[ITK] [ITK-users] Solved ! RE: stand-alone lib -- ITKApps/ITKFilterLib
Robert.Atwood at diamond.ac.uk
Robert.Atwood at diamond.ac.uk
Wed Mar 23 14:32:08 EDT 2016
Ok, adding –fPIC everywhere seemed to work , one of those was cmake_c_flags and also module_c_flags, I must have missed those before.
Then, downloading CMAKE 3.5.0 and adding the option Bradley has suggested, on the commandline, also worked ! Even for the original project with ITK I/o being used inside the wrapped filter chain!
(But, the option CMAKE_POSITION_INDEPENDENT_CODE is not initially presented in the ncurses interface ☹ )
Thanks , All!
Robert
From: Bradley Lowekamp [mailto:blowekamp at mail.nih.gov]
Sent: 23 March 2016 17:23
To: Atwood, Robert (DLSLtd,RAL,SCI)
Cc: matt.mccormick at kitware.com; insight-users at itk.org
Subject: Re: [ITK-users] stand-alone lib -- ITKApps/ITKFilterLib -- Solved (maybe)
Hello,
I think there are some plan old C file too. I just add the following to the cmake command line:
-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON
You could also add “-fPIC” to the CFLAGS too.
Brad
On Mar 23, 2016, at 1:04 PM, <Robert.Atwood at diamond.ac.uk<mailto:Robert.Atwood at diamond.ac.uk>> <Robert.Atwood at diamond.ac.uk<mailto:Robert.Atwood at diamond.ac.uk>> wrote:
Hi, Matt
I did that but it didn't work. Exactly the same error. See a little further back in the thread:
That's where I lost patience with 'combinatorial trial and error approach' , I added -fPIC everywhere I could think of
The position-independent-code seems to be generated for all libs except a small selction of i/o libs ; gdcm* ,Nrrd , and a couple of others (trial-and-error)
If I don't include these in the final link, then the link is successful. All other libraries appear to have PIC generated.
But, the final library isn't usable. I wonder what these ones have in common?? Is there a 'glitch' in the makefile generation that omits -fPIC in these cases somehow?
libitkgdcmjpeg8-4.10.a
libitkgdcmjpeg12-4.10.a
libitkgdcmjpeg16-4.10.a
libitkgdcmopenjpeg-4.10.a
libitkgdcmuuid-4.10.a
libITKEXPAT-4.10.a
libITKniftiio-4.10.a
libITKNrrdIO-4.10.a
libitkhdf5-4.10.a
libitksys-4.10.a
(using system jpeg, tiff, zlib and png)
Ironically , it's only .mhd I actually want to use and it is not on the problem list. But the io-objects need all these to be available just in case they get used, I suppose.
I have tried some combinations of these options but, you know, it
takes a while to rebuild ITK even though the computer is pretty good.
BUILD_POSITION_DEPENDENT_CODE OFF (I don’t think this should be ON
because that really wouldn’t work? )
BUILD_SHARED_LIBS OFF (or ON)
CMAKE_CXX_FLAGS -fPIC (or default)
CMAKE_EXE_LINKER_FLAGS -fPIC (or default)
CMAKE_STATIC_LINKER_FLAGS (should this be set too? )
Regards, Robert
-----Original Message-----
From: Matt McCormick [mailto:matt.mccormick at kitware.com]
Sent: 23 March 2016 16:29
To: Atwood, Robert (DLSLtd,RAL,SCI)
Cc: Dženan Zukić; insight-users at itk.org<mailto:insight-users at itk.org>
Subject: Re: [ITK-users] stand-alone lib -- ITKApps/ITKFilterLib -- Solved
(maybe)
Hi Robert,
/usr/bin/ld:
/dls_sw/apps/itk/itk-master-static/lib/libitkgdcmjpeg8-4.10.a(jerror.c
.o): relocation R_X86_64_32S against `.text' can not be used when
making a shared object; recompile with -fPIC
This means that "-fPIC" should be added to the CMAKE_CXX_FLAGS for ITK.
HTH,
Matt
On Wed, Mar 23, 2016 at 11:58 AM, <Robert.Atwood at diamond.ac.uk<mailto:Robert.Atwood at diamond.ac.uk>>
wrote:
Hi, Dženan, and List :
Thanks for the tips, but, building the executable by pointing to the
itk-build folder for linking is exactly what I did not want to do. I
want the compiled instances of the specific templated objects to be
put into a stand-alone library that could then be linked , in an
environment where the ITK build directory may not be available, and
within a project that’s not using cmake (yet? J ) just for a small
single-data-type-specific filter chain that would be a bit nontrivial to just re-
implement myself!
