReporting_SelfTest', 'CtkDicomDatabase')
self.layoutManager.selectModule("QuantitativeReporting")
slicer.mrmlScene.Clear(0)
self.setupTimer()

Expand All @@ -121,7 +123,6 @@ def loadTestVolume(self):
def runTest(self):
"""Run as few or as many tests as needed here.
"""

for testName in [f for f in QuantitativeReportingTest.__dict__.keys() if f.startswith('test_')]:
self.setUp()
getattr(self, testName)()
Expand All @@ -136,172 +137,171 @@ def loadTestData():
sampleData = TestDataLogic.downloadAndUnzipSampleData(self.collection)
TestDataLogic.importIntoDICOMDatabase(sampleData[imageType])

def checkFocusAndClickButton():
focus = slicer.app.focusWidget()
focus.parent().parent().yesButton.click()
with DICOMUtils.TemporaryDICOMDatabase(self.dicomDatabaseDir) as db:
self.assertTrue(db.isOpen)
self.assertEqual(slicer.dicomDatabase, db)

loadTestData()
loadTestData()

dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
checkbox = dicomWidget.detailsPopup.pluginSelector.checkBoxByPlugin["DICOMLongitudinalTID1500Plugin"]
crntState = checkbox.checked
checkbox.checked = False
# dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
# checkbox = dicomWidget.detailsPopup.pluginSelector.checkBoxByPlugin["DICOMLongitudinalTID1500Plugin"]
# crntState = checkbox.checked
# checkbox.checked = False

timer = qt.QTimer()
timer.setInterval(3000)
timer.setSingleShot(True)
timer.timeout.connect(checkFocusAndClickButton)
timer.start()
qrWidget = slicer.modules.QuantitativeReportingWidget

qrWidget = slicer.modules.QuantitativeReportingWidget
qrWidget.loadSeries(self.data['sr']['uid'])
settings = 'DICOM/automaticallyLoadReferences'
cacheAutoLoadReferences = qt.QSettings().value('DICOM/automaticallyLoadReferences')
qt.QSettings().setValue(settings, qt.QMessageBox.Yes)

qrWidget.loadSeries(self.data['sr']['uid'])

qt.QSettings().setValue(settings, cacheAutoLoadReferences)

checkbox.checked = crntState
# checkbox.checked = crntState

tableNodes = slicer.util.getNodesByClass("vtkMRMLTableNode")
tableNodes = slicer.util.getNodesByClass("vtkMRMLTableNode")

self.assertTrue(len(tableNodes),
"Loading SR into mrmlScene failed. No vtkMRMLTableNodes were found within the scene.")
self.assertTrue(len(tableNodes),
"Loading SR into mrmlScene failed. No vtkMRMLTableNodes were found within the scene.")

self.delayDisplay('Selecting measurements report')
self.delayDisplay('Selecting measurements report')

qrWidget.measurementReportSelector.setCurrentNode(tableNodes[0])
qrWidget.measurementReportSelector.setCurrentNode(tableNodes[0])

self.delayDisplay('Checking number of segments')
self.assertTrue(len(qrWidget.segmentEditorWidget.segments) == 3,
"Number of segments does not match expected count of 3")
self.delayDisplay('Checking number of segments')
self.assertTrue(len(qrWidget.segmentEditorWidget.segments) == 3,
"Number of segments does not match expected count of 3")

self.delayDisplay('Checking referenced master volume', 2000)
self.assertIsNotNone(qrWidget.segmentEditorWidget.masterVolumeNode,
"Master volume for the selected measurement report is None!")
self.delayDisplay('Checking referenced master volume', 2000)
self.assertIsNotNone(qrWidget.segmentEditorWidget.masterVolumeNode,
"Master volume for the selected measurement report is None!")

self.delayDisplay('Test passed!')
self.delayDisplay('Test passed!')

