def test_Part1Ruler(self,
enableScreenshotsFlag=0,
screenshotScaleFactor=1):
""" Test using rulers
"""
logic = RSNAQuantTutorialLogic()
logic.enableScreenshots = enableScreenshotsFlag
logic.screenshotScaleFactor = screenshotScaleFactor
self.delayDisplay("Starting the test")
#
# first, get some data
#
import SampleData
tumor = SampleData.downloadSample('MRBrainTumor1')
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)
logic.takeScreenshot('Ruler',
'Ruler used to measure tumor diameter', -1)
self.delayDisplay('Test passed!')
except Exception as 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
"""
logic = RSNAQuantTutorialLogic()
logic.enableScreenshots = enableScreenshotsFlag
logic.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);
logic.takeScreenshot('Ruler','Ruler used to measure tumor diameter',-1)
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
def test_SlicerCreateRulerCrashIssue4199(self):
""" Ideally you should have several levels of tests. At the lowest level
tests should 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.
"""
logic = SlicerCreateRulerCrashIssue4199Logic()
self.delayDisplay("Starting the test")
slicer.util.selectModule('Welcome')
# Add a ruler
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
rulerNode.SetPosition1(0, 0, 0)
rulerNode.SetPosition2(1, 1, 1)
rulerNode.Initialize(slicer.mrmlScene)
# Enter the Annotations module
slicer.util.selectModule('Annotations')
# If test reach this point without crashing it is a success
self.delayDisplay('Test passed!')
def test_LineIntersityProfile1(self):
""" Ideally you should have several levels of tests. At the lowest level
tests should 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:
logging.info(
'Requesting download %s from %s...\n' % (name, url))
urllib.urlretrieve(url, filePath)
if loader:
logging.info('Loading %s...' % (name,))
loader(filePath)
self.delayDisplay('Finished with download and loading')
volumeNode = slicer.util.getNode(pattern="FA")
logic = LineIntersityProfileLogic()
self.assertTrue(logic.hasImageData(volumeNode))
# self.delayDisplay('Test passed!')
# Add Test
# Initialise rule node in a know location
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
slicer.mrmlScene.AddNode(rulerNode)
rulerNode.SetPosition1(-65, 110, 60)
rulerNode.SetPosition2(-15, 60, 60)
rulerNode.SetName('Test')
# Initialise input selectors
moduleWidget = slicer.modules.LineIntersityProfileWidget
# Note: the end has no "()", or a __init__ function required!
moduleWidget.rulerSelector.setCurrentNode(rulerNode)
moduleWidget.inputSelector1.setCurrentNode(volumeNode)
moduleWidget.inputSelector2.setCurrentNode(volumeNode)
self.delayDisplay("Inputs initialised!")
# run the logic with the initialised inputs
moduleWidget.onApplyButton()
self.delayDisplay("if you see a ruler and a plot - test passed!")
def test_SlicerCreateRulerCrashIssue4199(self):
""" Ideally you should have several levels of tests. At the lowest level
tests should 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.
"""
logic = SlicerCreateRulerCrashIssue4199Logic()
self.delayDisplay("Starting the test")
slicer.util.selectModule('Welcome')
# Add a ruler
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
rulerNode.SetPosition1(0, 0, 0)
rulerNode.SetPosition2(1, 1, 1)
rulerNode.Initialize(slicer.mrmlScene)
# Enter the Annotations module
slicer.util.selectModule('Annotations')
# If test reach this point without crashing it is a success
self.delayDisplay('Test passed!')
