def storeSceneView(self, name, description=""):
"""
NOTE: Taken from here:
https://github.com/Slicer/Slicer/blob/master/Applications/SlicerApp/
Testing/Python/SlicerMRBTest.py#L273
Store a scene view into the current scene.
TODO: this might move to slicer.util
@param name: TheSceneViewName
@return: vtkImageData
"""
viewport = slicer.app.layoutManager().viewport()
qImage = qt.QPixmap().grabWidget(viewport).toImage()
imageData = vtk.vtkImageData()
slicer.qMRMLUtils().qImageToVtkImageData(qImage, imageData)
sceneViewNode = slicer.vtkMRMLSceneViewNode()
sceneViewNode.SetScreenShotType(4)
sceneViewNode.SetScreenShot(imageData)
return sceneViewNode.GetScreenShot()
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 storeSceneView(self, name, description=""):
"""
NOTE: Taken from here:
https://github.com/Slicer/Slicer/blob/master/Applications/SlicerApp/
Testing/Python/SlicerMRBTest.py#L273
Store a scene view into the current scene.
TODO: this might move to slicer.util
@param name: TheSceneViewName
@return: vtkImageData
"""
viewport = slicer.app.layoutManager().viewport()
qImage = qt.QPixmap().grabWidget(viewport).toImage()
imageData = vtk.vtkImageData()
slicer.qMRMLUtils().qImageToVtkImageData(qImage,imageData)
sceneViewNode = slicer.vtkMRMLSceneViewNode()
sceneViewNode.SetScreenShotType(4)
sceneViewNode.SetScreenShot(imageData)
return sceneViewNode.GetScreenShot()
def captureBitmap(self, threeDWidget, filePath):
# grab and convert to vtk image data
qpixMap = qt.QPixmap().grabWidget(threeDWidget)
qimage = qpixMap.toImage()
imageData = vtk.vtkImageData()
slicer.qMRMLUtils().qImageToVtkImageData(qimage, imageData)
qimage.save(filePath)
def onLoadFinished(self,worked): self.qImage.fill(0) self.webView.render(self.qImage) utils = slicer.qMRMLUtils() utils.qImageToVtkImageData(self.qImage,self.vtkImage) self.imageActor.SetInput(self.vtkImage) self.threeDView.scheduleRender()
def timeimage(self,cmd=''):
"""For debugging - return an image with the current time
rendered as text down to the hundredth of a second"""
# check arguments
p = urlparse.urlparse(cmd)
q = urlparse.parse_qs(p.query)
try:
color = "#" + q['color'][0].strip().lower()
except KeyError:
color = "#330"
#
# make a generally transparent image,
#
imageWidth = 128
imageHeight = 32
timeImage = qt.QImage(imageWidth, imageHeight, qt.QImage().Format_ARGB32)
timeImage.fill(0)
# a painter to use for various jobs
painter = qt.QPainter()
# draw a border around the pixmap
painter.begin(timeImage)
pen = qt.QPen()
color = qt.QColor(color)
color.setAlphaF(0.8)
pen.setColor(color)
pen.setWidth(5)
pen.setStyle(3) # dotted line (Qt::DotLine)
painter.setPen(pen)
rect = qt.QRect(1, 1, imageWidth-2, imageHeight-2)
painter.drawRect(rect)
color = qt.QColor("#333")
pen.setColor(color)
painter.setPen(pen)
position = qt.QPoint(10,20)
text = str(time.time()) # text to draw
painter.drawText(position, text)
painter.end()
# convert the image to vtk, then to png from there
vtkTimeImage = vtk.vtkImageData()
slicer.qMRMLUtils().qImageToVtkImageData(timeImage, vtkTimeImage)
pngData = self.vtkImageDataToPNG(vtkTimeImage)
return pngData
def _createMagnifiedPixmap(self, xyz, inputImageDataConnection, outputSize, crosshairColor, imageZoom=10):
