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<div class="section" id="module-cfelpyutils.crystfel_utils">
<span id="cfelpyutils-crystfel-utils-module"></span><h1>cfelpyutils.crystfel_utils module<a class="headerlink" href="#module-cfelpyutils.crystfel_utils" title="Permalink to this headline"></a></h1>
<p>CryystFEL utilities.</p>
<p>This module contains the implementation of several functions used to
interact with CrystFEL files and data (geometry files, stream files).</p>
<dl class="function">
<dt id="cfelpyutils.crystfel_utils.load_crystfel_geometry">
<code class="descclassname">cfelpyutils.crystfel_utils.</code><code class="descname">load_crystfel_geometry</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.crystfel_utils.load_crystfel_geometry" title="Permalink to this definition"></a></dt>
<dd><p>Load a CrystFEL geometry file into a dictionary.</p>
<p>Reimplementation of the get_detector_geometry_2 function from
CrystFEL in python. Return a dictionary with the geometry
information read from the file. Convert entries in the geometry
file to keys in the returned dictionary. For a full documentation
on the CrystFEL geometry format, see:</p>
<p><a class="reference external" href="http://www.desy.de/~twhite/crystfel/manual-crystfel_geometry.html">http://www.desy.de/~twhite/crystfel/manual-crystfel_geometry.html</a></p>
<p>The code of this function is synced with the code of the function
‘get_detector_geometry_2’ in CrystFEL at commit
41a8fa9819010fe8ddeb66676fee717f5226c7b8.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
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<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<em>str</em>) – filename of the geometry file.</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">dictionary with the geometry information loaded from the
file.</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">Dict</td>
</tr>
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<div class="section" id="module-cfelpyutils.geometry_utils">
<span id="cfelpyutils-geometry-utils-module"></span><h1>cfelpyutils.geometry_utils module<a class="headerlink" href="#module-cfelpyutils.geometry_utils" title="Permalink to this headline"></a></h1>
<p>Geometry utilities.</p>
<p>This module contains the implementation of several functions used to
manipulate geometry information.</p>
<dl class="class">
<dt id="cfelpyutils.geometry_utils.PixelMaps">
<em class="property">class </em><code class="descclassname">cfelpyutils.geometry_utils.</code><code class="descname">PixelMaps</code><span class="sig-paren">(</span><em>x</em>, <em>y</em>, <em>r</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.geometry_utils.PixelMaps" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
<p>Pixel maps storing data geometry.</p>
<p>A namedtuple that stores the pixel maps describing the geometry of a
dataset. The first two fields, named “x” and “y” respectively, store
the pixel maps for the x coordinate and the y coordinate. The third
field, named “r”, is instead a pixel map storing the distance of each
pixel in the data array from the center of the reference system.</p>
<dl class="attribute">
<dt id="cfelpyutils.geometry_utils.PixelMaps.r">
<code class="descname">r</code><a class="headerlink" href="#cfelpyutils.geometry_utils.PixelMaps.r" title="Permalink to this definition"></a></dt>
<dd><p>Alias for field number 2</p>
</dd></dl>
<dl class="attribute">
<dt id="cfelpyutils.geometry_utils.PixelMaps.x">
<code class="descname">x</code><a class="headerlink" href="#cfelpyutils.geometry_utils.PixelMaps.x" title="Permalink to this definition"></a></dt>
<dd><p>Alias for field number 0</p>
</dd></dl>
<dl class="attribute">
<dt id="cfelpyutils.geometry_utils.PixelMaps.y">
<code class="descname">y</code><a class="headerlink" href="#cfelpyutils.geometry_utils.PixelMaps.y" title="Permalink to this definition"></a></dt>
<dd><p>Alias for field number 1</p>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="cfelpyutils.geometry_utils.compute_min_array_size">
<code class="descclassname">cfelpyutils.geometry_utils.</code><code class="descname">compute_min_array_size</code><span class="sig-paren">(</span><em>pixel_maps</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.geometry_utils.compute_min_array_size" title="Permalink to this definition"></a></dt>
<dd><p>Compute the minimum array size storing data with applied geometry.</p>
<p>Return the minimum size of an array that can store data on which
