[Insight-developers] [Insight-users] Fast Marching Minimal Path Extraction error

Dan Mueller dan.muel at gmail.com
Mon Jul 14 01:49:14 EDT 2008 

Hi Luis,

Thanks for your response.

I am using ITK_SOURCE_DIR to construct a path to
{SOURCE}\Utilities\vxl\core\vnl so that "#include vnl_math.h" works.

What is the recommended way to add this directory to the include path
of a CMake generated project?

Regards, Dan

2008/7/13 Luis Ibanez <luis.ibanez at kitware.com>:
>
> Hi Dan,
>
> The use of ITK_SOURCE_DIR is discouraged because when you install ITK
> the actual source code may no longer be available.
>
> The ITK_SOURCE_DIR may make sense when you are building your application
> against a local build of ITK.
>
> If, on the other hand, you build against an installed ITK then only the
> header files and the compiled libraries will be available.
>
> If you are using a Debian installed ITK (or for that matter any Linux or
> Windows installation), then the ITK_SOURCE_DIR should not be available.
>
> BTW: Why is that you need "ITK_SOURCE_DIR" ?
>
>
>
> It seems that the problem is that
>
>
>                 FIND_PACKAGE(ITK REQUIRED)
>
>
> is not being used in this CMakeLists.txt file.
>
>
>  Please let us know,
>
>
>      Luis
>
>
>
> ----------------
> Dan Mueller wrote:
>>
>> Hi Alex,
>>
>> The problem is definitely in step 3. The VXL_INCLUDE_DIRS should have
>> the full path (with non-empty ITK_SOURCE_DIR). It seems ITK_SOURCE_DIR
>> is not being set...
>>
>> Insight Developers: do you know of any reason why ITK_SOURCE_DIR is
>> not being set using the below CMakeLists.txt on Linux(Debian)? (It
>> seems to work on Windows, cygwin, and the IJ Testing Environment...)
>>
>> Thanks for any insight.
>>
>> Regards, Dan
>>
>> #Set the project
>> CMAKE_MINIMUM_REQUIRED(VERSION 2.4)
>> PROJECT(MinimalPath)
>>
>> #Include some macros from another file...
>> INCLUDE(${CMAKE_SOURCE_DIR}/IJMacros.txt)
>>
>> #Setup required paths
>> SET(DATA_PATH ${CMAKE_SOURCE_DIR}/Data)
>> SET(SOURCE_PATH ${CMAKE_SOURCE_DIR}/Source)
>> SET(TESTING_PATH ${CMAKE_SOURCE_DIR}/Testing)
>>
>> SET(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/bin CACHE PATH "Single
>> output directory for building all libraries." FORCE)
>> SET(EXECUTABLE_OUTPUT_PATH ${CMAKE_BINARY_DIR}/bin CACHE PATH "Single
>> output directory for building all executables." FORCE)
>>
>> #The following lines are required to use Dart
>> ENABLE_TESTING()
>> INCLUDE(Dart)
>> FIND_PROGRAM(IMAGE_COMPARE ImageCompare)
>>
>> #Declare any external dependencies that your project may have here.
>> #examples include: ITK, VTK, JPEG, PNG, OpenGL, ZLIB, Perl, Java
>> #If you're not sure what name to use, look in the Modules directory of
>> your
>> #cmake install and check that a file named Find(Package).cmake exists
>> SET(Required_Packages
>>    ITK
>> )
>>
>> #this foreach loads all of the packages that you specified as required.
>> #It shouldn't need to be modified.
>> FOREACH(Package ${Required_Packages})
>>  LOADPACKAGE(${Package})
>> ENDFOREACH(Package)
>>
>> #Construct VXL/VNL includes
>> SET(VXL_INCLUDE_DIRS
>>    ${ITK_SOURCE_DIR}/Utilities/vxl
>>    ${ITK_SOURCE_DIR}/Utilities/vxl/core
>>    ${ITK_SOURCE_DIR}/Utilities/vxl/core/vnl
>>    ${ITK_SOURCE_DIR}/Utilities/vxl/vcl)
>>
>>
>> 2008/7/11 Oleksandr Dzyubak <adzyubak at gmail.com>:
>>
>>> Hi Daniel,
>>>
>>> Thanks for quick response.
>>>
>>> 1) Yes. My ITK_DIR is  /usr/local/lib/InsightToolkit
>>>
>>> 2) Yes.
>>> dzyubak at debian: /vnl$ pwd
>>> /usr/local/include/InsightToolkit/Utilities/vxl/core/vnl
>>>
>>> dzyubak at debian: /vnl$ ls | grep vnl_math
