Difference between revisions of "Slicer3:Execution Model Documentation:Python"

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Line 37: Line 37:
 
==Python Module collection==
 
==Python Module collection==
  
[[Slicer3:Execution Model Documentation:Python#PythonScript.py | PythonScript.py]]  
+
* [[Slicer3:Execution Model Documentation:Python#PythonScript.py | PythonScript.py]]  
 +
* [[Slicer3:Execution Model Documentation:Python#SurfaceConnectivity.py | SurfaceConnectivity.py]]
 +
* [[Slicer3:Execution Model Documentation:Python#SurfaceICPRegistration.py | SurfaceICPRegistration.py]]
 +
* [[Slicer3:Execution Model Documentation:Python#SurfaceToolbox.py | SurfaceToolbox.py]]
 +
 
  
 
===PythonScript.py===
 
===PythonScript.py===
Line 152: Line 156:
  
 
Setting of the filtered poly data to the outputSurface is left to the user (see last line).
 
Setting of the filtered poly data to the outputSurface is left to the user (see last line).
 +
 +
 +
===SurfaceConnectivity.py===
 +
 +
XML = """<?xml version="1.0" encoding="utf-8"?>
 +
<executable>
 +
 +
  <category>Python Modules</category>
 +
  <title>Python Surface Connectivity</title>
 +
  <description>
 +
Identify connected regions of a surface.
 +
</description>
 +
  <version>1.0</version>
 +
  <documentation-url></documentation-url>
 +
  <license></license>
 +
  <contributor>Luca Antiga and Daniel Blezek</contributor>
 +
 +
  <parameters>
 +
    <label>Surface Connectivity Parameters</label>
 +
    <description>Parameters for surface connectivity</description>
 +
 +
    <string-enumeration>
 +
      <name>connectivityMode</name>
 +
      <longflag>connectivityMode</longflag>
 +
      <description>Mode of operation of connectivity filter</description>
 +
      <label>Connectivity mode</label>
 +
      <default>AllRegions</default>
 +
      <element>AllRegions</element>
 +
      <element>ClosestToSeed</element>
 +
    </string-enumeration>
 +
 +
    <boolean>
 +
      <name>enableOutputFiducials</name>
 +
      <longflag>enableOutputFiducials</longflag>
 +
      <description>Toggle generation of labeled fiducials corresponding to each extracted region</description>
 +
      <label>Enable output fiducials</label>
 +
      <default>false</default>
 +
    </boolean>
 +
 +
    <point multiple="false">
 +
      <name>seedPoint</name>
 +
      <longflag>seedPoint</longflag>
 +
      <label>Seed Point</label>
 +
      <description>Fiducial to extract closest surface</description>
 +
    </point>
 +
  </parameters>
 +
 +
  <parameters>
 +
    <label>IO</label>
 +
    <description>Input/output parameters</description>
 +
 +
    <geometry>
 +
      <name>inputSurface</name>
 +
      <label>Input Surface</label>
 +
      <channel>input</channel>
 +
      <index>0</index>
 +
      <description>Input surface to be filtered</description>
 +
    </geometry>
 +
 +
    <geometry>
 +
      <name>outputSurface</name>
 +
      <label>Output Surface</label>
 +
      <channel>output</channel>
 +
      <index>1</index>
 +
      <description>Output filtered surface</description>
 +
    </geometry>
 +
  </parameters>
 +
 +
</executable>
 +
"""
 +
 +
 +
def Execute (inputSurface, outputSurface, connectivityMode="AllRegions", enableOutputFiducials=False, seedPoint=[0.0,0.0,0.0]):
 +
 +
    Slicer = __import__("Slicer")
 +
    slicer = Slicer.Slicer()
 +
    scene = slicer.MRMLScene
 +
    inputSurface = scene.GetNodeByID(inputSurface)
 +
    outputSurface = scene.GetNodeByID(outputSurface)
 +
 +
    connectivityFilter = slicer.vtkPolyDataConnectivityFilter.New()
 +
    connectivityFilter.SetInput(inputSurface.GetPolyData())
 +
    if connectivityMode == "AllRegions":
 +
        connectivityFilter.SetExtractionModeToAllRegions()
 +
        connectivityFilter.ColorRegionsOn()
 +
    elif connectivityMode == "ClosestToSeed":
 +
        connectivityFilter.SetExtractionModeToClosestPointRegion()
 +
        connectivityFilter.SetClosestPoint(seedPoint[0],seedPoint[1],seedPoint[2])
 +
    connectivityFilter.Update()
 +
 +
    if enableOutputFiducials:
 +
        fiducialList = scene.CreateNodeByClass("vtkMRMLFiducialListNode")
 +
        scene.AddNode(fiducialList)
 +
        thresholdPoints = slicer.vtkThresholdPoints.New()
 +
        thresholdPoints.SetInput(connectivityFilter.GetOutput())
 +
        numberOfRegions = connectivityFilter.GetNumberOfExtractedRegions()
 +
        for i in range(numberOfRegions):
 +
            lower = i - 0.5
 +
            upper = i + 0.5
 +
            thresholdPoints.ThresholdBetween(lower,upper)
 +
            thresholdPoints.Update()
 +
            if thresholdPoints.GetOutput().GetNumberOfPoints() > 0:
 +
                point = thresholdPoints.GetOutput().GetPoint(0)
 +
                fid = fiducialList.AddFiducial()
 +
                fiducialList.SetNthFiducialXYZ(fid,point[0],point[1],point[2])
 +
                fiducialList.SetNthFiducialLabelText(fid,"Region %d" % i)
 +
 +
    outputSurface.SetAndObservePolyData(connectivityFilter.GetOutput())
 +
 +
#    inputSurface.GetDisplayNode().SetVisibilityOff()
 +
#    outputSurface.GetDisplayNode().ScalarVisibilityOn()
 +
 +
    return
 +
 +
 +
===SurfaceICPRegistration.py===
 +
 +
 +
 +
===SurfaceToolbox.py===

