Slicer3 Q&A 2008-11-18 - Revision history

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

2017-07-10T17:58:22Z

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

Fedorov: /* Debugging */

2009-04-14T22:01:29Z

Debugging

Pieper: /* Debugging */

2008-12-04T15:24:44Z

Debugging

Fedorov at 23:43, 18 November 2008

2008-11-18T23:43:59Z

Fedorov: /* Event Management */

2008-11-18T23:38:30Z

Event Management

Fedorov: /* Debugging */

2008-11-18T23:30:07Z

Debugging

Fedorov: /* Memory Management and Leaks */

2008-11-18T23:28:38Z

Memory Management and Leaks

Fedorov: /* ITK Filters */

2008-11-18T23:27:15Z

ITK Filters

Fedorov: /* Volume Visualization */

2008-11-18T23:23:11Z

Volume Visualization

Fedorov: /* Tcl Interactor (tkcon) */

2008-11-18T23:09:48Z

Tcl Interactor (tkcon)

@@ Line 66: / Line 66: @@
 If you want to use ddd, set up the environment, launch ddd, attach to Slicer3-real, and "continue" as you do with gdb. To investigate a specific part of code, you need to go to menu "File->Open source", hit "Load shared library object symbols", and select the source file of your interest. Follow ddd instructions to insert breakpoints etc.
-''This approach also works for windows; for example, see [http://www.na-mic.org/Wiki/index.php/User:Pieper#Launching_visual_studio_for_slicer3_debugging these examples for visual studio].  Once you have a debugger in the right shell, you can single step through the startup procedure or [http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation:Debugging debug command line modules].''
+''This approach also works for windows; for example, see [http://www.na-mic.org/Wiki/index.php/User:Pieper#Launching_visual_studio_for_slicer3_debugging these examples for visual studio].  Once you have a debugger in the right shell, you can single step through the startup procedure or [https://www.slicer.org/wiki/Slicer3:Execution_Model_Documentation:Debugging debug command line modules].''
 ''On Windows, it is useful to install rxvt package in Cygwin -- it is much more convenient to use (window resizing, better mouse support).''
@@ Line 122: / Line 122: @@
 * High-level architecture/diagram of Slicer volume visualization: relationship between vtkMRMLScalarVolumeNode/vtkMRMLScalarVolumeDisplayNode/vtkMRMLScene, howto for volume rendering, ... (Fedorov)
-''There are three kinds of MRML nodes: data, display and storage nodes. In the context of the scalar images, data nodes keep information pertinent to the image contents (spacing, orientation, IJKtoRAS matrix, origin, etc.). Display nodes are used to render the image data. Storage nodes specify details on saving information stored in data nodes (e.g., see storage node specifically for NRRD image format). Refer to [http://www.slicer.org/slicerWiki/index.php/Image:Slicer3_MRML_Node_Hier.jpg MRML Node hierarchy slide] in [http://www.slicer.org/slicerWiki/index.php/Slicer3:Data_Model Slicer3 data model]. For the specific illustration of how nodes are added and display views are attached see Modules/Volumes::Logic implementation.''
+''There are three kinds of MRML nodes: data, display and storage nodes. In the context of the scalar images, data nodes keep information pertinent to the image contents (spacing, orientation, IJKtoRAS matrix, origin, etc.). Display nodes are used to render the image data. Storage nodes specify details on saving information stored in data nodes (e.g., see storage node specifically for NRRD image format). Refer to [https://www.slicer.org/wiki/Image:Slicer3_MRML_Node_Hier.jpg MRML Node hierarchy slide] in [https://www.slicer.org/wiki/Slicer3:Data_Model Slicer3 data model]. For the specific illustration of how nodes are added and display views are attached see Modules/Volumes::Logic implementation.''
 ''Volume rendering is currently not at the stage when you can do the render by adding MRML nodes and specifying properties. What is currently implemented in, for example, ChangeTracker module (ChangeTracker/Wizard/vtkChangeTrackerStep.cxx::CreateRender()) is the ok way to do it. In the future, volume rendering should be possible to do through the interaction with MRML scene (Alex is working on this). Also, the attendees have been referred to the M.S. thesis of Andreas Freudling (U. of Heidelberg), who developed Slicer3 VolumeRendering module (thesis to be found and linked here). Also, see [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:Volume_Rendering_Tutorials volume rendering tutorial materials ]''

← Older revision		Revision as of 22:01, 14 April 2009
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	Or you may wish to use ddd for a more graphical debugging experience.		Or you may wish to use ddd for a more graphical debugging experience.
		+
		+	If you want to use ddd, set up the environment, launch ddd, attach to Slicer3-real, and "continue" as you do with gdb. To investigate a specific part of code, you need to go to menu "File->Open source", hit "Load shared library object symbols", and select the source file of your interest. Follow ddd instructions to insert breakpoints etc.

