gprMax/toolboxes/Utilities/Paraview/gprMax.py

# Copyright (C) 2015-2023: The University of Edinburgh, United Kingdom
#                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
#
# This file is part of gprMax.
#
# gprMax is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# gprMax is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with gprMax.  If not, see <http://www.gnu.org/licenses/>.

import json
import os

from paraview.simple import (AppendDatasets, Box, GetActiveSource,
                             GetActiveView, GetParaViewVersion, Hide,
                             OpenDataFile, RenameSource, RenderAllViews,
                             SetActiveSource, Show, Threshold)


def threshold_filt(input, lt, ut, scalars):
    """Create threshold filter according to Paraview version.
    
    Args:
        input (array): input data to threshold filter
        lt, ut (int): lower and upper bounds of thresholding operation
        scalars (list/str): name of scalar array to perform thresholding

    Returns:
        threshold (object): threshold filter
    """

    # Read Paraview version number to set threshold filter method
    pvv = GetParaViewVersion()

    threshold = Threshold(Input=input)
    threshold.Scalars = scalars
  
    if pvv.major == 5 and pvv.minor < 10:
        threshold.ThresholdRange = [lt, ut]
    else:
        threshold.LowerThreshold = lt
        threshold.UpperThreshold = ut

    return threshold


def display_pmls(pmlthick, dx_dy_dz, nx_ny_nz):
    """Display PMLs as box sources using PML thickness values.
        Only suitable for gprMax >= v4

    Args:
        pmlthick (tuple): PML thickness values for each slab (cells)
        dx_dy_dz (tuple): Spatial resolution (m)
        nx_ny_dz (tuple): Domain size (cells)
    """

    pml_names = ['x0', 'y0', 'z0', 'xmax', 'ymax', 'zmax']
    pmls = dict.fromkeys(pml_names, None)
    SetActiveSource(pv_src)

    if pmlthick[0] != 0:
        x0 = Box(Center=[pmlthick[0] * dx_dy_dz[0] / 2,
                         nx_ny_nz[1] * dx_dy_dz[1] / 2,
                         nx_ny_nz[2] * dx_dy_dz[2] / 2],
                 XLength=pmlthick[0] * dx_dy_dz[0],
                 YLength=nx_ny_nz[1] * dx_dy_dz[1],
                 ZLength=nx_ny_nz[2] * dx_dy_dz[2])
        pmls['x0'] = x0

    if pmlthick[3] != 0:
        xmax = Box(Center=[dx_dy_dz[0] * (nx_ny_nz[0] - pmlthick[3] / 2),
                           nx_ny_nz[1] * dx_dy_dz[1] / 2,
                           nx_ny_nz[2] * dx_dy_dz[2] / 2],
                   XLength=pmlthick[3] * dx_dy_dz[0],
                   YLength=nx_ny_nz[1] * dx_dy_dz[1],
                   ZLength=nx_ny_nz[2] * dx_dy_dz[2])
        pmls['xmax'] = xmax

    if pmlthick[1] != 0:
        y0 = Box(Center=[nx_ny_nz[0] * dx_dy_dz[0] / 2,
                         pmlthick[1] * dx_dy_dz[1] / 2,
                         nx_ny_nz[2] * dx_dy_dz[2] / 2],
                 XLength=nx_ny_nz[0] * dx_dy_dz[0],
                 YLength=pmlthick[1] * dx_dy_dz[1],
                 ZLength=nx_ny_nz[2] * dx_dy_dz[2])
        pmls['y0'] = y0

    if pmlthick[4] != 0:
        ymax = Box(Center=[nx_ny_nz[0] * dx_dy_dz[0] / 2,
                           dx_dy_dz[1] * (nx_ny_nz[1] - pmlthick[4] / 2),
                           nx_ny_nz[2] * dx_dy_dz[2] / 2],
                   XLength=nx_ny_nz[0] * dx_dy_dz[0],
                   YLength=pmlthick[4] * dx_dy_dz[1],
                   ZLength=nx_ny_nz[2] * dx_dy_dz[2])
        pmls['ymax'] = ymax

