def GetModelSnapshot():
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
view = lm.threeDWidget(0).threeDView()
viewNode = view.mrmlViewNode()
view.resetFocalPoint()
viewNode.SetBackgroundColor((0,0,0))
viewNode.SetBackgroundColor2((0,0,0))
viewNode.SetAxisLabelsVisible(0)
viewNode.SetBoxVisible(0)
view.lookFromViewAxis(4)
view.setPitchRollYawIncrement(90)
view.pitch()
view.setPitchRollYawIncrement(30)
view.yaw()
view.pitchDirection = 1
view.pitch()
view.setZoomFactor(10)
view.zoomIn()
#view.setZoomFactor(5)
#view.zoomIn()
#view.zoomIn()
view.forceRender()
rw=view.renderWindow()
wti=vtk.vtkWindowToImageFilter()
wti.SetInput(rw)
slicer.app.processEvents()
wti.Update()
imgData3D = wti.GetOutput()
return(imgData3D)
def GetModelSnapshot():
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
view = lm.threeDWidget(0).threeDView()
viewNode = view.mrmlViewNode()
view.resetFocalPoint()
viewNode.SetBackgroundColor((0, 0, 0))
viewNode.SetBackgroundColor2((0, 0, 0))
viewNode.SetAxisLabelsVisible(0)
viewNode.SetBoxVisible(0)
view.lookFromViewAxis(4)
view.setPitchRollYawIncrement(90)
view.pitch()
view.setPitchRollYawIncrement(30)
view.yaw()
view.pitchDirection = 1
view.pitch()
view.setZoomFactor(10)
view.zoomIn()
#view.setZoomFactor(5)
#view.zoomIn()
#view.zoomIn()
view.forceRender()
rw = view.renderWindow()
wti = vtk.vtkWindowToImageFilter()
wti.SetInput(rw)
slicer.app.processEvents()
wti.Update()
imgData3D = wti.GetOutput()
return (imgData3D)
def run(self):
httpd = StoppableHttpServer(self.PORT)
self.httpdProcess = Process(target=httpd.serve_forever)
self.q= multiprocessing.Queue(1)
websocket_process = Process(target=startwebsocket, args=(8081,self.q))
import sys
oldstdin = sys.stdin;
oldstdout = sys.stdout;
oldstderr = sys.stderr;
filein = open("/home/utsav/tmp/stdin","r")
fileout = open("/home/utsav/tmp/stdout","w")
fileerr = open("/home/utsav/tmp/stderr","w")
sys.stdin = filein;
sys.stdout = fileout;
sys.stderr = fileerr;
print "starting"
websocket_process.start()
self.httpdProcess.start()
sys.stdin = oldstdin;
sys.stdout = oldstdout;
sys.stderr = oldstderr;
ren = slicer.app.layoutManager().activeThreeDRenderer()
self.w2i = vtk.vtkWindowToImageFilter()
self.w2i.SetInput(ren.GetRenderWindow())
self.w2i.SetInputBufferTypeToRGBA()
self.w2i.ShouldRerenderOff()
self.writer = vtk.vtkJPEGWriter()
self.writer.WriteToMemoryOn()
viewNode = slicer.util.getNodes('vtkMRMLViewNode*').values()[0]
viewNode.SetStereoType(6)
ren.GetRenderWindow().SetStereoTypeToSplitViewportHorizontal()
ren.GetRenderWindow().Render()
ren.AddObserver('EndEvent',self.OnRender)
def generate(self,
volumeRenderingNode,
filePattern="/tmp/slice_%04d.png"): # underscore not dash
self.cancelRequested = False
# Ensure view node and widget exists and cross-references are up-to-date
self.create3dView(volumeRenderingNode)
self.threeDViewNode.SetAndObserveParentLayoutNodeID(
volumeRenderingNode.GetID())
self.threeDWidget.setMRMLViewNode(self.threeDViewNode)
# Make sure the selected volume rendering node is visible in the capture view
if not volumeRenderingNode.IsDisplayableInView(
self.threeDViewNode.GetID()):
volumeRenderingNode.AddViewNodeID(self.threeDViewNode.GetID())
# Configure view and widget
self.threeDViewNode.SetBoxVisible(0)
self.threeDViewNode.SetAxisLabelsVisible(0)
self.threeDViewNode.SetVolumeRenderingQuality(
slicer.vtkMRMLViewNode.Normal
) # viewNode.Maximum could provide better quality but slower
self.threeDViewNode.SetRenderMode(slicer.vtkMRMLViewNode.Orthographic)
self.threeDViewNode.SetBackgroundColor((1, 1, 1))
self.threeDViewNode.SetBackgroundColor2((1, 1, 1))