def test_create_report(self):

self.delayDisplay('Starting %s' % inspect.stack()[0][3])

qrWidget = slicer.modules.QuantitativeReportingWidget

self.loadTestVolume()
success, err = qrWidget.saveReport()
self.assertFalse(success)
with DICOMUtils.TemporaryDICOMDatabase(self.dicomDatabaseDir) as db:
self.assertTrue(db.isOpen)
self.assertEqual(slicer.dicomDatabase, db)

self.delayDisplay('Add segments')
self.loadTestVolume()
success, err = qrWidget.saveReport()
self.assertFalse(success)

qrWidget = slicer.modules.QuantitativeReportingWidget
segmentation = qrWidget.segmentEditorWidget.segmentationNode.GetSegmentation()
self.delayDisplay('Add segments')

segmentGeometries = {
'Tumor': [[2, 30, 30, -127.7], [2, 40, 40, -127.7], [2, 50, 50, -127.7], [2, 40, 80, -127.7]],
'Air': [[2, 60, 100, -127.7], [2, 80, 30, -127.7]]
}
qrWidget = slicer.modules.QuantitativeReportingWidget
segmentation = qrWidget.segmentEditorWidget.segmentationNode.GetSegmentation()

segmentGeometries = {
'Tumor': [[2, 30, 30, -127.7], [2, 40, 40, -127.7], [2, 50, 50, -127.7], [2, 40, 80, -127.7]],
'Air': [[2, 60, 100, -127.7], [2, 80, 30, -127.7]]
}

for segmentName, segmentGeometry in segmentGeometries.iteritems():
appender = vtk.vtkAppendPolyData()
for segmentName, segmentGeometry in segmentGeometries.iteritems():
appender = vtk.vtkAppendPolyData()

for sphere in segmentGeometry:
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(sphere[0])
sphereSource.SetCenter(sphere[1], sphere[2], sphere[3])
appender.AddInputConnection(sphereSource.GetOutputPort())
for sphere in segmentGeometry:
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(sphere[0])
sphereSource.SetCenter(sphere[1], sphere[2], sphere[3])
appender.AddInputConnection(sphereSource.GetOutputPort())

segment = vtkSegmentationCore.vtkSegment()
segment.SetName(segmentation.GenerateUniqueSegmentID(segmentName))
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(segmentation.GenerateUniqueSegmentID(segmentName))

appender.Update()
representationName = vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName()
segment.AddRepresentation(representationName, appender.GetOutput())
segmentation.AddSegment(segment)
appender.Update()
representationName = vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName()
segment.AddRepresentation(representationName, appender.GetOutput())
segmentation.AddSegment(segment)

self.delayDisplay('Save report')
self.delayDisplay('Save report')

success, err = qrWidget.saveReport()
self.assertTrue(success)
success, err = qrWidget.saveReport()
self.assertTrue(success)

self.delayDisplay('Test passed!')
self.delayDisplay('Test passed!')

def test_import_labelmap(self):

self.delayDisplay('Starting %s' % inspect.stack()[0][3])

qrWidget = slicer.modules.QuantitativeReportingWidget
self.loadTestVolume()

sampleData = TestDataLogic.downloadAndUnzipSampleData(self.collection)
segmentationsDir = sampleData['seg_nrrd']
with DICOMUtils.TemporaryDICOMDatabase(self.dicomDatabaseDir) as db:
self.assertTrue(db.isOpen)
self.assertEqual(slicer.dicomDatabase, db)

labels = []
for f in [os.path.join(segmentationsDir, f) for f in os.listdir(segmentationsDir) if f.endswith(".nrrd")]:
_, label = slicer.util.loadVolume(f, {'labelmap': True}, returnNode=True)
if label:
labels.append(label)
self.loadTestVolume()

labelImportWidget = qrWidget.labelMapImportWidget

timer = qt.QTimer()
timer.setInterval(2000)
timer.timeout.connect(self._checkFocusAndClickButton)
timer.start()
sampleData = TestDataLogic.downloadAndUnzipSampleData(self.collection)
segmentationsDir = sampleData['seg_nrrd']

for label in labels:
labelImportWidget.labelMapSelector.setCurrentNode(label)
labelImportWidget.importButton.click()
labels = []
for f in [os.path.join(segmentationsDir, f) for f in os.listdir(segmentationsDir) if f.endswith(".nrrd")]:
_, label = slicer.util.loadVolume(f, {'labelmap': True}, returnNode=True)
if label:
labels.append(label)

