Documentation/Nightly/Developers/SlicerExecutionModel/Python - Revision history

Pieper at 22:27, 3 July 2018

2018-07-03T22:27:22Z

Lasso: moved Slicer3:Execution Model Documentation:Python to Documentation/Nightly/Developers/SlicerExecutionModel/Python: Slicer3 documentation is not maintained anymore and it is not clear for readers if the content is applicable to current Slicer

2015-06-16T21:32:51Z

moved Slicer3:Execution Model Documentation:Python to Documentation/Nightly/Developers/SlicerExecutionModel/Python: Slicer3 documentation is not maintained anymore and it is not clear for readers if the content is applicable to current Slicer

Lantiga: /* Python Module collection */

2009-06-29T10:47:49Z

Python Module collection

Show changes

Lantiga: /* Python Modules */

2008-09-05T17:19:49Z

Python Modules

Lantiga: /* SurfaceToolbox.py */

2008-09-05T16:37:29Z

SurfaceToolbox.py

Lantiga: /* SurfaceICPRegistration.py */

2008-09-05T16:36:41Z

SurfaceICPRegistration.py

Lantiga: /* SurfaceICPRegistration.py */

2008-09-05T16:35:19Z

SurfaceICPRegistration.py

Lantiga: /* SurfaceICPRegistration.py */

2008-09-05T16:34:43Z

SurfaceICPRegistration.py

Lantiga: Changes to the Python module examples with new style Python interface

2008-08-07T08:14:23Z

Changes to the Python module examples with new style Python interface

Marianna: /* Python Module collection */

2008-05-19T19:47:29Z

Python Module collection

← Older revision		Revision as of 22:27, 3 July 2018
Line 1:		Line 1:
		+	<big>'''''This page describes functionality in Slicer 3.x. To write a CLI in python for Slicer 4.9 and greater have a look at [https://github.com/Radiomics/SlicerRadiomics/tree/master/SlicerRadiomicsCLI this example script] from the SlicerRadiomics extension.'''''</big>
		+
	==Python Modules==		==Python Modules==

@@ Line 28: / Line 28: @@
       filter.Update()
       out.SetAndObserveImageData(filter.GetOutput())
       return

@@ Line 635: / Line 635: @@
   def Execute (inputSurface, outputSurface, \
       decimationEnabled=False, targetReduction=0.8, boundaryDeletion=True, \
-      smoothingEnabled=False, smoothingMethod="Taubin", boundarySmoothing=True, laplaceIterations=10, laplaceRelaxation=0.1, taubinIterations=10, taubinPassband=0.1, \
+      smoothingEnabled=False, smoothingMethod="Taubin", boundarySmoothing=True, \
       normalsEnabled=False, flipNormals=False, splitting=False, featureAngle=30.0, \
       cleanerEnabled=False):

@@ Line 322: / Line 322: @@
         <longflag>meanDistanceMode</longflag>
         <label>Mean distance mode</label>
-        <description>Set how the mean distance should be computed, RMS (square root of the average of the sum of squares of the closest point distances) or AbsoluteValue (mean of the sum of absolute values of the closest point distances)</description>
+        <description>Set how the mean distance should be computed, RMS (square root of the average of the sum of squares
         <default>RMS</default>
         <element>RMS</element>

@@ Line 322: / Line 322: @@
         <longflag>meanDistanceMode</longflag>
         <label>Mean distance mode</label>
-        <description>Set how the mean distance should be computed, RMS (square root of the average of the sum of squares of the closest point distances) or \
+        <description>Set how the mean distance should be computed, RMS (square root of the average of the sum of squares of the closest point distances) or AbsoluteValue (mean of the sum of absolute values of the closest point distances)</description>
         <default>RMS</default>
         <element>RMS</element>

← Older revision	Revision as of 21:32, 16 June 2015
(No difference)

