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Copyright 2020 United Kingdom Research and Innovation
.. Copyright 2020 United Kingdom Research and Innovation
Copyright 2020 The University of Manchester
Licensed under the Apache License, Version 2.0 (the "License");
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::

Copyright 2022 United Kingdom Research and Innovation
..Copyright 2022 United Kingdom Research and Innovation
Copyright 2022 The University of Manchester
Copyright [yyyy] [name of copyright owner]

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Copyright 2019 United Kingdom Research and Innovation
.. Copyright 2019 United Kingdom Research and Innovation
Copyright 2019 The University of Manchester
Licensed under the Apache License, Version 2.0 (the "License");
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Copyright 2019 United Kingdom Research and Innovation
.. Copyright 2019 United Kingdom Research and Innovation
Copyright 2019 The University of Manchester
Licensed under the Apache License, Version 2.0 (the "License");
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Copyright 2022 United Kingdom Research and Innovation
.. Copyright 2022 United Kingdom Research and Innovation
Copyright 2022 The University of Manchester
Licensed under the Apache License, Version 2.0 (the "License");
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Copyright 2019 United Kingdom Research and Innovation
.. Copyright 2019 United Kingdom Research and Innovation
Copyright 2019 The University of Manchester
Licensed under the Apache License, Version 2.0 (the "License");
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Copyright 2019 United Kingdom Research and Innovation
.. Copyright 2019 United Kingdom Research and Innovation
Copyright 2019 The University of Manchester
Licensed under the Apache License, Version 2.0 (the "License");
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Copyright 2019 United Kingdom Research and Innovation
.. Copyright 2019 United Kingdom Research and Innovation
Copyright 2019 The University of Manchester
Licensed under the Apache License, Version 2.0 (the "License");
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Copyright 2021 United Kingdom Research and Innovation
.. Copyright 2021 United Kingdom Research and Innovation
Copyright 2021 The University of Manchester
Licensed under the Apache License, Version 2.0 (the "License");
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Copyright 2021 United Kingdom Research and Innovation
.. Copyright 2021 United Kingdom Research and Innovation
Copyright 2021 The University of Manchester
Licensed under the Apache License, Version 2.0 (the "License");
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Copyright 2021 United Kingdom Research and Innovation
.. Copyright 2021 United Kingdom Research and Innovation
Copyright 2021 The University of Manchester
Licensed under the Apache License, Version 2.0 (the "License");
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Expand Up @@ -462,27 +462,7 @@ <h3><a href="../">Table of Contents</a></h3>
<div id="searchbox"></div>
<article class="bd-article" role="main">

<blockquote>
<div><blockquote>
<div><p>Copyright 2020 United Kingdom Research and Innovation
Copyright 2020 The University of Manchester</p>
<p>Licensed under the Apache License, Version 2.0 (the “License”);
you may not use this file except in compliance with the License.
You may obtain a copy of the License at</p>
<blockquote>
<div><p><a class="reference external" href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></p>
</div></blockquote>
<p>Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an “AS IS” BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.</p>
</div></blockquote>
<p>Authors:
CIL Developers, listed at: <a class="github reference external" href="https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt">TomographicImaging/CIL</a>
Kyle Pidgeon (UKRI-STFC)</p>
</div></blockquote>
<section id="developers-guide">
<section id="developers-guide">
<h1>Developers’ Guide<a class="headerlink" href="#developers-guide" title="Permalink to this headline">#</a></h1>
<p>CIL is an Object Orientated software. It has evolved during the years and it currently does not fully adheres to the following conventions. New additions must comply with
the following.</p>
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<section id="contributions-guidelines">
<h2>Contributions guidelines<a class="headerlink" href="#contributions-guidelines" title="Permalink to this headline">#</a></h2>
<p>Make sure that each contributed file contains the following text enclosed in the appropriate comment syntax for the file format. Please replace <cite>[yyyy]</cite> and <cite>[name of copyright owner]</cite> with your own identifying information. Optionally you may add author name and email.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Copyright</span> <span class="mi">2022</span> <span class="n">United</span> <span class="n">Kingdom</span> <span class="n">Research</span> <span class="ow">and</span> <span class="n">Innovation</span>
<span class="n">Copyright</span> <span class="mi">2022</span> <span class="n">The</span> <span class="n">University</span> <span class="n">of</span> <span class="n">Manchester</span>
<span class="n">Copyright</span> <span class="p">[</span><span class="n">yyyy</span><span class="p">]</span> <span class="p">[</span><span class="n">name</span> <span class="n">of</span> <span class="n">copyright</span> <span class="n">owner</span><span class="p">]</span>

<span class="n">Author</span><span class="p">(</span><span class="n">s</span><span class="p">):</span> <span class="p">[</span><span class="n">Author</span> <span class="n">name</span><span class="p">,</span> <span class="n">Author</span> <span class="n">email</span> <span class="p">(</span><span class="n">optional</span><span class="p">)]</span>

