def test_open(self):
"""
Open file and check a field.
"""
f = umfile.UMFile(self.restart_dump)
assert(len(f.fields) > 0)
assert(f.fields[2].__str__() == 'U COMPNT OF WIND AFTER TIMESTEP')
def test_array_read(self):
"""
Read data using array syntax.
"""
f = umfile.UMFile(self.restart_dump)
u_wnd = f.fields[2][:]
assert(u_wnd.shape == (145, 192))
assert(np.mean(u_wnd) > -0.1 and np.mean(u_wnd) < 0)
def test_array_write(self):
"""
Write data using array syntax.
"""
f = umfile.UMFile(self.restart_dump)
assert(np.sum(f.fields[2][:]) != 0)
f.fields[2][:] = 0
assert(np.sum(f.fields[2][:]) == 0)
def test_close(self):
"""
Modify data and check that changes are written out.
"""
# First make a copy of the test file.
restart_dump_copy = self.restart_dump + '.copy'
shutil.copyfile(self.restart_dump, restart_dump_copy)
f = umfile.UMFile(restart_dump_copy, 'r+')
assert(np.sum(f.fields[2][:]) != 0)
f.fields[2][:] = 0
assert(np.sum(f.fields[2][:]) == 0)
f.close()
f = umfile.UMFile(restart_dump_copy)
assert(np.sum(f.fields[2][:]) == 0)
os.remove(restart_dump_copy)
import umfile, stashvar
verbose = False
try:
optlist, args = getopt.getopt(sys.argv[1:], 'v')
for opt in optlist:
if opt[0] == '-v':
verbose = True
except getopt.error:
print "Usage: polar_anom [-v] ifile "
sys.exit(2)
if args:
ifile = args[0]
f = umfile.UMFile(ifile)
if not f.fieldsfile:
print "Not a UM fieldsfile"
sys.exit(1)
if f.fixhd[FH_HorizGrid] != 0:
print "Error - not a global grid"
sys.exit(1)
for k in range(f.fixhd[FH_LookupSize2]):
ilookup = f.ilookup[k]
rlookup = f.rlookup[k]
lbegin = ilookup[LBEGIN] # lbegin is offset from start
if lbegin == -99:
break
# Here check for this # Usage is check_land_overlap.py global_mask regional_mask # Note that this isn't going to work for rotated grids. # Martin Dix [email protected] import numpy as np import sys import umfile from um_fileheaders import * file1 = sys.argv[1] file2 = sys.argv[2] f = umfile.UMFile(file1) g = umfile.UMFile(file2) def getfld(f): # Expecting only a single field ilookup = f.ilookup[0] # Check field name and data type. # Expecting stash code 1 0 30 LAND MASK if ilookup[ITEM_CODE] != 30: print "Variable is not land mask, stashcode is", ilookup[ITEM_CODE] sys.exit(1) if ilookup[DATA_TYPE] != 3: print "Variable is not expected logical type, code is", ilookup[ DATA_TYPE]
#!/usr/bin/env python
# Change the calendar in a UM ancillary file from Gregorian to 360 day
# Assuming monthly data, change to appropriate middle of month dates.
from um_fileheaders import *
import umfile, sys
print sys.argv[1]
f = umfile.UMFile(sys.argv[1], 'r+')
if f.fixhd[FH_CalendarType] == 1:
f.fixhd[FH_CalendarType] = 2
print "Changing from Gregorian to 360 day"
else:
print "Already 360 day"
sys.exit(0)
for k in range(f.fixhd[FH_LookupSize2]):
ilookup = f.ilookup[k]
# print "Validity time", ilookup[LBYR], ilookup[LBMON], ilookup[LBDAT], \
# ilookup[LBHR], ilookup[LBMIN], ilookup[LBDAY]
# print "Data time", ilookup[LBYRD], ilookup[LBMOND], ilookup[LBDATD], \
# ilookup[LBHRD], ilookup[LBMIND], ilookup[LBDAYD]
# print "LBTIM", ilookup[LBTIM]
ilookup[LBDAT] = ilookup[LBDATD] = 16
ilookup[LBHR] = ilookup[LBHRD] = 0
ilookup[LBMIN] = ilookup[LBMIND] = 0
ilookup[LBDAY] = ilookup[LBDAYD] = 16 + (ilookup[LBMON] - 1) * 30
if ilookup[LBTIM] % 10 == 1:
# Reset units part of value from 1 to 2.
ilookup[LBTIM] += 1 # Crucial for CDMS.
