Updating of outputfiles_merge to allow it to be imported as a function.

docs/source/examples_simple_2D.rst

@@ -155,7 +155,7 @@ You should have produced 60 output files, one for each A-scan, with names ``cyli
 
     python -m tools.outputfiles_merge user_models/cylinder_Bscan_2D
 
-You should see a combined output file ``cylinder_Bscan_2D_merged.out``. The tool will ask you if you want to delete the original single A-scan output files or keep them.
+You should see a combined output file ``cylinder_Bscan_2D_merged.out``. You can add the optional argument ``--remove-files`` if you want to automatically delete the original single A-scan output files.
 
 You can now view an image of the B-scan using the command:
 
@@ -171,9 +171,3 @@ You can now view an image of the B-scan using the command:
     :width: 600px
 
     B-scan of model of a metal cylinder buried in a dielectric half-space.
-
-
-
-
-
-

docs/source/utils.rst

@@ -21,15 +21,16 @@ where ``inputfile`` is the name of input file including the path.
 outputfiles_merge.py
 --------------------
 
-gprMax produces a separate output file for each trace (A-scan) in a B-scan. This module combines the separate output files into a single file, and offers to remove the separate output files afterwards. Usage (from the top-level gprMax directory) is:
+gprMax produces a separate output file for each trace (A-scan) in a B-scan. This module combines the separate output files into a single file, and can remove the separate output files afterwards. Usage (from the top-level gprMax directory) is:
 
 .. code-block:: none
 
-    python -m tools.outputfiles_merge basefilename
+    python -m tools.outputfiles_merge basefilename --remove-files
 
 where:
 
 * ``basefilename`` is the base name file of the output file series, e.g. for ``myoutput1.out``, ``myoutput2.out`` the base file name would be ``myoutput``
+* ``remove-files`` is an optional argument (flag) that when given will remove the separate output files after the merge.
 
 
 convert_png2h5.py

tools/outputfiles_merge.py

@@ -25,25 +25,61 @@ import numpy as np
 
 from gprMax._version import __version__
 
-"""Merges traces (A-scans) from multiple output files into one new file, then removes the series of output files."""
 
-# Parse command line arguments
+def get_output_data(filename, rxnumber, rxcomponent):
-parser = argparse.ArgumentParser(description='Merges traces (A-scans) from multiple output files into one new file, then removes the series of output files.', usage='cd gprMax; python -m tools.outputfiles_merge basefilename')
+    """Gets B-scan output data from a model.
-parser.add_argument('basefilename', help='base name of output file series including path')
-args = parser.parse_args()
 
-basefilename = args.basefilename
+    Args:
-outputfile = basefilename + '_merged.out'
+        filename (string): Filename (including path) of output file.
-files = glob.glob(basefilename + '*.out')
+        rxnumber (int): Receiver output number.
-outputfiles = [filename for filename in files if '_merged' not in filename]
+        rxcomponent (str): Receiver output field/current component.
-modelruns = len(outputfiles)
-print('Found {} files to merge'.format(modelruns))
 
-# Combined output file
+    Returns:
-fout = h5py.File(outputfile, 'w')
+        outputdata (array): Array of A-scans, i.e. B-scan data.
+        dt (float): Temporal resolution of the model.
+    """
 
-# Add positional data for rxs
+    # Open output file and read some attributes
-for model in range(modelruns):
+    f = h5py.File(filename, 'r')
+    nrx = f.attrs['nrx']
+    dt = f.attrs['dt']
+
+    # Check there are any receivers
+    if nrx == 0:
+        raise CmdInputError('No receivers found in {}'.format(filename))
+
+    path = '/rxs/rx' + str(rxnumber) + '/'
+    availableoutputs = list(f[path].keys())
+
+    # Check if requested output is in file
+    if rxcomponent not in availableoutputs:
+        raise CmdInputError('{} output requested to plot, but the available output for receiver 1 is {}'.format(rxcomponent, ', '.join(availableoutputs)))
+
+    outputdata = f[path + '/' + rxcomponent]
+    outputdata = np.array(outputdata)
+
+    return outputdata, dt
+
+
+def merge_files(basefilename, removefiles=False):
+    """Merges traces (A-scans) from multiple output files into one new file,
+        then optionally removes the series of output files.
+
+    Args:
+        basefilename (string): Base name of output file series including path.
+        outputs (boolean): Flag to remove individual output files after merge.
+    """
+
+    outputfile = basefilename + '_merged.out'
+    files = glob.glob(basefilename + '*.out')
+    outputfiles = [filename for filename in files if '_merged' not in filename]
+    modelruns = len(outputfiles)
+
+    # Combined output file
+    fout = h5py.File(outputfile, 'w')
+
+    # Add positional data for rxs
+    for model in range(modelruns):
         fin = h5py.File(basefilename + str(model + 1) + '.out', 'r')
         nrx = fin.attrs['nrx']
 
@@ -71,10 +107,19 @@ for model in range(modelruns):
 
         fin.close()
 
-fout.close()
+    fout.close()
 
-check = input('Do you want to remove the multiple individual output files? [y] or n:')
+    if removefiles:
-if not check or check == 'y':
         for model in range(modelruns):
             file = basefilename + str(model + 1) + '.out'
             os.remove(file)
+
+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')
+    args = parser.parse_args()
+
+    merge_files(args.basefilename, removefiles=args.remove_files)

tools/plot_Bscan.py

@@ -25,45 +25,7 @@ import numpy as np
 import matplotlib.pyplot as plt
 
 from gprMax.exceptions import CmdInputError
-
+from .outputdata import get_output_data
-
-def get_output_data(filename, rxnumber, rxcomponent):
-    """Gets B-scan output data from a model.
-
-    Args:
-        filename (string): Filename (including path) of output file.
-        rxnumber (int): Receiver output number.
-        rxcomponent (str): Receiver output field/current component.
-
-    Returns:
-        outputdata (array): Array of A-scans, i.e. B-scan data.
-        dt (float): Temporal resolution of the model.
-    """
-
-    # Open output file and read some attributes
-    f = h5py.File(filename, 'r')
-    nrx = f.attrs['nrx']
-    dt = f.attrs['dt']
-
-    # Check there are any receivers
-    if nrx == 0:
-        raise CmdInputError('No receivers found in {}'.format(filename))
-
-    path = '/rxs/rx' + str(rxnumber) + '/'
-    availableoutputs = list(f[path].keys())
-
-    # Check if requested output is in file
-    if rxcomponent not in availableoutputs:
-        raise CmdInputError('{} output requested to plot, but the available output for receiver 1 is {}'.format(rxcomponent, ', '.join(availableoutputs)))
-
-    outputdata = f[path + '/' + rxcomponent]
-    outputdata = np.array(outputdata)
-
-    # Check that there is more than one A-scan present
-    if outputdata.shape[1] == 1:
-        raise CmdInputError('{} contains only a single A-scan.'.format(filename))
-
-    return outputdata, dt
 
 
 def mpl_plot(filename, outputdata, dt, rxnumber, rxcomponent):