Re: [Gimias-developers] help about the plugin
Hi Alex,
I'm glad to know that all things are working well. Regarding your
problems:
1. The default configuration of the MITK library should automatically
add the compilation flag /bigobj for MSVC compilar. This configuration is
defined in the file thirdParty\MITK_SVN2\CMakeLists.txt:
IF(WIN32)
#Visual C++, 32-bit, version 20081500 (vc90)
IF(MSVC_VERSION GREATER 1500 OR MSVC_VERSION EQUAL 1500)
SET(CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS} /bigobj)
ENDIF(MSVC_VERSION GREATER 1500 OR MSVC_VERSION EQUAL 1500)
ENDIF(WIN32)
If it does not work for your compiler, it means that the value of the
variable MSVC_VERSION is 1500. Could you please check it? You need to:
1. Add this line in the CMakeLists.txt file, just bellow the code above:
MESSAGE( MSVC_VERSION: ${MSVC_VERSION} )
2. Click Configure third party folders button in CSnake
3. Check the console output. In my computer it says:
MSVC_VERSION: 1600
2. For this problem, I think Yves can give you better support. He is
the main developer of CSnake. I put him in copy.
3. Do you have an example application using this feature? In what use
case do you need it? To know the orientation of an image, you can enable
the annotation cube (Ctrl+A). It shows the orientation of the image:
left/right, superior/inferior, anterior/posterior.
Best regards,
Xavi
2012/8/31 Zhijun Zhang zjzh...@gmail.com
hi Xavi:
Now all things are working well. Thank you very much for your help.
There are still two small problem in the cSnake,
1). when I generate the cmake file and compile the thirdparty projects
such as mitk and mitkext
I need manually add /bigobj in the compiler option under windows system,
2). and when I click the 'install files to build folder', for debug
version, it works.
for release version, it seems the library are not copied. so I manually
copied them.
I have another question about the viewing window of GIMIAS,
why the axes in the orthogonal view has no positive and negative
direction? sometimes it
is confusing to look for the positive axes directions.
Thank you very much.
regards,
Alex
--
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Re: [Gimias-developers] help about the plugin
From: Zhijun Zhang [mailto:zjzh...@gmail.com] Sent: lunes, 11 de junio de 2012 0:24 To: Xavier Planes; gimias-developers@lists.sourceforge.net Subject: Re: [Gimias-developers] help about the plugin hi Xavier: How are you these days? I have read some of the tutorials and now I can write a little code to have a two image registration plugin. Now I would like to write an image sequence registration tool. I would like to have the following problems: 1. for single image, if I open it in the GIMIAS menu file-open data, It shows in the data tree area, then how do I know the image pixel type, dimension? because I need to define an itk registration method with the template parameter of the pixel type and dimension. 2. If I open a 3D image sequences (lets say, ten analyze image or vtk image), how do I know the number of frames in this sequence and how I can get the pointer of each image frame in my processor functions? 3. I would like to call image registration functions in another library( like elastix ) in my plugin code, is there easy ways to add this library? is it necessary that the itk library that gimias based on and the itk elastix based on are the same version? thank you very much. regards, Alex -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Gimias-developers mailing list Gimias-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/gimias-developers
Re: [Gimias-developers] help about the plugin
hi Xavier: How are you these days? I have read some of the tutorials and now I can write a little code to have a two image registration plugin. Now I would like to write an image sequence registration tool. I would like to have the following problems: 1. for single image, if I open it in the GIMIAS menu file-open data, It shows in the data tree area, then how do I know the image pixel type, dimension? because I need to define an itk registration method with the template parameter of the pixel type and dimension. 2. If I open a 3D image sequences (lets say, ten analyze image or vtk image), how do I know the number of frames in this sequence and how I can get the pointer of each image frame in my processor functions? 3. I would like to call image registration functions in another library( like elastix ) in my plugin code, is there easy ways to add this library? is it necessary that the itk library that gimias based on and the itk elastix based on are the same version? thank you very much. regards, Alex 2012/6/1 Xavier Planes xavier.pla...@upf.edu Hi Alex, ** ** How is it going with the tutorials? Can I help you with any issue? ** ** Best regards, Xavi ** ** *From:* Xavier Planes [mailto:xavier.pla...