[ITK Community] Some questions about RegionGrowingSegmentation

Mon Feb 10 06:20:02 EST 2014

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<mailto: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$<file:///\\.fl$>" ".cxx" SRC "${f}")

      STRING(REGEX REPLACE ".*/([^/]*)$" "\\1<file:///\\1>" SRC "${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$<file:///\\.fl$>" ".cxx" SRC "${f}")

      STRING(REGEX REPLACE ".*/([^/]*)$" "\\1<file:///\\1>" SRC "${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<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<mailto: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<mailto: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<mailto: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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