Python Binding Error ... about clandmark HOT 22 OPEN

Hi @jiapei100,

what is your system, please?
The Python interface build is so far tested only on linux, where it seem to work without problems. So any help here is highly appreciated.

from clandmark.

I'm using Ubuntu 16.04 Beta 2, with GCC 5.3.1 and Python 3.5.1

from clandmark.

Hi @jiapei100,

then I guess the problem might be the version of Python. I never tried to compile with Python 3.+. Could you try to use Python 2.7 instead?

from clandmark.

Hi,
Actually, I've also tried this on Ubuntu 14.04 and get the same exact error with python 2.7

from clandmark.

Hi @jiapei100 @botev,

I have updated the library core, could you please try it now (with Python 2.7)? I have checked the build again and it works without problems for me.

from clandmark.

Still the same. Not matter it's python 2. 7 or python 3.5 .

Check my python.
jiapei@jiapei-GT72-6QE:/usr/bin$ ls -ls python* 0 lrwxrwxrwx 1 root root 9 Apr 15 01:57 python -> python2.7 0 lrwxrwxrwx 1 root root 9 Mar 27 05:15 python2 -> python2.7 3452 -rwxr-xr-x 1 root root 3533656 Mar 31 05:59 python2.7 0 lrwxrwxrwx 1 root root 33 Mar 31 05:59 python2.7-config -> x86_64-linux-gnu-python2.7-config 0 lrwxrwxrwx 1 root root 16 Dec 9 18:00 python2-config -> python2.7-config 0 lrwxrwxrwx 1 root root 9 Mar 23 04:00 python3 -> python3.5 4336 -rwxr-xr-x 2 root root 4439120 Mar 31 04:51 python3.5 0 lrwxrwxrwx 1 root root 33 Mar 31 04:51 python3.5-config -> x86_64-linux-gnu-python3.5-config 4336 -rwxr-xr-x 2 root root 4439120 Mar 31 04:51 python3.5m 0 lrwxrwxrwx 1 root root 34 Mar 31 04:51 python3.5m-config -> x86_64-linux-gnu-python3.5m-config 0 lrwxrwxrwx 1 root root 16 Mar 23 04:00 python3-config -> python3.5-config 0 lrwxrwxrwx 1 root root 10 Mar 23 04:00 python3m -> python3.5m 0 lrwxrwxrwx 1 root root 17 Mar 23 04:00 python3m-config -> python3.5m-config 0 lrwxrwxrwx 1 root root 16 Dec 9 18:00 python-config -> python2.7-config 0 lrwxrwxrwx 1 root root 58 Mar 25 15:01 pythontex -> ../share/texlive/texmf-dist/scripts/pythontex/pythontex.py

And while configuring clandmark with ccmake ../ out of source building:

` CMake Error at python_interface/CMakeLists.txt:3 (find_package):
By not providing "Findclandmark.cmake" in CMAKE_MODULE_PATH this project
has asked CMake to find a package configuration file provided by
"clandmark", but CMake did not find one.

Could not find a package configuration file provided by "clandmark" with
any of the following names:

 clandmarkConfig.cmake
 clandmark-config.cmake

Add the installation prefix of "clandmark" to CMAKE_PREFIX_PATH or set
"clandmark_DIR" to a directory containing one of the above files. If
"clandmark" provides a separate development package or SDK, be sure it has
been installed.

`

Any further suggestions?

Cheers
Pei

from clandmark.

Ok, I guess, I will need more information then. Just to check, could you capture screenshots from the complete cmake procedure?

1. Configure and compile clandmark with BUILD_SHARED=ON, BUILD_EXAMPLES=ON, BUILD_MATLAB_BINDINGS=OFF, BUILD_PYTHON_BINDINGS=OFF
2. Configure and compile clandmark with BUILD_SHARED=OFF, BUILD_EXAMPLES=OFF, (optionally BUILD_MATLAB_BINDINGS=ON), BUILD_PYTHON_BINDINGS=OFF
3. Configure and compile clandmark with BUILD_SHARED=ON and BUILD_PYTHON_BINDINGS=ON

set the clandmark_DIR and flandmark_DIR to your build/libclandmark when needed.

from clandmark.

The only thing I tried is:
BUILD_MATLAB_BINDINGS=OFF, BUILD_PYTHON_BINDINGS=ON
which brings me the errors.

Cheers
Pei

from clandmark.

