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https://gitee.com/sunhf/gprMax.git
已同步 2025-08-08 07:24:19 +08:00
Updated macro for old/new gprMax versions and old/new PV threshold filter
这个提交包含在：
Craig Warren
@@ -1,92 +0,0 @@
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# Copyright (C) 2015-2022: The University of Edinburgh
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# Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
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#
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# This file is part of gprMax.
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#
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# gprMax is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# gprMax is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with gprMax. If not, see <http://www.gnu.org/licenses/>.
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import mmap
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import os
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from xml.etree import ElementTree as ET
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import json
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def load_materials(ml):
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# create a threshold filter for each material type
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for i, m in enumerate(ml):
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threshold = Threshold(Input=model)
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threshold.ThresholdRange = [i, i]
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print(threshold.Scalars)
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threshold.Scalars = ['CELLS', 'Material']
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RenameSource(m, threshold)
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# Show data in view, except for free_space
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if i != 1:
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thresholddisplay = Show(threshold, renderview)
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thresholddisplay.ColorArrayName = ['CELLS', 'Material']
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threshold.UpdatePipeline()
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from paraview.simple import *
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# Get whatever source is loaded (should be model)
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model = GetActiveSource()
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# Get active view
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renderview = GetActiveView()
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# Show Data Axes Grid
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renderview.AxesGrid.Visibility = 1
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# Hide display of root data
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Hide(model)
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# one file only for now
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fp = model.FileName[0]
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# materials string
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ms = None
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# load json embedded in comment of line 3
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with open(fp, 'rb') as f:
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f.readline()
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f.readline()
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# comments
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c = f.readline().decode()
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# strip comment tags
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c = c[5:-5]
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# model information
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c = json.loads(c)
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# discretisation
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dl = c['dx_dy_dz']
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# n voxels
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nl = c['nx_ny_nz']
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# load material filters
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try:
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ml = c['Materials']
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load_materials(ml)
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except KeyError:
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print('No Materials to load')
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RenderAllViews()
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# Reset view to fit data
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renderview.ResetCamera()
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# Show color bar/color legend
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# thresholdDisplay.SetScalarBarVisibility(renderview, False)
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@@ -1,205 +0,0 @@
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# Copyright (C) 2015-2022: The University of Edinburgh
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# Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
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#
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# This file is part of gprMax.
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#
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||||
# 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.
|
||||
#
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# 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.
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||||
#
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# You should have received a copy of the GNU General Public License
|
||||
# along with gprMax. If not, see <http://www.gnu.org/licenses/>.
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import mmap
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import os
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from xml.etree import ElementTree as ET
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import json
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def display_pmls_new(pmlthick, dx_dy_dz, nx_ny_nz):
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"""Display PMLs as box sources using PML thickness values.
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Only suitable for gprMax > v.4
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Args:
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pmlthick (tuple): PML thickness values for each slab (cells)
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dx_dy_dz (tuple): Spatial resolution (m)
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nx_ny_dz (tuple): Domain size (cells)
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"""
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pml_names = ['x0', 'y0', 'z0', 'xmax', 'ymax', 'zmax']
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pmls = dict.fromkeys(pml_names, None)
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if pmlthick[0] != 0:
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x0 = Box(Center=[pmlthick[0] * dx_dy_dz[0] / 2,
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nx_ny_nz[1] * dx_dy_dz[1] / 2,
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nx_ny_nz[2] * dx_dy_dz[2] / 2],
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XLength=pmlthick[0] * dx_dy_dz[0],
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YLength=nx_ny_nz[1] * dx_dy_dz[1],
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ZLength=nx_ny_nz[2] * dx_dy_dz[2])
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pmls['x0'] = x0
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if pmlthick[3] != 0:
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xmax = Box(Center=[dx_dy_dz[0] * (nx_ny_nz[0] - pmlthick[3] / 2),
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nx_ny_nz[1] * dx_dy_dz[1] / 2,
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nx_ny_nz[2] * dx_dy_dz[2] / 2],
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XLength=pmlthick[3] * dx_dy_dz[0],
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YLength=nx_ny_nz[1] * dx_dy_dz[1],
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ZLength=nx_ny_nz[2] * dx_dy_dz[2])
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pmls['xmax'] = xmax
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if pmlthick[1] != 0:
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y0 = Box(Center=[nx_ny_nz[0] * dx_dy_dz[0] / 2,
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pmlthick[1] * dx_dy_dz[1] / 2,
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nx_ny_nz[2] * dx_dy_dz[2] / 2],
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XLength=nx_ny_nz[0] * dx_dy_dz[0],
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YLength=pmlthick[1] * dx_dy_dz[1],
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ZLength=nx_ny_nz[2] * dx_dy_dz[2])
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pmls['y0'] = y0
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if pmlthick[4] != 0:
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ymax = Box(Center=[nx_ny_nz[0] * dx_dy_dz[0] / 2,
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dx_dy_dz[1] * (nx_ny_nz[1] - pmlthick[4] / 2),
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nx_ny_nz[2] * dx_dy_dz[2] / 2],
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XLength=nx_ny_nz[0] * dx_dy_dz[0],
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YLength=pmlthick[4] * dx_dy_dz[1],
