default voxel and optional edge writing

gprMax/geometry_views.py

@@ -58,7 +58,7 @@ class GeometryView(object):
 
     def write_xdmf(self, modelrun, numbermodelruns, G):
         filename = self.filename[:-4]
-        write_output_file(filename, G)
+        write_output_file(filename, G, self.type)
 
     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.

gprMax/xdmf.py

@@ -39,41 +39,6 @@ class Coordinates:
         self.coordinate_count += 1
 
 
-def hexCellPicker(grid, i, j, k):
-    """
-        This is the ordering of nodes in the hexahedron cell.
-
-                7 --------- 6
-               /           /|
-              4 --------- 5 2
-              |  3        | /
-              | /         |/
-              0 --------- 1
-
-        0 1 2 3 4 5 6 7
-    """
-
-    cell = [
-        grid[i][j][k],
-        # 1
-        grid[i + 1][j][k],
-        # 2
-        grid[i + 1][j + 1][k],
-        # 3
-        grid[i][j + 1][k],
-        # 4
-        grid[i][j][k + 1],
-        # 5
-        grid[i + 1][j][k + 1],
-        # 6
-        grid[i + 1][j + 1][k + 1],
-        # 7
-        grid[i][j + 1][k + 1]
-    ]
-
-    return cell
-
-
 class Solids:
 
     def __init__(self, fdtd_grid):
@@ -96,9 +61,44 @@ class SolidLabels():
         self.total_solids = label_grid.n_cells()
         self.solid_labels = np.zeros((self.total_solids, 8), np.float32)
 
+    def hexCellPicker(self, grid, i, j, k):
+
+        """
+        This is the ordering of nodes in the hexahedron cell.
+
+                7 --------- 6
+               /           /|
+              4 --------- 5 2
+              |  3        | /
+              | /         |/
+              0 --------- 1
+
+        0 1 2 3 4 5 6 7
+        """
+
+        cell = [
+            grid[i][j][k],
+            # 1
+            grid[i + 1][j][k],
+            # 2
+            grid[i + 1][j + 1][k],
+            # 3
+            grid[i][j + 1][k],
+            # 4
+            grid[i][j][k + 1],
+            # 5
+            grid[i + 1][j][k + 1],
+            # 6
+            grid[i + 1][j + 1][k + 1],
+            # 7
+            grid[i][j + 1][k + 1]
+        ]
+
+        return cell
+
     def add(self, i, j, k):
 
-        solid_labels = hexCellPicker(self.label_grid.grid, i, j, k)
+        solid_labels = self.hexCellPicker(self.label_grid.grid, i, j, k)
         self.solid_labels[self.count] = solid_labels
         self.count += 1
 
@@ -119,25 +119,23 @@ class Materials:
 
         self.material_count += 1
 
-
+def process_grid(fdtd_grid, res):
-def process_grid(fdtd_grid):
 
     # Dimensions of the problem domain.
     nx = fdtd_grid.nx
     ny = fdtd_grid.ny
     nz = fdtd_grid.nz
 
+    # useful indices
+    i_max = nx - 1
+    j_max = ny - 1
+    k_max = nz - 1
+
     # label each node in the space
     labels = np.arange(nx * ny * nz).reshape(nx, ny, nz)
 
     label_grid = Grid(labels)
 
-    # Edges define the connectivity of the grid.
-    edges = Edges(label_grid)
-
-    # Material for each edge
-    edge_materials = Materials(fdtd_grid)
-
     # Define coordinates for each node
     coordinates = Coordinates(fdtd_grid)
 
@@ -147,9 +145,12 @@ def process_grid(fdtd_grid):
     # Connectivity for hexhahedron grid
     solid_labels = SolidLabels(label_grid)
 
-    i_max = nx - 1
+    if res == 'f':
-    j_max = ny - 1
+        # Edges define the connectivity of the grid.
-    k_max = nz - 1
+        edges = Edges(label_grid)
+
+        # Material for each edge
+        edge_materials = Materials(fdtd_grid)
 
     for i, ix in enumerate(labels):
         for j, jx in enumerate(ix):
@@ -157,80 +158,86 @@ def process_grid(fdtd_grid):
 
                 label = labels[i][j][k]
 
-                # Each vertex can have varying numbers of edges
-
-                # Type 1 vertex
                 if i < i_max and j < j_max and k < k_max:
-                    edges.add_edge(label, i + 1, j, k)
-                    edges.add_edge(label, i, j + 1, k)
-                    edges.add_edge(label, i, j, k + 1)
-
-                    edge_materials.add_material(i, j, k, 0)
-                    edge_materials.add_material(i, j, k, 1)
-                    edge_materials.add_material(i, j, k, 2)
-
-                    # Only this node can support a cell
                     solids.add_solid(i, j, k)
                     solid_labels.add(i, j, k)
 
