Make single output file for main and subgrids.

gprMax/fields_outputs.py

@@ -98,90 +98,77 @@ __global__ void store_outputs(int NRX, int iteration, const int* __restrict__ rx
 """)
 
 
-def write_hdf5_outputfiles(outputfile, G):
+def write_hdf5_outputfile(outputfile, G):
-    if G.rxs:
+    """Write an output file in HDF5 format.
-        write_hdf5_main_grid_outputfile(outputfile, G)
+
+    Args:
+        outputfile (str): Name of the output file.
+        G (FDTDGrid): Parameters describing a grid in a model.
+    """
+
+    # Check for any receivers in subgrids
     sg_rxs = [True for sg in G.subgrids if sg.rxs]
-    if sg_rxs:
-        write_hdf5_sub_grid_outputfile(outputfile, G)
-
-
-def write_hdf5_main_grid_outputfile(outputfile, G):
-    """Write an output file in HDF5 format.
-
-    Args:
-        outputfile (str): Name of the output file.
-        G (FDTDGrid): Parameters describing a grid in a model.
-    """
-
-    write_data(outputfile, G)
-    log.info(f'Written output file: {outputfile.name}')
-
-
-def write_hdf5_sub_grid_outputfile(outputfile, G):
-    """Write an output file in HDF5 format.
-
-    Args:
-        outputfile (str): Name of the output file.
-        G (FDTDGrid): Parameters describing a grid in a model.
-    """
-
-    stem = outputfile.stem
-    suffix = outputfile.suffix
-    parent = outputfile.parent
-
-    for sg in G.subgrids:
-        # Create an outputfile for each subgrid
-        fp = stem + '_' + sg.name + suffix
-        fp = parent / Path(fp)
-
-        f = write_data(fp, sg)
-
-        # Write some additional meta data about the subgrid
-        f.attrs['is_os_sep'] = sg.is_os_sep
-        f.attrs['pml_separation'] = sg.pml_separation
-        f.attrs['subgrid_pml_thickness'] = sg.pmlthickness['x0']
-        f.attrs['filter'] = sg.filter
-        f.attrs['ratio'] = sg.ratio
-        f.attrs['interpolation'] = sg.interpolation
-
-        log.info(f'Written output file: {fp.name}')
-
-def write_data(outputfile, G):
-    """Write an output file in HDF5 format.
-
-    Args:
-        outputfile (str): Name of the output file.
-        G (FDTDGrid): Parameters describing a grid in a model.
-
-    Returns:
-        f (file object): File object.
-    """
 
+    # Create output file and write top-level meta data
+    if G.rxs or sg_rxs:
         f = h5py.File(outputfile, 'w')
         f.attrs['gprMax'] = __version__
         f.attrs['Title'] = G.title
-    f.attrs['Iterations'] = G.iterations
+
-    f.attrs['nx_ny_nz'] = (G.nx, G.ny, G.nz)
+    # Write meta data and data for main grid
-    f.attrs['dx_dy_dz'] = (G.dx, G.dy, G.dz)
+    if G.rxs:
-    f.attrs['dt'] = G.dt
+        write_grid(f, G)
+
+    # Write meta data and data for any subgrids
+    if sg_rxs:
+        for sg in G.subgrids:
+            grp = f.create_group('/subgrids/' + sg.name)
+            write_grid(grp, sg, is_subgrid=True)
+
+    if G.rxs or sg_rxs:
+        log.info(f'Written output file: {outputfile.name}')
+
+
+def write_grid(basegrp, G, is_subgrid=False):
+    """Write grid meta data and data to HDF5 group.
+
+    Args:
+        basegrp (dict): HDF5 group.
+        G (FDTDGrid): Parameters describing a grid in a model.
+        is_subgrid (bool): Is grid instance the main grid or a subgrid.
+    """
+
+    # Write meta data for grid
+    basegrp.attrs['Iterations'] = G.iterations
+    basegrp.attrs['nx_ny_nz'] = (G.nx, G.ny, G.nz)
+    basegrp.attrs['dx_dy_dz'] = (G.dx, G.dy, G.dz)
+    basegrp.attrs['dt'] = G.dt
     nsrc = len(G.voltagesources + G.hertziandipoles + G.magneticdipoles + G.transmissionlines)
-    f.attrs['nsrc'] = nsrc
+    basegrp.attrs['nsrc'] = nsrc
-    f.attrs['nrx'] = len(G.rxs)
+    basegrp.attrs['nrx'] = len(G.rxs)
-    f.attrs['srcsteps'] = G.srcsteps
+    basegrp.attrs['srcsteps'] = G.srcsteps
-    f.attrs['rxsteps'] = G.rxsteps
+    basegrp.attrs['rxsteps'] = G.rxsteps
+
+    if is_subgrid:
+        # Write additional meta data about subgrid
+        basegrp.attrs['is_os_sep'] = G.is_os_sep
+        basegrp.attrs['pml_separation'] = G.pml_separation
+        basegrp.attrs['subgrid_pml_thickness'] = G.pmlthickness['x0']
+        basegrp.attrs['filter'] = G.filter
+        basegrp.attrs['ratio'] = G.ratio
+        basegrp.attrs['interpolation'] = G.interpolation
 
