SlicerWiki - Recent changes [en]

Developer Meetings/20120522

JChris.FillionR — Wed, 16 May 2012 22:32:15 GMT

To discuss:

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	== To discuss ==		== To discuss ==
		+	* [[#Meaning_of_vtkMRMLNode::ModifiedSinceRead\|Meaning_of_vtkMRMLNode::ModifiedSinceRead]]
		+	* [http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/008801.html Nicole / Andras: multiple colors within one Model saving as vtk?]
		+	* Update of download.slicer.org so that links can not easily be "downloaded" by malicious bots
		+	* Logo associated with CLI. Should we just recommend png ? See [http://www.na-mic.org/Bug/view.php?id=2072 #2072]
		+
		+	=== Meaning of vtkMRMLNode::ModifiedSinceRead ===
		+	<pre>
		+	From Julien - May 16, 2012:
		+	What is the exact meaning of vtkMRMLNode::ModifiedSinceRead ?
		+	From what I understand, it is a flag set to true if the "data" (e.g. vtkImageData, vtkPolyData) associated to the node has been modified since it has been set and observed.
		+	Currently, this information is only used by the Save Data dialog to know if the "data" needs to be saved or not. In the future, I believe it should be used by the SceneView node to know when saving "data".
		+	If my understanding is correct, then I don't understand your fix. Can you please comment ?
		+	Also, wouldn't it make sense that ModifiedSinceRead becomes a vtkMRMLStorableNode property instead of a vtkMRMLNode property?
		+	</pre>

	== Conclusion ==		== Conclusion ==

Documentation/4.1/Developers/Style Guide

Finetjul — Wed, 16 May 2012 21:16:59 GMT

number bullets for referencing

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	== Naming ==		== Naming ==

-	* Acronyms should be written in all CAPS.	+	# Acronyms should be written in all CAPS.
-	** ''RASToSlice'' not ''RasToSlice''	+	#: ''RASToSlice'' not ''RasToSlice''
-	** ''vtkMRML'' not ''vtkMrml''	+	#: ''vtkMRML'' not ''vtkMrml''
-	* Words should be spelled out and not abreviated	+	# Words should be spelled out and not abreviated
-	** ''GetWindow'' not ''GetWin''	+	#: ''GetWindow'' not ''GetWin''

	== Comments ==		== Comments ==

-	* include extensive comments in the header files	+	# include extensive comments in the header files
-	* keep the comments up to date as the code changes	+	# keep the comments up to date as the code changes
-	* use the keyword TODO to flag spots in the code that need to be revisited	+	# use the keyword TODO to flag spots in the code that need to be revisited
-	* do not leave blocks of commented out code in the source file -- if needed insert links to prior svn versions as comments	+	# do not leave blocks of commented out code in the source file -- if needed insert links to prior svn versions as comments

		+	== Functions ==
		+	# Don't mix different levels of abstraction
		+	#: Examples:
		+	#:: When dealing with files names and path, use [http://vtk.org/gitweb?p=VTK.git;a=blob;f=Utilities/KWSys/vtksys/SystemTools.hxx.in;h=04f197842695c5914d1a49d4738159d3bccb08e8;hb=HEAD kwsys::SystemTools] in VTK classes, [http://doc.qt.nokia.com/4.7.4/qfileinfo.html QFileInfo]/[http://doc.qt.nokia.com/4.7.4/qdir.html QDir] in Qt classes or [http://docs.python.org/library/os.path.html os.path] in python. Instead of doing string manipulation manually:
		+	#:::<code>QString filePath = directoryPath + "/" + fileName + ".exe"</code>)
		+	#:: prefer instead:
		+	#:::<code>SystemTools::JoinPath(), SystemTools::GetFilenameName()...</code>
		+	#:::<code>QFileInfo(QDir directory, QString fileName), QFileInfo::suffix(), QFileInfo::absoluteFilePath()...</code>
		+	#:::<code>os.path.join(), os.path.splitext(), os.path.abspath()...</code>
		+	#: References:
		+	#:* [http://www.amazon.com/gp/product/0132350882?ie=UTF8&tag=solisyntprog-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=0132350882 Clean Code] from ''Robert C. Martin'': ''Mixing levels of abstraction within a function is always confusing. Readers may not be able to tell whether a particular expression is an essential concept or a detail. Worse, like broken windows, once details are mixed with essential concepts, more and more details tend to accrete within the functions.''
		+	#:* http://zuskin.com/coding_habits__functions.htm#Abstraction_levels
		+	# Use STL where you can, but follow the VTK [http://www.vtk.org/Wiki/VTK_FAQ#Can_I_use_STL_with_VTK.3F guidelines]
		+	## However, prefer [http://doc.qt.nokia.com/4.7-snapshot/containers.html Qt Container classes] to STL classes in Qt files
		+	## Note that a [http://www.vtk.org/doc/nightly/html/classvtkCollection.html vtkCollection] is somewhat equivalent to <code>std::list<vtkSmartPointer<vtkObject*> ></code>
	== Language Specific ==		== Language Specific ==

-	* [[Documentation/{{documentation/version}}/Developers/Style Guide/Cpp \| C++]]	+	# [[Documentation/{{documentation/version}}/Developers/Style Guide/Cpp \| C++]]
-	* [[Documentation/{{documentation/version}}/Developers/Style Guide/Python \| Python]]	+	# [[Documentation/{{documentation/version}}/Developers/Style Guide/Python \| Python]]