<span class="n">Licensed</span> <span class="n">under</span> <span class="n">the</span> <span class="n">Apache</span> <span class="n">License</span><span class="p">,</span> <span class="n">Version</span> <span class="mf">2.0</span> <span class="p">(</span><span class="n">the</span> <span class="s2">&quot;License&quot;</span><span class="p">);</span>
<span class="n">you</span> <span class="n">may</span> <span class="ow">not</span> <span class="n">use</span> <span class="n">this</span> <span class="n">file</span> <span class="k">except</span> <span class="ow">in</span> <span class="n">compliance</span> <span class="k">with</span> <span class="n">the</span> <span class="n">License</span><span class="o">.</span>
<span class="n">You</span> <span class="n">may</span> <span class="n">obtain</span> <span class="n">a</span> <span class="n">copy</span> <span class="n">of</span> <span class="n">the</span> <span class="n">License</span> <span class="n">at</span>

<span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">www</span><span class="o">.</span><span class="n">apache</span><span class="o">.</span><span class="n">org</span><span class="o">/</span><span class="n">licenses</span><span class="o">/</span><span class="n">LICENSE</span><span class="o">-</span><span class="mf">2.0</span>

<span class="n">Unless</span> <span class="n">required</span> <span class="n">by</span> <span class="n">applicable</span> <span class="n">law</span> <span class="ow">or</span> <span class="n">agreed</span> <span class="n">to</span> <span class="ow">in</span> <span class="n">writing</span><span class="p">,</span> <span class="n">software</span>
<span class="n">distributed</span> <span class="n">under</span> <span class="n">the</span> <span class="n">License</span> <span class="ow">is</span> <span class="n">distributed</span> <span class="n">on</span> <span class="n">an</span> <span class="s2">&quot;AS IS&quot;</span> <span class="n">BASIS</span><span class="p">,</span>
<span class="n">WITHOUT</span> <span class="n">WARRANTIES</span> <span class="n">OR</span> <span class="n">CONDITIONS</span> <span class="n">OF</span> <span class="n">ANY</span> <span class="n">KIND</span><span class="p">,</span> <span class="n">either</span> <span class="n">express</span> <span class="ow">or</span> <span class="n">implied</span><span class="o">.</span>
<span class="n">See</span> <span class="n">the</span> <span class="n">License</span> <span class="k">for</span> <span class="n">the</span> <span class="n">specific</span> <span class="n">language</span> <span class="n">governing</span> <span class="n">permissions</span> <span class="ow">and</span>
<span class="n">limitations</span> <span class="n">under</span> <span class="n">the</span> <span class="n">License</span><span class="o">.</span>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">..</span><span class="n">Copyright</span> <span class="mi">2022</span> <span class="n">United</span> <span class="n">Kingdom</span> <span class="n">Research</span> <span class="ow">and</span> <span class="n">Innovation</span>
</pre></div>
</div>
<blockquote>
<div><p>Copyright 2022 The University of Manchester
Copyright [yyyy] [name of copyright owner]</p>
<p>Author(s): [Author name, Author email (optional)]</p>
<p>Licensed under the Apache License, Version 2.0 (the “License”);
you may not use this file except in compliance with the License.
You may obtain a copy of the License at</p>
<blockquote>
<div><p><a class="reference external" href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></p>
</div></blockquote>
<p>Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an “AS IS” BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.</p>
</div></blockquote>
</section>
</section>

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<div id="searchbox"></div>
<article class="bd-article" role="main">

<blockquote>
<div><blockquote>
<div><p>Copyright 2019 United Kingdom Research and Innovation
Copyright 2019 The University of Manchester</p>
<p>Licensed under the Apache License, Version 2.0 (the “License”);
you may not use this file except in compliance with the License.
You may obtain a copy of the License at</p>
<blockquote>
<div><p><a class="reference external" href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></p>
</div></blockquote>
<p>Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an “AS IS” BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.</p>
</div></blockquote>
<p>Authors:
CIL Developers, listed at: <a class="github reference external" href="https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt">TomographicImaging/CIL</a></p>
</div></blockquote>
<section id="framework">
<section id="framework">
<h1>Framework<a class="headerlink" href="#framework" title="Permalink to this headline">#</a></h1>
<section id="acquisitiongeometry">
<h2>AcquisitionGeometry<a class="headerlink" href="#acquisitiongeometry" title="Permalink to this headline">#</a></h2>
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<div id="searchbox"></div>
<article class="bd-article" role="main">

