Documentation/Nightly/Developers/Python scripting - Revision history

Lasso at 04:09, 24 April 2021

2021-04-24T04:09:57Z

Lasso: /* Running a CLI from Python */

2020-12-22T20:46:25Z

Running a CLI from Python

Lasso: /* Usage options */

2020-03-18T14:09:35Z

Usage options

Lasso: /* Usage options */

2020-03-18T14:08:27Z

Usage options

Lasso: /* Usage options */

2020-02-23T08:19:37Z

Usage options

Fernando: Replace xrange() by range()

2019-10-24T12:43:34Z

Replace xrange() by range()

Pieper: /* Start Here */

2019-09-12T13:58:35Z

Start Here

Pieper: /* Start Here */

2019-02-05T14:52:38Z

Start Here

JChris.FillionR at 07:18, 28 November 2018

2018-11-28T07:18:13Z

Inorton: /* Script Repository */

2018-09-12T13:20:33Z

Script Repository

@@ Line 7: / Line 7: @@
 Refer to [http://www.na-mic.org/Wiki/index.php/2013_Project_Week_Breakout_Session:Slicer4Python this description that includes links to all the documentation].
-Look at the [[Documentation/{{documentation/version}}/ScriptRepository |Script Repository]] for examples and inspiration.
+Look at the [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html Script repository] for examples and inspiration.
 = Background =
@@ Line 140: / Line 140: @@
 = Script Repository =
-See [[Documentation/Nightly/ScriptRepository|ScriptRepository]] for a larger collection of example code.
+See [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html Script repository] for a larger collection of example code.
 {{:Documentation/{{documentation/version}}/Developers/FAQ/Python Scripting|Python Scripting}}

@@ Line 118: / Line 118: @@
 === Running a CLI from Python ===
-Here's an example to create a model from a volume using the [[Documentation/4.0/Modules/GrayscaleModelMaker|Grayscale Model Maker]]
+[https://slicer.readthedocs.io/en/latest/developer_guide/python_faq.html#how-to-run-a-cli-module-from-python This documentation section has moved to ReadTheDocs.]
 ==== Accessing slice vtkRenderWindows from slice views ====

@@ Line 37: / Line 37: @@
 * Slicer can launch any external Python scripts (GUI is generated automatically from XML descriptor), running it by default in a background processing thread, without blocking the GUI. See example [https://github.com/lassoan/SlicerPythonCLIExample here].
-==Python Interactor==
+=Python Interactor=
 Use the Window->Python Interactor (Control-3 on window/linux, Command-3 on mac) to bring up the Qt-based console with access to the vtk, Qt, and Slicer wrapped APIs.
@@ Line 43: / Line 43: @@
 Most python code can be installed and run from this window, but because it exists in the event driven Qt GUI environment, some operations like, like parallel processing or headless operation, are not easily supported.
-=== Examples ===
+== Examples ==
 Start Slicer and bring up python console.  Load a sample volume like this:
@@ Line 61: / Line 61: @@
 You can use Tab to see lists of methods for a class instance.
-==== Accessing Volume data as numpy array ====
+=== Accessing Volume data as numpy array ===
 You can easily inspect and manipulate volume data using numpy and related code.  In slicer you can do this:
@@ Line 98: / Line 98: @@
 </pre>
-==== Accessing Model data as numpy array ====
+=== Accessing Model data as numpy array ===
 You can easily inspect and manipulate point coordinates of a model using numpy and related code by calling `arrayFromModelPoints`. After modification is completed, call Modified() method on the polydata to indicate that the model is modified and trigger display update.
@@ Line 116: / Line 116: @@
 </pre>
-==== Running a CLI from Python ====
+=== Running a CLI from Python ===
 Here's an example to create a model from a volume using the [[Documentation/4.0/Modules/GrayscaleModelMaker|Grayscale Model Maker]]

@@ Line 35: / Line 35: @@
 * Python debuggers (PyCharm, VS Code, Eclipse, etc.) can attach to a running Slicer application.
 * Slicer is accessible from Jupyter notebooks - SlicerJupyter extension makes Slicer application act as a Jupyter kernel, while keeping the application fully interactive.
-* Slicer can launch any external Python scripts (GUI is generated automatically from XML descriptor), running it by default in a background processing thread, without blocking the GUI.
+* Slicer can launch any external Python scripts (GUI is generated automatically from XML descriptor), running it by default in a background processing thread, without blocking the GUI. See example [https://github.com/lassoan/SlicerPythonCLIExample here].
 ==Python Interactor==

