Slicer3:Python:ScriptedModulesTipsNTricks - Revision history

Haehn at 02:19, 13 April 2011

2011-04-13T02:19:31Z

Haehn: /* Writing Tests in Python */

2011-04-13T02:15:47Z

Writing Tests in Python

Haehn: /* Writing Tests in Python */

2011-04-13T02:09:19Z

Writing Tests in Python

Haehn: /* Using KWWidget Callbacks */

2011-04-13T01:55:19Z

Using KWWidget Callbacks

Haehn: /* Use a custom MRML Node for your Scripted Module */

2011-04-13T01:43:41Z

Use a custom MRML Node for your Scripted Module

Haehn: /* Use a custom MRML Node for your Scripted Module */

2011-04-13T01:42:47Z

Use a custom MRML Node for your Scripted Module

Haehn: /* Use a custom MRML Node for your Scripted Module */

2011-04-13T01:41:54Z

Use a custom MRML Node for your Scripted Module

Haehn: /* Python Scripted Modules - Tips'N'Tricks */

2011-04-13T01:30:55Z

Python Scripted Modules - Tips'N'Tricks

Haehn: /* Adding your Logo to the Help&Acknowledgement Panel */

2011-04-13T01:07:58Z

Adding your Logo to the Help&Acknowledgement Panel

Haehn: /* Adding a Logo to the Help&Acknowledgement Panel */

2011-04-13T01:06:20Z

Adding a Logo to the Help&Acknowledgement Panel

← Older revision		Revision as of 02:19, 13 April 2011
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		+	Back to [[Slicer3:Python]]..
		+
	= Python Scripted Modules - Tips'N'Tricks =		= Python Scripted Modules - Tips'N'Tricks =

@@ Line 331: / Line 331: @@
 pathToData = os.path.normpath(slicer.Application.GetBinDir() + '/../share/Slicer3/Modules/AtlasCreator/TestData/')
 segPath = pathToData + os.sep + 'segmentations' + os.sep
 ...
@@ Line 372: / Line 380: @@
 === Distributing Images for Testing ===

