[ITK Community] Some questions about RegionGrowingSegmentation

[Girish, Gavaskar Ruturaj]

Yes I did. All the apps are working. I just want to build my own program based on RegionGrowingSegmentation.

Regards
Ruturaj

-----Original Message-----
From: Bill Lorensen [mailto:bill.lorensen at gmail.com]
Sent: Thursday, February 13, 2014 6:36 PM
To: Girish, Gavaskar Ruturaj
Cc: Jon Haitz Legarreta; community at itk.org
Subject: Re: [ITK Community] Some questions about RegionGrowingSegmentation

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:
> 2>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:
> 2>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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