Added a new function to read a COMMAND file for V9 (and maybe older v…

…ersions)

reflexible/conv2netcdf4/__init__.py

@@ -1,4 +1,4 @@
 # Import the public functions here
 from .data_structures import Header, Structure, BinaryFile, FDC
-from .flexpart_read import read_header, read_trajectories, read_command
+from .flexpart_read import read_header, read_trajectories, read_command, read_commandV9
 from .grid_read import read_grid, get_slabs, fill_grids

reflexible/conv2netcdf4/flexpart_read.py

@@ -10,6 +10,57 @@
 import reflexible.conv2netcdf4
 from .helpers import closest
 
+def read_commandV9(path, headerrows=7):
+    """Quick and dirty approach for reading COMMAND file for FP V9"""
+    COMMAND_KEYS = (
+        'SIM_DIR',
+        'SIM_START',
+        'SIM_END',
+        'AVG_CNC_INT',
+        'AVG_CNC_TAVG',
+        'CNC_SAMP_TIME',
+        'T_PARTSPLIT',
+        'SYNC',
+        'CTL',
+        'IFINE',
+        'IOUT',
+        'IPOUT',
+        'LSUBGRID',
+        'LCONVECTION',
+        'LAGESPECTRA',
+        'IPIN',
+        'OUTPUTFOREACHRELEASE',
+        'IFLUX',
+        'MDOMAINFILL',
+        'IND_SOURCE',
+        'IND_RECEPTOR',
+        'MQUASILAG',
+        'NESTED_OUTPUT',
+        'LINIT_COND')
+    float_keys = ['CTL']
+    date_keys = ['SIM_START', 'SIM_END']
+
+    COMMAND = {}
+    ncommand = 0
+    with open(path, 'r') as comfile:
+        for i in range(headerrows):
+            comfile.readline()
+        while ncommand < len(COMMAND_KEYS):
+            comfile.readline()
+            val = comfile.readline().strip().split()
+            key = COMMAND_KEYS[ncommand]
+            if key in date_keys:
+                val = val[:2]
+            elif key in float_keys:
+                val = float(val[0])
+            else:
+                val = int(val[0])
+            COMMAND[key] = val
+            comfile.readline()
+            comfile.readline()
+            ncommand += 1
+    return COMMAND
+
 
 def read_command(path, headerrows=7):
     """

reflexible/scripts/create_ncfile.py

@@ -18,10 +18,10 @@
 import os.path
 import netCDF4 as nc
 
-from reflexible.conv2netcdf4 import Header, read_grid
+from reflexible.conv2netcdf4 import Header, read_grid, read_command, read_commandV9
 
 
-def write_metadata(H, ncid):
+def write_metadata(H, command, ncid):
     # hes CF convention requires these attributes
     ncid.Conventions = 'CF-1.6'
     ncid.title = 'FLEXPART model output'
@@ -70,7 +70,7 @@ def write_metadata(H, ncid):
     # ncid.surf_only = H.surf_only
 
 
-def write_header(H, ncid):
+def write_header(H, command, ncid):
     nnx = H.numxgrid
     nny = H.numygrid
     nnz = H.numzgrid
@@ -138,6 +138,11 @@ def create_ncfile(fddir, nested, outfile=None):
         fprefix = 'grid_conc_'
     else:
         fprefix = 'grid_time_'
+
+    command_path = os.path.join(os.path.dirname(fddir), "options/COMMAND")
+    # XXX This needs to be checked out, as I am not sure when the new format started
+    command = read_commandV9(command_path)
+
     path = os.path.dirname(fddir)
     fprefix = os.path.join(path, fprefix)
     if outfile is None:
@@ -148,9 +153,10 @@ def create_ncfile(fddir, nested, outfile=None):
     else:
         ncfname = outfile
     cache_size = 16 * H.numxgrid * H.numygrid * H.numzgrid
+
     ncid = nc.Dataset(ncfname, 'w', chunk_cache=cache_size)
-    write_metadata(H, ncid)
-    write_header(H, ncid)
+    write_metadata(H, command, ncid)
+    write_header(H, command, ncid)
     ncid.close()
     return ncfname