Python interactor

The Python interactor is a very useful util to access run-time any 3DSlicer and SlicerAstro classes: MRML nodes, Widgets and Logics (e.g., the data of the fits file are stored in the MRML AstroVolume class). Python script can also be runned by typing on the terminal:

Slicer --python-script example.py

or by copying and pasting the code in the python console of 3DSlicer:

See also:

• https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Python_scripting
• http://www.slicer.org/slicerWiki/images/d/d7/Slicer4_ProgrammingTutorial_SPujol-SPieper_slicer4.4.pdf

Install Additional Python packages

3DSlicer and SlicerAstro binaries deliver its own Python environment. The Python version is 2.7 and it incorporates the additional package numpy. It is possible to install additional 'pure' python packages from the Python interactor as follow:

import pip 
pip.main(['install', 'astropy'])

3DSlicer Python scripts repository

• https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository

SlicerAstro Python scripts repository

• SmoothRenderSaveVideos.py:

  slicer.util.loadVolume("/full_path/galaxy.fits",{"center":True})
  mw = slicer.util.mainWindow()
  ms = mw.moduleSelector()
  # Smooth the datacube
  ms.selectModule('AstroSmoothing')
  smowidget = slicer.modules.astrosmoothing.widgetRepresentation()
  smomrmlpara = smowidget.mrmlAstroSmoothingParametersNode()
  smomrmlpara.SetMode("Manual")
  # only if a GPU is present:
  #smomrmlpara.SetHardware(1)
  smowidget.onApply()
  ms.selectModule('AstroVolume')
  # Setting maximum quality for the rendering
  astrovolumewidget = slicer.modules.astrovolume.widgetRepresentation()
  astrovolumewidget.onCurrentQualityControlChanged(1)
  volumes = slicer.mrmlScene.GetNodesByClass("vtkMRMLAstroVolumeNode")
  volumefiltered = volumes.GetItemAsObject(1)
  smomrmlpara.SetInputVolumeNodeID(volumefiltered.GetID())
  astrovolumewidget.onCurrentQualityControlChanged(1)
  # Create videos 
  ms.selectModule('ScreenCapture')
  screencapturewidget = slicer.modules.screencapture.widgetRepresentation()
  instance = screencapturewidget.self()
  viewNode = slicer.util.getNode('vtkMRMLViewNode1')
  instance.viewNodeSelector.setCurrentNode(viewNode)
  instance.numberOfStepsSliderWidget.setValue(360)
  instance.videoExportCheckBox.setChecked(1)
  instance.videoFormatWidget.setCurrentIndex(1)
  instance.videoFileNameWidget.setText("WEIN069.mp4")
  instance.videoLengthSliderWidget.setValue(6)
  instance.onCaptureButton()
  viewNode = slicer.util.getNode('vtkMRMLViewNode2')
  instance.viewNodeSelector.setCurrentNode(viewNode)
  instance.viewNodeSelector.setCurrentNode(viewNode)
  instance.numberOfStepsSliderWidget.setValue(360)
  instance.videoExportCheckBox.setChecked(1)
  instance.videoFormatWidget.setCurrentIndex(1)
  instance.videoFileNameWidget.setText("WEIN069_smoothed.mp4")
  instance.videoLengthSliderWidget.setValue(6)
  instance.onCaptureButton()

• Create(alike)MomentMap.py:

  # Get the data-cube volume
  volumeNode = getNode('name of the object')
  datacube = volumeNode.GetImageData()
  
  # Get dimensions
  N1 = int(volumeNode.GetAttribute("SlicerAstro.NAXIS1"))
  N2 = int(volumeNode.GetAttribute("SlicerAstro.NAXIS2"))
  RMS = float(volumeNode.GetAttribute("SlicerAstro.RMS"))
  
  # Create an empty 2-D image
  imageSize = [N1, N2, 1]
  imageSpacing = [1.0, 1.0, 1.0]
  voxelType = vtk.VTK_FLOAT
  imageDataTemp = vtk.vtkImageData()
  imageDataTemp.SetDimensions(imageSize)
  imageDataTemp.SetSpacing(imageSpacing)
  imageDataTemp.AllocateScalars(voxelType, 1)
  
  extentTemp = imageDataTemp.GetExtent()
  for i in xrange(extentTemp[0], extentTemp[1]+1):
      for j in xrange(extentTemp[2], extentTemp[3]+1):
         for k in xrange(extentTemp[4], extentTemp[5]+1):
            imageDataTemp.SetScalarComponentFromFloat(i,j,k,0,0.)
  
