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<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>
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