build error for python bindings with opencv_contrib modules

[avtomaton]

Build from latest version (1cd3c6f) with -DOPENCV_EXTRA_MODULES_PATH=<path to my contrib modules> produces the following error:

In file included from /home/avtomaton/arbeit/sdk/cxx/opencv/build/modules/python2/pyopencv_generated_include.h:11:0,
from /home/avtomaton/arbeit/sdk/cxx/opencv/modules/python/src2/cv2.cpp:12:
/home/avtomaton/arbeit/sdk/cxx/opencv_contrib/modules/hdf/include/opencv2/hdf/hdf5.hpp:40:18: fatal error: hdf5.h: No such file or directory

I attached makefile output for this error. It seems that for python2 and python3 modules there are no include paths for HDF5, i. e. dirty hardcoding

find_package(HDF5)
include_directories(${HDF5_INCLUDE_DIRS})

into modules/python/common.cmake solves the problem. I believe that it is not nice solution, that's why I don't attach pull request.

make-verbose.txt

[alalek]

Thanks for report!
Public includes of modules should not depend on external 3rdparty libraries. Violation of this rule provides this problem.
Line with #include <hdf5.h> must gone into internal implementation.

[auroua]

I have encountered exactly the same error in ubuntu 16.04, and have solved the problem using @avtomaton 's method

[cmdelatorre]

I have encountered exactly the same error with version 3.1.0 in Ubuntu 15.10, and have solved the problem using @avtomaton 's method.

[Yaffa1607]

What steps do I have to repeat after adding these lines to common.cmake?

[rtylecek]

I just run make once again and it compiled (U16.04).

[YuehChuan]

Works charm on ubuntu16.04.2 with ROS kinetic, thanks 😄

[RamitPahwa]

Where exactly do i need to add these lines ??
I am new to the area and not able to navigate to the common.cmake??
Please point me to the right direction.

[kvmanohar22]

@Ramit-Pahwa that file is located at <OpenCV_DIR>/modules/python

[NickCrews]

@Ramit-Pahwa And I added them on like the 3rd line of the file, so that

# This file is included from a subdirectory
set(PYTHON_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/../")

ocv_add_module(${MODULE_NAME} BINDINGS)

became

# This file is included from a subdirectory
set(PYTHON_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/../")

find_package(HDF5)
include_directories(${HDF5_INCLUDE_DIRS})

ocv_add_module(${MODULE_NAME} BINDINGS)

And this worked for me, I only had to run make again (Ubuntu 16.10)

[Sreekiranar]

Worked like a charm. Thanks a lot !! @avtomaton

[pravin382]

Worked for me, thanks

[DronPascal]

I made: $ sudo apt-get install -y libhdf5-dev
And it worked for me!

There's all that u need to QT and OpenCV if u need:
$ sudo apt install build-essential perl python git libx11-xcb-dev libxcb-composite0-dev libxcb-cursor-dev libxcb-damage0-dev libxcb-dpms0-dev libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-icccm4-dev libxcb-image0-dev libxcb-keysyms1-dev libxcb-present-dev libxcb-randr0-dev libxcb-render-util0-dev libxcb-render0-dev libxcb-shape0-dev libxcb-shm0-dev libxcb-sync-dev libxcb-xfixes0-dev libxcb-xinerama0-dev libxcb-xkb-dev libxcb-xtest0-dev libxcb1-dev flex bison gperf libicu-dev libxslt-dev ruby libssl-dev libxcursor-dev libxcomposite-dev libxdamage-dev libxrandr-dev libdbus-1-dev libfontconfig1-dev libcap-dev libxtst-dev libpulse-dev libudev-dev libpci-dev libnss3-dev libasound2-dev libxss-dev libegl1-mesa-dev gperf bison libasound2-dev make cmake libgl1-mesa-dev libglu1-mesa-dev build-essential cmake git libgtk2.0-dev pkg-config libavcodec-dev libavformat-dev libswscale-dev python-dev python-numpy libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libdc1394-22-dev ffmpeg libharfbuzz-dev libglib2.0-dev libpcre2-dev libgstreamer1.0-dev gstreamer1.0-tools gstreamer1.0-plugins-ugly gstreamer1.0-plugins-good gstreamer1.0-plugins-base gstreamer1.0-plugins-bad libgstreamer-plugins-base1.0-dev libdlib-dev libharfbuzz-dev libpcre3-dev libudev-dev libinput-dev libxcb-xinerama0-dev libxcb-xinerama0 libgdk3.0-cil-dev libgtk-3-dev libglib2.0-dev libglib2.0-cil-dev libglib3.0-cil-dev libegl1-mesa-dev libgles2-mesa-dev perl6 bison flex gperf python libdc1394-22-dev libdc1394-utils valgrind libhdf5-devsudo

[aismai01]

does anyone know by any chance if the procedure to install it is the same on a Raspberry Pi 3. I got the same error and I followed the recommendation that @avtomaton made but it didn't work

[Unlicensed-driver-ljx]

home/nvidia/opencv/opencv-3.4.5/build/modules/python_bindings_generator/pyopencv_generated_include.h:14:10: fatal error: opencv2/hdf/hdf5.hpp: No such file or directory
14 | #include "opencv2/hdf/hdf5.hpp"
| ^~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [modules/python2/CMakeFiles/opencv_python2.dir/build.make:63: modules/python2/CMakeFiles/opencv_python2.dir//src2/cv2.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:6674: modules/python2/CMakeFiles/opencv_python2.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
In file included from /home/nvidia/opencv/opencv-3.4.5/modules/python/src2/cv2.cpp:31:
/home/nvidia/opencv/opencv-3.4.5/build/modules/python_bindings_generator/pyopencv_generated_include.h:14:10: fatal error: opencv2/hdf/hdf5.hpp: No such file or directory
14 | #include "opencv2/hdf/hdf5.hpp"
| ^~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [modules/python3/CMakeFiles/opencv_python3.dir/build.make:63: modules/python3/CMakeFiles/opencv_python3.dir//src2/cv2.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:6719: modules/python3/CMakeFiles/opencv_python3.dir/all] Error 2
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