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ZLength=nx_ny_nz[2] * dx_dy_dz[2])
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pmls['ymax'] = ymax
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if pmlthick[2] != 0:
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z0 = Box(Center=[nx_ny_nz[0] * dx_dy_dz[0] / 2,
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nx_ny_nz[1] * dx_dy_dz[1] / 2,
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pmlthick[2] * dx_dy_dz[2] / 2],
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XLength=nx_ny_nz[0] * dx_dy_dz[0],
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YLength=nx_ny_nz[1] * dx_dy_dz[1],
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ZLength=pmlthick[2] * dx_dy_dz[2])
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pmls['z0'] = z0
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if pmlthick[5] != 0:
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zmax = Box(Center=[nx_ny_nz[0] * dx_dy_dz[0] / 2,
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nx_ny_nz[1] * dx_dy_dz[1] / 2,
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dx_dy_dz[2] * (nx_ny_nz[2] - pmlthick[5] / 2)],
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XLength=nx_ny_nz[0] * dx_dy_dz[0],
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YLength=nx_ny_nz[1] * dx_dy_dz[1],
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ZLength=pmlthick[5] * dx_dy_dz[2])
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pmls['zmax'] = zmax
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# Name PML sources and set opacity
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tmp = []
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for pml in pmls:
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if pmls[pml]:
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RenameSource('PML - ' + pml, pmls[pml])
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Hide(pmls[pml], renderview)
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tmp.append(pmls[pml])
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# Create a group of PMLs to switch on/off easily
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if tmp:
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pml_gp = AppendDatasets(Input=tmp)
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RenameSource('PML - All', pml_gp)
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pml_view = Show(pml_gp)
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pml_view.Opacity = 0.5
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def load_src_rx(srcs, dl):
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# Display sources and receivers as Paraview box sources
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for item in srcs:
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p = item['position']
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n = item['name']
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src_rx = Box(Center=[p[0] + dl[0]/2,
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p[1] + dl[1]/2,
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p[2] + dl[2]/2],
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XLength=dl[0], YLength=dl[1], ZLength=dl[2])
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RenameSource(n, src_rx)
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Show(src_rx)
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def load_materials(ml):
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# create a threshold filter for each material type
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for i, m in enumerate(ml):
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threshold = Threshold(Input=model)
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threshold.ThresholdRange = [i, i]
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threshold.Scalars = ['CELLS', 'Material']
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RenameSource(m, threshold)
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# Show data in view, except for free_space
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if i != 1:
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thresholddisplay = Show(threshold, renderview)
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thresholddisplay.ColorArrayName = ['CELLS', 'Material']
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threshold.UpdatePipeline()
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from paraview.simple import *
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# Get whatever source is loaded (should be model)
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model = GetActiveSource()
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# Get active view
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||||
renderview = GetActiveView()
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# Show Data Axes Grid
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renderview.AxesGrid.Visibility = 1
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# Hide display of root data
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||||
Hide(model)
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# one file only for now
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||||
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fp = model.FileName[0]
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# materials string
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ms = None
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||||
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||||
# load json embedded in comment of line 3
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||||
with open(fp, 'rb') as f:
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f.readline()
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f.readline()
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# comments
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||||
c = f.readline().decode()
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# strip comment tags
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c = c[5:-5]
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# model information
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c = json.loads(c)
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# discretisation
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dl = c['dx_dy_dz']
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# n voxels
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nl = c['nx_ny_nz']
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# load material filters
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try:
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ml = c['Materials']
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load_materials(ml)
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except KeyError:
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print('No Materials to load')
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# load sources
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try:
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srcs = c['Sources']
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load_src_rx(srcs, dl)
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except KeyError:
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print('No sources to load')
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# load rxs
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try:
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rxs = c['Receivers']
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load_src_rx(rxs, dl)
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except KeyError:
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print('No receivers to load')
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# load pmls
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try:
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pt = c['PMLthickness']
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display_pmls_new(pt, dl, nl)
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except KeyError:
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print('No PMLs to load')
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RenderAllViews()
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# Reset view to fit data
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renderview.ResetCamera()
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# Show color bar/color legend
|
||||
# thresholdDisplay.SetScalarBarVisibility(renderview, False)
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@@ -16,16 +16,67 @@
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# 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 mmap
|
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import os
|
||||
from xml.etree import ElementTree as ET
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||||
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from paraview.simple import *
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# Read Paraview version number to set threshold filter method
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pvv = GetParaViewVersion()
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if pvv.major == 5 and pvv.minor > 9:
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new_thres = True
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else:
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new_thres = False
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def display_pmls_new(pmlthick, dx_dy_dz, nx_ny_nz):
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def threshold_filt(input, lt, ut, scalars):
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"""Create threshold filter according to Paraview version.
