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镜像自地址 https://gitee.com/sunhf/gprMax.git 已同步 2025-08-08 07:24:19 +08:00
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Cleanup/rationalisation of code from writing geometry views.

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这个提交包含在：
Craig Warren
2018-07-09 11:13:54 +01:00
父节点 25e7d4b533
当前提交 ae243b1d03
共有 1 个文件被更改，包括 63 次插入 和 55 次删除
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118
gprMax/geometry_outputs.py
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@@ -64,27 +64,45 @@ class GeometryView(object):
if self.fileext == '.vti': if self.fileext == '.vti':
# Calculate number of cells according to requested sampling for geometry view # Calculate number of cells according to requested sampling for geometry view
self.vtk_xscells = self.xs // self.dx self.vtk_xscells = round_value(self.xs / self.dx)
self.vtk_xfcells = self.xf // self.dx self.vtk_xfcells = round_value(self.xf / self.dx)
self.vtk_yscells = self.ys // self.dy self.vtk_yscells = round_value(self.ys / self.dy)
self.vtk_yfcells = self.yf // self.dy self.vtk_yfcells = round_value(self.yf / self.dy)
self.vtk_zscells = self.zs // self.dz self.vtk_zscells = round_value(self.zs / self.dz)
self.vtk_zfcells = self.zf // self.dz self.vtk_zfcells = round_value(self.zf / self.dz)
self.vtk_nxcells = self.nx // self.dx self.vtk_nxcells = round_value(self.nx / self.dx)
self.vtk_nycells = self.ny // self.dy self.vtk_nycells = round_value(self.ny / self.dy)
self.vtk_nzcells = self.nz // self.dz self.vtk_nzcells = round_value(self.nz / self.dz)
self.n_vtk_cells = self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells self.vtk_ncells = self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells
self.datawritesize = int(np.dtype(np.uint32).itemsize * self.n_vtk_cells) + 2 * (int(np.dtype(np.int8).itemsize * self.n_vtk_cells)) 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': elif self.fileext == '.vtp':
self.vtk_numpoints = (self.nx + 1) * (self.ny + 1) * (self.nz + 1) self.vtk_numpoints = (self.nx + 1) * (self.ny + 1) * (self.nz + 1)
self.vtk_numpoint_components = 3 self.vtk_numpoint_components = 3
self.vtk_numlines = 2 * self.nx * self.ny + 2 * self.ny * self.nz + 2 * self.nx * self.nz + 3 * self.nx * self.ny * self.nz + self.nx + self.ny + self.nz
self.vtk_numline_components = 2 self.vtk_numline_components = 2
self.vtk_connectivity_offset = round_value((self.vtk_numpoints * self.vtk_numpoint_components * np.dtype(np.float32).itemsize) + np.dtype(np.uint32).itemsize) self.vtk_nxlines = self.nx * (self.ny + 1) * (self.nz + 1)
self.vtk_offsets_offset = round_value(self.vtk_connectivity_offset + (self.vtk_numlines * self.vtk_numline_components * np.dtype(np.uint32).itemsize) + np.dtype(np.uint32).itemsize) self.vtk_nylines = self.ny * (self.nx + 1) * (self.nz + 1)
self.vtk_materials_offset = round_value(self.vtk_offsets_offset + (self.vtk_numlines * np.dtype(np.uint32).itemsize) + np.dtype(np.uint32).itemsize) self.vtk_nzlines = self.nz * (self.nx + 1) * (self.ny + 1)
self.datawritesize = np.dtype(np.float32).itemsize * self.vtk_numpoints * self.vtk_numpoint_components + np.dtype(np.uint32).itemsize * self.vtk_numlines * self.vtk_numline_components + np.dtype(np.uint32).itemsize * self.vtk_numlines + np.dtype(np.uint32).itemsize * self.vtk_numlines self.vtk_numlines = self.vtk_nxlines + self.vtk_nylines + self.vtk_nzlines
self.vtk_connectivity_offset = round_value((self.vtk_numpoints *
self.vtk_numpoint_components *
np.dtype(np.float32).itemsize) +
np.dtype(np.uint32).itemsize)
self.vtk_offsets_offset = round_value(self.vtk_connectivity_offset +