And could you try those I mentioned? I think it is because you are missing the clandmark_DIR and flandmark_DIR, but to be sure, I need to see those screenshots.

from clandmark.

Yes, you are right...
clandmark_DIR must be set to "./libclandmark"

Thank you uricamic....

from clandmark.

Sorry, my fault. It looks like it's still the same.

1. If I disable Python Binding by
   BUILD_PYTHON_BINDINGS=OFF
   It's already cached. So, no matter I set clandmark_DIR or not, configure and make will go through.

2. I tried to enable BUILD_PYTHON_BINDINGS=ON at the very beginning,
   http://www.longervision.com/questions/clandmark/01_TryToEnablePython.png
   and see the following error message:
   http://www.longervision.com/questions/clandmark/02_ConfigureError.png

Then, I set the clandmark_DIR as
http://www.longervision.com/questions/clandmark/03_Setting_clandmark_DIR.png
but still get errors:
http://www.longervision.com/questions/clandmark/04_ConfigureErrorAgain.png

Finally, I even tried to modify CMakeCache.txt
http://www.longervision.com/questions/clandmark/05_WhereToSet_clandmark_DIR.png
but still get errors:
http://www.longervision.com/questions/clandmark/06_ConfigureErrorStill.png

Any further suggestions?

Cheers
Pei

from clandmark.

Hi @jiapei100,

could you please try the fullpath to libclandmark folder in clandmark_DIR? Another thing, which I have noticed is that in my case, the CMake asks not only for the clandmark_DIR, but also for the flandmark_DIR, they should be the same, however it is strange, that it is not asked for in your case...

from clandmark.

I tried fullpath as well, still as the issue mentioned
Yes, it seems I only have clandmark_DIR, but NO flandmark_DIR

Weird...
Pei

from clandmark.

Then, please, check all the CMakeLists.txt files if they are identical to those in repository.

To be more specific, check whether the CMakeLists.txt in the python_interface folder contains this line:

find_package(flandmark REQUIRED)

from clandmark.

This is my CMakeLists.txt under python_interface :

jiapei@jiapei-GT72-6QE:~/Downloads/patternrecognition/clandmark/python_interface$ cat CMakeLists.txt 
# python_interface/CMakeLists.txt

find_package(clandmark REQUIRED)
find_package(flandmark REQUIRED)
include_directories(
  ${CLANDMARK_INCLUDE_DIRS}
  ${FLANDMARK_INCLUDE_DIRS}
)

include_directories(${CMAKE_CURRENT_SOURCE_DIR}/include)
#include_directories( ${PROJECT_SOURCE_DIR}/libclandmark )
include_directories( ${PROJECT_SOURCE_DIR}/3rd_party/rapidxml-1.13 )
include_directories( ${PROJECT_SOURCE_DIR}/3rd_party/CImg-1.5.6 )
execute_process(COMMAND python -c "import numpy as np; print np.get_include()" OUTPUT_VARIABLE NUMPY_INCLUDE)
include_directories(${NUMPY_INCLUDE})


set(PY_NAME_interface python_interface)

set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wlong-long -Wl,-rpath,'$ORIGIN/'")

# Include the CMake script UseCython.cmake.  This defines add_cython_module().
# Instruction for use can be found at the top of cmake/UseCython.cmake.
include( UseCython )

# propagate precision definition
if(DOUBLE_PRECISION)
    add_definitions( -DDOUBLE_PRECISION=1 )
else(DOUBLE_PRECISION)
    add_definitions( -DDOUBLE_PRECISION=0 )
endif(DOUBLE_PRECISION)


# With CMake, a clean separation can be made between the source tree and the
# build tree.  When all source is compiled, as with pure C/C++, the source is
# no-longer needed in the build tree.  However, with pure *.py source, the
# source is processed directly.  To handle this, we reproduce the availability
# of the source files in the build tree.
add_custom_target( ReplicatePythonSourceTree ALL ${CMAKE_COMMAND} -P
  ${CMAKE_MODULE_PATH}/ReplicatePythonSourceTree.cmake
  ${CMAKE_CURRENT_BINARY_DIR}
  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )


# Process the CMakeLists.txt in the 'src' and 'bin' directory.
add_subdirectory( src )
add_subdirectory( bin )

from clandmark.

Hmm, looks the same to me.
Maybe you could try to add some message statements and check what is in the ${FLANDMARK_INCLUDE_DIRS} variable.

from clandmark.

