Added writiing for Paraview pvd wrapper file for multiple geometry views.

这个提交包含在:
craig-warren
2020-05-12 12:27:32 +01:00
父节点 d25717bf23
当前提交 562db983d1
共有 2 个文件被更改,包括 99 次插入84 次删除

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@@ -16,6 +16,10 @@
# You should have received a copy of the GNU General Public License
# along with gprMax. If not, see <http://www.gnu.org/licenses/>.
try:
import xml.etree.cElementTree as ET
except ImportError:
import xml.etree.ElementTree as ET
import logging
import os
from pathlib import Path
@@ -28,7 +32,7 @@ import numpy as np
from ._version import __version__
from .cython.geometry_outputs import (define_fine_geometry,
define_normal_geometry)
from .utilities import round_value
from .utilities import pretty_xml, round_value
logger = logging.getLogger(__name__)
@@ -61,6 +65,7 @@ class GeometryView:
self.dz = dz
self.filename = filename
self.fileext = fileext
self.set_filename_called = False
self.G = G
if self.fileext == '.vti':
@@ -76,7 +81,6 @@ class GeometryView:
self.vtk_nzcells = round_value(self.nz / self.dz)
self.vtk_ncells = self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells
self.datawritesize = (np.dtype(np.uint32).itemsize * self.vtk_ncells +
2 * np.dtype(np.int8).itemsize * self.vtk_ncells +
3 * np.dtype(np.uint32).itemsize)
elif self.fileext == '.vtp':
@@ -112,9 +116,11 @@ class GeometryView:
def set_filename(self):
"""Construct filename from user-supplied name and model run number."""
parts = config.get_model_config().output_file_path.parts
self.filename = Path(*parts[:-1], self.filename + config.get_model_config().appendmodelnumber)
self.filename = self.filename.with_suffix(self.fileext)
if not self.set_filename_called:
self.set_filename_called = True
parts = config.get_model_config().output_file_path.parts
self.filename = Path(*parts[:-1], self.filename + config.get_model_config().appendmodelnumber)
self.filename = self.filename.with_suffix(self.fileext)
def write_vtk(self, G, pbar):
"""Writes the geometry information to a VTK file.
@@ -129,42 +135,18 @@ class GeometryView:
"""
if self.fileext == '.vti':
# Create arrays and add numeric IDs for PML, sources and receivers
# (0 is not set, 1 is PML, srcs and rxs numbered thereafter)
self.srcs_pml = np.zeros((G.nx + 1, G.ny + 1, G.nz + 1), dtype=np.int8)
self.rxs = np.zeros((G.nx + 1, G.ny + 1, G.nz + 1), dtype=np.int8)
for pml in G.pmls:
self.srcs_pml[pml.xs:pml.xf, pml.ys:pml.yf, pml.zs:pml.zf] = 1
for index, src in enumerate(G.hertziandipoles + G.magneticdipoles + G.voltagesources + G.transmissionlines):
self.srcs_pml[src.xcoord, src.ycoord, src.zcoord] = index + 2
for index, rx in enumerate(G.rxs):
self.rxs[rx.xcoord, rx.ycoord, rx.zcoord] = index + 1
vtk_srcs_pml_offset = ((np.dtype(np.uint32).itemsize * self.vtk_nxcells *
self.vtk_nycells * self.vtk_nzcells) +
np.dtype(np.uint32).itemsize)
vtk_rxs_offset = ((np.dtype(np.uint32).itemsize * self.vtk_nxcells *
self.vtk_nycells * self.vtk_nzcells) +
np.dtype(np.uint32).itemsize +
(np.dtype(np.int8).itemsize * self.vtk_nxcells *
self.vtk_nycells * self.vtk_nzcells) +
np.dtype(np.uint32).itemsize)
with open(self.filename, 'wb') as f:
f.write('<?xml version="1.0"?>\n'.encode('utf-8'))
f.write(f'<VTKFile type="ImageData" version="1.0" byte_order="{config.sim_config.vtk_byteorder}">\n'.encode('utf-8'))
f.write(f'<ImageData WholeExtent="{self.vtk_xscells} {self.vtk_xfcells} {self.vtk_yscells} {self.vtk_yfcells} {self.vtk_zscells} {self.vtk_zfcells}" Origin="0 0 0" Spacing="{self.dx * G.dx:.3} {self.dy * G.dy:.3} {self.dz * G.dz:.3}">\n'.encode('utf-8'))
