[ITK] [ITK-users] FW: Lesion Sizing Toolkit Build not successful

Dženan Zukić dzenanz at gmail.com
Thu Oct 13 18:31:18 EDT 2016


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\
> lesionsizingtoolkit\examples\itkLesionSegmentationCommandLi
> neProgressReporter.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\visualization\
> 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\Visualization\
> 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\Visualization\
> 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\visualization\
> 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\Visualization\
> ViewImageAndSegmentationSurface.cxx                18
>
> Error      8              error C2039: 'MetaEvent' : is not a member of
> '`global namespace''                c:\itk2\src\modules\core\
> spatialobjects\include\itkMetaEvent.h             35
>
> Error      9              error C2499: 'itk::MetaEvent' : a class cannot
> be its own base class                c:\itk2\src\modules\core\
> spatialobjects\include\itkMetaEvent.h             35
>
> Error      10           error C2146: syntax error : missing ';' before
> identifier 'MetaObjectType'                c:\itk2\src\modules\core\
> spatialobjects\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\spatialobjects\include\
> itkMetaConverterBase.h          64
>
> Error      15           error C2143: syntax error : missing ';' before
> '*'                c:\itk2\src\modules\core\spatialobjects\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\spatialobjects\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\SpatialObjects\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\
> SpatialObjects\include\itkMetaSceneConverter.h   104
>
> Error      30           error C2065: 'MetaObject' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\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\SpatialObjects\include\itkMetaSceneConverter.h
> 116
>
> Error      33           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   117
>
> Error      34           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   117
>
> Error      35           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 121
>
> Error      36           error C2143: syntax error : missing ';' before
> '{'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 124
>
> Error      37           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   125
>
> Error      38           error C2653: 'TConverter' : is not a class or
> namespace name                C:\ITK2\src\Modules\Core\
> SpatialObjects\include\itkMetaSceneConverter.h   125
>
> Error      39           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 127
>
> Error      40           error C2065: 'transform' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 128
>
> Error      41           error C2143: syntax error : missing ',' before
> ')'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 128
>
> Error      42           error C2065: 'MetaObject' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      43           error C2065: 'obj' : undeclared
> identifier                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      44           error C2143: syntax error : missing ',' before
> ')'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 130
>
> Error      45           error C2143: syntax error : missing ';' before
> '}'                C:\ITK2\src\Modules\Core\SpatialObjects\include\itkMetaSceneConverter.h
> 141
>
> Error      46           fatal error C1004: unexpected end-of-file
> found                C:\ITK2\src\Modules\Core\SpatialObjects\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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