	== Library Dependencies ==		== Library Dependencies ==

-	* MRML classes should only depend on vtk and itk (not Slicer Logic or Qt)	+	# MRML classes should only depend on vtk and itk (not Slicer Logic or Qt)
-	* Logic classes depend on MRML to store state	+	# Logic classes depend on MRML to store state
-	* Logic classes should encapsulate vtk and itk pipelines to accomplish specific slicer tasks (such as resampling volumes for display)	+	# Logic classes should encapsulate vtk and itk pipelines to accomplish specific slicer tasks (such as resampling volumes for display)
-	* GUI classes can depend on MRML and Logic and Qt	+	# GUI classes can depend on MRML and Logic and Qt

	== Development Practices ==		== Development Practices ==

-	* While developing code, enable VTK_DEBUG_LEAKS (ON by default) in your vtk build and be sure to clean up any leaks that arise from your contributions.	+	# While developing code, enable VTK_DEBUG_LEAKS (ON by default) in your vtk build and be sure to clean up any leaks that arise from your contributions.

	== Coordinate Systems ==		== Coordinate Systems ==

-	* World space for 3D Views is in RAS (Right Anterior Superior) space. See [[Coordinate systems]].	+	# World space for 3D Views is in RAS (Right Anterior Superior) space. See [[Coordinate systems]].
-	* All units are expressed in Millimeters (mm)	+	# All units are expressed in Millimeters (mm)

	== Misc. ==		== Misc. ==
-
-	* Use STL where you can, but follow the VTK [http://www.vtk.org/Wiki/VTK_FAQ#Can_I_use_STL_with_VTK.3F guidelines]

	= Commits =		= Commits =

Documentation/4.1/Developers/Tutorials/Debug Instructions

JChris.FillionR — Wed, 16 May 2012 20:08:58 GMT

GDB debug by attaching to running process:

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	*<code>--gdb</code>: runs GDB then executes SlicerQT-real from within the debugger environment.		*<code>--gdb</code>: runs GDB then executes SlicerQT-real from within the debugger environment.

-	===GDB debug by attaching to running process===	+	===GDB debug by attaching to running process [RECOMMENDED] ===
	Run ./Slicer-build/Slicer		Run ./Slicer-build/Slicer

Documentation/4.1/Developers/Tutorials/ModuleWriting

Finetjul — Wed, 16 May 2012 19:07:10 GMT

Dependency between modules:

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	= Dependency between modules =		= Dependency between modules =
-	It is possible that your module needs to access information from another module. Typically the logic of a module.	+	It is possible that your module needs to access information from another module. Typically the logic or the custom MRML classes of a module.
	The following code is an example of what can be done to make your module dependent to the Volumes module logic:		The following code is an example of what can be done to make your module dependent to the Volumes module logic:
		+
	In CMakeLists.txt:		In CMakeLists.txt:
	set(qt_module_include_directories		set(qt_module_include_directories
Line 103:		Line 104:
	vtkSlicerVolumesModuleLogic		vtkSlicerVolumesModuleLogic
	)		)
		+
	In qSlicerMY_MODULE_NAMEModule.cxx:		In qSlicerMY_MODULE_NAMEModule.cxx:
	QStringList qSlicerMY_MODULE_NAMEModule::dependencies()const		QStringList qSlicerMY_MODULE_NAMEModule::dependencies()const
Line 123:		Line 125:
	moduleLogic->SetVolumesLogic(volumesLogic);		moduleLogic->SetVolumesLogic(volumesLogic);
	}		}
-	By specifying the module as a dependency, you are insured that the dependency will be setup before your module is setup.	+	By specifying the module as a dependency, you are insured that the dependency module will be setup before your module is setup.

	Follow the same pattern in CMakeLists.txt to add dependency on a module widgets:		Follow the same pattern in CMakeLists.txt to add dependency on a module widgets:
Line 137:		Line 139:
	qSlicerVolumesModuleWidgets		qSlicerVolumesModuleWidgets
	)		)
		+
		+	It works the same if you want to access the custom MRML (''vtkSlicerDEPENDENT_MODULEModuleMRML_SOURCE_DIR'') or displayable manager (''vtkSlicerDEPENDENT_MODULEModuleDisplayableManager_SOURCE_DIR'') classes.

Documentation/4.1/Developers/Tutorials/ExternalModuleWriting

JChris.FillionR — Wed, 16 May 2012 18:15:34 GMT

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-	~~Back to [[Documentation/{{documentation/version}}/Developers\|Developers Information]]←~~
-
	This tutorial describes how to make a (Slicer4 / QT) loadable module that is compiled outside of the slicer build tree.		This tutorial describes how to make a (Slicer4 / QT) loadable module that is compiled outside of the slicer build tree.

Documentation/4.1/Developers/Tutorials/Debug Instructions

JChris.FillionR — Wed, 16 May 2012 18:14:31 GMT

← Older revision		Revision as of 18:14, 16 May 2012
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-	~~Back to [[Documentation/{{documentation/version}}/Developers\|Developers Information]]←~~
-
	==Background==		==Background==
	The executable Slicer application ''Slicer-Superbuild/Slicer-build/Slicer'' (or Slicer.exe) is the [[Documentation/{{documentation/version}}/Developers/Launcher\|launcher]] of the real application binary ''Slicer-Superbuild/Slicer-build/bin/SlicerQT-real''.		The executable Slicer application ''Slicer-Superbuild/Slicer-build/Slicer'' (or Slicer.exe) is the [[Documentation/{{documentation/version}}/Developers/Launcher\|launcher]] of the real application binary ''Slicer-Superbuild/Slicer-build/bin/SlicerQT-real''.

