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<article id="content">
<header>
<h1 class="title">Module <code>pymskt.mesh.utils</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
from vtk.util.numpy_support import vtk_to_numpy, numpy_to_vtk
from pymskt.utils import sigma2fwhm
import pyvista as pv
import pymskt
# Some functions were originally based on the tutorial on ray casting in python + vtk
# by Adamos Kyriakou @:
# https://pyscience.wordpress.com/2014/09/21/ray-casting-with-python-and-vtk-intersecting-linesrays-with-surface-meshes/
def is_hit(obb_tree, source, target):
"""
Return True if line intersects mesh (`obb_tree`). The line starts at `source` and ends at `target`.
Parameters
----------
obb_tree : vtk.vtkOBBTree
OBBTree of a surface mesh.
source : list
x/y/z position of starting point of ray (to find intersection)
target : list
x/y/z position of ending point of ray (to find intersection)
Returns
-------
bool
Telling if the line (source to target) intersects the obb_tree.
"""
code = obb_tree.IntersectWithLine(source, target, None, None)
if code == 0:
return False
else:
return True
def get_intersect(obbTree, pSource, pTarget):
"""
Get intersecting points on the obbTree between a line from pSource to pTarget.
Parameters
----------
obb_tree : vtk.vtkOBBTree
OBBTree of a surface mesh.
pSource : list
x/y/z position of starting point of ray (to find intersection)
pTarget : list
x/y/z position of ending point of ray (to find intersection)
Returns
-------
tuple (list1, list2)
list1 is of the intersection points
list2 is the idx of the cells that were intersected.
"""
# Create an empty 'vtkPoints' object to store the intersection point coordinates
points = vtk.vtkPoints()
# Create an empty 'vtkIdList' object to store the ids of the cells that intersect
# with the cast rays
cell_ids = vtk.vtkIdList()
# Perform intersection
code = obbTree.IntersectWithLine(pSource, pTarget, points, cell_ids)
# Get point-data
point_data = points.GetData()
# Get number of intersection points found
n_points = point_data.GetNumberOfTuples()
# Get number of intersected cell ids
n_Ids = cell_ids.GetNumberOfIds()
assert (n_points == n_Ids)
# Loop through the found points and cells and store
# them in lists
points_inter = []
cell_ids_inter = []
for idx in range(n_points):
points_inter.append(point_data.GetTuple3(idx))
cell_ids_inter.append(cell_ids.GetId(idx))
return points_inter, cell_ids_inter
def get_surface_normals(surface,
point_normals_on=True,
cell_normals_on=True):
"""
Get the surface normals of a mesh (`surface`
Parameters
----------
surface : vtk.vtkPolyData
surface mesh to get normals from
point_normals_on : bool, optional
Whether or not to get normals of points (vertices), by default True
cell_normals_on : bool, optional
Whether or not to get normals from cells (faces?), by default True
Returns
-------
vtk.vtkPolyDataNormals
Normval vectors for points/cells.
"""
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(surface)
# Disable normal calculation at cell vertices
if point_normals_on is True:
normals.ComputePointNormalsOn()
elif point_normals_on is False:
normals.ComputePointNormalsOff()
# Enable normal calculation at cell centers
if cell_normals_on is True:
normals.ComputeCellNormalsOn()
elif cell_normals_on is False:
normals.ComputeCellNormalsOff()
# Disable splitting of sharp edges
normals.SplittingOff()
# Disable global flipping of normal orientation
normals.FlipNormalsOff()
# Enable automatic determination of correct normal orientation
normals.AutoOrientNormalsOn()
# Perform calculation
normals.Update()
return normals
def get_obb_surface(surface):
"""
Get vtk.vtkOBBTree for a surface mesh
Get obb of a surface mesh. This can be queried to see if a line etc. intersects a surface.
Parameters
----------
surface : vtk.vtkPolyData
The surface mesh to get an OBBTree for.
Returns
-------
vtk.vtkOBBTree
The OBBTree to be used to find intersections for calculating cartilage thickness etc.
"""
obb = vtk.vtkOBBTree()
obb.SetDataSet(surface)
obb.BuildLocator()
return obb
def vtk_deep_copy(mesh):
"""
"Deep" copy a vtk.vtkPolyData so that they are not connected in any way.
Parameters
----------
mesh : vtk.vtkPolyData
Mesh to copy.
Returns
-------
vtk.vtkPolyData
Copy of the input mesh.
"""
new_mesh = vtk.vtkPolyData()
new_mesh.DeepCopy(mesh)
return new_mesh
def estimate_mesh_scalars_FWHMs(mesh, scalar_name='thickness_mm'):
"""
Calculate the Full Width Half Maximum (FWHM) based on surface mesh scalars.