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||||
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||||
Args:
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||||
input (array): input data to threshold filter
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||||
lt, ut (int): lower and upper bounds of thresholding operation
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||||
scalars (list/str): name of scalar array to perform thresholding
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||||
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Returns:
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||||
threshold (object): threshold filter
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||||
"""
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||||
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||||
threshold = Threshold(Input=input)
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threshold.Scalars = scalars
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||||
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||||
if new_thres:
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||||
threshold.LowerThreshold = lt
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||||
threshold.UpperThreshold = ut
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||||
else:
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threshold.ThresholdRange = [lt, ut]
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||||
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return threshold
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||||
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||||
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||||
def display_src_rx(srcs_rxs, dl):
|
||||
"""Display sources and receivers as Paraview box sources.
|
||||
Only suitable for gprMax >= v4
|
||||
|
||||
Args:
|
||||
srcs_rxs (list): source/receiver names and positions
|
||||
dl (tuple): spatial discretisation
|
||||
"""
|
||||
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||||
for item in srcs_rxs:
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||||
pos = item['position']
|
||||
name = item['name']
|
||||
src_rx = Box(Center=[pos[0] + dl[0]/2,
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||||
pos[1] + dl[1]/2,
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||||
pos[2] + dl[2]/2],
|
||||
XLength=dl[0], YLength=dl[1], ZLength=dl[2])
|
||||
RenameSource(name, src_rx)
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||||
Show(src_rx)
|
||||
|
||||
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||||
def display_pmls(pmlthick, dx_dy_dz, nx_ny_nz):
|
||||
"""Display PMLs as box sources using PML thickness values.
|
||||
Only suitable for gprMax > v.4
|
||||
Only suitable for gprMax >= v4
|
||||
|
||||
Args:
|
||||
pmlthick (tuple): PML thickness values for each slab (cells)
|
||||
@@ -118,11 +169,17 @@ renderview.AxesGrid.Visibility = 1
|
||||
# Hide display of root data
|
||||
Hide(model)
|
||||
|
||||
# VTI or VTP file
|
||||
|
||||
#####################################
|
||||
# Get filename or list of filenames #
|
||||
#####################################
|
||||
|
||||
# Single .vti or .vtu file
|
||||
if len(model.FileName) == 1:
|
||||
files = model.FileName
|
||||
dirname = os.path.dirname(files[0])
|
||||
# PVD file
|
||||
|
||||
# Multiple .vti or .vtu files referenced in a .pvd file
|
||||
else:
|
||||
files = []
|
||||
dirname = os.path.dirname(model.FileName)
|
||||
@@ -130,152 +187,155 @@ else:
|
||||
root = tree.getroot()
|
||||
for elem in root:
|
||||
for subelem in elem.findall('DataSet'):
|
||||
tmp = os.path.join(dirname, subelem.get('file').encode('utf-8'))
|
||||
tmp = os.path.join(dirname, subelem.get('file'))
|
||||
files.append(tmp)
|
||||
|
||||
# Dictionaries to hold data - mainly for <v4 behaviour
|
||||