Developer Meetings/20120522

JChris.FillionR — Wed, 16 May 2012 18:13:40 GMT

Created page with 'Attendees: == To discuss == == Conclusion =='

New page

Attendees:

== To discuss ==

== Conclusion ==

Developer Meetings

JChris.FillionR — Wed, 16 May 2012 18:13:13 GMT

2012:

← Older revision		Revision as of 18:13, 16 May 2012
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	== 2012 ==		== 2012 ==
		+	* [[{{FULLPAGENAME}}/20120522\|May 22, 2012]]
	* [[{{FULLPAGENAME}}/20120515\|May 15, 2012]]		* [[{{FULLPAGENAME}}/20120515\|May 15, 2012]]
	* [[{{FULLPAGENAME}}/20120508\|May 8, 2012]]		* [[{{FULLPAGENAME}}/20120508\|May 8, 2012]]

Developer Meetings/20120515

JChris.FillionR — Wed, 16 May 2012 18:09:42 GMT

← Older revision		Revision as of 18:09, 16 May 2012
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-	Attendees:	+	Attendees: Alex, Chris, Jc, Julien, Nicole, Steve

	== To discuss ==		== To discuss ==
Line 13:		Line 13:
	** Every developer should make sure the issue assigned to him will be resolved 3 weeks before release date (August 1st)		** Every developer should make sure the issue assigned to him will be resolved 3 weeks before release date (August 1st)
	* Road map is forming: http://na-mic.org/Mantis/roadmap_page.php		* Road map is forming: http://na-mic.org/Mantis/roadmap_page.php
-	** VS2010: Slicer 4.2.0 ?	+	** VS2010: Slicer 4.2.0 ? http://www.na-mic.org/Bug/view.php?id=2002
	** ITKv4: Slicer 4.3.0 ? http://na-mic.org/Mantis/view.php?id=2007		** ITKv4: Slicer 4.3.0 ? http://na-mic.org/Mantis/view.php?id=2007
	** Qt 4.8.1: Slicer 4.3.0 ? See http://www.na-mic.org/Bug/view.php?id=2046		** Qt 4.8.1: Slicer 4.3.0 ? See http://www.na-mic.org/Bug/view.php?id=2046
Line 45:		Line 45:

	== Conclusion ==		== Conclusion ==
		+
		+	* Discussed release date for 4.1.1 and 4.2
		+	** 4.1.1
		+	*** Planned for June 1st. No feature freeze is expected.
		+	*** It will consist in creating a branch of 4.1 and integrating tweaks mainly related to extensions support. Related issues are listed [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&target_version=Slicer+4.1.1&sortby=last_updated&dir=DESC&hide_status_id=-2 here].
		+	** 4.2
		+	*** Need to clearly define which features and bug fixes we want to integrate. As of today, the list is [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&target_version=Slicer+4.2.0+AHM+Summer+2012&sortby=last_updated&dir=DESC&hide_status_id=-2 here].
		+	*** No special release will be done for RSNA (November). The plan will be to use 4.2.
		+	*** As of today, all issues labelled "crash" have been targeted for 4.2.
		+	*** '''TBD:''' Before NEXT Tuesday, developers are expected to review issue assigned to them and targeted for 4.2. If you believe an issue can't be resolved by mid-August / beginning of September, please let me know.
		+
		+	* Discussed update of DCMTK
		+	** Integration of DCMTK RT components/classes into official repository will be done at project week.
		+
		+	* Discussed VS2010 Support
		+	** Currently targeted for 4.2.0
		+	** Issue [http://www.na-mic.org/Bug/view.php?id=2002 #2002]
		+
		+	* Discussed ITKv4 Support
		+	** Currently targeted for 4.3.0
		+	** Issue [http://www.na-mic.org/Bug/view.php?id=2007 #2007]
		+
		+	* Discussed Qt 4.8.1 Support
		+	** Currently targeted for 4.3.0
		+	** Issue [http://www.na-mic.org/Bug/view.php?id=2046 #2046]
		+
		+	* Discussed transition to Git
		+	** Will definitively happen before the end of they year
		+	** Probably for 4.3.0
		+	** Issue [http://na-mic.org/Mantis/view.php?id=2059 #2059]
		+	** Before doing so, testing data will be moved into Midas. See [http://www.na-mic.org/Bug/view.php?id=2060 #2060]
		+
		+	* Discussed directory layout of scripted module in Slicer4
		+	** Scripted module will be moved into dedicated directory. Will be similar to scripted extension
		+	** Issue: [http://www.na-mic.org/Bug/view.php?id=2058 #2058]
		+
		+	* Discussed the layout of extensions
		+	** As of today, it will always be assumed a CMakeLists.txt will be available at the top level of your extension

