def processFile(self):
self._download_mesh_file()
reader = simple.OpenDataFile(_MeshViewer.meshFile)
reader.UpdatePipeline()
self.outline = simple.Show(reader)
self.outline.Representation = 'Outline'
# Get information about cell data arrays
nbFaces = 0
cdInfo = reader.GetCellDataInformation()
numberOfCellArrays = cdInfo.GetNumberOfArrays()
for idx in xrange(numberOfCellArrays):
array = cdInfo.GetArray(idx)
if array.GetName() != 'modelfaceids':
continue
nbFaces = int(array.GetRange(-1)[1])
# Extract each face and keep representation around
_MeshViewer.faces = []
for idx in range(nbFaces):
threshold = simple.Threshold(Scalars=['CELLS', 'modelfaceids'],
Input=reader,
ThresholdRange=[idx, idx])
rep = simple.Show(threshold)
_MeshViewer.faces.append(rep)
self.view = simple.Render()
self.view.Background = [0, 0, 0]
def reload_models(self):
self._clean_vizard_models()
# Apply clip filter
data = self._apply_clip(self.vtk_data)
# Iterate over every material
material_range = self.vtk_data_local.GetCellData().GetArray(
cfg.material_name).GetRange()
for material in range(int(material_range[0]),
int(material_range[1]) + 1):
# Separate the data by material
material_data = pv.Threshold(Input=data)
self._filters += [material_data]
# Settings are generated mostly by ParaView Trace function
material_data.Scalars = ['CELLS', cfg.material_name]
material_data.ThresholdRange = [material, material]
# Generate cloud
local = pv.servermanager.Fetch(material_data)
self.cloud_materials[material] = self.generate_cloud(
local, cfg.coloring_name)
self.cloud_materials[material].setParent(self.cloud_node)
# Apply ExtractSurface and Triangulate filter
extractSurface = pv.ExtractSurface(Input=material_data)
self._filters += [extractSurface]
# Settings are generated by ParaView Trace function
extractSurface.PieceInvariant = 1
extractSurface.NonlinearSubdivisionLevel = 1
triangulate = pv.Triangulate(Input=extractSurface)
self._filters += [triangulate]
# Generate surface
local = pv.servermanager.Fetch(triangulate)
self.surface_materials[material] = self.generate_surface(
local, cfg.coloring_name)
self.surface_materials[material].setParent(self.surface_node)
from paraview import simple
from paraview.web.dataset_builder import *
# -----------------------------------------------------------------------------
# Pipeline creation
# -----------------------------------------------------------------------------
core = simple.OpenDataFile(earthCore)
coreSurface = simple.ExtractSurface(Input=core)
coreWithNormals = simple.GenerateSurfaceNormals(Input=coreSurface)
reader = simple.OpenDataFile(inputFile % time[0])
reader.CellArrayStatus = ['temperature', 'salinity']
dataCleanUp = simple.Threshold(Input=reader,
Scalars=['CELLS', 'temperature'],
ThresholdRange=[-1000.0, 50.0])
dataToPoints = simple.CellDatatoPointData(Input=dataCleanUp)
sceneDescription = {
'size': [500, 500],
'light': ['intensity', 'normal'],
'camera': {
'CameraViewUp': [0.0, 0.0, 1.0],
'CameraPosition': [107823.5, -28000000, -44044.25],
'CameraFocalPoint': [107823.5, -7766.0, -44044.25]
},
'scene': [{
'name': 'Earth',
'source': coreWithNormals,
'colors': {
def _threshold_vtk(self, vtk, name):
threshold = ps.Threshold(Input=vtk)
threshold.Scalars = ["POINTS", name]
threshold.ThresholdRange = self._get_range(vtk)
return threshold
def get_curvatures(vtk_file, vtk_file_dir, output_file, output_file_dir,
arr_name, sample_rate, gauss_filter, mean_filter):
import paraview.simple as ps
import numpy as np
import paraview as pv
from vtk.util.numpy_support import vtk_to_numpy
# have paraview open the vtk data file
reader = ps.OpenDataFile(vtk_file_dir + vtk_file)
sys_data = pv.servermanager.Fetch(reader)
nx, ny, nz = sys_data.GetDimensions()
dx, dy, dz = sys_data.GetSpacing()
# downsample the data (makes for a smoother contour surface)
ds = ps.ExtractSubset(reader)
ds.SampleRateI = sample_rate
ds.SampleRateJ = sample_rate
ds.SampleRateK = sample_rate
ds.VOI[1] = nx - 1
ds.VOI[3] = ny - 1
ds.VOI[5] = nz - 1
ds.IncludeBoundary = 1
ds.UpdatePipeline()
# have paraview apply a contour surface at a concentration value of cont_val
contour = ps.Contour(ds)
cont_val = 0.0 # this might change depending on order parameter
contour.ContourBy = ['POINTS',
arr_name] # Viz is the name of the vtk array
contour.Isosurfaces = [cont_val]
contour.SetPropertyWithName('ComputeNormals', 0)
contour.UpdatePipeline()
# have paraview calculate the curvature (default is Gaussian)
curvature = ps.Curvature(contour)
# filter the curvatures
threshold = ps.Threshold(curvature)
threshold.Scalars = ['POINTS', 'Gauss_Curvature']
threshold.ThresholdRange = [-gauss_filter, gauss_filter]
threshold.AllScalars = 1
threshold.UpdatePipeline()