# Use existing instance of objects to avoid instanciating one at each event.
imageCrop = self.imageCrop
painter = self.painter
pen = self.pen
def _roundInt(value):
try:
return int(round(value))
except ValueError:
return 0
imageCrop.SetInputConnection(inputImageDataConnection)
xyzInt = [0, 0, 0]
xyzInt = [_roundInt(value) for value in xyz]
producer = inputImageDataConnection.GetProducer()
dims = producer.GetOutput().GetDimensions()
minDim = min(dims[0],dims[1])
imageSize = _roundInt(minDim/imageZoom/2.0)
imin = max(0,xyzInt[0]-imageSize)
imax = min(dims[0]-1, xyzInt[0]+imageSize)
jmin = max(0,xyzInt[1]-imageSize)
jmax = min(dims[1]-1, xyzInt[1]+imageSize)
if (imin <= imax) and (jmin <= jmax):
imageCrop.SetVOI(imin, imax, jmin, jmax, 0,0)
imageCrop.Update()
vtkImage = imageCrop.GetOutput()
if vtkImage:
qImage = qt.QImage()
slicer.qMRMLUtils().vtkImageDataToQImage(vtkImage, qImage)
imagePixmap = qt.QPixmap.fromImage(qImage)
imagePixmap = imagePixmap.scaled(outputSize, qt.Qt.KeepAspectRatio, qt.Qt.FastTransformation)
# draw crosshair
painter.begin(imagePixmap)
pen = qt.QPen()
pen.setColor(crosshairColor)
painter.setPen(pen)
painter.drawLine(0, imagePixmap.height()/2, imagePixmap.width(), imagePixmap.height()/2)
painter.drawLine(imagePixmap.width()/2,0, imagePixmap.width()/2, imagePixmap.height())
painter.end()
return imagePixmap
return None
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 == 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")
else:
# default to using the full window
widget = slicer.util.mainWindow()
# reset the type so that the node is set correctly
type = slicer.qMRMLScreenShotDialog.FullLayout
# 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 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 == 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")
else:
# default to using the full window
widget = slicer.util.mainWindow()
# reset the type so that the node is set correctly
type = slicer.qMRMLScreenShotDialog.FullLayout
# 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 saveScreenshot(self, name, filePath, description):
type = slicer.qMRMLScreenShotDialog.FullLayout
lm = slicer.app.layoutManager()
widget = lm.viewport()
# 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, 1, imageData)
snapshotNode = slicer.util.getNode(name)
if not snapshotNode:
print "Can't get snapshotNode"
return
if not slicer.util.saveNode(snapshotNode, filePath):
print "Can't save " + filePath
return
def __init__(self,
parent=None,
width=400,
height=400,
showWidget=False,
scale=False):
super(LayerReveal, self).__init__()
self.width = width
self.height = height
self.showWidget = showWidget
self.scale = scale
self.renderer = None
# utility Qt instances for use in methods
self.gray = qt.QColor()
self.gray.setRedF(0.5)
self.gray.setGreenF(0.5)
self.gray.setBlueF(0.5)
# a painter to use for various jobs
self.painter = qt.QPainter()
# make a qwidget display
if self.showWidget:
self.frame = qt.QFrame(parent)
mw = slicer.util.mainWindow()
self.frame.setGeometry(mw.x, mw.y, self.width, self.height)
self.frameLayout = qt.QVBoxLayout(self.frame)
self.label = qt.QLabel()
self.frameLayout.addWidget(self.label)
self.frame.show()
# make an image actor in the slice view
self.vtkImage = vtk.vtkImageData()
