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<!DOCTYPE html>
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<title>PySurfer Python Neuroimaging Visualization — PySurfer 0.10.0 documentation</title>
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<h3><a href="index.html">Table of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Changelog</a><ul>
<li><a class="reference internal" href="#version-0-10-0">Version 0.10.0</a></li>
<li><a class="reference internal" href="#version-0-9">Version 0.9</a></li>
<li><a class="reference internal" href="#version-0-8">Version 0.8</a></li>
<li><a class="reference internal" href="#version-0-7">Version 0.7</a></li>
<li><a class="reference internal" href="#version-0-6">Version 0.6</a></li>
<li><a class="reference internal" href="#version-0-5">Version 0.5</a></li>
<li><a class="reference internal" href="#version-0-4">Version 0.4</a><ul>
<li><a class="reference internal" href="#enhancements">Enhancements</a></li>
</ul>
</li>
<li><a class="reference internal" href="#version-0-3-1">Version 0.3.1</a><ul>
<li><a class="reference internal" href="#fixes">Fixes</a></li>
</ul>
</li>
<li><a class="reference internal" href="#version-0-3">Version 0.3</a><ul>
<li><a class="reference internal" href="#id1">Enhancements</a></li>
<li><a class="reference internal" href="#id2">Fixes</a></li>
</ul>
</li>
</ul>
</li>
</ul>
<h4>Previous topic</h4>
<p class="topless"><a href="generated/surfer.utils.coord_to_label.html"
title="previous chapter">surfer.utils.coord_to_label</a></p>
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<div class="document">
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<div class="body" role="main">
<div class="section" id="changelog">
<h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
<div class="section" id="version-0-10-0">
<h2>Version 0.10.0<a class="headerlink" href="#version-0-10-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><p>Added an option to smooth to nearest vertex in <a class="reference internal" href="generated/surfer.Brain.html#surfer.Brain.add_data" title="surfer.Brain.add_data"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Brain.add_data()</span></code></a> using
<code class="docutils literal notranslate"><span class="pre">smoothing_steps='nearest'</span></code></p></li>
<li><p>Added options for using offscreen mode</p></li>
<li><p>Improved integration with Jupyter notebook</p></li>
<li><p>Avoided view changes when using <a class="reference internal" href="generated/surfer.Brain.html#surfer.Brain.add_foci" title="surfer.Brain.add_foci"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Brain.add_foci()</span></code></a></p></li>
</ul>
</div>
<div class="section" id="version-0-9">
<h2>Version 0.9<a class="headerlink" href="#version-0-9" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><p>Fixed transparency issues with colormaps with
<a class="reference internal" href="generated/surfer.Brain.html#surfer.Brain.scale_data_colormap" title="surfer.Brain.scale_data_colormap"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Brain.scale_data_colormap()</span></code></a></p></li>
<li><p>Added an example of using custom colors</p></li>
<li><p>Added options for choosing units for <a class="reference internal" href="generated/surfer.Brain.html#surfer.Brain" title="surfer.Brain"><code class="xref py py-class docutils literal notranslate"><span class="pre">Brain</span></code></a> (<code class="docutils literal notranslate"><span class="pre">m</span></code> or <code class="docutils literal notranslate"><span class="pre">mm</span></code>)</p></li>
</ul>
</div>
<div class="section" id="version-0-8">
<h2>Version 0.8<a class="headerlink" href="#version-0-8" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><p>The surface geometry that is displayed can now be changed after initializing
a <code class="docutils literal notranslate"><span class="pre">Brain</span></code> instance with e.g. <code class="docutils literal notranslate"><span class="pre">brain.set_surf("smoothwm")</span></code>.</p></li>
<li><p>Allowed PySurfer to use custom matplotlib colormap objects or the names of
custom colormaps that have been registered with matplotlib.</p></li>
<li><p>Added four new colormaps from <code class="docutils literal notranslate"><span class="pre">seaborn</span></code>: <code class="docutils literal notranslate"><span class="pre">rocket</span></code>, <code class="docutils literal notranslate"><span class="pre">mako</span></code>, <code class="docutils literal notranslate"><span class="pre">icefire</span></code>,