@upf.edu *Sent:* miércoles, 23 de mayo de 2012 12:42 *To:* 'Zhijun Zhang'; 'gimias-developers@lists.sourceforge.net' *Subject:* RE: [Gimias-developers] help about the plugin ** ** Hi Alex, ** ** I recommend you to follow the tutorials: https://sourceforge.net/apps/mediawiki/gimias/index.php?title=Developer_tutorials_for_GIMIAS_1_4 ** ** After creating your plugin, you will have a default processor and widget: https://sourceforge.net/apps/mediawiki/gimias/index.php?title=HowToCreateYourPlugin ** ** For communicating the widget and the processor, I recommend you this tutorial: https://sourceforge.net/apps/mediawiki/gimias/index.php?title=HowToCommunicateBtwProcessorAndPanelWidget ** ** Best regards, Xavi ** ** *From:* Zhijun Zhang [mailto:zjzh...@gmail.com] *Sent:* miércoles, 23 de mayo de 2012 10:33 *To:* gimias-developers@lists.sourceforge.net *Subject:* Re: [Gimias-developers] help about the plugin ** ** hi Yves, thanks, after update the zlib, now I can build gimias code using csnake. Now I would like to know how to write plugin code: after I add some widget such as button and edit box using wxglade, how can I add a botton down function for the control? and where do I write the code for the processor? is there an example for this? regards, ** ** ** ** -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Gimias-developers mailing list Gimias-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/gimias-developers
Re: [Gimias-developers] help about the plugin
Hi Alex, These days we are working on several project deliverables and on a new release of GIMIAS-1.5. You can find more details here: http://www.gimias.org/download/gimias-15 Regarding your questions: 1. Read image properties: a. If using a Processor: The best way to know the pixel type and the dimension is to retrieve the vtk image from a DataEntity: Core::vtkImageDataPtr inputImage; GetProcessingData( 0, inputImage ); inputImage-GetDimensions() inputImage-GetSpacing(); inputImage-GetOrigin(); inputImage-GetScalarTypeAsString(); b. If using a CommandLinePlugin: You can use ITK directly. You can see an example in GaussianBlurImageFilter.cxx 2. Retrieve 3D+T data: a. For a Processor you can read the documentation: https://sourceforge.net/apps/mediawiki/gimias/index.php?title=Extensible_Exe cution_Component#3D.2BT_processing b. For a CommandLinePlugin: https://sourceforge.net/apps/mediawiki/gimias/index.php?title=HowToDevelopAC ommandLinePlugin#3D_.2B_T_processing 3. Elastix: I've been in an introductory presentation about Elastix some weeks ago and it was very interesting. However, I've never used it :(. It will be really great to integrate this library in GIMIAS. If you are integrating the source code of Elastix, I think you will not have any problem to use the same ITK version used in GIMIAS. If you are using the precompiled library, it could be more difficult. To integrate the precompiled library, it's very easy. You can take a look at this tutorial: https://sourceforge.net/apps/mediawiki/gimias/index.php?title=HowToCreateYou rThirdParty For the integration of Elastix, I'm thinking that it could be easier to use a command line plugin, instead of a GIMIAS native plugin because a command line plugin uses ITK directly. Best regards, Xavi From: Zhijun Zhang [mailto:zjzh...@gmail.com] Sent: lunes, 11 de junio de 2012 0:24 To: Xavier Planes; gimias-developers@lists.sourceforge.net Subject: Re: [Gimias-developers] help about the plugin hi Xavier: How are you these days? I have read some of the tutorials and now I can write a little code to have a two image registration plugin. Now I would like to write an image sequence registration tool. I would like to have the following problems: 1. for single image, if I open it in the GIMIAS menu file-open data, It shows in the data tree area, then how do I know the image pixel type, dimension? because I need to define an itk registration method with the template parameter of the pixel type and dimension. 2. If I open a 3D image sequences (lets say, ten analyze image or vtk image), how do I know the number of frames in this sequence and how I can get the pointer of each image frame in my processor functions? 3. I would like to call image registration functions in another library( like elastix ) in my plugin code, is there easy ways to add this library? is it necessary that the itk library that gimias based on and the itk elastix based on are the same version? thank you very much. regards, Alex -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Gimias-developers mailing list Gimias-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/gimias-developers
Re: [Gimias-developers] help about the plugin