f.write(f'<Piece Extent="{self.vtk_xscells} {self.vtk_xfcells} {self.vtk_yscells} {self.vtk_yfcells} {self.vtk_zscells} {self.vtk_zfcells}">\n'.encode('utf-8'))
extent = f'{self.vtk_xscells} {self.vtk_xfcells} {self.vtk_yscells} {self.vtk_yfcells} {self.vtk_zscells} {self.vtk_zfcells}'
f.write(f'<ImageData WholeExtent="{extent}" Origin="0 0 0" Spacing="{self.dx * G.dx:.3} {self.dy * G.dy:.3} {self.dz * G.dz:.3}">\n'.encode('utf-8'))
f.write(f'<Piece Extent="{extent}">\n'.encode('utf-8'))
f.write('<CellData Scalars="Material">\n'.encode('utf-8'))
f.write('<DataArray type="UInt32" Name="Material" format="appended" offset="0" />\n'.encode('utf-8'))
f.write(f'<DataArray type="Int8" Name="Sources_PML" format="appended" offset="{vtk_srcs_pml_offset}" />\n'.encode('utf-8'))
f.write(f'<DataArray type="Int8" Name="Receivers" format="appended" offset="{vtk_rxs_offset}" />\n'.encode('utf-8'))
f.write('</CellData>\n'.encode('utf-8'))
f.write('</Piece>\n</ImageData>\n<AppendedData encoding="raw">\n_'.encode('utf-8'))
solid_geometry = np.zeros((self.vtk_ncells), dtype=np.uint32)
srcs_pml_geometry = np.zeros((self.vtk_ncells), dtype=np.int8)
rxs_geometry = np.zeros((self.vtk_ncells), dtype=np.int8)
define_normal_geometry(
self.xs,
@@ -177,11 +159,7 @@ class GeometryView:
self.dy,
self.dz,
G.solid,
self.srcs_pml,
self.rxs,
solid_geometry,
srcs_pml_geometry,
rxs_geometry)
solid_geometry)
# Write number of bytes of appended data as UInt32
f.write(pack('I', solid_geometry.nbytes))
@@ -190,22 +168,7 @@ class GeometryView:
f.write(solid_geometry)
pbar.update(n=solid_geometry.nbytes)
# Write number of bytes of appended data as UInt32
f.write(pack('I', srcs_pml_geometry.nbytes))
pbar.update(n=4)
# Write sources and PML positions
f.write(srcs_pml_geometry)
pbar.update(n=srcs_pml_geometry.nbytes)
# Write number of bytes of appended data as UInt32
f.write(pack('I', rxs_geometry.nbytes))
pbar.update(n=4)
# Write receiver positions
f.write(rxs_geometry)
pbar.update(n=rxs_geometry.nbytes)
f.write('\n</AppendedData>\n</VTKFile>'.encode('utf-8'))
f.write('\n</AppendedData>\n</VTKFile>\n\n'.encode('utf-8'))
self.write_gprmax_info(f, G)
elif self.fileext == '.vtp':
@@ -293,7 +256,7 @@ class GeometryView:
f.write(z_materials)
pbar.update(n=z_materials.nbytes)
f.write('\n</AppendedData>\n</VTKFile>'.encode('utf-8'))
f.write('\n</AppendedData>\n</VTKFile>\n\n'.encode('utf-8'))
self.write_gprmax_info(f, G, materialsonly=True)
def write_gprmax_info(self, f, G, materialsonly=False):
@@ -306,16 +269,71 @@ class GeometryView:
materialsonly (bool): Only write information on materials
"""
f.write('\n\n<gprMax>\n'.encode('utf-8'))
root = ET.Element('gprMax')
root.set('Version', __version__)
root.set('dx_dy_dz', (G.dx, G.dy, G.dz))
root.set('nx_ny_nz', (G.nx, G.ny, G.nz))
# Write the name and numeric ID for each material
mats_el = ET.SubElement(root, 'Materials')
for material in G.materials:
f.write(f'<Material name="{material.ID}">{material.numID}</Material>\n'.encode('utf-8'))
mat_el = ET.SubElement(mats_el, 'Material')
mat_el.set('ID', material.ID)
mat_el.set('numID', str(material.numID))
# Write information on PMLs, sources, and receivers
if not materialsonly:
f.write('<PML name="PML boundary region">1</PML>\n'.encode('utf-8'))
for index, src in enumerate(G.hertziandipoles + G.magneticdipoles + G.voltagesources + G.transmissionlines):
f.write(f'<Sources name="{src.ID}">{index + 2}</Sources>\n'.encode('utf-8'))
for index, rx in enumerate(G.rxs):
f.write(f'<Receivers name="{rx.ID}">{index + 1}</Receivers>\n'.encode('utf-8'))