materials = {}
|
||||
srcs = {}
|
||||
srcs_old = {}
|
||||
rxs = {}
|
||||
rxs_old = {}
|
||||
pmls_old = {}
|
||||
pmls = {}
|
||||
|
||||
# To hold the maximum numerical ID for materials across multiple files
|
||||
material_ID_max = 0
|
||||
|
||||
#################################################################
|
||||
# Read and display data from file(s), i.e. materials, sources, #
|
||||
# receivers, and PMLs #
|
||||
# Method depends on gprMax version #
|
||||
#################################################################
|
||||
|
||||
for file in files:
|
||||
with open(file, 'rb') as f:
|
||||
# Get max numID of materials
|
||||
if model.CellData.GetArray('Material').GetRange()[1] > material_ID_max:
|
||||
material_ID_max = int(model.CellData.GetArray('Material').GetRange()[1])
|
||||
|
||||
# Read gprMax XML section
|
||||
#######################
|
||||
# Read data from file #
|
||||
#######################
|
||||
# Determine gprMax version
|
||||
# Read XML data
|
||||
mm = mmap.mmap(f.fileno(), 0, prot=mmap.PROT_READ)
|
||||
xml_pos = mm.find('<gprMax')
|
||||
mm.seek(xml_pos)
|
||||
xml = mm.read(mm.size() - xml_pos)
|
||||
root = ET.fromstring(xml)
|
||||
|
||||
# Print gprMax XML section that has been read for debugging
|
||||
# ET.dump(root)
|
||||
|
||||
# New behaviour - gprMax >v.4
|
||||
|
||||
# Look for <gprMax> tag which indicates version <4
|
||||
try:
|
||||
root.attrib['Version']
|
||||
v4 = True
|
||||
dx_dy_dz = tuple(float(s) for s in root.get(
|
||||
'dx_dy_dz').strip('()').split(','))
|
||||
nx_ny_nz = tuple(float(s) for s in root.get(
|
||||
'nx_ny_nz').strip('()').split(','))
|
||||
if any(x == 1 for x in nx_ny_nz):
|
||||
renderview.CameraParallelProjection = 1
|
||||
try:
|
||||
root.attrib['PMLthickness']
|
||||
pmlthick = tuple(int(s) for s in root.get(
|
||||
'PMLthickness').strip('[]').split(','))
|
||||
except:
|
||||
pass
|
||||
|
||||
# Old behaviour - gprMax <v.4
|
||||
except:
|
||||
xml_pos = mm.find(b'<gprMax')
|
||||
mm.seek(xml_pos)
|
||||
xml = mm.read(mm.size() - xml_pos)
|
||||
root = ET.fromstring(xml)
|
||||
# ET.dump(root)
|
||||
v4 = False
|
||||
|
||||
if v4:
|
||||
# Read material names and numeric IDs into a dict
|
||||
for elem in root:
|
||||
for subelem in elem.findall('Material'):
|
||||
materials[subelem.get('ID')] = int(subelem.get('numID'))
|
||||
|
||||
# Read sources
|
||||
for elem in root:
|
||||
for subelem in elem.findall('Source'):
|
||||
pos = tuple(float(s) for s in subelem.get(
|
||||
'position').strip('()').split(','))
|
||||
srcs[subelem.get('name')] = pos
|
||||
|
||||
# Read receivers
|
||||
for elem in root:
|
||||
for subelem in elem.findall('Receiver'):
|
||||
pos = tuple(float(s) for s in subelem.get(
|
||||
'position').strip('()').split(','))
|
||||
rxs[subelem.get('name')] = pos
|
||||
|
||||
else:
|
||||
print('\ngprMax version: < v.4.0.0')
|
||||
print(file)
|
||||
# Read material names and numeric IDs into a dict
|
||||
for elem in root.findall('Material'):
|
||||
materials[elem.get('name')] = int(elem.text)
|
||||
if int(elem.text) > material_ID_max:
|
||||
material_ID_max = int(elem.text)
|
||||
|
||||
# Read sources
|
||||
for elem in root.findall('Sources'):
|
||||
srcs_old[elem.get('name')] = int(elem.text)
|
||||
srcs[elem.get('name')] = int(elem.text)
|
||||
|
||||
# Read receivers
|
||||
for elem in root.findall('Receivers'):
|
||||
rxs_old[elem.get('name')] = int(elem.text)
|
||||
rxs[elem.get('name')] = int(elem.text)
|
||||
|
||||
# Read PMLs
|
||||
for elem in root.findall('PML'):
|
||||
pmls_old[elem.get('name')] = int(elem.text)
|
||||
pmls[elem.get('name')] = int(elem.text)
|
||||
|
||||
# Create a Threshold (filter) for each material
|
||||
except:
|
||||
v4 = True
|
||||
# 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 #
|
||||
################
|
||||
|
||||
if v4:
|
||||
# Discretisation
|
||||
dl = c['dx_dy_dz']