# Turn off shading. We do not want any lighting effect (specular reflections, etc.) to be baked into the image.
originalShade = volumeRenderingNode.GetVolumePropertyNode(
).GetVolumeProperty().GetShade()
volumeRenderingNode.GetVolumePropertyNode().GetVolumeProperty(
).SetShade(False)
self.threeDWidget.resize(self.width, self.height)
self.threeDWidget.show()
# Save original ROI
volumeRenderingNode.SetCroppingEnabled(True)
roi = volumeRenderingNode.GetROINode()
roiCenter = [0] * 3
roiRadius = [0] * 3
roi.GetXYZ(roiCenter)
roi.GetRadiusXYZ(roiRadius)
originalRoiVisibility = roi.GetDisplayVisibility()
roi.SetDisplayVisibility(False)
cameraPositionOffset = 100.0
cameraNode = slicer.modules.cameras.logic().GetViewActiveCameraNode(
self.threeDViewNode)
cameraNode.SetFocalPoint(roiCenter)
cameraNode.SetPosition(
roiCenter[0], roiCenter[1],
roiCenter[2] + roiRadius[2] + cameraPositionOffset)
cameraNode.SetViewUp((0, 1, 0))
cameraNode.GetCamera().SetClippingRange(
cameraPositionOffset / 2.0,
roiRadius[2] * 2 + cameraPositionOffset * 2.0)
windowSizeInPixels = self.threeDWidget.threeDView().renderWindow(
).GetSize()
pixelSizeInMm = 25.4 / self.yResolutionDpi
heightOfViewportInMm = windowSizeInPixels[
1] * pixelSizeInMm / self.printScale
cameraNode.SetParallelScale(heightOfViewportInMm)
# cycle through the slabs
slabRadius = list(roiRadius)
slabRadius[2] = self.slabThickness
roi.SetRadiusXYZ(slabRadius)
slabCounter = 0
slabCenter = [roiCenter[0], roiCenter[1], roiCenter[2] - roiRadius[2]]
slabTop = roiCenter[2] + roiRadius[2]
scaledSlabSpacingMm = self.slabSpacingMm / self.printScale
numberOfSlabs = int(roiRadius[2] * 2.0 / scaledSlabSpacingMm) + 1
threeDView = self.threeDWidget.threeDView()
renderWindow = threeDView.renderWindow()
renderer = renderWindow.GetRenderers().GetFirstRenderer()
originalCameraUserTransform = cameraNode.GetCamera().GetUserTransform()
originalPixelAspect = renderer.GetPixelAspect()
cameraUserTransform = vtk.vtkTransform()
cameraUserTransform.Scale(self.xResolutionDpi / self.yResolutionDpi,
1.0, 1.0)
cameraNode.GetCamera().SetUserTransform(cameraUserTransform)
if self.transparentBackground:
originalAlphaBitPlanes = renderWindow.GetAlphaBitPlanes()
renderWindow.SetAlphaBitPlanes(1)
originalGradientBackground = renderer.GetGradientBackground()
renderer.SetGradientBackground(False)
logging.info("Starting render...")
while slabCenter[2] <= slabTop:
slicer.app.processEvents()
if self.cancelRequested:
break
roi.SetXYZ(slabCenter)
threeDView.forceRender()
windowToImage = vtk.vtkWindowToImageFilter()
if self.transparentBackground:
windowToImage.SetInputBufferTypeToRGBA()
renderWindow.Render()
windowToImage.SetInput(renderWindow)
# Write to file with custom DPI
# (use Qt file writer to allow saving DPI values)
filename = "c:/tmp/test.png"
windowToImage.Update()
vtkImage = windowToImage.GetOutput()
qImage = qt.QImage()
slicer.qMRMLUtils().vtkImageDataToQImage(vtkImage, qImage)
inchesPerMeter = 1000 / 25.4
qImage.setDotsPerMeterX(self.xResolutionDpi * inchesPerMeter)
qImage.setDotsPerMeterY(self.yResolutionDpi * inchesPerMeter)
imagePixmap = qt.QPixmap.fromImage(qImage)
filePath = filePattern % slabCounter
imagePixmap.save(filePath)
slabCounter += 1
slabCenter[2] = slabCenter[2] + scaledSlabSpacingMm
logging.info("Slab {0}/{1} saved to {2}".format(
slabCounter, numberOfSlabs, filePath))
self.threeDWidget.hide()
# reset ROI
roi.SetXYZ(roiCenter)
roi.SetRadiusXYZ(roiRadius)
roi.SetDisplayVisibility(originalRoiVisibility)
cameraNode.GetCamera().SetUserTransform(originalCameraUserTransform)
if self.transparentBackground:
renderWindow.SetAlphaBitPlanes(originalAlphaBitPlanes)
renderer.SetGradientBackground(originalGradientBackground)
volumeRenderingNode.GetVolumePropertyNode().GetVolumeProperty(
).SetShade(originalShade)
# for debugging convenience
slicer.modules.BitmapGeneratorWidget.threeDWidget = self.threeDWidget
slicer.modules.BitmapGeneratorWidget.threeDViewNode = self.threeDViewNode
slicer.modules.BitmapGeneratorWidget.volumeRenderingNode = volumeRenderingNode
if self.cancelRequested:
raise ValueError('User requested cancel.')
