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<ul>
<li><a class="reference internal" href="#">cfelpyutils package</a><ul>
<li><a class="reference internal" href="#submodules">Submodules</a></li>
<li><a class="reference internal" href="#module-cfelpyutils.cfelfabio">cfelpyutils.cfelfabio module</a></li>
<li><a class="reference internal" href="#module-cfelpyutils.cfelgeom">cfelpyutils.cfelgeom module</a></li>
<li><a class="reference internal" href="#module-cfelpyutils.cfelhdf5">cfelpyutils.cfelhdf5 module</a></li>
<li><a class="reference internal" href="#module-cfelpyutils.cfeloptarg">cfelpyutils.cfeloptarg module</a></li>
<li><a class="reference internal" href="#module-cfelpyutils.cfelpsana">cfelpyutils.cfelpsana module</a></li>
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<div class="section" id="module-cfelpyutils">
<span id="cfelpyutils-package"></span><h1>cfelpyutils package<a class="headerlink" href="#module-cfelpyutils" title="Permalink to this headline">¶</a></h1>
<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>
<div class="section" id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="module-cfelpyutils.cfelfabio">
<span id="cfelpyutils-cfelfabio-module"></span><h2>cfelpyutils.cfelfabio module<a class="headerlink" href="#module-cfelpyutils.cfelfabio" title="Permalink to this headline">¶</a></h2>
<p>Utilities based on the fabio python module</p>
<p>This module contains utilities derived from the fabio python module.
This module allows python to understand and process several file format used in
x-ray crystallography. The utilites in this modules expand on what the fabio
module alread provides.</p>
<dl class="function">
<dt id="cfelpyutils.cfelfabio.read_cbf_from_stream">
<code class="descclassname">cfelpyutils.cfelfabio.</code><code class="descname">read_cbf_from_stream</code><span class="sig-paren">(</span><em>stream</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfelfabio.read_cbf_from_stream" title="Permalink to this definition">¶</a></dt>
<dd><p>“Reads a cbfimage object out of a data string buffer.</p>
<p>Read a data string buffer received as a payload from the PETRAIII P11
sender, and creates a cbfimage object from it (See the documentation of the
fabio python module).</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>stream</strong> (<em>str</em>) – a data string buffer received from the PETRAIII P11 sender.</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><strong>cbf_obj</strong> –
a cbfimage object containing the data
extracted from the string buffer.</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">fabio.cbfimage</td>
</tr>
</tbody>
</table>
</dd></dl>
</div>
<div class="section" id="module-cfelpyutils.cfelgeom">
<span id="cfelpyutils-cfelgeom-module"></span><h2>cfelpyutils.cfelgeom module<a class="headerlink" href="#module-cfelpyutils.cfelgeom" title="Permalink to this headline">¶</a></h2>
<p>Utilities for CrystFEL-style geometry files.</p>
<p>This module contains utilities for the processing of CrystFEL-style geometry
files.</p>
<dl class="function">
<dt id="cfelpyutils.cfelgeom.coffset_from_geometry_file">
<code class="descclassname">cfelpyutils.cfelgeom.</code><code class="descname">coffset_from_geometry_file</code><span class="sig-paren">(</span><em>fnam</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfelgeom.coffset_from_geometry_file" title="Permalink to this definition">¶</a></dt>
<dd><dl class="docutils">
<dt>Extracts detector distance offset information from a CrystFEL-style</dt>
<dd>geometry file.</dd>
</dl>
<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>fnam</strong> (<em>str</em>) – geometry filename.</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><strong>coffset</strong> –
the detector distance offset</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">float</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="cfelpyutils.cfelgeom.pixel_maps_from_geometry_file">
<code class="descclassname">cfelpyutils.cfelgeom.</code><code class="descname">pixel_maps_from_geometry_file</code><span class="sig-paren">(</span><em>fnam</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfelgeom.pixel_maps_from_geometry_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Extracts pixel maps from a CrystFEL-style geometry file.</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>fnam</strong> (<em>str</em>) – geometry filename.</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><strong>x,y,r</strong> –
slab-like pixel maps with respectively x, y coordinates of the pixel
and distance of the pixel from the center of the reference system
(usually the beam position).</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">numpy.ndarray float, numpy.ndarray float, numpy.ndarray float</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="cfelpyutils.cfelgeom.res_from_geometry_file">
<code class="descclassname">cfelpyutils.cfelgeom.</code><code class="descname">res_from_geometry_file</code><span class="sig-paren">(</span><em>fnam</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfelgeom.res_from_geometry_file" title="Permalink to this definition">¶</a></dt>
<dd><dl class="docutils">
<dt>Extracts pixel resolution information from a CrystFEL-style</dt>
<dd>geometry file.</dd>
</dl>
<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>fnam</strong> (<em>str</em>) – geometry filename.</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><strong>res</strong> –
the pixel resolution</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">float</td>
</tr>
</tbody>
</table>
</dd></dl>
</div>
<div class="section" id="module-cfelpyutils.cfelhdf5">
<span id="cfelpyutils-cfelhdf5-module"></span><h2>cfelpyutils.cfelhdf5 module<a class="headerlink" href="#module-cfelpyutils.cfelhdf5" title="Permalink to this headline">¶</a></h2>
<p>Utilities for HDF5 files.</p>
<p>This module contains utilities for the processing of HDF5. This module builds
on what the h5py module already provides.</p>
<dl class="function">
<dt id="cfelpyutils.cfelhdf5.load_nparray_from_hdf5_file">
<code class="descclassname">cfelpyutils.cfelhdf5.</code><code class="descname">load_nparray_from_hdf5_file</code><span class="sig-paren">(</span><em>data_filename</em>, <em>data_group</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfelhdf5.load_nparray_from_hdf5_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads a numpy.ndarray from an HDF5 file.</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_filename</strong> (<em>str</em>) – filename of the file to read.</li>
<li><strong>data_group</strong> (<em>str</em>) – internal HDF5 path of the data block to read.</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>nparray</strong> –
numpy array with the data read from the file.</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last">numpy.ndarray</p>
</td>
</tr>
</tbody>
</table>
</dd></dl>
</div>
<div class="section" id="module-cfelpyutils.cfeloptarg">
<span id="cfelpyutils-cfeloptarg-module"></span><h2>cfelpyutils.cfeloptarg module<a class="headerlink" href="#module-cfelpyutils.cfeloptarg" title="Permalink to this headline">¶</a></h2>
<p>Utilities for parsing command line options and configuration files.</p>
<p>This module contains utilities for parsing of command line options and
configuration files.</p>
<dl class="function">
<dt id="cfelpyutils.cfeloptarg.parse_cmdline_args">
<code class="descclassname">cfelpyutils.cfeloptarg.</code><code class="descname">parse_cmdline_args</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfeloptarg.parse_cmdline_args" title="Permalink to this definition">¶</a></dt>
<dd><p>Parses command line arguments for source and monitor.ini file.</p>
<p>Uses the argparse module to parse command line arguments.