← Older revision		Revision as of 02:09, 13 April 2011
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	== Writing Tests in Python ==		== Writing Tests in Python ==
		+	MRML Node tests or simple tests can be easily written in C++ but it is much easier to write tests which inspect observers or need the Slicer application in a scripting language. The following example shows how to test your Python Scripted Module with a combination of a C++ test and several Python tests.
		+
		+	1. It makes sense to create a ''Testing/'' subdirectory.
		+
		+	2. Then, define a testing kit using CMake. This is the standard template for C++ driven tests.
		+
		+	<pre>
		+
		+	SET(KIT AtlasCreatorLib)
		+	SET(CMAKE_TESTDRIVER_BEFORE_TESTMAIN "DEBUG_LEAKS_ENABLE_EXIT_ERROR();" )
		+	CREATE_TEST_SOURCELIST(Tests ${KIT}CxxTests.cxx
		+	vtkMRMLAtlasCreatorNodeTest1.cxx
		+	EXTRA_INCLUDE TestingMacros.h
		+	)
		+	SET (TestsToRun ${Tests})
		+	REMOVE (TestsToRun ${KIT}CxxTests.cxx)
		+
		+	SET(LIBRARY_NAME ${PROJECT_NAME})
		+
		+	ADD_EXECUTABLE(${KIT}CxxTests ${Tests})
		+	TARGET_LINK_LIBRARIES(${KIT}CxxTests ${lib_name})
		+
		+	SET( ${KIT}_TESTS ${CXX_TEST_PATH}/${KIT}CxxTests)
		+
		+	IF(WIN32)
		+	SET(${KIT}_TESTS ${CXX_TEST_PATH}/${CMAKE_BUILD_TYPE}/${KIT}CxxTests)
		+	ENDIF(WIN32)
		+
		+	MACRO( SIMPLE_TEST TESTNAME )
		+	ADD_TEST( ${TESTNAME} ${LAUNCH_EXE} ${${KIT}_TESTS} ${TESTNAME} )
		+	ENDMACRO( SIMPLE_TEST )
		+
		+	SIMPLE_TEST( vtkMRMLAtlasCreatorNodeTest1 )
		+
		+	</pre>
		+
		+	3. The following code can be appended to the ''Testing/CMakeLists.txt'' to include tests written in Python. Three different Python tests are appended in this case:
		+
		+	<pre>
		+
		+	# the following configures the Python tests to be copied into the build directory
		+	configure_file(
		+	${CMAKE_CURRENT_SOURCE_DIR}/vtkMRMLAtlasCreatorNodeLaunchTest1.py
		+	${CMAKE_BINARY_DIR}/${Slicer3_INSTALL_MODULES_LIB_DIR}/${PROJECT_NAME}/vtkMRMLAtlasCreatorNodeLaunchTest1.py
		+	COPYONLY)
		+
		+	configure_file(
		+	${CMAKE_CURRENT_SOURCE_DIR}/vtkMRMLAtlasCreatorNodeLaunchTest2.py
		+	${CMAKE_BINARY_DIR}/${Slicer3_INSTALL_MODULES_LIB_DIR}/${PROJECT_NAME}/vtkMRMLAtlasCreatorNodeLaunchTest2.py
		+	COPYONLY)
		+
		+	configure_file(
		+	${CMAKE_CURRENT_SOURCE_DIR}/vtkMRMLAtlasCreatorNodeLaunchTest3.py
		+	${CMAKE_BINARY_DIR}/${Slicer3_INSTALL_MODULES_LIB_DIR}/${PROJECT_NAME}/vtkMRMLAtlasCreatorNodeLaunchTest3.py
		+	COPYONLY)
		+
		+	install(
		+	FILES ${CMAKE_CURRENT_SOURCE_DIR}/vtkMRMLAtlasCreatorNodeLaunchTest1.py ${CMAKE_CURRENT_SOURCE_DIR}/vtkMRMLAtlasCreatorNodeLaunchTest2.py ${CMAKE_CURRENT_SOURCE_DIR}/vtkMRMLAtlasCreatorNodeLaunchTest3.py
		+	DESTINATION ${Slicer3_INSTALL_MODULES_LIB_DIR}/${PROJECT_NAME}
		+	)
		+
		+	</pre>
		+