I had some success with the following, for the example ITKFilterLib:
Using the itk-master-git-static as built before, (BUILD_SHARED_LIBS
OFF)
In CMakeLists.txt for the project, add SHARED keyword to the library
defninition:
15 ADD_LIBRARY(Example_ITKFilterLib SHARED ITKFilterLib.cxx )
Then use cmake + make to build the libExample_ITKFilterLib.so library.
Then I can invoke g++ as follows
build]$ g++ ../ITKFilterLib/ITKFilterLibTest.cxx -o testcomp -L . -l
Example_ITKFilterLib -I ../ITKFilterLib/
Even if the itk-master-static is not available in that environment,
this succeeds, and I believe this is what I want. I don’t want to have
a statically linked final executable, but rather a .so library.
However …
I encountered another hitch trying to apply this to my actual project.
If there were any FileWriter and FileReader present in the library, it
would not build, complaining about position-dependent symbols in
several IO libraries , most of which I was not actually wanting to use
at all. This happened at the step of trying to build the .so library
using the makefile created by cmake:
/usr/bin/ld:
/dls_sw/apps/itk/itk-master-static/lib/libitkgdcmjpeg8-4.10.a(jerror.c.o):
relocation R_X86_64_32S against `.text' can not be used when making a
shared object; recompile with -fPIC
/dls_sw/apps/itk/itk-master-static/lib/libitkgdcmjpeg8-4.10.a: could
not read symbols: Bad value
Removing any reference to FileReader and FileWriter gets rid of this
problem.
Thanks!
As a further note:
There are also some directions in the comments of the ITKFilterLib
example that did not turn out to be necessary in my project. I did not
have to create global objects for poitners or image containiers
outside the scope of the class and still did not have to #include itkImage.h in
the main program.
I placed the typedef’s inside the class and the instantiations of the
smart poitners in the class constructor. I don’t see that this extra
complication in the example is necessary unless it is platform dependent?
ITKFilterLib.cxx from ItkApps example:
23 #include "ITKFilterLib.h"
24
25 // Nasty local globals inside .cxx file to hide itk from the real world.
26 // Can't put this variable in the class definition otherwise we'd have
to
27 // include itkImage.h in every program using this class.
28 // The typedef h_itkFilterLibeDataType is in itkFilterLib.h to hide
29 // templates
30 typedef itk::Image<g_ItkFilterLibDataType,3> g_ImageType;
31 g_ImageType::Pointer g_InputImage;
32 g_ImageType::Pointer g_OutputImage;
I did not find this to be necessary in my project.
33
34
35 //
36 //
37 // The first filter in the .lib
38 //
39 //
40
41 /** The next lines are used to include the definition of the filter
42 * we want to install in the .lib, define a typedef for it, and create
43 * a "smart" pointer to hold it.
44 * CHANGE HERE: The filter to be instantiated.
45 **/
46 #include "itkCurvatureAnisotropicDiffusionImageFilter.h"
47 typedef itk::CurvatureAnisotropicDiffusionImageFilter<g_ImageType,
48 g_ImageType> g_AnisoFilterType;
49 g_AnisoFilterType::Pointer g_anisoFilter;
50
I also did not find it to be necessary to have this sort of typedef
and instantiation of the object at global scope in my project.
From: Dženan Zukić [mailto:dzenanz at gmail.com]
Sent: 23 March 2016 14:39
To: Atwood, Robert (DLSLtd,RAL,SCI)
Cc: Insight-users
Subject: Re: [ITK-users] stand-alone lib -- ITKApps/ITKFilterLib
Hi Robert,
BUILD_SHARED_LIBS OFF is the crucial setting. You can keep the rest of
options on defaults.
Your CMake code looks OK. You should execute the following from your
folder:
cmake .
make
During CMake step you should configure options (point to the itk-build
folder which was configured with BUILD_SHARED_LIBS OFF). Afterwards,
do not invoke g++ directly - invoke make, which supplies correct
include directories and link libraries so you don't run into a thousand errors.
Regards,
Dženan
On Tue, Mar 22, 2016 at 6:25 AM, <Robert.Atwood at diamond.ac.uk<mailto:Robert.Atwood at diamond.ac.uk>>
wrote:
Hi,
Thanks, Dženan, for the hint. But, does anyone have specific
information on exactly which options to set in each of: the ITK cmake
options; and the project cmake options, or the plain g++ for building
an external program to link to the library, for this to work ? There
appear to be a few that might be related to this. Because, so far,
simply changing the build options of the ITK installation didn’t work. See
below for even more details .
Thanks
Robert
Options selected in the project:
ITK_DIR
/dls_sw/apps/itk/itk-master-static/lib/cmake/ITK-4.10
In the ITK with installation to itk-master-static:
I have tried some combinations of these options but, you know, it
takes a while to rebuild ITK even though the computer is pretty good.