def test_LineIntensityProfile1(self):
""" Ideally you should have several levels of tests. At the lowest level
tests should 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:
logging.info('Requesting download %s from %s...\n' % (name, url))
urllib.urlretrieve(url, filePath)
if loader:
logging.info('Loading %s...' % (name,))
loader(filePath)
self.delayDisplay('Finished with download and loading')
volumeNode = slicer.util.getNode(pattern="FA")
logic = LineIntensityProfileLogic()
self.assertIsNotNone( logic.hasImageData(volumeNode) )
#initialize ruler in a known location
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
slicer.mrmlScene.AddNode(rulerNode)
rulerNode.SetPosition1(-65,110,60)
rulerNode.SetPosition2(-15,60,60)
rulerNode.SetName('Test')
# 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 initialized inputs
moduleWidget.onApplyButton()
self.delayDisplay('If you see a ruler and a plot - test passed')
def TestRulerAdd(renameFlag=1, visibilityFlag=1, numToAdd=20):
print("numToAdd = ", numToAdd)
if renameFlag > 0:
print("Index\tTime to add ruler\tDelta between adds\tTime to rename ruler\tDelta between renames")
print("%(index)04s\t" % {'index': "i"}, "t\tdt\tt\tdt")
else:
print("Index\tTime to add ruler\tDelta between adds")
print("%(index)04s\t" % {'index': "i"}, "t\tdt")
r1 = 0
a1 = 0
s1 = 0
r2 = 1
a2 = 1
s2 = 1
t1 = 0
t2 = 0
t3 = 0
t4 = 0
timeToAddThisRuler = 0
timeToAddLastRuler = 0
timeToRenameThisRuler = 0
timeToRenameLastRuler = 0
# iterate over the number of rulers to add
for i in range(numToAdd):
# print "i = ", i, "/", numToAdd, ", r = ", r, ", a = ", a, ", s = ", s
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
rulerNode.SetPosition1(r1, a1, s1)
rulerNode.SetPosition2(r2, a2, s2)
t1 = time.process_time()
rulerNode.Initialize(slicer.mrmlScene)
t2 = time.process_time()
timeToAddThisRuler = t2 - t1
dt = timeToAddThisRuler - timeToAddLastRuler
if renameFlag > 0:
t3 = time.process_time()
rulerNode.SetName(str(i))
t4 = time.process_time()
timeToRenameThisRuler = t4 - t3
dt2 = timeToRenameThisRuler - timeToRenameLastRuler
print('%(index)04d\t' % {'index': i}, timeToAddThisRuler, "\t", dt, "\t", timeToRenameThisRuler, "\t", dt2)
timeToRenameLastRuler = timeToRenameThisRuler
else:
print('%(index)04d\t' % {'index': i}, timeToAddThisRuler, "\t", dt)
r1 = r1 + 1.0
a1 = a1 + 1.0
s1 = s1 + 1.0
r2 = r2 + 1.5
a2 = a2 + 1.5
s2 = s2 + 1.5
timeToAddLastRuler = timeToAddThisRuler
def findAxisOfMotion(self, origins):
#Following guide from: http://sebastianraschka.com/Articles/2014_pca_step_by_step.html
#scale factor for better display:
scale = 100
#Calculate mean position
meanVector = [0, 0 ,0]
for i in range(3):
meanVector[i] = np.mean(origins[i, :])
#Computing covariance matrix
convMatrix = np.cov([origins[0, :], origins[1, :], origins[2, :]])
#Get eigenvectors
eig_val, eig_vec = np.linalg.eig(convMatrix)
# Make a list of (eigenvalue, eigenvector) tuples
eig_pairs = [(np.abs(eig_val[i]), eig_vec[:,i]) for i in range(len(eig_val))]
# Sort the (eigenvalue, eigenvector) tuples from high to low
eig_pairs.sort()
# eig_pairs.reverse()
matrix_w = np.hstack((eig_pairs[0][1].reshape(3, 1),
eig_pairs[1][1].reshape(3, 1),
eig_pairs[2][1].reshape(3, 1)))
print('Matrix W:\n', matrix_w)
#Create linear transform for contour propagation
vtkMatrix = vtk.vtkMatrix4x4()
transform = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(transform)
for i in range(3):
for j in range(3):
vtkMatrix.SetElement(j, i, matrix_w[i, j])
transform.SetAndObserveMatrixTransformFromParent(vtkMatrix)
#Plot eigenvectors from mean position
fiducials = slicer.vtkMRMLMarkupsFiducialNode()
displayNode = slicer.vtkMRMLMarkupsDisplayNode()
# vtkNew<vtkMRMLMarkupsFiducialStorageNode> wFStorageNode;
slicer.mrmlScene.AddNode(displayNode)
slicer.mrmlScene.AddNode(fiducials)
fiducials.SetAndObserveDisplayNodeID(displayNode.GetID())
fiducials.AddFiducialFromArray(meanVector, "Mean Position")
for i in range(len(eig_vec)):