f.write('</gprMax>\n'.encode('utf-8'))
# Information on PML thickness
if G.pmls:
root.set('PMLthickness', list(G.pmlthickness.values()))
# Location of sources and receivers
srcs = G.hertziandipoles + G.magneticdipoles + G.voltagesources + G.transmissionlines
if srcs:
srcs_el = ET.SubElement(root, 'Sources')
for src in srcs:
src_el = ET.SubElement(srcs_el, 'Source')
src_el.set('name', src.ID)
src_el.set('position', (src.xcoord * G.dx,
src.ycoord * G.dy,
src.zcoord * G.dz))
if G.rxs:
rxs_el = ET.SubElement(root, 'Receivers')
for rx in G.rxs:
rx_el = ET.SubElement(rxs_el, 'Receiver')
rx_el.set('name', rx.ID)
rx_el.set('position', (rx.xcoord * G.dx,
rx.ycoord * G.dy,
rx.zcoord * G.dz))
xml_string = pretty_xml(ET.tostring(root))
f.write(str.encode(xml_string))
def write_vtk_pvd(self, geometryviews):
"""Write a Paraview data file (.pvd) - PVD file provides pointers to the
collection of data files, i.e. GeometryViews.
Args:
geometryviews (list): list of GeometryViews to collect together.
"""
root = ET.Element('VTKFile')
root.set('type', 'Collection')
root.set('version', '0.1')
root.set('byte_order', str(config.sim_config.vtk_byteorder))
collection = ET.SubElement(root, 'Collection')
for gv in geometryviews:
gv.set_filename()
dataset = ET.SubElement(collection, 'DataSet')
dataset.set('timestep', '0')
dataset.set('group', '')
dataset.set('part', '0')
dataset.set('file', str(gv.filename.name))
xml_string = pretty_xml(ET.tostring(root))
self.pvdfile = config.get_model_config().output_file_path.with_suffix('.pvd')
with open(self.pvdfile, 'w') as f:
f.write(xml_string)
class GeometryObjects:
@@ -577,30 +595,8 @@ class GeometryViewFineMultiGrid:
f.write(sg_v.z_s_materials.tostring())
f.write('\n</AppendedData>\n</VTKFile>'.encode('utf-8'))
#self.write_gprmax_info(f, G, materialsonly=True)
def write_gprmax_info(self, f, G, materialsonly=False):
"""Writes gprMax specific information relating material, source,
and receiver names to numeric identifiers.
Args:
f (filehandle): VTK file.
G (FDTDGrid): Parameters describing a grid in a model.
materialsonly (bool): Only write information on materials.
"""
f.write('\n\n<gprMax>\n'.encode('utf-8'))
for material in G.materials:
f.write(f"""<Material name="{material.ID}">{material.numID}</Material>\n""".encode('utf-8'))
if not materialsonly:
f.write('<PML name="PML boundary region">1</PML>\n'.encode('utf-8'))
for index, src in enumerate(G.hertziandipoles + G.magneticdipoles + G.voltagesources + G.transmissionlines):
f.write(f"""<Sources name="{src.ID}">{index + 2}</Sources>\n""".encode('utf-8'))
for index, rx in enumerate(G.rxs):
f.write(f"""<Receivers name="{rx.ID}">{index + 1}</Receivers>\n""".encode('utf-8'))
f.write('</gprMax>\n'.encode('utf-8'))
class SubgridGeometryView:

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@@ -25,6 +25,7 @@ import re
import subprocess
import sys
import textwrap
import xml.dom.minidom
from contextlib import contextmanager
from copy import copy
from shutil import get_terminal_size
@@ -151,6 +152,24 @@ def logo(version):
logger.basic(textwrap.fill(licenseinfo3, width=get_terminal_width() - 1, initial_indent=' ', subsequent_indent=' '))
def pretty_xml(roughxml):
"""Nicely format XML string.
Args:
roughxml (str): XML string to format
Returns:
prettyxml (str): nicely formatted XML string
"""
prettyxml = xml.dom.minidom.parseString(roughxml).toprettyxml()
# Remove the weird newline issue
prettyxml = os.linesep.join(
[s for s in prettyxml.splitlines() if s.strip()])
return prettyxml
def round_value(value, decimalplaces=0):
"""Rounding function.