Parameters
----------
mesh : vtk.vtkPolyData
Surface mesh to estimate FWHM of the scalars from.
scalar_name : str, optional
Name of the scalars to calcualte FWHM for, by default 'thickness_mm'
Returns
-------
list
List of the FWHM values. Assuming they are for X/Y/Z
"""
gradient_filter = vtk.vtkGradientFilter()
gradient_filter.SetInputData(mesh)
gradient_filter.Update()
gradient_mesh = vtk.vtkPolyData()
gradient_mesh.DeepCopy(gradient_filter.GetOutput())
scalars = vtk_to_numpy(mesh.GetPointData().GetScalars())
location_non_zero = np.where(scalars != 0)
gradient_scalars = vtk_to_numpy(gradient_mesh.GetPointData().GetAbstractArray('Gradients'))
cartilage_gradients = gradient_scalars[location_non_zero, :][0]
thickness_scalars = vtk_to_numpy(gradient_mesh.GetPointData().GetAbstractArray(scalar_name))
cartilage_thicknesses = thickness_scalars[location_non_zero]
V0 = np.mean((cartilage_thicknesses - np.mean(cartilage_thicknesses)) ** 2)
V1 = np.mean((cartilage_gradients - np.mean(cartilage_gradients)) ** 2, axis=0)
sigma2s = -1 / (4 * np.log(1 - (V1 / (2 * V0))))
sigmas = np.sqrt(sigma2s)
FWHMs = [sigma2fwhm(x) for x in sigmas]
return FWHMs
def get_surface_distance(surface_1,
surface_2,
return_RMS=True,
return_individual_distances=False):
if (return_RMS is True) & (return_individual_distances is True):
raise Exception('Nothing to return - either return_RMS or return_individual_distances must be `True`')
pt_locator = vtk.vtkPointLocator()
pt_locator.SetDataSet(surface_2)
pt_locator.AutomaticOn()
pt_locator.BuildLocator()
distances = np.zeros(surface_1.GetNumberOfPoints())
for pt_idx in range(surface_1.GetNumberOfPoints()):
point_1 = np.asarray(surface_1.GetPoint(pt_idx))
pt_idx_2 = pt_locator.FindClosestPoint(point_1)
point_2 = np.asarray(surface_2.GetPoint(pt_idx_2))
distances[pt_idx] = np.sqrt(np.sum(np.square(point_2-point_1)))
RMS = np.sqrt(np.mean(np.square(distances)))
if return_individual_distances is True:
if return_RMS is True:
return RMS, distances
else:
return distances
else:
if return_RMS is True:
return RMS
def get_symmetric_surface_distance(surface_1, surface_2):
surf1_to_2_distances = get_surface_distance(surface_1, surface_2, return_RMS=False, return_individual_distances=True)
surf2_to_1_distances = get_surface_distance(surface_2, surface_1, return_RMS=False, return_individual_distances=True)
symmetric_distance = (np.sum(surf1_to_2_distances) + np.sum(surf2_to_1_distances)) / (len(surf1_to_2_distances) + len(surf2_to_1_distances))
return symmetric_distance
class GIF:
"""
Class for generating GIF of surface meshes.
Parameters
----------
plotter : pyvista.Plotter
Plotter to use for plotting.
color: str, optional
Color to use for object, by default 'orange'
show_edges: bool, optional
Whether to show edges on mesh, by default True
edge_color: str, optional
Color to use for edges, by default 'black'
camera_position: list or string, optional
Camera position to use, by default 'xz'
window_size: list, optional
Window size to use for GIF, by default [3000, 4000]
background_color: str, optional
Background color to use, by default 'white'
path_save: str, optional
Path to save GIF, by default '~/Downloads/ssm.gif'
Attributes
----------
_plotter : pyvista.Plotter
Plotter to use for plotting.
_color : str
Color to use for object.
_show_edges : bool
Whether to show edges on mesh.
_edge_color : str
Color to use for edges.
_camera_position : list or string
Camera position to use.
_window_size : list
Window size to use for GIF.
_background_color : str
Background color to use.
_path_save : str
Path to save GIF.
Methods
-------
add_mesh_frame(mesh)
Add a mesh to the GIF.
update_view()
Update the view of the plotter.
done()
Close the plotter.
"""
def __init__(
self,
plotter=None,
color='orange',
show_edges=True,
edge_color='black',
camera_position='xz',
window_size=[3000, 4000],
background_color='white',
path_save='~/Downloads/ssm.gif'
):
"""
Initialize the GIF class.
