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+<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):
+    &#34;&#34;&#34;
+    Turn 4x4 matrix into a vtkTransform
+
+    Parameters
+    ----------
+    transform_matrix : numpy.ndarray
+        4x4 transformation matrix to be converted to transform
+    &#34;&#34;&#34;
+
+    if np.allclose(transform_matrix.shape, [4, 4]):
+        pass
+    else:
+        raise Exception(&#39;transform matrix should be 4x4 matrix&#39;)
+    transform = vtk.vtkTransform()
+    transform.SetMatrix(transform_matrix.flatten())
+    return transform
+
+
+def apply_transform(source, transform):
+    &#34;&#34;&#34;
+    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. 
+    &#34;&#34;&#34;    
+    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):
+    &#34;&#34;&#34;
+    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. 
+    &#34;&#34;&#34;    
+    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:
+    &#34;&#34;&#34;
+    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 &#34;undoing&#34; of transformation. 
+
+    Methods
+    ----------
+
+    Notes
+    -----
+    There are remmnants of `three_by_three`, `translation` etc. to allow manual prescription of
+    this information. 
+
+    &#34;&#34;&#34;    
+    def __init__(self,
+                 sitk_image=None,
+                 three_by_three=None,
+                 translation=None,
+                 center=None
+                 ):
+        &#34;&#34;&#34;
+        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
+        &#34;&#34;&#34;        
+        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):
+        &#34;&#34;&#34;
+        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)
+        &#34;&#34;&#34;        
+        # 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):
+        &#34;&#34;&#34;
+        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)
+        &#34;&#34;&#34;        
+        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):
+        &#34;&#34;&#34;
+        Get `vtkTransformPolyDataFilter` using the `vtkTransform` of `transform_array`
+
+        Returns
+        -------
+        vtk.vtkTransformPolyDataFilter
+            Filter that can be applied to a vtk.vtkPolyData to transform it. 
+        &#34;&#34;&#34;        
+        # 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):
+        &#34;&#34;&#34;
+        Get `vtkTransformPolyDataFilter` using the `vtkTransform` of `inverse_transform_array`
+
+        Returns
+        -------
+        vtk.vtkTransformPolyDataFilter
+            Filter that can be applied to a vtk.vtkPolyData to transform it. 
+        &#34;&#34;&#34;        
+        inverse_transformer = vtk.vtkTransformPolyDataFilter()
+        inverse_transformer.SetTransform(self.get_inverse_transform())
+        return inverse_transformer
+
+    def apply_transform_to_mesh(self,
+                                mesh):
+        &#34;&#34;&#34;
+        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. 
+        &#34;&#34;&#34;        
+        transformer = self.get_transformer()
+        transformer.SetInputData(mesh)
+        transformer.Update()
+        return vtk_deep_copy(transformer.GetOutput())
+
+    def apply_inverse_transform_to_mesh(self,
+                                        mesh):
+        &#34;&#34;&#34;
+        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. 
+        &#34;&#34;&#34;                                        
+        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):
+    &#34;&#34;&#34;
+    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 &gt; 1 transformation.
+    Exception
+        If other error... ?? 
+    &#34;&#34;&#34;    
+    try:
+        versor = sitk.VersorRigid3DTransform(transform)
+    except RuntimeError:
+        try:
+            composite = sitk.CompositeTransform(transform)
+            if composite.GetNumberOfTransforms() == 1:
+                versor = sitk.VersorRigid3DTransform(composite.GetBackTransform())
+            else:
+                raise Exception (&#39;There is {} transforms in the composite transform, excpected 1!&#39;.format(composite.GetNumberOfTransforms()))
+        except BaseException as error:
+            raise Exception(error)
+    
+    return versor
+
+def break_versor_into_center_rotate_translate_transforms(versor):
+    &#34;&#34;&#34;
+    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). 
+    &#34;&#34;&#34;    
+    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> :&ensp;<code>vtk.vtkPolyData</code></dt>
+<dd>The source surface mesh to apply transformation (<code>transform</code>) to.</dd>
+<dt><strong><code>transform</code></strong> :&ensp;<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):
+    &#34;&#34;&#34;
+    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. 
+    &#34;&#34;&#34;    
+    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> :&ensp;<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):
+    &#34;&#34;&#34;
+    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). 
+    &#34;&#34;&#34;    
+    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> :&ensp;<code>vtk.vtkPolyData</code></dt>
+<dd>Mesh to transform</dd>
+<dt><strong><code>image</code></strong> :&ensp;<code>SimpleITK.Image</code></dt>
+<dd>Image that contains the transformation matrix of interest.</dd>
+<dt><strong><code>verbose</code></strong> :&ensp;<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):
+    &#34;&#34;&#34;
+    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. 