def threeD(self,cmd):
"""return a png for a threeD view
Args:
view={nodeid} (currently ignored)
"""
pngMethod = 'PIL'
if not hasImage:
pngMethod = 'VTK'
import numpy
import vtk.util.numpy_support
import slicer
try:
import cStringIO as StringIO
except ImportError:
import StringIO
p = urlparse.urlparse(cmd)
q = urlparse.parse_qs(p.query)
try:
view = q['view'][0].strip().lower()
except KeyError:
view = '1'
try:
size = int(q['size'][0].strip())
except (KeyError, ValueError):
size = None
try:
mode = str(q['mode'][0].strip())
except (KeyError, ValueError):
mode = None
try:
roll = float(q['roll'][0].strip())
except (KeyError, ValueError):
roll = None
try:
panX = float(q['panX'][0].strip())
except (KeyError, ValueError):
panX = None
try:
panY = float(q['panY'][0].strip())
except (KeyError, ValueError):
panY = None
try:
orbitX = float(q['orbitX'][0].strip())
except (KeyError, ValueError):
orbitX = None
try:
orbitY = float(q['orbitY'][0].strip())
except (KeyError, ValueError):
orbitY = None
layoutManager = slicer.app.layoutManager()
view = layoutManager.threeDWidget(0).threeDView()
view.renderEnabled = False
if mode:
cameraNode = slicer.util.getNode('*Camera*')
camera = cameraNode.GetCamera()
#if mode == 'start' or not self.interactionState.has_key('camera'):
#startCamera = vtk.vtkCamera()
#startCamera.DeepCopy(camera)
#self.interactionState['camera'] = startCamera
#startCamera = self.interactionState['camera']
cameraNode.DisableModifiedEventOn()
camera.DeepCopy(startCamera)
if roll:
camera.Roll(roll*100)
position = numpy.array(startCamera.GetPosition())
focalPoint = numpy.array(startCamera.GetFocalPoint())
viewUp = numpy.array(startCamera.GetViewUp())
viewPlaneNormal = numpy.array(startCamera.GetViewPlaneNormal())
viewAngle = startCamera.GetViewAngle()
viewRight = numpy.cross(viewUp,viewPlaneNormal)
viewDistance = numpy.linalg.norm(focalPoint - position)
self.logMessage("position", position)
self.logMessage("focalPoint", focalPoint)
self.logMessage("viewUp", viewUp)
self.logMessage("viewPlaneNormal", viewPlaneNormal)
self.logMessage("viewAngle", viewAngle)
self.logMessage("viewRight", viewRight)
self.logMessage("viewDistance", viewDistance)
if panX and panY:
offset = viewDistance * -panX * viewRight + viewDistance * viewUp * panY
newPosition = position + offset
newFocalPoint = focalPoint + offset
camera.SetPosition(newPosition)
camera.SetFocalPoint(newFocalPoint)
if orbitX and orbitY:
offset = viewDistance * -orbitX * viewRight + viewDistance * viewUp * orbitY
newPosition = position + offset
newFPToEye = newPosition - focalPoint
newPosition = focalPoint + viewDistance * newFPToEye / numpy.linalg.norm(newFPToEye)
camera.SetPosition(newPosition)
cameraNode.DisableModifiedEventOff()
cameraNode.InvokePendingModifiedEvent()
view.renderWindow().Render()
view.renderEnabled = True
w2i = vtk.vtkWindowToImageFilter()
w2i.SetInput(view.renderWindow())
w2i.SetReadFrontBuffer(0)
w2i.Update()
imageData = w2i.GetOutput()
pngData = self.vtkImageDataToPNG(imageData,method=pngMethod)
self.logMessage('threeD returning an image of %d length' % len(pngData))
return pngData
def modelHandler(imageNode, labelNode, Zind):
sliceZImageNode = extractMaxZSlice(imageNode, Zind)
sliceZLabelNode = extractMaxZSlice(labelNode, Zind)
volumesLogic = slicer.vtkSlicerVolumesLogic()
volumesLogic.SetVolumeAsLabelMap(sliceZLabelNode, True)
volumesLogic.SetVolumeAsLabelMap(labelNode, True)
sliceZLabelNodeDisplay = sliceZLabelNode.GetDisplayNode()
sliceZLabelNodeDisplay.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericColors.txt')
sliceZLabelNode.SetAndObserveDisplayNodeID(sliceZLabelNodeDisplay.GetID())
labelNodeDisplay = labelNode.GetDisplayNode()
labelNodeDisplay.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericColors.txt')
labelNode.SetAndObserveDisplayNodeID(labelNodeDisplay.GetID())
##
appLogic = slicer.app.applicationLogic()
selectionNode = appLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(sliceZImageNode.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(sliceZLabelNode.GetID())
appLogic.PropagateVolumeSelection()
##
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
redWidget = lm.sliceWidget('Red')
redLogic = redWidget.sliceLogic()
redView = redWidget.sliceView()
#redLogic.SetBackgroundWindowLevel(*windowLevel)
sln = slicer.util.getNode('vtkMRMLSliceNodeRed')
dims = list(sliceZImageNode.GetImageData().GetDimensions())