Parameters
----------
plotter : pyvista.Plotter, optional
Plotter to use for plotting, by default None
color: str, optional
Color to use for object, by default 'orange'
show_edges: bool, optional
Whether to show edges on mesh, by default True
edge_color: str, optional
Color to use for edges, by default 'black'
camera_position: list or string, optional
Camera position to use, by default 'xz'
window_size: list, optional
Window size to use for GIF, by default [3000, 4000]
background_color: str, optional
Background color to use, by default 'white'
path_save: str, optional
Path to save GIF, by default '~/Downloads/ssm.gif'
"""
if plotter is None:
self._plotter = pv.Plotter(notebook=False, off_screen=True)
else:
self._plotter = plotter
if path_save[-3:] != 'gif':
raise Exception('path must be to a file ending with suffix `.gif`')
self.counter = 0
self._plotter.open_gif(path_save)
self._color = color
self._show_edges = show_edges
self._edge_color = edge_color
self._camera_position = camera_position
self._window_size = window_size
self._background_color = background_color
self._path_save = path_save
def update_view(
self
):
self._plotter.camera_position = self._camera_position
self._plotter.window_size = self._window_size
self._plotter.set_background(color=self._background_color)
def add_mesh_frame(self, mesh):
if type(mesh) in (list, tuple):
actors = []
for mesh_ in mesh:
actors.append(self._plotter.add_mesh(
mesh_,
render=False,
color=self._color,
edge_color=self._edge_color,
show_edges=self._show_edges
))
else:
actor = self._plotter.add_mesh(
mesh,
render=False,
color=self._color,
edge_color=self._edge_color,
show_edges=self._show_edges
)
if self.counter == 0:
self.update_view()
self._plotter.write_frame()
if type(mesh) in (list, tuple):
for actor in actors:
self._plotter.remove_actor(actor)
else:
self._plotter.remove_actor(actor)
self.counter += 1
def done(self):
self._plotter.close()
@property
def color(self):
return self._color
@color.setter
def color(self, color):
self._color = color
@property
def show_edges(self):
return self._show_edges
@show_edges.setter
def show_edges(self, show_edges):
self._show_edges = show_edges
@property
def edge_color(self):
return self._edge_color
@edge_color.setter
def edge_color(self, edge_color):
self._edge_color = edge_color
@property
def camera_position(self):
return self._camera_position
@camera_position.setter
def camera_position(self, camera_position):
self._camera_position = camera_position
@property
def window_size(self):
return self._window_size
@window_size.setter
def window_size(self, window_size):
self._window_size = window_size
@property
def background_color(self):
return self._background_color
@background_color.setter
def background_color(self, background_color):
self._background_color = background_color
@property
def path_save(self):
return self._path_save
def get_arrow(
direction,
origin,
scale=100,
tip_length=0.25,
tip_radius=0.1,
tip_resolution=20,
shaft_radius=0.05,
shaft_resolution=20,
):
arrow = vtk.vtkArrowSource()
arrow.SetTipLength(tip_length)
arrow.SetTipRadius(tip_radius)
arrow.SetTipResolution(tip_resolution)
arrow.SetShaftRadius(shaft_radius)
arrow.SetShaftResolution(shaft_resolution)
arrow.Update()
arrow = arrow.GetOutput()
points = arrow.GetPoints().GetData()
array = vtk_to_numpy(points)
array *= scale
arrow.GetPoints().SetData(numpy_to_vtk(array))
normx = np.array(direction) / np.linalg.norm(direction)
normz = np.cross(normx, [0, 1.0, 0.0001])
normz /= np.linalg.norm(normz)
normy = np.cross(normz, normx)
four_by_four = np.identity(4)
four_by_four[:3,0] = normx
four_by_four[:3,1] = normy
four_by_four[:3,2] = normz
four_by_four[:3, 3] = origin
transform = pymskt.mesh.meshTransform.create_transform(four_by_four)
arrow = pymskt.mesh.meshTransform.apply_transform(arrow, transform)
return arrow</code></pre>
</details>
</section>
<section>
</section>
<section>
</section>
<section>
<h2 class="section-title" id="header-functions">Functions</h2>
<dl>
<dt id="pymskt.mesh.utils.estimate_mesh_scalars_FWHMs"><code class="name flex">
<span>def <span class="ident">estimate_mesh_scalars_FWHMs</span></span>(<span>mesh, scalar_name='thickness_mm')</span>
</code></dt>
<dd>
<div class="desc"><p>Calculate the Full Width Half Maximum (FWHM) based on surface mesh scalars. </p>
<h2 id="parameters">Parameters</h2>
<dl>
<dt><strong><code>mesh</code></strong> : <code>vtk.vtkPolyData</code></dt>
<dd>Surface mesh to estimate FWHM of the scalars from.</dd>
<dt><strong><code>scalar_name</code></strong> : <code>str</code>, optional</dt>
<dd>Name of the scalars to calcualte FWHM for, by default 'thickness_mm'</dd>
</dl>
<h2 id="returns">Returns</h2>
<dl>
<dt><code>list</code></dt>
<dd>List of the FWHM values. Assuming they are for X/Y/Z</dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def estimate_mesh_scalars_FWHMs(mesh, scalar_name='thickness_mm'):
"""
Calculate the Full Width Half Maximum (FWHM) based on surface mesh scalars.
Parameters
----------
mesh : vtk.vtkPolyData
Surface mesh to estimate FWHM of the scalars from.