Revision as of 13:27, 7 November 2007

Home < Slicer3:Execution Model Documentation:Python

A Python interpreter has been integrated into Slicer3. More details of the Python language can be found at Python.org. This interpreter may be used to execute Python script plugins. The modules have a few specific requirements to be correctly found and used as plugins. Like the standard executable and shared library plugins, Python plugins need to be self describing. To do this, the script must have a top level variable called XML or provide a toXML procedure. For example:

XML = """<?xml version="1.0" encoding="utf-8"?>
<executable>
  <category>Filtering.Denoising</category>
  ...

def toXML():
  return XML;


Details of the XML format are found in the main Execution Model documentation. Rather than construct a command line to pass into Python, Slicer3 directly calls an Execute procedure. It is assumed that the Execute function expects positional arguments first, and any optional arguments are passed in as keyword arguments. For instance, the GradientAnisotropicDiffusion.py module provides an Execute:

def Execute ( inputVolume, outputVolume, conductance=1.0, timeStep=0.0625, iterations=1 ):
    print "Executing Python Demo Application!"
    Slicer = __import__ ( "Slicer" );
    slicer = Slicer.Slicer()
    in = slicer.MRMLScene.GetNodeByID ( inputVolume );
    out = slicer.MRMLScene.GetNodeByID ( outputVolume );

    filter = slicer.vtkITKGradientAnisotropicDiffusionImageFilter.New()
    filter.SetConductanceParameter ( conductance )
    filter.SetTimeStep ( timeStep )
    filter.SetNumberOfIterations ( iterations )
    filter.SetInput ( in.GetImageData() )
    filter.Update()
    out.SetAndObserveImageData(filter.GetOutput())
    return


The function first constructs a Slicer object by importing the Slicer module. The Slicer object is the main interface into Slicer3 as a whole. The first two arguments, inputVolume and outputVolume are not proper MRMLVolumes, and must be looked up using the Slicer object (that is, the arguments are unique IDs rather than pointers to the objects). The filter is constructed through the Slicer object, and the parameters are set. After the filter is updated, the output image is put using the SetAndObserveImageData method on the output volume.