try:
optlist, args = getopt.getopt(sys.argv[1:], 'v:')
for opt in optlist:
if opt[0] == '-v':
oldindex, newindex = opt[1].split(",")
oldindex = int(oldindex)
newindex = int(newindex)
vdict[oldindex] = newindex
except getopt.error:
print "Usage: change_stashcode.py -v oldindex,newindex file"
print " Variables specified by STASH index = Section Number * 1000 + item number"
print " May use multiple -v arguments"
sys.exit(2)
ifile = args[0]
f = umfile.UMFile(ifile, 'r+')
changed = False
for k in range(f.fixhd[FH_LookupSize2]):
ilookup = f.ilookup[k]
lbegin = ilookup[LBEGIN]
if lbegin == -99:
break
# Format is Section Number * 1000 + item number
if ilookup[ITEM_CODE] in vdict:
changed = True
ilookup[ITEM_CODE] = vdict[ilookup[ITEM_CODE]]
if not changed:
print "Warning - no fields changed"
#!/usr/bin/env python
# Change the initial and valid date of a UM dump file
# Change both the file header and the date header of each record.
# The latter may not be strictly necessary but it makes looking at file with
# xconv less confusing.
import getopt, sys
import umfile
from um_fileheaders import *
ifile = sys.argv[1]
f = umfile.UMFile(ifile, "r+")
print "Initial Time", f.fixhd[FH_DTYear], f.fixhd[FH_DTMonth], f.fixhd[FH_DTDay], \
f.fixhd[FH_DTHour], f.fixhd[FH_DTMinute], f.fixhd[FH_DTSecond]
print "Valid Time", f.fixhd[FH_VTYear], f.fixhd[FH_VTMonth], f.fixhd[FH_VTDay], \
f.fixhd[FH_VTHour], f.fixhd[FH_VTMinute], f.fixhd[FH_VTSecond]
s = raw_input('Enter year month day\n')
s = s.split()
year = int(s[0])
month = int(s[1])
day = int(s[2])
print "Using", year, month, day
f.fixhd[FH_DTYear] = f.fixhd[FH_VTYear] = year
f.fixhd[FH_DTMonth] = f.fixhd[FH_VTMonth] = month
if opt[0] == '-i':
ifile = opt[1]
elif opt[0] == '-o':
ofile = opt[1]
elif opt[0] == '-v':
# Allow comma separated lists
for v in opt[1].split(","):
vlist.append(int(v))
except getopt.error:
print "Usage: um_copy_field.py -i ifile -o ofile -v var"
print " Copy fields from ifile to ofile"
print " Variables specified by STASH index = Section Number * 1000 + item number"
print " May use a list specififed as -v var1,var2,..."
sys.exit(2)
f = umfile.UMFile(ifile, "r")
g = umfile.UMFile(ofile, "r+")
# Find the indices of the desired fields in each file.
# This assumes that each is in normal stashcode order
# (as all files produced by model are)
findex = []
gindex = []
for k in range(f.fixhd[FH_LookupSize2]):
ilookup = f.ilookup[k]
lbegin = ilookup[LBEGIN] # lbegin is offset from start
if lbegin == -99:
break
if ilookup[ITEM_CODE] in vlist:
findex.append(k)
optlist, args = getopt.getopt(sys.argv[1:], 'i:o:m:')
for opt in optlist:
if opt[0] == '-i':
ifile = opt[1]
elif opt[0] == '-o':
ofile = opt[1]
elif opt[0] == '-m':
maskfile = opt[1]
except getopt.error:
usage()
if not ifile or not ofile or not maskfile:
print "Error: filenames undefined"
usage()
m = umfile.UMFile(maskfile)
f = umfile.UMFile(ifile)
# Target grid properties
nlon_target = m.inthead[IC_XLen]
nlat_target = m.inthead[IC_YLen]
# Create new axes for the output grid
outgrid = cdms2.createUniformGrid(m.realhead[RC_FirstLat], nlat_target,
m.realhead[RC_LatSpacing],
m.realhead[RC_FirstLong], nlon_target,
m.realhead[RC_LongSpacing])
g = umfile.UMFile(ofile, "w")
g.copyheader(f)
parser.add_argument('-o', dest='ofile', help='Output UM dump')
parser.add_argument('-f',
dest='fracfile',
help='New vegetation fraction (ancillary or netCDF)')
parser.add_argument('-v',
'--verbose',
dest='verbose',
action='store_true',
default=False,
help='verbose output')
args = parser.parse_args()
ntiles = 17
# Get old vegetation fraction from dump file
f = umfile.UMFile(args.ifile)
vlist = []
for k in range(f.fixhd[FH_LookupSize2]):
ilookup = f.ilookup[k]
lbegin = ilookup[LBEGIN]
if lbegin == -99:
break
if ilookup[ITEM_CODE] == 216:
a = f.readfld(k)
vlist.append(a)
assert len(vlist) == ntiles, 'Error - expected %d vegetation classes' % ntiles
old_vegfrac = np.array(vlist)
if args.fracfile.endswith(".nc"):