self.mrmlUtils = slicer.qMRMLUtils()
self.imageMapper = vtk.vtkImageMapper()
self.imageMapper.SetColorLevel(128)
self.imageMapper.SetColorWindow(255)
if vtk.VTK_MAJOR_VERSION <= 5:
self.imageMapper.SetInput(self.vtkImage)
else:
self.imageMapper.SetInputData(self.vtkImage)
self.actor2D = vtk.vtkActor2D()
self.actor2D.SetMapper(self.imageMapper)
def __init__(self,parent=None,width=400,height=400,showWidget=False,scale=False):
super(LayerReveal,self).__init__()
self.width = width
self.height = height
self.showWidget = showWidget
self.scale = scale
self.renderer = None
# utility Qt instances for use in methods
self.gray = qt.QColor()
self.gray.setRedF(0.5)
self.gray.setGreenF(0.5)
self.gray.setBlueF(0.5)
# a painter to use for various jobs
self.painter = qt.QPainter()
# make a qwidget display
if self.showWidget:
self.frame = qt.QFrame(parent)
mw = slicer.util.mainWindow()
self.frame.setGeometry(mw.x, mw.y, self.width, self.height)
self.frameLayout = qt.QVBoxLayout(self.frame)
self.label = qt.QLabel()
self.frameLayout.addWidget(self.label)
self.frame.show()
# make an image actor in the slice view
self.vtkImage = vtk.vtkImageData()
self.mrmlUtils = slicer.qMRMLUtils()
self.imageMapper = vtk.vtkImageMapper()
self.imageMapper.SetColorLevel(128)
self.imageMapper.SetColorWindow(255)
if vtk.VTK_MAJOR_VERSION <= 5:
self.imageMapper.SetInput(self.vtkImage)
else:
self.imageMapper.SetInputData(self.vtkImage)
self.actor2D = vtk.vtkActor2D()
self.actor2D.SetMapper(self.imageMapper)
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 __init__(self,parent=None,width=400,height=400,showWidget=False,scale=False):
super(ROIManager,self).__init__()
self.width = width
self.height = height
self.showWidget = showWidget
self.scale = scale
self.renderer = None
self.ROIRadius = 20.0
self.minValueBG=0
self.maxValueBG=0
self.minValueFG=0
self.maxValueFG=0
self.probeWidget = None
self.drawOverlay = 0
# utility Qt instances for use in methods
self.gray = qt.QColor()
self.gray.setRedF(0.5)
self.gray.setGreenF(0.5)
self.gray.setBlueF(0.5)
# a painter to use for various jobs
self.painter = qt.QPainter()
# make a qwidget display
if self.showWidget:
self.frame = qt.QFrame(parent)
mw = slicer.util.mainWindow()
self.frame.setGeometry(mw.x, mw.y, self.width, self.height)
self.frameLayout = qt.QVBoxLayout(self.frame)
self.label = qt.QLabel()
self.frameLayout.addWidget(self.label)
self.frame.show()
# make an image actor in the slice view
self.vtkImage = vtk.vtkImageData()
self.mrmlUtils = slicer.qMRMLUtils()
self.imageMapper = vtk.vtkImageMapper()
self.imageMapper.SetColorLevel(128)
self.imageMapper.SetColorWindow(255)
if vtk.VTK_MAJOR_VERSION <= 5:
self.imageMapper.SetInput(self.vtkImage)
else:
self.imageMapper.SetInputData(self.vtkImage)
self.actor2D = vtk.vtkActor2D()
self.actor2D.SetMapper(self.imageMapper)
# make a circle actor
self.circle = vtk.vtkRegularPolygonSource()
self.circle.SetNumberOfSides(50)
self.circle.SetRadius(5)
self.circle.SetCenter(0,0,0)
self.circle.GeneratePolylineOn()
self.circle.GeneratePolygonOff()
self.circle.Update()
self.mapper = vtk.vtkPolyDataMapper2D()
self.actor = vtk.vtkActor2D()
if vtk.VTK_MAJOR_VERSION <= 5:
self.mapper.SetInput(self.circle.GetOutput())
else:
