[ITK-users] FW: Lesion Sizing Toolkit Build not successful
Dženan Zukić
dzenanz at gmail.com
Fri Oct 14 09:21:18 EDT 2016
Hi Christina,
I pushed a new commit to my fork
<https://github.com/dzenanz/LesionSizingToolkit> which resolves all build
and link errors on my VS2013 setup. Can you give it a try?
Regards,
Dženan
On Thu, Oct 13, 2016 at 6:31 PM, Dženan Zukić <dzenanz at gmail.com> wrote:
> Hi Constance,
>
> I am using a recent VTK master.
>
> I am right now looking into lesion sizing toolkit. I have push a commit to
> my fork:
> https://github.com/dzenanz/LesionSizingToolkit
>
> This solves compile errors for me. I still have link errors (when building
> outside of ITK build tree, your first approach).
>
> It is end of workday in US Eastern so I will probably have to postpone
> this for tomorrow. But maybe someone else on the list will suggest a fix
> meanwhile :)
>
> Regards,
> Dženan
>
> On Thu, Oct 13, 2016 at 6:20 PM, Owens,Constance A <CAOwens at mdanderson.org
> > wrote:
>
>> Hi Dženan,
>>
>> My advisor wanted me to ask you what VTK version did you use exactly? He
>> tried with VS2015 and still gets the same error. Below was his response to
>> me:
>>
>>
>>
>> Using the VS2015 doesn’t help. Same errors.
>>
>>
>>
>> I believe it’s the problem of combination of ITK and VTK. Try to check
>> with Dzenan what the VTK version he used and the cmake options for VTK. It
>> seems that when VTK was included, all ITK header files could not be
>> located. No ITK directories were included (as shown).
>>
>>
>>
>>
>>
>>
>>
>> Thanks,
>>
>> Constance
>>
>>
>>
>> *From:* Dženan Zukić [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 1:45 PM
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>> *Subject:* Re: FW: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> I am using 3.6.2.
>>
>>
>>
>> On Thu, Oct 13, 2016 at 2:22 PM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> Hi Dženan,
>>
>> What version of Cmake are you using? So I can rule it out as being a
>> possible cause for the issues.
>>
>>
>>
>> Thanks,
>>
>> Constance
>>
>>
>>
>> *From:* Dženan Zukić [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 1:17 PM
>>
>>
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> Hi Constance,
>>
>>
>>
>> those are the steps. What could be going on is that LesionSizingToolkit
>> does not support such an old VisualStudio. You could try a newer VS, such
>> as 2013 or 2015.
>>
>>
>>
>> Also, I will try to figure out the problem in standalone build later.
>>
>>
>>
>> Regards,
>>
>> Dženan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 1:10 PM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> Hi Dženan,
>>
>> These are the steps that I followed:
>>
>>
>>
>> § Download ITK
>>
>> - Use Git Clone and place in folder C:\ITK-v4.11\src
>>
>> o https://itk.org/Wiki/ITK/Git/Download
>>
>> - Open Cmake
>>
>> o Set source to folder C:\ITK-v4.11\src\ITK
>>
>> o Set build to folder C:\ITK-v4.11\bin-x64
>>
>> o Click ‘configure’
>>
>> · Set settings to ‘Visual Studio 9 2008 Win64’
>>
>> - Once configuration is complete:
>>
>> o These configuration parameters were suggested by ITK
>>
>> o Enable
>>
>> · Module_LesionSizingToolkit
>>
>> · LSTK_USE_VTK (Maybe I should not have done this?)
>>
>> o Disable
>>
>> · Build_Shared_Libs
>>
>> · Build_Examples
>>
>> · Build_Testing
>>
>> o Click ‘Configure’, again
>>
>> - Generate
>>
>> - Double click on file ‘ITK.sln’
>>
>> o This can be found in folder: C:\ITK-v4.11\bin-x64
>>
>> - Right click on ‘ALL_BUILD’
>>
>> o Select ‘Build’
>>
>> And I still got all the errors that I mentioned in the first e-mail. My
>> apologies if I am not understanding the steps you suggested. I am very new
>> to Cmake and Visual Studio, having experience only with MATLAB prior to
>> this.
>>
>>
>>
>> I would like to be able to see the segmentation results when using LSTK.
>> The goal would be to run LSTK with their data first, and then to use it on
>> our data.
