[Insight-users] Fast Marching Minimal Path Extraction error

Oleksandr Dzyubak adzyubak at gmail.com
Fri Jul 11 12:53:22 EDT 2008 

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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