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"""
.. _slice_example:
Slicing
~~~~~~~
Extract thin planar slices from a volume.
"""
from __future__ import annotations
import matplotlib.pyplot as plt
import numpy as np
# sphinx_gallery_thumbnail_number = 2
import pyvista as pv
from pyvista import examples
# %%
# PyVista meshes have several slicing filters bound directly to all datasets.
# These filters allow you to slice through a volumetric dataset to extract and
# view sections through the volume of data.
#
# One of the most common slicing filters used in PyVista is the
# :func:`pyvista.DataSetFilters.slice_orthogonal` filter which creates three
# orthogonal slices through the dataset parallel to the three Cartesian planes.
# For example, let's slice through the sample geostatistical training image
# volume. First, load up the volume and preview it:
mesh = examples.load_channels()
# define a categorical colormap
cmap = plt.get_cmap("viridis", 4)
mesh.plot(cmap=cmap)
# %%
# Note that this dataset is a 3D volume and there might be regions within this
# volume that we would like to inspect. We can create slices through the mesh
# to gain further insight about the internals of the volume.
slices = mesh.slice_orthogonal()
slices.plot(cmap=cmap)
# %%
# The orthogonal slices can be easily translated throughout the volume:
slices = mesh.slice_orthogonal(x=20, y=20, z=30)
slices.plot(cmap=cmap)
# %%
# We can also add just a single slice of the volume by specifying the origin
# and normal of the slicing plane with the :func:`pyvista.DataSetFilters.slice`
# filter:
# Single slice - origin defaults to the center of the mesh
single_slice = mesh.slice(normal=[1, 1, 0])
p = pv.Plotter()
p.add_mesh(mesh.outline(), color="k")
p.add_mesh(single_slice, cmap=cmap)
p.show()
# %%
# Adding slicing planes uniformly across an axial direction can also be
# automated with the :func:`pyvista.DataSetFilters.slice_along_axis` filter:
slices = mesh.slice_along_axis(n=7, axis="y")
slices.plot(cmap=cmap)
# %%
# Slice Along Line
# ++++++++++++++++
#
# We can also slice a dataset along a :func:`pyvista.Spline` or
# :func:`pyvista.Line` using the :func:`pyvista.DataSetFilters.slice_along_line` filter.
#
# First, define a line source through the dataset of interest. Please note
# that this type of slicing is computationally expensive and might take a while
# if there are a lot of points in the line - try to keep the resolution of
# the line low.
model = examples.load_channels()
def path(y):
"""Equation: x = a(y-h)^2 + k"""
a = 110.0 / 160.0**2
x = a * y**2 + 0.0
return x, y
x, y = path(np.arange(model.bounds[2], model.bounds[3], 15.0))
zo = np.linspace(9.0, 11.0, num=len(y))
points = np.c_[x, y, zo]
spline = pv.Spline(points, 15)
spline
# %%
# Then run the filter
slc = model.slice_along_line(spline)
slc
# %%
p = pv.Plotter()
p.add_mesh(slc, cmap=cmap)
p.add_mesh(model.outline())
p.show(cpos=[1, -1, 1])
# %%
# Multiple Slices in Vector Direction
# +++++++++++++++++++++++++++++++++++
#
# Slice a mesh along a vector direction perpendicularly.
mesh = examples.download_brain()
# Create vector
vec = np.array([1.0, 2.0, 1.0])
# Normalize the vector
normal = vec / np.linalg.norm(vec)
# Make points along that vector for the extent of your slices
a = mesh.center + normal * mesh.length / 3.0
b = mesh.center - normal * mesh.length / 3.0
# Define the line/points for the slices
n_slices = 5
line = pv.Line(a, b, n_slices)
# Generate all of the slices
slices = pv.MultiBlock()
for point in line.points:
slices.append(mesh.slice(normal=normal, origin=point))
# %%
p = pv.Plotter()
p.add_mesh(mesh.outline(), color="k")
p.add_mesh(slices, opacity=0.75)
p.add_mesh(line, color="red", line_width=5)
p.show()
# %%
# Slice At Different Bearings
# +++++++++++++++++++++++++++
#
# From `pyvista-support#23 <https://github.com/pyvista/pyvista-support/issues/23>`_
#
# An example of how to get many slices at different bearings all centered
# around a user-chosen location.
#
# Create a point to orient slices around
ranges = np.ptp(np.array(model.bounds).reshape(-1, 2), axis=1)
point = np.array(model.center) - ranges * 0.25
# %%
# Now generate a few normal vectors to rotate a slice around the z-axis.
# Use equation for circle since its about the Z-axis.
increment = np.pi / 6.0
# use a container to hold all the slices
slices = pv.MultiBlock() # treat like a dictionary/list
for theta in np.arange(0, np.pi, increment):
normal = np.array([np.cos(theta), np.sin(theta), 0.0]).dot(np.pi / 2.0)
name = f'Bearing: {np.rad2deg(theta):.2f}'
slices[name] = model.slice(origin=point, normal=normal)
slices
# %%
# And now display it.
p = pv.Plotter()
p.add_mesh(slices, cmap=cmap)
p.add_mesh(model.outline())
p.show()
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