Merge branch 'devel-reframe' into mpi

toolboxes/STLtoVoxel/convert.py

@@ -26,7 +26,13 @@ def convert_files(input_file_paths, discretization, colors=[(0, 0, 0)], pad=1, p
 
     for input_file_path in input_file_paths:
         mesh_obj = mesh.Mesh.from_file(input_file_path)
-        org_mesh = np.hstack((mesh_obj.v0[:, np.newaxis], mesh_obj.v1[:, np.newaxis], mesh_obj.v2[:, np.newaxis]))
+        org_mesh = np.hstack(
+            (
+                mesh_obj.v0[:, np.newaxis],
+                mesh_obj.v1[:, np.newaxis],
+                mesh_obj.v2[:, np.newaxis],
+            )
+        )
         meshes.append(org_mesh)
     vol, scale, shift = convert_meshes(meshes, discretization, parallel)
     vol = np.transpose(vol)

toolboxes/STLtoVoxel/slice.py

@@ -19,7 +19,12 @@ def mesh_to_plane(mesh, bounding_box, parallel):
 
     current_mesh_indices = set()
     z = 0
-    with tqdm(total=bounding_box[2], desc="Processing Layers", ncols=get_terminal_width() - 1, file=sys.stdout) as pbar:
+    with tqdm(
+        total=bounding_box[2],
+        desc="Processing Layers",
+        ncols=get_terminal_width() - 1,
+        file=sys.stdout,
+    ) as pbar:
         for event_z, status, tri_ind in generate_tri_events(mesh):
             while event_z - z >= 0:
                 mesh_subset = [mesh[ind] for ind in current_mesh_indices]

toolboxes/STLtoVoxel/stltovoxel.py

@@ -17,9 +17,15 @@ if __name__ == "__main__":
         usage="cd gprMax; python -m toolboxes.STLtoVoxel.stltovoxel stlfilename -matindex -dxdydz",
     )
     parser.add_argument(
-        "stlfiles", help="can be the filename of a single STL file, or the path to folder containing multiple STL files"
+        "stlfiles",
+        help="can be the filename of a single STL file, or the path to folder containing multiple STL files",
+    )
+    parser.add_argument(
+        "-dxdydz",
+        type=float,
+        required=True,
+        help="discretisation to use in voxelisation process",
     )
-    parser.add_argument("-dxdydz", type=float, required=True, help="discretisation to use in voxelisation process")
     args = parser.parse_args()
 
     if os.path.isdir(args.stlfiles):
@@ -29,16 +35,18 @@ if __name__ == "__main__":
         filename_mats = os.path.join(path, os.path.basename(path) + "_mats.txt")
     elif os.path.isfile(args.stlfiles):
         path = os.path.dirname(args.stlfiles)
-        files = args.stlfiles
-        filename_hdf5 = os.path.join(path, os.path.split(os.path.basename(path))[0] + "_geo.h5")
-        filename_mats = os.path.join(path, os.path.split(os.path.basename(path))[0] + "_mats.txt")
+        files = [args.stlfiles]
+        filename_hdf5 = os.path.splitext(args.stlfiles)[0] + "_geo.h5"
+        filename_mats = os.path.splitext(args.stlfiles)[0] + "_mats.txt"
 
     dxdydz = (args.dxdydz, args.dxdydz, args.dxdydz)
 
     newline = "\n\t"
     logger.info(f"\nConverting STL file(s): {newline.join(files)}")
     model_array = convert_files(files, dxdydz)
-    logger.info(f"Number of voxels: {model_array.shape[0]} x {model_array.shape[1]} x {model_array.shape[2]}")
+    logger.info(
+        f"Number of voxels: {model_array.shape[0]} x {model_array.shape[1]} x {model_array.shape[2]}"
+    )
     logger.info(f"Spatial discretisation: {dxdydz[0]} x {dxdydz[1]} x {dxdydz[2]}m")
 
     # Write HDF5 file for gprMax using voxels