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plotChargeAll.py
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plotChargeAll.py
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from __future__ import print_function
import h5py
import numpy as np
from vtk import *
hfl = []
hfl.append(h5py.File('data/charge-He-electrons-000026.h5','r'))
hfl.append(h5py.File('data/charge-beam-driver-000026.h5','r'))
hfl.append(h5py.File('data/charge-plasma-000026.h5','r'))
window = vtk.vtkRenderWindow()
# ... and set window size.
window.SetSize(1280, 800)
renderer = vtk.vtkRenderer()
# Set background
renderer.SetBackground(0,0,0)
# renderer.TexturedBackgroundOn()
# Other colors
# nc = vtk.vtkNamedColors()
# renderer.SetBackground(nc.GetColor3d('MidnightBlue'))
data = []
npdata = []
npdatauchar = []
dataImport = []
volume = []
mapper = []
for i, hf in enumerate(hfl):
data.append(hf.get('charge'))
axisz = hf.get('AXIS/AXIS1')
axisy = hf.get('AXIS/AXIS2')
axisx = hf.get('AXIS/AXIS3')
dz = (axisz[1]-axisz[0])/data[i].shape[2]
dy = (axisy[1]-axisy[0])/data[i].shape[1]
dx = (axisx[1]-axisx[0])/data[i].shape[0]
print('\nFilename : ',hf.filename)
print('Axis z range: [%.2f,%.2f] Nbins = %i dz = %.4f' % (axisz[0],axisz[1],data[i].shape[2],dz) )
print('Axis x range: [%.2f,%.2f] Nbins = %i dx = %.4f' % (axisx[0],axisx[1],data[i].shape[0],dx) )
print('Axis y range: [%.2f,%.2f] Nbins = %i dy = %.4f' % (axisy[0],axisy[1],data[i].shape[1],dy) )
# Changing to positive integer types (particle density)
# it is required by vtkVolumeRayCastMapper
npdata.append(np.array(np.absolute(data[i])))
minvalue = np.amin(npdata[i])
maxvalue = np.amax(npdata[i])
print('Minimum value = %.2f Maximum = %.2f' % (minvalue,maxvalue))
# Rescale data
den1 = 255.0/maxvalue
if "He-electrons" in hf.filename:
den1 *= 100
elif "plasma" in hf.filename:
den1 *= 50
npdata[i] = np.round(den1 * npdata[i])
npdatauchar.append(np.array(npdata[i], dtype=np.uint8))
print('Shape of the array: ', npdatauchar[i].shape,' Type: ',npdatauchar[i].dtype)
minvalue = np.amin(npdatauchar[i])
maxvalue = np.amax(npdatauchar[i])
print('Minimum value = %.2f Maximum = %.2f' % (minvalue,maxvalue))
# For VTK to be able to use the data, it must be stored as a VTK-image.
# This can be done by the vtkImageImport which
# imports raw data and stores it.
dataImport.append(vtk.vtkImageImport())
# The array is converted to a string of chars and imported.
#data_string = npdatauchar[i].tostring()
#dataImport[i].CopyImportVoidPointer(data_string, len(data_string))
dataImport[i].SetImportVoidPointer(npdatauchar[i])
# The type of the newly imported data is set to float.
dataImport[i].SetDataScalarTypeToUnsignedChar()
# dataImport[i].SetDataScalarTypeToFloat()
# Because the data that is imported only contains an intensity value,
# the importer must be told this is the case.
dataImport[i].SetNumberOfScalarComponents(1)
