Added a pre-commit config file and reformatted all the files accordingly by using it.

toolboxes/Utilities/outputfiles_merge.py

@@ -44,26 +44,28 @@ def get_output_data(filename, rxnumber, rxcomponent):
     """
 
     # Open output file and read some attributes
-    with h5py.File(filename, 'r') as f:
-        nrx = f.attrs['nrx']
-        dt = f.attrs['dt']
+    with h5py.File(filename, "r") as f:
+        nrx = f.attrs["nrx"]
+        dt = f.attrs["dt"]
 
         # Check there are any receivers
         if nrx == 0:
-            logger.exception(f'No receivers found in {filename}')
+            logger.exception(f"No receivers found in {filename}")
             raise ValueError
 
-        path = '/rxs/rx' + str(rxnumber) + '/'
+        path = "/rxs/rx" + str(rxnumber) + "/"
         availableoutputs = list(f[path].keys())
 
         # Check if requested output is in file
         if rxcomponent not in availableoutputs:
-            logger.exception(f"{rxcomponent} output requested to plot, but the " +
-                             f"available output for receiver 1 is " +
-                             f"{', '.join(availableoutputs)}")
+            logger.exception(
+                f"{rxcomponent} output requested to plot, but the "
+                + f"available output for receiver 1 is "
+                + f"{', '.join(availableoutputs)}"
+            )
             raise ValueError
 
-        outputdata = f[path + '/' + rxcomponent]
+        outputdata = f[path + "/" + rxcomponent]
         outputdata = np.array(outputdata)
 
     return outputdata, dt
@@ -78,43 +80,43 @@ def merge_files(outputfiles, removefiles=False):
         removefiles: boolean flag to remove individual output files after merge.
     """
 
-    merged_outputfile = os.path.commonprefix(outputfiles) + '_merged.h5'
+    merged_outputfile = os.path.commonprefix(outputfiles) + "_merged.h5"
 
     # Combined output file
-    fout = h5py.File(merged_outputfile, 'w')
+    fout = h5py.File(merged_outputfile, "w")
 
     for i, outputfile in enumerate(outputfiles):
-        fin = h5py.File(outputfile, 'r')
-        nrx = fin.attrs['nrx']
+        fin = h5py.File(outputfile, "r")
+        nrx = fin.attrs["nrx"]
 
         # Write properties for merged file on first iteration
         if i == 0:
-            fout.attrs['gprMax'] = __version__
-            fout.attrs['Iterations'] = fin.attrs['Iterations']
-            fout.attrs['nx_ny_nz'] = fin.attrs['nx_ny_nz']
-            fout.attrs['dx_dy_dz'] = fin.attrs['dx_dy_dz']
-            fout.attrs['dt'] = fin.attrs['dt']
-            fout.attrs['nsrc'] = fin.attrs['nsrc']
-            fout.attrs['nrx'] = fin.attrs['nrx']
-            fout.attrs['srcsteps'] = fin.attrs['srcsteps']
-            fout.attrs['rxsteps'] = fin.attrs['rxsteps']
+            fout.attrs["gprMax"] = __version__
+            fout.attrs["Iterations"] = fin.attrs["Iterations"]
+            fout.attrs["nx_ny_nz"] = fin.attrs["nx_ny_nz"]
+            fout.attrs["dx_dy_dz"] = fin.attrs["dx_dy_dz"]
+            fout.attrs["dt"] = fin.attrs["dt"]
+            fout.attrs["nsrc"] = fin.attrs["nsrc"]
+            fout.attrs["nrx"] = fin.attrs["nrx"]
+            fout.attrs["srcsteps"] = fin.attrs["srcsteps"]
+            fout.attrs["rxsteps"] = fin.attrs["rxsteps"]
 
             for rx in range(1, nrx + 1):
-                path = '/rxs/rx' + str(rx)
+                path = "/rxs/rx" + str(rx)
                 grp = fout.create_group(path)
                 availableoutputs = list(fin[path].keys())
                 for output in availableoutputs:
-                    grp.create_dataset(output, 
-                                       (fout.attrs['Iterations'], len(outputfiles)), 
-                                       dtype=fin[path + '/' + output].dtype)
+                    grp.create_dataset(
+                        output, (fout.attrs["Iterations"], len(outputfiles)), dtype=fin[path + "/" + output].dtype
+                    )
 
         # For all receivers
         for rx in range(1, nrx + 1):
-            path = '/rxs/rx' + str(rx) + '/'
+            path = "/rxs/rx" + str(rx) + "/"
             availableoutputs = list(fin[path].keys())
             # For all receiver outputs
             for output in availableoutputs:
-                fout[path + '/' + output][:, i] = fin[path + '/' + output][:]
+                fout[path + "/" + output][:, i] = fin[path + "/" + output][:]
 
         fin.close()
     fout.close()
@@ -123,19 +125,22 @@ def merge_files(outputfiles, removefiles=False):
         for outputfile in outputfiles:
             os.remove(outputfile)
 
-if __name__ == "__main__":
 
+if __name__ == "__main__":
     # Parse command line arguments
-    parser = argparse.ArgumentParser(description='Merges traces (A-scans) from multiple ' +
-                                                 'output files into one new file, then ' +
-                                                 'optionally removes the series of output files.', 
-                                     usage='cd gprMax; python -m tools.outputfiles_merge basefilename')
-    parser.add_argument('basefilename', help='base name of output file series including path')
-    parser.add_argument('--remove-files', action='store_true', default=False, 
-                        help='flag to remove individual output files after merge')
+    parser = argparse.ArgumentParser(
+        description="Merges traces (A-scans) from multiple "
+        + "output files into one new file, then "
+        + "optionally removes the series of output files.",
+        usage="cd gprMax; python -m tools.outputfiles_merge basefilename",
+    )
+    parser.add_argument("basefilename", help="base name of output file series including path")
+    parser.add_argument(
+        "--remove-files", action="store_true", default=False, help="flag to remove individual output files after merge"
+    )
     args = parser.parse_args()
 
-    files = glob.glob(args.basefilename + '*.h5')
-    outputfiles = [filename for filename in files if '_merged' not in filename]
+    files = glob.glob(args.basefilename + "*.h5")
+    outputfiles = [filename for filename in files if "_merged" not in filename]
     outputfiles.sort(key=natural_keys)
     merge_files(outputfiles, removefiles=args.remove_files)