the geometry information described by the pixel maps has been
applied.</p>
<p>The returned array shape is big enough to display all the input
pixel values in the reference system of the physical detector. The
array is also supposed to be centered at the center of the
reference system of the detector (i.e: the beam interaction point).</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>[</strong><strong>PixelMaps</strong><strong>]</strong> (<em>pixel_maps</em>) – a PixelMaps tuple.</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">a numpy-style shape tuple storing the minimum
array size.</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">Tuple[int, int]</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="cfelpyutils.geometry_utils.compute_pix_maps">
<code class="descclassname">cfelpyutils.geometry_utils.</code><code class="descname">compute_pix_maps</code><span class="sig-paren">(</span><em>geometry</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.geometry_utils.compute_pix_maps" title="Permalink to this definition"></a></dt>
<dd><p>Compute pixel maps from a CrystFEL geometry object.</p>
<p>Take as input a CrystFEL-style geometry object (A dictionary
returned by the function load_crystfel_geometry function in the
crystfel_utils module) and return a PixelMap tuple . The origin the
reference system used by the pixel maps is set at the beam
interaction point.</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>geometry</strong> (<em>dict</em>) – A CrystFEL geometry object (A dictionary
returned by the
<a class="reference internal" href="cfelpyutils.crystfel_utils.html#cfelpyutils.crystfel_utils.load_crystfel_geometry" title="cfelpyutils.crystfel_utils.load_crystfel_geometry"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cfelpyutils.crystfel_utils.load_crystfel_geometry</span></code></a>
function).</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A PixelMaps tuple storing the pixel maps (ndarrays
of type float).</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#cfelpyutils.geometry_utils.PixelMaps" title="cfelpyutils.geometry_utils.PixelMaps">PixelMaps</a></td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="cfelpyutils.geometry_utils.compute_visualization_pix_maps">
<code class="descclassname">cfelpyutils.geometry_utils.</code><code class="descname">compute_visualization_pix_maps</code><span class="sig-paren">(</span><em>geometry</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.geometry_utils.compute_visualization_pix_maps" title="Permalink to this definition"></a></dt>
<dd><p>Compute pixel maps for visualization of the data.</p>
<p>The pixel maps can be used for to display the data in a Pyqtgraph
ImageView widget.</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>geometry</strong> (<em>dict</em>) – A CrystFEL geometry object (A dictionary
returned by the
<a class="reference internal" href="cfelpyutils.crystfel_utils.html#cfelpyutils.crystfel_utils.load_crystfel_geometry" title="cfelpyutils.crystfel_utils.load_crystfel_geometry"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cfelpyutils.crystfel_utils.load_crystfel_geometry</span></code></a>
function).</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="docutils">
<dt>A PixelMaps tuple containing the adjusted pixel</dt>
<dd>maps. The first two fields, named “x” and “y” respectively,
store the pixel maps for the x coordinate and the y
coordinates (as ndarrays of type int). The third field
(“r”) is just set to None.</dd>
</dl>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#cfelpyutils.geometry_utils.PixelMaps" title="cfelpyutils.geometry_utils.PixelMaps">PixelMaps</a></td>
</tr>
</tbody>
</table>
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<h1>cfelpyutils package<a class="headerlink" href="#cfelpyutils-package" title="Permalink to this headline"></a></h1>
<div class="section" id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline"></a></h2>
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<li class="toctree-l1"><a class="reference internal" href="cfelpyutils.parameter_utils.html">cfelpyutils.parameter_utils module</a></li>
</ul>
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<div class="section" id="module-cfelpyutils">
<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-cfelpyutils" title="Permalink to this headline"></a></h2>
<p>Utilities for CFEL software projects.</p>
<p>This module provides utilities (functions, classes, etc.) used by many CFEL projects.</p>