scalar_name : str, optional
Name of the scalars to calcualte FWHM for, by default 'thickness_mm'
Returns
-------
list
List of the FWHM values. Assuming they are for X/Y/Z
"""
gradient_filter = vtk.vtkGradientFilter()
gradient_filter.SetInputData(mesh)
gradient_filter.Update()
gradient_mesh = vtk.vtkPolyData()
gradient_mesh.DeepCopy(gradient_filter.GetOutput())
scalars = vtk_to_numpy(mesh.GetPointData().GetScalars())
location_non_zero = np.where(scalars != 0)
gradient_scalars = vtk_to_numpy(gradient_mesh.GetPointData().GetAbstractArray('Gradients'))
cartilage_gradients = gradient_scalars[location_non_zero, :][0]
thickness_scalars = vtk_to_numpy(gradient_mesh.GetPointData().GetAbstractArray(scalar_name))
cartilage_thicknesses = thickness_scalars[location_non_zero]
V0 = np.mean((cartilage_thicknesses - np.mean(cartilage_thicknesses)) ** 2)
V1 = np.mean((cartilage_gradients - np.mean(cartilage_gradients)) ** 2, axis=0)
sigma2s = -1 / (4 * np.log(1 - (V1 / (2 * V0))))
sigmas = np.sqrt(sigma2s)
FWHMs = [sigma2fwhm(x) for x in sigmas]
return FWHMs</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.get_arrow"><code class="name flex">
<span>def <span class="ident">get_arrow</span></span>(<span>direction, origin, scale=100, tip_length=0.25, tip_radius=0.1, tip_resolution=20, shaft_radius=0.05, shaft_resolution=20)</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def get_arrow(
direction,
origin,
scale=100,
tip_length=0.25,
tip_radius=0.1,
tip_resolution=20,
shaft_radius=0.05,
shaft_resolution=20,
):
arrow = vtk.vtkArrowSource()
arrow.SetTipLength(tip_length)
arrow.SetTipRadius(tip_radius)
arrow.SetTipResolution(tip_resolution)
arrow.SetShaftRadius(shaft_radius)
arrow.SetShaftResolution(shaft_resolution)
arrow.Update()
arrow = arrow.GetOutput()
points = arrow.GetPoints().GetData()
array = vtk_to_numpy(points)
array *= scale
arrow.GetPoints().SetData(numpy_to_vtk(array))
normx = np.array(direction) / np.linalg.norm(direction)
normz = np.cross(normx, [0, 1.0, 0.0001])
normz /= np.linalg.norm(normz)
normy = np.cross(normz, normx)
four_by_four = np.identity(4)
four_by_four[:3,0] = normx
four_by_four[:3,1] = normy
four_by_four[:3,2] = normz
four_by_four[:3, 3] = origin
transform = pymskt.mesh.meshTransform.create_transform(four_by_four)
arrow = pymskt.mesh.meshTransform.apply_transform(arrow, transform)
return arrow</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.get_intersect"><code class="name flex">
<span>def <span class="ident">get_intersect</span></span>(<span>obbTree, pSource, pTarget)</span>
</code></dt>
<dd>
<div class="desc"><p>Get intersecting points on the obbTree between a line from pSource to pTarget. </p>
<h2 id="parameters">Parameters</h2>
<dl>
<dt><strong><code>obb_tree</code></strong> : <code>vtk.vtkOBBTree</code></dt>
<dd>OBBTree of a surface mesh.</dd>
<dt><strong><code>pSource</code></strong> : <code>list</code></dt>
<dd>x/y/z position of starting point of ray (to find intersection)</dd>
<dt><strong><code>pTarget</code></strong> : <code>list</code></dt>
<dd>x/y/z position of ending point of ray (to find intersection)</dd>
</dl>
<h2 id="returns">Returns</h2>
<dl>
<dt><code>tuple (list1, list2)</code></dt>
<dd>list1 is of the intersection points
list2 is the idx of the cells that were intersected.</dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def get_intersect(obbTree, pSource, pTarget):
"""
Get intersecting points on the obbTree between a line from pSource to pTarget.
Parameters
----------
obb_tree : vtk.vtkOBBTree
OBBTree of a surface mesh.
pSource : list
x/y/z position of starting point of ray (to find intersection)
pTarget : list
x/y/z position of ending point of ray (to find intersection)
Returns
-------
tuple (list1, list2)
list1 is of the intersection points
list2 is the idx of the cells that were intersected.
"""
# Create an empty 'vtkPoints' object to store the intersection point coordinates
points = vtk.vtkPoints()
# Create an empty 'vtkIdList' object to store the ids of the cells that intersect
# with the cast rays
cell_ids = vtk.vtkIdList()
# Perform intersection
code = obbTree.IntersectWithLine(pSource, pTarget, points, cell_ids)
# Get point-data
point_data = points.GetData()
# Get number of intersection points found
n_points = point_data.GetNumberOfTuples()
# Get number of intersected cell ids
n_Ids = cell_ids.GetNumberOfIds()
assert (n_points == n_Ids)
# Loop through the found points and cells and store
# them in lists
points_inter = []
cell_ids_inter = []
for idx in range(n_points):
points_inter.append(point_data.GetTuple3(idx))
cell_ids_inter.append(cell_ids.GetId(idx))
return points_inter, cell_ids_inter</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.get_obb_surface"><code class="name flex">
<span>def <span class="ident">get_obb_surface</span></span>(<span>surface)</span>
</code></dt>
<dd>
<div class="desc"><p>Get vtk.vtkOBBTree for a surface mesh
Get obb of a surface mesh. This can be queried to see if a line etc. intersects a surface.</p>
<h2 id="parameters">Parameters</h2>
<dl>
<dt><strong><code>surface</code></strong> : <code>vtk.vtkPolyData</code></dt>
<dd>The surface mesh to get an OBBTree for.</dd>
</dl>
<h2 id="returns">Returns</h2>
<dl>
<dt><code>vtk.vtkOBBTree</code></dt>
<dd>The OBBTree to be used to find intersections for calculating cartilage thickness etc.</dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def get_obb_surface(surface):
"""
Get vtk.vtkOBBTree for a surface mesh
Get obb of a surface mesh. This can be queried to see if a line etc. intersects a surface.
Parameters
----------
surface : vtk.vtkPolyData
The surface mesh to get an OBBTree for.
Returns
-------
vtk.vtkOBBTree
The OBBTree to be used to find intersections for calculating cartilage thickness etc.