BUILD_POSITION_DEPENDENT_CODE OFF (I don’t think this should be ON
because that really wouldn’t work? )
BUILD_SHARED_LIBS OFF (or ON)
CMAKE_CXX_FLAGS -fPIC (or default)
CMAKE_EXE_LINKER_FLAGS -fPIC (or default)
CMAKE_STATIC_LINKER_FLAGS (should this be set too? )
The CMakeLists in the project file – only small modification from the
original to ‘BUILD_OUTSIDE_INSIGHT_APPICATIONS’. The project builds
using the Cmake makefile, producing the library and the executable
But trying to build either the ‘main’ procedure provided with linking
to that library, or even simplifying the ‘main’ to do virtually
nothing except instantiate the object, results in 1000 error messages
of ‘undefined symbols’
1 PROJECT(Example_ITKFilterLib)
2
3 #REMOVED 'IF (BUILD_OUTSIDE_INSIGHT_APPLICATIONS)'
4
5 FIND_PACKAGE(ITK)
6 IF(ITK_FOUND)
7 INCLUDE(${ITK_USE_FILE})
8 ELSE(ITK_FOUND)
9 MESSAGE(FATAL_ERROR
10 "Cannot build ITKApps without ITK. Please set ITK_DIR.")
11 ENDIF(ITK_FOUND)
12
13 #REMOVED 'ENDIF(BUILD_OUTSIDE_INSIGHT_APPLICATIONS)'
14
15 ADD_LIBRARY(Example_ITKFilterLib ITKFilterLib.cxx )
16 INSTALL_TARGETS(/lib Example_ITKFilterLib)
17 TARGET_LINK_LIBRARIES(Example_ITKFilterLib ${ITK_LIBRARIES})
18
19 ADD_EXECUTABLE(Example_ITKFilterLibTest ITKFilterLibTest.cxx )
20 INSTALL_TARGETS(/bin Example_ITKFilterLibTest)
21 TARGET_LINK_LIBRARIES(Example_ITKFilterLibTest
Example_ITKFilterLib)
build]$ ls -l
total 2508
-rw-rw-r-- 1 kny48981 kny48981 14393 Mar 22 10:02 CMakeCache.txt
drwxrwxr-x 6 kny48981 kny48981 4096 Mar 22 10:05 CMakeFiles
-rwxrwxr-x 1 kny48981 kny48981 1417263 Mar 22 10:05
Example_ITKFilterLibTest
drwxrwxr-x 2 kny48981 kny48981 4096 Mar 22 10:02
ITKIOFactoryRegistration
-rw-rw-r-- 1 kny48981 kny48981 7933 Mar 22 10:02 Makefile
-rw-rw-r-- 1 kny48981 kny48981 1092874 Mar 22 10:05
libExample_ITKFilterLib.a
build]$ g++ -o testcomp ../ITKFilterLib/ITKFilterLibTest.cxx -I
../ITKFilterLib -L . -l Example_ITKFilterLib >& out &
… generates 1100 messages …
1 ./libExample_ITKFilterLib.a(ITKFilterLib.o): In function
`itk::MemoryAllocationError::MemoryAllocationError(std::basic_string<c
har,
std::char_traits<char>, std::allocat
2
ITKFilterLib.cxx:(.text._ZN3itk21MemoryAllocationErrorC2ERKSsjS2_S2_[_ZN3
itk21MemoryAllocationErrorC5ERKSsjS2_S2_]+0x39):
undefined reference to `itk::ExceptionObject:
…
1106
ITKFilterLib.cxx:(.text._ZNK3itk12NeighborhoodIPfLj3ENS_21Neighborhood
AllocatorIS1_EEE9PrintSelfERSoNS_6IndentE[itk::Neighborhood<float*,
3u, itk::NeighborhoodAllocato
1107 collect2: ld returned 1 exit status
Minimal example main:
1 #include "ITKFilterLib.h"
2 int main(int, char **) {
3 int inputDimSize[3];
4 float inputOrigin[3];
5 float inputSpacing[3];
6 inputDimSize[0] = 5;
7 inputDimSize[1] = 5;
8 inputDimSize[2] = 5;
9 inputOrigin[0] = 0;
10 inputOrigin[1] = 0;
11 inputOrigin[2] = 0;
12 inputSpacing[0] = 1;
13 inputSpacing[1] = 1;
14 inputSpacing[2] = 1;
15
16 itkFilterLib filter(inputDimSize, inputOrigin, inputSpacing);
17 return (true);
18 }
g++ -o testmin minimal_example.cxx -I ../ITKFilterLib -L . -l
Example_ITKFilterLib >& out
Same output AFAICT:
1 ./libExample_ITKFilterLib.a(ITKFilterLib.o): In function
`itk::MemoryAllocationError::MemoryAllocationError(std::basic_string<c
har,
std::char_traits<char>, std::alloca
2
ITKFilterLib.cxx:(.text._ZN3itk21MemoryAllocationErrorC2ERKSsjS2_S2_[_ZN3
itk21MemoryAllocationErrorC5ERKSsjS2_S2_]+0x39):
undefined reference to `itk::ExceptionObject:
….
