def takeScreenshot(self,name,description,type=-1,screenshotScaleFactor=1):
lm = slicer.app.layoutManager()
# switch on the type to get the requested window
widget = 0
if type == -1:
# full window
widget = slicer.util.mainWindow()
elif type == slicer.qMRMLScreenShotDialog().FullLayout:
# full layout
widget = lm.viewport()
elif type == slicer.qMRMLScreenShotDialog().ThreeD:
# just the 3D window
widget = lm.threeDWidget(0).threeDView()
elif type == slicer.qMRMLScreenShotDialog().Red:
# red slice window
widget = lm.sliceWidget("Red")
elif type == slicer.qMRMLScreenShotDialog().Yellow:
# yellow slice window
widget = lm.sliceWidget("Yellow")
elif type == slicer.qMRMLScreenShotDialog().Green:
# green slice window
widget = lm.sliceWidget("Green")
# grab and convert to vtk image data
qpixMap = qt.QPixmap().grabWidget(widget)
qimage = qpixMap.toImage()
imageData = vtk.vtkImageData()
slicer.qMRMLUtils().qImageToVtkImageData(qimage,imageData)
annotationLogic = slicer.modules.annotations.logic()
annotationLogic.CreateSnapShot(name, description, type, screenshotScaleFactor, imageData)
def run(self,node,enableScreenshots=0,screenshotScaleFactor=1):
"""
Run the actual algorithm
"""
self.enableScreenshots = enableScreenshots
self.screenshotScaleFactor = screenshotScaleFactor
name = 'Lung001'
#self.takeScreenshot('Lung001_PT',slicer.qMRMLScreenShotDialog().ThreeD)
self.takeScreenshot(name,slicer.qMRMLScreenShotDialog().ThreeD)
print "Finished!"
return True
def takeScreenshot(self, name, description, type=-1):
# show the message even if not taking a screen shot
self.delayDisplay(description)
if self.enableScreenshots == 0:
return
lm = slicer.app.layoutManager()
# switch on the type to get the requested window
widget = 0
if type == -1:
# full window
widget = slicer.util.mainWindow()
elif type == slicer.qMRMLScreenShotDialog().FullLayout:
# full layout
widget = lm.viewport()
elif type == slicer.qMRMLScreenShotDialog().ThreeD:
# just the 3D window
widget = lm.threeDWidget(0).threeDView()
elif type == slicer.qMRMLScreenShotDialog().Red:
# red slice window
widget = lm.sliceWidget("Red")
elif type == slicer.qMRMLScreenShotDialog().Yellow:
# yellow slice window
widget = lm.sliceWidget("Yellow")
elif type == slicer.qMRMLScreenShotDialog().Green:
# green slice window
widget = lm.sliceWidget("Green")
# grab and convert to vtk image data
qpixMap = qt.QPixmap().grabWidget(widget)
qimage = qpixMap.toImage()
imageData = vtk.vtkImageData()
slicer.qMRMLUtils().qImageToVtkImageData(qimage, imageData)
annotationLogic = slicer.modules.annotations.logic()
annotationLogic.CreateSnapShot(name, description, type,
self.screenshotScaleFactor, imageData)
def onSave(self):
"""save the label statistics
"""
self.onApplyButton() #selects Apply in case it is accidentally not pressed
self.logic.takeScreenshot('Slice-label','slice',slicer.qMRMLScreenShotDialog().Red)
baseDir = os.path.dirname(self.resultsFilePath)
folderName = self.helper.master.GetName()
dirName = os.path.join(baseDir, folderName)
if not os.path.exists(dirName):
os.mkdir(dirName)
l = slicer.app.applicationLogic()
l.SaveSceneToSlicerDataBundleDirectory(dirName, None)
# saves the csv files to selected folder
csvFileName = os.path.join(dirName, "{0}_waist_circumference.csv".format(folderName))
self.logic.saveStats(csvFileName)
self.logic.appendStats(self.resultsFilePath)
self.resetTableModel()
self.logic.startNextImage()
def run(self, enableScreenshots=0, screenshotScaleFactor=1):
"""
Run the actual algorithm
"""
self.delayDisplay('Running the aglorithm')
self.enableScreenshots = enableScreenshots
self.screenshotScaleFactor = screenshotScaleFactor
# Start in conventional layout
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
# without this delayed display, when running from the cmd line Slicer starts
# up in a different layout and the seed won't get rendered in the right spot
self.delayDisplay("Conventional view")
# Download MRHead from sample data
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
print("Getting MR Head Volume")
mrHeadVolume = sampleDataLogic.downloadMRHead()
