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

Dan Mueller dan.muel at gmail.com
Tue Jul 15 01:47:24 EDT 2008 

Hi Luis,

2008/7/14 Luis Ibanez <luis.ibanez at kitware.com>:
> The standard practice for including vnl_math.h is to do
>              #include "vnl/vnl_math.h"

This was the first thing I asked Alex to try:
    http://www.itk.org/pipermail/insight-users/2008-July/026687.html

He reported that it did not work:
    http://www.itk.org/pipermail/insight-users/2008-July/026708.html

Obviously I'm doing something wrong in my CMakeLists.txt so that
"Utilities/vxl/core" is not set as an include directory. Could it be
that it is an installed version of ITK? (Alex?) Any other suggestions?

Regards, Dan

2008/7/14 Luis Ibanez <luis.ibanez at kitware.com>:
>
> Hi Dan,
>
>
> The standard practice for including vnl_math.h is to do
>
>
>              #include "vnl/vnl_math.h"
>
>
> You will find several examples of this use in Insight/Code/Common.
>
>
>
> In general, ITK_SOURCE_DIR shouldn't be used because it will not
> exist in an installed ITK.
>
>
>   Regards,
>
>
>      Luis
>
>
> ------------------
> Dan Mueller wrote:
>>
>> 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
>>>>>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> Insight-developers mailing list
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>>>> http://www.itk.org/mailman/listinfo/insight-developers
>>>>
>>>
>>
>

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