diff --git a/gprMax/geometry_views.py b/gprMax/geometry_views.py
index 784eb604..eade70b9 100644
--- a/gprMax/geometry_views.py
+++ b/gprMax/geometry_views.py
@@ -34,8 +34,8 @@ class GeometryView:
def __init__(self, xs=None, ys=None, zs=None, xf=None, yf=None, zf=None, dx=None, dy=None, dz=None, filename=None, type=None):
"""
Args:
- xs, xf, ys, yf, zs, zf (float): Extent of the volume.
- dx, dy, dz (float): Spatial discretisation.
+ xs, xf, ys, yf, zs, zf (int): Extent of the volume in cells.
+ dx, dy, dz (int): Spatial discretisation in cells.
filename (str): Filename to save to.
type (str): Either 'n' for a per cell geometry view, or 'f' for a per cell edge geometry view.
"""
@@ -54,10 +54,9 @@ class GeometryView:
self.dz = dz
self.filename = filename
self.type = type
- self.srcs_rxs = np.zeros((self.nx / self.dx, self.ny / self.dy, self.nz / self.dz), dtype=np.int8)
def write_vtk(self, modelrun, numbermodelruns, G):
- """Writes the geometry information to a VTK file. Either ImageData (.vti) for a per cell geometry view, or PolygonalData (.vtp) for a per cell edge geometry view.
+ """Writes the geometry information to a VTK file. Either ImageData (.vti) for a per-cell geometry view, or PolygonalData (.vtp) for a per-cell-edge geometry view.
N.B. No Python 3 support for VTK at time of writing (03/2015)
@@ -76,19 +75,25 @@ class GeometryView:
if self.type == 'n':
self.filename += '.vti'
- # Calculate number of cells according to requested sampling
+ # Calculate number of cells according to requested sampling for geometry view
self.vtk_xscells = round_value(self.xs / self.dx)
self.vtk_xfcells = round_value(self.xf / self.dx)
self.vtk_yscells = round_value(self.ys / self.dy)
self.vtk_yfcells = round_value(self.yf / self.dy)
self.vtk_zscells = round_value(self.zs / self.dz)
self.vtk_zfcells = round_value(self.zf / self.dz)
+ self.vtk_nxcells = self.vtk_xfcells - self.vtk_xscells
+ self.vtk_nycells = self.vtk_yfcells - self.vtk_yscells
+ self.vtk_nzcells = self.vtk_zfcells - self.vtk_zscells
- # Add a numeric ID for receivers and sources to an array
+ # Create an array and add numeric IDs for PML, sources and receivers
+ self.srcs_rxs_pml = np.zeros((G.nx + 1, G.ny + 1, G.nz + 1), dtype=np.int8)
+ for pml in G.pmls:
+ self.srcs_rxs_pml[pml.xs:pml.xf, pml.ys:pml.yf, pml.zs:pml.zf] = 1
for index, srcrx in enumerate(G.rxs + G.hertziandipoles + G.magneticdipoles + G.voltagesources + G.transmissionlines):
- self.srcs_rxs[srcrx.xcoord, srcrx.ycoord, srcrx.zcoord] = index + 1
-
- vtk_srcs_rxs_offset = round_value((np.dtype(np.uint32).itemsize * (self.nx / self.dx) * (self.ny / self.dy) * (self.nz / self.dz)) + np.dtype(np.uint32).itemsize)
+ self.srcs_rxs_pml[srcrx.xcoord, srcrx.ycoord, srcrx.zcoord] = index + 2
+
+ vtk_srcs_rxs_pml_offset = round_value((np.dtype(np.uint32).itemsize * self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells) + np.dtype(np.uint32).itemsize)
with open(self.filename, 'wb') as f:
f.write('\n'.encode('utf-8'))
@@ -97,11 +102,12 @@ class GeometryView:
f.write('\n'.format(self.vtk_xscells, self.vtk_xfcells, self.vtk_yscells, self.vtk_yfcells, self.vtk_zscells, self.vtk_zfcells).encode('utf-8'))
f.write('\n'.encode('utf-8'))
f.write('\n'.encode('utf-8'))
- f.write('\n'.format(vtk_srcs_rxs_offset).encode('utf-8'))
- f.write('\n\n\n\n_'.encode('utf-8'))
+ f.write('\n'.format(vtk_srcs_rxs_pml_offset).encode('utf-8'))
+ f.write('\n'.encode('utf-8'))
+ f.write('\n\n\n_'.encode('utf-8'))
- # Calculate number of bytes of appended data section
- datasize = int(np.dtype(np.uint32).itemsize * (self.nx / self.dx) * (self.ny / self.dy) * (self.nz / self.dz))
+ # Write material IDs
+ datasize = int(np.dtype(np.uint32).itemsize * self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells)