self.mapper.SetInputConnection(self.circle.GetOutputPort())
self.actor.SetMapper(self.mapper)
property_ = self.actor.GetProperty()
property_.SetColor(1,1,0)
property_.SetLineWidth(1)
def processEvent(self,observee,event):
# TODO: use a timer to delay calculation and compress events
insideView = False
ras = [0.0,0.0,0.0]
xyz = [0.0,0.0,0.0]
sliceNode = None
if self.CrosshairNode:
insideView = self.CrosshairNode.GetCursorPositionRAS(ras)
sliceNode = self.CrosshairNode.GetCursorPositionXYZ(xyz)
sliceLogic = None
if sliceNode:
appLogic = slicer.app.applicationLogic()
if appLogic:
sliceLogic = appLogic.GetSliceLogic(sliceNode)
if not insideView or not sliceNode or not sliceLogic:
self.currentLayoutName = None
# reset all the readouts
self.viewerColor.text = ""
self.viewInfo.text = ""
layers = ('L', 'F', 'B')
for layer in layers:
self.layerNames[layer].setText( "" )
self.layerIJKs[layer].setText( "" )
self.layerValues[layer].setText( "" )
self.imageLabel.hide()
self.viewerColor.hide()
self.viewInfo.hide()
self.viewerFrame.hide()
self.showImageBox.show()
return
self.viewerColor.show()
self.viewInfo.show()
self.viewerFrame.show()
self.showImageBox.hide()
self.currentLayoutName = sliceNode.GetLayoutName()
# populate the widgets
self.viewerColor.setText( " " )
rgbColor = sliceNode.GetLayoutColor();
color = qt.QColor.fromRgbF(rgbColor[0], rgbColor[1], rgbColor[2])
if hasattr(color, 'name'):
self.viewerColor.setStyleSheet('QLabel {background-color : %s}' % color.name())
# Described below are the details for the ras coordinate width set to 6:
# 1: sign
# 3: suggested number of digits before decimal point
# 1: decimal point:
# 1: number of digits after decimal point
spacing = "%.1f" % sliceLogic.GetLowestVolumeSliceSpacing()[2]
if sliceNode.GetSliceSpacingMode() == slicer.vtkMRMLSliceNode.PrescribedSliceSpacingMode:
spacing = "(%s)" % spacing
self.viewInfo.text = \
" {layoutName: <8s} RAS: ({ras_x:6.1f}, {ras_y:6.1f}, {ras_z:6.1f}) {orient: >8s} Sp: {spacing:s}" \
.format(layoutName=sliceNode.GetLayoutName(),
ras_x=ras[0],
ras_y=ras[1],
ras_z=ras[2],
orient=sliceNode.GetOrientationString(),
spacing=spacing
)
def _roundInt(value):
try:
return int(round(value))
except ValueError:
return 0
hasVolume = False
layerLogicCalls = (('L', sliceLogic.GetLabelLayer),
('F', sliceLogic.GetForegroundLayer),
('B', sliceLogic.GetBackgroundLayer))
for layer,logicCall in layerLogicCalls:
layerLogic = logicCall()
volumeNode = layerLogic.GetVolumeNode()
ijk = [0, 0, 0]
if volumeNode:
hasVolume = True
xyToIJK = layerLogic.GetXYToIJKTransform()
ijkFloat = xyToIJK.TransformDoublePoint(xyz)
ijk = [_roundInt(value) for value in ijkFloat]
self.layerNames[layer].setText(
"<b>%s</b>" % (self.fitName(volumeNode.GetName()) if volumeNode else "None"))
self.layerIJKs[layer].setText(
"({i:4d}, {j:4d}, {k:4d})".format(i=ijk[0], j=ijk[1], k=ijk[2]) if volumeNode else "")
self.layerValues[layer].setText(
"<b>%s</b>" % self.getPixelString(volumeNode,ijk) if volumeNode else "")
# set image
if (not slicer.mrmlScene.IsBatchProcessing()) and sliceLogic and hasVolume and self.showImage:
self.imageCrop.SetInputConnection(sliceLogic.GetBlend().GetOutputPort())
xyzInt = [0, 0, 0]
xyzInt = [_roundInt(value) for value in xyz]
dims = sliceLogic.GetBlend().GetOutput().GetDimensions()