and <code class="docutils literal notranslate"><span class="pre">vlag</span></code>.</p></li>
<li><p>Terrain interaction is now possible via the <code class="docutils literal notranslate"><span class="pre">interaction</span></code> keyword argument.</p></li>
<li><p>An API reference page is now available.</p></li>
<li><p>Support is now provided for visualizing vector-valued (3 values per vertex)
data.</p></li>
</ul>
</div>
<div class="section" id="version-0-7">
<h2>Version 0.7<a class="headerlink" href="#version-0-7" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><p>Support for Python 3.3 and up.</p></li>
<li><p>A new <code class="docutils literal notranslate"><span class="pre">alpha</span></code> keyword to the <code class="docutils literal notranslate"><span class="pre">Brain</span></code> constructor now controls
opacity of the rendered brain surface.</p></li>
<li><p>The <code class="docutils literal notranslate"><span class="pre">curv</span></code> keyword to the <code class="docutils literal notranslate"><span class="pre">Brain</span></code> constructor has been
deprecated. To replicate previous behavior when <code class="docutils literal notranslate"><span class="pre">curv</span></code> was set to
<code class="docutils literal notranslate"><span class="pre">True</span></code> simply omit the <code class="docutils literal notranslate"><span class="pre">curv</span></code> keyword. To replicate previous
behavior when <code class="docutils literal notranslate"><span class="pre">curv</span></code> was set to <code class="docutils literal notranslate"><span class="pre">False</span></code>, simply set the
<code class="docutils literal notranslate"><span class="pre">cortex</span></code> keyword to None. To ease transition the <code class="docutils literal notranslate"><span class="pre">curv</span></code> argument
will still be caught and processed, but it will be removed in a
future release.</p></li>
<li><p>The <code class="docutils literal notranslate"><span class="pre">cortex</span></code> keyword to the <code class="docutils literal notranslate"><span class="pre">Brain</span></code> constructor now also accepts
a valid color specification (such as a 3-tuple with RGB values or a
color name) to render the cortical surface in that color without
rendering binary curvature values. Additionally it now also accepts
a dictionary with keyword arguments that are passed on to the call
to <code class="docutils literal notranslate"><span class="pre">mlab.pipeline.surface</span></code>.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Brain.save_movie</span></code> now uses the <code class="docutils literal notranslate"><span class="pre">imageio</span></code> library, eliminating the need
to manually install <code class="docutils literal notranslate"><span class="pre">ffmpeg</span></code>. <code class="docutils literal notranslate"><span class="pre">imageio</span></code> has been added as an optional
dependency which can be installed with
<code class="docutils literal notranslate"><span class="pre">$</span> <span class="pre">pip</span> <span class="pre">install</span> <span class="pre">pysurfer[save_movie]</span></code>.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Brain.save_image</span></code> now has the option to save with alpha channel and
antialiasing.</p></li>
</ul>
</div>
<div class="section" id="version-0-6">
<h2>Version 0.6<a class="headerlink" href="#version-0-6" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><p>Values that were previously selected using a <code class="docutils literal notranslate"><span class="pre">config_opts</span></code>
dictionary in the <code class="docutils literal notranslate"><span class="pre">Brain</span></code> constructor are now keyword arguments.
This should make it easier to use tab-completion in IPython, and will
generally simplify your scripts. To ease transition, a <code class="docutils literal notranslate"><span class="pre">config_opts</span></code>
argument will still be caught, and its entries will be used (overriding
the keyword arguments), but it will be removed in a future release.</p></li>
<li><p>The ability to set default values in a config file has been removed.
While convenient, this approach encourages code that is not fully
reproducible. While existing code that was written expecting a config
file will still run, the visualization will fall back to default values.