Documentation/4.1/Modules/DWIRicianLMMSEFilter

Finetjul — Tue, 15 May 2012 22:12:04 GMT

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	{{documentation/{{documentation/version}}/module-introduction-start\|{{documentation/modulename}}}}		{{documentation/{{documentation/version}}/module-introduction-start\|{{documentation/modulename}}}}
	{{documentation/{{documentation/version}}/module-introduction-row}}		{{documentation/{{documentation/version}}/module-introduction-row}}
		+	Partially founded by grant number TEC2007-67073/TCM from the Comision Interministerial de Ciencia y Tecnologia (Spain).<br>
	This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>		This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>
-	Author: ~~FIRSTNAME LASTNAME~~, ~~AFFILIATION~~<br>	+	Author: Antonio Tristan Vega, Universidad de Valladolid, {{collaborator\|longname\|lmi}}<br>
-	Contributor1: ~~FIRSTNAME LASTNAME~~, ~~AFFILIATION~~<br>	+	Contributor1: Santiago Aja Fernandez, Universidad de Valladolid<br>
-	Contributor2: ~~FIRSTNAME LASTNAME~~, ~~AFFILIATION~~<br>	+	Contributor2: Marc Niethammer, {{collaborator\|longname\|unc}}<br>
-	Contact: ~~FIRSTNAME LASTNAME~~, <email>~~john~~@~~doe~~.~~org~~</email><br>	+	Contact: Antonio Tristan Vega, <email>atriveg@bwh.harvard.edu</email><br>
	{{documentation/{{documentation/version}}/module-introduction-row}}		{{documentation/{{documentation/version}}/module-introduction-row}}
	{{documentation/{{documentation/version}}/module-introduction-logo-gallery		{{documentation/{{documentation/version}}/module-introduction-logo-gallery
-	\|{{collaborator\|logo\|~~isomics~~}}\|{{collaborator\|longname\|~~isomics~~}} ~~<- Replace this logo with yours~~	+	\|{{collaborator\|logo\|lmi}}\|{{collaborator\|longname\|lmi}}
-	\|{{collaborator\|logo\|~~spl~~}}\|{{collaborator\|longname\|~~spl~~}} ~~<-Replace this logo with yours~~	+	\|{{collaborator\|logo\|unc}}\|{{collaborator\|longname\|unc}}
	}}		}}
	{{documentation/{{documentation/version}}/module-introduction-end}}		{{documentation/{{documentation/version}}/module-introduction-end}}
Line 41:		Line 42:
	<!-- ---------------------------- -->		<!-- ---------------------------- -->
	{{documentation/{{documentation/version}}/module-section\|References}}		{{documentation/{{documentation/version}}/module-section\|References}}
-	~~N/A~~	+	S. Aja-Fernandez, M. Niethammer, M. Kubicki, M. Shenton, and C.-F. Westin. Restoration of DWI data using a Rician LMMSE estimator. IEEE Transactions on Medical Imaging, 27(10): pp. 1389-1403, Oct. 2008.

	<!-- ---------------------------- -->		<!-- ---------------------------- -->

Developer Meetings/20120515

JChris.FillionR — Tue, 15 May 2012 20:17:16 GMT

← Older revision		Revision as of 20:17, 15 May 2012
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	* Road map is forming: http://na-mic.org/Mantis/roadmap_page.php		* Road map is forming: http://na-mic.org/Mantis/roadmap_page.php
	** VS2010: Slicer 4.2.0 ?		** VS2010: Slicer 4.2.0 ?
-	** ITKv4: Slicer 4.3.0 ?	+	** ITKv4: Slicer 4.3.0 ? http://na-mic.org/Mantis/view.php?id=2007
	** Qt 4.8.1: Slicer 4.3.0 ? See http://www.na-mic.org/Bug/view.php?id=2046		** Qt 4.8.1: Slicer 4.3.0 ? See http://www.na-mic.org/Bug/view.php?id=2046
	* Let's think about Slicer 4.4		* Let's think about Slicer 4.4

Documentation/4.1/Developers/Build Instructions/Prerequisites/Qt

JChris.FillionR — Tue, 15 May 2012 19:58:28 GMT

Download links:

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	\|align="center" colspan="1"\| [http://sw.nokia.com/id/14b2039c-0e1f-4774-a4f2-9aa60b6d5313/Qt_SDK_Lin64_offline SDK-1.2]		\|align="center" colspan="1"\| [http://sw.nokia.com/id/14b2039c-0e1f-4774-a4f2-9aa60b6d5313/Qt_SDK_Lin64_offline SDK-1.2]
	\|style="background-color:#C0C0C0;" align="center" colspan="1"\| <del>[http://get.qt.nokia.com/qt/source/qt-mac-carbon-opensource-4.7.0.dmg carbon_4.7.0]</del>		\|style="background-color:#C0C0C0;" align="center" colspan="1"\| <del>[http://get.qt.nokia.com/qt/source/qt-mac-carbon-opensource-4.7.0.dmg carbon_4.7.0]</del>
-	\|align="center" colspan="1"\| [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4.dmg 4.7.4 SDK] [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4-debug-libs.dmg ~~cocoa_4~~.7.4 (optional debug libs)]	+	\|align="center" colspan="1"\| [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4.dmg 4.7.4 SDK] <br> [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4-debug-libs.dmg 4.7.4 SDK (optional: with debug libs)]

	\|align="center" colspan="1"\| [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.7.4-vs2008.exe 4.7.4]		\|align="center" colspan="1"\| [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.7.4-vs2008.exe 4.7.4]

Developer Meetings/20120515

JChris.FillionR — Tue, 15 May 2012 19:53:43 GMT

← Older revision		Revision as of 19:53, 15 May 2012
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	== To discuss ==		== To discuss ==