# Place a fiducial on the red slice
markupsLogic = slicer.modules.markups.logic()
eye = [33.4975, 79.4042, -10.2143]
fidIndex = markupsLogic.AddFiducial(eye[0], eye[1], eye[2])
fidID = markupsLogic.GetActiveListID()
fidNode = slicer.mrmlScene.GetNodeByID(fidID)
self.delayDisplay("Placed a fiducial")
# Pan and zoom
sliceWidget = slicer.app.layoutManager().sliceWidget('Red')
sliceLogic = sliceWidget.sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
sliceNode = sliceLogic.GetSliceNode()
sliceNode.SetXYZOrigin(-71.7, 129.7, 0.0)
sliceNode.SetFieldOfView(98.3, 130.5, 1.0)
self.delayDisplay("Panned and zoomed")
# Get the seed widget seed location
startingSeedDisplayCoords = [0.0, 0.0, 0.0]
helper = self.getFiducialSliceDisplayableManagerHelper('Red')
if helper != None:
seedWidget = helper.GetWidget(fidNode)
seedRepresentation = seedWidget.GetSeedRepresentation()
handleRep = seedRepresentation.GetHandleRepresentation(fidIndex)
startingSeedDisplayCoords = handleRep.GetDisplayPosition()
print('Starting seed display coords = %d, %d, %d' %
(startingSeedDisplayCoords[0], startingSeedDisplayCoords[1],
startingSeedDisplayCoords[2]))
self.takeScreenshot('FiducialLayoutSwitchBug1914-StartingPosition',
'Fiducial starting position',
slicer.qMRMLScreenShotDialog().Red)
# Switch to red slice only
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
self.delayDisplay("Red Slice only")
# Switch to conventional layout
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
self.delayDisplay("Conventional layout")
# Get the current seed widget seed location
endingSeedDisplayCoords = [0.0, 0.0, 0.0]
helper = self.getFiducialSliceDisplayableManagerHelper('Red')
if helper != None:
seedWidget = helper.GetWidget(fidNode)
seedRepresentation = seedWidget.GetSeedRepresentation()
handleRep = seedRepresentation.GetHandleRepresentation(fidIndex)
endingSeedDisplayCoords = handleRep.GetDisplayPosition()
print('Ending seed display coords = %d, %d, %d' %
(endingSeedDisplayCoords[0], endingSeedDisplayCoords[1],
endingSeedDisplayCoords[2]))
self.takeScreenshot('FiducialLayoutSwitchBug1914-EndingPosition',
'Fiducial ending position',
slicer.qMRMLScreenShotDialog().Red)
# Compare to original seed widget location
diff = math.pow(
(startingSeedDisplayCoords[0] - endingSeedDisplayCoords[0]),
2) + math.pow(
(startingSeedDisplayCoords[1] - endingSeedDisplayCoords[1]),
2) + math.pow((startingSeedDisplayCoords[2] -
endingSeedDisplayCoords[2]), 2)
if diff != 0.0:
diff = math.sqrt(diff)
self.delayDisplay(
"Difference between starting and ending seed display coordinates = %g"
% diff)
if diff > 1.0:
# raise Exception("Display coordinate difference is too large!\nExpected < 1.0 but got %g" % (diff))
print(
"Display coordinate difference is too large!\nExpected < 1.0 but got %g"
% (diff))
return False
if enableScreenshots == 1:
# compare the screen snapshots
startView = slicer.mrmlScene.GetFirstNodeByName(
'FiducialLayoutSwitchBug1914-StartingPosition')
startShot = startView.GetScreenShot()
endView = slicer.mrmlScene.GetFirstNodeByName(
'FiducialLayoutSwitchBug1914-EndingPosition')
endShot = endView.GetScreenShot()
imageMath = vtk.vtkImageMathematics()
imageMath.SetOperationToSubtract()
imageMath.SetInput1(startShot)
imageMath.SetInput2(endShot)
imageMath.Update()
shotDiff = imageMath.GetOutput()
# save it as a scene view
annotationLogic = slicer.modules.annotations.logic()
annotationLogic.CreateSnapShot(
"FiducialLayoutSwitchBug1914-Diff",
"Difference between starting and ending fiducial seed positions",
slicer.qMRMLScreenShotDialog().Red, screenshotScaleFactor,
shotDiff)
# calculate the image difference
imageStats = vtk.vtkImageHistogramStatistics()
imageStats.SetInput(shotDiff)
imageStats.GenerateHistogramImageOff()
imageStats.Update()
meanVal = imageStats.GetMean()
self.delayDisplay("Mean of image difference = %g" % meanVal)
if meanVal > 5.0:
# raise Exception("Image difference is too great!\nExpected <= 5.0, but got %g" % (meanVal))
print(
"Image difference is too great!\nExpected <= 5.0, but got %g"
% (meanVal))
return False
self.delayDisplay('Test passed!')