minDim = min(dims[0],dims[1])
imageSize = _roundInt(minDim/self.imageZoom/2.0)
imin = max(0,xyzInt[0]-imageSize)
imax = min(dims[0]-1, xyzInt[0]+imageSize)
jmin = max(0,xyzInt[1]-imageSize)
jmax = min(dims[1]-1, xyzInt[1]+imageSize)
if (imin <= imax) and (jmin <= jmax):
self.imageCrop.SetVOI(imin, imax, jmin, jmax, 0,0)
self.imageCrop.Update()
vtkImage = self.imageCrop.GetOutput()
if vtkImage:
qImage = qt.QImage()
slicer.qMRMLUtils().vtkImageDataToQImage(vtkImage, qImage)
self.imagePixmap = self.imagePixmap.fromImage(qImage)
self.imagePixmap = self.imagePixmap.scaled(self.imageLabel.size, qt.Qt.KeepAspectRatio, qt.Qt.FastTransformation)
# draw crosshair
self.painter.begin(self.imagePixmap)
self.pen.setColor(color)
self.painter.setPen(self.pen)
self.painter.drawLine(0,self.imagePixmap.height()/2, self.imagePixmap.width(), self.imagePixmap.height()/2)
self.painter.drawLine(self.imagePixmap.width()/2,0, self.imagePixmap.width()/2, self.imagePixmap.height())
self.painter.end()
self.imageLabel.setPixmap(self.imagePixmap)
self.onShowImage(self.showImage)
sceneName = slicer.mrmlScene.GetURL()
if sceneName != "":
self.frame.parent().text = "Data Probe: %s" % self.fitName(sceneName,nameSize=2*self.nameSize)
else:
self.frame.parent().text = "Data Probe"
def processEvent(self,observee,event):
# TODO: use a timer to delay calculation and compress events
insideView = False
ras = [0.0,0.0,0.0]
xyz = [0.0,0.0,0.0]
sliceNode = None
if self.CrosshairNode:
insideView = self.CrosshairNode.GetCursorPositionRAS(ras)
sliceNode = self.CrosshairNode.GetCursorPositionXYZ(xyz)
sliceLogic = None
if sliceNode:
appLogic = slicer.app.applicationLogic()
if appLogic:
sliceLogic = appLogic.GetSliceLogic(sliceNode)
if not insideView or not sliceNode or not sliceLogic:
self.currentLayoutName = None
# reset all the readouts
self.viewerColor.text = ""
self.viewInfo.text = ""
layers = ('L', 'F', 'B')
for layer in layers:
self.layerNames[layer].setText( "" )
self.layerIJKs[layer].setText( "" )
self.layerValues[layer].setText( "" )
self.imageLabel.hide()
self.viewerColor.hide()
self.viewInfo.hide()
self.viewerFrame.hide()
self.showImageBox.show()
return
self.viewerColor.show()
self.viewInfo.show()
self.viewerFrame.show()
self.showImageBox.hide()
self.currentLayoutName = sliceNode.GetLayoutName()
# populate the widgets
self.viewerColor.setText( " " )
rgbColor = sliceNode.GetLayoutColor();
color = qt.QColor.fromRgbF(rgbColor[0], rgbColor[1], rgbColor[2])
if hasattr(color, 'name'):
self.viewerColor.setStyleSheet('QLabel {background-color : %s}' % color.name())
# Described below are the details for the ras coordinate width set to 6:
# 1: sign
# 3: suggested number of digits before decimal point
# 1: decimal point:
# 1: number of digits after decimal point
spacing = "%.1f" % sliceLogic.GetLowestVolumeSliceSpacing()[2]
if sliceNode.GetSliceSpacingMode() == slicer.vtkMRMLSliceNode.PrescribedSliceSpacingMode:
spacing = "(%s)" % spacing
self.viewInfo.text = \
" {layoutName: <8s} RAS: ({ras_x:6.1f}, {ras_y:6.1f}, {ras_z:6.1f}) {orient: >8s} Sp: {spacing:s}" \
.format(layoutName=sliceNode.GetLayoutName(),
ras_x=ras[0],
ras_y=ras[1],
ras_z=ras[2],
orient=sliceNode.GetOrientationString(),
spacing=spacing
)
