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<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>
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