These should be updated directly in your plotting scripts.</p></li>
<li><p>Figure size is now specified only through the <code class="docutils literal notranslate"><span class="pre">size</span></code> keyword argument
of <a class="reference internal" href="generated/surfer.Brain.html#surfer.Brain" title="surfer.Brain"><code class="xref py py-class docutils literal notranslate"><span class="pre">Brain</span></code></a>. To make a rectangular window, pass a <code class="docutils literal notranslate"><span class="pre">(width,</span> <span class="pre">height)</span></code>
tuple. Passing a single value to <code class="docutils literal notranslate"><span class="pre">size</span></code> will still make a square window.</p></li>
<li><p>The <code class="docutils literal notranslate"><span class="pre">cortex</span></code> keyword argument can now be a mayavi colormap name or
a <code class="docutils literal notranslate"><span class="pre">(colormap,</span> <span class="pre">min,</span> <span class="pre">max,</span> <span class="pre">reverse)</span></code> tuple for full control.</p></li>
<li><p>Morphometry plotting was made more flexible with the ability to pass
a specific colormap and anchor points for that colormap. Additionally,
the default anchor points now use robust statistics to give better
values.</p></li>
<li><p>Contour overlay plotting was made more flexible by adding keyword arguments
to control whether a colorbar should be shown and whether existing contour
overlays should be removed before plotting.</p></li>
</ul>
</div>
<div class="section" id="version-0-5">
<h2>Version 0.5<a class="headerlink" href="#version-0-5" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><p>Added control over the width of outlines when plotting the borders of
annotations or labels.</p></li>
<li><p>The visual display of the surfaces was improved by using surface normals.</p></li>
<li><p>Made colormap specification in Brain.add_data and Brain.add_contour_overlay
more flexible, with better defaults.</p></li>
<li><p>Brain.save_montage() can now produce 2d grids of views in addition to
horizontal and vertical arrangements.</p></li>
<li><p>Fixed some installation issues and added explicit checks for dependencies
on install.</p></li>
<li><p>Updated the installation docs with information about getting PySurfer
running on OSX, and changed the official environment recommendation to
Anaconda.</p></li>
</ul>
</div>
<div class="section" id="version-0-4">
<h2>Version 0.4<a class="headerlink" href="#version-0-4" title="Permalink to this headline">¶</a></h2>
<div class="section" id="enhancements">
<h3>Enhancements<a class="headerlink" href="#enhancements" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><p>Display data from both hemispheres simultaneously</p></li>
<li><p>Display multiple views simultaneously</p></li>
<li><p>Toggling Mayavi toolbars</p></li>
<li><p>Use nibabel for IO functions</p></li>
</ul>
</div>
</div>
<div class="section" id="version-0-3-1">
<h2>Version 0.3.1<a class="headerlink" href="#version-0-3-1" title="Permalink to this headline">¶</a></h2>
<div class="section" id="fixes">
<h3>Fixes<a class="headerlink" href="#fixes" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><p>Reverted change in io.py that broke Python 2.6 compatibility</p></li>
<li><p>Updated traitsui import while keeping backgrounds compatibility</p></li>
</ul>
</div>
</div>
<div class="section" id="version-0-3">
<h2>Version 0.3<a class="headerlink" href="#version-0-3" title="Permalink to this headline">¶</a></h2>
<div class="section" id="id1">
<h3>Enhancements<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><p>TimeViewer GUI to control data exploration in the time dimension</p></li>
<li><p>Support for reading and visualizing MEG data from MNE</p></li>
<li><p>Function to project volume-based data using mri_vol2surf</p></li>
<li><p>Label routines can read scalar data and threshold visualization</p></li>
<li><p>Utility function to smooth overlay data along the cortical manifold</p></li>
<li><p>Example for displaying parcellation-based ROI analysis results</p></li>
<li><p>Example for displaying ROI labels</p></li>
<li><p>Example for plotting probabilistic labels</p></li>
<li><p>Improved color flexibility using matplotlib for many visualization modes</p></li>
<li><p>Exposed alpha channel for many visualization modes</p></li>
</ul>
</div>
<div class="section" id="id2">
<h3>Fixes<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><p>Big-endian overlay data should now display properly on 64-bit systems.</p></li>
<li><p>Colorbar text displays properly on light backgrounds</p></li>
<li><p>Lights are oriented depending on hemisphere so surfaces are equally lit</p></li>
</ul>
</div>
</div>
</div>
</div>
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