Permalink
Browse files

Updating docs and license text

  • Loading branch information...
jamesgao committed Nov 14, 2013
1 parent 8386495 commit ca60b4ac8efd76da5cb12b6b0fe4f3a8b07362bb
Showing with 347 additions and 28 deletions.
  1. +9 −19 LICENSE
  2. +294 −0 MANIFEST
  3. +2 −0 MANIFEST.in
  4. +2 −2 docs/conf.py
  5. +1 −1 docs/index.rst
  6. +20 −4 docs/install.rst
  7. +16 −1 docs/segmentation.rst
  8. +3 −1 setup.py
View
28 LICENSE
@@ -1,23 +1,13 @@
Copyright (c) 2013, James Gao
Copyright (c) 2013, The Regents of the University of California (Regents).
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
Permission to use, copy, modify, and distribute this software and its documentation for educational,
research, and not-for-profit purposes, without fee and without a signed licensing agreement, is hereby granted,
provided that the above copyright notice, this paragraph and the following two paragraphs appear in all copies,
modifications, and distributions. Contact The Office of Technology Licensing, UC Berkeley,
2150 Shattuck Avenue, Suite 510, Berkeley, CA 94720-1620, (510) 643-7201, for commercial licensing opportunities.
Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
Created by James Gao, University of California, Berkeley.
Redistributions in binary form must reproduce the above copyright notice, this
list of conditions and the following disclaimer in the documentation and/or
other materials provided with the distribution.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
IN NO EVENT SHALL REGENTS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF REGENTS HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". REGENTS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
View
294 MANIFEST
@@ -0,0 +1,294 @@
# file GENERATED by distutils, do NOT edit
setup.py
OpenCTM-1.0.3/lib/compressMG1.c
OpenCTM-1.0.3/lib/compressMG2.c
OpenCTM-1.0.3/lib/compressRAW.c
OpenCTM-1.0.3/lib/openctm.c
OpenCTM-1.0.3/lib/stream.c
OpenCTM-1.0.3/lib/liblzma/Alloc.c
OpenCTM-1.0.3/lib/liblzma/LzFind.c
OpenCTM-1.0.3/lib/liblzma/LzmaDec.c
OpenCTM-1.0.3/lib/liblzma/LzmaEnc.c
OpenCTM-1.0.3/lib/liblzma/LzmaLib.c
cortex/__init__.py
cortex/align.py
cortex/anat.py
cortex/appdirs.py
cortex/brainctm.py
cortex/db.py
cortex/defaults.cfg
cortex/formats.c
cortex/formats_old.py
cortex/freesurfer.py
cortex/mayavi_aligner.py
cortex/mp.py
cortex/openctm.c
cortex/options.py
cortex/polyutils.py
cortex/quickflat.py
cortex/rois.py
cortex/segment.py
cortex/surfinfo.py
cortex/svgbase.xml
cortex/svgroi.py
cortex/utils.py
cortex/volume.py
cortex/xfm.py
cortex/blender/__init__.py
cortex/blender/blendlib.py
cortex/dataset/__init__.py
cortex/dataset/braindata.py
cortex/dataset/views.py
cortex/mapper/__init__.py
cortex/mapper/line.py
cortex/mapper/patch.py
cortex/mapper/point.py
cortex/mapper/samplers.py
cortex/mapper/volume.py
cortex/webgl/FallbackLoader.py
cortex/webgl/__init__.py
cortex/webgl/data.py
cortex/webgl/favicon.ico
cortex/webgl/htmlembed.py
cortex/webgl/mixer.html
cortex/webgl/public.html
cortex/webgl/serve.py
cortex/webgl/simple.html
cortex/webgl/static.html
cortex/webgl/template.html
cortex/webgl/view.py
cortex/webgl/wngraph-minimal.html
cortex/webgl/wngraph.html
cortex/webgl/resources/css/jquery.miniColors.css
cortex/webgl/resources/css/jsplot.css
cortex/webgl/resources/css/mriview.css
cortex/webgl/resources/css/w2ui-1.2.min.css
cortex/webgl/resources/css/ui-lightness/jquery-ui-1.8.21.custom-2.css
cortex/webgl/resources/css/ui-lightness/jquery-ui-1.8.21.custom.css
cortex/webgl/resources/css/ui-lightness/images/ui-bg_diagonals-thick_18_b81900_40x40.png
cortex/webgl/resources/css/ui-lightness/images/ui-bg_diagonals-thick_20_666666_40x40.png
cortex/webgl/resources/css/ui-lightness/images/ui-bg_flat_10_000000_40x100.png