return True
def takeScreenshot(self,name,type=-1):
# show the message even if not taking a screen shot
filePath = '/u/kanderle/Transfer/Movie/'+name+'.png'
if self.enableScreenshots == 0:
return
lm = slicer.app.layoutManager()
description = '4D'
# switch on the type to get the requested window
widget = 0
if type == -1:
# full window
widget = slicer.util.mainWindow()
elif type == slicer.qMRMLScreenShotDialog().FullLayout:
# full layout
widget = lm.viewport()
elif type == slicer.qMRMLScreenShotDialog().ThreeD:
# just the 3D window
widget = lm.threeDWidget(0).threeDView()
elif type == slicer.qMRMLScreenShotDialog().Red:
# red slice window
widget = lm.sliceWidget("Red")
elif type == slicer.qMRMLScreenShotDialog().Yellow:
# yellow slice window
widget = lm.sliceWidget("Yellow")
elif type == slicer.qMRMLScreenShotDialog().Green:
# green slice window
widget = lm.sliceWidget("Green")
# grab and convert to vtk image data
if type == slicer.qMRMLScreenShotDialog().ThreeD:
degrees = 71
n = 0 #
heartBeat = 0
heartDisplayNode = None
color = [0.56,0,0]
widget = lm.threeDWidget(0).threeDView()
for i in range(0,degrees):
if i < 10:
number = '0' + str(i)
else:
number = str(i)
filePath = '/u/kanderle/Transfer/Movie/'+name+'_'+number+'.png'
#if i%heartBeat == 0:
#if heartDisplayNode:
#heartDisplayNode.SetVisibility(0)
#n += 1
#if n>10:
#n = 1
#print "Changing state to: " + str(n)
#heartNode = slicer.util.getNode('Heart_' + str(n))
#if not heartNode:
#print "No Heart Node"
#n = n+1
#continue
#heartDisplayNode = heartNode.GetDisplayNode()
#heartDisplayNode.SetColor(color)
#heartDisplayNode.SetVisibility(1)
#heartDisplayNode.SetOpacity(0.8)
rw = widget.renderWindow()
wti = vtk.vtkWindowToImageFilter()
wti.SetInput(rw)
wti.Update()
writer = vtk.vtkPNGWriter()
writer.SetFileName(filePath)
writer.SetInputConnection(wti.GetOutputPort())
writer.Write()
widget.yaw()
widget.forceRender()
else:
qpixMap = qt.QPixmap().grabWidget(widget)
qimage = qpixMap.toImage()
imageData = vtk.vtkImageData()
slicer.qMRMLUtils().qImageToVtkImageData(qimage,imageData)
annotationLogic = slicer.modules.annotations.logic()
annotationLogic.CreateSnapShot(name, description, type, self.screenshotScaleFactor, imageData)
def run(self,enableScreenshots=0,screenshotScaleFactor=1):
"""
Run the actual algorithm
"""
self.delayDisplay('Running the aglorithm')
self.enableScreenshots = enableScreenshots
self.screenshotScaleFactor = screenshotScaleFactor
# Start in conventional layout
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
# without this delayed display, when running from the cmd line Slicer starts
# up in a different layout and the seed won't get rendered in the right spot
self.delayDisplay("Conventional view")
# Download MRHead from sample data
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
print("Getting MR Head Volume")
mrHeadVolume = sampleDataLogic.downloadMRHead()
# Place a fiducial on the red slice
markupsLogic = slicer.modules.markups.logic()
eye = [33.4975, 79.4042, -10.2143]
fidIndex = markupsLogic.AddFiducial(eye[0], eye[1], eye[2])
fidID = markupsLogic.GetActiveListID()
fidNode = slicer.mrmlScene.GetNodeByID(fidID)
self.delayDisplay("Placed a fiducial")
# Pan and zoom
sliceWidget = slicer.app.layoutManager().sliceWidget('Red')
sliceLogic = sliceWidget.sliceLogic()
compositeNode = sliceLogic.GetSliceCompositeNode()
sliceNode = sliceLogic.GetSliceNode()
sliceNode.SetXYZOrigin(-71.7, 129.7, 0.0)
sliceNode.SetFieldOfView(98.3, 130.5, 1.0)