-	* Review recently created issue	+	* Fix release date
-	* Fix release date ~~for~~ Slicer 4.1.1 and 4.2	+	** Slicer 4.1.1:
		+	*** Freeze: NA - Release date: June 1st
		+	** Slicer 4.2
		+	*** Freeze: August 1st - Release date: August 20
		+	* Before next week meeting:
		+	** Define all issues (bug and feature) associated with target 4.2
		+	** Which issues/feature should we expect for 4.2 ?
		+	** Every developer should make sure the issue assigned to him will be resolved 3 weeks before release date (August 1st)
		+	* Road map is forming: http://na-mic.org/Mantis/roadmap_page.php
		+	** VS2010: Slicer 4.2.0 ?
		+	** ITKv4: Slicer 4.3.0 ?
		+	** Qt 4.8.1: Slicer 4.3.0 ? See http://www.na-mic.org/Bug/view.php?id=2046
		+	* Let's think about Slicer 4.4
		+	* Transition to git ? Slicer 4.3.0 ?
		+
	* [[#.3D_Volume_streaming_and_MRML\|Volume_streaming_and_MRML]]		* [[#.3D_Volume_streaming_and_MRML\|Volume_streaming_and_MRML]]

Documentation/4.1/Developers/Build Instructions/Prerequisites/Qt

Pieper — Tue, 15 May 2012 19:14:49 GMT

Download links:

← Older revision		Revision as of 19:14, 15 May 2012
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	\|align="center" colspan="1"\| [http://sw.nokia.com/id/14b2039c-0e1f-4774-a4f2-9aa60b6d5313/Qt_SDK_Lin64_offline SDK-1.2]		\|align="center" colspan="1"\| [http://sw.nokia.com/id/14b2039c-0e1f-4774-a4f2-9aa60b6d5313/Qt_SDK_Lin64_offline SDK-1.2]
	\|style="background-color:#C0C0C0;" align="center" colspan="1"\| <del>[http://get.qt.nokia.com/qt/source/qt-mac-carbon-opensource-4.7.0.dmg carbon_4.7.0]</del>		\|style="background-color:#C0C0C0;" align="center" colspan="1"\| <del>[http://get.qt.nokia.com/qt/source/qt-mac-carbon-opensource-4.7.0.dmg carbon_4.7.0]</del>
-	\|align="center" colspan="1"\| [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4~~-debug-libs~~.dmg ~~cocoa_4~~.7.4 ~~debug libs~~] [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4.dmg 4.7.4 ~~SDK~~]	+	\|align="center" colspan="1"\| [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4.dmg 4.7.4 SDK] [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4-debug-libs.dmg cocoa_4.7.4 (optional debug libs)]

	\|align="center" colspan="1"\| [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.7.4-vs2008.exe 4.7.4]		\|align="center" colspan="1"\| [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.7.4-vs2008.exe 4.7.4]

User:Finetjul

Finetjul — Tue, 15 May 2012 18:22:11 GMT

← Older revision		Revision as of 18:22, 15 May 2012
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	* vtkMRML::CopyWithSingleModifiedEvent should do StartModify and EndModify() instead (dito for CopyWithSceneWithSingleModifiedEvent)		* vtkMRML::CopyWithSingleModifiedEvent should do StartModify and EndModify() instead (dito for CopyWithSceneWithSingleModifiedEvent)
	* Singleton node vtkMRMLLayoutNode has an ID of vtkMRMLLayoutNodevtkMRMLLayoutNode		* Singleton node vtkMRMLLayoutNode has an ID of vtkMRMLLayoutNodevtkMRMLLayoutNode
		+
	=What am I working on?=		=What am I working on?=
-	*~~CTK Layout flickering (to be merged)~~	+	* Various mantis issues
-	*VTK callback speed-up (to be merged)	+
		+	=On hold =
		+	*VTK callback speed-up (in VTK 6.0, to be merged on Slicer/VTK)

	=What's coming next?=		=What's coming next?=
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	*Investigate (not necessarily be the one to fix it): [http://www.na-mic.org/Bug/view.php?id=1980 1980], [http://www.na-mic.org/Bug/view.php?id=1952 1952]...		*Investigate (not necessarily be the one to fix it): [http://www.na-mic.org/Bug/view.php?id=1980 1980], [http://www.na-mic.org/Bug/view.php?id=1952 1952]...
	=Done=		=Done=
		+	*CTK Layout flickering
	*Volume Rendering supports color transfer function		*Volume Rendering supports color transfer function
	*Scene view speed-up		*Scene view speed-up
	*QtTesting integration		*QtTesting integration
	*Crash when restoring sceneview		*Crash when restoring sceneview

Documentation/4.1/FAQ

Meier — Tue, 15 May 2012 16:39:03 GMT

Registration is too slow. How can I speed up my registration?:

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	== How important is bias field correction / intensity inhomogeneity correction? ==		== How important is bias field correction / intensity inhomogeneity correction? ==
-	While registration may still succeed with mild cases of inhomogeneity, moderate to severe inhomogeneity can negatively affect automated registration quality. It is recommended to run an automated bias-field correction on both images before registration. [http://~~www~~.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection see here for documentation on this module]. Masking of non-essential peripheral structures can also help to reduce distracting image content. ~~[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/~~FAQ~~#What.27s_the_purpose_of_masking_.2F_VOI_in_registration.3F See here~~ for more ~~on masking]~~	+	[[Image:Slicer41VerifiedIcon.png\|50px\|left]]
		+	While registration may still succeed with mild cases of inhomogeneity, moderate to severe inhomogeneity can negatively affect automated registration quality. It is recommended to run an automated bias-field correction on both images before registration. [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/N4ITKBiasFieldCorrection see here for documentation on this module]. Masking of non-essential peripheral structures can also help to reduce distracting image content. See the FAQ on masking for more details.

