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"""
.. _volumetric_analysis_example:
Volumetric Analysis
~~~~~~~~~~~~~~~~~~~
Calculate mass properties such as the volume or area of datasets
"""
# sphinx_gallery_thumbnail_number = 4
from __future__ import annotations
import numpy as np
from pyvista import examples
# %%
# Computing mass properties such as the volume or area of datasets in PyVista
# is quite easy using the :func:`pyvista.DataObjectFilters.compute_cell_sizes`
# filter and the :attr:`pyvista.DataSet.volume` property on all PyVista meshes.
#
# Let's get started with a simple gridded mesh:
# Load a simple example mesh
dataset = examples.load_uniform()
dataset.set_active_scalars('Spatial Cell Data')
# %%
# We can then calculate the volume of every cell in the array using the
# ``.compute_cell_sizes`` filter which will add arrays to the cell data of the
# mesh core the volume and area by default.
# Compute volumes and areas
sized = dataset.compute_cell_sizes()
# Grab volumes for all cells in the mesh
cell_volumes = sized.cell_data['Volume']
# %%
# We can also compute the total volume of the mesh using the ``.volume``
# property:
# Compute the total volume of the mesh
volume = dataset.volume
# %%
# But what if we have a dataset that we threshold with two
# volumetric bodies left over in one dataset? Take this for example:
threshed = dataset.threshold_percent([0.15, 0.50], invert=True)
threshed.plot(show_grid=True, cpos=[-2, 5, 3])
# %%
# We could then assign a classification array for the two bodies, compute the
# cell sizes, then extract the volumes of each body. Note that there is a
# simpler implementation of this below in :ref:`split_vol`.
# Create a classifying array to ID each body
rng = dataset.get_data_range()
cval = ((rng[1] - rng[0]) * 0.20) + rng[0]
classifier = threshed.cell_data['Spatial Cell Data'] > cval
# Compute cell volumes
sizes = threshed.compute_cell_sizes()
volumes = sizes.cell_data['Volume']
# Split volumes based on classifier and get the volumes
idx = np.argwhere(classifier)
hvol = np.sum(volumes[idx])
idx = np.argwhere(~classifier)
lvol = np.sum(volumes[idx])
print(f'Low grade volume: {lvol}')
print(f'High grade volume: {hvol}')
print(f'Original volume: {dataset.volume}')
# %%
# Or better yet, you could simply extract the largest volume from your
# dataset directly by passing ``'largest'`` to the ``connectivity`` and
# specifying the scalar range of interest.
# Grab the largest connected volume within a scalar range
scalar_range = [0, 77] # Range corresponding to bottom 15% of values
largest = threshed.connectivity('largest', scalar_range=scalar_range)
# Get volume as numeric value
large_volume = largest.volume
# Display it
largest.plot(show_grid=True, cpos=[-2, 5, 3])
# %%
# -----
#
# .. _split_vol:
#
# Splitting Volumes
# +++++++++++++++++
#
# What if instead, we wanted to split all the different connected bodies /
# volumes in a dataset like the one above? We could use the
# :func:`pyvista.DataSetFilters.split_bodies` filter to extract all the
# different connected volumes in a dataset into blocks in a
# :class:`pyvista.MultiBlock` dataset. For example, lets split the thresholded
# volume in the example above:
# Load a simple example mesh
dataset = examples.load_uniform()
dataset.set_active_scalars('Spatial Cell Data')
threshed = dataset.threshold_percent([0.15, 0.50], invert=True)
bodies = threshed.split_bodies()
for i, body in enumerate(bodies):
print(f'Body {i} volume: {body.volume:.3f}')
# %%
bodies.plot(show_grid=True, multi_colors=True, cpos=[-2, 5, 3])
# %%
# -----
#
# A Real Dataset
# ++++++++++++++
#
# Here is a realistic training dataset of fluvial channels in the subsurface.
# This will threshold the channels from the dataset then separate each
# significantly large body and compute the volumes for each.
#
# Load up the data and threshold the channels:
data = examples.load_channels()
channels = data.threshold([0.9, 1.1])
# %%
# Now extract all the different bodies and compute their volumes:
bodies = channels.split_bodies()
# Now remove all bodies with a small volume
for key in bodies.keys():
b = bodies[key]
vol = b.volume
if vol < 1000.0:
del bodies[key]
continue
# Now lets add a volume array to all blocks
b.cell_data['TOTAL VOLUME'] = np.full(b.n_cells, vol)
# %%
# Print out the volumes for each body:
for i, body in enumerate(bodies):
print(f'Body {i:02d} volume: {body.volume:.3f}')
# %%
# And visualize all the different volumes:
bodies.plot(scalars='TOTAL VOLUME', cmap='viridis', show_grid=True)
# %%
# .. tags:: filter
|