>>
>>
>>
>> Thanks,
>> Constance
>>
>>
>>
>>
>>
>> *From:* Dženan Zukić [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 11:57 AM
>>
>>
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> Hi Constance,
>>
>>
>>
>> the "master version" is master branch in the official git repository:
>>
>> git://itk.org/ITK.git
>>
>> To see how to get it you can take a look here:
>>
>> itk.org/Wiki/ITK/Git/Develop
>>
>>
>>
>> Regards,
>>
>> Dženan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 12:48 PM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> Hi Dženan,
>>
>> What exactly is meant by ‘master version’ of ITK? Am I correct to assume
>> that it is the most current release available at the link provided below?
>>
>> https://itk.org/ITK/resources/software.html
>>
>>
>>
>> Thanks,
>> Constance
>>
>>
>>
>> *From:* Dženan Zukić [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 10:44 AM
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>>
>>
>> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> Yes, that's what was successful for me. You can also try turning
>> Build_Examples and Build_Testing on later. I mainly keep them off to reduce
>> build time - as you might guess, I rebuild ITK a lot :)
>>
>>
>>
>> Regards,
>>
>> Dženan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 11:38 AM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> Hi Dženan,
>>
>>
>>
>> Just to confirm, when I configure in Cmake, I should turn OFF
>> Build_Examples and Build_Testing, but turn ON Module_LesionSizingToolkit?
>>
>>
>>
>> Thanks,
>>
>> Constance
>>
>>
>>
>>
>>
>> *From:* Dženan Zukić [mailto:dzenanz at gmail.com]
>> *Sent:* Thursday, October 13, 2016 10:29 AM
>> *To:* Owens,Constance A <CAOwens at mdanderson.org>
>> *Cc:* insight-users at itk.org
>> *Subject:* Re: [ITK-users] Lesion Sizing Toolkit Build not successful
>>
>>
>>
>> Hi Constance,
>>
>>
>>
>> building it outside of ITK I also get similar errors, e.g.:
>>
>> 5>C:\Misc\LesionSizingToolkit\Utilities\Visualization\IsoSurfaceVolumeEstimation.cxx(21):
>> fatal error C1083: Cannot open include file: 'vtkPolyDataWriter.h': No such
>> file or directory
>>
>>
>>
>> I will investigate later, and in the meantime you can try building it as
>> part of ITK (turn Module_LesionSizingToolkit ON).
>>
>>
>>
>> Regards,
>>
>> Dženan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 11:20 AM, Dženan Zukić <dzenanz at gmail.com> wrote:
>>
>> Hi Constance,
>>
>>
>>
>> the lesion sizing toolkit builds with master version of ITK with examples
>> and tests turned off. I will now try building with those on to see if some
>> problems appear. I used VS2013 x64.
>>
>>
>>
>> Regards,
>>
>> Dženan
>>
>>
>>
>> On Thu, Oct 13, 2016 at 10:48 AM, Owens,Constance A <
>> CAOwens at mdanderson.org> wrote:
>>
>> I was hoping to speak with someone who may be able to help me with
>> installing and building Lesion Sizing Toolkit. Originally I tried to build
>> LSTK with ITK v4.2.0 and VTK v7.0.0 but during the build process (I’m using
>> Visual Studio 9 2008 64x), 6 projects fail with the following errors:
>>
>>
>>
>> Error 1 fatal error C1083: Cannot open include file:
>> 'itkLesionSegmentationImageFilter8.h': No such file or
>> directory c:\itk2\src\modules\remote\les
>> ionsizingtoolkit\examples\itkLesionSegmentationCommandLinePr
>> ogressReporter.h 22
>>
>> Error 2 fatal error C1083: Cannot open include file:
>> 'itkImageFileReader.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Examples\LesionSegmentation.cxx
>> 1
>>
>> Error 3 fatal error C1083: Cannot open include file:
>> 'itkVector.h': No such file or directory
>> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\vis
>> ualization\vtkContourVisualizationModule.h 22
>>
>> Error 4 fatal error C1083: Cannot open include file:
>> 'vtkPolyDataWriter.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\LesionSurfaceExtraction.cxx 21
>>
>> Error 5 fatal error C1083: Cannot open include file:
>> 'vtkPolyDataWriter.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\IsoSurfaceVolumeEstimation.cxx 21
>>
>> Error 6 fatal error C1083: Cannot open include file:
>> 'itkVector.h': No such file or directory
>> c:\itk2\src\modules\remote\lesionsizingtoolkit\utilities\vis
>> ualization\vtkContourVisualizationModule.h 22
>>
>> Error 7 fatal error C1083: Cannot open include file:
>> 'itkCommand.h': No such file or directory
>> c:\ITK2\src\Modules\Remote\LesionSizingToolkit\Utilities\Vis
>> ualization\ViewImageAndSegmentationSurface.cxx 18
>>
>> Error 8 error C2039: 'MetaEvent' : is not a member of
>> '`global namespace'' c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaEvent.h 35
>>
>> Error 9 error C2499: 'itk::MetaEvent' : a class cannot
>> be its own base class c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaEvent.h 35
>>
>> Error 10 error C2146: syntax error : missing ';' before
>> identifier 'MetaObjectType' c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h 55
>>
>> Error 11 error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 55
>>
