Datasets
Models
Diff of
/docs/mesh/meshTransform.html
[000000]
..
[9173ee]
Switch to side-by-side view
--- a +++ b/docs/mesh/meshTransform.html @@ -0,0 +1,1068 @@ +<!doctype html> +<html lang="en"> +<head> +<meta charset="utf-8"> +<meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" /> +<meta name="generator" content="pdoc 0.10.0" /> +<title>pymskt.mesh.meshTransform API documentation</title> +<meta name="description" content="" /> +<link rel="preload stylesheet" as="style" href="https://cdnjs.cloudflare.com/ajax/libs/10up-sanitize.css/11.0.1/sanitize.min.css" integrity="sha256-PK9q560IAAa6WVRRh76LtCaI8pjTJ2z11v0miyNNjrs=" crossorigin> +<link rel="preload stylesheet" as="style" href="https://cdnjs.cloudflare.com/ajax/libs/10up-sanitize.css/11.0.1/typography.min.css" integrity="sha256-7l/o7C8jubJiy74VsKTidCy1yBkRtiUGbVkYBylBqUg=" crossorigin> +<link rel="stylesheet preload" as="style" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.1.1/styles/github.min.css" crossorigin> +<style>:root{--highlight-color:#fe9}.flex{display:flex !important}body{line-height:1.5em}#content{padding:20px}#sidebar{padding:30px;overflow:hidden}#sidebar > *:last-child{margin-bottom:2cm}.http-server-breadcrumbs{font-size:130%;margin:0 0 15px 0}#footer{font-size:.75em;padding:5px 30px;border-top:1px solid #ddd;text-align:right}#footer p{margin:0 0 0 1em;display:inline-block}#footer p:last-child{margin-right:30px}h1,h2,h3,h4,h5{font-weight:300}h1{font-size:2.5em;line-height:1.1em}h2{font-size:1.75em;margin:1em 0 .50em 0}h3{font-size:1.4em;margin:25px 0 10px 0}h4{margin:0;font-size:105%}h1:target,h2:target,h3:target,h4:target,h5:target,h6:target{background:var(--highlight-color);padding:.2em 0}a{color:#058;text-decoration:none;transition:color .3s ease-in-out}a:hover{color:#e82}.title code{font-weight:bold}h2[id^="header-"]{margin-top:2em}.ident{color:#900}pre code{background:#f8f8f8;font-size:.8em;line-height:1.4em}code{background:#f2f2f1;padding:1px 4px;overflow-wrap:break-word}h1 code{background:transparent}pre{background:#f8f8f8;border:0;border-top:1px solid #ccc;border-bottom:1px solid #ccc;margin:1em 0;padding:1ex}#http-server-module-list{display:flex;flex-flow:column}#http-server-module-list div{display:flex}#http-server-module-list dt{min-width:10%}#http-server-module-list p{margin-top:0}.toc ul,#index{list-style-type:none;margin:0;padding:0}#index code{background:transparent}#index h3{border-bottom:1px solid #ddd}#index ul{padding:0}#index h4{margin-top:.6em;font-weight:bold}@media (min-width:200ex){#index .two-column{column-count:2}}@media (min-width:300ex){#index .two-column{column-count:3}}dl{margin-bottom:2em}dl dl:last-child{margin-bottom:4em}dd{margin:0 0 1em 3em}#header-classes + dl > dd{margin-bottom:3em}dd dd{margin-left:2em}dd p{margin:10px 0}.name{background:#eee;font-weight:bold;font-size:.85em;padding:5px 10px;display:inline-block;min-width:40%}.name:hover{background:#e0e0e0}dt:target .name{background:var(--highlight-color)}.name > span:first-child{white-space:nowrap}.name.class > span:nth-child(2){margin-left:.4em}.inherited{color:#999;border-left:5px solid #eee;padding-left:1em}.inheritance em{font-style:normal;font-weight:bold}.desc h2{font-weight:400;font-size:1.25em}.desc h3{font-size:1em}.desc dt code{background:inherit}.source summary,.git-link-div{color:#666;text-align:right;font-weight:400;font-size:.8em;text-transform:uppercase}.source summary > *{white-space:nowrap;cursor:pointer}.git-link{color:inherit;margin-left:1em}.source pre{max-height:500px;overflow:auto;margin:0}.source pre code{font-size:12px;overflow:visible}.hlist{list-style:none}.hlist li{display:inline}.hlist li:after{content:',\2002'}.hlist li:last-child:after{content:none}.hlist .hlist{display:inline;padding-left:1em}img{max-width:100%}td{padding:0 .5em}.admonition{padding:.1em .5em;margin-bottom:1em}.admonition-title{font-weight:bold}.admonition.note,.admonition.info,.admonition.important{background:#aef}.admonition.todo,.admonition.versionadded,.admonition.tip,.admonition.hint{background:#dfd}.admonition.warning,.admonition.versionchanged,.admonition.deprecated{background:#fd4}.admonition.error,.admonition.danger,.admonition.caution{background:lightpink}</style> +<style media="screen and (min-width: 700px)">@media screen and (min-width:700px){#sidebar{width:30%;height:100vh;overflow:auto;position:sticky;top:0}#content{width:70%;max-width:100ch;padding:3em 4em;border-left:1px solid #ddd}pre code{font-size:1em}.item .name{font-size:1em}main{display:flex;flex-direction:row-reverse;justify-content:flex-end}.toc ul ul,#index ul{padding-left:1.5em}.toc > ul > li{margin-top:.5em}}</style> +<style media="print">@media print{#sidebar h1{page-break-before:always}.source{display:none}}@media print{*{background:transparent !important;color:#000 !