(self.vtk_numlines * self.vtk_numline_components * np.dtype(np.uint32).itemsize) +
np.dtype(np.uint32).itemsize)
self.vtk_materials_offset = round_value(self.vtk_offsets_offset +
(self.vtk_numlines * np.dtype(np.uint32).itemsize) +
np.dtype(np.uint32).itemsize)
vtk_cell_offsets = ((self.vtk_numline_components * self.vtk_numlines) +
self.vtk_numline_components - self.vtk_numline_components - 1) // self.vtk_numline_components + 1
self.datawritesize = (np.dtype(np.float32).itemsize * self.vtk_numpoints * self.vtk_numpoint_components +
np.dtype(np.uint32).itemsize * self.vtk_numlines * self.vtk_numline_components +
np.dtype(np.uint32).itemsize * self.vtk_numlines +
np.dtype(np.uint32).itemsize * vtk_cell_offsets +
np.dtype(np.uint32).itemsize * 4)
def set_filename(self, appendmodelnumber, G): def set_filename(self, appendmodelnumber, G):
""" """
@@ -137,9 +155,9 @@ class GeometryView(object):
f.write('</CellData>\n'.encode('utf-8')) f.write('</CellData>\n'.encode('utf-8'))
f.write('</Piece>\n</ImageData>\n<AppendedData encoding="raw">\n_'.encode('utf-8')) f.write('</Piece>\n</ImageData>\n<AppendedData encoding="raw">\n_'.encode('utf-8'))
solid_geometry = np.zeros((self.n_vtk_cells), dtype=np.uint32) solid_geometry = np.zeros((self.vtk_ncells), dtype=np.uint32)
srcs_pml_geometry = np.zeros((self.n_vtk_cells), dtype=np.int8) srcs_pml_geometry = np.zeros((self.vtk_ncells), dtype=np.int8)
rxs_geometry = np.zeros((self.n_vtk_cells), dtype=np.int8) rxs_geometry = np.zeros((self.vtk_ncells), dtype=np.int8)
define_normal_geometry( define_normal_geometry(
self.xs, self.xs,
@@ -158,25 +176,26 @@ class GeometryView(object):
srcs_pml_geometry, srcs_pml_geometry,
rxs_geometry) rxs_geometry)
# Write material IDs
datasize = solid_geometry.nbytes
# Write number of bytes of appended data as UInt32 # Write number of bytes of appended data as UInt32
f.write(pack('I', datasize)) f.write(pack('I', solid_geometry.nbytes))
pbar.update(n=4) pbar.update(n=4)
# Write solid array
f.write(solid_geometry) f.write(solid_geometry)
pbar.update(n=datasize) pbar.update(n=solid_geometry.nbytes)
datasize = srcs_pml_geometry.nbytes # Write number of bytes of appended data as UInt32
f.write(pack('I', datasize)) f.write(pack('I', srcs_pml_geometry.nbytes))
pbar.update(n=4) pbar.update(n=4)
# Write sources and PML positions
f.write(srcs_pml_geometry) f.write(srcs_pml_geometry)
pbar.update(n=datasize) pbar.update(n=srcs_pml_geometry.nbytes)
datasize = rxs_geometry.nbytes # Write number of bytes of appended data as UInt32
f.write(pack('I', datasize)) f.write(pack('I', rxs_geometry.nbytes))
pbar.update(n=4) pbar.update(n=4)
# Write receiver positions
f.write(rxs_geometry) f.write(rxs_geometry)
pbar.update(n=datasize) pbar.update(n=rxs_geometry.nbytes)
f.write('\n</AppendedData>\n</VTKFile>'.encode('utf-8')) f.write('\n</AppendedData>\n</VTKFile>'.encode('utf-8'))
@@ -199,23 +218,20 @@ class GeometryView(object):
f.write('</Piece>\n</PolyData>\n<AppendedData encoding="raw">\n_'.encode('utf-8')) f.write('</Piece>\n</PolyData>\n<AppendedData encoding="raw">\n_'.encode('utf-8'))
# Coordinates of each point # Coordinates of each point
n_points = (self.nx + 1) * (self.ny + 1) * (self.nz + 1) points = np.zeros((self.vtk_numpoints, 3), dtype=np.float32)
points = np.zeros((n_points, 3), dtype=np.float32)
# Number of x components # Number of x components
n_x_lines = self.nx * (self.ny + 1) * (self.nz + 1)
# Node connectivity. Each index contains a pair of connected x nodes # Node connectivity. Each index contains a pair of connected x nodes
x_lines = np.zeros((n_x_lines, 2), dtype=np.uint32) x_lines = np.zeros((self.vtk_nxlines, 2), dtype=np.uint32)
