Fixed documentation

dmpelt · Nov 25, 2013 · 6cf2f28 · 6cf2f28
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diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,6 @@
 build/
 dist/
-docSRC/_build/
+docSRC/_build/doctrees
 
 *.c
 *.cpp

diff --git a/astra/functions.py b/astra/functions.py
@@ -109,6 +109,14 @@ def add_noise_to_sino(sinogram_in, I0):
     return sinogram_out
 
 def geom_size(geom, dim=None):
+    """Returns the size of a volume or sinogram, based on the projection or volume geometry.
+    
+    :param geom: Geometry to calculate size from
+    :type geometry: :class:`dict`
+    :param dim: Optional axis index to return
+    :type dim: :class:`int`
+    """
+
     if 'GridSliceCount' in geom:
         # 3D Volume geometry?
         s = (geom['GridSliceCount'],geom['GridRowCount'], geom['GridColCount'])

diff --git a/docSRC/_build/html/.buildinfo b/docSRC/_build/html/.buildinfo
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+    <title>Helper class: the ASTRAProjector module &mdash; PyASTRAToolbox 1.0 documentation</title>
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+
+  <div class="section" id="module-astra.ASTRAProjector">
+<span id="helper-class-the-astraprojector-module"></span><h1>Helper class: the <tt class="xref py py-mod docutils literal"><span class="pre">ASTRAProjector</span></tt> module<a class="headerlink" href="#module-astra.ASTRAProjector" title="Permalink to this headline">¶</a></h1>
+<dl class="class">
+<dt id="astra.ASTRAProjector.ASTRAProjector2D">
+<em class="property">class </em><tt class="descclassname">astra.ASTRAProjector.</tt><tt class="descname">ASTRAProjector2D</tt><big>(</big><em>proj_geom</em>, <em>vol_geom</em>, <em>proj_type</em>, <em>useCUDA=False</em><big>)</big><a class="reference internal" href="_modules/astra/ASTRAProjector.html#ASTRAProjector2D"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.ASTRAProjector.ASTRAProjector2D" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">object</span></tt></p>
+<p>Helps with various common ASTRA Toolbox 2D operations.</p>
+<p>This class can perform several often used toolbox operations, such as:</p>
+<ul class="simple">
+<li>Forward projecting</li>
+<li>Back projecting</li>
+<li>Reconstructing</li>
+</ul>
+<p>Note that this class has a some computational overhead, because it
+copies a lot of data. If you use many repeated operations, directly
+using the PyAstraToolbox methods directly is faster.</p>
+<p>You can use this class as an abstracted weight matrix <span class="math">\(W\)</span>: multiplying an instance
+<tt class="docutils literal"><span class="pre">proj</span></tt> of this class by an image results in a forward projection of the image, and multiplying
+<tt class="docutils literal"><span class="pre">proj.T</span></tt> by a sinogram results in a backprojection of the sinogram:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">proj</span> <span class="o">=</span> <span class="n">ASTRAProjector2D</span><span class="p">(</span><span class="o">...</span><span class="p">)</span>
+<span class="n">fp</span> <span class="o">=</span> <span class="n">proj</span><span class="o">*</span><span class="n">image</span>
+<span class="n">bp</span> <span class="o">=</span> <span class="n">proj</span><span class="o">.</span><span class="n">T</span><span class="o">*</span><span class="n">sinogram</span>
+</pre></div>
+</div>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>proj_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) &#8211; The projection geometry.</li>
+<li><strong>vol_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) &#8211; The volume geometry.</li>
+<li><strong>proj_type</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) &#8211; Projector type, such as <tt class="docutils literal"><span class="pre">'line'</span></tt>, <tt class="docutils literal"><span class="pre">'linear'</span></tt>, ...</li>
+<li><strong>useCUDA</strong> (<tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt>) &#8211; If <tt class="docutils literal"><span class="pre">True</span></tt>, use CUDA for calculations, when possible.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="method">
+<dt id="astra.ASTRAProjector.ASTRAProjector2D.backProject">
+<tt class="descname">backProject</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="_modules/astra/ASTRAProjector.html#ASTRAProjector2D.backProject"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.ASTRAProjector.ASTRAProjector2D.backProject" title="Permalink to this definition">¶</a></dt>
+<dd><p>Backproject a sinogram.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.8)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <tt class="xref py py-class docutils literal"><span class="pre">int</span></tt>) &#8211; The sinogram data or ID.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.8)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> &#8211; The backprojection.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="astra.ASTRAProjector.ASTRAProjector2D.forwardProject">
+<tt class="descname">forwardProject</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="_modules/astra/ASTRAProjector.html#ASTRAProjector2D.forwardProject"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.ASTRAProjector.ASTRAProjector2D.forwardProject" title="Permalink to this definition">¶</a></dt>
+<dd><p>Forward project an image.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.8)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <tt class="xref py py-class docutils literal"><span class="pre">int</span></tt>) &#8211; The image data or ID.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.8)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> &#8211; The forward projection.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="astra.ASTRAProjector.ASTRAProjector2D.reconstruct">
+<tt class="descname">reconstruct</tt><big>(</big><em>data</em>, <em>method</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="_modules/astra/ASTRAProjector.html#ASTRAProjector2D.reconstruct"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.ASTRAProjector.ASTRAProjector2D.reconstruct" title="Permalink to this definition">¶</a></dt>
+<dd><p>Reconstruct an image from a sinogram.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.8)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <tt class="xref py py-class docutils literal"><span class="pre">int</span></tt>) &#8211; The sinogram data or ID.</li>
+<li><strong>method</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) &#8211; Name of the reconstruction algorithm.</li>
+<li><strong>kwargs</strong> &#8211; Additional named parameters to pass to <a class="reference internal" href="creators.html#astra.creators.create_reconstruction" title="astra.creators.create_reconstruction"><tt class="xref py py-func docutils literal"><span class="pre">astra.creators.create_reconstruction()</span></tt></a>.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.8)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> &#8211; The reconstruction.</p>
+</td>
+</tr>
+</tbody>
+</table>
+<p>Example of a SIRT reconstruction using CUDA:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">proj</span> <span class="o">=</span> <span class="n">ASTRAProjector2D</span><span class="p">(</span><span class="o">...</span><span class="p">)</span>
+<span class="n">rec</span> <span class="o">=</span> <span class="n">proj</span><span class="o">.</span><span class="n">reconstruct</span><span class="p">(</span><span class="n">sinogram</span><span class="p">,</span><span class="s">&#39;SIRT_CUDA&#39;</span><span class="p">,</span><span class="n">iterations</span><span class="o">=</span><span class="mi">1000</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="astra.ASTRAProjector.ASTRAProjector2DTranspose">
+<em class="property">class </em><tt class="descclassname">astra.ASTRAProjector.</tt><tt class="descname">ASTRAProjector2DTranspose</tt><big>(</big><em>parentProj</em><big>)</big><a class="reference internal" href="_modules/astra/ASTRAProjector.html#ASTRAProjector2DTranspose"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.ASTRAProjector.ASTRAProjector2DTranspose" title="Permalink to this definition">¶</a></dt>
+<dd><p>Implements the <tt class="docutils literal"><span class="pre">proj.T</span></tt> functionality.</p>
+<p>Do not use directly, since it can be accessed as member <tt class="docutils literal"><span class="pre">.T</span></tt> of
+an <a class="reference internal" href="#astra.ASTRAProjector.ASTRAProjector2D" title="astra.ASTRAProjector.ASTRAProjector2D"><tt class="xref py py-class docutils literal"><span class="pre">ASTRAProjector2D</span></tt></a> object.</p>
+</dd></dl>
+
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