# dims[0] is x, dims[1] is y, dims [2] is Z
redWidget.setFixedSize(720,660)
slncw = redWidget.sliceController()
slncw.showLabelOutline(1)
slncw.fitSliceToBackground()
#sln.SetFieldOfView(dims[0],dims[1],1)
#sln.SetDimensions(dims[0],dims[1],1)
sliceannotations = slicer.modules.DataProbeInstance.infoWidget.sliceAnnoations
if sliceannotations.sliceViewAnnotationsCheckBox.checkState() == 2:
sliceannotations.sliceViewAnnotationsCheckBox.click()
slicer.app.processEvents()
wti=vtk.vtkWindowToImageFilter()
wti.SetInput(redView.renderWindow())
wti.Update()
imgDataRedSlice = wti.GetOutput()
modelMakerCLI(labelNode)
imgData3D = GetModelSnapshot()
append = vtk.vtkImageAppend()
append.SetAppendAxis(0)
append.AddInputData(imgDataRedSlice)
append.AddInputData(imgData3D)
append.Update()
finalImage = append.GetOutput()
return finalImage
def generate(self,
volumeRenderingNode,
filePattern="/tmp/slice_%04d.png"): # underscore not dash
"""
"""
lm = slicer.app.layoutManager()
# switch on the type to get the requested window
# just the 3D window
mainThreeDWidget = lm.threeDWidget(0).threeDView()
viewNode = mainThreeDWidget.mrmlViewNode()
# create the dummy threeD widget
threeDWidget = slicer.qMRMLThreeDWidget()
threeDWidget.resize(self.width, self.height)
threeDWidget.setObjectName("ThreeDWidget%s" %
viewNode.GetLayoutLabel())
threeDWidget.setMRMLScene(slicer.mrmlScene)
threeDWidget.setMRMLViewNode(viewNode)
self.threeDWidget = threeDWidget
threeDWidget.show()
# configure the view
cacheViewNode = slicer.vtkMRMLViewNode()
cacheViewNode.Copy(viewNode)
viewNode.SetBoxVisible(0)
viewNode.SetAxisLabelsVisible(0)
viewNode.SetBackgroundColor((1, 1, 1))
viewNode.SetBackgroundColor2((1, 1, 1))
roi = volumeRenderingNode.GetROINode()
roiCenter = [
0,
] * 3
roiRadius = [
0,
] * 3
roi.GetXYZ(roiCenter)
roi.GetRadiusXYZ(roiRadius)
roi.SetDisplayVisibility(0)
camera = vtk.vtkCamera()
camera.SetFocalPoint(roiCenter)
camera.SetPosition(roiCenter[0], roiCenter[1],
roiCenter[2] + roiRadius[2])
camera.SetViewUp((0, 1, 0))
mrmlCamera = slicer.util.getNode('Default Scene Camera')
cacheCamera = vtk.vtkCamera()
cacheCamera.DeepCopy(mrmlCamera.GetCamera())
mrmlCamera.GetCamera().DeepCopy(camera)
viewNode.SetRenderMode(slicer.vtkMRMLViewNode.Orthographic)
# cycle through the slabs
slabRadius = list(roiRadius)
slabRadius[2] = self.slabThickness
roi.SetRadiusXYZ(slabRadius)
slabCounter = 0
slabCenter = [roiCenter[0], roiCenter[1], roiCenter[2] - roiRadius[2]]
slabTop = roiCenter[2] + roiRadius[2]
threeDView = threeDWidget.threeDView()
renderWindow = threeDView.renderWindow()
self.delayDisplay("Starting render...", 300)
while slabCenter[2] <= slabTop:
roi.SetXYZ(slabCenter)
threeDView.forceRender()
windowToImage = vtk.vtkWindowToImageFilter()
windowToImage.SetInput(renderWindow)
writer = vtk.vtkPNGWriter()
writer.SetInputConnection(windowToImage.GetOutputPort())
filePath = filePattern % slabCounter
windowToImage.Update()
writer.SetFileName(filePath)
writer.Write()
slabCounter += 1
slabCenter[2] = slabCenter[2] + self.slabSpacing
# reset things
viewNode.Copy(cacheViewNode)
mrmlCamera.GetCamera().DeepCopy(cacheCamera)
roi.SetXYZ(roiCenter)
roi.SetRadiusXYZ(roiRadius)
roi.SetDisplayVisibility(1)
def test_ShadedModels1(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")
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
print("Getting MR Head Volume")
mrHeadVolume = sampleDataLogic.downloadMRHead()
resize = vtk.vtkImageResize()
resize.SetInputDataObject(mrHeadVolume.GetImageData())
resize.SetOutputDimensions(256,256,128)
resize.Update()
tdw = slicer.qMRMLThreeDWidget()
tdw.setMRMLScene(slicer.mrmlScene)
tdw.setMRMLViewNode(slicer.util.getNode("*ViewNode*"))
tdw.show()
from vtkSlicerShadedActorModuleLogicPython import *
shadedActor=vtkOpenGLShadedActor()
tdv = tdw.threeDView()
rw = tdv.renderWindow()
rens = rw.GetRenderers()
ren = rens.GetItemAsObject(0)
ren.AddActor(shadedActor)
mapper = vtk.vtkPolyDataMapper()
shadedActor.SetMapper(mapper)
shadedActor.SetVertexShaderSource("""
#version 120
attribute vec3 vertexAttribute;
attribute vec2 textureCoordinateAttribute;
varying vec4 interpolatedColor;
varying vec3 interpolatedTextureCoordinate;
void main()
{
interpolatedColor = vec4(0.5) + vec4(vertexAttribute, 1.);
interpolatedTextureCoordinate = vec3(textureCoordinateAttribute, .5);
gl_Position = vec4(vertexAttribute, 1.);
}
""")
shadedActor.SetFragmentShaderSource("""