# fiducials.AddFiducialFromArray(meanVector + scale * eig_vec[i], " P " + str(i+1))
#Plot ruler
ruler = slicer.vtkMRMLAnnotationRulerNode()
displayRuler = slicer.vtkMRMLAnnotationLineDisplayNode()
displayRuler.SetLabelVisibility(0)
displayRuler.SetMaxTicks(0)
displayRuler.SetLineWidth(5)
slicer.mrmlScene.AddNode(displayRuler)
slicer.mrmlScene.AddNode(ruler)
ruler.SetAndObserveDisplayNodeID(displayRuler.GetID())
ruler.SetPosition1(meanVector)
ruler.SetPosition2(meanVector + scale * eig_vec[i])
return matrix_w
def get3DEuclideanDistance(pos1, pos2):
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
rulerNode.SetPosition1(pos1)
rulerNode.SetPosition2(pos2)
distance3D = rulerNode.GetDistanceMeasurement()
return distance3D
def get3DEuclideanDistance(pos1, pos2): rulerNode = slicer.vtkMRMLAnnotationRulerNode() rulerNode.SetPosition1(pos1) rulerNode.SetPosition2(pos2) distance3D = rulerNode.GetDistanceMeasurement() return distance3D
def loadAdditionalMeasurements(self, srUID):
"""
Loads length measements as annotation rulers
TODO: need to generalize to other report contents
"""
srFilePath = slicer.dicomDatabase.fileForInstance(srUID)
sr = dicom.read_file(srFilePath)
if not self.isConcept(sr, "imagingMeasurementReport"):
return sr
contents = {}
measurements = []
contents['measurements'] = measurements
for item in sr.ContentSequence:
if self.isConcept(item, "personObserver"):
contents['personObserver'] = item.PersonName
if self.isConcept(item, "imagingMeasuremnts"):
for contentItem in item.ContentSequence:
if self.isConcept(contentItem, "measurementGroup"):
measurement = {}
for measurementItem in contentItem.ContentSequence:
if self.isConcept(measurementItem,
"trackingIdentifier"):
measurement[
'trackingIdentifier'] = measurementItem.TextValue
if self.isConcept(measurementItem,
"trackingUniqueIdentifier"):
measurement[
'trackingUniqueIdentifier'] = measurementItem.UID
if self.isConcept(measurementItem, "findingSite"):
measurement[
'findingSite'] = measurementItem.ConceptCodeSequence[
0].CodeMeaning
if self.isConcept(measurementItem, "length"):
for lengthItem in measurementItem.ContentSequence:
measurement[
'polyline'] = lengthItem.GraphicData
for selectionItem in lengthItem.ContentSequence:
if selectionItem.RelationshipType == "SELECTED FROM":
for reference in selectionItem.ReferencedSOPSequence:
measurement[
'referencedSOPInstanceUID'] = reference.ReferencedSOPInstanceUID
if hasattr(
reference,
"ReferencedFrameNumber"
) and reference.ReferencedFrameNumber != "1":
print(
'Error - only single frame references supported'
)
measurements.append(measurement)
for measurement in contents['measurements']:
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
rulerNode.SetLocked(True)
rulerNode.SetName(contents['personObserver'])
referenceFilePath = slicer.dicomDatabase.fileForInstance(
measurement['referencedSOPInstanceUID'])
reference = dicom.read_file(referenceFilePath)
origin = numpy.array(reference.ImagePositionPatient)
alongColumnVector = numpy.array(
reference.ImageOrientationPatient[:3])
alongRowVector = numpy.array(reference.ImageOrientationPatient[3:])
alongColumnVector *= reference.PixelSpacing[1]
alongRowVector *= reference.PixelSpacing[0]
col1, row1, col2, row2 = measurement['polyline']
lpsToRAS = numpy.array([-1, -1, 1])
p1 = (origin + col1 * alongColumnVector +
row1 * alongRowVector) * lpsToRAS
p2 = (origin + col2 * alongColumnVector +
row2 * alongRowVector) * lpsToRAS
rulerNode.SetPosition1(*p1)
rulerNode.SetPosition2(*p2)
rulerNode.Initialize(slicer.mrmlScene)
colorIndex = 1 + len(
slicer.util.getNodesByClass('vtkMRMLAnnotationRulerNode'))
colorNode = slicer.util.getNode("GenericAnatomyColors")
color = [
0,
] * 4
colorNode.GetColor(colorIndex, color)
rulerNode.GetDisplayNode().SetColor(*color[:3])
rulerNode.GetAnnotationTextDisplayNode().SetColor(*color[:3])
rulerNode.GetAnnotationPointDisplayNode().SetColor(*color[:3])
rulerNode.GetAnnotationPointDisplayNode().SetGlyphScale(2)
rulerNode.GetAnnotationLineDisplayNode().SetLabelPosition(
random.random())
