Re: [scipion-users] OpenCV not found for Xmipp

[David M. <dma...@cn...>]

Hi David, Wolfgang and Scipion users,

Regarding the first question of why the openCV code of Xmipp is not
compailing when OpenCV is in a alternate location, Xmipp needs the headers
files of OpenCV to compile that part of the code, thus you must have
installed the devel version of the OpenCV package and, also, the include
folder of the openCV must be seeable during the compilation time.

Regarding the libtiff versions fight, yes Scipion has libtiff5, then if
other libtiff is used to compile the system's openCV, it will fail.

Both issues might be fixed by installing OpenCV inside Scipion via

$ cd $SCIPION_HOME
$ ./scipion install opencv -j N

where N is the number of processors (take into account that this
installation takes a while, thus the bigger N is better).

NOTE: Regarding the OpenCV inside Scipion, we have using the OpenCV-v2.4.13
by default and we have checked that it works fine for Centos7 and Ubuntu16.
However, for Ubuntu 18, we have observed that the OpenCV-v3.4.1 should be
used. Therefore, if you use Ubuntu18, you should edit the
$SCIPION_HOME/config/scipion.conf in such a way that OPENCV_VER=3.4.1 and
then install opencv using the command above (this only works if Scipion is
installed from sources, not from binaries).


Finally, just to note that OpenCV is used by Xmipp only for two non
critical protocols (Optical Alignment and Enric -former Volume
Homogenizer-). Therefore, if you don't need this two protocols and it still
not working even with the hints pointed out above, the OpenCV code in Xmipp
can be ignored by editing $SCIPION_HOME/config/scipion.conf in such a way
that OPENCV=False and, then, trying to compile Xmipp again.


I hope tht it will help and my appologies for the late reply.


Thanks for reporting!

<http://ucm.es/>

*_____Dr. David Maluenda Niubó*
dma...@cn... - (+34) 619 029 310
CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
BioComputing Unit <http://biocomputingunit.es/>

This email message and any documents attached to it may contain
confidential or legally protected material and are intended solely for the
use of the individual or organization to whom they are addressed. We remind
you that if you are not the intended recipient of this email message or the
person responsible for processing it, then you are not authorized to read,
save, modify, send, copy or disclose any of its contents. If you have
received this email message by mistake, we kindly ask you to inform the
sender of this and to eliminate both the message and any attachments it
carries from your account. Thank you for your collaboration.



On Tue, May 28, 2019 at 6:12 PM Hoover, David (NIH/CIT) [E] via
scipion-users <sci...@li...> wrote:

> No.  I've been attempting to compile Xmipp from source, but that is even
> harder.
>
> David Hoover
> HPC @ NIH
>
> On 5/27/2019 11:28 AM, Pablo Conesa wrote:
> > Hi David! Have we ever replied to you with a solution?
> >
> > On 23/5/19 17:09, Hoover, David (NIH/CIT) [E] via scipion-users wrote:
> >> Hi,
> >>
> >> I recently installed Scipion 2.0 and all the plugins, and attempted to
> run the tutorials.  We have OpenCV installed in an alternate location, and
> I make it available by setting $PATH and $LD_LIBRARY_PATH.  I keep getting
> complaints that it is not installed, and that I should fix this and
> reinstall Xmipp.
> >>
> >> How does Xmipp know where OpenCV is?  Can I set a configuration
> somewhere stating where it is located?
> >>
> >> David Hoover
> >> HPC @ NIH
> >>
> >>
> >> _______________________________________________
> >> scipion-users mailing list
> >> sci...@li...
> >> https://lists.sourceforge.net/lists/listinfo/scipion-users
> >
> >
> > _______________________________________________
> > scipion-users mailing list
> > sci...@li...
> > https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>