[AniMov] Assistance with Animove Plugin on QGIS for Mac OSX

Patrick Freeman freeman1 at stanford.edu
Tue Aug 6 17:59:01 CEST 2013


Hi Victor,

To answer your first question, yes, the MCP option is available for use. So
we're good there. As for SciPy, things get a little hairy. When I ask QGIS
to import SciPy I get the following read-out:

Traceback (most recent call last):

File "<input>", line 1, in <module>

File
"/Applications/QGIS.app/Contents/MacOS/../Resources/python/qgis/utils.py",
line 309, in _import

mod = _builtin_import(name, globals, locals, fromlist, level)

ImportError: No module named scipy


I assume this means I don't have the SciPy package installed in the correct
folder. I know this sounds super basic, but can you tell me how I should
install SciPy so that QGIS can read it? I just don't want to screw up my
entire QGIS program on accident. I have downloaded the SciPy 0.11.0 version
but Jorge, you thought that there was an issue with the plugin requiring
the 0.12 version yes? Should I give the 0.11.0 version a shot with any
instructions that you might provide or should I just try to install the
0.12 version. Should I also plan to download the Numpy package as well?


Also, I did attempt your other fix of checking and unchecking the options
box in Sextante and it doesn't make the KDE option appear unfortunately.


Thanks again guys, I really appreciate it and so do the rhinos!


Patrick

On Tue, Aug 6, 2013 at 12:00 PM, <animov-request at faunalia.it> wrote:

