AHM2012-Slicer-Python - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T18:07:13Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Pieper: /* VTK and MRML */

2012-01-07T23:21:34Z

VTK and MRML

Pieper: /* Qt */

2012-01-07T23:20:40Z

Pieper: /* Qt */

2012-01-07T23:20:09Z

Pieper: /* Limitations of python */

2012-01-07T23:19:37Z

Limitations of python

Pieper: /* Refining the code and UI with slicerrc */

2012-01-07T23:13:17Z

Refining the code and UI with slicerrc

Pieper: /* Refining the code and UI with slicerrc */

2012-01-07T23:12:54Z

Refining the code and UI with slicerrc

Pieper: /* Refining the code and UI with slicerrc */

2012-01-07T23:09:08Z

Refining the code and UI with slicerrc

Pieper: /* Writing a Scripted Module */

2012-01-07T23:03:55Z

Writing a Scripted Module

Pieper: /* Using the console */

2012-01-07T23:01:05Z

Using the console

@@ Line 250: / Line 250: @@
 The Endoscopy module is a good example to look at for writing a scripted module.
-You can get started by using the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers/ModuleWizard ModuleWizard] to create your skeleton module.
+You can get started by using the [https://www.slicer.org/wiki/Documentation/4.0/Developers/ModuleWizard ModuleWizard] to create your skeleton module.
 Then you implement the functionality using the methods described above:

← Older revision		Revision as of 23:21, 7 January 2012
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	=== VTK and MRML ===		=== VTK and MRML ===

−	It is possible to ~~implement the logic of the effect using~~ [http://www.vtk.org/Wiki/VTK/Python_Wrapping_FAQ VTK Python binding]. You can get ideas of what is possible from [http://www.itk.org/Wiki/VTK/Tutorials the VTK tutorials].	+	It is possible to use [http://www.vtk.org/Wiki/VTK/Python_Wrapping_FAQ VTK Python binding]. You can get ideas of what is possible from [http://www.itk.org/Wiki/VTK/Tutorials the VTK tutorials].

@@ Line 3: / Line 3: @@
 === Qt ===
-[http://pythonqt.sourceforge.net/ PythonQt] exposes most of the [http://qt.nokia.com Qt] interface so that sophisticated interfaces can be easily created.
+[http://pythonqt.sourceforge.net/ PythonQt] exposes most of the [http://qt.nokia.com Qt] interface so that sophisticated interfaces can be easily created.  PythonQt also allows introspection and modification of the interface at runtime.
 [[Image:SlicerQT-real 174.png|thumb|300px|right|Run-time query of all Qt widgets in the application]]

@@ Line 3: / Line 3: @@
 === Qt ===
-Interfaces are build with [http://pythonqt.sourceforge.net/ PythonQt] which exposes most of the [http://qt.nokia.com Qt] interface so that sophisticated interfaces can be easily created.
+[http://pythonqt.sourceforge.net/ PythonQt] exposes most of the [http://qt.nokia.com Qt] interface so that sophisticated interfaces can be easily created.
 [[Image:SlicerQT-real 174.png|thumb|300px|right|Run-time query of all Qt widgets in the application]]

← Older revision		Revision as of 23:19, 7 January 2012
Line 318:		Line 318:

	== Limitations of python ==		== Limitations of python ==
		+
		+	Although python gives almost everything you need to write a full-featured slicer module, there are some things you cannot do:
		+
		+	* PythonQt does not allow you to inherit from QWidget, so you need to build interfaces by composition rather than inheritance (although you can use python inheritance to organize your code).
		+	* Computation in python is slower than C++, so most of your numerical and graphical code should be written in C++ can exposed to python via one of several mechanisms:
		+	** Write a CLI module
		+	** Write a VTK class to implement the function
		+	** Write an ITK class to implement the function and wrap it via vtkITK
		+	** Write an ITK class to implement the function and wrap it via SimpleITK (coming soon)
		+	* Python provides many libraries and modules, but not all are available with slicer
		+	** scipy is a large collection of code that is not easy to compile across platforms (enthought sells compiled versions so users won't need to compile it themselves)
		+	** matplotlib is not available in slicer
		+	** ipython is not available in slicer (yet)
		+	* Some aspects of the underlying Qt, VTK, CTK, APIs are not exposed via python. Usually this isn't an issue but it can sometimes bite you.