It parses the following arguments:</p>
<blockquote>
<div><p>source (1st positional argument): data source (file list, psana source
string, etc.).</p>
<p>configuration file (-i/–ini): file containing user-provided
parameters.</p>
</div></blockquote>
</dd></dl>
<dl class="function">
<dt id="cfelpyutils.cfeloptarg.parse_parameters">
<code class="descclassname">cfelpyutils.cfeloptarg.</code><code class="descname">parse_parameters</code><span class="sig-paren">(</span><em>config</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfeloptarg.parse_parameters" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets correct types for parameter dictionaries.</p>
<p>Reads a parameter dictionary returned by the ConfigParser python modue,
and assigns correct types to parameters, without changing the structure of
the dictionary.</p>
<p>The parser tries to interpret each entry in the dictionary according to the
following rules:</p>
<ul>
<li><p class="first">If the entry starts and ends with a single quote, it is interpreted as a
string.</p>
</li>
<li><p class="first">If the entry is the word None, without quotes, then the entry is
interpreted as NoneType.</p>
</li>
<li><p class="first">If the entry is the word False, without quotes, then the entry is
interpreted as a boolean False.</p>
</li>
<li><p class="first">If the entry is the word True, without quotes, then the entry is
interpreted as a boolean True.</p>
</li>
<li><p class="first">If non of the previous options match the content of the entry,
the parser tries 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>
<p>The first choice that succeeds determines the entry type.</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"><strong>config</strong> (<em>dict</em>) – parameter dictionary returned by ConfigParser.</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><strong>monitor_params</strong> –
dictionary with the same structure as the input
dictionary, but with correct types assigned to each entry.</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">dict</td>
</tr>
</tbody>
</table>
</dd></dl>
</div>
<div class="section" id="module-cfelpyutils.cfelpsana">
<span id="cfelpyutils-cfelpsana-module"></span><h2>cfelpyutils.cfelpsana module<a class="headerlink" href="#module-cfelpyutils.cfelpsana" title="Permalink to this headline">¶</a></h2>
<p>Utilities based on the psana python module.</p>
<p>This module provides utilities that build on the functionality provided by the
psana python module.</p>
<dl class="function">
<dt id="cfelpyutils.cfelpsana.dirname_from_source_runs">
<code class="descclassname">cfelpyutils.cfelpsana.</code><code class="descname">dirname_from_source_runs</code><span class="sig-paren">(</span><em>source</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfelpsana.dirname_from_source_runs" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a directory name based on a psana source string.</p>
<p>Takes a psana source string (e.g exp=CXI/cxix....) and returns
a string that can be used as a subdirectory name or a prefix for files and
directories.</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>source</strong> (<em>str</em>) – a psana source string (e.g. exp=CXI/cxi....).</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><strong>dirname</strong> –
a string that can be used as a filename or a prefix .</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">str</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="cfelpyutils.cfelpsana.psana_event_inspection">
<code class="descclassname">cfelpyutils.cfelpsana.</code><code class="descname">psana_event_inspection</code><span class="sig-paren">(</span><em>source</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfelpsana.psana_event_inspection" title="Permalink to this definition">¶</a></dt>
<dd><p>Prints the structure of psana events.</p>
<p>Takes a psana source string (e.g. exp=CXI/cxix....) and inspects the
structure of the first event in the data, printing information about
the the content of the event.</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>source</strong> (<em>str</em>) – a psana source string (e.g. exp=CXI/cxix....).</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="cfelpyutils.cfelpsana.psana_obj_from_string">
<code class="descclassname">cfelpyutils.cfelpsana.</code><code class="descname">psana_obj_from_string</code><span class="sig-paren">(</span><em>name</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfelpsana.psana_obj_from_string" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts a string into a psana object type.</p>
<p>Takes a string and returns the python object type described by the string.</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>name</strong> (<em>str</em>) – a string describing a python type.</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><strong>mod</strong> –
the python type described by the string.</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">type</td>
</tr>
</tbody>
</table>
</dd></dl>
</div>
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