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<!DOCTYPE html>
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<title>liger_iris_pipeline Documentation — liger_iris_pipeline v0.5.dev</title>
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<section id="liger-iris-pipeline-documentation">
<h1>liger_iris_pipeline Documentation<a class="headerlink" href="#liger-iris-pipeline-documentation" title="Link to this heading">¶</a></h1>
<p>The Liger-IRIS Data Reduction System is based on the suite of packages from Space Telescope Science Institute
used to process data from JWST and NGRST.</p>
<p>With <code class="docutils literal notranslate"><span class="pre">stpipe</span></code> and <code class="docutils literal notranslate"><span class="pre">stdatamodels</span></code> we can configure each step of a pipeline through one or more text based .INI style files,
then we provide one input FITS file or a set of multiple inputs defined in JSON (named <a class="reference external" href="https://jwst-pipeline.readthedocs.io/en/latest/jwst/associations/overview.html">Associations</a>).
Custom analysis steps and pipelines for IRIS are defined as classes in the current repository <code class="docutils literal notranslate"><span class="pre">liger_iris_pipeline</span></code></p>
<p>Then execute the pipeline from the command line using the <code class="docutils literal notranslate"><span class="pre">tmtrun</span></code> executable or using
directly the Python library.</p>
<p>The pipeline also dynamically interfaces to the <code class="docutils literal notranslate"><span class="pre">CRDS</span></code> the Calibration References Data System,
to retrieve the best calibration datasets given the metadata in the headers of the input FITS files.
The <code class="docutils literal notranslate"><span class="pre">CRDS</span></code> client can also load data from a local cache, so for now we do not have a actual
<code class="docutils literal notranslate"><span class="pre">CRDS</span></code> server and we only rely on a local cache.</p>
<p>The <code class="docutils literal notranslate"><span class="pre">CRDS</span></code> is not under our control, the Thirty Meter Telescope will deliver a database system
to replace the <code class="docutils literal notranslate"><span class="pre">CRDS</span></code> and we can adapt our code to that in the future.</p>
<section id="getting-started">
<h2>Getting Started<a class="headerlink" href="#getting-started" title="Link to this heading">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="getting-started.html">Getting Started</a><ul>
<li class="toctree-l2"><a class="reference internal" href="getting-started.html#python-environment">Python Environment</a></li>
<li class="toctree-l2"><a class="reference internal" href="getting-started.html#crds">CRDS</a></li>
<li class="toctree-l2"><a class="reference internal" href="getting-started.html#compilation-of-readout-code">Compilation of Readout Code</a></li>
<li class="toctree-l2"><a class="reference internal" href="getting-started.html#development-install">Development Install</a></li>
<li class="toctree-l2"><a class="reference internal" href="getting-started.html#run-the-unit-tests">Run the unit tests</a></li>
</ul>
</li>
</ul>
</div>
</section>
<section id="example-run">
<h2>Example run<a class="headerlink" href="#example-run" title="Link to this heading">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="example-run.html">Example pipeline execution</a><ul>
<li class="toctree-l2"><a class="reference internal" href="example-run.html#Setup-CRDS">Setup CRDS</a></li>
<li class="toctree-l2"><a class="reference internal" href="example-run.html#Get-input-simulations">Get input simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="example-run.html#Preprocess-the-flat-frame">Preprocess the flat frame</a></li>
<li class="toctree-l2"><a class="reference internal" href="example-run.html#Configure-the-image-processing-pipeline">Configure the image processing pipeline</a></li>
<li class="toctree-l2"><a class="reference internal" href="example-run.html#Define-the-input-data">Define the input data</a></li>
