[ITK Community] Some questions about RegionGrowingSegmentation
Bill Lorensen
bill.lorensen at gmail.com
Thu Feb 13 08:05:58 EST 2014
Did you build ITKApps as a superbuild?
On Thu, Feb 13, 2014 at 1:22 AM, Girish, Gavaskar Ruturaj
<gavaskar.ruturaj.girish at philips.com> wrote:
> Dear Jon and Bill,
>
>
>
> After 2 days of trying to compile my program, during which I learnt some
> CMake commands, made many modifications to my CMakeLists.txt file based on
> what both of you suggested, and encountered various types of linker errors
> which are too numerous to list here, I can only share my latest
> CMakeLists.txt file here, and hope you or any other community members can
> tell me what exactly I am doing wrong.
>
> For the record, I am now getting the following errors in VS 2010:
>
>
>
> C:\Program Files\FLTK\include\FL\math.h(22): fatal error C1083: Cannot open
> include file: '/usr/include/math.h': No such file or directory
>
> 2> RegionGrowingSegmentationImageDisplay.cpp
>
> 2>C:\Program Files\FLTK\include\FL\math.h(22): fatal error C1083: Cannot
> open include file: '/usr/include/math.h': No such file or directory
>
> 2> RGS_main.cpp
>
> 2>C:\Program Files\FLTK\include\FL\math.h(22): fatal error C1083: Cannot
> open include file: '/usr/include/math.h': No such file or directory
>
>
>
> Since I am not using Linux, I don't really know what to do with these
> errors. I was previously getting linker errors, but now I am getting the
> above errors again.
>
>
>
> It would be very helpful to me if you can have a look at my attached
> CMakeLists.txt file. I have included relevant information as comments.
>
> Thanks a lot for your help.
>
>
>
> Regards
>
> Ruturaj
>
>
>
>
>
> From: Jon Haitz Legarreta [mailto:jhlegarreta at vicomtech.org]
> Sent: Monday, February 10, 2014 6:21 PM
>
>
> To: Girish, Gavaskar Ruturaj
> Cc: community at itk.org
> Subject: Re: [ITK Community] Some questions about RegionGrowingSegmentation
>
>
>
> Hi Ruturaj,
>
> you are right. However, if you are using CMake you shouldn't modify your
> compiler's include/link libraries within your compiler's environment; CMake
> does it for you.
>
>
>
> Thus, concerning the errors you are getting, in CMake's terms, you would
> interpret that you are not including FLTK as a library in your CMakeLists.
>
> If the error persisted even after you manually added the FLTK folder, then
> the file fltkImageViewer.h is not within that folder.
>
> But anyway, try not to alter the project's properties within your compiler;
> you can do that through your CMakeLists.
>
> Make sure also that you include it in your target link libraries' list.
>
> If errors persist, sharing your CMakeLists may be useful.
>
> HTH,
> JON HAITZ
>
>
>
> On 10 February 2014 12:20, Girish, Gavaskar Ruturaj
> <gavaskar.ruturaj.girish at philips.com> wrote:
>
> Dear Jon,
>
>
>
> I did as you told. Actually I am using FLTK only to view the images
> (fltkImageViewer.h). I am not using it for user interaction. After making
> the relevant changes in CMakeLists.txt, I am able to configure and generate
> the Visual Studio project. However, now I get errors while building the
> solution in Visual Studio. Here are the 2 errors I get:
>
> (In my main header file:) fatal error C1083: Cannot open
> include file: 'fltkImageViewer.h': No such file or directory
>
> and
>
> C:\Program Files\FLTK\include\FL\math.h(22): fatal error
> C1083: Cannot open include file: '/usr/include/math.h': No such file or
> directory
>
>
>
> I think the issue is something to do with the directories where VS searches
> for the #included files. I have added the following directories in
> 'Additional Include Directories' in C/C++ Properties for the project (don't
> know if all are needed):
>
> <My source directory for cmake>
>
> <My build directory for cmake>
>
> C:\Program Files\ITK\include\ITK-4.6
>
> C:\Program Files\FLTK\include\FL
>
> <Binary directory of superbuild>
> \ITKApps-build\Auxiliary\ITKFlFileWriter
>
> <Binary directory of superbuild>
> \ITKApps-build\Auxiliary\FltkImageViewer
>
> <Binary directory of superbuild>
> \ITKApps-build\Auxiliary\VtkFltk
>
>
>
> Any idea why these errors are occurring? Do I need to include any other
> directories?
>
>
>
> Thanks in advance & also for your previous reply.