#version 120
varying vec4 interpolatedColor;
varying vec3 interpolatedTextureCoordinate;
uniform sampler3D volumeSampler;
void main()
{
gl_FragColor = vec4 ( 1.0, 0.0, 0.0, 1.0 );
gl_FragColor = interpolatedColor;
vec4 volumeSample = texture3D(volumeSampler, interpolatedTextureCoordinate);
volumeSample *= 100;
gl_FragColor = mix( volumeSample, interpolatedColor, 0.5);
vec4 integratedRay = vec4(0.);
for (int i = 0; i < 256; i++) {
vec3 samplePoint = vec3(interpolatedTextureCoordinate.st, i/256.);
vec4 volumeSample = texture3D(volumeSampler, samplePoint);
integratedRay += volumeSample;
}
gl_FragColor = integratedRay;
}
""")
shadedActor.SetTextureImageData(resize.GetOutputDataObject(0))
#shadedActor.SetTextureImageData(mrHeadVolume.GetImageData())
sphereSource = vtk.vtkSphereSource()
mapper.SetInputConnection(sphereSource.GetOutputPort())
actor = vtk.vtkActor()
actor.SetScale(20,20,20)
actor.SetMapper(mapper)
ren.AddActor(actor)
rw.Render()
wti = vtk.vtkWindowToImageFilter()
wti.SetInput(rw)
iv = vtk.vtkImageViewer()
iv.SetColorLevel(128)
iv.SetColorWindow(256)
iv.SetInputConnection(wti.GetOutputPort())
iv.Render()
extensionManager = vtk.vtkOpenGLExtensionManager()
extensionManager.SetRenderWindow(rw)
extensionManager.Update()
print(extensionManager)
print(extensionManager.GetDriverGLVendor())
print(extensionManager.GetDriverGLVersion())
print(extensionManager.GetDriverGLRenderer())
slicer.modules.ShadedModelsWidget.tdw = tdw
slicer.modules.ShadedModelsWidget.iv = iv
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 modelHandler(ImageFilePath, imageNode, labelNode, imgOutputDir,
IDcurrPatient, Zind):
"""
imageBuffer = vtk.vtkImageData()
label = growCut(imageNode.GetImageData(),labelNode.GetImageData(),imageBuffer)
q = labelNode.GetImageData()
q.DeepCopy(label)
if labelNode.GetImageDataConnection():
labelNode.GetImageDataConnection().GetProducer().Update()
if labelNode.GetImageData().GetPointData().GetScalars() != None:
labelNode.GetImageData().GetPointData().GetScalars().Modified()
labelNode.GetImageData().Modified()
labelNode.Modified()
pdb.set_trace()
"""
imageSeriesDescription = os.path.basename(ImageFilePath).replace(
'.nrrd', '')
imagePatientID = os.path.basename(
os.path.dirname(os.path.dirname(os.path.dirname((ImageFilePath)))))
imageStudyDate = os.path.basename(
os.path.dirname(os.path.dirname((ImageFilePath))))
imagePatientID_StudyDate = imagePatientID + '_' + imageStudyDate
inputImage = su.PullFromSlicer(imageNode.GetName())
inputLabel = su.PullFromSlicer(labelNode.GetName())
pixelID = inputImage.GetPixelIDValue()
FlipYAxis = sitk.FlipImageFilter()
FlipYAxis.SetFlipAxes([False, True, False])
sizeZ = list(inputImage.GetSize())
sizeZ[2] = 0
indexZ = [0, 0, Zind]
ExtractorZ = sitk.ExtractImageFilter()
ExtractorZ.SetSize(sizeZ)
ExtractorZ.SetIndex(indexZ)
sliceZImage = ExtractorZ.Execute(inputImage)
sliceZLabel = ExtractorZ.Execute(inputLabel)
imageName = 'Axial_Slice_Image' + IDcurrPatient
labelName = 'Axial_Slice_Label' + IDcurrPatient
su.PushToSlicer(sliceZImage, imageName)
su.PushToSlicer(sliceZLabel, labelName)
sliceZImageNode = slicer.util.getNode(imageName)
sliceZLabelNode = slicer.util.getNode(labelName)
volumesLogic = slicer.vtkSlicerVolumesLogic()
volumesLogic.SetVolumeAsLabelMap(sliceZLabelNode, True)
volumesLogic.SetVolumeAsLabelMap(labelNode, True)
#sliceZLabelNode = binarizeLabelMapToValue(sliceZLabelNode, labelValue=296)
#labelNode = binarizeLabelMapToValue(labelNode, labelValue=296)
sliceZLabelNodeDisplay = sliceZLabelNode.GetDisplayNode()
sliceZLabelNodeDisplay.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericColors.txt')
sliceZLabelNode.SetAndObserveDisplayNodeID(sliceZLabelNodeDisplay.GetID())
labelNodeDisplay = labelNode.GetDisplayNode()
labelNodeDisplay.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericColors.txt')
labelNode.SetAndObserveDisplayNodeID(labelNodeDisplay.GetID())
##
appLogic = slicer.app.applicationLogic()
selectionNode = appLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(sliceZImageNode.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(sliceZLabelNode.GetID())
appLogic.PropagateVolumeSelection()
##
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
redWidget = lm.sliceWidget('Red')
redLogic = redWidget.sliceLogic()
redView = redWidget.sliceView()
#redLogic.SetBackgroundWindowLevel(*windowLevel)
sln = slicer.util.getNode('vtkMRMLSliceNodeRed')