>>> vnl_math.h
>>>
>>> 3) After adding a line as you advised
>>> MESSAGE(SEND_ERROR ${VXL_INCLUDE_DIRS}) # Add this line (it is now
>>> located
>>> on the line 41),
>>> I got an error message below.
>>>
>>> CMake Error at CMakeLists.txt:41 (MESSAGE):
>>>
>>> /Utilities/vxl/Utilities/vxl/core/Utilities/vxl/core/vnl/Utilities/vxl/vcl
>>>
>>> 4) The content of the flags.make file is below.
>>>
>>> *********Begin flags.make ********
>>> # CMAKE generated file: DO NOT EDIT!
>>> # Generated by "Unix Makefiles" Generator, CMake Version 2.6
>>>
>>> # compile CXX with /usr/bin/c++
>>> CXX_FLAGS =   -ftemplate-depth-50 -Wall
>>> -I/usr/local/include/InsightToolkit/Review
>>> -I/usr/local/include/InsightToolkit/Patented
>>> -I/usr/local/include/InsightToolkit/gdcm/src
>>> -I/usr/local/include/InsightToolkit/gdcm
>>> -I/usr/local/include/InsightToolkit/Utilities/vxl/core
>>> -I/usr/local/include/InsightToolkit/Utilities/vxl/vcl
>>> -I/usr/local/include/InsightToolkit/Utilities/vxl/v3p/netlib
>>> -I/usr/local/include/InsightToolkit/Utilities
>>> -I/usr/local/include/InsightToolkit/Utilities/itkExtHdrs
>>> -I/usr/local/include/InsightToolkit/Utilities/nifti/znzlib
>>> -I/usr/local/include/InsightToolkit/Utilities/nifti/niftilib
>>> -I/usr/local/include/InsightToolkit/Utilities/expat
>>> -I/usr/local/include/InsightToolkit/Utilities/DICOMParser
>>> -I/usr/local/include/InsightToolkit/Utilities/NrrdIO
>>> -I/usr/local/include/InsightToolkit/Utilities/MetaIO
>>> -I/usr/local/include/InsightToolkit/SpatialObject
>>> -I/usr/local/include/InsightToolkit/Numerics/NeuralNetworks
>>> -I/usr/local/include/InsightToolkit/Numerics/Statistics
>>> -I/usr/local/include/InsightToolkit/Numerics/FEM
>>> -I/usr/local/include/InsightToolkit/IO
>>> -I/usr/local/include/InsightToolkit/Numerics
>>> -I/usr/local/include/InsightToolkit/Common
>>> -I/usr/local/include/InsightToolkit/BasicFilters
>>> -I/usr/local/include/InsightToolkit/Algorithms
>>> -I/usr/local/include/InsightToolkit
>>> -I/mnt/Public/ITK_Test/Fast_Marching_Minimal_Path_Extraction_in_ITK
>>>
>>> -I/mnt/Public/ITK_Test/Fast_Marching_Minimal_Path_Extraction_in_ITK/Source
>>> -I/Utilities/vxl -I/Utilities/vxl/core -I/Utilities/vxl/core/vnl
>>> -I/Utilities/vxl/vcl
>>> CXX_DEFINES =
>>>
>>> *********Begin flags.make ********
>>>
>>>
>>> Thanks for your help,
>>>
>>> Alex
>>>
>>> Dan Mueller wrote:
>>>
>>>> Hi Alex,
>>>>
>>>> Sorry, I meant "itkSingleImageCostFunction.txx".
>>>>
>>>> Yes, the main CMakeLists.txt should take care of everything (at least
>>>> it does on my builds and the IJ).
>>>>
>>>> Basically the problem seems to be that "vnl_math.h" is not being
>>>> included. It should be a simple matter of some detective work to find
>>>> out where things go wrong.
>>>>
>>>> Can you please check a couple of things:
>>>> 1. When you configure the project, I assume you are specifying the
>>>> ITK_DIR variable?
>>>> 2. Do you have the "{ITK_SOURCE_DIR}\Utilities\vxl\core\vnl"
>>>> directory? Is the "vnl_math.h" file inside?
>>>> 3. Can you please add the following line to the main CMakeLists.txt
>>>> and let me know the result?
>>>> #Construct VXL/VNL includes
>>>> SET(VXL_INCLUDE_DIRS
>>>>  ${ITK_SOURCE_DIR}/Utilities/vxl
>>>>  ${ITK_SOURCE_DIR}/Utilities/vxl/core
>>>>  ${ITK_SOURCE_DIR}/Utilities/vxl/core/vnl
>>>>  ${ITK_SOURCE_DIR}/Utilities/vxl/vcl)
>>>> MESSAGE(SEND_ERROR ${VXL_INCLUDE_DIRS}) # Add this line
>>>>  4. Can you please report the include paths generated by CMake? They
>>>> should include the directories shown above. (On my cygwin system,
>>>> these go into
>>>>