>
>
>
> Regards
>
> Ruturaj
>
> From: Jon Haitz Legarreta [mailto:jhlegarreta at vicomtech.org]
> Sent: Friday, February 07, 2014 5:57 PM
>
>
> To: Girish, Gavaskar Ruturaj
> Cc: community at itk.org
> Subject: Re: [ITK Community] Some questions about RegionGrowingSegmentation
>
>
>
> Dear Ruturaj,
>
> if you don't need FLTK (as you mentioned, you don't need a GUI), then you
> need to modify the CMakeLists accordingly, i.e. remove all FLTK-related
> CMake variables in your new, fresh CMakeLists.txt
>
> You will just need to tell CMake that your projects depends only on ITK.
>
> In the ITK wiki, you will find quite a few examples on how to do this [1].
> You even have a segmentation section there.
>
>
> HTH,
> JON HAITZ
>
> [1] http://www.itk.org/Wiki/ITK/Examples#About_the_Examples
>
>
>
> On 7 February 2014 12:36, Girish, Gavaskar Ruturaj
> <gavaskar.ruturaj.girish at philips.com> wrote:
>
> Dear Friends,
>
>
>
> I am not able to build the app RegionGrowingSegmentation separately without
> using Superbuild. I have already installed Superbuild once. Here is what I
> did:
>
>
>
> In cmake, I gave the source directory as ITKApps/RegionGrowingSegmentation
> and hit 'Configure', upon which CMake showed me the following error.
>
>
>
> CMake Error: Error required internal CMake variable not set, cmake may be
> not be built correctly.
> Missing variable is:
> FLTK_FLUID_EXECUTABLE
>
> CMake Error: Error required internal CMake variable not set, cmake may be
> not be built correctly.
> Missing variable is:
> FLTK_FLUID_EXECUTABLE
>
> CMake Error at CMakeLists.txt:42 (ITK_DISABLE_FLTK_GENERATED_WARNINGS):
> Unknown CMake command "ITK_DISABLE_FLTK_GENERATED_WARNINGS".
>
> CMake Warning (dev) in CMakeLists.txt:
> No cmake_minimum_required command is present. A line of code such as
>
> cmake_minimum_required(VERSION 2.8)
>
> should be added at the top of the file. The version specified may be lower
> if you wish to support older CMake versions for this project. For more
> information run "cmake --help-policy CMP0000".
> This warning is for project developers. Use -Wno-dev to suppress it.
>
> FLTK_WRAP_UI was called with a target that was never created:
> RegionGrowingSegmentation. The problem was found while processing the source
> directory: D:/ITKApps-27-01-2014/RegionGrowingSegmentation. This
> FLTK_WRAP_UI call will be ignored.
>
> FLTK_WRAP_UI was called with a target that was never created:
> RegionGrowingSegmentation2D. The problem was found while processing the
> source directory: D:/ITKApps-27-01-2014/RegionGrowingSegmentation. This
> FLTK_WRAP_UI call will be ignored.
>
> Configuring incomplete, errors occurred!
>
> See also "D:/RegionGrowingSegmentation-Build/CMakeFiles/CMakeOutput.log".
>
>
>
> So I added the following 3 commands to CMakeLists.txt:
>
>
>
> 1) SET(FLTK_FLUID_EXECUTABLE "C:/Program Files/FLTK/bin/fluid.exe")
>
> 2) CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
>
> 3) (Copied from ITKApps/CMakeLists.txt)
>
> MACRO(ITK_DISABLE_FLTK_GENERATED_WARNINGS files)
>
> IF(CMAKE_COMPILER_IS_GNUCXX)
>
> FOREACH(f ${files})
>
> STRING(REGEX REPLACE "\\.fl$" ".cxx" SRC "${f}")
>
> STRING(REGEX REPLACE ".*/([^/]*)$" "\\1" SRC "${SRC}")
>
> SET_SOURCE_FILES_PROPERTIES(${SRC} PROPERTIES COMPILE_FLAGS -w)
>
> ENDFOREACH(f)
>
> ENDIF(CMAKE_COMPILER_IS_GNUCXX)
>
> IF(MSVC)
>
> FOREACH(f ${files})
>
> STRING(REGEX REPLACE "\\.fl$" ".cxx" SRC "${f}")
>
> STRING(REGEX REPLACE ".*/([^/]*)$" "\\1" SRC "${SRC}")
>
> SET_SOURCE_FILES_PROPERTIES(${SRC} PROPERTIES COMPILE_FLAGS /w)
>
> ENDFOREACH(f)
>
> ENDIF(MSVC)
>
> ENDMACRO(ITK_DISABLE_FLTK_GENERATED_WARNINGS)
>
>
>
> Then I got the following error in cmake:
>
>
>
> CMake Error at CMakeLists.txt:82 (ADD_GUI_EXECUTABLE):
> Unknown CMake command "ADD_GUI_EXECUTABLE".