		+	4. The following lines are required to actually add the Python tests to the Testing kit. They will be run by using the Slicer launcher in test-mode with the '''-p''' argument for an external Python script.
		+
		+	<pre>
		+
		+	# add a tcl test
		+	# ADD_TEST(MeasurementsTest1 ${Slicer3_BINARY_DIR}/Slicer3 --test-mode --script ${Slicer3_SOURCE_DIR}/Modules/Measurements/Testing/Tcl/MeasurementsTest1.tcl)
		+
		+	# add python tests by using the Slicer launcher in test-mode
		+	ADD_TEST(AtlasCreatorLaunchFixedTest ${Slicer3_BINARY_DIR}/Slicer3 --test-mode -p ${Slicer3_BINARY_DIR}/${Slicer3_INSTALL_MODULES_LIB_DIR}/${PROJECT_NAME}/vtkMRMLAtlasCreatorNodeLaunchTest1.py)
		+	ADD_TEST(AtlasCreatorLaunchFixedFailProofTest ${Slicer3_BINARY_DIR}/Slicer3 --test-mode -p ${Slicer3_BINARY_DIR}/${Slicer3_INSTALL_MODULES_LIB_DIR}/${PROJECT_NAME}/vtkMRMLAtlasCreatorNodeLaunchTest2.py)
		+	ADD_TEST(AtlasCreatorLaunchDynamicTest ${Slicer3_BINARY_DIR}/Slicer3 --test-mode -p ${Slicer3_BINARY_DIR}/${Slicer3_INSTALL_MODULES_LIB_DIR}/${PROJECT_NAME}/vtkMRMLAtlasCreatorNodeLaunchTest3.py)
		+
		+	</pre>
		+
		+	5. To define the '''actual Python tests''', the following template is helpful. This shows the base of vtkMRMLAtlasCreatorNodeLaunchTest1.py:
		+
		+	<pre>
		+	from Slicer import slicer
		+	import sys
		+	import os
		+	import shutil
		+	import tempfile
		+
		+	#
		+	# AtlasCreator Test 1
		+
		+	# setting some paths
		+	pathToData = os.path.normpath(slicer.Application.GetBinDir() + '/../share/Slicer3/Modules/AtlasCreator/TestData/')
		+	segPath = pathToData + os.sep + 'segmentations' + os.sep
		+
		+	...
		+
		+	# create the node
		+	n = slicer.vtkMRMLAtlasCreatorNode()
		+
		+	# call some methods
		+	n.InitializeByDefault()
		+
		+	# test on a condition
		+	if CONDITION:
		+	# all there
		+	ret = True
		+	else:
		+	# error
		+	ret = False
		+
		+	# exit test with the corresponding exit code (0 on Success, 1 on Failure)
		+	if ret:
		+	slicer.Application.Evaluate("exit 0")
		+	else:
		+	slicer.Application.Evaluate("exit 1")
		+
		+	</pre>
		+
		+	6. If everything is glued together properly, a '''make test''' in the ScriptedModule directory runs the C++ and Python tests together.
		+
		+	<pre>
		+	Running tests...
		+	Test project /Users/daniel/SLICER/TRUNK/Slicer3-build/Modules/AtlasCreator
		+	Start 1: vtkMRMLAtlasCreatorNodeTest1
		+	1/4 Test #1: vtkMRMLAtlasCreatorNodeTest1 ........... Passed 0.70 sec
		+	Start 2: AtlasCreatorLaunchFixedTest
		+	2/4 Test #2: AtlasCreatorLaunchFixedTest ............ Passed 29.78 sec
		+	Start 3: AtlasCreatorLaunchFixedFailProofTest
		+	3/4 Test #3: AtlasCreatorLaunchFixedFailProofTest ... Passed 37.10 sec
		+	Start 4: AtlasCreatorLaunchDynamicTest
		+	4/4 Test #4: AtlasCreatorLaunchDynamicTest .......... Passed 37.09 sec
		+	</pre>
		+
		+	=== Distributing Images for Testing ===

