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README.txt
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README.txt
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MotionClouds: installing and running the python scripts
MotionClouds are parameterized stimuli with controlled motion content
and no spatial coherence. They are precisely tuned in the frequency
space.
A full description can be found in Paula S. Leon, Ivo Vanzetta,
Guillaume S. Masson, Laurent U. Perrinet. Motion Clouds:
Model-based stimulus synthesis of natural-like random textures for
the study of motion perception, URL . Journal of Neurophysiology,
107(11):3217--3226, 2012, see
http://www.ncbi.nlm.nih.gov/pubmed/22423003 or
http://jn.physiology.org/content/107/11/3217 .
The latest changes are available from this web site:
https://github.com/NeuralEnsemble/MotionClouds
Installing and running the python scripts:
This package consists of:
MotionClouds.py : the API with all the math and display routines,
test_*.py : different types of stimuli are tested,
experiment_*py : different experiments.
fig_*py : different scripts used to generate wiki pages.
figures : resulting figures of tests and experiments (as set in
the variable MotionClouds.figpath.
Makefile : a GNUmake file to edit files make edit, generate
figures make figures or compile the documentation make doc.
Installation
Installation of MotionClouds consists simply in downloading the
MotionClouds.py file which contains all routines to compute and
use the MotionClouds textures. This script uses python] which
comes (pre-installed / easy to download and install) on many
operating systems. Installation has some dependencies:
mandatory: numpy is the core library used to compute textures,
optional: mayavi is used to visualize envelopes,
optional: ffmpeg is used to generate movies.
optional: matplotlib, scipy (with PIL support) and imagemagick
are used to generate figures in the documentation.
optional: progressbar for displaying progress of encoding.
installation using custom scripts
depending on your system you should use in a terminal window
sh install_dependencies_debian.sh
or
sh install_dependencies_macosx.sh
an alternative is to use a virtual machine such as for instance
the one provided by the NeuroDebian team.
Installation in Debian-based distributions (such as Ubuntu)
Use the aptitude front end to install packages: (or alternatively
apt -get if you feel confident with that tool instead)
python is supported by most distribution and should already be
installed. You can check which version is installed :
python -V
The same libraries as for MacOsX need to be installed :
sudo aptitude install python-scipy python-numpy python-matplotlib
Idem for the progress bar module
sudo easy_install progressbar
Install the ffmpeg encoder to work with mpeg, avi, etc, videos:
sudo aptitude install ffmpeg
when creating MoiMoin pages, it is useful to package images in a
zip file:
aptitude install zip
Installation on MacOsX: EPD
Enthought distributes a battery-included installation of
python. It is recommended to use the i386 version as the 64-bits
version lacks a proper compilation of MayaVi. You will still need
ffmpeg to make movies (see HomeBrew or MacPorts section below).
Installation on MacOsX: HomeBrew (for more experienced users)
install it following their instructions :
ruby -e "$(curl -fsSL https://raw.github.com/gist/323731)"
then install the following packages
# install python through HomeBrew as a framework
brew install python --framework
# bootstrap pip
/usr/local/share/python/easy_install pip
/usr/local/share/python/pip install --upgrade distribute
# libraries
brew install gfortran
pip install -U ipython
# useful packages
pip install -U nose
pip install -U progressbar
easy_install pyreport
easy_install -f http://dist.plone.org/thirdparty/ -U PIL==1.1.7
# numpy et al
pip install -U numpy
pip install -U scipy
pip install -U -e git+git@github.com:matplotlib/matplotlib.git#egg=matplotlib
# pip install -f http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.0/matplotlib-1.0.0.tar.gz matplotlib
# IDE
pip install -U sphinx pyflakes rope
brew install sip
brew install pyqt
pip install -U spyder
# mayavi
brew install vtk --python
pip install -U traitsbackendqt
pip install -U configobj
pip install -U "Mayavi[app]"
be sure to install ffmpeg :
brew install ffmpeg
brew install zip
Installation on MacOsX: MacPorts (outdated documentation)
On MacOsX, this may be achieved using MacPorts:
MacPorts is a generic package manager, somewhat related to
Debian's apt scheme. You will need the XCode package which sits in
your MacOSX installation DVD or may downloaded on Apple's site or
even borrowed to me. Once installed, do the following on the
command-line
on Leopard (python 26 works fine too):
sudo port install python25 python_select
sudo python_select python25
sudo port install py25-pil py25-numpy py25-scipy py25-ipython py25-matplotlib
+cairo+latex+tkinter
sudo port install py25-enthoughtbase py25-mayavi py25-traitsbackendqt
on Snow Leopard:
sudo port install python26 python_select
sudo python_select python26
sudo port install py26-pil py26-numpy py26-scipy py26-ipython py26-matplotlib
+cairo+latex+tkinter
sudo port install py26-enthoughtbase py26-mayavi py26-traitsbackendqt
* then optionally, {{{
sudo easy_install progressbar pygarrayimage pyglet
be sure to install ffmpeg :
sudo port install ffmpeg