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镜像自地址 https://gitee.com/sunhf/gprMax.git 已同步 2025-08-07 15:10:13 +08:00
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Update Paraview macro to use field data

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nmannall
2024-11-12 14:34:10 +00:00
父节点 67d6d63072
当前提交 98b77504e3
共有 1 个文件被更改，包括 175 次插入 和 107 次删除
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282
toolboxes/Utilities/Paraview/gprMax.py
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@@ -16,69 +16,103 @@
# 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.servermanager import Proxy, SourceProxy
from paraview.simple import (
AppendDatasets,
Box,
ColorBy,
FetchData,
GetActiveSource,
GetActiveView,
GetDisplayProperties,
GetParaViewVersion,
Hide,
OpenDataFile,
RenameSource,
RenderAllViews,
SetActiveSource,
Show,
Threshold,
)
from paraview.vtk.numpy_interface import dataset_adapter as dsa
from vtkmodules.vtkCommonCore import vtkStringArray
COLOUR_SCALARS = ("CELLS", "Material")
def threshold_filt(input, lt, ut, scalars):
def threshold_materials(source: SourceProxy, view: Proxy, material_ids: vtkStringArray):
"""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
source: Input to the threshold filter.
view: The view proxy to show the threshold in.
material_ids: Array of material ids. A new threshold filter will
be created for each material.
"""
# Read Paraview version number to set threshold filter method
pvv = GetParaViewVersion()
threshold = Threshold(Input=input)
threshold.Scalars = scalars
for index in range(material_ids.GetNumberOfValues()):
threshold = Threshold(Input=source, Scalars=COLOUR_SCALARS)
if pvv.major == 5 and pvv.minor < 10:
threshold.ThresholdRange = [lt, ut]
else:
threshold.LowerThreshold = lt
threshold.UpperThreshold = ut
if pvv.major == 5 and pvv.minor < 10:
threshold.ThresholdRange = [index, index]
else:
threshold.LowerThreshold = index
threshold.UpperThreshold = index
return threshold
RenameSource(material_ids.GetValue(index), threshold)
# Show data in view, except for free_space
if index != 1:
Show(threshold, view)
threshold.UpdatePipeline()
def display_pmls(pmlthick, dx_dy_dz, nx_ny_nz):
"""Display PMLs as box sources using PML thickness values.
Only suitable for gprMax >= v4
def create_box_sources(names: vtkStringArray, positions: dsa.VTKArray, dl: dsa.VTKArray):
"""Create new single cell box sources.
Args:
pmlthick (tuple): PML thickness values for each slab (cells)
dx_dy_dz (tuple): Spatial resolution (m)
nx_ny_dz (tuple): Domain size (cells)
names: Array of N names for the new sources.
positions: x, y, z coordinates of the new sources. This should
have shape (N, 3).
dl: x, y, z spatial resolution.
"""
for index in range(names.GetNumberOfValues()):
name = names.GetValue(index)
pos = positions[index]
src = Box(
Center=pos + dl / 2,
XLength=dl[0],
YLength=dl[1],
ZLength=dl[2],
)
RenameSource(name, src)
Show(src)
def display_pmls(pmlthick: dsa.VTKArray, dx_dy_dz: dsa.VTKArray, nx_ny_nz: dsa.VTKArray):
"""Display PMLs as box sources using PML thickness values.
Only suitable for gprMax >= v4.
Args:
pmlthick: PML thickness values for each slab (cells).
dx_dy_dz: Spatial resolution (m).
nx_ny_dz: Domain size (cells).
"""
pml_names = ["x0", "y0", "z0", "xmax", "ymax", "zmax"]
pmls = dict.fromkeys(pml_names, None)
SetActiveSource(pv_data)
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],
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],
@@ -100,7 +134,11 @@ def display_pmls(pmlthick, dx_dy_dz, nx_ny_nz):
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],
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],
@@ -122,7 +160,11 @@ def display_pmls(pmlthick, dx_dy_dz, nx_ny_nz):
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],
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],
@@ -158,96 +200,122 @@ def display_pmls(pmlthick, dx_dy_dz, nx_ny_nz):
pml_view.Opacity = 0.5
# Get whatever source is loaded - should be loaded file (.vt*) or files (.pvd)
pv_data = GetActiveSource()
def is_valid_key(key: str, dictionary: dict) -> bool:
"""Check key exists and is not an empty array (i.e. VTKNoneArray).