cortex/webgl/resources/css/ui-lightness/images/ui-bg_glass_100_f6f6f6_1x400.png
cortex/webgl/resources/css/ui-lightness/images/ui-bg_glass_100_fdf5ce_1x400.png
cortex/webgl/resources/css/ui-lightness/images/ui-bg_glass_65_ffffff_1x400.png
cortex/webgl/resources/css/ui-lightness/images/ui-bg_gloss-wave_35_f6a828_500x100.png
cortex/webgl/resources/css/ui-lightness/images/ui-bg_highlight-soft_100_eeeeee_1x100.png
cortex/webgl/resources/css/ui-lightness/images/ui-bg_highlight-soft_75_ffe45c_1x100.png
cortex/webgl/resources/css/ui-lightness/images/ui-icons_222222_256x240.png
cortex/webgl/resources/css/ui-lightness/images/ui-icons_228ef1_256x240.png
cortex/webgl/resources/css/ui-lightness/images/ui-icons_ef8c08_256x240.png
cortex/webgl/resources/css/ui-lightness/images/ui-icons_ffd27a_256x240.png
cortex/webgl/resources/css/ui-lightness/images/ui-icons_ffffff_256x240.png
cortex/webgl/resources/images/colors.png
cortex/webgl/resources/images/control-pause.png
cortex/webgl/resources/images/control-play.png
cortex/webgl/resources/images/loading.gif
cortex/webgl/resources/images/trigger.png
cortex/webgl/resources/js/LandscapeControls.js
cortex/webgl/resources/js/Three.js
cortex/webgl/resources/js/canvg.js
cortex/webgl/resources/js/datamodel.js
cortex/webgl/resources/js/dataset.js
cortex/webgl/resources/js/facepick.js
cortex/webgl/resources/js/facepick_worker.js
cortex/webgl/resources/js/figure.js
cortex/webgl/resources/js/graphview.js
cortex/webgl/resources/js/hoverintent.min.js
cortex/webgl/resources/js/jgestures.min.js
cortex/webgl/resources/js/jquery-1.7.2.min.js
cortex/webgl/resources/js/jquery-1.8.0.min.js
cortex/webgl/resources/js/jquery-ui-1.8.21.custom.min.js
cortex/webgl/resources/js/jquery-ui-1.8.23.custom.min.js
cortex/webgl/resources/js/jquery.ddslick.min.js
cortex/webgl/resources/js/jquery.miniColors.js
cortex/webgl/resources/js/jquery.svg.min.js
cortex/webgl/resources/js/jquery.svganim.min.js
cortex/webgl/resources/js/jquery.ui.touch-punch.min.js
cortex/webgl/resources/js/kdTree-min.js
cortex/webgl/resources/js/mriview.js
cortex/webgl/resources/js/mriview_utils.js
cortex/webgl/resources/js/python_interface.js
cortex/webgl/resources/js/rgbcolor.js
cortex/webgl/resources/js/shaderlib.js
cortex/webgl/resources/js/shadowtex.js
cortex/webgl/resources/js/surfgeometry.js
cortex/webgl/resources/js/surfload.js
cortex/webgl/resources/js/svgroi.js
cortex/webgl/resources/js/w2ui-1.2.min.js
cortex/webgl/resources/js/ctm/CTMLoader.js
cortex/webgl/resources/js/ctm/CTMWorker.js
cortex/webgl/resources/js/ctm/ctm.js
cortex/webgl/resources/js/ctm/lzma.js
cortex/webgl/resources/js/ctm/license/OpenCTM.txt
cortex/webgl/resources/js/ctm/license/js-lzma.txt
cortex/webgl/resources/js/ctm/license/js-openctm.txt
cortex/webgl/resources/json/wngraph-definitions.json
cortex/webgl/resources/json/wngraph-nodenames.json
cortex/webgl/resources/json/wngraph-rgbcolors.json
cortex/webgl/resources/json/wngraph-testvoxwts.json
filestore/colormaps/Accent.png
filestore/colormaps/Accent_r.png
filestore/colormaps/Blues.png
filestore/colormaps/Blues_r.png
filestore/colormaps/BrBG.png
filestore/colormaps/BrBG_r.png
filestore/colormaps/BuGn.png
filestore/colormaps/BuGn_r.png
filestore/colormaps/BuPu.png
filestore/colormaps/BuPu_r.png
filestore/colormaps/CyanBlueGrayRedPink.png
filestore/colormaps/Dark2.png
filestore/colormaps/Dark2_r.png
filestore/colormaps/GnBu.png
filestore/colormaps/GnBu_r.png
filestore/colormaps/Greens.png
filestore/colormaps/Greens_r.png
filestore/colormaps/Greys.png
filestore/colormaps/Greys_r.png
filestore/colormaps/J4.png
filestore/colormaps/J4R.png
filestore/colormaps/J4s.png
filestore/colormaps/J5.png
filestore/colormaps/J5R.png
filestore/colormaps/J6.png
filestore/colormaps/J6R.png
filestore/colormaps/OrRd.png
filestore/colormaps/OrRd_r.png