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.mesh.meshTransform</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 SimpleITK as sitk +from pymskt.mesh.utils import vtk_deep_copy +from pymskt.utils import create_4x4_from_3x3 + +# import pyfocusr + +def create_transform(transform_matrix): + """ + Turn 4x4 matrix into a vtkTransform + + Parameters + ---------- + transform_matrix : numpy.ndarray + 4x4 transformation matrix to be converted to transform + """ + + if np.allclose(transform_matrix.shape, [4, 4]): + pass + else: + raise Exception('transform matrix should be 4x4 matrix') + transform = vtk.vtkTransform() + transform.SetMatrix(transform_matrix.flatten()) + return transform + + +def apply_transform(source, transform): + """ + Apply transform to surface mesh + + Parameters + ---------- + source : vtk.vtkPolyData + The source surface mesh to apply transformation (`transform`) to. + transform : vtk.vtkTransform + The transofrm to apply to the surface mesh (`source`) + + Returns + ------- + vtk.vtkPolyData + The transformed surface mesh. + """ + transform_filter = vtk.vtkTransformPolyDataFilter() + transform_filter.SetInputData(source) + transform_filter.SetTransform(transform) + transform_filter.Update() + return transform_filter.GetOutput() + +def copy_image_transform_to_mesh(mesh, image, verbose=False): + """ + Copy the transformation matrix from a SimpleITK image onto a + vtk.vtkPolyData + + Parameters + ---------- + mesh : vtk.vtkPolyData + Mesh to transform + image : SimpleITK.Image + Image that contains the transformation matrix of interest. + verbose : bool, optional + Should we print the transform to the console?, by default False + + Returns + ------- + vtk.vtkPolyData + The surface `mesh` after apply the transformation matrix from the `image` to it. + """ + transform_array = create_4x4_from_3x3(image.GetDirection(), translation=image.GetOrigin()) + + transform = create_transform(transform_array) + + if verbose is True: + print(transform) + + return apply_transform(source=mesh, transform=transform) + +class SitkVtkTransformer: + """ + An class to helping apply SimpleITK image transformation to vtk.vtkPolyData + + Parameters + ---------- + sitk_image : SimpleITK.Image, optional + Image whos transformation matrix should be used, by default None + three_by_three : numpy.ndarray, optional + 3x3 transformation matrix to build the transformer based on, by default None + translation : numpy.ndarray, optional + 1x3 translation to apply, by default None + center : numpy.ndarray, optional + center of the image volume to enable centering before applying transform, by default None + + + Attributes + ---------- + transform_array : numpy.ndarray + 4x4 transformation matrix + inverse_transform_array : np.ndarray + Inverse of transform array to allow "undoing" of transformation. + + Methods + ---------- + + Notes + ----- + There are remmnants of `three_by_three`, `translation` etc. to allow manual prescription of + this information. + + """ + def __init__(self, + sitk_image=None, + three_by_three=None, + translation=None, + center=None + ): + """ + Class to enable transformation of vtk.vtkPolyData based on SimpleITK.Image. + + Parameters + ---------- + sitk_image : SimpleITK.Image, optional + Image whos transformation matrix should be used, by default None + three_by_three : numpy.ndarray, optional + 3x3 transformation matrix to build the transformer based on, by default None + translation : numpy.ndarray, optional + 1x3 translation to apply, by default None + center : numpy.ndarray, optional + center of the image volume to enable centering before applying transform, by default None + """ + if sitk_image is not None: + self.transform_array = create_4x4_from_3x3(sitk_image.GetDirection(), translation=sitk_image.GetOrigin()) + # Need to setup below code to receive 3x3, translation, and center to apply a transform. + + # elif three_by_three is not None: + # self.transform_array = create_4x4_from_3x3(three_by_three) + # # if translation is not None: + # # # self.transform_array[:3, 3] = translation + # self.translation = translation + + # # Center is in this, but is not currently used. Below is commented out to show how it could be automatically applied. + # self.center = center + + + # Easier to rotate mesh to image instead of image to mesh. So take inverse of transform. + self.inverse_transform_array = np.linalg.inv(self.transform_array) + + def get_transform(self): + """ + Get vtkTransform of the `transform_array` created in `__init__` + + Returns + ------- + vtk.vtkTransform + VTK transform object that can be used for transforming a vtk object (e.g., vtk.vtkPolyData) + """ + # create vtk transform. + transform = vtk.vtkTransform() + # if self.center is not None: + # transform.PostMultiply() + # transform.Translate(-self.center[0], -self.center[1], -self.center[2]) + transform.SetMatrix(self.transform_array.flatten()) + # if self.translation is not None: + # transform.Translate(self.translation) + # if self.center is not None: + # transform.Translate(self.center[0], self.center[1], self.center[2]) + return transform + + def get_inverse_transform(self): + """ + Get vtkTransform of the `inverse_transform_array` created in `__init__` + + Returns + ------- + vtk.vtkTransform + VTK transform object that can be used for transforming a vtk object (e.g., vtk.vtkPolyData) + """ + transform = vtk.vtkTransform() + transform.SetMatrix(self.inverse_transform_array.flatten()) + # if self.translation is not None: + # transform.Translate(tuple([-x for x in self.translation])) + return transform + + def get_transformer(self): + """ + Get `vtkTransformPolyDataFilter` using the `vtkTransform` of `transform_array` + + Returns + ------- + vtk.vtkTransformPolyDataFilter + Filter that can be applied to a vtk.vtkPolyData to transform it. + """ + # Get transform filter and apply transform to bone mesh. + transformer = vtk.vtkTransformPolyDataFilter() + transformer.SetTransform(self.get_transform()) + # Now, can use this later to transform the bone/ + return transformer + + def get_inverse_transformer(self): + """ + Get `vtkTransformPolyDataFilter` using the `vtkTransform` of `inverse_transform_array` + + Returns + ------- + vtk.vtkTransformPolyDataFilter + Filter that can be applied to a vtk.vtkPolyData to transform it. + """ + inverse_transformer = vtk.vtkTransformPolyDataFilter() + inverse_transformer.SetTransform(self.get_inverse_transform()) + return inverse_transformer + + def apply_transform_to_mesh(self, + mesh): + """ + Transform surface mesh using transformation matrix from the image data. + + Parameters + ---------- + mesh : vtk.vtkPolyData + surface mesh to apply transform to. + + Returns + ------- + vtk.vtkPolyData + copy of the `mesh` object after being transformed using image data transformation matrix. + """ + transformer = self.get_transformer() + transformer.SetInputData(mesh) + transformer.Update() + return vtk_deep_copy(transformer.GetOutput()) + + def apply_inverse_transform_to_mesh(self, + mesh): + """ + Transform surface mesh using the inverse of the transformation matrix from the image data. + + Parameters + ---------- + mesh : vtk.vtkPolyData + surface mesh to apply transform to. + + Returns + ------- + vtk.vtkPolyData + copy of the `mesh` object after being transformed using the inverse of the image data transformation matrix. + """ + inverse_transformer = self.get_inverse_transformer() + inverse_transformer.SetInputData(mesh) + inverse_transformer.Update() + return vtk_deep_copy(inverse_transformer.GetOutput()) + +def get_versor_from_transform(transform): + """ + Get a `sitk.VersorRigid3DTransform` from a regular transform. + + Parameters + ---------- + transform : sitk.sitkTransform + Transformation to turn into a versor transform. + + Returns + ------- + sitk.VersorRigid3DTransform + The transform converted into a versor transform. + + Raises + ------ + Exception + If the transform is a composite of > 1 transformation. + Exception + If other error... ?? + """ + try: + versor = sitk.VersorRigid3DTransform(transform) + except RuntimeError: + try: + composite = sitk.CompositeTransform(transform) + if composite.GetNumberOfTransforms() == 1: + versor = sitk.VersorRigid3DTransform(composite.GetBackTransform()) + else: + raise Exception ('There is {} transforms in the composite transform, excpected 1!'.format(composite.GetNumberOfTransforms())) + except BaseException as error: + raise Exception(error) + + return versor + +def break_versor_into_center_rotate_translate_transforms(versor): + """ + Convert a sitk.VersorRigid3DTransform into a 3 vtk.vtkTransform objects: + 1. center transformation, 2. rotation transform, 3. translation transform. + + Parameters + ---------- + versor : sitk.VersorRigid3DTransform + The sitk transformation matrix that we want to break into its constituent parts. + + Returns + ------- + tuple of 3x vtk.vtkTransform + Tuple of transformations to be applied to surface mesh to align it with the original image(s). + """ + center_of_rotation = versor.GetCenter() + center_transform = vtk.vtkTransform() + center_transform.Translate(center_of_rotation[0], center_of_rotation[1], center_of_rotation[2]) + + rotate_transform = vtk.vtkTransform() + four_by_four = np.identity(4) + four_by_four[:3,:3] = np.reshape(versor.GetMatrix(), (3,3)) + rotate_transform.SetMatrix(four_by_four.flatten()) + + translate_transform = vtk.vtkTransform() + translate_transform.Translate(versor.GetTranslation()) + + return center_transform, rotate_transform, translate_transform</code></pre> +</details> +</section> +<section> +</section> +<section> +</section> +<section> +<h2 class="section-title" id="header-functions">Functions</h2> +<dl> +<dt id="pymskt.mesh.meshTransform.apply_transform"><code class="name flex"> +<span>def <span class="ident">apply_transform</span></span>(<span>source, transform)</span> +</code></dt> +<dd> +<div class="desc"><p>Apply transform to surface mesh</p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>source</code></strong> : <code>vtk.vtkPolyData</code></dt> +<dd>The source surface mesh to apply transformation (<code>transform</code>) to.