ToDo
  • Progress functionality
  • Casting image arguments to proper MRML volume objects before calling Execute

Python Module collection


PythonScript.py

This module allows to run external Python code saved in a .py file on an image or surface (or both), and have the results loaded back in Slicer. It doesn't really do anything itself, but it's handy for:

  • writing Python modules, since one can store the actual module code in a file without having to copy it to Slicer3-build/lib/Slicer3/Plugins
  • writing quick one-shot filtering operations that are not elegible to become full-fledged modules
  • experimenting with Python in Slicer.
XML = """<?xml version="1.0" encoding="utf-8"?>
<executable>

  <category>Python Modules</category>
  <title>Python Script</title>
  <description>Run external Python code on a surface or image.</description>
  <version>1.0</version>
  <documentation-url></documentation-url>
  <license></license>
  <contributor>Luca Antiga and Daniel Blezek</contributor>

  <parameters>
    <label>Python Script Parameters</label>
    <description>Parameters for Python script</description>
    <file>
      <name>scriptFileName</name>
      <longflag>scriptFileName</longflag>
      <description>File containing Python code to run</description>
      <label>Script file</label>
    </file>
  </parameters>

  <parameters>
    <label>IO</label>
    <description>Input/output parameters</description>

    <geometry>
      <name>inputSurface</name>
      <longflag>inputSurface</longflag>
      <label>Input Surface</label>
      <channel>input</channel>
      <description>Input surface to be filtered</description>
    </geometry>

    <image>
      <name>inputVolume</name>
      <longflag>inputVolume</longflag>
      <label>Input Volume</label>
      <channel>input</channel>
      <description>Input image to be filtered</description>
    </image>

    <geometry>
      <name>outputSurface</name>
      <longflag>outputSurface</longflag>
      <label>Output Surface</label>
      <channel>output</channel>
      <description>Output filtered surface</description>
    </geometry>

    <image>
     <name>outputVolume</name>
     <longflag>outputVolume</longflag>
     <label>Output Volume</label>
     <channel>output</channel>
     <description>Output filtered volume</description>
   </image>


  </parameters>

</executable>
"""


def Execute (scriptFileName="", inputSurface="", inputVolume="", outputSurface="", outputVolume=""):

    Slicer = __import__("Slicer")
    slicer = Slicer.Slicer()
    scene = slicer.MRMLScene

    if inputSurface:
        inputSurface = scene.GetNodeByID(inputSurface)

    if inputVolume:
        inputVolume = scene.GetNodeByID(inputVolume)

    if outputSurface:
        outputSurface = scene.GetNodeByID(outputSurface)

   if outputVolume:
       outputVolume = scene.GetNodeByID(outputVolume)

    try:
        execfile(scriptFileName)
    except Exception, error:
        slicer.Application.ErrorMessage("Python script error: %s" % error)

    return

Note how the try...except block intercepts Python exceptions generated while running the external script and prints messages out in Slicer's message console.

Now let's see what an external script code could look like. Say we want to take the input surface and decimate it.

inputPolyData = inputSurface.GetPolyData()

decimation = slicer.vtkDecimatePro.New()
decimation.SetInput(inputSurface.GetPolyData())
decimation.SetTargetReduction(0.99)
decimation.Update()

outputSurface.SetAndObservePolyData(decimation.GetOutput())

In the script (which we can save in a .py file), we don't have to start by importing Slicer module, since it's already done in the PythonScript.py module. We have to assume that inputSurface, outputSurface, inputVolume and outputVolume are already available as MRML nodes (vtkMRMLModelNode and vtkMRMLVolumeNode, respectively), and that the slicer module is also already imported.

Setting of the filtered poly data to the outputSurface is left to the user (see last line).