timer.stop()
labelImportLogic = qrWidget.labelMapImportWidget.logic

segmentation = qrWidget.segmentEditorWidget.segmentationNode.GetSegmentation()
self.assertEquals(segmentation.GetNumberOfSegments(), len(labels))
for label in labels:
labelImportLogic.labelmap = label
labelImportLogic.run(resampleIfNecessary=True)

self.delayDisplay('Test passed!')
segmentation = qrWidget.segmentEditorWidget.segmentationNode.GetSegmentation()
self.assertEquals(segmentation.GetNumberOfSegments(), len(labels))

def _checkFocusAndClickButton(self):
focus = slicer.app.focusWidget()
if type(focus) is qt.QPushButton:
focus.click()
self.delayDisplay('Test passed!')

def test_import_segmentation(self):

self.delayDisplay('Starting %s' % inspect.stack()[0][3])

uid = self.data["seg_dcm"]["uid"]

self.loadTestVolume()
with DICOMUtils.TemporaryDICOMDatabase(self.dicomDatabaseDir) as db:
self.assertTrue(db.isOpen)
self.assertEqual(slicer.dicomDatabase, db)

if not len(slicer.dicomDatabase.filesForSeries(uid)):
sampleData = TestDataLogic.downloadAndUnzipSampleData(self.collection)
TestDataLogic.importIntoDICOMDatabase(sampleData["seg_dcm"])
self.loadTestVolume()

def checkFocusAndClickButton():
focus = slicer.app.focusWidget()
focus.parent().parent().noButton.click()
if not len(slicer.dicomDatabase.filesForSeries(uid)):
sampleData = TestDataLogic.downloadAndUnzipSampleData(self.collection)
TestDataLogic.importIntoDICOMDatabase(sampleData["seg_dcm"])

timer = qt.QTimer()
timer.setInterval(3000)
timer.setSingleShot(True)
timer.timeout.connect(checkFocusAndClickButton)
timer.start()
qrWidget = slicer.modules.QuantitativeReportingWidget

qrWidget = slicer.modules.QuantitativeReportingWidget
qrWidget.loadSeries(uid)
settings = 'DICOM/automaticallyLoadReferences'
cacheAutoLoadReferences = qt.QSettings().value('DICOM/automaticallyLoadReferences')
qt.QSettings().setValue(settings, qt.QMessageBox.Yes)

qrWidget.loadSeries(uid)

qt.QSettings().setValue(settings, cacheAutoLoadReferences)

segmentationNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[-1]
segmentationNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[-1]

qrWidget.importSegmentationCollapsibleButton.collapsed = False
qrWidget.importSegmentationCollapsibleButton.collapsed = False

importWidget = qrWidget.segmentImportWidget
importWidget.otherSegmentationNodeSelector.setCurrentNode(segmentationNode)
importWidget = qrWidget.segmentImportWidget
importWidget.otherSegmentationNodeSelector.setCurrentNode(segmentationNode)

segmentIDs = qrWidget.segmentEditorWidget.logic.getSegmentIDs(segmentationNode, False)
importWidget.otherSegmentsTableView.setSelectedSegmentIDs(segmentIDs)
segmentIDs = qrWidget.segmentEditorWidget.logic.getSegmentIDs(segmentationNode, False)
importWidget.otherSegmentsTableView.setSelectedSegmentIDs(segmentIDs)

importWidget.copyOtherToCurrentButton.click()
importWidget.copyOtherToCurrentButton.click()

self.delayDisplay('Checking number of imported segments')
self.assertTrue(len(qrWidget.segmentEditorWidget.segments) == 3,
"Number of segments does not match expected count of 3")
self.delayDisplay('Checking number of imported segments')
self.assertTrue(len(qrWidget.segmentEditorWidget.segments) == 3,
"Number of segments does not match expected count of 3")

self.delayDisplay('Test passed!')
self.delayDisplay('Test passed!')

def _selectModule(self):
self.layoutManager.selectModule("QuantitativeReporting")