I had the same problem. It seems to happen because of the upper cases.
after copying and renaming the cmake files like the following I could compile.

ls cmake/Modules/
FindCImg.cmake                   FindCython.cmake                 FindRapidXML.cmake
Findclandmark.cmake              Findflandmark.cmake              ReplicatePythonSourceTree.cmake
FindCLANDMARK.cmake              FindFLANDMARK.cmake              UseCython.cmake

from clandmark.

Do I have to download a binary named "rectangle-props"? I could only use setup.py when I commented out this file.

  1 from setuptools import setup
  2 from distutils.sysconfig import get_python_lib
  3 import glob
  4 import os
  5 import sys
  6 
  7 if os.path.exists('readme.rst'):
  8     print("""The setup.py script should be executed from the build directory.
  9 
 10 Please see the file 'readme.rst' for further instructions.""")
 11     sys.exit(1)
 12 
 13 
 14 setup(
 15     name = "cythoncmakeexample",
 16     package_dir = {'': 'src'},
 17 #    data_files = [(get_python_lib(), glob.glob('src/*.so')),
 18 #        ('bin', ['bin/rectangle-props'])],
 19     data_files = [(get_python_lib(), glob.glob('src/*.so'))],
 20     author = 'Matt McCormick',
 21     description = 'Use the CMake build system to make Cython modules.',
 22     license = 'Apache',
 23     keywords = 'cmake cython build',
 24     url = 'http://github.com/thewtex/cython-cmake-example',
 25     # test_require = ['nose'],
 26     # zip_safe = False,
 27     )

from clandmark.

@jiapei100 could you please check whether the renaming of files as suggested by @andreas128 solves the problem for you? If it does, I will rename the files in the repository...

from clandmark.

Hi @andreas128,

I think it is not needed, it remained there for some historical development reasons probably.

from clandmark.

It seems "andreas128's suggestions" does help a bit. Now, I didn't have those warnings due to the upper-case and lower-case issue. However, I meet another issue:

I fact, I checked .../clandmark/python_interface/CMakeLists.txt , and line 14~15 are correct.

execute_process(COMMAND python -c "import numpy as np; print np.get_include()" OUTPUT_VARIABLE NUMPY_INCLUDE)
include_directories(${NUMPY_INCLUDE})

I checked these 2 lines by:

>>> import numpy as np
>>> print(np.get_include())
/usr/local/lib/python3.5/dist-packages/numpy/core/include
>>> exit()
jiapei@jiapei-GT72-6QE:/usr/local/lib/python3.5/dist-packages$ cd /usr/local/lib/python3.5/dist-packages/numpy/core/include
jiapei@jiapei-GT72-6QE:/usr/local/lib/python3.5/dist-packages/numpy/core/include$ ls -ls numpy/ufuncobject.h
16 -rw-r--r-- 1 root staff 12323 Apr 20 10:56 numpy/ufuncobject.h

However, "make" still results in the following error message:

/home/jiapei/Downloads/patternrecognition/clandmark/build/python_interface/src/py_featurePool.cxx:283:31: fatal error: numpy/ufuncobject.h: No such file or directory
compilation terminated.
python_interface/src/CMakeFiles/py_featurePool.dir/build.make:70: recipe for target 'python_interface/src/CMakeFiles/py_featurePool.dir/py_featurePool.cxx.o' failed
make[2]: *** [python_interface/src/CMakeFiles/py_featurePool.dir/py_featurePool.cxx.o] Error 1
CMakeFiles/Makefile2:339: recipe for target 'python_interface/src/CMakeFiles/py_featurePool.dir/all' failed
make[1]: *** [python_interface/src/CMakeFiles/py_featurePool.dir/all] Error 2
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2

And, if I ignore python building, by ticking off BUILD_PYTHON_BINDINGS, and do
sudo python setup.py install
directly from within python_interface subdirectory, I got the following error message:
error: can't copy 'bin/rectangle-props': doesn't exist or not a regular file

Oh, BTW, my numpy version

>>> import numpy
>>> numpy.__version__
'1.11.0'

So, any further suggestions?

Cheers
Pei

from clandmark.

Hi @jiapei100,

I am not sure, since I am not a Python expert, but I think the problem might be the Python version.

I was checking the build system only for Python 2.7, while in your post, I see that you are still referring to Python 3.5.
So, the question is, do you use Python 2.7 in CMake configuration? If you do, do you have numpy for Python 2.7 as well?

Best,

Michal

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