@@ Line 16: / Line 16: @@
   def Execute ( inputVolume, outputVolume, conductance=1.0, timeStep=0.0625, iterations=1 ):
       print "Executing Python Demo Application!"
-      Slicer = __import__ ( "Slicer" );
+      Slicer = __import__ ( "Slicer" )
-      slicer = Slicer.Slicer()
+      slicer = Slicer.slicer
       in = slicer.MRMLScene.GetNodeByID ( inputVolume );
       out = slicer.MRMLScene.GetNodeByID ( outputVolume );
-      filter = slicer.vtkITKGradientAnisotropicDiffusionImageFilter.New()
+      filter = slicer.vtkITKGradientAnisotropicDiffusionImageFilter()
       filter.SetConductanceParameter ( conductance )
       filter.SetTimeStep ( timeStep )
@@ Line 126: / Line 126: @@
       Slicer = __import__("Slicer")
-      slicer = Slicer.Slicer()
+      slicer = Slicer.slicer
       scene = slicer.MRMLScene
@@ Line 154: / Line 154: @@
   inputPolyData = inputSurface.GetPolyData()
-  decimation = slicer.vtkDecimatePro.New()
+  decimation = slicer.vtkDecimatePro()
   decimation.SetInput(inputSurface.GetPolyData())
   decimation.SetTargetReduction(0.99)
@@ Line 165: / Line 165: @@
 Setting of the filtered poly data to the outputSurface is left to the user (see last line).
-In general, the syntax used to use VTK classes in a Slicer Python module is very similar to using VTK from Python. There are just two main differences:
+In general, the syntax used to use VTK classes in a Slicer Python module is very similar to using VTK from Python. There is just one main difference: classes have to be looked for in slicer, not vtk (i.e. slicer.vtkImageData() instead of vtk.vtkImageData())
 ===SurfaceConnectivity.py===
@@ Line 249: / Line 243: @@
          Slicer = __import__("Slicer")
-         slicer = Slicer.Slicer()
+         slicer = Slicer.slicer
          scene = slicer.MRMLScene
          inputSurface = scene.GetNodeByID(inputSurface)
          outputSurface = scene.GetNodeByID(outputSurface)
-         connectivityFilter = slicer.vtkPolyDataConnectivityFilter.New()
+         connectivityFilter = slicer.vtkPolyDataConnectivityFilter()
          connectivityFilter.SetInput(inputSurface.GetPolyData())
          if connectivityMode == "AllRegions":
@@ Line 268: / Line 262: @@
              fiducialList.DisableModifiedEventOn()
              fiducialList.SetScene(scene)
-             thresholdPoints = slicer.vtkThresholdPoints.New()
+             thresholdPoints = slicer.vtkThresholdPoints()
              thresholdPoints.SetInput(connectivityFilter.GetOutput())
              numberOfRegions = connectivityFilter.GetNumberOfExtractedRegions()
@@ Line 425: / Line 419: @@
       Slicer = __import__("Slicer")
-      slicer = Slicer.Slicer()
+      slicer = Slicer.slicer
       scene = slicer.MRMLScene
       inputSurface = scene.GetNodeByID(inputSurface)
@@ Line 431: / Line 425: @@
       outputSurface = scene.GetNodeByID(outputSurface)
-      icpTransform = slicer.vtkIterativeClosestPointTransform.New()
+      icpTransform = slicer.vtkIterativeClosestPointTransform()
       icpTransform.SetSource(inputSurface.GetPolyData())
       icpTransform.SetTarget(targetSurface.GetPolyData())
@@ Line 450: / Line 444: @@
       icpTransform.SetMaximumMeanDistance(maximumMeanDistance)
-      transformFilter = slicer.vtkTransformPolyDataFilter.New()
+      transformFilter = slicer.vtkTransformPolyDataFilter()
       transformFilter.SetInput(inputSurface.GetPolyData())
       transformFilter.SetTransform(icpTransform)
@@ Line 645: / Line 639: @@
       Slicer = __import__("Slicer")
-      slicer = Slicer.Slicer()
+      slicer = Slicer.slicer
       scene = slicer.MRMLScene
       inputSurface = scene.GetNodeByID(inputSurface)
@@ Line 653: / Line 647: @@
       if decimationEnabled:
-          decimation = slicer.vtkDecimatePro.New()
+          decimation = slicer.vtkDecimatePro()
           decimation.SetInput(surface)
           decimation.SetTargetReduction(targetReduction)
@@ Line 666: / Line 660: @@
       if smoothingEnabled:
           if smoothingMethod == "Laplace":
-              smoothing = slicer.vtkSmoothPolyDataFilter.New()
+              smoothing = slicer.vtkSmoothPolyDataFilter()
               smoothing.SetInput(surface)
               if boundarySmoothing:
@@ Line 689: / Line 683: @@
       if normalsEnabled:
-          normals = slicer.vtkPolyDataNormals.New()
+          normals = slicer.vtkPolyDataNormals()
           normals.SetInput(surface)
           normals.AutoOrientNormalsOn()
@@ Line 706: / Line 700: @@
       if cleanerEnabled:
-          cleaner = slicer.vtkCleanPolyData.New()
+          cleaner = slicer.vtkCleanPolyData()
           cleaner.SetInput(surface)
           cleaner.Update()

@@ Line 49: / Line 49: @@
 * ResliceAsVolume.py
-You can download the zipfile with all these files here: [[Image:PythonModules.zip]]. Either place all the files in the Slicer3/Modules/Python directory (replacing the existing files) or just throw the .py files you're interested in into Slicer3-build/lib/Slicer3/Plugins directory and launch Slicer3.
+You can download the zipfile with all these files  [[Media:PythonModules.zip|here]]. Either place all the files in the Slicer3/Modules/Python directory (replacing the existing files) or just throw the .py files you're interested in into Slicer3-build/lib/Slicer3/Plugins directory and launch Slicer3.
 ===PythonScript.py===