	''This approach also works for windows; for example, see [http://www.na-mic.org/Wiki/index.php/User:Pieper#Launching_visual_studio_for_slicer3_debugging these examples for visual studio]. Once you have a debugger in the right shell, you can single step through the startup procedure or [http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation:Debugging debug command line modules].''		''This approach also works for windows; for example, see [http://www.na-mic.org/Wiki/index.php/User:Pieper#Launching_visual_studio_for_slicer3_debugging these examples for visual studio]. Once you have a debugger in the right shell, you can single step through the startup procedure or [http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation:Debugging debug command line modules].''

← Older revision		Revision as of 15:24, 4 December 2008
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	./Slicer3 --launch xterm		./Slicer3 --launch xterm
		+
		+	''in the newly launched xterm, you can then run:''
		+
		+	gdb bin/Slicer3-real
		+
		+	Or you may wish to use ddd for a more graphical debugging experience.

	''This approach also works for windows; for example, see [http://www.na-mic.org/Wiki/index.php/User:Pieper#Launching_visual_studio_for_slicer3_debugging these examples for visual studio]. Once you have a debugger in the right shell, you can single step through the startup procedure or [http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation:Debugging debug command line modules].''		''This approach also works for windows; for example, see [http://www.na-mic.org/Wiki/index.php/User:Pieper#Launching_visual_studio_for_slicer3_debugging these examples for visual studio]. Once you have a debugger in the right shell, you can single step through the startup procedure or [http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation:Debugging debug command line modules].''

@@ Line 116: / Line 116: @@
 ''There are three kinds of MRML nodes: data, display and storage nodes. In the context of the scalar images, data nodes keep information pertinent to the image contents (spacing, orientation, IJKtoRAS matrix, origin, etc.). Display nodes are used to render the image data. Storage nodes specify details on saving information stored in data nodes (e.g., see storage node specifically for NRRD image format). Refer to [http://www.slicer.org/slicerWiki/index.php/Image:Slicer3_MRML_Node_Hier.jpg MRML Node hierarchy slide] in [http://www.slicer.org/slicerWiki/index.php/Slicer3:Data_Model Slicer3 data model]. For the specific illustration of how nodes are added and display views are attached see Modules/Volumes::Logic implementation.''
-''Volume rendering is currently not at the stage when you can do the render by adding MRML nodes and specifying properties. What is currently implemented in, for example, ChangeTracker module (ChangeTracker/Wizard/vtkChangeTrackerStep.cxx::CreateRender()) is the ok way to do it. In the future, volume rendering should be possible to do through the interaction with MRML scene (Alex is working on this). Also, the attendees have been referred to the M.S. thesis of Andreas Freudling (U. of Heidelberg), who developed Slicer3 VolumeRendering module (thesis to be found and linked here).''
+''Volume rendering is currently not at the stage when you can do the render by adding MRML nodes and specifying properties. What is currently implemented in, for example, ChangeTracker module (ChangeTracker/Wizard/vtkChangeTrackerStep.cxx::CreateRender()) is the ok way to do it. In the future, volume rendering should be possible to do through the interaction with MRML scene (Alex is working on this). Also, the attendees have been referred to the M.S. thesis of Andreas Freudling (U. of Heidelberg), who developed Slicer3 VolumeRendering module (thesis to be found and linked here). Also, see [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:Volume_Rendering_Tutorials volume rendering tutorial materials ]''
 === ITK Filters ===
@@ Line 168: / Line 168: @@
 ''The best approach here is to write a small test program that confirms how you think the pipeline *should* work.  I write these in tcl, but C++ or python work too.  Ideally if you can factor out the parts which depend on slicer-specific data structures you can quickly narrow down how to use the VTK classes in a pipeline.  Sometimes there are bugs in VTK that need to get fixed.  Having the standalone test case is crucial for demonstrating these bugs and getting them fixed.''

