import os
import numpy as np
import openpnm as op
import pandas as pd
[docs]
def project_to_paraview(project, filename): # pragma: no cover
r"""
Exports an OpenPNM network to a paraview state file.
Parameters
----------
network : Network
The network containing the desired data.
filename : str
Path to saved .vtp file.
Notes
-----
Outputs a pvsm file that can be opened in Paraview. The pvsm file will
be saved with the same name as .vtp file
"""
try:
import paraview.simple
except ModuleNotFoundError:
msg = (
"The paraview python bindings must be installed using "
"conda install -c conda-forge paraview, however this may require"
" using a virtualenv since conflicts with other packages are common."
" This is why it is not explicitly included as a dependency in"
" OpenPNM."
)
raise ModuleNotFoundError(msg)
paraview.simple._DisableFirstRenderCameraReset()
file = os.path.splitext(filename)[0]
network = project.network
x, y, z = np.ptp(network.coords, axis=0)
if sum(op.topotools.dimensionality(network)) == 2:
zshape = 0
xshape = y
yshape = x
elif sum(op.topotools.dimensionality(network)) == 3:
zshape = x
xshape = z
yshape = y
maxshape = max(xshape, yshape, zshape)
shape = np.array([xshape, yshape, zshape])
# Create a new 'XML PolyData Reader'
Path = os.getcwd() + "\\" + file + '.vtp'
net_vtp = paraview.simple.XMLPolyDataReader(FileName=[Path])
p = op.io.Dict.to_dict(project=project, element=['pore'],
flatten=False,
categorize_by=['data' 'object'])
# The folloing lines are bit complex but avoid using the flatdict lib
p = pd.json_normalize(p, sep='.').to_dict(orient='records')[0]
for k in list(p.keys()):
p[k.replace('.', ' | ')] = p.pop(k)
t = op.io.Dict.to_dict(project=project, element=['throat'],
flatten=False,
categorize_by=['data' 'object'])
t = pd.json_normalize(t, sep='.').to_dict(orient='records')[0]
for k in list(t.keys()):
t[k.replace('.', '/')] = t.pop(k)
# Now write the p and t dictionaries
net_vtp.CellArrayStatus = t.keys()
net_vtp.PointArrayStatus = p.keys()
# Get active view
render_view = paraview.simple.GetActiveViewOrCreate('RenderView')
# Uncomment following to set a specific view size
# render_view.ViewSize = [1524, 527]
# Get layout
_ = paraview.simple.GetLayout()
# Show data in view
net_vtp_display = paraview.simple.Show(
net_vtp, render_view, 'GeometryRepresentation'
)
# Trace defaults for the display properties.
net_vtp_display.Representation = 'Surface'
net_vtp_display.ColorArrayName = [None, '']
net_vtp_display.OSPRayScaleArray = [
f'network | {network.name} | labels | pore.all']
net_vtp_display.OSPRayScaleFunction = 'PiecewiseFunction'
net_vtp_display.SelectOrientationVectors = 'None'
net_vtp_display.ScaleFactor = (maxshape-1)/10
net_vtp_display.SelectScaleArray = 'None'
net_vtp_display.GlyphType = 'Arrow'
net_vtp_display.GlyphTableIndexArray = 'None'
net_vtp_display.GaussianRadius = (maxshape-1)/200
net_vtp_display.SetScaleArray = \
['POINTS', 'network | ' + network.name + ' | labels | pore.all']
net_vtp_display.ScaleTransferFunction = 'PiecewiseFunction'
net_vtp_display.OpacityArray = \
['POINTS', 'network | ' + network.name + ' | labels | pore.all']
net_vtp_display.OpacityTransferFunction = 'PiecewiseFunction'
net_vtp_display.DataAxesGrid = 'GridAxesRepresentation'
net_vtp_display.PolarAxes = 'PolarAxesRepresentation'
# Init the 'PiecewiseFunction' selected for 'ScaleTransferFunction'
net_vtp_display.ScaleTransferFunction.Points = [1, 0, 0.5, 0, 1, 1, 0.5, 0]
# Init the 'PiecewiseFunction' selected for 'OpacityTransferFunction'
net_vtp_display.OpacityTransferFunction.Points = [1, 0, 0.5, 0, 1, 1, 0.5, 0]
# Reset view to fit data
render_view.ResetCamera()
# Get the material library
_ = paraview.simple.GetMaterialLibrary()
# Update the view to ensure updated data information
render_view.Update()
# Create a new 'Glyph'
glyph = paraview.simple.Glyph(Input=net_vtp, GlyphType='Arrow')
glyph.OrientationArray = ['POINTS', 'No orientation array']
glyph.ScaleArray = ['POINTS', 'No scale array']
glyph.ScaleFactor = 1
glyph.GlyphTransform = 'Transform2'
# Properties modified on glyph
glyph.GlyphType = 'Sphere'
glyph.ScaleArray = \
['POINTS', 'network | ' + network.name + ' | properties | pore.diameter']
# Show data in view
glyph_display = paraview.simple.Show(
glyph, render_view, 'GeometryRepresentation')