filestore/colormaps/Oranges.png
filestore/colormaps/Oranges_r.png
filestore/colormaps/PRGn.png
filestore/colormaps/PRGn_r.png
filestore/colormaps/Paired.png
filestore/colormaps/Paired_r.png
filestore/colormaps/Pastel1.png
filestore/colormaps/Pastel1_r.png
filestore/colormaps/Pastel2.png
filestore/colormaps/Pastel2_r.png
filestore/colormaps/PiYG.png
filestore/colormaps/PiYG_r.png
filestore/colormaps/PuBu.png
filestore/colormaps/PuBuGn.png
filestore/colormaps/PuBuGn_r.png
filestore/colormaps/PuBu_r.png
filestore/colormaps/PuOr.png
filestore/colormaps/PuOr_r.png
filestore/colormaps/PuRd.png
filestore/colormaps/PuRd_r.png
filestore/colormaps/Purples.png
filestore/colormaps/Purples_r.png
filestore/colormaps/RGrB_tsi.png
filestore/colormaps/RdBu.png
filestore/colormaps/RdBu_2D.png
filestore/colormaps/RdBu_covar.png
filestore/colormaps/RdBu_covar_alpha.png
filestore/colormaps/RdBu_r.png
filestore/colormaps/RdGy.png
filestore/colormaps/RdGy_r.png
filestore/colormaps/RdPu.png
filestore/colormaps/RdPu_r.png
filestore/colormaps/RdYlBu.png
filestore/colormaps/RdYlBu_r.png
filestore/colormaps/RdYlGn.png
filestore/colormaps/RdYlGn_r.png
filestore/colormaps/Reds.png
filestore/colormaps/Reds_r.png
filestore/colormaps/Retinotopy_RYBCR.png
filestore/colormaps/Retinotopy_RYBCR_2D.png
filestore/colormaps/Set1.png
filestore/colormaps/Set1_r.png
filestore/colormaps/Set2.png
filestore/colormaps/Set2_r.png
filestore/colormaps/Set3.png
filestore/colormaps/Set3_r.png
filestore/colormaps/Spectral.png
filestore/colormaps/Spectral_r.png
filestore/colormaps/YlGn.png
filestore/colormaps/YlGnBu.png
filestore/colormaps/YlGnBu_r.png
filestore/colormaps/YlGn_r.png
filestore/colormaps/YlOrBr.png
filestore/colormaps/YlOrBr_r.png
filestore/colormaps/YlOrRd.png
filestore/colormaps/YlOrRd_r.png
filestore/colormaps/afmhot.png
filestore/colormaps/afmhot_r.png
filestore/colormaps/autumn.png
filestore/colormaps/autumn_r.png
filestore/colormaps/binary.png
filestore/colormaps/binary_r.png
filestore/colormaps/bone.png
filestore/colormaps/bone_r.png
filestore/colormaps/brg.png
filestore/colormaps/brg_r.png
filestore/colormaps/bwr.png
filestore/colormaps/bwr_r.png
filestore/colormaps/cool.png
filestore/colormaps/cool_r.png
filestore/colormaps/coolwarm.png
filestore/colormaps/coolwarm_r.png
filestore/colormaps/copper.png
filestore/colormaps/copper_r.png
filestore/colormaps/cubehelix.png
filestore/colormaps/cubehelix_r.png
filestore/colormaps/flag.png
filestore/colormaps/flag_r.png
filestore/colormaps/gist_earth.png
filestore/colormaps/gist_earth_r.png
filestore/colormaps/gist_gray.png
filestore/colormaps/gist_gray_r.png
filestore/colormaps/gist_heat.png
filestore/colormaps/gist_heat_r.png
filestore/colormaps/gist_ncar.png
filestore/colormaps/gist_ncar_r.png
filestore/colormaps/gist_rainbow.png
filestore/colormaps/gist_rainbow_r.png
filestore/colormaps/gist_stern.png
filestore/colormaps/gist_stern_r.png
filestore/colormaps/gist_yarg.png
filestore/colormaps/gist_yarg_r.png
filestore/colormaps/gnuplot.png
filestore/colormaps/gnuplot2.png
filestore/colormaps/gnuplot2_r.png
filestore/colormaps/gnuplot_r.png
filestore/colormaps/gray.png
filestore/colormaps/gray_r.png
filestore/colormaps/hot.png
filestore/colormaps/hot_r.png
filestore/colormaps/hsv.png
filestore/colormaps/hsv_r.png
filestore/colormaps/jet.png
filestore/colormaps/jet_r.png
filestore/colormaps/ocean.png
filestore/colormaps/ocean_r.png
filestore/colormaps/pink.png
filestore/colormaps/pink_r.png
filestore/colormaps/prism.png
filestore/colormaps/prism_r.png
filestore/colormaps/rainbow.png
filestore/colormaps/rainbow_r.png
filestore/colormaps/seismic.png
filestore/colormaps/seismic_r.png
filestore/colormaps/spectral.png
filestore/colormaps/spectral_r.png
filestore/colormaps/spring.png
filestore/colormaps/spring_r.png