	== Have the Slicer registration methods been validated? ==		== Have the Slicer registration methods been validated? ==
		+	[[Image:Slicer41VerifiedIcon.png\|50px\|left]]
	The Slicer3.6 registration modules share the same same underlying ITK registration engines. For validation of those basic algorithms refer to the ITK software guide or the Insight Journal. Slicer registration of images and surfaces has been applied successfully in many cases, some of which are documented here [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:UseCaseInventory here]. For ongoing efforts on improving/validating Slicer registration performance please contact the [mailto:slicer-users@bwh.harvard.edu Slicer User Mailing List] or the [mailto:slicer-devel@bwh.harvard.edu Slicer Developer Mailing List].		The Slicer3.6 registration modules share the same same underlying ITK registration engines. For validation of those basic algorithms refer to the ITK software guide or the Insight Journal. Slicer registration of images and surfaces has been applied successfully in many cases, some of which are documented here [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:UseCaseInventory here]. For ongoing efforts on improving/validating Slicer registration performance please contact the [mailto:slicer-users@bwh.harvard.edu Slicer User Mailing List] or the [mailto:slicer-devel@bwh.harvard.edu Slicer Developer Mailing List].

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	== How can I save the parameter settings I have selected for later use or sharing? ==		== How can I save the parameter settings I have selected for later use or sharing? ==
-	The ''Parameter Set'' menu at the top tab of each module serves this purpose of saving and recalling instances of parameter settings. To save the current settings select ''Rename'' from the menu, give it a descriptive name and then select ''Create New Commandline Module'' from the menu. New settings are added to the menu as created. These settings are saved together with the Slicer Scene.mrml file. To save only ~~tthe~~ presets without any associate data, first save your entire scene, then delete all nodes in the MRML tree except the top ''Scene'' node, and then save this under a new name like "Slicer_Presets.mrml" etc. To load the presets in, use ''Import'' from the File menu, which will add the MRML entries to the existing scene. Do not load presets via "Load Scene", since that will ~~delete all currently~~ loaded data. [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:ParameterPresetsTutorial A detailed user guide on loading presets can be found here]	+	[[Image:Slicer41VerifiedIcon.png\|50px\|left]]
		+	The ''Parameter Set'' menu at the top tab of each module serves this purpose of saving and recalling instances of parameter settings. To save the current settings select ''Rename'' from the menu, give it a descriptive name and then select ''Create New Commandline Module'' from the menu. New settings are added to the menu as created. These settings are saved together with the Slicer Scene.mrml file. To save only the presets without any associate data, first save your entire scene, then delete all nodes in the MRML tree except the top ''Scene'' node, and then save this under a new name like "Slicer_Presets.mrml" etc. To load the presets in, use ''Import'' from the File menu, which will add the MRML entries to the existing scene. Do '''not''' load presets via "Load Scene", since that will replace the loaded data rather than add to it. [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:ParameterPresetsTutorial A detailed user guide on loading presets can be found here]. Note that the content and format of the Slicer Scene file tends to change and evolve with newer versions, and presets may not be compatible across very different versions.

	== Registration is too slow. How can I speed up my registration? ==		== Registration is too slow. How can I speed up my registration? ==
-	The key parameters that influence registration speed are the number of sample points, the degrees of freedom of the transform, the type of similarity metric and the initial misalignment and image contrast/content differences. If registration quality is ok, try reducing the sample points first. [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/FAQ#How_many_sample_points_should_I_choose_for_my_registration.3F Guidelines on selecting sample points are given here]. The degrees of freedom usually are given by the overall task and not subject to variation, but depending on initial misalignment, both speed and robustness can improve by an iterative approach that gradually increases DOF rather than starting with a high DOF setting. ~~Thehttp~~://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit ~~BRAINSfit module~~] and [http://~~www~~.slicer.org/slicerWiki/index.php/Modules~~:RegisterImages~~ Expert Automated Registration ~~module~~] both allow prescriptions of iterative DOF.<br>	+	[[Image:Slicer41VerifiedIcon.png\|50px\|left]]
-	If using a cost/criterion function other than mutual information, note that the corresponding ITK implementation may not have been parallelized and hence may not be taking advantage of multi-threading/multi-CPU cores on your computer. This can slow down performance significantly. ~~<br>~~	+	The key parameters that influence registration speed are the number of sample points, the degrees of freedom of the transform, the type of similarity metric and the initial misalignment and image contrast/content differences. If registration quality is ok, try reducing the sample points first. [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/FAQ#How_many_sample_points_should_I_choose_for_my_registration.3F Guidelines on selecting sample points are given here]. The degrees of freedom usually are given by the overall task and not subject to variation, but depending on initial misalignment, both speed and robustness can improve by an iterative approach that gradually increases DOF rather than starting with a high DOF setting. The [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit ''General Registration (BRAINS)''] and [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ExpertAutomatedRegistration ''Expert Automated Registration''] both allow prescriptions of iterative DOF.<br>
-	[http://~~www~~.slicer.org/slicerWiki/index.php/~~Slicer3~~:Registration Also see the ''Slicer Registration ~~Portal~~ Page'' for help on selecting registration methods based on criteria of speed, precision etc.]	+	If using a cost/criterion function other than mutual information, note that the corresponding ITK implementation may not have been parallelized and hence may not be taking advantage of multi-threading/multi-CPU cores on your computer. This can slow down performance significantly.
		+	[http://wiki.slicer.org/slicerWiki/index.php/Category:Documentation/4.1/Modules/Registration Also see the ''Slicer Registration Page'' for help on selecting registration methods based on criteria of speed, precision etc.]. <br> General tips:
		+	*the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit ''General Registration (BRAINS)''] module is parallelized and tends to be fastest
		+	*try reducing the number of sample points; see [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/FAQ#How_many_sample_points_should_I_choose_for_my_registration.3F here for guidelines on selecting sample points]
		+	*try a lower DOF registration first to determine if initial position differences are causing excessive search that slows down registration.
		+	*use mutual information as cost function (default)
		+	*if your image is very large (512x512 in plane or greater) try a lower resolution version of your image. You can use the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleVolume Resample Volume] module to subsample your image.