  # calculate moment map
  imageData = volumeNode.GetImageData()
  extent = imageData.GetExtent()
  for i in xrange(extent[0], extent[1]+1):
      for j in xrange(extent[2], extent[3]+1):
         sum = 0.
         for k in xrange(extent[4], extent[5]+1):
            value = imageData.GetScalarComponentAsFloat(i,j,k,0)
            if value > 3 * RMS:
               sum += value
         imageDataTemp.SetScalarComponentFromFloat(i,j,0,0,sum)
  
  imageDataTemp.Modified()
  point = imageDataTemp.GetPointData()
  array = point.GetArray("ImageScalars")
  point.Modified()
  array.Modified()
  array.GetValueRange()
  
  # create Astro Volume for the moment map
  astroVolumeLogic = slicer.modules.astrovolume.logic()
  volumeNodeMomentMap = astroVolumeLogic.CloneVolume(slicer.mrmlScene, volumeNode, 'MomentMap')
  
  # modify fits attributes
  volumeNodeMomentMap.SetAttribute("SlicerAstro.NAXIS", "2")
  volumeNodeMomentMap.RemoveAttribute("SlicerAstro.NAXIS3")
  volumeNodeMomentMap.RemoveAttribute("SlicerAstro.CROTA3")
  volumeNodeMomentMap.RemoveAttribute("SlicerAstro.CRPIX3")
  volumeNodeMomentMap.RemoveAttribute("SlicerAstro.CRVAL3")
  volumeNodeMomentMap.RemoveAttribute("SlicerAstro.CTYPE3")
  volumeNodeMomentMap.RemoveAttribute("SlicerAstro.CUNIT3")
  volumeNodeMomentMap.RemoveAttribute("SlicerAstro.DTYPE3")
  volumeNodeMomentMap.RemoveAttribute("SlicerAstro.DRVAL3")
  volumeNodeMomentMap.RemoveAttribute("SlicerAstro.DUNIT3")
  
  # copy 2-D image into the Astro Volume object
  volumeNodeMomentMap.SetAndObserveImageData(imageDataTemp)
  volumeNodeMomentMap.UpdateNoiseAttributes()
  volumeNodeMomentMap.UpdateRangeAttributes()
  
  # change colorMap of the 2-D image
  displayNode = volumeNodeMomentMap.GetDisplayNode()
  displayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeRainbow')
  
  # changing the colorMap parameters
  #displayNode.AutoWindowLevelOff()
  #displayNode.SetWindow(??)
  #displayNode.SetLevel(??)
  
  
  

• AccessDataAsNumpy.py:

  def array(pattern = "", index = 0):
    """Return the array you are "most likely to want" from the indexth
    MRML node that matches the pattern.  Meant to be used in the python
    console for quick debugging/testing.
    """
  
    import vtk.util.numpy_support
    n = getNode(pattern=pattern, index=index)
    i = n.GetImageData()
    shape = list(n.GetImageData().GetDimensions())
    shape.reverse()
    a = vtk.util.numpy_support.vtk_to_numpy(i.GetPointData().GetScalars()).reshape(shape)
    return a
  
  

• maskVolumeWithLabelVolume.py:

  # Get the data-cube volumes
  volumeNode = getNode('Name')
  volumeLabelNode = getNode('LabelName')
  
  # masking
  imageData = volumeNode.GetImageData()
  imageDataLabel = volumeLabelNode.GetImageData()
  extent = imageData.GetExtent()
  for i in xrange(extent[0], extent[1]+1):
     for j in xrange(extent[2], extent[3]+1):
        for k in xrange(extent[4], extent[5]+1):
           if imageDataLabel.GetScalarComponentAsFloat(i,j,k,0) < 1 :
              imageData.SetScalarComponentFromFloat(i,j,k,0, 0.)
  
  # update volume keywords
  volumeNode.UpdateNoiseAttributes()
  volumeNode.UpdateRangeAttributes()
  
  

• more to come...