dims = list(sliceZImageNode.GetImageData().GetDimensions())
# dims[0] is x, dims[1] is y, dims [2] is Z
redWidget.setFixedSize(720, 660)
slncw = redWidget.sliceController()
slncw.showLabelOutline(1)
slncw.fitSliceToBackground()
#sln.SetFieldOfView(dims[0],dims[1],1)
#sln.SetDimensions(dims[0],dims[1],1)
sliceannotations = slicer.modules.DataProbeInstance.infoWidget.sliceAnnoations
if sliceannotations.sliceViewAnnotationsCheckBox.checkState() == 2:
sliceannotations.sliceViewAnnotationsCheckBox.click()
slicer.app.processEvents()
wti = vtk.vtkWindowToImageFilter()
wti.SetInput(redView.renderWindow())
wti.Update()
imgDataRedSlice = wti.GetOutput()
modelMakerCLI(labelNode)
imgData3D = GetModelSnapshot()
append = vtk.vtkImageAppend()
append.SetAppendAxis(0)
append.AddInputData(imgDataRedSlice)
append.AddInputData(imgData3D)
append.Update()
finalImage = append.GetOutput()
#finalImagePath = str(os.path.join(imgOutputDir, IDcurrPatient + '_axial_sliceZ.png'))
finalImagePath = str(
os.path.join(
imgOutputDir,
imagePatientID_StudyDate + '_' + imageSeriesDescription + '.png'))
writer = vtk.vtkPNGWriter()
writer.SetFileName(finalImagePath)
writer.SetInputData(finalImage)
writer.Write()
def threeD(self, cmd):
"""return a png for a threeD view
Args:
view={nodeid} (currently ignored)
"""
pngMethod = 'PIL'
if not hasImage:
pngMethod = 'VTK'
import numpy
import vtk.util.numpy_support
import slicer
try:
import cStringIO as StringIO
except ImportError:
import StringIO
p = urlparse.urlparse(cmd)
q = urlparse.parse_qs(p.query)
try:
view = q['view'][0].strip().lower()
except KeyError:
view = '1'
try:
size = int(q['size'][0].strip())
except (KeyError, ValueError):
size = None
try:
mode = str(q['mode'][0].strip())
except (KeyError, ValueError):
mode = None
try:
roll = float(q['roll'][0].strip())
except (KeyError, ValueError):
roll = None
try:
panX = float(q['panX'][0].strip())
except (KeyError, ValueError):
panX = None
try:
panY = float(q['panY'][0].strip())
except (KeyError, ValueError):
panY = None
try:
orbitX = float(q['orbitX'][0].strip())
except (KeyError, ValueError):
orbitX = None
try:
orbitY = float(q['orbitY'][0].strip())
except (KeyError, ValueError):
orbitY = None
layoutManager = slicer.app.layoutManager()
view = layoutManager.threeDWidget(0).threeDView()
view.renderEnabled = False
if mode:
cameraNode = slicer.util.getNode('*Camera*')
camera = cameraNode.GetCamera()
#if mode == 'start' or not self.interactionState.has_key('camera'):
#startCamera = vtk.vtkCamera()
#startCamera.DeepCopy(camera)
#self.interactionState['camera'] = startCamera
#startCamera = self.interactionState['camera']
cameraNode.DisableModifiedEventOn()
camera.DeepCopy(startCamera)
if roll:
camera.Roll(roll * 100)
position = numpy.array(startCamera.GetPosition())
focalPoint = numpy.array(startCamera.GetFocalPoint())
viewUp = numpy.array(startCamera.GetViewUp())
viewPlaneNormal = numpy.array(startCamera.GetViewPlaneNormal())
viewAngle = startCamera.GetViewAngle()
viewRight = numpy.cross(viewUp, viewPlaneNormal)
viewDistance = numpy.linalg.norm(focalPoint - position)
self.logMessage("position", position)
self.logMessage("focalPoint", focalPoint)
self.logMessage("viewUp", viewUp)
self.logMessage("viewPlaneNormal", viewPlaneNormal)
self.logMessage("viewAngle", viewAngle)
self.logMessage("viewRight", viewRight)
self.logMessage("viewDistance", viewDistance)
if panX and panY:
offset = viewDistance * -panX * viewRight + viewDistance * viewUp * panY
newPosition = position + offset
newFocalPoint = focalPoint + offset
camera.SetPosition(newPosition)
camera.SetFocalPoint(newFocalPoint)
if orbitX and orbitY:
offset = viewDistance * -orbitX * viewRight + viewDistance * viewUp * orbitY
newPosition = position + offset
newFPToEye = newPosition - focalPoint
newPosition = focalPoint + viewDistance * newFPToEye / numpy.linalg.norm(
newFPToEye)
camera.SetPosition(newPosition)
cameraNode.DisableModifiedEventOff()
cameraNode.InvokePendingModifiedEvent()
view.renderWindow().Render()
view.renderEnabled = True
w2i = vtk.vtkWindowToImageFilter()
w2i.SetInput(view.renderWindow())
w2i.SetReadFrontBuffer(0)
w2i.Update()
imageData = w2i.GetOutput()
pngData = self.vtkImageDataToPNG(imageData, method=pngMethod)
self.logMessage('threeD returning an image of %d length' %
len(pngData))
return pngData
def modelHandler(imageNode, labelNode, Zind):
sliceZImageNode = extractMaxZSlice(imageNode, Zind)