</dd> +<dt><strong><code>transform</code></strong> : <code>vtk.vtkTransform</code></dt> +<dd>The transofrm to apply to the surface mesh (<code>source</code>)</dd> +</dl> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>vtk.vtkPolyData</code></dt> +<dd>The transformed surface mesh.</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def apply_transform(source, transform): + """ + Apply transform to surface mesh + + Parameters + ---------- + source : vtk.vtkPolyData + The source surface mesh to apply transformation (`transform`) to. + transform : vtk.vtkTransform + The transofrm to apply to the surface mesh (`source`) + + Returns + ------- + vtk.vtkPolyData + The transformed surface mesh. + """ + transform_filter = vtk.vtkTransformPolyDataFilter() + transform_filter.SetInputData(source) + transform_filter.SetTransform(transform) + transform_filter.Update() + return transform_filter.GetOutput()</code></pre> +</details> +</dd> +<dt id="pymskt.mesh.meshTransform.break_versor_into_center_rotate_translate_transforms"><code class="name flex"> +<span>def <span class="ident">break_versor_into_center_rotate_translate_transforms</span></span>(<span>versor)</span> +</code></dt> +<dd> +<div class="desc"><p>Convert a sitk.VersorRigid3DTransform into a 3 vtk.vtkTransform objects: +1. center transformation, 2. rotation transform, 3. translation transform. </p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>versor</code></strong> : <code>sitk.VersorRigid3DTransform</code></dt> +<dd>The sitk transformation matrix that we want to break into its constituent parts.</dd> +</dl> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>tuple</code> of <code>3x vtk.vtkTransform</code></dt> +<dd>Tuple of transformations to be applied to surface mesh to align it with the original image(s).</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def break_versor_into_center_rotate_translate_transforms(versor): + """ + Convert a sitk.VersorRigid3DTransform into a 3 vtk.vtkTransform objects: + 1. center transformation, 2. rotation transform, 3. translation transform. + + Parameters + ---------- + versor : sitk.VersorRigid3DTransform + The sitk transformation matrix that we want to break into its constituent parts. + + Returns + ------- + tuple of 3x vtk.vtkTransform + Tuple of transformations to be applied to surface mesh to align it with the original image(s). + """ + center_of_rotation = versor.GetCenter() + center_transform = vtk.vtkTransform() + center_transform.Translate(center_of_rotation[0], center_of_rotation[1], center_of_rotation[2]) + + rotate_transform = vtk.vtkTransform() + four_by_four = np.identity(4) + four_by_four[:3,:3] = np.reshape(versor.GetMatrix(), (3,3)) + rotate_transform.SetMatrix(four_by_four.flatten()) + + translate_transform = vtk.vtkTransform() + translate_transform.Translate(versor.GetTranslation()) + + return center_transform, rotate_transform, translate_transform</code></pre> +</details> +</dd> +<dt id="pymskt.mesh.meshTransform.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 a SimpleITK image onto a +vtk.vtkPolyData</p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>mesh</code></strong> : <code>vtk.vtkPolyData</code></dt> +<dd>Mesh to transform</dd> +<dt><strong><code>image</code></strong> : <code>SimpleITK.Image</code></dt> +<dd>Image that contains the transformation matrix of interest.</dd> +<dt><strong><code>verbose</code></strong> : <code>bool</code>, optional</dt> +<dd>Should we print the transform to the console?, by default False</dd> +</dl> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>vtk.vtkPolyData</code></dt> +<dd>The surface <code>mesh</code> after apply the transformation matrix from the <code>image</code> to it.</dd> +</dl></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 a SimpleITK image onto a + vtk.vtkPolyData + + Parameters + ---------- + mesh : vtk.vtkPolyData + Mesh to transform + image : SimpleITK.Image + Image that contains the transformation matrix of interest. + verbose : bool, optional + Should we print the transform to the console?, by default False + + Returns + ------- + vtk.vtkPolyData + The surface `mesh` after apply the transformation matrix from the `image` to it. + """ + transform_array = create_4x4_from_3x3(image.GetDirection(), translation=image.GetOrigin()) + + transform = create_transform(transform_array) + + if verbose is True: + print(transform) + + return apply_transform(source=mesh, transform=transform)</code></pre> +</details> +</dd> +<dt id="pymskt.mesh.meshTransform.create_transform"><code class="name flex"> +<span>def <span class="ident">create_transform</span></span>(<span>transform_matrix)</span> +</code></dt> +<dd> +<div class="desc"><p>Turn 4x4 matrix into a vtkTransform</p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>transform_matrix</code></strong> : <code>numpy.ndarray</code></dt> +<dd>4x4 transformation matrix to be converted to transform</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def create_transform(transform_matrix): + """ + Turn 4x4 matrix into a vtkTransform + + Parameters + ---------- + transform_matrix : numpy.ndarray + 4x4 transformation matrix to be converted to transform + """ + + if np.allclose(transform_matrix.shape, [4, 4]): + pass + else: + raise Exception('transform matrix should be 4x4 matrix') + transform = vtk.vtkTransform() + transform.SetMatrix(transform_matrix.flatten()) + return transform</code></pre> +</details> +</dd> +<dt id="pymskt.mesh.meshTransform.get_versor_from_transform"><code class="name flex"> +<span>def <span class="ident">get_versor_from_transform</span></span>(<span>transform)</span> +</code></dt> +<dd> +<div class="desc"><p>Get a <code>sitk.VersorRigid3DTransform</code> from a regular transform. </p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>transform</code></strong> : <code>sitk.sitkTransform</code></dt> +<dd>Transformation to turn into a versor transform.</dd> +</dl> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>sitk.VersorRigid3DTransform</code></dt> +<dd>The transform converted into a versor transform.</dd> +</dl> +<h2 id="raises">Raises</h2> +<dl> +<dt><code>Exception</code></dt> +<dd>If the transform is a composite of > 1 transformation.</dd> +<dt><code>Exception</code></dt> +<dd>If other error… ??</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def get_versor_from_transform(transform): + """ + Get a `sitk.VersorRigid3DTransform` from a regular transform. + + Parameters + ---------- + transform : sitk.sitkTransform + Transformation to turn into a versor transform. + + Returns + ------- + sitk.VersorRigid3DTransform + The transform converted into a versor transform. + + Raises + ------ + Exception + If the transform is a composite of > 1 transformation. + Exception + If other error... ?? + """ + try: + versor = sitk.VersorRigid3DTransform(transform) + except RuntimeError: + try: + composite = sitk.CompositeTransform(transform) + if composite.GetNumberOfTransforms() == 1: + versor = sitk.VersorRigid3DTransform(composite.GetBackTransform()) + else: + raise Exception ('There is {} transforms in the composite transform, excpected 1!'.format(composite.GetNumberOfTransforms())) + except BaseException as error: + raise Exception(error) + + return versor</code></pre> +</details> +</dd> +</dl> +</section> +<section> +<h2 class="section-title" id="header-classes">Classes</h2> +<dl> +<dt id="pymskt.mesh.meshTransform.SitkVtkTransformer"><code class="flex name class"> +<span>class <span class="ident">SitkVtkTransformer</span></span> +<span>(</span><span>sitk_image=None, three_by_three=None, translation=None, center=None)</span> +</code></dt> +<dd> +<div class="desc"><p>An class to helping apply SimpleITK image transformation to vtk.vtkPolyData</p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>sitk_image</code></strong> : <code>SimpleITK.Image</code>, optional</dt> +<dd>Image whos transformation matrix should be used, by default None</dd> +<dt><strong><code>three_by_three</code></strong> : <code>numpy.ndarray</code>, optional</dt> +<dd>3x3 transformation matrix to build the transformer based on, by default None</dd> +<dt><strong><code>translation</code></strong> : <code>numpy.ndarray</code>, optional</dt> +<dd>1x3 translation to apply, by default None</dd> +<dt><strong><code>center</code></strong> : <code>numpy.ndarray</code>, optional</dt> +<dd>center of the image volume to enable centering before applying transform, by default None</dd> +</dl> +<h2 id="attributes">Attributes</h2> +<dl> +<dt><strong><code>transform_array</code></strong> : <code>numpy.ndarray</code></dt> +<dd>4x4 transformation matrix</dd> +<dt><strong><code>inverse_transform_array</code></strong> : <code>np.ndarray</code></dt> +<dd>Inverse of transform array to allow "undoing" of transformation.</dd> +</dl> +<h2 id="methods">Methods</h2> +<h2 id="notes">Notes</h2> +<p>There are remmnants of <code>three_by_three</code>, <code>translation</code> etc. to allow manual prescription of +this information. </p> +<p>Class to enable transformation of vtk.vtkPolyData based on SimpleITK.Image.</p> +<h2 id="parameters_1">Parameters</h2> +<dl> +<dt><strong><code>sitk_image</code></strong> : <code>SimpleITK.Image</code>, optional</dt> +<dd>Image whos transformation matrix should be used, by default None</dd> +<dt><strong><code>three_by_three</code></strong> : <code>numpy.ndarray</code>, optional</dt> +<dd>3x3 transformation matrix to build the transformer based on, by default None</dd> +<dt><strong><code>translation</code></strong> : <code>numpy.ndarray</code>, optional</dt> +<dd>1x3 translation to apply, by default None</dd> +<dt><strong><code>center</code></strong> : <code>numpy.ndarray</code>, optional</dt> +<dd>center of the image volume to enable centering before applying transform, by default None</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">class SitkVtkTransformer: + """ + An class to helping apply SimpleITK image transformation to vtk.vtkPolyData + + Parameters + ---------- + sitk_image : SimpleITK.Image, optional + Image whos transformation matrix should be used, by default None + three_by_three : numpy.ndarray, optional + 3x3 transformation matrix to build the transformer based on, by default None + translation : numpy.ndarray, optional + 1x3 translation to apply, by default None + center : numpy.ndarray, optional + center of the image volume to enable centering before applying transform, by default None + + + Attributes + ---------- + transform_array : numpy.ndarray + 4x4 transformation matrix + inverse_transform_array : np.ndarray + Inverse of transform array to allow "undoing" of transformation. + + Methods + ---------- + + Notes + ----- + There are remmnants of `three_by_three`, `translation` etc. to allow manual prescription of + this information. + + """ + def __init__(self, + sitk_image=None, + three_by_three=None, + translation=None, + center=None + ): + """ + Class to enable transformation of vtk.vtkPolyData based on SimpleITK.Image. + + Parameters + ---------- + sitk_image : SimpleITK.Image, optional + Image whos transformation matrix should be used, by default None + three_by_three : numpy.ndarray, optional + 3x3 transformation matrix to build the transformer based on, by default None + translation : numpy.ndarray, optional + 1x3 translation to apply, by default None + center : numpy.ndarray, optional + center of the image volume to enable centering before applying transform, by default None + """ + if sitk_image is not None: + self.transform_array = create_4x4_from_3x3(sitk_image.GetDirection(), translation=sitk_image.GetOrigin()) + # Need to setup below code to receive 3x3, translation, and center to apply a transform. + + # elif three_by_three is not None: + # self.transform_array = create_4x4_from_3x3(three_by_three) + # # if translation is not None: + # # # self.transform_array[:3, 3] = translation + # self.translation = translation + + # # Center is in this, but is not currently used. Below is commented out to show how it could be automatically applied. + # self.center = center + + + # Easier to rotate mesh to image instead of image to mesh. So take inverse of transform. + self.inverse_transform_array = np.linalg.inv(self.transform_array) + + def get_transform(self): + """ + Get vtkTransform of the `transform_array` created in `__init__` + + Returns + ------- + vtk.vtkTransform + VTK transform object that can be used for transforming a vtk object (e.g., vtk.vtkPolyData) + """ + # create vtk transform. + transform = vtk.vtkTransform() + # if self.center is not None: + # transform.PostMultiply() + # transform.Translate(-self.center[0], -self.center[1], -self.center[2]) + transform.SetMatrix(self.transform_array.flatten()) + # if self.translation is not None: + # transform.Translate(self.translation) + # if self.center is not None: + # transform.Translate(self.center[0], self.center[1], self.center[2]) + return transform + + def get_inverse_transform(self): + """ + Get vtkTransform of the `inverse_transform_array` created in `__init__` + + Returns + ------- + vtk.vtkTransform + VTK transform object that can be used for transforming a vtk object (e.g., vtk.vtkPolyData) + """ + transform = vtk.vtkTransform() + transform.SetMatrix(self.inverse_transform_array.flatten()) + # if self.translation is not None: + # transform.Translate(tuple([-x for x in self.translation])) + return transform + + def get_transformer(self): + """ + Get `vtkTransformPolyDataFilter` using the `vtkTransform` of `transform_array` + + Returns + ------- + vtk.vtkTransformPolyDataFilter + Filter that can be applied to a vtk.vtkPolyData to transform it. + """ + # Get transform filter and apply transform to bone mesh. + transformer = vtk.vtkTransformPolyDataFilter() + transformer.SetTransform(self.get_transform()) + # Now, can use this later to transform the bone/ + return transformer + + def get_inverse_transformer(self): + """ + Get `vtkTransformPolyDataFilter` using the `vtkTransform` of `inverse_transform_array` + + Returns + ------- + vtk.vtkTransformPolyDataFilter + Filter that can be applied to a vtk.vtkPolyData to transform it. + """ + inverse_transformer = vtk.vtkTransformPolyDataFilter() + inverse_transformer.SetTransform(self.get_inverse_transform()) + return inverse_transformer + + def apply_transform_to_mesh(self, + mesh): + """ + Transform surface mesh using transformation matrix from the image data. + + Parameters + ---------- + mesh : vtk.vtkPolyData + surface mesh to apply transform to. + + Returns + ------- + vtk.vtkPolyData + copy of the `mesh` object after being transformed using image data transformation matrix. + """ + transformer = self.get_transformer() + transformer.SetInputData(mesh) + transformer.Update() + return vtk_deep_copy(transformer.GetOutput()) + + def apply_inverse_transform_to_mesh(self, + mesh): + """ + Transform surface mesh using the inverse of the transformation matrix from the image data. + + Parameters + ---------- + mesh : vtk.vtkPolyData + surface mesh to apply transform to. + + Returns + ------- + vtk.vtkPolyData + copy of the `mesh` object after being transformed using the inverse of