# Write number of bytes of appended data as UInt32
f.write(pack('I', datasize))
for k in range(self.zs, self.zf, self.dz):
@@ -109,14 +115,14 @@ class GeometryView:
for i in range(self.xs, self.xf, self.dx):
f.write(pack('I', G.solid[i, j, k]))
- # Calculate number of bytes of appended data section
- datasize = int(np.dtype(np.int8).itemsize * (self.nx / self.dx) * (self.ny / self.dy) * (self.nz / self.dz))
+ # Write source/receiver IDs
+ datasize = int(np.dtype(np.int8).itemsize * self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells)
f.write(pack('I', datasize))
- # Write number of bytes of appended data as UInt32
for k in range(self.zs, self.zf, self.dz):
for j in range(self.ys, self.yf, self.dy):
for i in range(self.xs, self.xf, self.dx):
- f.write(pack('b', self.srcs_rxs[i, j, k]))
+ f.write(pack('b', self.srcs_rxs_pml[i, j, k]))
+
f.write('\n\n'.encode('utf-8'))
self.write_gprmax_info(f, G)
@@ -128,19 +134,24 @@ class GeometryView:
vtk_numpoint_components = 3
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
vtk_numline_components = 2;
+
vtk_connectivity_offset = round_value((vtk_numpoints * vtk_numpoint_components * np.dtype(np.float32).itemsize) + np.dtype(np.uint32).itemsize)
vtk_offsets_offset = round_value(vtk_connectivity_offset + (vtk_numlines * vtk_numline_components * np.dtype(np.uint32).itemsize) + np.dtype(np.uint32).itemsize)
- vtk_id_offset = round_value(vtk_offsets_offset + (vtk_numlines * np.dtype(np.uint32).itemsize) + np.dtype(np.uint32).itemsize)
- vtk_offsets_size = vtk_numlines
+ vtk_materials_offset = round_value(vtk_offsets_offset + (vtk_numlines * np.dtype(np.uint32).itemsize) + np.dtype(np.uint32).itemsize)
with open(self.filename, 'wb') as f:
f.write('\n'.encode('utf-8'))
f.write('\n'.format(GeometryView.byteorder).encode('utf-8'))
f.write('\n\n'.format(vtk_numpoints, vtk_numlines).encode('utf-8'))
+
f.write('\n\n\n'.encode('utf-8'))
f.write('\n\n'.format(vtk_connectivity_offset).encode('utf-8'))
f.write('\n\n'.format(vtk_offsets_offset).encode('utf-8'))
- f.write('\n\n\n'.format(vtk_id_offset).encode('utf-8'))
+
+ f.write('\n'.encode('utf-8'))
+ f.write('\n'.format(vtk_materials_offset).encode('utf-8'))
+ f.write('\n'.encode('utf-8'))
+
f.write('\n\n\n_'.encode('utf-8'))
# Write points
@@ -186,12 +197,12 @@ class GeometryView:
# Write cell type (line) offsets
vtk_cell_pts = 2
- datasize = np.dtype(np.uint32).itemsize * vtk_offsets_size
+ datasize = np.dtype(np.uint32).itemsize * vtk_numlines
f.write(pack('I', datasize))
for vtk_offsets in range(vtk_cell_pts, (vtk_numline_components * vtk_numlines) + vtk_cell_pts, vtk_cell_pts):
f.write(pack('I', vtk_offsets))
- # Write Ex, Ey, Ez values from ID array
+ # Write material IDs per-cell-edge, i.e. from ID array
datasize = np.dtype(np.uint32).itemsize * vtk_numlines
f.write(pack('I', datasize))
for i in range(self.xs, self.xf):
@@ -211,21 +222,25 @@ class GeometryView:
f.write('\n\n'.encode('utf-8'))
- self.write_gprmax_info(f, G)
+ self.write_gprmax_info(f, G, materialsonly=True)
- def write_gprmax_info(self, f, G):
+
+ 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 (class): Grid class instance - holds essential parameters describing the model.
+ materialsonly (boolean): Only write information on materials
"""
f.write('\n\n\n'.encode('utf-8'))
for material in G.materials:
f.write('{}\n'.format(material.ID, material.numID).encode('utf-8'))
- for index, srcrx in enumerate(G.rxs + G.hertziandipoles + G.magneticdipoles + G.voltagesources + G.transmissionlines):
- f.write('{}\n'.format(srcrx.ID, index + 1).encode('utf-8'))
+ if not materialsonly:
+ f.write('1\n'.encode('utf-8'))
+ for index, srcrx in enumerate(G.rxs + G.hertziandipoles + G.magneticdipoles + G.voltagesources + G.transmissionlines):
+ f.write('{}\n'.format(srcrx.ID, index + 2).encode('utf-8'))
f.write('\n'.encode('utf-8'))