<li class="toctree-l2"><a class="reference internal" href="example-run.html#Execute-the-pipeline-from-the-command-line">Execute the pipeline from the command line</a></li>
<li class="toctree-l2"><a class="reference internal" href="example-run.html#Plot-the-reduced-frame">Plot the reduced frame</a></li>
</ul>
</li>
</ul>
</div>
</section>
<section id="design">
<h2>Design<a class="headerlink" href="#design" title="Link to this heading">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="design.html">IRIS Data Reduction System design</a></li>
<li class="toctree-l1"><a class="reference internal" href="design.html#purpose">Purpose</a></li>
<li class="toctree-l1"><a class="reference internal" href="design.html#software-infrastructure">Software infrastructure</a></li>
<li class="toctree-l1"><a class="reference internal" href="design.html#processing-levels-and-data-product-stages">Processing levels and data product stages</a></li>
<li class="toctree-l1"><a class="reference internal" href="design.html#file-format">File format</a></li>
<li class="toctree-l1"><a class="reference internal" href="design.html#example-run">Example run</a></li>
<li class="toctree-l1"><a class="reference internal" href="design.html#access-calibration-files-via-the-calibration-reference-data-system-crds">Access calibration files via the Calibration Reference Data System (CRDS)</a></li>
<li class="toctree-l1"><a class="reference internal" href="design.html#metadata">Metadata</a></li>
</ul>
</div>
</section>
<section id="calibration-and-crds">
<h2>Calibration and CRDS<a class="headerlink" href="#calibration-and-crds" title="Link to this heading">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="calibration-database.html">Calibration</a><ul>
<li class="toctree-l2"><a class="reference internal" href="calibration-database.html#calibration-files">Calibration files</a></li>
<li class="toctree-l2"><a class="reference internal" href="calibration-database.html#access-calibration-files-via-the-calibration-reference-data-system-crds">Access calibration files via the Calibration Reference Data System (CRDS)</a></li>
</ul>
</li>
</ul>
</div>
</section>
<section id="algorithms">
<h2>Algorithms<a class="headerlink" href="#algorithms" title="Link to this heading">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="available-steps.html">Available algorithms</a></li>
<li class="toctree-l1"><a class="reference internal" href="algorithms.html">Algorithms</a></li>
<li class="toctree-l1"><a class="reference internal" href="algorithms.html#imager-algorithms">Imager Algorithms</a></li>
<li class="toctree-l1"><a class="reference internal" href="algorithms.html#ifs-algorithms">IFS Algorithms</a></li>
<li class="toctree-l1"><a class="reference internal" href="algorithms.html#advanced-algorithms">Advanced Algorithms</a></li>
<li class="toctree-l1"><a class="reference internal" href="algorithms.html#calibration-algorithms">Calibration algorithms</a></li>
</ul>
</div>
</section>
<section id="subarrays">
<h2>Subarrays<a class="headerlink" href="#subarrays" title="Link to this heading">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="subarrays.html">Support for subarrays</a></li>
</ul>
</div>
</section>
<section id="reference-api">
<h2>Reference/API<a class="headerlink" href="#reference-api" title="Link to this heading">¶</a></h2>
<section id="module-liger_iris_pipeline">
<span id="liger-iris-pipeline-package"></span><h3>liger_iris_pipeline Package<a class="headerlink" href="#module-liger_iris_pipeline" title="Link to this heading">¶</a></h3>
<section id="functions">
<h4>Functions<a class="headerlink" href="#functions" title="Link to this heading">¶</a></h4>
<table class="autosummary longtable docutils align-default">
<tbody>
<tr class="row-odd"><td><p><a class="reference internal" href="api/liger_iris_pipeline.monkeypatch_jwst_datamodels.html#liger_iris_pipeline.monkeypatch_jwst_datamodels" title="liger_iris_pipeline.monkeypatch_jwst_datamodels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">monkeypatch_jwst_datamodels</span></code></a>()</p></td>
<td><p></p></td>
</tr>
</tbody>
</table>