sliceZLabelNode = extractMaxZSlice(labelNode, Zind)
volumesLogic = slicer.vtkSlicerVolumesLogic()
volumesLogic.SetVolumeAsLabelMap(sliceZLabelNode, True)
volumesLogic.SetVolumeAsLabelMap(labelNode, True)
sliceZLabelNodeDisplay = sliceZLabelNode.GetDisplayNode()
sliceZLabelNodeDisplay.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericColors.txt')
sliceZLabelNode.SetAndObserveDisplayNodeID(sliceZLabelNodeDisplay.GetID())
labelNodeDisplay = labelNode.GetDisplayNode()
labelNodeDisplay.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericColors.txt')
labelNode.SetAndObserveDisplayNodeID(labelNodeDisplay.GetID())
##
appLogic = slicer.app.applicationLogic()
selectionNode = appLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(sliceZImageNode.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(sliceZLabelNode.GetID())
appLogic.PropagateVolumeSelection()
##
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
redWidget = lm.sliceWidget('Red')
redLogic = redWidget.sliceLogic()
redView = redWidget.sliceView()
#redLogic.SetBackgroundWindowLevel(*windowLevel)
sln = slicer.util.getNode('vtkMRMLSliceNodeRed')
dims = list(sliceZImageNode.GetImageData().GetDimensions())
# dims[0] is x, dims[1] is y, dims [2] is Z
redWidget.setFixedSize(720, 660)
slncw = redWidget.sliceController()
slncw.showLabelOutline(1)
slncw.fitSliceToBackground()
#sln.SetFieldOfView(dims[0],dims[1],1)
#sln.SetDimensions(dims[0],dims[1],1)
sliceannotations = slicer.modules.DataProbeInstance.infoWidget.sliceAnnoations
if sliceannotations.sliceViewAnnotationsCheckBox.checkState() == 2:
sliceannotations.sliceViewAnnotationsCheckBox.click()
slicer.app.processEvents()
wti = vtk.vtkWindowToImageFilter()
wti.SetInput(redView.renderWindow())
wti.Update()
imgDataRedSlice = wti.GetOutput()
modelMakerCLI(labelNode)
imgData3D = GetModelSnapshot()
append = vtk.vtkImageAppend()
append.SetAppendAxis(0)
append.AddInputData(imgDataRedSlice)
append.AddInputData(imgData3D)
append.Update()
finalImage = append.GetOutput()
return finalImage
def modelHandler(ImageFilePath, imageNode, labelNode, imgOutputDir, IDcurrPatient, Zind):
"""
imageBuffer = vtk.vtkImageData()
label = growCut(imageNode.GetImageData(),labelNode.GetImageData(),imageBuffer)
q = labelNode.GetImageData()
q.DeepCopy(label)
if labelNode.GetImageDataConnection():
labelNode.GetImageDataConnection().GetProducer().Update()
if labelNode.GetImageData().GetPointData().GetScalars() != None:
labelNode.GetImageData().GetPointData().GetScalars().Modified()
labelNode.GetImageData().Modified()
labelNode.Modified()
pdb.set_trace()
"""
imageSeriesDescription = os.path.basename(ImageFilePath).replace('.nrrd','')
imagePatientID = os.path.basename(os.path.dirname(os.path.dirname(os.path.dirname((ImageFilePath)))))
imageStudyDate = os.path.basename(os.path.dirname(os.path.dirname((ImageFilePath))))
imagePatientID_StudyDate = imagePatientID + '_' + imageStudyDate
inputImage = su.PullFromSlicer(imageNode.GetName())
inputLabel = su.PullFromSlicer(labelNode.GetName())
pixelID = inputImage.GetPixelIDValue()
FlipYAxis = sitk.FlipImageFilter()
FlipYAxis.SetFlipAxes([False, True, False])
sizeZ = list(inputImage.GetSize())
sizeZ[2] = 0
indexZ = [0, 0, Zind]
ExtractorZ = sitk.ExtractImageFilter()
ExtractorZ.SetSize(sizeZ)
ExtractorZ.SetIndex(indexZ)
sliceZImage = ExtractorZ.Execute(inputImage)
sliceZLabel = ExtractorZ.Execute(inputLabel)
imageName = 'Axial_Slice_Image' + IDcurrPatient
labelName = 'Axial_Slice_Label' + IDcurrPatient
su.PushToSlicer(sliceZImage, imageName)
su.PushToSlicer(sliceZLabel, labelName)
sliceZImageNode = slicer.util.getNode(imageName)
sliceZLabelNode = slicer.util.getNode(labelName)
volumesLogic = slicer.vtkSlicerVolumesLogic()
volumesLogic.SetVolumeAsLabelMap(sliceZLabelNode, True)
volumesLogic.SetVolumeAsLabelMap(labelNode, True)
#sliceZLabelNode = binarizeLabelMapToValue(sliceZLabelNode, labelValue=296)
#labelNode = binarizeLabelMapToValue(labelNode, labelValue=296)
sliceZLabelNodeDisplay = sliceZLabelNode.GetDisplayNode()
sliceZLabelNodeDisplay.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericColors.txt')
sliceZLabelNode.SetAndObserveDisplayNodeID(sliceZLabelNodeDisplay.GetID())
labelNodeDisplay = labelNode.GetDisplayNode()
labelNodeDisplay.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericColors.txt')
labelNode.SetAndObserveDisplayNodeID(labelNodeDisplay.GetID())
