diff --git a/.gitignore b/.gitignore index 6cd3bbc77..5f70fb3d7 100644 --- a/.gitignore +++ b/.gitignore @@ -66,4 +66,11 @@ neo/test/io/neurosharemergeio.py files_for_testing_neo /venv /neo/test/resources -doc/source/examples +doc/examples +doc/*.abf +doc/*.png +doc/*.plx +doc/*.nev +doc/*.ns5 +doc/*.nix +doc/*.nwb \ No newline at end of file diff --git a/doc/source/bug_reports.rst b/doc/source/bug_reports.rst index 7cf3934b7..4dcae32c3 100644 --- a/doc/source/bug_reports.rst +++ b/doc/source/bug_reports.rst @@ -3,7 +3,7 @@ Reporting bugs, requesting new features ======================================= If you find a bug, unclear documentation, or would like to add a new feature to Neo, -please go to https://github.com/NeuralEnsemble/PyNN/issues/. +please go to https://github.com/NeuralEnsemble/python-neo/issues/. Searching the issue tracker diff --git a/doc/source/conf.py b/doc/source/conf.py index 6dd546e71..6e372256a 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -111,15 +111,16 @@ # The theme to use for HTML and HTML Help pages. Major themes that come with # Sphinx are currently 'default' and 'sphinxdoc'. # html_theme = 'default' -html_theme = 'sphinxdoc' +# html_theme = 'sphinxdoc' # html_theme = 'haiku' # html_theme = 'scrolls' # html_theme = 'agogo' +html_theme = 'alabaster' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. -# html_theme_options = {} +html_theme_options = {'logo': 'neologo_transparent.png'} # Add any paths that contain custom themes here, relative to this directory. # html_theme_path = [] @@ -133,13 +134,13 @@ # The name of an image file (relative to this directory) to place at the top # of the sidebar. -html_logo = 'images/neologo_light.png' +# html_logo = 'images/neologo_transparent.png' # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. -html_favicon = None +html_favicon = 'images/neologo_favicon.png' # Add any paths that contain custom static files (such as style sheets) here, diff --git a/doc/source/images/neologo_favicon.png b/doc/source/images/neologo_favicon.png new file mode 100644 index 000000000..9ec09bb5c Binary files /dev/null and b/doc/source/images/neologo_favicon.png differ diff --git a/doc/source/images/neologo_transparent.png b/doc/source/images/neologo_transparent.png new file mode 100644 index 000000000..67445bef4 Binary files /dev/null and b/doc/source/images/neologo_transparent.png differ diff --git a/doc/source/share_data.rst b/doc/source/share_data.rst index 01682fe7f..6f306a692 100644 --- a/doc/source/share_data.rst +++ b/doc/source/share_data.rst @@ -106,7 +106,7 @@ To quickly take a look at the data, let's plot it: In [16]: plt.savefig("open_format_example_cc_step.png") -.. image:: open_format_example_cc_step.png +.. image:: ../open_format_example_cc_step.png Now we've read the data into Neo, we're ready to write them to an open format. diff --git a/examples/igorio.ipynb b/examples/igorio.ipynb deleted file mode 100644 index 00fc29fb6..000000000 --- a/examples/igorio.ipynb +++ /dev/null @@ -1,130 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": { - "deletable": true, - "editable": true - }, - "source": [ - "## IgorProIO Demo" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": { - "collapsed": false, - "deletable": true, - "editable": true - }, - "outputs": [], - "source": [ - "%matplotlib inline\n", - "import matplotlib.pyplot as plt\n", - "import neo" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "deletable": true, - "editable": true - }, - "source": [ - "### IBW support" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": { - "collapsed": false, - "deletable": true, - "editable": true - }, - "outputs": [ - { - "data": { - "image/png": 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- "text/plain": [ - "" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "# Downloaded from Human Brain Project Collaboratory\n", - "# Digital Reconstruction of Neocortical Microcircuitry (nmc-portal)\n", - "# http://microcircuits.epfl.ch/#/animal/8ecde7d1-b2d2-11e4-b949-6003088da632\n", - "x = neo.io.IgorIO(filename='nmc-portal/grouped_ephys/B95/B95_Ch0_IDRest_107.ibw')\n", - "signal = x.read_analogsignal()\n", - "plt.plot(signal.times,signal)\n", - "plt.xlabel(signal.sampling_period.dimensionality)\n", - "plt.ylabel(signal.dimensionality);" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "deletable": true, - "editable": true - }, - "source": [ - "### PXP support" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": { - "collapsed": false, - "deletable": true, - "editable": true - }, - "outputs": [ - { - "data": { - "image/png": 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aG3XeEQP7sq+mnrFDB7D4jssBuGnOYt7Zspebpk/mvk+fC8Csa1o27u8XlQDw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\nEZGY/j+DnKE7AWKkdQAAAABJRU5ErkJggg==\n", - "text/plain": [ - "" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "# Same as above, but the .ibw file was loaded into Igor and saved as part of a .pxp file. \n", - "x = neo.io.IgorIO(filename='nmc-portal/grouped_ephys/B95/B95_Ch0_IDRest_107.pxp')\n", - "signal = x.read_analogsignal(path='root:AA_IDRest_Ch0_107')\n", - "plt.plot(signal.times,signal)\n", - "plt.xlabel(signal.sampling_period.dimensionality)\n", - "plt.ylabel(signal.dimensionality);" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.5.2" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/igorio.py b/examples/igorio.py new file mode 100644 index 000000000..abcd5c8af --- /dev/null +++ b/examples/igorio.py @@ -0,0 +1,31 @@ +""" +IgorProIO Demo +=========================== + +""" + +import os +from urllib.request import urlretrieve +import zipfile +import matplotlib.pyplot as plt +from neo.io import get_io + + +# Downloaded from Human Brain Project Collaboratory +# Digital Reconstruction of Neocortical Microcircuitry (nmc-portal) +# http://microcircuits.epfl.ch/#/animal/8ecde7d1-b2d2-11e4-b949-6003088da632 +datafile_url = "https://microcircuits.epfl.ch/data/released_data/B95.zip" +filename_zip = "B95.zip" +filename = 'grouped_ephys/B95/B95_Ch0_IDRest_107.ibw' +urlretrieve(datafile_url, filename_zip) + +zip_ref = zipfile.ZipFile(filename_zip) # create zipfile object +zip_ref.extract(path='.', member=filename) # extract file to dir +zip_ref.close() + + +reader = get_io(filename) +signal = reader.read_analogsignal() +plt.plot(signal.times, signal) +plt.xlabel(signal.sampling_period.dimensionality) +plt.ylabel(signal.dimensionality) diff --git a/examples/nmc-portal/grouped_ephys/B95/B95_Ch0_IDRest_107.ibw b/examples/nmc-portal/grouped_ephys/B95/B95_Ch0_IDRest_107.ibw deleted file mode 100644 index 45d550d4b..000000000 Binary files a/examples/nmc-portal/grouped_ephys/B95/B95_Ch0_IDRest_107.ibw and /dev/null differ diff --git a/examples/nmc-portal/grouped_ephys/B95/B95_Ch0_IDRest_107.pxp b/examples/nmc-portal/grouped_ephys/B95/B95_Ch0_IDRest_107.pxp deleted file mode 100644 index 254f1015e..000000000 Binary files a/examples/nmc-portal/grouped_ephys/B95/B95_Ch0_IDRest_107.pxp and /dev/null differ diff --git a/examples/plot_with_matplotlib.py b/examples/plot_with_matplotlib.py index 3616ce068..89439aace 100644 --- a/examples/plot_with_matplotlib.py +++ b/examples/plot_with_matplotlib.py @@ -13,7 +13,7 @@ import neo distantfile = 'https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/plexon/File_plexon_3.plx' -localfile = './File_plexon_3.plx' +localfile = 'File_plexon_3.plx' urllib.request.urlretrieve(distantfile, localfile) diff --git a/examples/read_files_neo_io.py b/examples/read_files_neo_io.py index e5b3f2f57..09dea7e0d 100644 --- a/examples/read_files_neo_io.py +++ b/examples/read_files_neo_io.py @@ -12,7 +12,7 @@ # Plexon files distantfile = url_repo + 'plexon/File_plexon_3.plx' -localfile = './File_plexon_3.plx' +localfile = 'File_plexon_3.plx' urllib.request.urlretrieve(distantfile, localfile) # create a reader diff --git a/examples/read_files_neo_rawio.py b/examples/read_files_neo_rawio.py index e8b0b9aec..c2e0c6960 100644 --- a/examples/read_files_neo_rawio.py +++ b/examples/read_files_neo_rawio.py @@ -12,7 +12,7 @@ # Get Plexon files distantfile = url_repo + 'plexon/File_plexon_3.plx' -localfile = './File_plexon_3.plx' +localfile = 'File_plexon_3.plx' urllib.request.urlretrieve(distantfile, localfile) # create a reader @@ -56,7 +56,7 @@ # Read event timestamps and times (take another file) distantfile = url_repo + 'plexon/File_plexon_2.plx' -localfile = './File_plexon_2.plx' +localfile = 'File_plexon_2.plx' urllib.request.urlretrieve(distantfile, localfile) # Count events per channel