|
||||
# Number of voxels
|
||||
nl = c['nx_ny_nz']
|
||||
|
||||
# Store materials
|
||||
try:
|
||||
mats = c['Materials']
|
||||
for i, material in enumerate(mats):
|
||||
materials[material] = i
|
||||
if i > material_ID_max:
|
||||
material_ID_max = i
|
||||
except KeyError:
|
||||
print('No materials to load')
|
||||
|
||||
# Display any sources
|
||||
try:
|
||||
srcs = c['Sources']
|
||||
display_src_rx(srcs, dl)
|
||||
except KeyError:
|
||||
print('No sources to load')
|
||||
|
||||
# Display any receivers
|
||||
try:
|
||||
rxs = c['Receivers']
|
||||
display_src_rx(rxs, dl)
|
||||
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')
|
||||
|
||||
else:
|
||||
# Display any sources and PMLs
|
||||
srcs_pmls = dict(srcs)
|
||||
srcs_pmls.update(pmls)
|
||||
if srcs_pmls:
|
||||
for k, v in srcs_pmls.items():
|
||||
threshold = threshold_filt(model, v, v, 'Sources_PML')
|
||||
RenameSource(k, threshold)
|
||||
|
||||
# Show data in view
|
||||
thresholddisplay = Show(threshold, renderview)
|
||||
thresholddisplay.ColorArrayName = 'Sources_PML'
|
||||
if v == 1:
|
||||
thresholddisplay.Opacity = 0.5
|
||||
threshold.UpdatePipeline()
|
||||
|
||||
# Display any receivers
|
||||
if rxs:
|
||||
for k, v in rxs.items():
|
||||
threshold = threshold_filt(model, v, v, 'Receivers')
|
||||
RenameSource(k, threshold)
|
||||
|
||||
# Show data in view
|
||||
thresholddisplay = Show(threshold, renderview)
|
||||
thresholddisplay.ColorArrayName = 'Receivers'
|
||||
threshold.UpdatePipeline()
|
||||
|
||||
# Display materials
|
||||
material_range = range(0, material_ID_max + 1)
|
||||
for k, v in sorted(materials.items(), key=lambda x: x[1]):
|
||||
if v in material_range:
|
||||
threshold = Threshold(Input=model)
|
||||
threshold.Scalars = 'Material'
|
||||
threshold.ThresholdRange = [v, v]
|
||||
threshold = threshold_filt(model, v, v, ['CELLS', 'Material'])
|
||||
RenameSource(k, threshold)
|
||||
|
||||
# Show data in view, except for free_space
|
||||
if v != 1:
|
||||
thresholddisplay = Show(threshold, renderview)
|
||||
thresholddisplay.ColorArrayName = 'Material'
|
||||
thresholddisplay.ColorArrayName = ['CELLS', 'Material']
|
||||
threshold.UpdatePipeline()
|
||||
|
||||
# New behaviour
|
||||
if v4:
|
||||
# Display sources and receivers as Paraview box sources
|
||||
for k, v in srcs.items() + rxs.items():
|
||||
src_rx = Box(Center=[v[0] + dx_dy_dz[0]/2,
|
||||
v[1] + dx_dy_dz[1]/2,
|
||||
v[2] + dx_dy_dz[2]/2],
|
||||
XLength=dx_dy_dz[0], YLength=dx_dy_dz[1], ZLength=dx_dy_dz[2])
|
||||
RenameSource(k, src_rx)
|
||||
Show(src_rx)
|
||||
|
||||
# Display PMLs as Paraview box sources
|
||||
try:
|
||||
pmlthick
|
||||
display_pmls_new(pmlthick, dx_dy_dz, nx_ny_nz)
|
||||
except:
|
||||
pass
|
||||
|
||||
# Old behaviour
|
||||
else:
|
||||
# Create threshold for sources/pml(name and numeric value)
|
||||
srcs_pmls_old = dict(srcs_old.items() + pmls_old.items())
|
||||
if srcs_pmls_old:
|
||||
for k, v in srcs_pmls_old.items():
|
||||
threshold = Threshold(Input=model)
|
||||
threshold.Scalars = 'Sources_PML'
|
||||
threshold.ThresholdRange = [v, v]
|
||||
RenameSource(k, threshold)
|
||||
|
||||
# Show data in view
|
||||
thresholddisplay = Show(threshold, renderview)
|
||||
thresholddisplay.ColorArrayName = 'Sources_PML'
|
||||
|
||||
if v == 1:
|
||||
thresholddisplay.Opacity = 0.5
|
||||
|
||||
if rxs_old:
|
||||
# Create threshold for receivers (name and numeric value)
|
||||
for k, v in rxs_old.items():
|
||||
threshold = Threshold(Input=model)
|
||||
threshold.Scalars = 'Receivers'
|
||||
threshold.ThresholdRange = [v, v]
|
||||
RenameSource(k, threshold)
|
||||
|
||||
# Show data in view
|
||||
thresholddisplay = Show(threshold, renderview)
|
||||
thresholddisplay.ColorArrayName = 'Receivers'
|
||||
|
||||
RenderAllViews()
|
||||
|
||||
|
||||
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