"""
obb = vtk.vtkOBBTree()
obb.SetDataSet(surface)
obb.BuildLocator()
return obb</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.get_surface_distance"><code class="name flex">
<span>def <span class="ident">get_surface_distance</span></span>(<span>surface_1, surface_2, return_RMS=True, return_individual_distances=False)</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def get_surface_distance(surface_1,
surface_2,
return_RMS=True,
return_individual_distances=False):
if (return_RMS is True) & (return_individual_distances is True):
raise Exception('Nothing to return - either return_RMS or return_individual_distances must be `True`')
pt_locator = vtk.vtkPointLocator()
pt_locator.SetDataSet(surface_2)
pt_locator.AutomaticOn()
pt_locator.BuildLocator()
distances = np.zeros(surface_1.GetNumberOfPoints())
for pt_idx in range(surface_1.GetNumberOfPoints()):
point_1 = np.asarray(surface_1.GetPoint(pt_idx))
pt_idx_2 = pt_locator.FindClosestPoint(point_1)
point_2 = np.asarray(surface_2.GetPoint(pt_idx_2))
distances[pt_idx] = np.sqrt(np.sum(np.square(point_2-point_1)))
RMS = np.sqrt(np.mean(np.square(distances)))
if return_individual_distances is True:
if return_RMS is True:
return RMS, distances
else:
return distances
else:
if return_RMS is True:
return RMS</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.get_surface_normals"><code class="name flex">
<span>def <span class="ident">get_surface_normals</span></span>(<span>surface, point_normals_on=True, cell_normals_on=True)</span>
</code></dt>
<dd>
<div class="desc"><p>Get the surface normals of a mesh (<code>surface</code></p>
<h2 id="parameters">Parameters</h2>
<dl>
<dt><strong><code>surface</code></strong> : <code>vtk.vtkPolyData</code></dt>
<dd>surface mesh to get normals from</dd>
<dt><strong><code>point_normals_on</code></strong> : <code>bool</code>, optional</dt>
<dd>Whether or not to get normals of points (vertices), by default True</dd>
<dt><strong><code>cell_normals_on</code></strong> : <code>bool</code>, optional</dt>
<dd>Whether or not to get normals from cells (faces?), by default True</dd>
</dl>
<h2 id="returns">Returns</h2>
<dl>
<dt><code>vtk.vtkPolyDataNormals</code></dt>
<dd>Normval vectors for points/cells.</dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def get_surface_normals(surface,
point_normals_on=True,
cell_normals_on=True):
"""
Get the surface normals of a mesh (`surface`
Parameters
----------
surface : vtk.vtkPolyData
surface mesh to get normals from
point_normals_on : bool, optional
Whether or not to get normals of points (vertices), by default True
cell_normals_on : bool, optional
Whether or not to get normals from cells (faces?), by default True
Returns
-------
vtk.vtkPolyDataNormals
Normval vectors for points/cells.
"""
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(surface)
# Disable normal calculation at cell vertices
if point_normals_on is True:
normals.ComputePointNormalsOn()
elif point_normals_on is False:
normals.ComputePointNormalsOff()
# Enable normal calculation at cell centers
if cell_normals_on is True:
normals.ComputeCellNormalsOn()
elif cell_normals_on is False:
normals.ComputeCellNormalsOff()
# Disable splitting of sharp edges
normals.SplittingOff()
# Disable global flipping of normal orientation
normals.FlipNormalsOff()
# Enable automatic determination of correct normal orientation
normals.AutoOrientNormalsOn()
# Perform calculation
normals.Update()
return normals</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.get_symmetric_surface_distance"><code class="name flex">
<span>def <span class="ident">get_symmetric_surface_distance</span></span>(<span>surface_1, surface_2)</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def get_symmetric_surface_distance(surface_1, surface_2):
surf1_to_2_distances = get_surface_distance(surface_1, surface_2, return_RMS=False, return_individual_distances=True)
surf2_to_1_distances = get_surface_distance(surface_2, surface_1, return_RMS=False, return_individual_distances=True)
symmetric_distance = (np.sum(surf1_to_2_distances) + np.sum(surf2_to_1_distances)) / (len(surf1_to_2_distances) + len(surf2_to_1_distances))
return symmetric_distance</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.is_hit"><code class="name flex">
<span>def <span class="ident">is_hit</span></span>(<span>obb_tree, source, target)</span>
</code></dt>
<dd>
<div class="desc"><p>Return True if line intersects mesh (<code>obb_tree</code>). The line starts at <code>source</code> and ends at <code>target</code>.</p>
<h2 id="parameters">Parameters</h2>
<dl>
<dt><strong><code>obb_tree</code></strong> : <code>vtk.vtkOBBTree</code></dt>
<dd>OBBTree of a surface mesh.</dd>
<dt><strong><code>source</code></strong> : <code>list</code></dt>
<dd>x/y/z position of starting point of ray (to find intersection)</dd>
<dt><strong><code>target</code></strong> : <code>list</code></dt>
<dd>x/y/z position of ending point of ray (to find intersection)</dd>
</dl>
<h2 id="returns">Returns</h2>
<dl>
<dt><code>bool</code></dt>
<dd>Telling if the line (source to target) intersects the obb_tree.</dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def is_hit(obb_tree, source, target):
"""
Return True if line intersects mesh (`obb_tree`). The line starts at `source` and ends at `target`.