##
appLogic = slicer.app.applicationLogic()
selectionNode = appLogic.GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(sliceZImageNode.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(sliceZLabelNode.GetID())
appLogic.PropagateVolumeSelection()
##
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
redWidget = lm.sliceWidget('Red')
redLogic = redWidget.sliceLogic()
redView = redWidget.sliceView()
#redLogic.SetBackgroundWindowLevel(*windowLevel)
sln = slicer.util.getNode('vtkMRMLSliceNodeRed')
dims = list(sliceZImageNode.GetImageData().GetDimensions())
# dims[0] is x, dims[1] is y, dims [2] is Z
redWidget.setFixedSize(720,660)
slncw = redWidget.sliceController()
slncw.showLabelOutline(1)
slncw.fitSliceToBackground()
#sln.SetFieldOfView(dims[0],dims[1],1)
#sln.SetDimensions(dims[0],dims[1],1)
sliceannotations = slicer.modules.DataProbeInstance.infoWidget.sliceAnnoations
if sliceannotations.sliceViewAnnotationsCheckBox.checkState() == 2:
sliceannotations.sliceViewAnnotationsCheckBox.click()
slicer.app.processEvents()
wti=vtk.vtkWindowToImageFilter()
wti.SetInput(redView.renderWindow())
wti.Update()
imgDataRedSlice = wti.GetOutput()
modelMakerCLI(labelNode)
imgData3D = GetModelSnapshot()
append = vtk.vtkImageAppend()
append.SetAppendAxis(0)
append.AddInputData(imgDataRedSlice)
append.AddInputData(imgData3D)
append.Update()
finalImage = append.GetOutput()
#finalImagePath = str(os.path.join(imgOutputDir, IDcurrPatient + '_axial_sliceZ.png'))
finalImagePath = str(os.path.join(imgOutputDir, imagePatientID_StudyDate + '_' + imageSeriesDescription +'.png'))
writer=vtk.vtkPNGWriter()
writer.SetFileName(finalImagePath)
writer.SetInputData(finalImage)
writer.Write()
def test_ShadedModels1(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")
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
print("Getting MR Head Volume")
mrHeadVolume = sampleDataLogic.downloadMRHead()
resize = vtk.vtkImageResize()
resize.SetInputDataObject(mrHeadVolume.GetImageData())
resize.SetOutputDimensions(256, 256, 128)
resize.Update()
tdw = slicer.qMRMLThreeDWidget()
tdw.setMRMLScene(slicer.mrmlScene)
tdw.setMRMLViewNode(slicer.util.getNode("*ViewNode*"))
tdw.show()
from vtkSlicerShadedActorModuleLogicPython import *
shadedActor = vtkOpenGLShadedActor()
tdv = tdw.threeDView()
rw = tdv.renderWindow()
rens = rw.GetRenderers()
ren = rens.GetItemAsObject(0)
ren.AddActor(shadedActor)
mapper = vtk.vtkPolyDataMapper()
shadedActor.SetMapper(mapper)
shadedActor.SetVertexShaderSource("""
#version 120
attribute vec3 vertexAttribute;
attribute vec2 textureCoordinateAttribute;
varying vec4 interpolatedColor;
varying vec3 interpolatedTextureCoordinate;
void main()
{
interpolatedColor = vec4(0.5) + vec4(vertexAttribute, 1.);
interpolatedTextureCoordinate = vec3(textureCoordinateAttribute, .5);
gl_Position = vec4(vertexAttribute, 1.);
}
""")
shadedActor.SetFragmentShaderSource("""
#version 120
varying vec4 interpolatedColor;
varying vec3 interpolatedTextureCoordinate;
uniform sampler3D volumeSampler;
void main()
{
gl_FragColor = vec4 ( 1.0, 0.0, 0.0, 1.0 );
gl_FragColor = interpolatedColor;
vec4 volumeSample = texture3D(volumeSampler, interpolatedTextureCoordinate);
volumeSample *= 100;
gl_FragColor = mix( volumeSample, interpolatedColor, 0.5);
vec4 integratedRay = vec4(0.);
for (int i = 0; i < 256; i++) {
vec3 samplePoint = vec3(interpolatedTextureCoordinate.st, i/256.);
vec4 volumeSample = texture3D(volumeSampler, samplePoint);
integratedRay += volumeSample;
}
gl_FragColor = integratedRay;
}
""")
shadedActor.SetTextureImageData(resize.GetOutputDataObject(0))
#shadedActor.SetTextureImageData(mrHeadVolume.GetImageData())
sphereSource = vtk.vtkSphereSource()
mapper.SetInputConnection(sphereSource.GetOutputPort())
actor = vtk.vtkActor()
actor.SetScale(20, 20, 20)
actor.SetMapper(mapper)
ren.AddActor(actor)
rw.Render()
wti = vtk.vtkWindowToImageFilter()
wti.SetInput(rw)
iv = vtk.vtkImageViewer()
iv.SetColorLevel(128)
iv.SetColorWindow(256)
iv.SetInputConnection(wti.GetOutputPort())
iv.Render()
extensionManager = vtk.vtkOpenGLExtensionManager()
extensionManager.SetRenderWindow(rw)
extensionManager.Update()
print(extensionManager)
print(extensionManager.GetDriverGLVendor())
print(extensionManager.GetDriverGLVersion())
print(extensionManager.GetDriverGLRenderer())
slicer.modules.ShadedModelsWidget.tdw = tdw
slicer.modules.ShadedModelsWidget.iv = iv