# Trace defaults for the display properties.
glyph_display.Representation = 'Surface'
glyph_display.ColorArrayName = [None, '']
glyph_display.OSPRayScaleArray = 'Normals'
glyph_display.OSPRayScaleFunction = 'PiecewiseFunction'
glyph_display.SelectOrientationVectors = 'None'
glyph_display.ScaleFactor = (maxshape - 1) / 10
glyph_display.SelectScaleArray = 'None'
glyph_display.GlyphType = 'Arrow'
glyph_display.GlyphTableIndexArray = 'None'
glyph_display.GaussianRadius = (maxshape - 1) / 200
glyph_display.SetScaleArray = ['POINTS', 'Normals']
glyph_display.ScaleTransferFunction = 'PiecewiseFunction'
glyph_display.OpacityArray = ['POINTS', 'Normals']
glyph_display.OpacityTransferFunction = 'PiecewiseFunction'
glyph_display.DataAxesGrid = 'GridAxesRepresentation'
glyph_display.PolarAxes = 'PolarAxesRepresentation'
# Init the 'PiecewiseFunction' selected for 'ScaleTransferFunction'
glyph_display.ScaleTransferFunction.Points = [-0.97, 0, 0.5, 0, 0.97, 1, 0.5, 0]
# Init the 'PiecewiseFunction' selected for 'OpacityTransferFunction'
glyph_display.OpacityTransferFunction.Points = [-0.97, 0, 0.5, 0, 0.97, 1, 0.5, 0]
# Update the view to ensure updated data information
render_view.Update()
# Set active source
paraview.simple.SetActiveSource(net_vtp)
# Create a new 'Shrink'
shrink1 = paraview.simple.Shrink(Input=net_vtp)
# Properties modified on shrink1
shrink1.ShrinkFactor = 1.0
# Show data in view
shrink_display = paraview.simple.Show(
shrink1, render_view, 'UnstructuredGridRepresentation')
# Trace defaults for the display properties.
shrink_display.Representation = 'Surface'
shrink_display.ColorArrayName = [None, '']
shrink_display.OSPRayScaleArray = \
['network | ' + network.name + ' | labels | pore.all']
shrink_display.OSPRayScaleFunction = 'PiecewiseFunction'
shrink_display.SelectOrientationVectors = 'None'
shrink_display.ScaleFactor = (maxshape-1)/10
shrink_display.SelectScaleArray = 'None'
shrink_display.GlyphType = 'Arrow'
shrink_display.GlyphTableIndexArray = 'None'
shrink_display.GaussianRadius = (maxshape-1)/200
shrink_display.SetScaleArray = \
['POINTS', 'network | ' + network.name + ' | labels | pore.all']
shrink_display.ScaleTransferFunction = 'PiecewiseFunction'
shrink_display.OpacityArray = \
['POINTS', 'network | ' + network.name + ' | labels | pore.all']
shrink_display.OpacityTransferFunction = 'PiecewiseFunction'
shrink_display.DataAxesGrid = 'GridAxesRepresentation'
shrink_display.PolarAxes = 'PolarAxesRepresentation'
shrink_display.ScalarOpacityUnitDistance = 1.0349360947089783
# Init the 'PiecewiseFunction' selected for 'ScaleTransferFunction'
shrink_display.ScaleTransferFunction.Points = [1, 0, 0.5, 0, 1, 1, 0.5, 0]
# Init the 'PiecewiseFunction' selected for 'OpacityTransferFunction'
shrink_display.OpacityTransferFunction.Points = [1, 0, 0.5, 0, 1, 1, 0.5, 0]
# Hide data in view
paraview.simple.Hide(net_vtp, render_view)
# Update the view to ensure updated data information
render_view.Update()
# Create a new 'Cell Data to Point Data'
cellDatatoPointData1 = paraview.simple.CellDatatoPointData(Input=shrink1)
cellDatatoPointData1.CellDataArraytoprocess = t
# Show data in view
cell_data_to_point_data_display = paraview.simple.Show(
cellDatatoPointData1, render_view, 'UnstructuredGridRepresentation'
)
