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

Luis Ibanez luis.ibanez at kitware.com
Sun Jul 13 17:17:59 EDT 2008 

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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