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I2PC / scipion

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)
http://scipion.i2pc.es
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Optical flow missing in 1.2-beta? #1448

Closed JuhaHuiskonen closed 6 years ago

JuhaHuiskonen commented 6 years ago

Hi, I installed 1.2-beta. we're running relion13 betagal tutorial. However we noticed that movie alignment fails, and this is because xmipp_movie_optical_alignment_cpu program is not in the software/em/xmipp/bin folder. Scipion did install without any errors

delarosatrevin commented 6 years ago

Hi @JuhaHuiskonen, can you check if the OpenCV option is set to True in the scipion/config/scipion.conf file? xmipp_movie_optical_alignment_cpu depends on OpenCV and if it False it will not be compiled. If it is False and you change it to True, you will need to launch the ./scipion install command again (hopefully only will install the missing part).

JuhaHuiskonen commented 6 years ago

you're right @delarosatrevin OpenCV installation hadn't worked so I had compiled with option --no-opencv. If I try to install it this is what happens:

[ 14%] Building CXX object modules/highgui/CMakeFiles/opencv_highgui.dir/src/grfmt_jpeg2000.cpp.o In file included from /usr/include/jasper/jasper.h:77:0, from /wrk/project_cryoem/apps/taito-gpu/scipion-1.2.beta/software/tmp/opencv-2.4.13/modules/highgui/src/grfmt_jpeg2000.cpp:58: /usr/include/jasper/jas_math.h: In function ‘bool jas_safe_size_mul(size_t, size_t, size_t)’: /usr/include/jasper/jas_math.h:143:15: error: ‘SIZE_MAX’ was not declared in this scope if (x && y > SIZE_MAX / x) { ^ /usr/include/jasper/jas_math.h: In function ‘bool jas_safe_size_add(size_t, size_t, size_t)’: /usr/include/jasper/jas_math.h:170:10: error: ‘SIZE_MAX’ was not declared in this scope if (y > SIZE_MAX - x) { ^ make[2]: [modules/highgui/CMakeFiles/opencv_highgui.dir/src/grfmt_jpeg2000.cpp.o] Error 1 make[1]: [modules/highgui/CMakeFiles/opencv_highgui.dir/all] Error 2 make: *** [all] Error 2

delarosatrevin commented 6 years ago

Do you have OpenCV (and it devel ) libraries installed in your system? It is a huge library with many dependencies...so if you can install in the standard way, we could workaround the Scipion install script to use it instead of compiling from scratch. See the related issue #1445 .

pconesa commented 6 years ago

@JuhaHuiskonen , is this solved?

JuhaHuiskonen commented 6 years ago

yes. opencv compilation had failed

pconesa commented 6 years ago

Thanks!