+    &#34;&#34;&#34;    
+    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> :&ensp;<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):
+    &#34;&#34;&#34;
+    Turn 4x4 matrix into a vtkTransform
+
+    Parameters
+    ----------
+    transform_matrix : numpy.ndarray
+        4x4 transformation matrix to be converted to transform
+    &#34;&#34;&#34;
+
+    if np.allclose(transform_matrix.shape, [4, 4]):
+        pass
+    else:
+        raise Exception(&#39;transform matrix should be 4x4 matrix&#39;)
+    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> :&ensp;<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 &gt; 1 transformation.</dd>
+<dt><code>Exception</code></dt>
+<dd>If other error&hellip; ??</dd>
+</dl></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def get_versor_from_transform(transform):
+    &#34;&#34;&#34;
+    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 &gt; 1 transformation.
+    Exception
+        If other error... ?? 
+    &#34;&#34;&#34;    
+    try:
+        versor = sitk.VersorRigid3DTransform(transform)
+    except RuntimeError:
+        try:
+            composite = sitk.CompositeTransform(transform)
+            if composite.GetNumberOfTransforms() == 1:
+                versor = sitk.VersorRigid3DTransform(composite.GetBackTransform())
+            else:
+                raise Exception (&#39;There is {} transforms in the composite transform, excpected 1!&#39;.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> :&ensp;<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> :&ensp;<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> :&ensp;<code>numpy.ndarray</code>, optional</dt>
+<dd>1x3 translation to apply, by default None</dd>
+<dt><strong><code>center</code></strong> :&ensp;<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> :&ensp;<code>numpy.ndarray</code></dt>
+<dd>4x4 transformation matrix</dd>
+<dt><strong><code>inverse_transform_array</code></strong> :&ensp;<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> :&ensp;<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> :&ensp;<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> :&ensp;<code>numpy.ndarray</code>, optional</dt>
+<dd>1x3 translation to apply, by default None</dd>
+<dt><strong><code>center</code></strong> :&ensp;<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:
+    &#34;&#34;&#34;
+    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 &#34;undoing&#34; of transformation. 
+
+    Methods
+    ----------
+
+    Notes
+    -----
+    There are remmnants of `three_by_three`, `translation` etc. to allow manual prescription of
+    this information. 
+
+    &#34;&#34;&#34;    
+    def __init__(self,
+                 sitk_image=None,
+                 three_by_three=None,
+                 translation=None,
+                 center=None
+                 ):
+        &#34;&#34;&#34;
+        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
+        &#34;&#34;&#34;        
+        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):
+        &#34;&#34;&#34;
+        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)
+        &#34;&#34;&#34;        
+        # 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):
+        &#34;&#34;&#34;
+        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)
+        &#34;&#34;&#34;        
+        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):
+        &#34;&#34;&#34;
+        Get `vtkTransformPolyDataFilter` using the `vtkTransform` of `transform_array`
+
+        Returns
+        -------
+        vtk.vtkTransformPolyDataFilter
+            Filter that can be applied to a vtk.vtkPolyData to transform it. 
+        &#34;&#34;&#34;        
+        # 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):
+        &#34;&#34;&#34;
+        Get `vtkTransformPolyDataFilter` using the `vtkTransform` of `inverse_transform_array`
+
+        Returns
+        -------
+        vtk.vtkTransformPolyDataFilter
+            Filter that can be applied to a vtk.vtkPolyData to transform it. 
+        &#34;&#34;&#34;        
+        inverse_transformer = vtk.vtkTransformPolyDataFilter()
+        inverse_transformer.SetTransform(self.get_inverse_transform())
+        return inverse_transformer
+
+    def apply_transform_to_mesh(self,
+                                mesh):
+        &#34;&#34;&#34;
+        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. 
+        &#34;&#34;&#34;        
+        transformer = self.get_transformer()
+        transformer.SetInputData(mesh)
+        transformer.Update()
+        return vtk_deep_copy(transformer.GetOutput())
+
+    def apply_inverse_transform_to_mesh(self,
+                                        mesh):
+        &#34;&#34;&#34;
+        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. 
+        &#34;&#34;&#34;                                        
+        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> :&ensp;<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):
+    &#34;&#34;&#34;
+    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. 
+    &#34;&#34;&#34;                                        
+    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> :&ensp;<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):
+    &#34;&#34;&#34;
+    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. 
+    &#34;&#34;&#34;        
+    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):
+    &#34;&#34;&#34;
+    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)
+    &#34;&#34;&#34;        
+    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):
+    &#34;&#34;&#34;
+    Get `vtkTransformPolyDataFilter` using the `vtkTransform` of `inverse_transform_array`
+
+    Returns
+    -------
+    vtk.vtkTransformPolyDataFilter
+        Filter that can be applied to a vtk.vtkPolyData to transform it. 
+    &#34;&#34;&#34;        
+    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):
+    &#34;&#34;&#34;
+    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)
+    &#34;&#34;&#34;        
+    # 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):
+    &#34;&#34;&#34;
+    Get `vtkTransformPolyDataFilter` using the `vtkTransform` of `transform_array`
+
+    Returns
+    -------
+    vtk.vtkTransformPolyDataFilter
+        Filter that can be applied to a vtk.vtkPolyData to transform it. 
+    &#34;&#34;&#34;        
+    # 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">
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