self.delayDisplay("Panned and zoomed")
# Get the seed widget seed location
startingSeedDisplayCoords = [0.0, 0.0, 0.0]
helper = self.getFiducialSliceDisplayableManagerHelper('Red')
if helper != None:
seedWidget = helper.GetWidget(fidNode)
seedRepresentation = seedWidget.GetSeedRepresentation()
handleRep = seedRepresentation.GetHandleRepresentation(fidIndex)
startingSeedDisplayCoords = handleRep.GetDisplayPosition()
print('Starting seed display coords = %d, %d, %d' % (startingSeedDisplayCoords[0], startingSeedDisplayCoords[1], startingSeedDisplayCoords[2]))
self.takeScreenshot('FiducialLayoutSwitchBug1914-StartingPosition','Fiducial starting position',slicer.qMRMLScreenShotDialog().Red)
# Switch to red slice only
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
self.delayDisplay("Red Slice only")
# Switch to conventional layout
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
self.delayDisplay("Conventional layout")
# Get the current seed widget seed location
endingSeedDisplayCoords = [0.0, 0.0, 0.0]
helper = self.getFiducialSliceDisplayableManagerHelper('Red')
if helper != None:
seedWidget = helper.GetWidget(fidNode)
seedRepresentation = seedWidget.GetSeedRepresentation()
handleRep = seedRepresentation.GetHandleRepresentation(fidIndex)
endingSeedDisplayCoords = handleRep.GetDisplayPosition()
print('Ending seed display coords = %d, %d, %d' % (endingSeedDisplayCoords[0], endingSeedDisplayCoords[1], endingSeedDisplayCoords[2]))
self.takeScreenshot('FiducialLayoutSwitchBug1914-EndingPosition','Fiducial ending position',slicer.qMRMLScreenShotDialog().Red)
# Compare to original seed widget location
diff = math.pow((startingSeedDisplayCoords[0] - endingSeedDisplayCoords[0]),2) + math.pow((startingSeedDisplayCoords[1] - endingSeedDisplayCoords[1]),2) + math.pow((startingSeedDisplayCoords[2] - endingSeedDisplayCoords[2]),2)
if diff != 0.0:
diff = math.sqrt(diff)
self.delayDisplay("Difference between starting and ending seed display coordinates = %g" % diff)
if diff > 1.0:
# raise Exception("Display coordinate difference is too large!\nExpected < 1.0 but got %g" % (diff))
print("Display coordinate difference is too large!\nExpected < 1.0 but got %g" % (diff))
return False
if enableScreenshots == 1:
# compare the screen snapshots
startView = slicer.mrmlScene.GetFirstNodeByName('FiducialLayoutSwitchBug1914-StartingPosition')
startShot = startView.GetScreenShot()
endView = slicer.mrmlScene.GetFirstNodeByName('FiducialLayoutSwitchBug1914-EndingPosition')
endShot = endView.GetScreenShot()
imageMath = vtk.vtkImageMathematics()
imageMath.SetOperationToSubtract()
imageMath.SetInput1(startShot)
imageMath.SetInput2(endShot)
imageMath.Update()
shotDiff = imageMath.GetOutput()
# save it as a scene view
annotationLogic = slicer.modules.annotations.logic()
annotationLogic.CreateSnapShot("FiducialLayoutSwitchBug1914-Diff", "Difference between starting and ending fiducial seed positions",slicer.qMRMLScreenShotDialog().Red, screenshotScaleFactor, shotDiff)
# calculate the image difference
imageStats = vtk.vtkImageHistogramStatistics()
imageStats.SetInput(shotDiff)
imageStats.GenerateHistogramImageOff()
imageStats.Update()
meanVal = imageStats.GetMean()
self.delayDisplay("Mean of image difference = %g" % meanVal)
if meanVal > 5.0:
# raise Exception("Image difference is too great!\nExpected <= 5.0, but got %g" % (meanVal))
print("Image difference is too great!\nExpected <= 5.0, but got %g" % (meanVal))
return False
self.delayDisplay('Test passed!')
return True