# Read from a netCDF version of a dump file
# Usage is show_land_overlap.py global_mask regional_mask disallowed # Note that this isn't going to work for rotated grids. # Martin Dix [email protected] import numpy as np import sys import umfile from um_fileheaders import * file1 = sys.argv[1] file2 = sys.argv[2] file3 = sys.argv[3] f = umfile.UMFile(file1) g = umfile.UMFile(file2, 'r+') h = umfile.UMFile(file3, 'w') h.copyheader(g) h.ilookup[:] = -99 # Used as missing value h.rlookup[:] = np.fromstring(np.array([-99],h.int).tostring(),h.float) def getfld(f): # Expecting only a single field ilookup = f.ilookup[0] # Check field name and data type. # Expecting stash code 1 0 30 LAND MASK if ilookup[ITEM_CODE] != 30: print "Variable is not land mask, stashcode is", ilookup[ITEM_CODE]
#!/usr/bin/env python
# List of valid data times in a file
from um_fileheaders import *
import umfile, sys, collections, datetime
f = umfile.UMFile(sys.argv[1])
times=collections.defaultdict(int)
for k in range(f.fixhd[FH_LookupSize2]):
ilookup = f.ilookup[k]
if ilookup[LBEGIN] == -99:
break
t = datetime.datetime(ilookup[LBYR], ilookup[LBMON],
ilookup[LBDAT], ilookup[LBHR],
ilookup[LBMIN], ilookup[LBDAY])
times[t] += 1
print "Valid_times",
for t in sorted(times.keys()):
print t.strftime('%Y%m%d%H%M'),
print
if len(set(times.values())) > 1:
print "Warning - not all times have same number of fields"
elif opt[0] == '-y':
y0 = int(opt[1].split(',')[0])
ny = int(opt[1].split(',')[1])
except getopt.error:
usage()
sys.exit(2)
if len(args) != 3:
print "Missing filename arguments"
usage()
# Section to take
if verbose:
print "Section", x0, y0, nx, ny
f1 = umfile.UMFile(args[0])
f2 = umfile.UMFile(args[1])
g = umfile.UMFile(args[2], "w")
g.copyheader(f1)
for k in range(f1.fixhd[FH_LookupSize2]):
if f1.ilookup[k][LBEGIN] == -99 or f2.ilookup[k][LBEGIN] == -99:
break
if f1.ilookup[k][ITEM_CODE] != f2.ilookup[k][ITEM_CODE]:
raise Exception(
"files do not match %d %d %d" %
(k, f1.ilookup[k][ITEM_CODE], f2.ilookup[k][ITEM_CODE]))
data1 = f1.readfld(k)
dataout = f2.readfld(k)
from um_fileheaders import *
def usage():
print "Usage: mergefiles.py -file1 file2 outputfile"
sys.exit(2)
vlist = []
xlist = []
nfields = 9999999999
prognostic = False
if len(sys.argv) != 4:
print "Missing filename arguments"
usage()
f1 = umfile.UMFile(sys.argv[1])
f2 = umfile.UMFile(sys.argv[2])
g = umfile.UMFile(sys.argv[3], "w")
g.copyheader(f)
print "Lookup sizes", f1.fixhd[FH_LookupSize2], f1.fixhd[FH_LookupSize1], \
f2.fixhd[FH_LookupSize2], f2.fixhd[FH_LookupSize1]
g.ilookup[:] = -99 # Used as missing value
# Start of data is at fixhd[FH_DataStart],
# This should be a multiple of 2048 + 1
# Start of lookup table fixhd[FH_LookupStart]
min_dstart = g.fixhd[FH_LookupStart] + np.prod(olookup.shape)
import getopt, sys
import umfile
from um_fileheaders import *
try:
optlist, args = getopt.getopt(sys.argv[1:], 'i:o:')
for opt in optlist:
if opt[0] == '-i':
ifile = opt[1]
elif opt[0] == '-o':
ofile = opt[1]
except getopt.error:
print "Usage: change_endianness.py -i ifile -o ofile"
sys.exit(2)
f = umfile.UMFile(ifile)
g = umfile.UMFile(ofile, "w")
g.copyheader(f)
g.rlookup = g.rlookup.byteswap()
# Set output byteorder to be opposite of input
if f.byteorder == '>':
g.byteorder = '<'
elif f.byteorder == '<':
g.byteorder = '>'
else:
# Native
if sys.byteorder == 'little':
g.byteorder = '>' # Big
else:
dest='ncvarname',
required=True,
help='netCDF variable name')
parser.add_argument('target', help='UM File to change')
args = parser.parse_args()
d = cdms2.open(args.ncfile)
try:
# Remove singleton dimensions (time or level in surface fields)
ncvar = d.variables[args.ncvarname](squeeze=1)
except KeyError:
print "\nError: variable %s not in %s" % (args.ncvarname, args.ncfile)
sys.exit(1)
f = umfile.UMFile(args.target, "r+")
# Set new missing value to match the UM missing value
arr = MV2.array(ncvar[:])
arr.setMissing(f.missval_r)
arr = MV2.filled(arr).astype(f.float)
# Loop over all the fields
replaced = False
for k in range(f.fixhd[FH_LookupSize2]):
ilookup = f.ilookup[k]
lbegin = ilookup[LBEGIN] # lbegin is offset from start
if lbegin == -99:
break
if ilookup[ITEM_CODE] == args.varcode:
print "Replacing field", k, ilookup[ITEM_CODE]
