gprMax/toolboxes/Utilities/outputfiles_merge.py

# Copyright (C) 2015-2022: The University of Edinburgh, United Kingdom
#                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
#
# This file is part of gprMax.
#
# gprMax is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# gprMax is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with gprMax.  If not, see <http://www.gnu.org/licenses/>.

import argparse
import glob
import logging
import os
from pathlib import Path

import h5py
import numpy as np
from gprMax._version import __version__
from gprMax.utilities.utilities import natural_keys

logger = logging.getLogger(__name__)


def get_output_data(filename, rxnumber, rxcomponent):
    """Gets B-scan output data from a model.

    Args:
        filename: string of tilename (including path) of output file.
        rxnumber: int of receiver output number.
        rxcomponent: string of receiver output field/current component.

    Returns:
        outputdata: array of A-scans, i.e. B-scan data.
        dt: float of temporal resolution of the model.
    """

    # Open output file and read some attributes
    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}')
            raise ValueError

        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)}")
            raise ValueError

        outputdata = f[path + '/' + rxcomponent]
        outputdata = np.array(outputdata)

    return outputdata, dt


def merge_files(outputfiles, removefiles=False):
    """Merges traces (A-scans) from multiple output files into one new file,
        then optionally removes the series of output files.

    Args:
        outputfiles: list of output files to be merged.
        removefiles: boolean flag to remove individual output files after merge.
    """

    merged_outputfile = os.path.commonprefix(outputfiles) + '_merged.h5'

    # Combined output file
    fout = h5py.File(merged_outputfile, 'w')

    for i, outputfile in enumerate(outputfiles):
        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']

            for rx in range(1, nrx + 1):
                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)

        # For all receivers
        for rx in range(1, nrx + 1):
            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][:]

        fin.close()
    fout.close()

    if removefiles:
        for outputfile in outputfiles:
            os.remove(outputfile)

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()

    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)