# Material at Ex location in Yee cell. # Material at Ex location in Yee cell.
x_materials = np.zeros((n_x_lines), dtype=np.uint32) x_materials = np.zeros((self.vtk_nxlines), dtype=np.uint32)
n_y_lines = self.ny * (self.nx + 1) * (self.nz + 1) y_lines = np.zeros((self.vtk_nylines, 2), dtype=np.uint32)
y_lines = np.zeros((n_y_lines, 2), dtype=np.uint32) y_materials = np.zeros((self.vtk_nylines), dtype=np.uint32)
y_materials = np.zeros((n_y_lines), dtype=np.uint32)
n_z_lines = self.nz * (self.nx + 1) * (self.ny + 1) z_lines = np.zeros((self.vtk_nzlines, 2), dtype=np.uint32)
z_lines = np.zeros((n_z_lines, 2), dtype=np.uint32) z_materials = np.zeros((self.vtk_nzlines), dtype=np.uint32)
z_materials = np.zeros((n_z_lines), dtype=np.uint32)
define_fine_geometry(self.nx, define_fine_geometry(self.nx,
self.ny, self.ny,
@@ -239,16 +255,13 @@ class GeometryView(object):
z_materials) z_materials)
# Write point data # Write point data
datasize = points.nbytes f.write(pack('I', points.nbytes))
f.write(pack('I', datasize))
f.write(points) f.write(points)
pbar.update(n=datasize) pbar.update(n=points.nbytes)
# Write connectivity data # Write connectivity data
datasize = np.dtype(np.uint32).itemsize * self.vtk_numlines * self.vtk_numline_components f.write(pack('I', np.dtype(np.uint32).itemsize * self.vtk_numlines * self.vtk_numline_components))
f.write(pack('I', datasize))
pbar.update(n=4) pbar.update(n=4)
f.write(x_lines) f.write(x_lines)
pbar.update(n=x_lines.nbytes) pbar.update(n=x_lines.nbytes)
f.write(y_lines) f.write(y_lines)
@@ -257,19 +270,15 @@ class GeometryView(object):
pbar.update(n=z_lines.nbytes) pbar.update(n=z_lines.nbytes)
# Write cell type (line) offsets # Write cell type (line) offsets
vtk_cell_pts = 2 f.write(pack('I', np.dtype(np.uint32).itemsize * self.vtk_numlines))
datasize = np.dtype(np.uint32).itemsize * self.vtk_numlines
f.write(pack('I', datasize))
pbar.update(n=4) pbar.update(n=4)
for vtk_offsets in range(vtk_cell_pts, (self.vtk_numline_components * self.vtk_numlines) + vtk_cell_pts, vtk_cell_pts): for vtk_offsets in range(self.vtk_numline_components, (self.vtk_numline_components * self.vtk_numlines) + self.vtk_numline_components, self.vtk_numline_components):
f.write(pack('I', vtk_offsets)) f.write(pack('I', vtk_offsets))
pbar.update(n=4) pbar.update(n=4)
# Write material IDs per-cell-edge, i.e. from ID array # Write material IDs per-cell-edge, i.e. from ID array
datasize = np.dtype(np.uint32).itemsize * self.vtk_numlines f.write(pack('I', np.dtype(np.uint32).itemsize * self.vtk_numlines))
f.write(pack('I', datasize))
pbar.update(n=4) pbar.update(n=4)
f.write(x_materials) f.write(x_materials)
pbar.update(n=x_materials.nbytes) pbar.update(n=x_materials.nbytes)
f.write(y_materials) f.write(y_materials)
@@ -278,7 +287,6 @@ class GeometryView(object):
pbar.update(n=z_materials.nbytes) pbar.update(n=z_materials.nbytes)
f.write('\n</AppendedData>\n</VTKFile>'.encode('utf-8')) f.write('\n</AppendedData>\n</VTKFile>'.encode('utf-8'))
self.write_gprmax_info(f, G, materialsonly=True) self.write_gprmax_info(f, G, materialsonly=True)
def write_gprmax_info(self, f, G, materialsonly=False): def write_gprmax_info(self, f, G, materialsonly=False):
@@ -344,7 +352,7 @@ class GeometryObjects(object):
fdata = h5py.File(os.path.abspath(os.path.join(G.inputdirectory, self.filename)), 'w') fdata = h5py.File(os.path.abspath(os.path.join(G.inputdirectory, self.filename)), 'w')
fdata.attrs['gprMax'] = __version__ fdata.attrs['gprMax'] = __version__
fdata.attrs['Title'] = G.title fdata.attrs['Title'] = G.title
fdata.attrs['dx, dy, dz'] = (G.dx, G.dy, G.dz) fdata.attrs['dx_dy_dz'] = (G.dx, G.dy, G.dz)
# Get minimum and maximum integers of materials in geometry objects volume # Get minimum and maximum integers of materials in geometry objects volume
minmat = np.amin(G.ID[:, self.xs:self.xf + 1, self.ys:self.yf + 1, self.zs:self.zf + 1]) minmat = np.amin(G.ID[:, self.xs:self.xf + 1, self.ys:self.yf + 1, self.zs:self.zf + 1])