     # Create group for sources (except transmission lines); add type and positional data attributes
     srclist = G.voltagesources + G.hertziandipoles + G.magneticdipoles
     for srcindex, src in enumerate(srclist):
-        grp = f.create_group('/srcs/src' + str(srcindex + 1))
+        grp = basegrp.create_group('srcs/src' + str(srcindex + 1))
         grp.attrs['Type'] = type(src).__name__
         grp.attrs['Position'] = (src.xcoord * G.dx, src.ycoord * G.dy, src.zcoord * G.dz)
 
     # Create group for transmission lines; add positional data, line resistance and
     # line discretisation attributes; write arrays for line voltages and currents
     for tlindex, tl in enumerate(G.transmissionlines):
-        grp = f.create_group('/tls/tl' + str(tlindex + 1))
+        grp = basegrp.create_group('tls/tl' + str(tlindex + 1))
         grp.attrs['Position'] = (tl.xcoord * G.dx, tl.ycoord * G.dy, tl.zcoord * G.dz)
         grp.attrs['Resistance'] = tl.resistance
         grp.attrs['dl'] = tl.dl
@@ -189,17 +176,15 @@ def write_data(outputfile, G):
         grp['Vinc'] = tl.Vinc
         grp['Iinc'] = tl.Iinc
         # Save total voltage and current
-        f['/tls/tl' + str(tlindex + 1) + '/Vtotal'] = tl.Vtotal
+        basegrp['tls/tl' + str(tlindex + 1) + '/Vtotal'] = tl.Vtotal
-        f['/tls/tl' + str(tlindex + 1) + '/Itotal'] = tl.Itotal
+        basegrp['tls/tl' + str(tlindex + 1) + '/Itotal'] = tl.Itotal
 
     # Create group, add positional data and write field component arrays for receivers
     for rxindex, rx in enumerate(G.rxs):
-        grp = f.create_group('/rxs/rx' + str(rxindex + 1))
+        grp = basegrp.create_group('rxs/rx' + str(rxindex + 1))
         if rx.ID:
             grp.attrs['Name'] = rx.ID
         grp.attrs['Position'] = (rx.xcoord * G.dx, rx.ycoord * G.dy, rx.zcoord * G.dz)
 
         for output in rx.outputs:
-            f['/rxs/rx' + str(rxindex + 1) + '/' + output] = rx.outputs[output]
+            basegrp['rxs/rx' + str(rxindex + 1) + '/' + output] = rx.outputs[output]
-
-    return f

gprMax/model_build_run.py

@@ -35,7 +35,7 @@ import gprMax.config as config
 from .cython.yee_cell_build import build_electric_components
 from .cython.yee_cell_build import build_magnetic_components
 from .exceptions import GeneralError
-from .fields_outputs import write_hdf5_outputfiles
+from .fields_outputs import write_hdf5_outputfile
 from .grid import dispersion_analysis
 from .hash_cmds_file import parse_hash_commands
 from .materials import Material
@@ -213,8 +213,8 @@ class ModelBuildRun:
             to file(s).
         """
 
-        # Write an output file(s) in HDF5 format
+        # Write an output file in HDF5 format
-        write_hdf5_outputfiles(config.get_model_config().output_file_path_ext, self.G)
+        write_hdf5_outputfile(config.get_model_config().output_file_path_ext, self.G)
 
         # Write any snapshots to file
         if self.G.snapshots:

tools/plot_Ascan.py

@@ -45,17 +45,36 @@ def mpl_plot(filename, outputs=Rx.defaultoutputs, fft=False):
 
     file = Path(filename)
 