# Trace defaults for the display properties.
cell_data_to_point_data_display.Representation = 'Surface'
cell_data_to_point_data_display.ColorArrayName = [None, '']
cell_data_to_point_data_display.OSPRayScaleArray = \
['network | ' + network.name + ' | labels | pore.all']
cell_data_to_point_data_display.OSPRayScaleFunction = 'PiecewiseFunction'
cell_data_to_point_data_display.SelectOrientationVectors = 'None'
cell_data_to_point_data_display.ScaleFactor = (maxshape-1)/10
cell_data_to_point_data_display.SelectScaleArray = 'None'
cell_data_to_point_data_display.GlyphType = 'Arrow'
cell_data_to_point_data_display.GlyphTableIndexArray = 'None'
cell_data_to_point_data_display.GaussianRadius = (maxshape-1)/200
cell_data_to_point_data_display.SetScaleArray = \
['POINTS', 'network | ' + network.name + ' | labels | pore.all']
cell_data_to_point_data_display.ScaleTransferFunction = 'PiecewiseFunction'
cell_data_to_point_data_display.OpacityArray = \
['POINTS', 'network | ' + network.name + ' | labels | pore.all']
cell_data_to_point_data_display.OpacityTransferFunction = 'PiecewiseFunction'
cell_data_to_point_data_display.DataAxesGrid = 'GridAxesRepresentation'
cell_data_to_point_data_display.PolarAxes = 'PolarAxesRepresentation'
cell_data_to_point_data_display.ScalarOpacityUnitDistance = 1.0349360947089783
# Init the 'PiecewiseFunction' selected for 'ScaleTransferFunction'
cell_data_to_point_data_display.ScaleTransferFunction.Points = [
1, 0, 0.5, 0, 1, 1, 0.5, 0]
# Init the 'PiecewiseFunction' selected for 'OpacityTransferFunction'
cell_data_to_point_data_display.OpacityTransferFunction.Points = [
1, 0, 0.5, 0, 1, 1, 0.5, 0]
# Hide data in view
paraview.simple.Hide(shrink1, render_view)
# Update the view to ensure updated data information
render_view.Update()
# Set active source
paraview.simple.SetActiveSource(shrink1)
# Set active source
paraview.simple.SetActiveSource(cellDatatoPointData1)
# Set active source
paraview.simple.SetActiveSource(shrink1)
# Create a new 'Extract Surface'
extractSurface1 = paraview.simple.ExtractSurface(Input=shrink1)
# Show data in view
extract_surface_display = paraview.simple.Show(
extractSurface1, render_view, 'GeometryRepresentation')