>>>> "{MinimalPath_BUILD_DIR}\Source\CMakeFiles\MinimalPathMain.dir\flags.make")
>>>>
>>>> Let me know regarding these things.
>>>>
>>>> Cheers, Dan
>>>>
>>>> 2008/7/10 Oleksandr Dzyubak <adzyubak at gmail.com>:
>>>>
>>>>
>>>>> Hi Daniel,
>>>>>
>>>>> Thanks for your prompt reply.
>>>>> I am using Linux(Debian) or UNIX(FreeBSD). Mostly Linux.
>>>>> Yes, I am using rev.6. Just downloaded once again to make sure it is.
>>>>> There no such a file like "itkSingleImageCostFunction.cxx" in the
>>>>> downloaded
>>>>> archive.
>>>>> Did you mean the template file "itkSingleImageCostFunction.txx"?
>>>>>
>>>>> Following your advice, I have changed the includes but no magic
>>>>> happened.
>>>>> The same error.
>>>>>
>>>>> I thought that it is the CMakeLists.txt in concert with cmake which
>>>>> should
>>>>> take care of that.
>>>>> It is not?
>>>>>
>>>>> Regards,
>>>>>
>>>>> Alex
>>>>>
>>>>> Dan Mueller wrote:
>>>>>
>>>>>
>>>>>> Hi Alex,
>>>>>>
>>>>>> Strange. It compiles fine for me on Windows with Visual Studio 8.0 and
>>>>>> on the IJ Testing Environment (some flavour of Linux, I think)...
>>>>>>
>>>>>> Are you using revision 6?
>>>>>>
>>>>>> Perhaps try changing this line in itkSingleImageCostFunction.cxx
>>>>>>  #include "vnl_math.h"
>>>>>> to
>>>>>>  #include "vnl/vnl_math.h"
>>>>>>
>>>>>> Let me know if you still have problems.
>>>>>>
>>>>>> Regards, Dan
>>>>>>
>>>>>> 2008/7/10 Oleksandr Dzyubak <adzyubak at gmail.com>:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Dear ITKers,
>>>>>>>
>>>>>>> After reading the articles by J. Sethian,
>>>>>>> I decided to downloaded the Fast Marching Minimal Path Extraction
>>>>>>> program
>>>>>>> and give it a try.
>>>>>>>
>>>>>>> Surprisingly I could not even compile it.
>>>>>>> The errors I got are below. Did somebody try it?
>>>>>>>
>>>>>>> Just in case. I am using Debian Linux with
>>>>>>> gcc version 4.1.2 20061115 (prerelease) (Debian 4.1.1-21).
>>>>>>>
>>>>>>> Thanks,,
>>>>>>> Alex
>>>>>>>
>>>>>>> *********Begin Errors********
>>>>>>>
>>>>>>> dzyubak at debian: /BUILD$ make
>>>>>>> Scanning dependencies of target MinimalPathMain
>>>>>>> [ 33%] Building CXX object
>>>>>>> Source/CMakeFiles/MinimalPathMain.dir/main.o
>>>>>>> In file included from
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> /mnt/Public/ITK_Test/Fast_Marching_Minimal_Path_Extraction_in_ITK/Source/itkSingleImageCostFunction.h:147,
>>>>>>>            from
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> /mnt/Public/ITK_Test/Fast_Marching_Minimal_Path_Extraction_in_ITK/Source/itkArrivalFunctionToPathFilter.h:23,
>>>>>>>            from
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> /mnt/Public/ITK_Test/Fast_Marching_Minimal_Path_Extraction_in_ITK/Testing/MinimalPathTests.cxx:39,
>>>>>>>            from
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> /mnt/Public/ITK_Test/Fast_Marching_Minimal_Path_Extraction_in_ITK/Source/main.cxx:10:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> /mnt/Public/ITK_Test/Fast_Marching_Minimal_Path_Extraction_in_ITK/Source/itkSingleImageCostFunction.txx:20:22:
>>>>>>> error: vnl_math.h: No such file or directory
>>>>>>> make[2]: *** [Source/CMakeFiles/MinimalPathMain.dir/main.o] Error 1
>>>>>>> make[1]: *** [Source/CMakeFiles/MinimalPathMain.dir/all] Error 2
>>>>>>> make: *** [all] Error 2
>>>>>>> dzyubak at debian: /BUILD$
>>>>>>>
>>>>>>>
>>>>>>> **********End Errors******
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Insight-users mailing list
>>>>>>> Insight-users at itk.org
>>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>>>
>>>
>>>
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