-    # Open output file and read some attributes
+    # Open output file and read iterations
     f = h5py.File(file, 'r')
-    nrx = f.attrs['nrx']
+
-    dt = f.attrs['dt']
+    # Paths to grid(s) to traverse for outputs
-    iterations = f.attrs['Iterations']
+    paths = ['/']
-    time = np.linspace(0, (iterations - 1) * dt, num=iterations)
+
+    # Check if any subgrids and add path(s)
+    is_subgrids = "/subgrids" in f
+    if is_subgrids:
+        paths = paths + ['/subgrids/' + path + '/' for path in f['/subgrids'].keys()]
+
+    # Get number of receivers in grid(s)
+    nrxs = []
+    for path in paths:
+        if f[path].attrs['nrx'] > 0:
+            nrxs.append(f[path].attrs['nrx'])
+        else:
+            paths.remove(path)
 
     # Check there are any receivers
-    if nrx == 0:
+    if not paths:
         raise CmdInputError(f'No receivers found in {file}')
 
+    # Loop through all grids
+    for path in paths:
+        iterations = f[path].attrs['Iterations']
+        nrx = f[path].attrs['nrx']
+        dt = f[path].attrs['dt']
+        time = np.linspace(0, (iterations - 1) * dt, num=iterations)
+
         # Check for single output component when doing a FFT
         if fft:
             if not len(outputs) == 1:
@@ -63,8 +82,8 @@ def mpl_plot(filename, outputs=Rx.defaultoutputs, fft=False):
 
         # New plot for each receiver
         for rx in range(1, nrx + 1):
-        path = '/rxs/rx' + str(rx) + '/'
+            rxpath = path + 'rxs/rx' + str(rx) + '/'
-        availableoutputs = list(f[path].keys())
+            availableoutputs = list(f[rxpath].keys())
 
             # If only a single output is required, create one subplot
             if len(outputs) == 1:
@@ -82,7 +101,7 @@ def mpl_plot(filename, outputs=Rx.defaultoutputs, fft=False):
                 if output not in availableoutputs:
                     raise CmdInputError(f"{output} output requested to plot, but the available output for receiver 1 is {', '.join(availableoutputs)}")
 
-            outputdata = f[path + output][:] * polarity
+                outputdata = f[rxpath + output][:] * polarity
 
                 # Plotting if FFT required
                 if fft:
@@ -100,7 +119,8 @@ def mpl_plot(filename, outputs=Rx.defaultoutputs, fft=False):
                     pltrange = np.s_[0:pltrange]
 
                     # Plot time history of output component
-                fig, (ax1, ax2) = plt.subplots(nrows=1, ncols=2, num='rx' + str(rx),
+                    fig, (ax1, ax2) = plt.subplots(nrows=1, ncols=2,
+                                                   num=rxpath + ' - ' + f[rxpath].attrs['Name'],
                                                    figsize=(20, 10), facecolor='w',
                                                    edgecolor='w')
                     line1 = ax1.plot(time, outputdata, 'r', lw=2, label=outputtext)
@@ -141,8 +161,8 @@ def mpl_plot(filename, outputs=Rx.defaultoutputs, fft=False):
                 else:
                     fig, ax = plt.subplots(subplot_kw=dict(xlabel='Time [s]',
                                            ylabel=outputtext + ' field strength [V/m]'),
-                                       num='rx' + str(rx), figsize=(20, 10),
+                                           num=rxpath + ' - ' + f[rxpath].attrs['Name'],
-                                       facecolor='w', edgecolor='w')
+                                           figsize=(20, 10), facecolor='w', edgecolor='w')
                     line = ax.plot(time, outputdata, 'r', lw=2, label=outputtext)
                     ax.set_xlim([0, np.amax(time)])
                     # ax.set_ylim([-15, 20])
@@ -158,8 +178,8 @@ def mpl_plot(filename, outputs=Rx.defaultoutputs, fft=False):
             # If multiple outputs required, create all nine subplots and populate only the specified ones
             else:
                 fig, ax = plt.subplots(subplot_kw=dict(xlabel='Time [s]'),
-                                   num='rx' + str(rx), figsize=(20, 10),
+                                       num=rxpath + ' - ' + f[rxpath].attrs['Name'],
-                                   facecolor='w', edgecolor='w')
+                                       figsize=(20, 10), facecolor='w', edgecolor='w')
                 if len(outputs) == 9:
                     gs = gridspec.GridSpec(3, 3, hspace=0.3, wspace=0.3)
                 else:
@@ -179,7 +199,7 @@ def mpl_plot(filename, outputs=Rx.defaultoutputs, fft=False):
                     if output not in availableoutputs:
                         raise CmdInputError(f"Output(s) requested to plot: {', '.join(outputs)}, but available output(s) for receiver {rx} in the file: {', '.join(availableoutputs)}")
 
-                outputdata = f[path + output][:] * polarity
+                    outputdata = f[rxpath + output][:] * polarity
 
                     if output == 'Ex':
                         ax = plt.subplot(gs[0, 0])