def _roundInt(value):
try:
return int(round(value))
except ValueError:
return 0
hasVolume = False
layerLogicCalls = (('L', sliceLogic.GetLabelLayer),
('F', sliceLogic.GetForegroundLayer),
('B', sliceLogic.GetBackgroundLayer))
for layer,logicCall in layerLogicCalls:
layerLogic = logicCall()
volumeNode = layerLogic.GetVolumeNode()
ijk = [0, 0, 0]
if volumeNode:
hasVolume = True
xyToIJK = layerLogic.GetXYToIJKTransform()
ijkFloat = xyToIJK.TransformDoublePoint(xyz)
ijk = [_roundInt(value) for value in ijkFloat]
self.layerNames[layer].setText(
"<b>%s</b>" % (self.fitName(volumeNode.GetName()) if volumeNode else "None"))
self.layerIJKs[layer].setText(
"({i:4d}, {j:4d}, {k:4d})".format(i=ijk[0], j=ijk[1], k=ijk[2]) if volumeNode else "")
self.layerValues[layer].setText(
"<b>%s</b>" % self.getPixelString(volumeNode,ijk) if volumeNode else "")
# set image
if (not slicer.mrmlScene.IsBatchProcessing()) and sliceLogic and hasVolume and self.showImage:
self.imageCrop.SetInputConnection(sliceLogic.GetBlend().GetOutputPort())
xyzInt = [0, 0, 0]
xyzInt = [_roundInt(value) for value in xyz]
dims = sliceLogic.GetBlend().GetOutput().GetDimensions()
minDim = min(dims[0],dims[1])
imageSize = _roundInt(minDim/self.imageZoom/2.0)
imin = max(0,xyzInt[0]-imageSize)
imax = min(dims[0]-1, xyzInt[0]+imageSize)
jmin = max(0,xyzInt[1]-imageSize)
jmax = min(dims[1]-1, xyzInt[1]+imageSize)
if (imin <= imax) and (jmin <= jmax):
self.imageCrop.SetVOI(imin, imax, jmin, jmax, 0,0)
self.imageCrop.Update()
vtkImage = self.imageCrop.GetOutput()
if vtkImage:
qImage = qt.QImage()
slicer.qMRMLUtils().vtkImageDataToQImage(vtkImage, qImage)
self.imagePixmap = self.imagePixmap.fromImage(qImage)
self.imagePixmap = self.imagePixmap.scaled(self.imageLabel.size, qt.Qt.KeepAspectRatio, qt.Qt.FastTransformation)
# draw crosshair
self.painter.begin(self.imagePixmap)
self.pen.setColor(color)
self.painter.setPen(self.pen)
self.painter.drawLine(0,self.imagePixmap.height()/2, self.imagePixmap.width(), self.imagePixmap.height()/2)
self.painter.drawLine(self.imagePixmap.width()/2,0, self.imagePixmap.width()/2, self.imagePixmap.height())
self.painter.end()
self.imageLabel.setPixmap(self.imagePixmap)
self.onShowImage(self.showImage)
sceneName = slicer.mrmlScene.GetURL()
if sceneName != "":
self.frame.parent().text = "Data Probe: %s" % self.fitName(sceneName,nameSize=2*self.nameSize)
else:
self.frame.parent().text = "Data Probe"
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 revealPixmap(self, xy):
"""fill a pixmap with an image that has a reveal pattern
at xy with the fg drawn over the bg"""
# Get QImages for the two layers
bgVTKImage = self.layerLogics['B'].GetImageData()
fgVTKImage = self.layerLogics['F'].GetImageData()
bgQImage = qt.QImage()
fgQImage = qt.QImage()
slicer.qMRMLUtils().vtkImageDataToQImage(bgVTKImage, bgQImage)
slicer.qMRMLUtils().vtkImageDataToQImage(fgVTKImage, fgQImage)
# get the geometry of the focal point (xy) and images
# noting that vtk has the origin at the bottom left and qt has
# it at the top left. yy is the flipped version of y
imageWidth = bgQImage.width()
imageHeight = bgQImage.height()
x,y=xy
yy = imageHeight-y
#
# make a generally transparent image,
# then fill quadrants with the fg image
#
overlayImage = qt.QImage(imageWidth, imageHeight, qt.QImage().Format_ARGB32)