>
> FLTK_WRAP_UI was called with a target that was never created:
> RegionGrowingSegmentation. The problem was found while processing the source
> directory: D:/ITKApps-27-01-2014/RegionGrowingSegmentation. This
> FLTK_WRAP_UI call will be ignored.
>
> FLTK_WRAP_UI was called with a target that was never created:
> RegionGrowingSegmentation2D. The problem was found while processing the
> source directory: D:/ITKApps-27-01-2014/RegionGrowingSegmentation. This
> FLTK_WRAP_UI call will be ignored.
>
> Configuring incomplete, errors occurred!
>
>
>
> Please tell me if I did anything wrong and what I need to do to build this
> app. I need to find a way to build it separately since I wish to modify it a
> little. Thanks.
>
>
>
> Regards
>
> Ruturaj
>
>
>
>
>
> From: Community [mailto:community-bounces at itk.org] On Behalf Of Girish,
> Gavaskar Ruturaj
> Sent: Friday, February 07, 2014 1:37 PM
> To: Jon Haitz Legarreta
>
>
> Cc: community at itk.org
> Subject: Re: [ITK Community] Some questions about RegionGrowingSegmentation
>
>
>
> Dear Jon,
>
>
>
> Thanks for your suggestion. I am looking to modify the source code to accept
> multiple seed points so that more than one region can be segmented. I find
> it much easier without a GUI as I never worked with developing a GUI before.
> I will go through the links you posted.
>
>
>
> Regards
>
> Ruturaj
>
>
>
>
>
> From: Jon Haitz Legarreta [mailto:jhlegarreta at vicomtech.org]
> Sent: Friday, February 07, 2014 1:15 PM
> To: Girish, Gavaskar Ruturaj
> Cc: community at itk.org
> Subject: Re: [ITK Community] Some questions about RegionGrowingSegmentation
>
>
>
> Dear Ruturaj,
>
> 1.- Haven't got the example with me, but if you intend to use a region
> growing segmentation filter a good point to start is the ITK software guide,
> chapter 9.1 [1]. There, you will be able to see which are the available
> build-in algorithms/strategies, and you will see which are the methods you
> need to call in order to make them work. Please, bear in mind that
> segmentation is highly application-specific, and you may need to at least
> adjust the parameters, when it's not to develop your own strategy based on
> what's available in ITK, for example. Nevertheless, the available examples
> in ITK are quite useful.
>
> 2.- Sure. The seed point can be read from wherever you need (user
> interaction, program arguments, external file). The seed-setting method (or
> whichever method actually requiring the seed point) will only require a
> vector/array or individual coordinates, regardless of where you picked up
> them.
>
> 3.- As said, haven't got the app in front of me, but surely you will be able
> to build your own application for region growing segmentation without any
> GUI. ITK is independent of any GUI (now, the apps may use a specific one);
> you can just build an application with the GUI library that you most like.
> Having said, that, may be the most common and easiest choice is Qt [2],
> which has an open source version.
>
>
>
> [1] http://www.itk.org/ItkSoftwareGuide.pdf
> [2] http://qt-project.org/
>
>
>
> On 7 February 2014 06:27, Girish, Gavaskar Ruturaj
> <gavaskar.ruturaj.girish at philips.com> wrote:
>
> Hello All,
>
>
>
> I am new to ITK & C++ and I have some questions related to the ITK app
> RegionGrowingSegmentation:
>
> 1. Please explain to me the purpose of the function
> RegionGrowingSegmentation:: ClickSelectCallback(float x, float y, float z,
> float itkNotUsed(value), void * args), along with the meaning of the
> arguments (Line 451 in RegionGrowingSegmentation.cxx)
>
> 2. Is it possible to pass the coordinates of the seed point without
> user interaction (for example, as arguments or by storing them in a file
> etc.) ?
>
> 3. Can this app be built without a GUI, so that the coordinates of the
> seed point, along with other parameters, can be directly passed from the
> command line? If yes, what is the procedure to build it?
>
>
>
> Thanks.
>
>
>
> Regards
>
> Ruturaj
>
>
>
>
>
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