← Older revision		Revision as of 08:19, 23 February 2020
Line 25:		Line 25:

	= Usage options =		= Usage options =
		+
		+	Slicer is an application that embeds a Python interpreter, similarly to [https://docs.blender.org/api/blender_python_api_current/info_overview.html Blender], [https://www.freecadweb.org/wiki/Embedding_FreeCAD FreeCAD], [https://manual.calibre-ebook.com/develop.html#using-an-interactive-python-interpreter Calibre], [https://developers.maxon.net/docs/Cinema4DPythonSDK/html/manuals/introduction/python_in_c4d.html Cinema4D], etc.
		+
		+	While Slicer has a set of core libraries that could be packaged in a way so that they can be imported in any Python environment (<code>import slicer</code>), but currently we don't offer this option. This exists only as limited, experimental option for most other applications, too.
		+
		+	We rather focus our efforts on other kind of Python integrations:
		+
		+	* Official, recommended way of running Python processing scripts is to execute them using Slicer's embedded Python interpreter (e.g., the Python interactor). Any additional required python packages can be installed using pip (<code>pip_install('scipy'</code>).
		+	* Python debuggers (PyCharm, VS Code, Eclipse, etc.) can attach to a running Slicer application.
		+	* Slicer is accessible from Jupyter notebooks - SlicerJupyter extension makes Slicer application act as a Jupyter kernel, while keeping the application fully interactive.
		+	* Slicer can launch any external Python scripts (GUI is generated automatically from XML descriptor), running it by default in a background processing thread, without blocking the GUI.

	==Python Interactor==		==Python Interactor==

@@ Line 113: / Line 113: @@
    parameters["InputVolume"] = volumeNode.GetID()
    outModel = slicer.vtkMRMLModelNode()
-   slicer.mrmlScene.AddNode( outModel )
+   slicer.mrmlScene.AddNode(outModel)
    parameters["OutputGeometry"] = outModel.GetID()
    grayMaker = slicer.modules.grayscalemodelmaker
-   return (slicer.cli.runSync(grayMaker, None, parameters))
+   return slicer.cli.runSync(grayMaker, None, parameters)
 </pre>
@@ Line 179: / Line 179: @@
 cliModule = slicer.modules.grayscalemodelmaker
 n=cliModule.cliModuleLogic().CreateNode()
-for groupIndex in xrange(0,n.GetNumberOfParameterGroups()):
+for groupIndex in range(n.GetNumberOfParameterGroups()):
-   for parameterIndex in xrange(0,n.GetNumberOfParametersInGroup(groupIndex)):
+   for parameterIndex in range(n.GetNumberOfParametersInGroup(groupIndex)):
-     print('  Parameter ({0}/{1}): {2} ({3})'.format(groupIndex, parameterIndex, n.GetParameterName(groupIndex, parameterIndex), n.GetParameterLabel(groupIndex, parameterIndex)))
+     print('Parameter ({0}/{1}): {2} ({3})'.format(groupIndex, parameterIndex, n.GetParameterName(groupIndex, parameterIndex), n.GetParameterLabel(groupIndex, parameterIndex)))
 </pre>

@@ Line 3: / Line 3: @@
 = Start Here =
-Please read [https://docs.google.com/presentation/d/1JXIfs0rAM7DwZAho57Jqz14MRn2BIMrjB17Uj_7Yztc/edit?usp=sharing these slides] and work through the example code.
+Please read [https://docs.google.com/presentation/d/1JXIfs0rAM7DwZAho57Jqz14MRn2BIMrjB17Uj_7Yztc/edit?usp=sharing these slides] and [https://www.slicer.org/wiki/Documentation/Nightly/Training#PerkLab.27s_Slicer_bootcamp_training_materials these slides].  This will give you an overall idea what is possible, and you can use a binary download of Slicer to work through the example code.
 Refer to [http://www.na-mic.org/Wiki/index.php/2013_Project_Week_Breakout_Session:Slicer4Python this description that includes links to all the documentation].

← Older revision		Revision as of 14:52, 5 February 2019
Line 7:		Line 7:
	Refer to [http://www.na-mic.org/Wiki/index.php/2013_Project_Week_Breakout_Session:Slicer4Python this description that includes links to all the documentation].		Refer to [http://www.na-mic.org/Wiki/index.php/2013_Project_Week_Breakout_Session:Slicer4Python this description that includes links to all the documentation].

		+	Look at the [[Documentation/{{documentation/version}}/ScriptRepository \|Script Repository]] for examples and inspiration.

	= Background =		= Background =