filestore/colormaps/summer.png
filestore/colormaps/summer_r.png
filestore/colormaps/terrain.png
filestore/colormaps/terrain_r.png
filestore/colormaps/winter.png
filestore/colormaps/winter_r.png
filestore/db/S1/rois.svg
filestore/db/S1/anatomicals/raw.nii.gz
filestore/db/S1/surfaces/flat_lh.npz
filestore/db/S1/surfaces/flat_rh.npz
filestore/db/S1/surfaces/inflated_lh.npz
filestore/db/S1/surfaces/inflated_rh.npz
filestore/db/S1/surfaces/pia_lh.npz
filestore/db/S1/surfaces/pia_rh.npz
filestore/db/S1/surfaces/wm_lh.npz
filestore/db/S1/surfaces/wm_rh.npz
filestore/db/S1/transforms/fullhead/matrices.xfm
filestore/db/S1/transforms/fullhead/reference.nii.gz
filestore/db/S1/transforms/retinotopy/matrices.xfm
filestore/db/S1/transforms/retinotopy/reference.nii.gz
View
@@ -0,0 +1,2 @@
recursive-include filestore *
recursive-include cortex/webgl/resources *
View
@@ -25,8 +25,8 @@
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', 'numpydoc', "sphinx.ext.autosummary"]
autosummary_generate = True
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', "sphinx.ext.autosummary"]
#autosummary_generate = True
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
View
@@ -26,9 +26,9 @@ Contents:
install
segmentation
database
rois
align
dataset
rois
transforms
Indices and tables
View
@@ -1,7 +1,6 @@
Installation
============
Pycortex is available on the Python Packaging Index. The easiest way to install it is with the Anaconda_. To use pycortex with Anaconda_, first install anaconda as instructed, then type the following commands into a terminal::
Pycortex is available on the Python Packaging Index. The easiest way to install it is with Anaconda_. To use pycortex with Anaconda_, first install anaconda as instructed, then type the following commands into a terminal::
sudo pip install nibabel
sudo pip install pycortex
@@ -11,15 +10,32 @@ If you are running Ubuntu, the built-in python packages should be sufficient. Us
sudo apt-get install python-dev python-numpy python-scipy python-matplotlib python-h5py python-nibabel python-lxml python-shapely python-html5lib
sudo pip install pycortex
If you wish to run the latest bleeding-edge version of pycortex, use the following instructions::
git clone https://github.com/jamesgao/pycortex.git
cd pycortex
sudo python setup.py install
.. _Anaconda: https://store.continuum.io/cshop/anaconda/
Demo
----
To test if your install went well, first download the `example dataset <http://gallantlab.org/pycortex/S1_retinotopy.hdf>`_. Then run the following commands at a terminal::
$ ipython
In [1]: import cortex
In [2]: ds = cortex.openFile("S1_retinotopy.hdf")
In [3]: cortex.webshow(ds)
If everything went well, this should pop up a web browser window with the same view as http://gallantlab.org/pycortex/retinotopy_demo/.
Configuration
-------------
The pycortex configuration file is located in :file:`~/.config/pycortex/options.cfg`. The location of the *filestore* (i.e. database) needs to be written into the file under the ``[basic]`` header::
Pycortex will automatically create a database filestore when it is first installed. In Linux, this filestore is located at :file:`/usr/local/share/pycortex/`. On first import, it will also create a configuration file in your user directory which allows you to specify additional options, including alternate filestore locations.
In Linux, this user configuration file is located in :file:`~/.config/pycortex/options.cfg`. The location of the *filestore* (i.e. database) needs to be written into the file under the ``[basic]`` header::
[basic]
filestore=/abs/path/to/filestore
By default, the filestore is automatically installed in
.. todo:: Additional option documentation
Oops, something went wrong.

0 comments on commit ca60b4a

Please sign in to comment.