Merge pull request #37 from qurit/lukework

Update Documentation, Remove Device as Argument, Fix HU2Mu for DICOM Loading

docs/build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 72bf9ae685372f8bf6cc3975765c68e5
+config: 6b4e5210114709da477b15a4da7ff9db
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/.doctrees/nbsphinx/notebooks/conventions.ipynb

@@ -81,9 +81,9 @@
     "\n",
     "PyTomography is built around two fundamental operations used in image reconstruction: **Forward Projection** and **Back Projection**.\n",
     "\n",
-    "* **Forward Projection**: Takes something in object space $\\mathbb{U}$ and converts it to something in image space $\\mathbb{V}$ using the system matrix: $b_j = \\sum_{i} H_{ji} a_i$ (or $b = Ha$). This operation is implemented in the class `ForwardProjectionNet` from `pytomography.projections`. \n",
+    "* **Forward Projection**: Takes something in object space $\\mathbb{U}$ and converts it to something in image space $\\mathbb{V}$ using the system matrix: $b_j = \\sum_{i} H_{ji} a_i$ (or $b = Ha$). This operation is implemented by the `forward` method of the `SystemMatrix` class.\n",
     "\n",
-    "* **Back Projection**: Takes something in image space $\\mathbb{V}$ and converts it to something in object space $\\mathbb{U}$ using the system matrix: $a_i' = \\frac{1}{\\sum_j H_{ji}}\\sum_{j} H_{ji} b_j$ (or $a'=\\frac{1}{H^T \\vec{1}}H^T b$). This operation is implemented in the class `BackProjectionNet` from `pytomography.projections`. \n",
+    "* **Back Projection**: Takes something in image space $\\mathbb{V}$ and converts it to something in object space $\\mathbb{U}$ using the system matrix: $a_i' = \\frac{1}{\\sum_j H_{ji}}\\sum_{j} H_{ji} b_j$ (or $a'=\\frac{1}{H^T \\vec{1}}H^T b$). This operation is implemented by the `backward` method of the `SystemMatrix` class. \n",
     "\n",
     "It's worth noting that $a_i$ and $b_j$ don't have to represent physical objects or images. In the case of the OSEM algorithm, it is the ratio of two quantities that is forward projected: such a ratio does not represent a physical object.\n",
     "\n",
@@ -104,10 +104,7 @@
     "\n",
     "**Example:**: Modeling of a PET scanner (2D mode, no scatter) can be written as $H_{\\text{PET}} = \\sum_{\\theta} B_1(\\theta) B_2(\\theta) P(\\theta) \\otimes \\hat{\\theta}$. The operator $B_2(\\theta)$ implements atteunation modeling in PET. Unlike SPECT, where attenuation modeling is done in object space, it is implemented for PET in image space due to the fact that the probability of detection is adjusted by the same value for each LOR in PET. The matrix $B_1$ implements PSF blurring: unlike in SPECT, it is assumed that the blurring is constant as a function from distance to the scanner, and thus the operation can be implemented in image space. The matrix $P(\\theta)$ sums all the voxels together in the direction of the scanner, turning a 3D object into a 2D projection.\n",
     "\n",
-    "Operations $A_i$ and $B_i$ are referred to as mappings: many predefined mappings are located in the `mappings` folder. \n",
-    "\n",
-    "(INSERT TUTORIAL SHOWING HOW TO MAKE MAPPING).\n",
-    "\n"
+    "Operations $A_i$ and $B_i$ are referred to as **transforms**: many predefined transforms are located in the `transforms` folder. "
    ]
   },
   {