# Trace defaults for the display properties.
extract_surface_display.Representation = 'Surface'
extract_surface_display.ColorArrayName = [None, '']
extract_surface_display.OSPRayScaleArray = \
['network | ' + network.name + ' | labels | pore.all']
extract_surface_display.OSPRayScaleFunction = 'PiecewiseFunction'
extract_surface_display.SelectOrientationVectors = 'None'
extract_surface_display.ScaleFactor = (maxshape-1)/10
extract_surface_display.SelectScaleArray = 'None'
extract_surface_display.GlyphType = 'Arrow'
extract_surface_display.GlyphTableIndexArray = 'None'
extract_surface_display.GaussianRadius = (maxshape-1)/200
extract_surface_display.SetScaleArray = \
['POINTS', 'network | ' + network.name + ' | labels | pore.all']
extract_surface_display.ScaleTransferFunction = 'PiecewiseFunction'
extract_surface_display.OpacityArray = \
['POINTS', 'network | ' + network.name + ' | labels | pore.all']
extract_surface_display.OpacityTransferFunction = 'PiecewiseFunction'
extract_surface_display.DataAxesGrid = 'GridAxesRepresentation'
extract_surface_display.PolarAxes = 'PolarAxesRepresentation'
# Init the 'PiecewiseFunction' selected for 'ScaleTransferFunction'
extract_surface_display.ScaleTransferFunction.Points = [
1, 0, 0.5, 0, 1, 1, 0.5, 0]
# Init the 'PiecewiseFunction' selected for 'OpacityTransferFunction'
extract_surface_display.OpacityTransferFunction.Points = [
1, 0, 0.5, 0, 1, 1, 0.5, 0]
# Hide data in view
paraview.simple.Hide(shrink1, render_view)
# Update the view to ensure updated data information
render_view.Update()
# create a new 'Tube'
tube = paraview.simple.Tube(Input=extractSurface1)
tube.Scalars = ['POINTS', 'network |' + network.name + '| labels | pore.all']
tube.Vectors = [None, '1']
tube.Radius = 0.04
# Set active source
paraview.simple.SetActiveSource(extractSurface1)
# Destroy tube
paraview.simple.Delete(tube)
del tube
# Set active source
paraview.simple.SetActiveSource(shrink1)
# Set active source
paraview.simple.SetActiveSource(cellDatatoPointData1)
# Set active source
paraview.simple.SetActiveSource(extractSurface1)
# Create a new 'Tube'
tube = paraview.simple.Tube(Input=extractSurface1)
tube.Scalars = [
'POINTS', 'network |' + network.name + ' | labels | pore.all']
tube.Vectors = [None, '1']
tube.Radius = 0.04
# Properties modified on tube
tube.Vectors = ['POINTS', '1']
# Show data in view
tube_display = paraview.simple.Show(tube, render_view,
'GeometryRepresentation')
# Trace defaults for the display properties.
tube_display.Representation = 'Surface'
tube_display.ColorArrayName = [None, '']
tube_display.OSPRayScaleArray = 'TubeNormals'
tube_display.OSPRayScaleFunction = 'PiecewiseFunction'
tube_display.SelectOrientationVectors = 'None'
tube_display.ScaleFactor = (maxshape)/10
tube_display.SelectScaleArray = 'None'
tube_display.GlyphType = 'Arrow'
tube_display.GlyphTableIndexArray = 'None'
tube_display.GaussianRadius = (maxshape)/200
tube_display.SetScaleArray = ['POINTS', 'TubeNormals']
tube_display.ScaleTransferFunction = 'PiecewiseFunction'
tube_display.OpacityArray = ['POINTS', 'TubeNormals']
tube_display.OpacityTransferFunction = 'PiecewiseFunction'
tube_display.DataAxesGrid = 'GridAxesRepresentation'
tube_display.PolarAxes = 'PolarAxesRepresentation'
# Init the 'PiecewiseFunction' selected for 'ScaleTransferFunction'
tube_display.ScaleTransferFunction.Points = [-1, 0, 0.5, 0, 1, 1, 0.5, 0]
# Init the 'PiecewiseFunction' selected for 'OpacityTransferFunction'
tube_display.OpacityTransferFunction.Points = [-1, 0, 0.5, 0, 1, 1, 0.5, 0]
# Hide data in view
paraview.simple.Hide(extractSurface1, render_view)
# Update the view to ensure updated data information
render_view.Update()
# Saving camera placements for all active views
# Current camera placement for render_view
render_view.CameraPosition = [
(xshape + 1) / 2, (yshape + 1) / 2, 4.3 * np.sqrt(np.sum(shape / 2)**2)
]
render_view.CameraFocalPoint = [(xi+1) / 2 for xi in shape]
render_view.CameraParallelScale = np.sqrt(np.sum(shape / 2)**2)
paraview.simple.SaveState(f"{file}.pvsm")