-                # Type 2 vertex
+                if res == 'f':
-                elif i < i_max and j == j_max and k == k_max:
+                    # Each vertex can have varying numbers of edges
-                    edges.add_edge(label, i + 1, j, k)
+                    # Type 1 vertex
-                    edge_materials.add_material(i, j, k, 0)
+                    if i < i_max and j < j_max and k < k_max:
+                        edges.add_edge(label, i + 1, j, k)
+                        edges.add_edge(label, i, j + 1, k)
+                        edges.add_edge(label, i, j, k + 1)
 
-                # Type 7 vertex
+                        edge_materials.add_material(i, j, k, 0)
-                elif i < i_max and j == j_max and k < k_max:
+                        edge_materials.add_material(i, j, k, 1)
-                    edges.add_edge(label, i + 1, j, k)
+                        edge_materials.add_material(i, j, k, 2)
-                    edges.add_edge(label, i, j, k + 1)
-                    edge_materials.add_material(i, j, k, 0)
-                    edge_materials.add_material(i, j, k, 2)
 
-                # Type 6 vertex
+                        # Only this node can support a cell
-                elif i == i_max and j == j_max and k < k_max:
-                    edges.add_edge(label, i, j, k + 1)
-                    edge_materials.add_material(i, j, k, 2)
 
-                # Type 5 vertex
+                    # Type 2 vertex
-                elif i == i_max and j < j_max and k < k_max:
+                    elif i < i_max and j == j_max and k == k_max:
-                    edges.add_edge(label, i, j, k + 1)
+                        edges.add_edge(label, i + 1, j, k)
-                    edges.add_edge(label, i, j + 1, k)
+                        edge_materials.add_material(i, j, k, 0)
-                    edge_materials.add_material(i, j, k, 2)
-                    edge_materials.add_material(i, j, k, 1)
 
-                # Type 4 vertex
+                    # Type 7 vertex
-                elif i == i_max and j < j_max and k == k_max:
+                    elif i < i_max and j == j_max and k < k_max:
-                    edges.add_edge(label, i, j + 1, k)
+                        edges.add_edge(label, i + 1, j, k)
-                    edge_materials.add_material(i, j, k, 1)
+                        edges.add_edge(label, i, j, k + 1)
+                        edge_materials.add_material(i, j, k, 0)
+                        edge_materials.add_material(i, j, k, 2)
 
-                # Type 8 vertex
+                    # Type 6 vertex
-                elif i < i_max and j < j_max and k == k_max:
+                    elif i == i_max and j == j_max and k < k_max:
-                    edges.add_edge(label, i, j + 1, k)
+                        edges.add_edge(label, i, j, k + 1)
-                    edges.add_edge(label, i + 1, j, k)
+                        edge_materials.add_material(i, j, k, 2)
-                    edge_materials.add_material(i, j, k, 1)
-                    edge_materials.add_material(i, j, k, 0)
 
-                # Type 3 vertex
+                    # Type 5 vertex
-                # Has no new connectivity
+                    elif i == i_max and j < j_max and k < k_max:
-                elif i == i_max and j == j_max and k == k_max:
+                        edges.add_edge(label, i, j, k + 1)
-                    pass
+                        edges.add_edge(label, i, j + 1, k)
-                else:
+                        edge_materials.add_material(i, j, k, 2)
-                    print('oh no')
+                        edge_materials.add_material(i, j, k, 1)
+
+                    # Type 4 vertex
+                    elif i == i_max and j < j_max and k == k_max:
+                        edges.add_edge(label, i, j + 1, k)
+                        edge_materials.add_material(i, j, k, 1)
+
+                    # Type 8 vertex
+                    elif i < i_max and j < j_max and k == k_max:
+                        edges.add_edge(label, i, j + 1, k)
+                        edges.add_edge(label, i + 1, j, k)
+                        edge_materials.add_material(i, j, k, 1)
+                        edge_materials.add_material(i, j, k, 0)
+
+                    # Type 3 vertex
+                    # Has no new connectivity
+                    elif i == i_max and j == j_max and k == k_max:
+                        pass
+                    else:
+                        print('oh no')
 
                 # Add the coordinates
                 coordinates.add_coordinate(i, j, k)
 
-    return {
+    data = {
         'coordinates': coordinates,
         'solids': solids,
         'solid_labels': solid_labels,
-        'edges': edges,
-        'edge_materials': edge_materials,
     }
 
+    if res == 'f':
+        data['edges'] = edges
+        data['edge_materials'] = edge_materials
 