the image data transformation matrix. + """ + inverse_transformer = self.get_inverse_transformer() + inverse_transformer.SetInputData(mesh) + inverse_transformer.Update() + return vtk_deep_copy(inverse_transformer.GetOutput())</code></pre> +</details> +<h3>Methods</h3> +<dl> +<dt id="pymskt.mesh.meshTransform.SitkVtkTransformer.apply_inverse_transform_to_mesh"><code class="name flex"> +<span>def <span class="ident">apply_inverse_transform_to_mesh</span></span>(<span>self, mesh)</span> +</code></dt> +<dd> +<div class="desc"><p>Transform surface mesh using the inverse of the transformation matrix from the image data. </p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>mesh</code></strong> : <code>vtk.vtkPolyData</code></dt> +<dd>surface mesh to apply transform to.</dd> +</dl> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>vtk.vtkPolyData</code></dt> +<dd>copy of the <code>mesh</code> object after being transformed using the inverse of the image data transformation matrix.</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def apply_inverse_transform_to_mesh(self, + mesh): + """ + Transform surface mesh using the inverse of the transformation matrix from the image data. + + Parameters + ---------- + mesh : vtk.vtkPolyData + surface mesh to apply transform to. + + Returns + ------- + vtk.vtkPolyData + copy of the `mesh` object after being transformed using the inverse of the image data transformation matrix. + """ + inverse_transformer = self.get_inverse_transformer() + inverse_transformer.SetInputData(mesh) + inverse_transformer.Update() + return vtk_deep_copy(inverse_transformer.GetOutput())</code></pre> +</details> +</dd> +<dt id="pymskt.mesh.meshTransform.SitkVtkTransformer.apply_transform_to_mesh"><code class="name flex"> +<span>def <span class="ident">apply_transform_to_mesh</span></span>(<span>self, mesh)</span> +</code></dt> +<dd> +<div class="desc"><p>Transform surface mesh using transformation matrix from the image data. </p> +<h2 id="parameters">Parameters</h2> +<dl> +<dt><strong><code>mesh</code></strong> : <code>vtk.vtkPolyData</code></dt> +<dd>surface mesh to apply transform to.</dd> +</dl> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>vtk.vtkPolyData</code></dt> +<dd>copy of the <code>mesh</code> object after being transformed using image data transformation matrix.</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def apply_transform_to_mesh(self, + mesh): + """ + Transform surface mesh using transformation matrix from the image data. + + Parameters + ---------- + mesh : vtk.vtkPolyData + surface mesh to apply transform to. + + Returns + ------- + vtk.vtkPolyData + copy of the `mesh` object after being transformed using image data transformation matrix. + """ + transformer = self.get_transformer() + transformer.SetInputData(mesh) + transformer.Update() + return vtk_deep_copy(transformer.GetOutput())</code></pre> +</details> +</dd> +<dt id="pymskt.mesh.meshTransform.SitkVtkTransformer.get_inverse_transform"><code class="name flex"> +<span>def <span class="ident">get_inverse_transform</span></span>(<span>self)</span> +</code></dt> +<dd> +<div class="desc"><p>Get vtkTransform of the <code>inverse_transform_array</code> created in <code>__init__</code></p> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>vtk.vtkTransform</code></dt> +<dd>VTK transform object that can be used for transforming a vtk object (e.g., vtk.vtkPolyData)</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def get_inverse_transform(self): + """ + Get vtkTransform of the `inverse_transform_array` created in `__init__` + + Returns + ------- + vtk.vtkTransform + VTK transform object that can be used for transforming a vtk object (e.g., vtk.vtkPolyData) + """ + transform = vtk.vtkTransform() + transform.SetMatrix(self.inverse_transform_array.flatten()) + # if self.translation is not None: + # transform.Translate(tuple([-x for x in self.translation])) + return transform</code></pre> +</details> +</dd> +<dt id="pymskt.mesh.meshTransform.SitkVtkTransformer.get_inverse_transformer"><code class="name flex"> +<span>def <span class="ident">get_inverse_transformer</span></span>(<span>self)</span> +</code></dt> +<dd> +<div class="desc"><p>Get <code>vtkTransformPolyDataFilter</code> using the <code>vtkTransform</code> of <code>inverse_transform_array</code></p> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>vtk.vtkTransformPolyDataFilter</code></dt> +<dd>Filter that can be applied to a vtk.vtkPolyData to transform it.