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> Today's Topics:
>
>    1. Assistance with Animov Plugin on QGIS for Mac OSX
>       (Patrick Freeman)
>    2. Re: Assistance with Animov Plugin on QGIS for Mac OSX
>       (Victor Gonzalez)
>    3. Re: Assistance with Animov Plugin on QGIS for Mac OSX
>       (Jorge Arevalo)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 5 Aug 2013 16:00:34 +0200
> From: Patrick Freeman <freeman1 at stanford.edu>
> To: animov at faunalia.it
> Subject: [AniMov] Assistance with Animov Plugin on QGIS for Mac OSX
> Message-ID:
>         <
> CAFUu_5nQa53BkQaGmrEGJu1Krgehf358gWur1DcGduT1cdZJ8Q at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> My name is Patrick Freeman and I'm currently a master's student from
> Stanford University interning with a conservation research organization in
> South Africa. I've been tasked with using a database of VHF telemetry data
> and GPS collar readings from the regional population of black rhinos to
> develop a working knowledge of their home ranges, home range overlap and
> habitat usage. The organization here employs QGIS to do all of their map
> work and thus I've learned how to use the program as much as I can over the
> past month. However, I'm still completely blind to the workings of Python,
> etc.
>
> I am desperately trying to get the kernel density estimation tool in the
> Animove plugin in the Sextante toolbox to work but it simply won't appear.
> I've read plenty on various different sites that this is a result of a
> missing SciPy package. I have downloaded the SciPy package for Mac but
> don't know how to install it properly to my QGIS directory. I'm currently
> using a Mac OSx (Lion) and I'm working with QGIS 1.8. I *believe* my Python
> is version 2.7, but I'm not entirely sure how to check it properly (again,
> I'm new to QGIS and the world of Python). I have spent several weeks
> combing the Internet for help with this issue to no avail despite there
> being plenty of information about how to make this plugin work for the
> Windows version of QGIS. I was wondering if I went straight to the source I
> could potentially get a little assistance with getting the KDE to be
> functional for the plugin? Paolo has graciously directed me to this
> conversation (
> http://lists.faunalia.it/pipermail/animov/2013-August/001113.html) but it
> is again more focused on the Windows installation process. I am just
> worried that if I try to reinstall a developer version of QGIS that I'll
> screw up a bunch of the work that I've already done on this project/make my
> computer implode so I want to make sure what I'm doing is correct. This
> black rhino project is of urgent importance to the conservation managers in
> this area given the spike in rhino poaching incidents in the area so I
> thank you in advance for any and all support!
>
> Cheers,
>
> Patrick Freeman
>
> --
> Patrick T. Freeman
> Stanford University
> Head Teaching Assistant - Stanford University Earth Systems Program
> B.S. Candidate '13, M.S. Candidate '14 | Earth Systems
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>
> ------------------------------
>
> Message: 2
> Date: Tue, 6 Aug 2013 09:33:01 +0200
> From: Victor Gonzalez <victor.gonzalez at geomati.co>
> To: Animal Movement <animov at faunalia.it>
> Subject: Re: [AniMov] Assistance with Animov Plugin on QGIS for Mac
>         OSX
> Message-ID:
>         <CAKMYNK=
> 789PauJAEqi3_UmiO3NNMPknaGaxu2OY-mQXHZj+EYw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Patrick,
>
> I never used Mac OS, so I'm not sure I can help, but I'll try. Does the
> "Minimum Convex Polygon" algorithm appear in the SEXTANTE toolbox?
>
> If so, AniMove is installed and configured correctly, but scipy may not be
> installed with the required version and thus the "Kernel Density
> Estimation" algorithm does not appear. To check your scipy version, you can
> try this: open the Plugins -> Python console and write this:
>
>   >>> import sys
>   >>> sys.version
>   (check Python version)
>   >>> import scipy
>   >>> scipy.version.version
>   (check scipy version)
>   >>> import numpy
>   >>> numpy.version.version
>   (check numpy version)
>
> If no AniMove algorithm appears in the SEXTANTE toolbox, you can try this:
> open the Analysis -> SEXTANTE options and configuration and check the box
> under AniMove (MCP and Kernel analysis UD).
> If it is already checked, try to uncheck and check it again.
>
> If the AniMove (MCP and Kernel analysis UD) option does not appear in the
> SEXTANTE options and configuration, then the AniMove plugin is not
> installed correctly.
>
> Please, let us know if you find something.
> Regards,
> V?ctor.
>
>
>
> 2013/8/5 Patrick Freeman <freeman1 at stanford.edu>
>
> >  My name is Patrick Freeman and I'm currently a master's student from
> > Stanford University interning with a conservation research organization
> in
> > South Africa. I've been tasked with using a database of VHF telemetry
> data
> > and GPS collar readings from the regional population of black rhinos to
> > develop a working knowledge of their home ranges, home range overlap and
> > habitat usage. The organization here employs QGIS to do all of their map
> > work and thus I've learned how to use the program as much as I can over
> the
> > past month. However, I'm still completely blind to the workings of
> Python,
> > etc.
> >
> > I am desperately trying to get the kernel density estimation tool in the
> > Animove plugin in the Sextante toolbox to work but it simply won't
> appear.
> > I've read plenty on various different sites that this is a result of a
> > missing SciPy package. I have downloaded the SciPy package for Mac but
> > don't know how to install it properly to my QGIS directory. I'm currently
> > using a Mac OSx (Lion) and I'm working with QGIS 1.8. I *believe* my
> Python
> > is version 2.7, but I'm not entirely sure how to check it properly
> (again,
> > I'm new to QGIS and the world of Python). I have spent several weeks
> > combing the Internet for help with this issue to no avail despite there
> > being plenty of information about how to make this plugin work for the
> > Windows version of QGIS. I was wondering if I went straight to the
> source I
> > could potentially get a little assistance with getting the KDE to be
> > functional for the plugin? Paolo has graciously directed me to this
> > conversation (
> > http://lists.faunalia.it/pipermail/animov/2013-August/001113.html) but
> it
> > is again more focused on the Windows installation process. I am just