gauss_data = pv.servermanager.Fetch(threshold)
size_gauss = gauss_data.GetPointData().GetArray(0).GetSize()
# convert vtk array to numpy array
gauss_curv = vtk_to_numpy(gauss_data.GetPointData().GetArray(0))
# integrate the surface area and curvature
summed_curv = ps.IntegrateVariables(threshold)
summed_curv_data = pv.servermanager.Fetch(summed_curv)
g_surf_area = summed_curv_data.GetCellData().GetArray(0).GetValue(0)
# have paraview recalculate the mean curvature
curvature.SetPropertyWithName('CurvatureType', 'Mean')
curvature.UpdatePipeline()
threshold = ps.Threshold(curvature)
threshold.Scalars = ['POINTS', 'Mean_Curvature']
threshold.ThresholdRange = [-mean_filter, mean_filter]
threshold.UpdatePipeline()
summed_curv = ps.IntegrateVariables(threshold)
summed_curv.UpdatePipeline()
summed_curv_data = pv.servermanager.Fetch(summed_curv)
m_surf_area = summed_curv_data.GetCellData().GetArray(0).GetValue(0)
mean_data = pv.servermanager.Fetch(threshold)
# convert vtk array to numpy array
mean_curv = vtk_to_numpy(mean_data.GetPointData().GetArray(0))
# calculate the surface area to volume ratio
g_surf_to_vol = g_surf_area / (nx * dx * ny * dy * nz * dz)
m_surf_to_vol = m_surf_area / (nx * dx * ny * dy * nz * dz)
# calculate percent of data used in threshold
curvature_data = pv.servermanager.Fetch(curvature)
size_curv = curvature_data.GetPointData().GetArray(0).GetSize()
# save the numpy arrays for later manipulation
np.savez(output_file_dir + output_file, gauss_curv, mean_curv,
g_surf_to_vol, g_surf_area, m_surf_to_vol, m_surf_area)
# delete paraview sources and filters
ps.Delete(summed_curv)
ps.Delete(contour)
ps.Delete(ds)
ps.Delete(reader)
del (sys_data)
del (summed_curv_data)
return 0
class Pipeline:
# Create data source "input" (provides simulation fields)
simData = coprocessor.CreateProducer(datadescription, "input")
# Write VTK output if requested
if writeVtkOutput:
fullWriter = pvs.XMLHierarchicalBoxDataWriter(
Input=simData, DataMode="Appended", CompressorType="ZLib")
# Set freq=1 to ensure that output is written whenever the pipeline runs
coprocessor.RegisterWriter(fullWriter,
filename='bg_out_%t.vth',
freq=1)
# Create a new render view to generate images
renderView = pvs.CreateView('RenderView')
renderView.ViewSize = [1500, 768]
renderView.InteractionMode = '2D'
renderView.AxesGrid = 'GridAxes3DActor'
renderView.CenterOfRotation = [2.8, 1.7, 0.0]
renderView.StereoType = 0
renderView.CameraPosition = [2.8, 1.7, 10000.0]
renderView.CameraFocalPoint = [2.8, 1.7, 0.0]
renderView.CameraParallelScale = 3.386
renderView.Background = [0.32, 0.34, 0.43]
renderView.ViewTime = datadescription.GetTime()
# Show simulation time with 1 digit after decimal point
annotateTime = pvs.AnnotateTime()
annotateTime.Format = 'time: %.1f'
timeDisplay = pvs.Show(annotateTime, renderView)
# Combine uu and vv components into velocity vector field
calculatorVelField = pvs.Calculator(Input=simData)
calculatorVelField.AttributeType = 'Cell Data'
calculatorVelField.ResultArrayName = 'velocity'
calculatorVelField.Function = 'uu*iHat+vv*jHat'
# Compute velocity field magnitudes
calculatorVelMag = pvs.Calculator(Input=calculatorVelField)
calculatorVelMag.AttributeType = 'Cell Data'
calculatorVelMag.ResultArrayName = 'mag'
calculatorVelMag.Function = 'mag(velocity)'
# Remove cells with vanishing velocity magnitude
velMagThreshold = pvs.Threshold(calculatorVelMag)
velMagThreshold.Scalars = ['CELLS', 'mag']
velMagThreshold.ThresholdRange = [1.0e-6, 1.0e30]
# Visualise remaining velocity vector field using arrows with fixed length
# and skipping cells to avoid crowding
glyphs = pvs.Glyph(Input=velMagThreshold, GlyphType='Arrow')
glyphs.Vectors = ['CELLS', 'velocity']
glyphs.ScaleFactor = 0.2
glyphs.GlyphMode = 'Every Nth Point'
glyphs.Stride = 100
glyphs.GlyphTransform = 'Transform2'
# Register the view with coprocessor and provide it with information such as
# the filename to use. Set freq=1 to ensure that images are rendered whenever
# the pipeline runs
coprocessor.RegisterView(renderView,
filename='bg_out_%t.png',
freq=1,
fittoscreen=0,
magnification=1,
width=1500,
height=768,
cinema={})
# Create colour transfer function for field
LUT = pvs.GetColorTransferFunction('hh')
LUT.RGBPoints = [
9.355e-05, 0.231, 0.298, 0.753, 0.0674, 0.865, 0.865, 0.865,
0.135, 0.706, 0.0157, 0.149
]
LUT.ScalarRangeInitialized = 1.0
# Render data field and colour by field value using lookup table
fieldDisplay = pvs.Show(simData, renderView)
fieldDisplay.Representation = 'Surface'
fieldDisplay.ColorArrayName = ['CELLS', 'hh']
fieldDisplay.LookupTable = LUT
# Add velocity field visualisation
velfieldDisplay = pvs.Show(glyphs, renderView)