    if pmlthick[2] != 0:
        z0 = Box(Center=[nx_ny_nz[0] * dx_dy_dz[0] / 2,
                         nx_ny_nz[1] * dx_dy_dz[1] / 2,
                         pmlthick[2] * dx_dy_dz[2] / 2],
                 XLength=nx_ny_nz[0] * dx_dy_dz[0],
                 YLength=nx_ny_nz[1] * dx_dy_dz[1],
                 ZLength=pmlthick[2] * dx_dy_dz[2])
        pmls['z0'] = z0

    if pmlthick[5] != 0:
        zmax = Box(Center=[nx_ny_nz[0] * dx_dy_dz[0] / 2,
                           nx_ny_nz[1] * dx_dy_dz[1] / 2,
                           dx_dy_dz[2] * (nx_ny_nz[2] - pmlthick[5] / 2)],
                   XLength=nx_ny_nz[0] * dx_dy_dz[0],
                   YLength=nx_ny_nz[1] * dx_dy_dz[1],
                   ZLength=pmlthick[5] * dx_dy_dz[2])
        pmls['zmax'] = zmax

    # Name PML sources and set opacity
    tmp = []
    for pml in pmls:
        if pmls[pml]:
            RenameSource('PML - ' + pml, pmls[pml])
            Hide(pmls[pml], pv_view)
            tmp.append(pmls[pml])

    # Create a group of PMLs to switch on/off easily
    if tmp:
        pml_gp = AppendDatasets(Input=tmp)
        RenameSource('PML - All', pml_gp)
        pml_view = Show(pml_gp)
        pml_view.Opacity = 0.5


# Get whatever source is loaded - should be loaded file (.vt*) or files (.pvd)
data = GetActiveSource()

# Hide display of root data
Hide(data)


# Single .vti or .vtu file
file = data.FileName
dirname = os.path.dirname(file[0])

# Read and display data from file, i.e. materials, sources,  receivers, and PMLs
with open(file, 'rb') as f:
    # Comments () embedded in line 3 of file
    f.readline()
    f.readline()
    c = f.readline().decode()
    # Strip comment tags
    c = c[5:-5]
    # Model information
    c = json.loads(c)
    print('\ngprMax version: ' + c['gprMax_version'])
    print(file)            

################
# Display data #
################
pv_view = GetActiveView()
pv_view.AxesGrid.Visibility = 1 # Show Data Axes Grid
pv_data = OpenDataFile(file)
pv_disp = Show(pv_data, pv_view)
pv_src = GetActiveSource()
Hide(pv_src)
src_name = os.path.split(file)
RenameSource(src_name[1])

# Discretisation
dl = c['dx_dy_dz']
# Number of voxels
nl = c['nx_ny_nz']

# Materials
try:
    for i, mat in enumerate(c['Materials']):
        threshold = threshold_filt(pv_src, i, i, ['CELLS', 'Material'])
        RenameSource(mat, threshold)

        # Show data in view, except for free_space
        if i != 1:
            thresholddisplay = Show(threshold, pv_view)
            thresholddisplay.ColorArrayName = ['CELLS', 'Material']
        threshold.UpdatePipeline()
except KeyError:
    print('No materials to load')

# Display any sources
try:
    for item in c['Sources']:
        pos = item['position']
        name = item['name']
        src = Box(Center=[pos[0] + dl[0]/2,
                            pos[1] + dl[1]/2,
                            pos[2] + dl[2]/2],
                    XLength=dl[0], YLength=dl[1], ZLength=dl[2])
        RenameSource(name, src)
        Show(src)
except KeyError:
    print('No sources to load')

# Display any receivers
try:
    for item in c['Receivers']:
        pos = item['position']
        name = item['name']
        rx = Box(Center=[pos[0] + dl[0]/2,
                            pos[1] + dl[1]/2,
                            pos[2] + dl[2]/2],
                    XLength=dl[0], YLength=dl[1], ZLength=dl[2])
        RenameSource(name, rx)
        Show(rx)
except KeyError:
    print('No receivers to load')

# Display any PMLs
try:
    pt = c['PMLthickness']
    display_pmls(pt, dl, nl)
except KeyError:
    print('No PMLs to load')

        
RenderAllViews()

# Reset view to fit data
pv_view.ResetCamera()