Merge branch 'logger_write_snapshot' into 'master'

Implement conversion between logger and snapshot

See merge request !1258

logger/examples/create_snapshot.py

+#!/usr/bin/env python3
+"""
+Read a logger file by using an index file and then write a snapshot.
+Example: python3 create_snapshot -t 0.1 -o out.hdf5 ../../examples/SedovBlast_3D/index_*dump
+"""
+import sys
+import h5py
+import numpy as np
+from glob import glob
+import argparse
+sys.path.append("../.libs/")
+
+import liblogger as logger
+
+
+def parse_arguments():
+    parser = argparse.ArgumentParser(
+        description='Read a logfile and plots some basic properties')
+
+    default_files = "../../examples/HydroTests/SedovBlast_3D/index_*dump"
+    default_files = glob(default_files)
+
+    parser.add_argument("-o", '--output', dest='out',
+                        type=str, default="out.hdf5",
+                        help='Output filename')
+    parser.add_argument("-t", '--time', dest='time',
+                        type=float, default=0.01,
+                        help='Simulation time')
+    parser.add_argument('files', metavar='filenames', type=str, nargs="*",
+                        help='The filenames of the logfiles')
+    args = parser.parse_args()
+    if len(args.files) == 0:
+        args.files = default_files
+    return args
+
+
+def write_particle_type(snap, part_type, args):
+    """
+    Write a particle type inside an HDF5 file.
+
+    Parameters
+    ----------
+
+    snap: h5py.File
+        The output file.
+
+    part_type: int
+        The particle type to write
+
+    args: ArgumentParser
+        The argument parser
+
+    Returns
+    -------
+
+    npart: int
+        The number of particles of the given type.
+    """
+    fields = None
+    fields_name = None
+
+    # Read all the fields
+    for f in args.files:
+        if f.endswith(".dump"):
+            filename = f[:-5]
+        else:
+            raise Exception("It seems that you are not providing a logfile (.dump)")
+
+        # Open the logger
+        with logger.Reader(filename, verbose=0) as reader:
+
+            # Get the list of fields
+            if fields_name is None:
+                fields_name = reader.get_list_fields(part_type)
+
+            # Abort if only requesting a type not implemented
+            if "SpecialFlags" in fields_name:
+                print("Part type %i not implemented, skipping it" % part_type)
+                continue
+
+            # Read the fields
+            fields_tmp = reader.get_particle_data(fields_name, args.time, part_type)
+            if fields is None:
+                fields = fields_tmp
+            else:
+                for i, field in enumerate(fields):
+                    fields[i] = np.append(fields[i], fields_tmp[i], axis=0)
+
+    # Do we have this particle type?
+    if fields is None or fields[0].shape[0] == 0:
+        return 0
+
+    # Get the number of particles
+    npart = fields[0].shape[0]
+
+    # Create the group
+    name = "PartType%i" % part_type
+    grp = snap.create_group(name)
+
+    # Save the data
+    for i, field in enumerate(fields_name):
+        grp.create_dataset(field, data=fields[i])
+
+    return npart
+
+
+if __name__ == "__main__":
+    args = parse_arguments()
+    print("Output: %s" % args.out)
+    print("basename: %s" % args.files)
+    print("time: %g" % args.time)
+
+    # read the logger
+    n_types = 6
+
+    # Create a snapshot
+    with h5py.File(args.out, "w") as snap:
+        npart = np.zeros(n_types)
+        for part_type in range(n_types):
+            npart[part_type] = write_particle_type(snap, part_type, args)
+
+
+        # Write the header
+        grp = snap.create_group("Header")
+        grp.attrs["NumPart_Total"] = npart
+        grp.attrs["NumPart_Total_HighWord"] = [0] * n_types
+        grp.attrs["NumPart_ThisFile"] = npart
+        grp.attrs["Time"] = args.time
+        grp.attrs["NumFilesPerSnapshot"] = 1
+        grp.attrs["MassTable"] = [0.0] * n_types
+

logger/examples/reader_example.py

 #!/usr/bin/env python3
 """
 Read a logger file by using an index file.
-Example: ./reader_example.py ../../examples/SedovBlast_3D/index 0.1
+Example: ./reader_example.py -t 0.1 ../../examples/SedovBlast_3D/index_*dump
 """
 import sys
 import numpy as np