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+</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):
+    &#34;&#34;&#34;
+    convert list to numpy array
+    Parameters
+    ----------
+    l : list
+        list to convert to numpy array
+    Returns
+    -------
+    numpy.ndarray
+        array created from inputted list `l`
+    &#34;&#34;&#34;
+    return np.array(l)
+def n2l(n):
+    &#34;&#34;&#34;
+    convert numpy array into list
+    Parameters
+    ----------
+    n : numpy.ndarray
+        array to convert into list.
+    Returns
+    -------
+    list
+        list created from inputted numpy array `n`.
+    &#34;&#34;&#34;
+    return list(n)
+def create_4x4_from_3x3(three_by_three, translation=None):
+    &#34;&#34;&#34;
+    Create a 4x4 transformation matrix from a 3x3 transformation matrix.
+    Parameters
+    ----------
+    three_by_three : numpy.ndarray
+x3 transformation matrix to convert into a 4x4
+    translation : numpy.ndarray, optional
+        translation to include in the 4x4, by default None
+    Returns
+    -------
+    numpy.ndarray
+x4 transformation matrix created from inputted
+        `three_by_three` and `translation`.
+    &#34;&#34;&#34;
+    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):
+    &#34;&#34;&#34;
+    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&#39;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]
+    &#34;&#34;&#34;
+    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):
+    &#34;&#34;&#34;
+    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.
+    &#34;&#34;&#34;
+    return sigma * np.sqrt(8 * np.log(2))
+def fwhm2sigma(fwhm):
+    &#34;&#34;&#34;
+    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.
+    &#34;&#34;&#34;
+    return fwhm / np.sqrt(8 * np.log(2))
+def safely_delete_tmp_file(location,
+                           filename):
+    &#34;&#34;&#34;
+    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
+    &#34;&#34;&#34;
+    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> :&ensp;<code>vtk.vtkPolyData</code></dt>
+<dd>Surface mesh to transform.</dd>
+<dt><strong><code>image</code></strong> :&ensp;<code>SimpleITK.Image</code></dt>
+<dd>Image who's transform to apply to the <code>mesh</code>.</dd>
+<dt><strong><code>verbose</code></strong> :&ensp;<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):
+    &#34;&#34;&#34;
+    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&#39;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]
+    &#34;&#34;&#34;
+    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> :&ensp;<code>numpy.ndarray</code></dt>
+<dd>3x3 transformation matrix to convert into a 4x4</dd>
+<dt><strong><code>translation</code></strong> :&ensp;<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):
+    &#34;&#34;&#34;
+    Create a 4x4 transformation matrix from a 3x3 transformation matrix.
+    Parameters
+    ----------
+    three_by_three : numpy.ndarray
+x3 transformation matrix to convert into a 4x4
+    translation : numpy.ndarray, optional
+        translation to include in the 4x4, by default None
+    Returns
+    -------
+    numpy.ndarray
+x4 transformation matrix created from inputted
+        `three_by_three` and `translation`.
+    &#34;&#34;&#34;
+    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> :&ensp;<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):
+    &#34;&#34;&#34;
+    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.
+    &#34;&#34;&#34;
+    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> :&ensp;<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):
+    &#34;&#34;&#34;
+    convert list to numpy array
+    Parameters
+    ----------
+    l : list
+        list to convert to numpy array
+    Returns
+    -------
+    numpy.ndarray
+        array created from inputted list `l`
+    &#34;&#34;&#34;
+    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> :&ensp;<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):
+    &#34;&#34;&#34;
+    convert numpy array into list
+    Parameters
+    ----------
+    n : numpy.ndarray
+        array to convert into list.
+    Returns
+    -------
+    list
+        list created from inputted numpy array `n`.
+    &#34;&#34;&#34;
+    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> :&ensp;<code>str</code></dt>
+<dd>location of the temporary file to remove</dd>
+<dt><strong><code>filename</code></strong> :&ensp;<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):
+    &#34;&#34;&#34;
+    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
+    &#34;&#34;&#34;
+    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> :&ensp;<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):
+    &#34;&#34;&#34;
+    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.
+    &#34;&#34;&#34;
+    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>
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+</html>