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!important;box-shadow:none !important;text-shadow:none !important}a[href]:after{content:" (" attr(href) ")";font-size:90%}a[href][title]:after{content:none}abbr[title]:after{content:" (" attr(title) ")"}.ir a:after,a[href^="javascript:"]:after,a[href^="#"]:after{content:""}pre,blockquote{border:1px solid #999;page-break-inside:avoid}thead{display:table-header-group}tr,img{page-break-inside:avoid}img{max-width:100% !important}@page{margin:0.5cm}p,h2,h3{orphans:3;widows:3}h1,h2,h3,h4,h5,h6{page-break-after:avoid}}</style> +<script defer src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.1.1/highlight.min.js" integrity="sha256-Uv3H6lx7dJmRfRvH8TH6kJD1TSK1aFcwgx+mdg3epi8=" crossorigin></script> +<script>window.addEventListener('DOMContentLoaded', () => hljs.initHighlighting())</script> +</head> +<body> +<main> +<article id="content"> +<header> +<h1 class="title">Module <code>pymskt.utils.main</code></h1> +</header> +<section id="section-intro"> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">import vtk +import numpy as np +import os +import errno + + + +def l2n(l): + """ + convert list to numpy array + + Parameters + ---------- + l : list + list to convert to numpy array + + Returns + ------- + numpy.ndarray + array created from inputted list `l` + """ + return np.array(l) + + +def n2l(n): + """ + convert numpy array into list + + Parameters + ---------- + n : numpy.ndarray + array to convert into list. + + Returns + ------- + list + list created from inputted numpy array `n`. + """ + return list(n) + + +def create_4x4_from_3x3(three_by_three, translation=None): + """ + Create a 4x4 transformation matrix from a 3x3 transformation matrix. + + Parameters + ---------- + three_by_three : numpy.ndarray + 3x3 transformation matrix to convert into a 4x4 + translation : numpy.ndarray, optional + translation to include in the 4x4, by default None + + Returns + ------- + numpy.ndarray + 4x4 transformation matrix created from inputted + `three_by_three` and `translation`. + """ + if len(three_by_three) == 9: + three_by_three = np.reshape(three_by_three, (3, 3)) + four_by_four = np.identity(4) + four_by_four[:3, :3] = three_by_three + + # if translation is provided, put it in the last column + if translation is not None: + four_by_four[:3, 3] = translation + return four_by_four + + +def copy_image_transform_to_mesh(mesh, image, verbose=False): + """ + Copy the transformation matrix from image to mesh. + This is the same as the function `meshTransform.copy_image_transform_to_mesh` and + `meshTransform.apply_transform`. + + Parameters + ---------- + mesh : vtk.vtkPolyData + Surface mesh to transform. + image : SimpleITK.Image + Image who's transform to apply to the `mesh`. + verbose : bool, optional + Whether or not to print the transform to console, by default False + + Returns + ------- + [type] + [description] + """ + transform_array = create_4x4_from_3x3(image.GetDirection()) + transform_array[:3, 3] = image.GetOrigin() + transform = vtk.vtkTransform() + transform.SetMatrix(transform_array.flatten()) + # transform.Translate(image.GetOrigin()) + + if verbose is True: + print(transform) + + transformer = vtk.vtkTransformPolyDataFilter() + transformer.SetTransform(transform) + transformer.SetInputData(mesh) + transformer.Update() + return transformer.GetOutput() + + +def sigma2fwhm(sigma): + """ + Converting sigma to Full Width Half Maximum (FWHM). + + Parameters + ---------- + sigma : float + The standard deviation (sigma) to convert to FWHM + + Returns + ------- + float + The FWHM that is equivalent to the inputted sigma. + """ + return sigma * np.sqrt(8 * np.log(2)) + +def fwhm2sigma(fwhm): + """ + Convert a Full Width Half Maximum into sigma. + + Parameters + ---------- + fwhm : float + The FWHM to convert to sigma. + + Returns + ------- + float + The sigma that is equivalent to the inputted FWHM. + """ + return fwhm / np.sqrt(8 * np.log(2)) + +def safely_delete_tmp_file(location, + filename): + """ + Function to safely remove a temporary file. + + Parameters + ---------- + location : str + location of the temporary file to remove + filename : str + the filename of the temporary file to delete + """ + try: + os.remove(os.path.join(location, filename)) + except OSError as exc: + if exc.errno != errno.ENOENT: + raise + pass</code></pre> +</details> +</section> +<section> +</section> +<section> +</section> +<section> +<h2 class="section-title" id="header-functions">Functions</h2> +<dl> +<dt id="pymskt.utils.main.copy_image_transform_to_mesh"><code class="name flex"> +<span>def <span class="ident">copy_image_transform_to_mesh</span></span>(<span>mesh, image, verbose=False)</span> +</code></dt> +<dd> +<div class="desc"><p>Copy the transformation matrix from image to mesh. +This is the same as the function <code>meshTransform.copy_image_transform_to_mesh</code> and +<code>meshTransform.apply_transform</code>. </p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>mesh</code></strong> : <code>vtk.vtkPolyData</code></dt> +<dd>Surface mesh to transform.