docs/build/html/_modules/index.html

@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" />
 
     <!-- Generated with Sphinx 6.1.3 and Furo 2022.12.07 -->
-        <title>Overview: module code - PyTomography 0.3.3 documentation</title>
+        <title>Overview: module code - PyTomography 0.4.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?digest=91d0f0d1c444bdcb17a68e833c7a53903343c195" />
     <link rel="stylesheet" type="text/css" href="../_static/graphviz.css" />
@@ -123,7 +123,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">PyTomography 0.3.3 documentation</div></a>
+      <a href="../index.html"><div class="brand">PyTomography 0.4.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
-  <span class="sidebar-brand-text">PyTomography 0.3.3 documentation</span>
+  <span class="sidebar-brand-text">PyTomography 0.4.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -173,31 +173,34 @@
 <li class="toctree-l4"><a class="reference internal" href="../autoapi/pytomography/io/simind/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.io.simind</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l3 has-children"><a class="reference internal" href="../autoapi/pytomography/mappings/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.mappings</span></code></a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" role="switch" type="checkbox"/><label for="toctree-checkbox-6"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l4 has-children"><a class="reference internal" href="../autoapi/pytomography/mappings/SPECT/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.mappings.SPECT</span></code></a><input class="toctree-checkbox" id="toctree-checkbox-7" name="toctree-checkbox-7" role="switch" type="checkbox"/><label for="toctree-checkbox-7"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l5"><a class="reference internal" href="../autoapi/pytomography/mappings/SPECT/atteunation/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.mappings.SPECT.atteunation</span></code></a></li>
-<li class="toctree-l5"><a class="reference internal" href="../autoapi/pytomography/mappings/SPECT/psf/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.mappings.SPECT.psf</span></code></a></li>
+<li class="toctree-l3 has-children"><a class="reference internal" href="../autoapi/pytomography/metadata/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.metadata</span></code></a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" role="switch" type="checkbox"/><label for="toctree-checkbox-6"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l4"><a class="reference internal" href="../autoapi/pytomography/metadata/metadata/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.metadata.metadata</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l4"><a class="reference internal" href="../autoapi/pytomography/mappings/mapping/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.mappings.mapping</span></code></a></li>
+<li class="toctree-l3 has-children"><a class="reference internal" href="../autoapi/pytomography/priors/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.priors</span></code></a><input class="toctree-checkbox" id="toctree-checkbox-7" name="toctree-checkbox-7" role="switch" type="checkbox"/><label for="toctree-checkbox-7"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l4"><a class="reference internal" href="../autoapi/pytomography/priors/nearest_neighbour/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.priors.nearest_neighbour</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../autoapi/pytomography/priors/prior/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.priors.prior</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l3 has-children"><a class="reference internal" href="../autoapi/pytomography/metadata/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.metadata</span></code></a><input class="toctree-checkbox" id="toctree-checkbox-8" name="toctree-checkbox-8" role="switch" type="checkbox"/><label for="toctree-checkbox-8"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l4"><a class="reference internal" href="../autoapi/pytomography/metadata/metadata/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.metadata.metadata</span></code></a></li>
+<li class="toctree-l3 has-children"><a class="reference internal" href="../autoapi/pytomography/projections/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.projections</span></code></a><input class="toctree-checkbox" id="toctree-checkbox-8" name="toctree-checkbox-8" role="switch" type="checkbox"/><label for="toctree-checkbox-8"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l4"><a class="reference internal" href="../autoapi/pytomography/projections/system_matrix/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.projections.system_matrix</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l3 has-children"><a class="reference internal" href="../autoapi/pytomography/priors/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.priors</span></code></a><input class="toctree-checkbox" id="toctree-checkbox-9" name="toctree-checkbox-9" role="switch" type="checkbox"/><label for="toctree-checkbox-9"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l4"><a class="reference internal" href="../autoapi/pytomography/priors/nearest_neighbour/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.priors.nearest_neighbour</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../autoapi/pytomography/priors/prior/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.priors.prior</span></code></a></li>