	== Registration results are inconsistent and don't work on some image pairs. Are there ways to make registration more robust? ==		== Registration results are inconsistent and don't work on some image pairs. Are there ways to make registration more robust? ==

Developer Meetings/20120515

JChris.FillionR — Tue, 15 May 2012 16:15:38 GMT

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	== To discuss ==		== To discuss ==
		+
		+	* Review recently created issue
		+	* Fix release date for Slicer 4.1.1 and 4.2
		+	* [[#.3D_Volume_streaming_and_MRML\|Volume_streaming_and_MRML]]
		+
		+	=== Volume streaming and MRML ==
		+	<pre>
		+	From Laurent:
		+
		+	Hello,
		+
		+	I've seen Andriy is using vtkMRMLDiffusionWeightedImageNode to store several volumes in his 4D module.
		+	I would like to use it with the same purpose, but with streaming volumes.
		+
		+	The major difference is I don't know number of volumes I will receive. I looked at the vtkMRMLDiffusionWeightedImageNode and, when we call SetNumberOfGradient, it seems, it's reseting BValue array and gradient array.
		+
		+	If I understood it, we use gradient array to store our ImageData.
		+
		+	My first thought has been, when I receive a volume, increase the value of NumberOfGradients, then, add the new volume in the gradient array.
		+	However, if SetNumberOfGradient is reseting these arrays, this will erase my previous volumes store in it.
		+
		+	I still can copy them before, then SetNumberOfGradient, then put them in the array (with the new size) and add my new volume at the end, but this is not efficient at all (especially when number of volumes is increasing).
		+
		+	Please, could you let me know if I misunderstood something. If not, is there any workaround ?
		+
		+	Thank you.
		+	</pre>

	== Conclusion ==		== Conclusion ==

Documentation/4.1/FAQ

Meier — Tue, 15 May 2012 16:06:44 GMT

I want to register two images with different intensity/contrast.:

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	== I want to register two images with different intensity/contrast. ==		== I want to register two images with different intensity/contrast. ==
-	*The two most critical image features that determine automated registration accuracy and robustness are image contrast and resolution. Differences in image contrast are best addressed with the appropriate cost function. The cost function that has proven most reliable for registering images with different contrast (e.g. a T1 MRI to a T2 or an MRI to CT or PET) is '''mutual information'''. All intensity-based registration modules use mutual information as the default cost function. Only the [http://www.slicer.org/slicerWiki/index.php/Modules~~:RegisterImages~~ ''Expert Automated Registration''] module lets you choose alternative cost function.	+	[[Image:Slicer41VerifiedIcon.png\|50px\|left]]
-		+	The two most critical image features that determine automated registration accuracy and robustness are image contrast and resolution. Differences in image contrast are best addressed with the appropriate cost function. The cost function that has proven most reliable for registering images with different contrast (e.g. a T1 MRI to a T2 or an MRI to CT or PET) is '''mutual information'''. All intensity-based registration modules use mutual information as the default cost function. Only the[http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ExpertAutomatedRegistration ''Expert Automated Registration''] module (under ''All Modules'') lets you choose alternative cost function.
-	No extra adjustment is therefore needed in terms of adjusting parameters to register images of different contrast. Depending on the amount of differences you may consider masking to exclude distracting image content or adjusting the ''Histogram Bins'' setting to increase/decrease the level of intensity detail the algorithm is aware of.	+	No extra adjustment is therefore needed in terms of adjusting parameters to register images of different contrast. Depending on the amount of differences you may consider masking to exclude distracting image content or adjusting the ''Histogram Bins'' setting to increase/decrease the level of intensity detail the algorithm is aware of.
		+	*Modules that allow control of ''Histogram Bins'':
		+	**[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/LinearRegistration Linear Registration (under: "All Modules" menu)]
		+	**[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/AffineRegistration Affine Registration (under: "All Modules" menu)]
		+	**[http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BSplineDeformableRegistration BSpline Deformable Registration (under: "All Modules" menu)]

	== How important is bias field correction / intensity inhomogeneity correction? ==		== How important is bias field correction / intensity inhomogeneity correction? ==