</dd> +<dt><strong><code>image</code></strong> : <code>SimpleITK.Image</code></dt> +<dd>Image who's transform to apply to the <code>mesh</code>.</dd> +<dt><strong><code>verbose</code></strong> : <code>bool</code>, optional</dt> +<dd>Whether or not to print the transform to console, by default False</dd> +</dl> +<h2 id="returns">Returns</h2> +<p>[type] +[description]</p></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def copy_image_transform_to_mesh(mesh, image, verbose=False): + """ + Copy the transformation matrix from image to mesh. + This is the same as the function `meshTransform.copy_image_transform_to_mesh` and + `meshTransform.apply_transform`. + + Parameters + ---------- + mesh : vtk.vtkPolyData + Surface mesh to transform. + image : SimpleITK.Image + Image who's transform to apply to the `mesh`. + verbose : bool, optional + Whether or not to print the transform to console, by default False + + Returns + ------- + [type] + [description] + """ + transform_array = create_4x4_from_3x3(image.GetDirection()) + transform_array[:3, 3] = image.GetOrigin() + transform = vtk.vtkTransform() + transform.SetMatrix(transform_array.flatten()) + # transform.Translate(image.GetOrigin()) + + if verbose is True: + print(transform) + + transformer = vtk.vtkTransformPolyDataFilter() + transformer.SetTransform(transform) + transformer.SetInputData(mesh) + transformer.Update() + return transformer.GetOutput()</code></pre> +</details> +</dd> +<dt id="pymskt.utils.main.create_4x4_from_3x3"><code class="name flex"> +<span>def <span class="ident">create_4x4_from_3x3</span></span>(<span>three_by_three, translation=None)</span> +</code></dt> +<dd> +<div class="desc"><p>Create a 4x4 transformation matrix from a 3x3 transformation matrix. </p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>three_by_three</code></strong> : <code>numpy.ndarray</code></dt> +<dd>3x3 transformation matrix to convert into a 4x4</dd> +<dt><strong><code>translation</code></strong> : <code>numpy.ndarray</code>, optional</dt> +<dd>translation to include in the 4x4, by default None</dd> +</dl> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>numpy.ndarray</code></dt> +<dd>4x4 transformation matrix created from inputted +<code>three_by_three</code> and <code>translation</code>.</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def create_4x4_from_3x3(three_by_three, translation=None): + """ + Create a 4x4 transformation matrix from a 3x3 transformation matrix. + + Parameters + ---------- + three_by_three : numpy.ndarray + 3x3 transformation matrix to convert into a 4x4 + translation : numpy.ndarray, optional + translation to include in the 4x4, by default None + + Returns + ------- + numpy.ndarray + 4x4 transformation matrix created from inputted + `three_by_three` and `translation`. + """ + if len(three_by_three) == 9: + three_by_three = np.reshape(three_by_three, (3, 3)) + four_by_four = np.identity(4) + four_by_four[:3, :3] = three_by_three + + # if translation is provided, put it in the last column + if translation is not None: + four_by_four[:3, 3] = translation + return four_by_four</code></pre> +</details> +</dd> +<dt id="pymskt.utils.main.fwhm2sigma"><code class="name flex"> +<span>def <span class="ident">fwhm2sigma</span></span>(<span>fwhm)</span> +</code></dt> +<dd> +<div class="desc"><p>Convert a Full Width Half Maximum into sigma. </p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>fwhm</code></strong> : <code>float</code></dt> +<dd>The FWHM to convert to sigma.</dd> +</dl> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>float</code></dt> +<dd>The sigma that is equivalent to the inputted FWHM.