+<li class="toctree-l3 has-children"><a class="reference internal" href="../autoapi/pytomography/transforms/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.transforms</span></code></a><input class="toctree-checkbox" id="toctree-checkbox-9" name="toctree-checkbox-9" role="switch" type="checkbox"/><label for="toctree-checkbox-9"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l4 has-children"><a class="reference internal" href="../autoapi/pytomography/transforms/PET/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.transforms.PET</span></code></a><input class="toctree-checkbox" id="toctree-checkbox-10" name="toctree-checkbox-10" role="switch" type="checkbox"/><label for="toctree-checkbox-10"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l5"><a class="reference internal" href="../autoapi/pytomography/transforms/PET/attenuation/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.transforms.PET.attenuation</span></code></a></li>
+<li class="toctree-l5"><a class="reference internal" href="../autoapi/pytomography/transforms/PET/psf/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.transforms.PET.psf</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l4 has-children"><a class="reference internal" href="../autoapi/pytomography/transforms/SPECT/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.transforms.SPECT</span></code></a><input class="toctree-checkbox" id="toctree-checkbox-11" name="toctree-checkbox-11" role="switch" type="checkbox"/><label for="toctree-checkbox-11"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l5"><a class="reference internal" href="../autoapi/pytomography/transforms/SPECT/atteunation/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.transforms.SPECT.atteunation</span></code></a></li>
+<li class="toctree-l5"><a class="reference internal" href="../autoapi/pytomography/transforms/SPECT/psf/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.transforms.SPECT.psf</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l3 has-children"><a class="reference internal" href="../autoapi/pytomography/projections/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.projections</span></code></a><input class="toctree-checkbox" id="toctree-checkbox-10" name="toctree-checkbox-10" role="switch" type="checkbox"/><label for="toctree-checkbox-10"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l4"><a class="reference internal" href="../autoapi/pytomography/projections/back_projection/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.projections.back_projection</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../autoapi/pytomography/projections/forward_projection/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.projections.forward_projection</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../autoapi/pytomography/projections/projection/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.projections.projection</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../autoapi/pytomography/transforms/transform/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.transforms.transform</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l3 has-children"><a class="reference internal" href="../autoapi/pytomography/utils/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.utils</span></code></a><input class="toctree-checkbox" id="toctree-checkbox-11" name="toctree-checkbox-11" role="switch" type="checkbox"/><label for="toctree-checkbox-11"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l3 has-children"><a class="reference internal" href="../autoapi/pytomography/utils/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.utils</span></code></a><input class="toctree-checkbox" id="toctree-checkbox-12" name="toctree-checkbox-12" role="switch" type="checkbox"/><label for="toctree-checkbox-12"><div class="visually-hidden">Toggle child pages in navigation</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
 <li class="toctree-l4"><a class="reference internal" href="../autoapi/pytomography/utils/helper_functions/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pytomography.utils.helper_functions</span></code></a></li>
 </ul>
 </li>
@@ -244,15 +247,15 @@ <h1>All modules for which code is available</h1>
 <li><a href="pytomography/callbacks/callback.html">pytomography.callbacks.callback</a></li>
 <li><a href="pytomography/io/dicom.html">pytomography.io.dicom</a></li>
 <li><a href="pytomography/io/simind.html">pytomography.io.simind</a></li>
-<li><a href="pytomography/mappings/SPECT/atteunation.html">pytomography.mappings.SPECT.atteunation</a></li>
-<li><a href="pytomography/mappings/SPECT/psf.html">pytomography.mappings.SPECT.psf</a></li>
-<li><a href="pytomography/mappings/mapping.html">pytomography.mappings.mapping</a></li>
 <li><a href="pytomography/metadata/metadata.html">pytomography.metadata.metadata</a></li>
 <li><a href="pytomography/priors/nearest_neighbour.html">pytomography.priors.nearest_neighbour</a></li>
 <li><a href="pytomography/priors/prior.html">pytomography.priors.prior</a></li>
-<li><a href="pytomography/projections/back_projection.html">pytomography.projections.back_projection</a></li>
-<li><a href="pytomography/projections/forward_projection.html">pytomography.projections.forward_projection</a></li>
-<li><a href="pytomography/projections/projection.html">pytomography.projections.projection</a></li>
+<li><a href="pytomography/projections/system_matrix.html">pytomography.projections.system_matrix</a></li>
+<li><a href="pytomography/transforms/PET/attenuation.html">pytomography.transforms.PET.attenuation</a></li>
+<li><a href="pytomography/transforms/PET/psf.html">pytomography.transforms.PET.psf</a></li>
+<li><a href="pytomography/transforms/SPECT/atteunation.html">pytomography.transforms.SPECT.atteunation</a></li>
+<li><a href="pytomography/transforms/SPECT/psf.html">pytomography.transforms.SPECT.psf</a></li>
+<li><a href="pytomography/transforms/transform.html">pytomography.transforms.transform</a></li>
 <li><a href="pytomography/utils/helper_functions.html">pytomography.utils.helper_functions</a></li>
 </ul></ul>
         </article>