# Hide display of root data
Hide(pv_data)
Args:
key: Name of key to check.
dictionary: Dictionary like object that should contain the key.
# Single .vti or .vtu file
file = pv_data.FileName[0]
Returns:
is_valid_key: True if the key is in the dictionary and is not
of type VTKNoneArray. False otherwise.
"""
return key in dictionary.keys() and not isinstance(dictionary[key], dsa.VTKNoneArray)
# 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_disp = Show(pv_data, pv_view)
pv_disp.ColorArrayName = ["CELLS", "Material"]
class HaltException(Exception):
pass
# 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_data, i, i, ["CELLS", "Material"])
RenameSource(mat, threshold)
print("=============== Running gprMax macro ===============", end="\n\n")
# 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")
# Get active source - should be loaded file (.vtkhdf)
pv_source = GetActiveSource()
# 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],
if pv_source is None:
raise HaltException("ERROR: No active source.")
pv_source.UpdatePipeline()
raw_data = FetchData(pv_source)[0]
data = dsa.WrapDataObject(raw_data)
# Check the necessary metadata is attached to the file
metadata_keys = data.FieldData.keys()
compulsory_keys = ["gprMax_version", "nx_ny_nz", "dx_dy_dz", "material_ids"]
missing_keys = []
for key in compulsory_keys:
if key not in metadata_keys:
missing_keys.append(key)
if len(missing_keys) > 0:
keys = "\n- ".join(missing_keys)
print(f"Missing metadata fields: \n- {keys}\n")
if len(metadata_keys) > 0:
keys = "\n- ".join(metadata_keys)
print(f"Found: \n- {keys}\n")
raise HaltException(
"ERROR: Missing gprMax metadata information. Do you have the correct source selected?"
)
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")
# gprMax version
version = data.FieldData["gprMax_version"].GetValue(0)
# Number of voxels
nl = data.FieldData["nx_ny_nz"]
# Discretisation
dl = data.FieldData["dx_dy_dz"]
# Display any PMLs
try:
pt = c["PMLthickness"]
display_pmls(pt, dl, nl)
except KeyError:
print("No PMLs to load")
print("gprMax version:", data.FieldData["gprMax_version"].GetValue(0))
print("nx_ny_nz:", nl)
print("dx_dy_dz:", dl, end="\n\n")
################
# Display data #
################
RenderAllViews()
# Get active view
pv_view = GetActiveView()
pv_view.AxesGrid.Visibility = 1 # Show Data Axes Grid
# Reset view to fit data
pv_view.ResetCamera()
# Get display properties
pv_disp = GetDisplayProperties(pv_source, view=pv_view)
# Set scalar colouring
ColorBy(pv_disp, COLOUR_SCALARS)
# Materials
print("Loading materials... ", end="\t")
if is_valid_key("material_ids", data.FieldData):
threshold_materials(pv_source, pv_view, data.FieldData["material_ids"])
print("Done.")
else:
print("No materials to load.")
# Display any sources
print("Loading sources... ", end="\t\t")
if is_valid_key("source_ids", data.FieldData) and is_valid_key("sources", data.FieldData):
create_box_sources(data.FieldData["source_ids"], data.FieldData["sources"], dl)
print("Done.")
else:
print("No sources to load.")
# Display any receivers
print("Loading receivers... ", end="\t")
if is_valid_key("receiver_ids", data.FieldData) and is_valid_key("receivers", data.FieldData):
create_box_sources(data.FieldData["receiver_ids"], data.FieldData["receivers"], dl)
print("Done.")
else:
print("No receivers to load.")
# Display any PMLs
print("Loading PMLs... ", end="\t\t")
if is_valid_key("pml_thickness", data.FieldData):
display_pmls(data.FieldData["pml_thickness"], dl, nl)
print("Done.")
else:
print("No PMLs to load.")
RenderAllViews()
SetActiveSource(pv_source)
Hide(pv_source)
# Reset view to fit data
pv_view.ResetCamera()
except HaltException as e:
print(e)
print()