overlayImage.fill(0)
halfWidth = imageWidth/2
halfHeight = imageHeight/2
topLeft = qt.QRect(0,0, x, yy)
bottomRight = qt.QRect(x, yy, imageWidth-x-1, imageHeight-yy-1)
self.painter.begin(overlayImage)
self.painter.drawImage(topLeft, fgQImage, topLeft)
self.painter.drawImage(bottomRight, fgQImage, bottomRight)
self.painter.end()
# draw the bg and fg on top of gray background
compositePixmap = qt.QPixmap(self.width,self.height)
compositePixmap.fill(self.gray)
self.painter.begin(compositePixmap)
self.painter.drawImage(
-1 * (x -self.width/2),
-1 * (yy -self.height/2),
bgQImage)
self.painter.drawImage(
-1 * (x -self.width/2),
-1 * (yy -self.height/2),
overlayImage)
self.painter.end()
if self.scale:
compositePixmap = self.scalePixmap(compositePixmap)
# draw a border around the pixmap
self.painter.begin(compositePixmap)
self.pen = qt.QPen()
self.color = qt.QColor("#FF0")
self.color.setAlphaF(0.3)
self.pen.setColor(self.color)
self.pen.setWidth(5)
self.pen.setStyle(3) # dotted line (Qt::DotLine)
self.painter.setPen(self.pen)
rect = qt.QRect(1, 1, self.width-2, self.height-2)
self.painter.drawRect(rect)
self.painter.end()
return compositePixmap
def revealPixmap(self, xy):
"""fill a pixmap with an image that has a reveal pattern
at xy with the fg drawn over the bg"""
# Get QImages for the two layers
bgVTKImage = self.layerLogics['B'].GetImageData()
fgVTKImage = self.layerLogics['F'].GetImageData()
bgQImage = qt.QImage()
fgQImage = qt.QImage()
slicer.qMRMLUtils().vtkImageDataToQImage(bgVTKImage, bgQImage)
slicer.qMRMLUtils().vtkImageDataToQImage(fgVTKImage, fgQImage)
# get the geometry of the focal point (xy) and images
# noting that vtk has the origin at the bottom left and qt has
# it at the top left. yy is the flipped version of y
imageWidth = bgQImage.width()
imageHeight = bgQImage.height()
x, y = xy
yy = imageHeight - y
#
# make a generally transparent image,
# then fill quadrants with the fg image
#
overlayImage = qt.QImage(imageWidth, imageHeight,
qt.QImage().Format_ARGB32)
overlayImage.fill(0)
halfWidth = imageWidth / 2
halfHeight = imageHeight / 2
topLeft = qt.QRect(0, 0, x, yy)
bottomRight = qt.QRect(x, yy, imageWidth - x - 1, imageHeight - yy - 1)
self.painter.begin(overlayImage)
self.painter.drawImage(topLeft, fgQImage, topLeft)
self.painter.drawImage(bottomRight, fgQImage, bottomRight)
self.painter.end()
# draw the bg and fg on top of gray background
compositePixmap = qt.QPixmap(self.width, self.height)
compositePixmap.fill(self.gray)
self.painter.begin(compositePixmap)
self.painter.drawImage(-1 * (x - self.width / 2),
-1 * (yy - self.height / 2), bgQImage)
self.painter.drawImage(-1 * (x - self.width / 2),
-1 * (yy - self.height / 2), overlayImage)
self.painter.end()
if self.scale:
compositePixmap = self.scalePixmap(compositePixmap)
# draw a border around the pixmap
self.painter.begin(compositePixmap)
self.pen = qt.QPen()
self.color = qt.QColor("#FF0")
self.color.setAlphaF(0.3)
self.pen.setColor(self.color)
self.pen.setWidth(5)
self.pen.setStyle(3) # dotted line (Qt::DotLine)
self.painter.setPen(self.pen)
rect = qt.QRect(1, 1, self.width - 2, self.height - 2)
self.painter.drawRect(rect)
self.painter.end()
return compositePixmap