@@ Line 155: / Line 155: @@
 * Overview of different classes of events in Slicer, and what action should be done in what observer (GUI events, MRML events, Logic events, Scene events, anything else?...) (Fedorov/Haytham)
-* How do the Logic Methods keep track of the MRML node events? Which Logic Methods are involved? Are Macros used, and if so, where are they defined? (Haytham)
+''GUI responds to MRML changes by observing MRML events. GUI is also watching GUI events and updates MRML. This can become tricky when an update triggers another update, and care should be taken not to create event handling loops. This can be done with guard variables (e.g., no MRML event processing while handling GUI events). Logic events are rarely necessary, and currently are only used in slice rendering in the main GUI. Try to stay away from Logic events so that another layer of complexity is not introduced. According to Steve, debugging events is the most challenging task, fixing memory leaks is simple compared to this.''
 === Debugging VTK Pipelines ===

← Older revision		Revision as of 23:30, 18 November 2008
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	''Note, that if you update CMakeLists.txt, add new files, and such, on Windows, you need to re-run cmake before compiling your project in VC. Exit VC before you do this.''		''Note, that if you update CMakeLists.txt, add new files, and such, on Windows, you need to re-run cmake before compiling your project in VC. Exit VC before you do this.''
		+
		+	''Message output should be done with vtkDebugMacro(), vtkErrorMacro() and vtkWarningMacro(). The output from these macros will go to the Slicer error console (open it by clicking red button in the bottom-right corner.''

	=== Example Code ===		=== Example Code ===

← Older revision		Revision as of 23:28, 18 November 2008
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	''You can also use the --ignore-module <module name> command line argument to suppress a particular module to see if it is the source of the leak. See [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Testing/LeakTest.tcl?rev=7767&view=markup this leak test script] for an example of how this can be used systematically to find a leaking module (note this script is still in development).''		''You can also use the --ignore-module <module name> command line argument to suppress a particular module to see if it is the source of the leak. See [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Testing/LeakTest.tcl?rev=7767&view=markup this leak test script] for an example of how this can be used systematically to find a leaking module (note this script is still in development).''
		+
		+	''Rule of thumb: if something is set with vtkSet...() macro, the pointer can (should!) be deleted. Delete() will only decrement the reference count.''

	=== Event Management ===		=== Event Management ===

@@ Line 123: / Line 123: @@
 ''The current 'best practice' for simple filters, per Steve Pieper and Jim Miller, is to encapsulate the ITK code inside a VTK class as done in [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/vtkITK/vtkITKWandImageFilter.h?rev=7807&view=markup Libs/vtkITK/vtkITKWandImageFilter.h] and [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/vtkITK/vtkITKWandImageFilter.cxx?rev=7807&view=markup Libs/vtkITK/vtkITKWandImageFilter.cxx]''
 * Is there a framework for creating a workflow of command line modules programmatically? (Fedorov)
 === Memory Management and Leaks ===

← Older revision		Revision as of 23:09, 18 November 2008
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	''This is one of the most powerful tools in slicer. See the [http://tkcon.sourceforge.net/ tkcon documentation] for general capabilities. The tkcon has been enhanced in slicer to support method name completion for vtk classes (shift-tab) and wrapping statements in square brackets (control-]). See this (partly out-of-date) [http://www.slicer.org/archives/faq/index.html#14 slicer2 documentation of what you can do with tkcon].''		''This is one of the most powerful tools in slicer. See the [http://tkcon.sourceforge.net/ tkcon documentation] for general capabilities. The tkcon has been enhanced in slicer to support method name completion for vtk classes (shift-tab) and wrapping statements in square brackets (control-]). See this (partly out-of-date) [http://www.slicer.org/archives/faq/index.html#14 slicer2 documentation of what you can do with tkcon].''
		+
		+	''Some useful shortcuts: Ctrl+] will wrap the code in brackets -- this can be handy with multiple nesting levels common in Tcl. Shift+Tab does function auto-completion.''
		+
		+	''$::slicer3 -- namespace for all Slicer3 variables and methods. Explore MRMLScene, ListMethods can be called to list methods. MRMLWatcher includes all nodes in the MRML scene.''

	=== Volume Visualization ===		=== Volume Visualization ===