SurfaceConnectivity.py

XML = """<?xml version="1.0" encoding="utf-8"?>
<executable>

  <category>Python Modules</category>
  <title>Python Surface Connectivity</title>
  <description>
Identify connected regions of a surface.
</description>
  <version>1.0</version>
  <documentation-url></documentation-url>
  <license></license>
  <contributor>Luca Antiga and Daniel Blezek</contributor>

  <parameters>
    <label>Surface Connectivity Parameters</label>
    <description>Parameters for surface connectivity</description>

    <string-enumeration>
      <name>connectivityMode</name>
      <longflag>connectivityMode</longflag>
      <description>Mode of operation of connectivity filter</description>
      <label>Connectivity mode</label>
      <default>AllRegions</default>
      <element>AllRegions</element>
      <element>ClosestToSeed</element>
    </string-enumeration>

    <boolean>
      <name>enableOutputFiducials</name>
      <longflag>enableOutputFiducials</longflag>
      <description>Toggle generation of labeled fiducials corresponding to each extracted region</description>
      <label>Enable output fiducials</label>
      <default>false</default>
    </boolean>

    <point multiple="false">
      <name>seedPoint</name>
      <longflag>seedPoint</longflag>
      <label>Seed Point</label>
      <description>Fiducial to extract closest surface</description>
    </point>
  </parameters>

  <parameters>
    <label>IO</label>
    <description>Input/output parameters</description>

    <geometry>
      <name>inputSurface</name>
      <label>Input Surface</label>
      <channel>input</channel>
      <index>0</index>
      <description>Input surface to be filtered</description>
    </geometry>

    <geometry>
      <name>outputSurface</name>
      <label>Output Surface</label>
      <channel>output</channel>
      <index>1</index>
      <description>Output filtered surface</description>
    </geometry>
  </parameters>

</executable>
"""


def Execute (inputSurface, outputSurface, connectivityMode="AllRegions", enableOutputFiducials=False, seedPoint=[0.0,0.0,0.0]):

    Slicer = __import__("Slicer")
    slicer = Slicer.Slicer()
    scene = slicer.MRMLScene
    inputSurface = scene.GetNodeByID(inputSurface)
    outputSurface = scene.GetNodeByID(outputSurface)

    connectivityFilter = slicer.vtkPolyDataConnectivityFilter.New()
    connectivityFilter.SetInput(inputSurface.GetPolyData())
    if connectivityMode == "AllRegions":
        connectivityFilter.SetExtractionModeToAllRegions()
        connectivityFilter.ColorRegionsOn()
    elif connectivityMode == "ClosestToSeed":
        connectivityFilter.SetExtractionModeToClosestPointRegion()
        connectivityFilter.SetClosestPoint(seedPoint[0],seedPoint[1],seedPoint[2])
    connectivityFilter.Update()

    if enableOutputFiducials:
        fiducialList = scene.CreateNodeByClass("vtkMRMLFiducialListNode")
        scene.AddNode(fiducialList)
        thresholdPoints = slicer.vtkThresholdPoints.New()
        thresholdPoints.SetInput(connectivityFilter.GetOutput())
        numberOfRegions = connectivityFilter.GetNumberOfExtractedRegions()
        for i in range(numberOfRegions):
            lower = i - 0.5
            upper = i + 0.5
            thresholdPoints.ThresholdBetween(lower,upper)
            thresholdPoints.Update()
            if thresholdPoints.GetOutput().GetNumberOfPoints() > 0:
                point = thresholdPoints.GetOutput().GetPoint(0)
                fid = fiducialList.AddFiducial()
                fiducialList.SetNthFiducialXYZ(fid,point[0],point[1],point[2])
                fiducialList.SetNthFiducialLabelText(fid,"Region %d" % i)

    outputSurface.SetAndObservePolyData(connectivityFilter.GetOutput())

#    inputSurface.GetDisplayNode().SetVisibilityOff()
#    outputSurface.GetDisplayNode().ScalarVisibilityOn()

    return


SurfaceICPRegistration.py

SurfaceToolbox.py