> > worried that if I try to reinstall a developer version of QGIS that I'll
> > screw up a bunch of the work that I've already done on this project/make
> my
> > computer implode so I want to make sure what I'm doing is correct. This
> > black rhino project is of urgent importance to the conservation managers
> in
> > this area given the spike in rhino poaching incidents in the area so I
> > thank you in advance for any and all support!
> >
> > Cheers,
> >
> > Patrick Freeman
> >
> > --
> > Patrick T. Freeman
> > Stanford University
> > Head Teaching Assistant - Stanford University Earth Systems Program
> > B.S. Candidate '13, M.S. Candidate '14 | Earth Systems
> >
> >
> >
> > _______________________________________________
> > AniMov mailing list
> > AniMov at faunalia.it
> > http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
> >
> >
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>
> ------------------------------
>
> Message: 3
> Date: Tue, 6 Aug 2013 11:08:08 +0200
> From: Jorge Arevalo <jorge.arevalo at geomati.co>
> To: Animal Movement <animov at faunalia.it>
> Subject: Re: [AniMov] Assistance with Animov Plugin on QGIS for Mac
>         OSX
> Message-ID:
>         <
> CAC4KD+FCnFpYhCfnkecGvyGcD7xir2D5xTVQqh0domZbuOzoag at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello,
>
> As Mac OS user, I have the same problem. I'm almost 100% secure is a
> problem with scipy version. I think the plugin requires scipy 0.12
> and, by default, 0.11.1 is installed. I'm investigating it, to include
> a Mac OS installation guide in the official documentation. I'll keep
> you updated.
>
> Best regards,
> Jorge
>
> On Tue, Aug 6, 2013 at 9:33 AM, Victor Gonzalez
> <victor.gonzalez at geomati.co> wrote:
> > Hi Patrick,
> >
> > I never used Mac OS, so I'm not sure I can help, but I'll try. Does the
> > "Minimum Convex Polygon" algorithm appear in the SEXTANTE toolbox?
> >
> > If so, AniMove is installed and configured correctly, but scipy may not
> be
> > installed with the required version and thus the "Kernel Density
> Estimation"
> > algorithm does not appear. To check your scipy version, you can try this:
> > open the Plugins -> Python console and write this:
> >
> >   >>> import sys
> >   >>> sys.version
> >   (check Python version)
> >   >>> import scipy
> >   >>> scipy.version.version
> >   (check scipy version)
> >   >>> import numpy
> >   >>> numpy.version.version
> >   (check numpy version)
> >
> > If no AniMove algorithm appears in the SEXTANTE toolbox, you can try
> this:
> > open the Analysis -> SEXTANTE options and configuration and check the box
> > under AniMove (MCP and Kernel analysis UD).
> > If it is already checked, try to uncheck and check it again.
> >
> > If the AniMove (MCP and Kernel analysis UD) option does not appear in the
> > SEXTANTE options and configuration, then the AniMove plugin is not
> installed
> > correctly.
> >
> > Please, let us know if you find something.
> > Regards,
> > V?ctor.
> >
> >
> >
> > 2013/8/5 Patrick Freeman <freeman1 at stanford.edu>
> >>
> >> My name is Patrick Freeman and I'm currently a master's student from
> >> Stanford University interning with a conservation research organization
> in
> >> South Africa. I've been tasked with using a database of VHF telemetry
> data
> >> and GPS collar readings from the regional population of black rhinos to
> >> develop a working knowledge of their home ranges, home range overlap and
> >> habitat usage. The organization here employs QGIS to do all of their map
> >> work and thus I've learned how to use the program as much as I can over
> the
> >> past month. However, I'm still completely blind to the workings of
> Python,
> >> etc.
> >>
> >> I am desperately trying to get the kernel density estimation tool in the
> >> Animove plugin in the Sextante toolbox to work but it simply won't
> appear.
> >> I've read plenty on various different sites that this is a result of a
> >> missing SciPy package. I have downloaded the SciPy package for Mac but
> don't
> >> know how to install it properly to my QGIS directory. I'm currently
> using a
> >> Mac OSx (Lion) and I'm working with QGIS 1.8. I *believe* my Python is
> >> version 2.7, but I'm not entirely sure how to check it properly (again,
> I'm
> >> new to QGIS and the world of Python). I have spent several weeks
> combing the
> >> Internet for help with this issue to no avail despite there being
> plenty of
> >> information about how to make this plugin work for the Windows version
> of
> >> QGIS. I was wondering if I went straight to the source I could
> potentially
> >> get a little assistance with getting the KDE to be functional for the
> >> plugin? Paolo has graciously directed me to this conversation
> >> (http://lists.faunalia.it/pipermail/animov/2013-August/001113.html)
> but it
> >> is again more focused on the Windows installation process. I am just
> worried
> >> that if I try to reinstall a developer version of QGIS that I'll screw
> up a
> >> bunch of the work that I've already done on this project/make my
> computer
> >> implode so I want to make sure what I'm doing is correct. This black
> rhino
> >> project is of urgent importance to the conservation managers in this
> area
> >> given the spike in rhino poaching incidents in the area so I thank you
> in
> >> advance for any and all support!
> >>
> >> Cheers,
> >>
> >> Patrick Freeman
> >>
> >> --
> >> Patrick T. Freeman
> >> Stanford University
> >> Head Teaching Assistant - Stanford University Earth Systems Program
> >> B.S. Candidate '13, M.S. Candidate '14 | Earth Systems
> >>
> >>
> >>
> >> _______________________________________________
> >> AniMov mailing list
> >> AniMov at faunalia.it
> >> http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
> >>
> >
> >
> > _______________________________________________
> > AniMov mailing list
> > AniMov at faunalia.it
> > http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
> >
>
>
>
> --
> Jorge Ar?valo
> http://geomati.co
>
>
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>
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> AniMov at faunalia.it
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> ------------------------------
>
> End of AniMov Digest, Vol 90, Issue 3
> *************************************
>



-- 
Patrick T. Freeman
Stanford University
Head Teaching Assistant - Stanford University Earth Systems Program
B.S. Candidate '13, M.S. Candidate '14 | Earth Systems
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