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

Dan Mueller dan.muel at gmail.com
Sat Jul 12 00:44:56 EDT 2008 

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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