Parameters
----------
obb_tree : vtk.vtkOBBTree
OBBTree of a surface mesh.
source : list
x/y/z position of starting point of ray (to find intersection)
target : list
x/y/z position of ending point of ray (to find intersection)
Returns
-------
bool
Telling if the line (source to target) intersects the obb_tree.
"""
code = obb_tree.IntersectWithLine(source, target, None, None)
if code == 0:
return False
else:
return True</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.vtk_deep_copy"><code class="name flex">
<span>def <span class="ident">vtk_deep_copy</span></span>(<span>mesh)</span>
</code></dt>
<dd>
<div class="desc"><p>"Deep" copy a vtk.vtkPolyData so that they are not connected in any way. </p>
<h2 id="parameters">Parameters</h2>
<dl>
<dt><strong><code>mesh</code></strong> : <code>vtk.vtkPolyData</code></dt>
<dd>Mesh to copy.</dd>
</dl>
<h2 id="returns">Returns</h2>
<dl>
<dt><code>vtk.vtkPolyData</code></dt>
<dd>Copy of the input mesh.</dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def vtk_deep_copy(mesh):
"""
"Deep" copy a vtk.vtkPolyData so that they are not connected in any way.
Parameters
----------
mesh : vtk.vtkPolyData
Mesh to copy.
Returns
-------
vtk.vtkPolyData
Copy of the input mesh.
"""
new_mesh = vtk.vtkPolyData()
new_mesh.DeepCopy(mesh)
return new_mesh</code></pre>
</details>
</dd>
</dl>
</section>
<section>
<h2 class="section-title" id="header-classes">Classes</h2>
<dl>
<dt id="pymskt.mesh.utils.GIF"><code class="flex name class">
<span>class <span class="ident">GIF</span></span>
<span>(</span><span>plotter=None, color='orange', show_edges=True, edge_color='black', camera_position='xz', window_size=[3000, 4000], background_color='white', path_save='~/Downloads/ssm.gif')</span>
</code></dt>
<dd>
<div class="desc"><p>Class for generating GIF of surface meshes.</p>
<h2 id="parameters">Parameters</h2>
<dl>
<dt><strong><code>plotter</code></strong> : <code>pyvista.Plotter</code></dt>
<dd>Plotter to use for plotting.</dd>
<dt><strong><code>color</code></strong> : <code>str</code>, optional</dt>
<dd>Color to use for object, by default 'orange'</dd>
<dt><strong><code>show_edges</code></strong> : <code>bool</code>, optional</dt>
<dd>Whether to show edges on mesh, by default True</dd>
<dt><strong><code>edge_color</code></strong> : <code>str</code>, optional</dt>
<dd>Color to use for edges, by default 'black'</dd>
<dt><strong><code>camera_position</code></strong> : <code>list</code> or <code>string</code>, optional</dt>
<dd>Camera position to use, by default 'xz'</dd>
<dt><strong><code>window_size</code></strong> : <code>list</code>, optional</dt>
<dd>Window size to use for GIF, by default [3000, 4000]</dd>
<dt><strong><code>background_color</code></strong> : <code>str</code>, optional</dt>
<dd>Background color to use, by default 'white'</dd>
<dt><strong><code>path_save</code></strong> : <code>str</code>, optional</dt>
<dd>Path to save GIF, by default '~/Downloads/ssm.gif'</dd>
</dl>
<h2 id="attributes">Attributes</h2>
<dl>
<dt><strong><code>_plotter</code></strong> : <code>pyvista.Plotter</code></dt>
<dd>Plotter to use for plotting.</dd>
<dt><strong><code>_color</code></strong> : <code>str</code></dt>
<dd>Color to use for object.</dd>
<dt><strong><code>_show_edges</code></strong> : <code>bool</code></dt>
<dd>Whether to show edges on mesh.</dd>
<dt><strong><code>_edge_color</code></strong> : <code>str</code></dt>
<dd>Color to use for edges.</dd>
<dt><strong><code>_camera_position</code></strong> : <code>list</code> or <code>string</code></dt>
<dd>Camera position to use.</dd>
<dt><strong><code>_window_size</code></strong> : <code>list</code></dt>
<dd>Window size to use for GIF.</dd>
<dt><strong><code>_background_color</code></strong> : <code>str</code></dt>
<dd>Background color to use.</dd>
<dt><strong><code>_path_save</code></strong> : <code>str</code></dt>
<dd>Path to save GIF.</dd>
</dl>
<h2 id="methods">Methods</h2>
<p>add_mesh_frame(mesh)
Add a mesh to the GIF.
update_view()
Update the view of the plotter.
done()
Close the plotter.</p>
<p>Initialize the GIF class.</p>
<h2 id="parameters_1">Parameters</h2>
<dl>
<dt><strong><code>plotter</code></strong> : <code>pyvista.Plotter</code>, optional</dt>
<dd>Plotter to use for plotting, by default None</dd>
<dt><strong><code>color</code></strong> : <code>str</code>, optional</dt>
<dd>Color to use for object, by default 'orange'</dd>
<dt><strong><code>show_edges</code></strong> : <code>bool</code>, optional</dt>
<dd>Whether to show edges on mesh, by default True</dd>
<dt><strong><code>edge_color</code></strong> : <code>str</code>, optional</dt>
<dd>Color to use for edges, by default 'black'</dd>
<dt><strong><code>camera_position</code></strong> : <code>list</code> or <code>string</code>, optional</dt>
<dd>Camera position to use, by default 'xz'</dd>
<dt><strong><code>window_size</code></strong> : <code>list</code>, optional</dt>
<dd>Window size to use for GIF, by default [3000, 4000]</dd>
<dt><strong><code>background_color</code></strong> : <code>str</code>, optional</dt>
<dd>Background color to use, by default 'white'</dd>
<dt><strong><code>path_save</code></strong> : <code>str</code>, optional</dt>
<dd>Path to save GIF, by default '~/Downloads/ssm.gif'</dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">class GIF:
"""
Class for generating GIF of surface meshes.