</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def fwhm2sigma(fwhm): + """ + Convert a Full Width Half Maximum into sigma. + + Parameters + ---------- + fwhm : float + The FWHM to convert to sigma. + + Returns + ------- + float + The sigma that is equivalent to the inputted FWHM. + """ + return fwhm / np.sqrt(8 * np.log(2))</code></pre> +</details> +</dd> +<dt id="pymskt.utils.main.l2n"><code class="name flex"> +<span>def <span class="ident">l2n</span></span>(<span>l)</span> +</code></dt> +<dd> +<div class="desc"><p>convert list to numpy array</p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>l</code></strong> : <code>list</code></dt> +<dd>list to convert to numpy array</dd> +</dl> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>numpy.ndarray</code></dt> +<dd>array created from inputted list <code>l</code></dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def l2n(l): + """ + convert list to numpy array + + Parameters + ---------- + l : list + list to convert to numpy array + + Returns + ------- + numpy.ndarray + array created from inputted list `l` + """ + return np.array(l)</code></pre> +</details> +</dd> +<dt id="pymskt.utils.main.n2l"><code class="name flex"> +<span>def <span class="ident">n2l</span></span>(<span>n)</span> +</code></dt> +<dd> +<div class="desc"><p>convert numpy array into list</p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>n</code></strong> : <code>numpy.ndarray</code></dt> +<dd>array to convert into list.</dd> +</dl> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>list</code></dt> +<dd>list created from inputted numpy array <code>n</code>.</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def n2l(n): + """ + convert numpy array into list + + Parameters + ---------- + n : numpy.ndarray + array to convert into list. + + Returns + ------- + list + list created from inputted numpy array `n`. + """ + return list(n)</code></pre> +</details> +</dd> +<dt id="pymskt.utils.main.safely_delete_tmp_file"><code class="name flex"> +<span>def <span class="ident">safely_delete_tmp_file</span></span>(<span>location, filename)</span> +</code></dt> +<dd> +<div class="desc"><p>Function to safely remove a temporary file. </p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>location</code></strong> : <code>str</code></dt> +<dd>location of the temporary file to remove</dd> +<dt><strong><code>filename</code></strong> : <code>str</code></dt> +<dd>the filename of the temporary file to delete</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def safely_delete_tmp_file(location, + filename): + """ + Function to safely remove a temporary file. + + Parameters + ---------- + location : str + location of the temporary file to remove + filename : str + the filename of the temporary file to delete + """ + try: + os.remove(os.path.join(location, filename)) + except OSError as exc: + if exc.errno != errno.ENOENT: + raise + pass</code></pre> +</details> +</dd> +<dt id="pymskt.utils.main.sigma2fwhm"><code class="name flex"> +<span>def <span class="ident">sigma2fwhm</span></span>(<span>sigma)</span> +</code></dt> +<dd> +<div class="desc"><p>Converting sigma to Full Width Half Maximum (FWHM). </p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>sigma</code></strong> : <code>float</code></dt> +<dd>The standard deviation (sigma) to convert to FWHM</dd> +</dl> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>float</code></dt> +<dd>The FWHM that is equivalent to the inputted sigma.</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def sigma2fwhm(sigma): + """ + Converting sigma to Full Width Half Maximum (FWHM). + + Parameters + ---------- + sigma : float + The standard deviation (sigma) to convert to FWHM + + Returns + ------- + float + The FWHM that is equivalent to the inputted sigma. + """ + return sigma * np.sqrt(8 * np.log(2))</code></pre> +</details> +</dd> +</dl> +</section> +<section> +</section> +</article> +<nav id="sidebar"> +<h1>Index</h1> +<div class="toc"> +<ul></ul> +</div> +<ul id="index"> +<li><h3>Super-module</h3> +<ul> +<li><code><a title="pymskt.utils" href="index.html">pymskt.utils</a></code></li> +</ul> +</li> +<li><h3><a href="#header-functions">Functions</a></h3> +<ul class=""> +<li><code><a title="pymskt.utils.main.copy_image_transform_to_mesh" href="#pymskt.utils.main.copy_image_transform_to_mesh">copy_image_transform_to_mesh</a></code></li> +<li><code><a title="pymskt.utils.main.create_4x4_from_3x3" href="#pymskt.utils.main.create_4x4_from_3x3">create_4x4_from_3x3</a></code></li> +<li><code><a title="pymskt.utils.main.fwhm2sigma" href="#pymskt.utils.main.fwhm2sigma">fwhm2sigma</a></code></li> +<li><code><a title="pymskt.utils.main.l2n" href="#pymskt.utils.main.l2n">l2n</a></code></li> +<li><code><a title="pymskt.utils.main.n2l" href="#pymskt.utils.main.n2l">n2l</a></code></li> +<li><code><a title="pymskt.utils.main.safely_delete_tmp_file" href="#pymskt.utils.main.safely_delete_tmp_file">safely_delete_tmp_file</a></code></li> +<li><code><a title="pymskt.utils.main.sigma2fwhm" href="#pymskt.utils.main.sigma2fwhm">sigma2fwhm</a></code></li> +</ul> +</li> +</ul> +</nav> +</main> +<footer id="footer"> +<p>Generated by <a href="https://pdoc3.github.io/pdoc" title="pdoc: Python API documentation generator"><cite>pdoc</cite> 0.10.0</a>.</p> +</footer> +</body> +</html> \ No newline at end of file