-def write_output_file(filename, grid):
+    return data
 
-    data = process_grid(grid)
+
+def write_output_file(filename, grid, res):
+
+    data = process_grid(grid, res)
     data['filename'] = filename
     data['xml_doc'] = create_xdmf_markup(data)
 
@@ -246,14 +253,17 @@ def write_xml_doc(options):
 
 def write_H5file(options):
 
-        f = h5py.File(options['filename'] + '.h5', "w")
+    f = h5py.File(options['filename'] + '.h5', "w")
-        coords = f.create_group("mesh")
+    coords = f.create_group("mesh")
-        coords.create_dataset('coordinates', data=options['coordinates'].coordinates)
+    data = f.create_group("data")
-        coords.create_dataset('connectivity', data=options['edges'].edges)
+
-        coords.create_dataset('solid_connectivity', data=options['solid_labels'].solid_labels)
+    coords.create_dataset('coordinates', data=options['coordinates'].coordinates)
-        data = f.create_group("data")
+    coords.create_dataset('solid_connectivity', data=options['solid_labels'].solid_labels)
+    data.create_dataset('solids', data=options['solids'].solids)
+
+    if 'edges' in options:
         data.create_dataset('materials', data=options['edge_materials'].materials)
-        data.create_dataset('solids', data=options['solids'].solids)
+        coords.create_dataset('connectivity', data=options['edges'].edges)
 
 
 def create_xdmf_markup(options):
@@ -264,36 +274,40 @@ def create_xdmf_markup(options):
     domain_el = etree.Element("Domain")
     xdmf_el.append(domain_el)
 
-    grid_el = etree.Element("Grid", Name="Edges", GridType="Uniform")
-    domain_el.append(grid_el)
-
-    # Create the grid node
-    topology_el = etree.Element("Topology", TopologyType="Polyline", NumberOfElements=str(options['edges'].total_edges))
-    grid_el.append(topology_el)
-
-    topology_dimensions = "{} 2".format(options['edges'].total_edges)
-    top_data_el = etree.Element("DataItem", Dimensions=topology_dimensions, NumberType="Float", Precision="8", Format="HDF")
-    top_data_el.text = "{}:/mesh/connectivity".format(options['filename'] + '.h5')
-    topology_el.append(top_data_el)
-
-    # Create the Geometry node
     geometry_el = etree.Element("Geometry", GeometryType="XYZ")
-    grid_el.append(geometry_el)
-
-    # Create the origin coordinates
     coordinates_dimensions = "{} 3".format(options['coordinates'].total_coordinates)
     origin_el = etree.Element("DataItem", Dimensions=coordinates_dimensions, NumberType="Float", Precision="8", Format="HDF")
     origin_el.text = "{}:/mesh/coordinates".format(options['filename'] + '.h5')
     geometry_el.append(origin_el)
 
-    # Create the materials attribute
+    # Check if there are edges to write
-    attr_el = etree.Element("Attribute", Center="Cell", Name="Edge_Materials")
+    if 'edges' in options:
-    grid_el.append(attr_el)
 
-    materials_dimensions = "{} 1".format(options['edge_materials'].material_count)
+        grid_el = etree.Element("Grid", Name="Edges", GridType="Uniform")
-    materials_el = etree.Element("DataItem", Dimensions=materials_dimensions, NumberType="Float", Precision="8", Format="HDF")
+        domain_el.append(grid_el)
-    materials_el.text = "{}:/data/materials".format(options['filename'] + '.h5')
+
-    attr_el.append(materials_el)
+        # Create the grid node
+        topology_el = etree.Element("Topology", TopologyType="Polyline", NumberOfElements=str(options['edges'].total_edges))
+        grid_el.append(topology_el)
+
+        topology_dimensions = "{} 2".format(options['edges'].total_edges)
+        top_data_el = etree.Element("DataItem", Dimensions=topology_dimensions, NumberType="Float", Precision="8", Format="HDF")
+        top_data_el.text = "{}:/mesh/connectivity".format(options['filename'] + '.h5')
+        topology_el.append(top_data_el)
+
+        # Create the Geometry node
+        grid_el.append(copy.deepcopy(geometry_el))
+
+        # Create the origin coordinates
+
+        # Create the materials attribute
+        attr_el = etree.Element("Attribute", Center="Cell", Name="Edge_Materials")
+        grid_el.append(attr_el)
+
+        materials_dimensions = "{} 1".format(options['edge_materials'].material_count)
+        materials_el = etree.Element("DataItem", Dimensions=materials_dimensions, NumberType="Float", Precision="8", Format="HDF")
+        materials_el.text = "{}:/data/materials".format(options['filename'] + '.h5')
+        attr_el.append(materials_el)
 
     v_grid_el = etree.Element("Grid", Name="Voxel", GridType="Uniform")
     domain_el.append(v_grid_el)