<blockquote>
<div><blockquote>
<div><p>Copyright 2019 United Kingdom Research and Innovation
Copyright 2019 The University of Manchester</p>
<p>Licensed under the Apache License, Version 2.0 (the “License”);
you may not use this file except in compliance with the License.
You may obtain a copy of the License at</p>
<blockquote>
<div><p><a class="reference external" href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></p>
</div></blockquote>
<p>Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an “AS IS” BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.</p>
</div></blockquote>
<p>Authors:
CIL Developers, listed at: <a class="github reference external" href="https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt">TomographicImaging/CIL</a></p>
</div></blockquote>
<section id="welcome-to-cil-s-documentation">
<section id="welcome-to-cil-s-documentation">
<h1>Welcome to CIL’s documentation!<a class="headerlink" href="#welcome-to-cil-s-documentation" title="Permalink to this headline">#</a></h1>
<p>The aim of this package is to enable rapid prototyping of optimisation-based
reconstruction problems, i.e. defining and solving different optimization problems to enforce different properties on the reconstructed image, while being
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<div id="searchbox"></div>
<article class="bd-article" role="main">

<blockquote>
<div><blockquote>
<div><p>Copyright 2022 United Kingdom Research and Innovation
Copyright 2022 The University of Manchester</p>
<p>Licensed under the Apache License, Version 2.0 (the “License”);
you may not use this file except in compliance with the License.
You may obtain a copy of the License at</p>
<blockquote>
<div><p><a class="reference external" href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></p>
</div></blockquote>
<p>Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an “AS IS” BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.</p>
</div></blockquote>
<p>Authors:
CIL Developers, listed at: <a class="github reference external" href="https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt">TomographicImaging/CIL</a></p>
</div></blockquote>
<section id="introduction">
<section id="introduction">
<h1>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">#</a></h1>
<p>The goal of the Core Imaging Library is to allow the user to simply create iterative reconstruction methods which
go beyond the standard filter back projection technique and which better suit the data characteristics.
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<div id="searchbox"></div>
<article class="bd-article" role="main">

<blockquote>
<div><blockquote>
<div><p>Copyright 2019 United Kingdom Research and Innovation
Copyright 2019 The University of Manchester</p>
<p>Licensed under the Apache License, Version 2.0 (the “License”);
you may not use this file except in compliance with the License.
You may obtain a copy of the License at</p>
<blockquote>
<div><p><a class="reference external" href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></p>
</div></blockquote>
<p>Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an “AS IS” BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.</p>
</div></blockquote>
<p>Authors:
CIL Developers, listed at: <a class="github reference external" href="https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt">TomographicImaging/CIL</a>
Kyle Pidgeon (UKRI-STFC)</p>
</div></blockquote>
<section id="read-write-acquisitiondata-and-imagedata">
<section id="read-write-acquisitiondata-and-imagedata">
<h1>Read/ write AcquisitionData and ImageData<a class="headerlink" href="#read-write-acquisitiondata-and-imagedata" title="Permalink to this headline">#</a></h1>
<section id="nexus">
<h2>NeXuS<a class="headerlink" href="#nexus" title="Permalink to this headline">#</a></h2>
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Expand Up @@ -498,26 +498,7 @@ <h3><a href="../">Table of Contents</a></h3>
<div id="searchbox"></div>
<article class="bd-article" role="main">

<blockquote>
<div><blockquote>
<div><p>Copyright 2019 United Kingdom Research and Innovation
Copyright 2019 The University of Manchester</p>
<p>Licensed under the Apache License, Version 2.0 (the “License”);
you may not use this file except in compliance with the License.
You may obtain a copy of the License at</p>
<blockquote>
<div><p><a class="reference external" href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></p>
</div></blockquote>
<p>Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an “AS IS” BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.</p>
</div></blockquote>
<p>Authors:
CIL Developers, listed at: <a class="github reference external" href="https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt">TomographicImaging/CIL</a></p>
</div></blockquote>
<section id="optimisation-framework">
<section id="optimisation-framework">
<h1>Optimisation framework<a class="headerlink" href="#optimisation-framework" title="Permalink to this headline">#</a></h1>
<p>This package allows rapid prototyping of optimisation-based reconstruction problems, i.e. defining and solving different optimization problems to enforce different properties on the reconstructed image.</p>
<p>Firstly, it provides an object-oriented framework for defining mathematical operators and functions as well a collection of useful example operators and functions. Both smooth and non-smooth functions can be used.</p>
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<div id="searchbox"></div>
<article class="bd-article" role="main">

<blockquote>
<div><blockquote>
<div><p>Copyright 2019 United Kingdom Research and Innovation
Copyright 2019 The University of Manchester</p>
<p>Licensed under the Apache License, Version 2.0 (the “License”);
you may not use this file except in compliance with the License.
You may obtain a copy of the License at</p>
<blockquote>
<div><p><a class="reference external" href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></p>
</div></blockquote>
<p>Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an “AS IS” BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.</p>
</div></blockquote>
<p>Authors:
CIL Developers, listed at: <a class="github reference external" href="https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt">TomographicImaging/CIL</a></p>
</div></blockquote>
<section id="cil-plugins">
<section id="cil-plugins">
<h1>CIL Plugins<a class="headerlink" href="#cil-plugins" title="Permalink to this headline">#</a></h1>
<section id="ccpi-regularisation">
<h2>CCPi Regularisation<a class="headerlink" href="#ccpi-regularisation" title="Permalink to this headline">#</a></h2>
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