← Older revision		Revision as of 01:55, 13 April 2011
Line 186:		Line 186:

	== Using KWWidget Callbacks ==		== Using KWWidget Callbacks ==
		+	Best practice to check if the GUI has changed is to observe the KWWidgets for triggered events. Unfortunately, this is not always possible since not all widgets fire all available events. To still be able to monitor changes in the GUI, KWWidget Callbacks can be used in connection with the '''Invoke''' method of the Scripted Module. This also helps to realize wizards in Scripted Modules :).
		+
		+	This example shows how to use callbacks on a vtkKWComboBoxWithLabel to monitor changes in the selection. Certain callbacks attach additional information to the method which gets fired. For example the comboBox callback adds the current selected item as String.
		+
		+	1. Create a method in your ScriptedModule which gets called when the comboBox changes. In connection with a comboBox callback, this method needs an additional argument.
		+
		+	<pre>
		+	...
		+	'''=========================================================================================='''
		+	def UpdateMRMLFromCallback(self,dummyArgument=None):
		+	'''
		+	Just passes through to UpdateMRML.
		+
		+	The dummyArgument is a placeholder when this function is called by a ComboBox callback and the current
		+	value is attached automatically by KWWidgets.
		+	'''
		+	self.UpdateMRML()
		+	...
		+	</pre>
		+
		+	2. Add the callback after the widget was created using the '''Invoke''' functionality.
		+
		+	<pre>
		+	...
		+	self._toolkitCombo = slicer.vtkKWComboBoxWithLabel()
		+	...
		+
		+	'''=========================================================================================='''
		+	def BuildGUI(self):
		+	'''
		+	Creates the Graphical User Interface (GUI) of the AtlasCreator. Gets called once during loading of the module.
		+	'''
		+	...
		+	self._toolkitCombo.SetParent(self._parametersFrame.GetFrame())
		+	self._toolkitCombo.Create()
		+	self._toolkitCombo.GetWidget().ReadOnlyOn()
		+	self._toolkitCombo.SetLabelText("Toolkit:")
		+	self._toolkitCombo.SetLabelWidth(20)
		+	self._toolkitCombo.SetBalloonHelpString("The toolkit to use for Registration.")
		+	slicer.TkCall("pack %s -side top -anchor nw -fill x -padx 2 -pady 2" % self._toolkitCombo.GetWidgetName())
		+
		+	self._toolkitCombo.GetWidget().AddValue("'BRAINSFit'")
		+	self._toolkitCombo.GetWidget().AddValue("'CMTK'")
		+	self._toolkitCombo.GetWidget().SetValue("'BRAINSFit'")
		+
		+	# the following callback invokes the UpdateMRMLFromCallback method in this module after each change
		+	self._toolkitCombo.GetWidget().SetCommand(self.vtkScriptedModuleGUI, "Invoke UpdateMRMLFromCallback")
		+	...
		+	</pre>
		+
		+	3. In this special case, KWWidgets add the current selected item as String to the callback. The Invoke functionality can only handle strings correctly if they are wrapped in quotes as seen above (e.g. "'BRAINSFit'"..). This is not necessary for integers, for example if the Callback adds coordinates.

	== Writing Tests in Python ==		== Writing Tests in Python ==

@@ Line 181: / Line 181: @@
 </pre>
-. All the pieces can be glued together with CMake which also handles the Python interface through Tcl wrapping.
+. All the pieces can be glued together with CMake which also handles the Python interface through Tcl wrapping (using Subdirs(..) and vtk_wrap_tcl3 commands).
 . In the Scripted Module observe for MRMLScene::NodeAddedEvents as seen above and save pointers to your custom MRML Node IDs. Then, the UpdateMRML() and UpdateGUI() methods should use the pointers to update the node or the GUI.

@@ Line 162: / Line 162: @@
 . The MRML Node itself can be written by using the default practices.
-. After creating the MRML Node, the '''RegisterNodes()''' method in the logic should be used to register the custom MRML Node within the MRML Scene. This is required for Loading and Saving the scene.
+. After creating the MRML Node, the '''RegisterNodes()''' method in the logic should be used to register the custom MRML Node within the MRML Scene. This is required for Loading and Saving the scene. This is the only real code the gui-less module has to include.
 <pre>

@@ Line 154: / Line 154: @@
 === Use a custom MRML Node for your Scripted Module ===
 == Using KWWidget Callbacks ==
 == Writing Tests in Python ==

@@ Line 1: / Line 1: @@
 = Python Scripted Modules - Tips'N'Tricks =
-This page shows tips and tricks for writing Python Scripted Modules in Slicer3.
+This page shows tips and tricks for writing Python Scripted Modules in Slicer3. Most examples are taken from the AtlasCreator module.
 == Adding your Logo to the Help&Acknowledgement Panel ==
@@ Line 55: / Line 55: @@
 == MRML Events ==
 === Observe MRML Scene events ===
 === Observe MRML Node events ===
 === Use a custom MRML Node for your Scripted Module ===

@@ Line 23: / Line 23: @@
 </pre>
-. In your ScriptedModuleGUI class, edit the BuildGUI function and add the following code after calling '''self.BuildHelpAndAboutFrame''':
+. In your ScriptedModuleGUI class, edit the BuildGUI function and add the following code '''after calling ''self.BuildHelpAndAboutFrame''''':
 <pre>
@@ Line 50: / Line 50: @@
          slicer.TkCall("pack %s -side top -anchor nw -fill x -padx 2 -pady 2" % self._logoLabel.GetWidgetName())
 ...
 </pre>
 == MRML Events ==