# The following two functions describe how the data is stored
# and the dimensions of the array it is stored in.
dataImport[i].SetDataExtent(0, npdatauchar[i].shape[2]-1, 0, npdatauchar[i].shape[1]-1, 0, npdatauchar[i].shape[0]-1)
dataImport[i].SetWholeExtent(0, npdatauchar[i].shape[2]-1, 0, npdatauchar[i].shape[1]-1, 0, npdatauchar[i].shape[0]-1)
dataImport[i].SetDataSpacing(dz,dy,dx)
dataImport[i].SetDataOrigin(0.0,axisy[0],axisx[0])
dataImport[i].Update()
# Opacity and color scales
opacity = vtk.vtkPiecewiseFunction()
color = vtk.vtkColorTransferFunction()
if "plasma" in hf.filename:
opacity.AddPoint(0, 0.0)
opacity.AddPoint(den1, 0.01)
opacity.AddPoint(10*den1, 0.8)
opacity.AddPoint(maxvalue, 1.0)
color.AddRGBPoint(0, 0.078, 0.078, 0.078)
color.AddRGBPoint(den1, 0.188, 0.247, 0.294)
color.AddRGBPoint(maxvalue, 1.0, 1.0, 1.0)
# other palette
#color.AddRGBPoint(0.0, 0.865, 0.865, 0.865)
#color.AddRGBPoint(den1, 0.2313, 0.298, 0.753)
#color.AddRGBPoint(maxvalue, 1.0, 1.0, 1.0)
elif "beam" in hf.filename :
opacity.AddPoint(0, 0.0)
opacity.AddPoint(maxvalue, 1.0)
color.AddRGBPoint(0.0, 0.220, 0.039, 0.235)
color.AddRGBPoint(0.2*maxvalue, 0.390, 0.050, 0.330)
color.AddRGBPoint(0.4*maxvalue, 0.700, 0.200, 0.300)
color.AddRGBPoint(1.0*maxvalue, 1.000, 1.000, 0.200)
elif "He-electrons" in hf.filename:
opacity.AddPoint(0.0, 0.0)
opacity.AddPoint(1, 0.1)
opacity.AddPoint(100, 0.8)
opacity.AddPoint(255, 1.0)
color.AddRGBPoint(0.0, 0.220, 0.039, 0.235)
color.AddRGBPoint(0.01*maxvalue, 0.627, 0.125, 0.235)
color.AddRGBPoint(0.10*maxvalue, 0.700, 0.200, 0.300)
color.AddRGBPoint(1.00*maxvalue, 1.000, 1.000, 0.200)
volumeprop = vtk.vtkVolumeProperty()
volumeprop.SetColor(color)
volumeprop.SetScalarOpacity(opacity)
volumeprop.ShadeOff()
#volumeprop.ShadeOn()
volumeprop.SetInterpolationTypeToLinear()
#
#compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
#mapper = vtk.vtkVolumeRayCastMapper()
#mapper.SetVolumeRayCastFunction(compositeFunction)
#
#mapper = vtkFixedPointVolumeRayCastMapper()
#mapper = vtk.vtkVolumeTextureMapper2D()
mapper.append(vtk.vtkGPUVolumeRayCastMapper())
#mapper[i].SetBlendModeToMaximumIntensity();
#mapper[i].SetSampleDistance(0.1)
#mapper[i].SetAutoAdjustSampleDistances(0)
# Add data to the mapper
mapper[i].SetInputConnection(dataImport[i].GetOutputPort())
# The class vtkVolume is used to pair the previously declared volume
# as well as the properties to be used when rendering that volume.
volume.append(vtk.vtkVolume())
volume[i].SetMapper(mapper[i])
volume[i].SetProperty(volumeprop)
# Add the volume to the renderer ...
renderer.AddVolume(volume[i])
if (1) & ( ("beam" in hf.filename) | ("He-electrons" in hf.filename)):
threshold = vtk.vtkImageThreshold()
threshold.SetInputConnection(dataImport[i].GetOutputPort())
threshold.ThresholdBetween(110,200)
threshold.ReplaceInOn()
threshold.SetInValue(100) # set all values in range to 1
threshold.ReplaceOutOn()
threshold.SetOutValue(0) # set all values out range to 0
threshold.Update()
dmc = vtk.vtkDiscreteMarchingCubes()
dmc.SetInputConnection(threshold.GetOutputPort())
#dmc.SetInputConnection(dataImport[i].GetOutputPort())
dmc.GenerateValues(1, 100, 100)
dmc.Update()
mapper2 = vtk.vtkPolyDataMapper()
mapper2.SetInputConnection(dmc.GetOutputPort())
mapper2.SetLookupTable(color)
mapper2.SetColorModeToMapScalars()
actor = vtk.vtkActor()
actor.SetMapper(mapper2)
actor.GetProperty().SetOpacity(0.8)
renderer.AddActor(actor)
window.AddRenderer(renderer)
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(window)
#style = vtkInteractorStyleTrackballCamera();
#interactor.SetInteractorStyle(style);
window.Render()
interactor.Initialize()
interactor.Start()