Parameters
----------
plotter : pyvista.Plotter
Plotter to use for plotting.
color: str, optional
Color to use for object, by default 'orange'
show_edges: bool, optional
Whether to show edges on mesh, by default True
edge_color: str, optional
Color to use for edges, by default 'black'
camera_position: list or string, optional
Camera position to use, by default 'xz'
window_size: list, optional
Window size to use for GIF, by default [3000, 4000]
background_color: str, optional
Background color to use, by default 'white'
path_save: str, optional
Path to save GIF, by default '~/Downloads/ssm.gif'
Attributes
----------
_plotter : pyvista.Plotter
Plotter to use for plotting.
_color : str
Color to use for object.
_show_edges : bool
Whether to show edges on mesh.
_edge_color : str
Color to use for edges.
_camera_position : list or string
Camera position to use.
_window_size : list
Window size to use for GIF.
_background_color : str
Background color to use.
_path_save : str
Path to save GIF.
Methods
-------
add_mesh_frame(mesh)
Add a mesh to the GIF.
update_view()
Update the view of the plotter.
done()
Close the plotter.
"""
def __init__(
self,
plotter=None,
color='orange',
show_edges=True,
edge_color='black',
camera_position='xz',
window_size=[3000, 4000],
background_color='white',
path_save='~/Downloads/ssm.gif'
):
"""
Initialize the GIF class.
Parameters
----------
plotter : pyvista.Plotter, optional
Plotter to use for plotting, by default None
color: str, optional
Color to use for object, by default 'orange'
show_edges: bool, optional
Whether to show edges on mesh, by default True
edge_color: str, optional
Color to use for edges, by default 'black'
camera_position: list or string, optional
Camera position to use, by default 'xz'
window_size: list, optional
Window size to use for GIF, by default [3000, 4000]
background_color: str, optional
Background color to use, by default 'white'
path_save: str, optional
Path to save GIF, by default '~/Downloads/ssm.gif'
"""
if plotter is None:
self._plotter = pv.Plotter(notebook=False, off_screen=True)
else:
self._plotter = plotter
if path_save[-3:] != 'gif':
raise Exception('path must be to a file ending with suffix `.gif`')
self.counter = 0
self._plotter.open_gif(path_save)
self._color = color
self._show_edges = show_edges
self._edge_color = edge_color
self._camera_position = camera_position
self._window_size = window_size
self._background_color = background_color
self._path_save = path_save
def update_view(
self
):
self._plotter.camera_position = self._camera_position
self._plotter.window_size = self._window_size
self._plotter.set_background(color=self._background_color)
def add_mesh_frame(self, mesh):
if type(mesh) in (list, tuple):
actors = []
for mesh_ in mesh:
actors.append(self._plotter.add_mesh(
mesh_,
render=False,
color=self._color,
edge_color=self._edge_color,
show_edges=self._show_edges
))
else:
actor = self._plotter.add_mesh(
mesh,
render=False,
color=self._color,
edge_color=self._edge_color,
show_edges=self._show_edges
)
if self.counter == 0:
self.update_view()
self._plotter.write_frame()
if type(mesh) in (list, tuple):
for actor in actors:
self._plotter.remove_actor(actor)
else:
self._plotter.remove_actor(actor)
self.counter += 1
def done(self):
self._plotter.close()
@property
def color(self):
return self._color
@color.setter
def color(self, color):
self._color = color
@property
def show_edges(self):
return self._show_edges
@show_edges.setter
def show_edges(self, show_edges):
self._show_edges = show_edges
@property
def edge_color(self):
return self._edge_color
@edge_color.setter
def edge_color(self, edge_color):
self._edge_color = edge_color
@property
def camera_position(self):
return self._camera_position
@camera_position.setter
def camera_position(self, camera_position):
self._camera_position = camera_position
@property
def window_size(self):
return self._window_size
@window_size.setter
def window_size(self, window_size):
self._window_size = window_size
@property
def background_color(self):
return self._background_color
@background_color.setter
def background_color(self, background_color):
self._background_color = background_color
@property
def path_save(self):
return self._path_save</code></pre>
</details>
<h3>Instance variables</h3>
<dl>
<dt id="pymskt.mesh.utils.GIF.background_color"><code class="name">var <span class="ident">background_color</span></code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">@property
def background_color(self):
return self._background_color</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.GIF.camera_position"><code class="name">var <span class="ident">camera_position</span></code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">@property
def camera_position(self):
return self._camera_position</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.GIF.color"><code class="name">var <span class="ident">color</span></code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">@property
def color(self):
return self._color</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.GIF.edge_color"><code class="name">var <span class="ident">edge_color</span></code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">@property