@@ Line 268: / Line 268: @@
 In practice, it is very convenient for developers to use the this feature to make shortcuts for interacting with their code.
-See [https://github.com/pieper/SlicerRC] for examples that you can build from.
+See [https://github.com/pieper/SlicerRC https://github.com/pieper/SlicerRC] for examples that you can build from.
 Here's an excerpt from that example:

← Older revision		Revision as of 23:12, 7 January 2012
Line 309:		Line 309:

	</pre>		</pre>
		+
		+	What this does is:
		+	* Registers a hot-key for the application so that when Control-Shift-2 is entered the endoscopy() python function is invoked
		+	* This hot-key reloads the source code for the module and creates a new instance of the module GUI
		+	* The module GUI is accessible via the python console in a global variable 'e'
		+	* The the 'e' variable lets you access internal state, call methods, and otherwise debug your module.
		+	* You can typically edit the module python code and reload the module with Control-Shift-2 without exiting slicer, making the development process very efficient

	== Limitations of python ==		== Limitations of python ==

← Older revision		Revision as of 23:09, 7 January 2012
Line 258:		Line 258:

	== Refining the code and UI with slicerrc ==		== Refining the code and UI with slicerrc ==
		+
		+	Slicer supports a user-specific startup script called slicerrc
		+	* Can be either in ~/.slicerrc.py or in location pointed to by SLICERRC environment variable
		+	* Can do arbitrary startup actions:
		+	** load data
		+	** change the GUI
		+	** initiate computation
		+
		+	In practice, it is very convenient for developers to use the this feature to make shortcuts for interacting with their code.
		+
		+	See [https://github.com/pieper/SlicerRC] for examples that you can build from.
		+
		+	Here's an excerpt from that example:
		+	<pre>
		+	def endoscopy():
		+	print "SlicerRC - endoscopy setup..."
		+	import imp, sys, os
		+	endoPath = '%s/../../Slicer4/Modules/Scripted/Scripts' % slicer.app.slicerHome
		+	if not sys.path.__contains__(endoPath):
		+	sys.path.insert(0,endoPath)
		+
		+	mod = "Endoscopy"
		+	sourceFile = endoPath + "/Endoscopy.py"
		+	fp = open(sourceFile, "r")
		+	globals()[mod] = imp.load_module(mod, fp, sourceFile, ('.py', 'r', imp.PY_SOURCE))
		+	fp.close()
		+
		+	globals()['e'] = e = globals()[mod].EndoscopyWidget()
		+
		+
		+	def setupMacros():
		+	"""Set up hot keys for various development scenarios"""
		+
		+	import qt
		+	global endoscopy
		+
		+	macros = (
		+	("Shift+Ctrl+2", endoscopy),
		+	)
		+
		+	for keys,f in macros:
		+	k = qt.QKeySequence(keys)
		+	s = qt.QShortcut(k,mainWindow())
		+	s.connect('activated()', f)
		+	s.connect('activatedAmbiguously()', f)
		+	print "SlicerRC - '%s' -> '%s'" % (keys, f.__name__)
		+
		+	# Install macros
		+	if mainWindow(verbose=False): setupMacros()
		+
		+	</pre>

	== Limitations of python ==		== Limitations of python ==

@@ Line 248: / Line 248: @@
 == Writing a Scripted Module ==
-*** PythonQt interface
+The Endoscopy module is a good example to look at for writing a scripted module.
-*** Logic with vtk/vtkITK/CLI Modules
-*** Accessing MRML Data via numpy
+You can get started by using the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers/ModuleWizard ModuleWizard] to create your skeleton module.
 == Refining the code and UI with slicerrc ==
 == Limitations of python ==

@@ Line 239: / Line 239: @@
 ==Using the console==
 (See [http://vimeo.com/33236047 J2's excellent demo video])
 == Writing a Scripted Module ==