>> Error 12 error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 55
>>
>> Error 13 error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 64
>>
>> Error 14 error C2143: syntax error : missing ',' before
>> '*' c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h 64
>>
>> Error 15 error C2143: syntax error : missing ';' before
>> '*' c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h 67
>>
>> Error 16 error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
>> : 'virtual' not permitted on data declarations
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error 17 error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error 18 error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 67
>>
>> Error 20 error C2143: syntax error : missing ';' before
>> '*' c:\itk2\src\modules\core\spati
>> alobjects\include\itkMetaConverterBase.h 77
>>
>> Error 21 error C2433: 'itk::MetaConverterBase<VDimension>::MetaObjectType'
>> : 'virtual' not permitted on data declarations
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error 22 error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error 23 error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> c:\itk2\src\modules\core\spatialobjects\include\itkMetaConverterBase.h
>> 77
>>
>> Error 25 error C2143: syntax error : missing ';' before
>> '*' C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 100
>>
>> Error 26 error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 100
>>
>> Error 27 error C4430: missing type specifier - int
>> assumed. Note: C++ does not support default-int
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 102
>>
>> Error 29 error C2061: syntax error : identifier
>> 'MetaScene' C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 104
>>
>> Error 30 error C2065: 'MetaObject' : undeclared
>> identifier C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 112
>>
>> Error 31 error C2059: syntax error : '>'
>> C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
>> 112
>>
>> Error 32 error C2143: syntax error : missing ';' before
>> '{' C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 116
>>
>> Error 33 error C2653: 'TConverter' : is not a class or
>> namespace name C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 117
>>
>> Error 34 error C2653: 'TConverter' : is not a class or
>> namespace name C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 117
>>
>> Error 35 error C2143: syntax error : missing ';' before
>> '}' C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 121
>>
>> Error 36 error C2143: syntax error : missing ';' before
>> '{' C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 124
>>
>> Error 37 error C2653: 'TConverter' : is not a class or
>> namespace name C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 125
>>
>> Error 38 error C2653: 'TConverter' : is not a class or
>> namespace name C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 125
>>
>> Error 39 error C2143: syntax error : missing ';' before
>> '}' C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 127
>>
>> Error 40 error C2065: 'transform' : undeclared
>> identifier C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 128
>>
>> Error 41 error C2143: syntax error : missing ',' before
>> ')' C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 128
>>
>> Error 42 error C2065: 'MetaObject' : undeclared
>> identifier C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 130
>>
>> Error 43 error C2065: 'obj' : undeclared
>> identifier C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 130
>>
>> Error 44 error C2143: syntax error : missing ',' before
>> ')' C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 130
>>
>> Error 45 error C2143: syntax error : missing ';' before
>> '}' C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 141
>>
>> Error 46 fatal error C1004: unexpected end-of-file
>> found C:\ITK2\src\Modules\Core\Spati
>> alObjects\include\itkMetaSceneConverter.h 141
>>
>>
>>
>> Additionally, I am using CMake v3.6.1.
>>
>>
>>
>> I also tried to build it with VTK v5.10 and ITK v4.2 as suggested by the
>> ITK Bar Camp document provided by this link:
>>
>> http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/
>> ITK/LungNoduleSegmentationWithLSTK.html
>>
>>
>>
>> However, cmake showed an error requesting a version of VTK 6.0.0 or
>> newer. I will try this version in the meantime, but was hoping to get some
>> help on building LSTK.
>>
>>
>>
>>
>>
>> Thanks,
>>
>> Constance Owens
>>
>> Graduate Research Assistant
>>
>> *The University of Texas Graduate School of Biomedical Sciences at
>> Houston*
>> Medical Physics
>>
>> CAOwens at mdanderson.org
>> <https://mailbox.mdanderson.org/owa/redir.aspx?REF=1_J6y-0UTLZALKHOYAqJgthiuCumt3SSyTDe5aCeIfM-m0qTq4TTCAFtYWlsdG86Q0FPd2Vuc0BtZGFuZGVyc29uLm9yZw..>
>> tel 713-745-3679 | cel 281-770-5210
>>
>>
>>
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>> The information contained in this e-mail message may be privileged,
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