def edge_color(self):
return self._edge_color</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.GIF.path_save"><code class="name">var <span class="ident">path_save</span></code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">@property
def path_save(self):
return self._path_save</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.GIF.show_edges"><code class="name">var <span class="ident">show_edges</span></code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">@property
def show_edges(self):
return self._show_edges</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.GIF.window_size"><code class="name">var <span class="ident">window_size</span></code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">@property
def window_size(self):
return self._window_size</code></pre>
</details>
</dd>
</dl>
<h3>Methods</h3>
<dl>
<dt id="pymskt.mesh.utils.GIF.add_mesh_frame"><code class="name flex">
<span>def <span class="ident">add_mesh_frame</span></span>(<span>self, mesh)</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def add_mesh_frame(self, mesh):
if type(mesh) in (list, tuple):
actors = []
for mesh_ in mesh:
actors.append(self._plotter.add_mesh(
mesh_,
render=False,
color=self._color,
edge_color=self._edge_color,
show_edges=self._show_edges
))
else:
actor = self._plotter.add_mesh(
mesh,
render=False,
color=self._color,
edge_color=self._edge_color,
show_edges=self._show_edges
)
if self.counter == 0:
self.update_view()
self._plotter.write_frame()
if type(mesh) in (list, tuple):
for actor in actors:
self._plotter.remove_actor(actor)
else:
self._plotter.remove_actor(actor)
self.counter += 1</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.GIF.done"><code class="name flex">
<span>def <span class="ident">done</span></span>(<span>self)</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def done(self):
self._plotter.close()</code></pre>
</details>
</dd>
<dt id="pymskt.mesh.utils.GIF.update_view"><code class="name flex">
<span>def <span class="ident">update_view</span></span>(<span>self)</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def update_view(
self
):
self._plotter.camera_position = self._camera_position
self._plotter.window_size = self._window_size
self._plotter.set_background(color=self._background_color)</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.utils.estimate_mesh_scalars_FWHMs" href="#pymskt.mesh.utils.estimate_mesh_scalars_FWHMs">estimate_mesh_scalars_FWHMs</a></code></li>
<li><code><a title="pymskt.mesh.utils.get_arrow" href="#pymskt.mesh.utils.get_arrow">get_arrow</a></code></li>
<li><code><a title="pymskt.mesh.utils.get_intersect" href="#pymskt.mesh.utils.get_intersect">get_intersect</a></code></li>
<li><code><a title="pymskt.mesh.utils.get_obb_surface" href="#pymskt.mesh.utils.get_obb_surface">get_obb_surface</a></code></li>
<li><code><a title="pymskt.mesh.utils.get_surface_distance" href="#pymskt.mesh.utils.get_surface_distance">get_surface_distance</a></code></li>
<li><code><a title="pymskt.mesh.utils.get_surface_normals" href="#pymskt.mesh.utils.get_surface_normals">get_surface_normals</a></code></li>
<li><code><a title="pymskt.mesh.utils.get_symmetric_surface_distance" href="#pymskt.mesh.utils.get_symmetric_surface_distance">get_symmetric_surface_distance</a></code></li>
<li><code><a title="pymskt.mesh.utils.is_hit" href="#pymskt.mesh.utils.is_hit">is_hit</a></code></li>
<li><code><a title="pymskt.mesh.utils.vtk_deep_copy" href="#pymskt.mesh.utils.vtk_deep_copy">vtk_deep_copy</a></code></li>
</ul>
</li>
<li><h3><a href="#header-classes">Classes</a></h3>
<ul>
<li>
<h4><code><a title="pymskt.mesh.utils.GIF" href="#pymskt.mesh.utils.GIF">GIF</a></code></h4>
<ul class="two-column">
<li><code><a title="pymskt.mesh.utils.GIF.add_mesh_frame" href="#pymskt.mesh.utils.GIF.add_mesh_frame">add_mesh_frame</a></code></li>
<li><code><a title="pymskt.mesh.utils.GIF.background_color" href="#pymskt.mesh.utils.GIF.background_color">background_color</a></code></li>
<li><code><a title="pymskt.mesh.utils.GIF.camera_position" href="#pymskt.mesh.utils.GIF.camera_position">camera_position</a></code></li>
<li><code><a title="pymskt.mesh.utils.GIF.color" href="#pymskt.mesh.utils.GIF.color">color</a></code></li>
<li><code><a title="pymskt.mesh.utils.GIF.done" href="#pymskt.mesh.utils.GIF.done">done</a></code></li>
<li><code><a title="pymskt.mesh.utils.GIF.edge_color" href="#pymskt.mesh.utils.GIF.edge_color">edge_color</a></code></li>
<li><code><a title="pymskt.mesh.utils.GIF.path_save" href="#pymskt.mesh.utils.GIF.path_save">path_save</a></code></li>
<li><code><a title="pymskt.mesh.utils.GIF.show_edges" href="#pymskt.mesh.utils.GIF.show_edges">show_edges</a></code></li>
<li><code><a title="pymskt.mesh.utils.GIF.update_view" href="#pymskt.mesh.utils.GIF.update_view">update_view</a></code></li>
<li><code><a title="pymskt.mesh.utils.GIF.window_size" href="#pymskt.mesh.utils.GIF.window_size">window_size</a></code></li>
</ul>
</li>
</ul>
</li>
</ul>
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