</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def get_inverse_transformer(self): + """ + Get `vtkTransformPolyDataFilter` using the `vtkTransform` of `inverse_transform_array` + + Returns + ------- + vtk.vtkTransformPolyDataFilter + Filter that can be applied to a vtk.vtkPolyData to transform it. + """ + inverse_transformer = vtk.vtkTransformPolyDataFilter() + inverse_transformer.SetTransform(self.get_inverse_transform()) + return inverse_transformer</code></pre> +</details> +</dd> +<dt id="pymskt.mesh.meshTransform.SitkVtkTransformer.get_transform"><code class="name flex"> +<span>def <span class="ident">get_transform</span></span>(<span>self)</span> +</code></dt> +<dd> +<div class="desc"><p>Get vtkTransform of the <code>transform_array</code> created in <code>__init__</code></p> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>vtk.vtkTransform</code></dt> +<dd>VTK transform object that can be used for transforming a vtk object (e.g., vtk.vtkPolyData)</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def get_transform(self): + """ + Get vtkTransform of the `transform_array` created in `__init__` + + Returns + ------- + vtk.vtkTransform + VTK transform object that can be used for transforming a vtk object (e.g., vtk.vtkPolyData) + """ + # create vtk transform. + transform = vtk.vtkTransform() + # if self.center is not None: + # transform.PostMultiply() + # transform.Translate(-self.center[0], -self.center[1], -self.center[2]) + transform.SetMatrix(self.transform_array.flatten()) + # if self.translation is not None: + # transform.Translate(self.translation) + # if self.center is not None: + # transform.Translate(self.center[0], self.center[1], self.center[2]) + return transform</code></pre> +</details> +</dd> +<dt id="pymskt.mesh.meshTransform.SitkVtkTransformer.get_transformer"><code class="name flex"> +<span>def <span class="ident">get_transformer</span></span>(<span>self)</span> +</code></dt> +<dd> +<div class="desc"><p>Get <code>vtkTransformPolyDataFilter</code> using the <code>vtkTransform</code> of <code>transform_array</code></p> +<h2 id="returns">Returns</h2> +<dl> +<dt><code>vtk.vtkTransformPolyDataFilter</code></dt> +<dd>Filter that can be applied to a vtk.vtkPolyData to transform it.</dd> +</dl></div> +<details class="source"> +<summary> +<span>Expand source code</span> +</summary> +<pre><code class="python">def get_transformer(self): + """ + Get `vtkTransformPolyDataFilter` using the `vtkTransform` of `transform_array` + + Returns + ------- + vtk.vtkTransformPolyDataFilter + Filter that can be applied to a vtk.vtkPolyData to transform it. + """ + # Get transform filter and apply transform to bone mesh. + transformer = vtk.vtkTransformPolyDataFilter() + transformer.SetTransform(self.get_transform()) + # Now, can use this later to transform the bone/ + return transformer</code></pre> +</details> +</dd> +</dl> +</dd> +</dl> +</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.mesh" href="index.html">pymskt.mesh</a></code></li> +</ul> +</li> +<li><h3><a href="#header-functions">Functions</a></h3> +<ul class=""> +<li><code><a title="pymskt.mesh.meshTransform.apply_transform" href="#pymskt.mesh.meshTransform.apply_transform">apply_transform</a></code></li> +<li><code><a title="pymskt.mesh.meshTransform.break_versor_into_center_rotate_translate_transforms" href="#pymskt.mesh.meshTransform.break_versor_into_center_rotate_translate_transforms">break_versor_into_center_rotate_translate_transforms</a></code></li> +<li><code><a title="pymskt.mesh.meshTransform.copy_image_transform_to_mesh" href="#pymskt.mesh.meshTransform.copy_image_transform_to_mesh">copy_image_transform_to_mesh</a></code></li> +<li><code><a title="pymskt.mesh.meshTransform.create_transform" href="#pymskt.mesh.meshTransform.create_transform">create_transform</a></code></li> +<li><code><a title="pymskt.mesh.meshTransform.get_versor_from_transform" href="#pymskt.mesh.meshTransform.get_versor_from_transform">get_versor_from_transform</a></code></li> +</ul> +</li> +<li><h3><a href="#header-classes">Classes</a></h3> +<ul> +<li> +<h4><code><a title="pymskt.mesh.meshTransform.SitkVtkTransformer" href="#pymskt.mesh.meshTransform.SitkVtkTransformer">SitkVtkTransformer</a></code></h4> +<ul class=""> +<li><code><a title="pymskt.mesh.meshTransform.SitkVtkTransformer.apply_inverse_transform_to_mesh" href="#pymskt.mesh.meshTransform.SitkVtkTransformer.apply_inverse_transform_to_mesh">apply_inverse_transform_to_mesh</a></code></li> +<li><code><a title="pymskt.mesh.meshTransform.SitkVtkTransformer.apply_transform_to_mesh" href="#pymskt.mesh.meshTransform.SitkVtkTransformer.apply_transform_to_mesh">apply_transform_to_mesh</a></code></li> +<li><code><a title="pymskt.mesh.meshTransform.SitkVtkTransformer.get_inverse_transform" href="#pymskt.mesh.meshTransform.SitkVtkTransformer.get_inverse_transform">get_inverse_transform</a></code></li> +<li><code><a title="pymskt.mesh.meshTransform.SitkVtkTransformer.get_inverse_transformer" href="#pymskt.mesh.meshTransform.SitkVtkTransformer.get_inverse_transformer">get_inverse_transformer</a></code></li> +<li><code><a title="pymskt.mesh.meshTransform.SitkVtkTransformer.get_transform" href="#pymskt.mesh.meshTransform.SitkVtkTransformer.get_transform">get_transform</a></code></li> +<li><code><a title="pymskt.mesh.meshTransform.SitkVtkTransformer.get_transformer" href="#pymskt.mesh.meshTransform.SitkVtkTransformer.get_transformer">get_transformer</a></code></li> +</ul> +</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