<p>It contains the following submodules (non of which are automatically imported):</p>
<p>cfelfabio: utilities based on the fabio python module (a module that allows
python to work with several file format used in x-ray imaging).</p>
<p>cfelgeom: utilities for processing CrystFEL-style geometry files.</p>
<p>cfelhdf5: utilities for processing HDF5 files (based on the h5py python module).</p>
<p>cfeloptarg: utilities to parse command line arguments and parameter files.</p>
<p>cfelpsana: utilities that expand the functionality of the psana python module.</p>
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<div class="section" id="module-cfelpyutils.parameter_utils">
<span id="cfelpyutils-parameter-utils-module"></span><h1>cfelpyutils.parameter_utils module<a class="headerlink" href="#module-cfelpyutils.parameter_utils" title="Permalink to this headline"></a></h1>
<p>Parameter parsing utilities.</p>
<p>This module contains the implementation of several utilities used
to parse and manipulate dictionaries that store options and parameters.</p>
<dl class="function">
<dt id="cfelpyutils.parameter_utils.convert_parameters">
<code class="descclassname">cfelpyutils.parameter_utils.</code><code class="descname">convert_parameters</code><span class="sig-paren">(</span><em>config_dict</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.parameter_utils.convert_parameters" title="Permalink to this definition"></a></dt>
<dd><p>Convert strings in parameter dictionaries to the correct data type.</p>
<p>Convert a dictionary return by the configparse module to a
dictionar contaning the same parameters converted from string to
their correct type (int, float, string, etc.)</p>
<p>Try to convert each entry in the dictionary according to the
following rules. The first rule that applies to the entry
determines the type.</p>
<ul>
<li><p class="first">If the entry starts and ends with a single quote or double quote,
leave it as a string.</p>
</li>
<li><p class="first">If the entry starts and ends with a square bracket, convert it to
a list.</p>
</li>
<li><p class="first">If the entry starts and ends with a curly braces, convert it to a
dictionary or a set.</p>
</li>
<li><p class="first">If the entry is the word None, without quotes, convert it to
NoneType.</p>
</li>
<li><p class="first">If the entry is the word False, without quotes, convert it to a
boolean False.</p>
</li>
<li><p class="first">If the entry is the word True, without quotes, convert it to a
boolean True.</p>
</li>
<li><p class="first">If none of the previous options match the content of the entry,
try to interpret the entry in order as:</p>
<blockquote>
<div><ul class="simple">
<li>An integer number.</li>
<li>A float number.</li>
<li>A string.</li>
</ul>
</div></blockquote>
</li>
<li><p class="first">If all else fails, raise an exception.</p>
</li>
</ul>
<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"><p class="first"><strong>config</strong> (<em>Dict</em>) – a dictionary containing strings (the dictionary
returned by Config Parser).</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">dictionary with the same structure as the input
dictionary, but with correct types assigned to each entry.</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first">Dict</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><ul class="first last simple">
<li><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> – if an entry cannot be converted to any supported</li>
<li><code class="xref py py-exc docutils literal notranslate"><span class="pre">type.</span></code></li>
</ul>
</td>
</tr>
</tbody>
</table>
</dd></dl>
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cfelpyutils\.crystfel\_utils module
===================================
.. automodule:: cfelpyutils.crystfel_utils
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cfelpyutils\.geometry\_utils module
===================================
.. automodule:: cfelpyutils.geometry_utils
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cfelpyutils\.parameter\_utils module
====================================
.. automodule:: cfelpyutils.parameter_utils
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cfelpyutils package
===================
Submodules
----------
.. toctree::
cfelpyutils.crystfel_utils
cfelpyutils.geometry_utils
cfelpyutils.parameter_utils
Module contents
---------------
.. automodule:: cfelpyutils
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