</section>
<section id="classes">
<h4>Classes<a class="headerlink" href="#classes" title="Link to this heading">¶</a></h4>
<table class="autosummary longtable docutils align-default">
<tbody>
<tr class="row-odd"><td><p><a class="reference internal" href="api/liger_iris_pipeline.AssignWcsStep.html#liger_iris_pipeline.AssignWcsStep" title="liger_iris_pipeline.AssignWcsStep"><code class="xref py py-obj docutils literal notranslate"><span class="pre">AssignWcsStep</span></code></a>([name, parent, config_file, ...])</p></td>
<td><p>AssignWcsStep: Create a gWCS object and store it in <code class="docutils literal notranslate"><span class="pre">Model.meta</span></code>.</p></td>
</tr>
<tr class="row-even"><td><p><a class="reference internal" href="api/liger_iris_pipeline.BackgroundStep.html#liger_iris_pipeline.BackgroundStep" title="liger_iris_pipeline.BackgroundStep"><code class="xref py py-obj docutils literal notranslate"><span class="pre">BackgroundStep</span></code></a>([name, parent, config_file, ...])</p></td>
<td><p>BackgroundStep: Subtract background exposures from target exposures.</p></td>
</tr>
<tr class="row-odd"><td><p><a class="reference internal" href="api/liger_iris_pipeline.DQInitStep.html#liger_iris_pipeline.DQInitStep" title="liger_iris_pipeline.DQInitStep"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DQInitStep</span></code></a>([name, parent, config_file, ...])</p></td>
<td><p>Initialize the Data Quality extension from the mask reference file.</p></td>
</tr>
<tr class="row-even"><td><p><a class="reference internal" href="api/liger_iris_pipeline.DarkCurrentStep.html#liger_iris_pipeline.DarkCurrentStep" title="liger_iris_pipeline.DarkCurrentStep"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DarkCurrentStep</span></code></a>([name, parent, config_file, ...])</p></td>
<td><p>DarkCurrentStep: Performs dark current correction by subtracting dark current reference data from the input science data model.</p></td>
</tr>
<tr class="row-odd"><td><p><a class="reference internal" href="api/liger_iris_pipeline.FlatFieldStep.html#liger_iris_pipeline.FlatFieldStep" title="liger_iris_pipeline.FlatFieldStep"><code class="xref py py-obj docutils literal notranslate"><span class="pre">FlatFieldStep</span></code></a>([name, parent, config_file, ...])</p></td>
<td><p>Flat-field a science image using a flatfield reference image.</p></td>
</tr>
<tr class="row-even"><td><p><a class="reference internal" href="api/liger_iris_pipeline.MergeSubarraysStep.html#liger_iris_pipeline.MergeSubarraysStep" title="liger_iris_pipeline.MergeSubarraysStep"><code class="xref py py-obj docutils literal notranslate"><span class="pre">MergeSubarraysStep</span></code></a>([name, parent, ...])</p></td>
<td><p>ParseSubarrayMapStep: Parse a subarray map extension, if available, and create header metadata and data quality flag accordingly.</p></td>
</tr>
<tr class="row-odd"><td><p><a class="reference internal" href="api/liger_iris_pipeline.NormalizeStep.html#liger_iris_pipeline.NormalizeStep" title="liger_iris_pipeline.NormalizeStep"><code class="xref py py-obj docutils literal notranslate"><span class="pre">NormalizeStep</span></code></a>([name, parent, config_file, ...])</p></td>
<td><p>NormalizeStep: Normalize a frame by dividing by its own mean, median or mode</p></td>
</tr>
<tr class="row-even"><td><p><a class="reference internal" href="api/liger_iris_pipeline.ParseSubarrayMapStep.html#liger_iris_pipeline.ParseSubarrayMapStep" title="liger_iris_pipeline.ParseSubarrayMapStep"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ParseSubarrayMapStep</span></code></a>([name, parent, ...])</p></td>
<td><p>ParseSubarrayMapStep: Parse a subarray map extension, if available, and create header metadata and data quality flag accordingly</p></td>
</tr>
<tr class="row-odd"><td><p><a class="reference internal" href="api/liger_iris_pipeline.ProcessFlatfieldL2.html#liger_iris_pipeline.ProcessFlatfieldL2" title="liger_iris_pipeline.ProcessFlatfieldL2"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ProcessFlatfieldL2</span></code></a>(*args, **kwargs)</p></td>