From: Dženan Zukić [mailto:dzenanz at gmail.com]
Sent: 21 March 2016 20:21
To: Atwood, Robert (DLSLtd,RAL,SCI)
Cc: Insight-users
Subject: Re: [ITK-users] stand-alone lib -- ITKApps/ITKFilterLib
Hi Robert,
maybe you need to link to ITK statically? To accomplish this you
probably need to build ITK as static libraries (it is a configuration
option in CMake).
Regards,
Dženan
On Mon, Mar 21, 2016 at 12:50 PM, <Robert.Atwood at diamond.ac.uk<mailto:Robert.Atwood at diamond.ac.uk>>
wrote:
Hi,
This example, ITKApps/ITKFilterLib, appears to be an example of what I
want to do , bundle or encapsulate a specific ITK-based filter into a
library so that another program may just call it without having to
have the ITK source installation available.
However, a basic test for me is not working.
I just tried to compile the test example from command line after
building the library with Cmake as usual. I get hundreds of 'undefined
reference', as if I have to link with all the ITK libs anyways.
Am I missing something?
Thanks
g++ -o testcomp ../ITKFilterLib/ITKFilterLibTest.cxx -I
g++ ../ITKFilterLib/ -L
. -l Example_ITKFilterLib
First few lines of output:
./libExample_ITKFilterLib.a(ITKFilterLib.o): In function
`itk::MemoryAllocationError::MemoryAllocationError(std::basic_string<c
har, std::char_traits<char>, std::allocator<char> > const&, unsigned
int, std::basic_string<char, std::char_traits<char>,
std::allocator<char> > const&, std::basic_string<char,
std::char_traits<char>, std::allocator<char>
const&)':
ITKFilterLib.cxx:(.text._ZN3itk21MemoryAllocationErrorC2ERKSsjS2_S2_[_ZN3
itk21MemoryAllocationErrorC5ERKSsjS2_S2_]+0x39):
undefined reference to
`itk::ExceptionObject::ExceptionObject(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&, unsigned int,
std::basic_string<char, std::char_traits<char>, std::allocator<char> >
const&, std::basic_string<char, std::char_trait
ITKFilterLib.cxx:(.text._ZN3itk21MemoryAllocationErrorC2ERKSsjS2_S2_[_ZN3
itk21MemoryAllocationErrorC5ERKSsjS2_S2_]+0x44):
undefined reference to `vtable for itk::MemoryAllocationError'
./libExample_ITKFilterLib.a(ITKFilterLib.o): In function
`itk::ProcessAborted::ProcessAborted(char const*, unsigned int)':
ITKFilterLib.cxx:(.text._ZN3itk14ProcessAbortedC2EPKcj[_ZN3itk14ProcessAb
ortedC5EPKcj]+0x33):
undefined reference to `itk::ExceptionObject::ExceptionObject(char
const*, unsigned int, char const*, char const*)'
ITKFilterLib.cxx:(.text._ZN3itk14ProcessAbortedC2EPKcj[_ZN3itk14ProcessAb
ortedC5EPKcj]+0x3e):
undefined reference to `vtable for itk::ProcessAborted'
ITKFilterLib.cxx:(.text._ZN3itk14ProcessAbortedC2EPKcj[_ZN3itk14ProcessAb
ortedC5EPKcj]+0x4f):
undefined reference to `itk::ExceptionObject::SetDescription(char const*)'
ITKFilterLib.cxx:(.text._ZN3itk14ProcessAbortedC2EPKcj[_ZN3itk14ProcessAb
ortedC5EPKcj]+0x62):
undefined reference to `itk::ExceptionObject::~ExceptionObject()'
This is on a Linux Red Hat with ITK git master today (March 21 2016)
cmake --version
cmake version 2.8.12.2
/proc/version:
Linux version 2.6.32-573.18.1.el6.x86_64
(mockbuild at x86-010.build.bos.redhat.com<mailto:mockbuild at x86-010.build.bos.redhat.com>) (gcc version 4.4.7 20120313
(Red Hat 4.4.7-16) (GCC) ) #1 SMP Wed Jan 6 11:20:49 EST 2016
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may be transmitted in or with the message.
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Any opinions expressed within this e-mail are those of the individual
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any
attachments are free from viruses and we cannot accept liability for
any damage which you may sustain as a result of software viruses which
may be transmitted in or with the message.
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