Hi Alex, Analyze images contain orientation information and by default are realigned to LPS when loading these in GIMIAS. You can disable this option in the Edit-Preferences-Global-Orient images to LPS orientation when reading. If this does not work, could you please send me your files? I can take a look at it. Best, Xavi From: Zhijun Zhang [mailto:zjzh...@gmail.com] Sent: viernes, 01 de junio de 2012 10:19 To: gimias-developers@lists.sourceforge.net Subject: Re: [Gimias-developers] help about the plugin hi all: I have a problem with the hdr(.img) image and vtk image displaying. I have segment some mesh model and save into vtk files. In the paraview, I can see that the mesh and the analyze image file (or same image in .vtk format) aligns perfect. However, neither vtk format nor the img(hdr) format images aligns well with the mesh file. I do not know whether there is problem with this. Thank you for your help. Alex -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Gimias-developers mailing list Gimias-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/gimias-developers
Re: [Gimias-developers] help about the plugin
Hi Alex, This error means that csnake cannot find the third party module called ZLIB. This is a third party library that is included in gimias under the thirdParty folder. So either you do not have the folder or its path has not been given to csnake (it needs to be set in the Third Party folders section of the context tab). If this is not the problem, could you send me either a snapshot of the context tab or the *.CSnakeGUI file in which you save your configuration. Best, Yves From: Zhijun Zhang [mailto:zjzh...@gmail.com] Sent: sábado, 19 de mayo de 2012 9:37 To: gimias-developers@lists.sourceforge.net; xavier.pla...@upf.edu Subject: [Gimias-developers] help about the plugin hi Xavi and Yves, Thank you for your help. Following my problem, I have installed the csnake 2.5 version. but now I still have problem, I have added the gimias1.4.2 source directory together with my plugin directory in the csnake 'root folders' blanks, and I have set up the directories for the compiler, python and cmake, then I choose the csnake file for my plugin, and press the update, now the Csnake pops a dialog says stopped exception in process. no module named csnZLIB'. I have tried to build the gimias source as described in the User manual 1.2.0, it gives the same complain dialog info. I copy the info here: Working, patience please... Action: Update List Of Targets. Traceback (most recent call last): File csnGUI.py, line 966, in DoActions File csnGUI.py, line 893, in ActionUpdateListOfTargets File csnGUIHandler.pyc, line 301, in GetListOfPossibleTargets File csnGUIHandler.pyc, line 137, in __GetProjectModule File csnUtility.pyc, line 106, in LoadModule File D:/zjzhang/work/gimiasApp/gimiasApp_src\csngimiasApp.py, line 8, in module File D:/zjzhang/Library/GIMIAS_1_4_2/src\csnGIMIASDef.py, line 108, in CreateGimiasApp File D:/zjzhang/Library/GIMIAS_1_4_2/src\Apps\Gimias\csnGIMIAS.py, line 20, in module File csnAPIImplementation.pyc, line 145, in AddProjects File csnAPIImplementation.pyc, line 96, in _UnwrapProject File D:/zjzhang/Library/GIMIAS_1_4_2/src\csnGIMIASDef.py, line 148, in gmCoreLight File D:/zjzhang/Library/GIMIAS_1_4_2/src\Apps\Gimias\csnGMCoreLight.py, line 14, in module File csnAPIImplementation.pyc, line 145, in AddProjects File csnAPIImplementation.pyc, line 96, in _UnwrapProject File D:/zjzhang/Library/GIMIAS_1_4_2/src\csnGIMIASDef.py, line 112, in gmCommonObjects File D:/zjzhang/Library/GIMIAS_1_4_2/src\Apps\Gimias\Core\CommonObjects\csnGMCom monObjects.py, line 11, in module File csnAPIImplementation.pyc, line 145, in AddProjects File csnAPIImplementation.pyc, line 96, in _UnwrapProject File D:/zjzhang/Library/GIMIAS_1_4_2/src\csnToolkitOpen.py, line 60, in baseLib File D:/zjzhang/Library/GIMIAS_1_4_2/src\Modules\BaseLib\csnBaseLib.py, line 56, in module File csnAPIImplementation.pyc, line 145, in AddProjects File csnAPIImplementation.pyc, line 96, in _UnwrapProject File D:/zjzhang/Library/GIMIAS_1_4_2/src\csnToolkitOpen.py, line 34, in cgns File csnAPIImplementation.pyc, line 639, in LoadThirdPartyModule File csnProject.pyc, line 62, in LoadThirdPartyModule File csnUtility.pyc, line 119, in LoadModules File D:/zjzhang/Library/GIMIAS_1_4_2/thirdParty/CGNS\csnCGNS.py, line 8, in module File csnAPIImplementation.pyc, line 145, in AddProjects File csnAPIImplementation.pyc, line 96, in _UnwrapProject File D:/zjzhang/Library/GIMIAS_1_4_2/src\csnGIMIASDef.py, line 34, in hdf5 File csnAPIImplementation.pyc, line 639, in LoadThirdPartyModule File csnProject.pyc, line 62, in LoadThirdPartyModule File csnUtility.pyc, line 119, in LoadModules File D:/zjzhang/Library/GIMIAS_1_4_2/thirdParty/HDF5\csnHDF5.py, line 8, in module File csnAPIImplementation.pyc, line 145, in AddProjects File csnAPIImplementation.pyc, line 96, in _UnwrapProject File D:/zjzhang/Library/GIMIAS_1_4_2/src\csnGIMIASDef.py, line 10, in zlib File csnAPIImplementation.pyc, line 639, in LoadThirdPartyModule File csnProject.pyc, line 62, in LoadThirdPartyModule File csnUtility.pyc, line 119, in LoadModules ImportError: No module named csnZLIB Done (3mn 46.83s). I would like to know how to do ? Thank you very much. regards, Alex -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Gimias-developers mailing list Gimias-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/gimias-developers