<td><p>ProcessFlatfieldL2: Remove dark and normalize exposure to create a flat field to be later added to the CRDS.</p></td>
</tr>
<tr class="row-even"><td><p><a class="reference internal" href="api/liger_iris_pipeline.ProcessImagerL2Pipeline.html#liger_iris_pipeline.ProcessImagerL2Pipeline" title="liger_iris_pipeline.ProcessImagerL2Pipeline"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ProcessImagerL2Pipeline</span></code></a>(*args, **kwargs)</p></td>
<td><p>ProcessImagerL2Pipeline: Processes JWST imaging-mode slope data from Level-2a to Level-2b.</p></td>
</tr>
<tr class="row-odd"><td><p><a class="reference internal" href="api/liger_iris_pipeline.ROPPipeline.html#liger_iris_pipeline.ROPPipeline" title="liger_iris_pipeline.ROPPipeline"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ROPPipeline</span></code></a>(*args, **kwargs)</p></td>
<td><p>Detector1Pipeline for IRIS</p></td>
</tr>
<tr class="row-even"><td><p><a class="reference internal" href="api/liger_iris_pipeline.SubtractImagesStep.html#liger_iris_pipeline.SubtractImagesStep" title="liger_iris_pipeline.SubtractImagesStep"><code class="xref py py-obj docutils literal notranslate"><span class="pre">SubtractImagesStep</span></code></a>([name, parent, ...])</p></td>
<td><p>SubtractImagesStep: Subtract two exposures from one another to accomplish background subtraction.</p></td>
</tr>
<tr class="row-odd"><td><p><a class="reference internal" href="api/liger_iris_pipeline.UnsupportedPythonError.html#liger_iris_pipeline.UnsupportedPythonError" title="liger_iris_pipeline.UnsupportedPythonError"><code class="xref py py-obj docutils literal notranslate"><span class="pre">UnsupportedPythonError</span></code></a></p></td>
<td><p></p></td>
</tr>
</tbody>
</table>
</section>
<section id="class-inheritance-diagram">
<h4>Class Inheritance Diagram<a class="headerlink" href="#class-inheritance-diagram" title="Link to this heading">¶</a></h4>
<div class="graphviz"><object data="_images/inheritance-1629473b8671124fcbbbd99e7e066a198cb2004a.svg" type="image/svg+xml" class="inheritance graphviz">
<p class="warning">Inheritance diagram of liger_iris_pipeline.assign_wcs.assign_wcs_step.AssignWcsStep, liger_iris_pipeline.background.background_step.BackgroundStep, liger_iris_pipeline.dq_init.dq_init_step.DQInitStep, liger_iris_pipeline.dark_current.dark_current_step.DarkCurrentStep, liger_iris_pipeline.flatfield.flat_field_step.FlatFieldStep, liger_iris_pipeline.merge_subarrays.merge_subarrays.MergeSubarraysStep, liger_iris_pipeline.normalize.normalize_step.NormalizeStep, liger_iris_pipeline.parse_subarray_map.parse_subarray_map_step.ParseSubarrayMapStep, liger_iris_pipeline.pipeline.preprocess_flatfield.ProcessFlatfieldL2, liger_iris_pipeline.pipeline.image2.ProcessImagerL2Pipeline, liger_iris_pipeline.pipeline.rop.ROPPipeline, liger_iris_pipeline.background.subtract_images_step.SubtractImagesStep, liger_iris_pipeline.UnsupportedPythonError</p></object></div>
</section>
</section>
</section>
</section>
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<div class="sphinxsidebarwrapper"><h3>Page Contents</h3>
<ul>
<li><a class="reference internal" href="#">liger_iris_pipeline Documentation</a><ul>
<li><a class="reference internal" href="#getting-started">Getting Started</a></li>
<li><a class="reference internal" href="#example-run">Example run</a></li>
<li><a class="reference internal" href="#design">Design</a></li>
<li><a class="reference internal" href="#calibration-and-crds">Calibration and CRDS</a></li>
<li><a class="reference internal" href="#algorithms">Algorithms</a></li>
<li><a class="reference internal" href="#subarrays">Subarrays</a></li>
<li><a class="reference internal" href="#reference-api">Reference/API</a><ul>
<li><a class="reference internal" href="#module-liger_iris_pipeline">liger_iris_pipeline Package</a><ul>
<li><a class="reference internal" href="#functions">Functions</a></li>
<li><a class="reference internal" href="#classes">Classes</a></li>
<li><a class="reference internal" href="#class-inheritance-diagram">Class Inheritance Diagram</a></li>
</ul>
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