Documentation/4.1/Modules/Models

Finetjul — Tue, 15 May 2012 15:56:10 GMT

Link "Similar modules" properly

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	<!-- ---------------------------- -->		<!-- ---------------------------- -->
	{{documentation/{{documentation/version}}/module-section\|Similar Modules}}		{{documentation/{{documentation/version}}/module-section\|Similar Modules}}
-	* The Annotations module uses geometry to mark locations and so has similar functionality to the models module.	+	* The [[Documentation/{{documentation/version}}/Modules/Annotations\|Annotations]] module uses geometry to mark locations and so has similar functionality to the models module.
-	* The [~~http:~~//~~www.slicer.org/slicerWiki/index.php/Documentation/4.1~~/Modules/ProbeVolumeWithModel Probe Volume With Model] module allows a user to apply a scalar overlay to a model by sampling a volume.	+	* The [[Documentation/{{documentation/version}}/Modules/ProbeVolumeWithModel\|Probe Volume With Model]] module allows a user to apply a scalar overlay to a model by sampling a volume.
-	* The [~~http:~~//~~www.slicer.org/slicerWiki/index.php/Documentation/4.1~~/Modules/MergeModels Merge Models] module will allow you to create a single model from two models	+	* The [[Documentation/{{documentation/version}}/Modules/MergeModels\|Merge Models]] module will allow you to create a single model from two models

	<!-- ---------------------------- -->		<!-- ---------------------------- -->

Documentation/4.1/Modules/Models

Nicole — Tue, 15 May 2012 15:04:29 GMT

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	{{documentation/{{documentation/version}}/module-section\|Similar Modules}}		{{documentation/{{documentation/version}}/module-section\|Similar Modules}}
	* The Annotations module uses geometry to mark locations and so has similar functionality to the models module.		* The Annotations module uses geometry to mark locations and so has similar functionality to the models module.
-	* The Probe Volume With Model module allows a user to apply a scalar overlay to a model by sampling a volume.	+	* The [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ProbeVolumeWithModel Probe Volume With Model] module allows a user to apply a scalar overlay to a model by sampling a volume.
		+	* The [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/MergeModels Merge Models] module will allow you to create a single model from two models

	<!-- ---------------------------- -->		<!-- ---------------------------- -->
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	{{documentation/{{documentation/version}}/module-section\|Information for Developers}}		{{documentation/{{documentation/version}}/module-section\|Information for Developers}}
	{{documentation/{{documentation/version}}/module-developerinfo}}		{{documentation/{{documentation/version}}/module-developerinfo}}
		+
		+	It's possible to have multiple models combined into one model and have each shape assigned different color values, but it requires either using Merge Models to merge the shapes into one file and using python to create a scalar overlay to assign values to each vertex (assuming the user can determine which vertex belongs to which shape), or using Paraview, as per [http://slicer-users.65878.n3.nabble.com/saving-multiple-colors-Models-within-one-STL-or-VTK-tp3974004p3974701.html Andras Lasso]:
		+
		+	Merge multiple STL files into a single colored VTK file in Paraview:
		+
		+	*Load all the models
		+	*Assign a constant scalar to the points by using the Calculator filter (use a different constant for each model, e.g., 1, 2, 3, 4, ...)
		+	*Merge the Calculator outputs with the Append Geometry filter
		+	*Save the Append Geometry filter output with File / Save Data / File type VTK or VTP (download the sample ParaView state file from [http://dl.dropbox.com/u/1528749/SlicerHelp/merge.pvsm here])
		+
		+	Then in Slicer you can load the model, open the Models module, open Scalars, enable "Visible", select "Result" as active scalar, select a color table.

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	\|align="center" colspan="1"\| [http://sw.nokia.com/id/14b2039c-0e1f-4774-a4f2-9aa60b6d5313/Qt_SDK_Lin64_offline SDK-1.2]		\|align="center" colspan="1"\| [http://sw.nokia.com/id/14b2039c-0e1f-4774-a4f2-9aa60b6d5313/Qt_SDK_Lin64_offline SDK-1.2]
	\|style="background-color:#C0C0C0;" align="center" colspan="1"\| <del>[http://get.qt.nokia.com/qt/source/qt-mac-carbon-opensource-4.7.0.dmg carbon_4.7.0]</del>		\|style="background-color:#C0C0C0;" align="center" colspan="1"\| <del>[http://get.qt.nokia.com/qt/source/qt-mac-carbon-opensource-4.7.0.dmg carbon_4.7.0]</del>
-	\|align="center" colspan="1"\| [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4.dmg 4.7.4 SDK] [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4-debug-libs.dmg ~~cocoa_4~~.7.4 (optional debug libs)]	+	\|align="center" colspan="1"\| [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4.dmg 4.7.4 SDK] <br> [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4-debug-libs.dmg 4.7.4 SDK (optional: with debug libs)]

	\|align="center" colspan="1"\| [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.7.4-vs2008.exe 4.7.4]		\|align="center" colspan="1"\| [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.7.4-vs2008.exe 4.7.4]

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	\|style="background-color:#C0C0C0;" align="center" colspan="1"\| <del>[http://get.qt.nokia.com/qt/source/qt-mac-carbon-opensource-4.7.0.dmg carbon_4.7.0]</del>		\|style="background-color:#C0C0C0;" align="center" colspan="1"\| <del>[http://get.qt.nokia.com/qt/source/qt-mac-carbon-opensource-4.7.0.dmg carbon_4.7.0]</del>
-	\|align="center" colspan="1"\| [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4~~-debug-libs~~.dmg ~~cocoa_4~~.7.4 ~~debug libs~~] [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4.dmg 4.7.4 ~~SDK~~]	+	\|align="center" colspan="1"\| [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4.dmg 4.7.4 SDK] [ftp://ftp.qt.nokia.com/qt/source/qt-mac-opensource-4.7.4-debug-libs.dmg cocoa_4.7.4 (optional debug libs)]

	\|align="center" colspan="1"\| [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.7.4-vs2008.exe 4.7.4]		\|align="center" colspan="1"\| [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.7.4-vs2008.exe 4.7.4]