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extract_hwsd_latlon_rebin.py
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#!/usr/bin/env python
import netCDF4 as nc
import matplotlib.pyplot as plt
import sys
import numpy as np
import argparse
import getpass
import datetime as dt
from scipy import stats
################################################################################
################################################################################
#
# Define class
#
################################################################################
################################################################################
class extract:
def parse_input(self):
parser=argparse.ArgumentParser(description='Extract a subset of a binary file to a netcdf file')
# optional
parser.add_argument('--inmissing',type=float,help='Missing value in input file',required=False,default=None)
parser.add_argument('--outmissing',type=float,help='Missing value in output file',required=False,default=None)
parser.add_argument('--lat_binsize',type=float,help='Binsize of latitudinal aggregation',required=False,default=None)
parser.add_argument('--lon_binsize',type=float,help='Binsize of longitudinal aggregation',required=False,default=None)
# positional
parser.add_argument('infile',help='Input file')
parser.add_argument('outfile',help='Output file')
parser.add_argument('latmin',help='Minimum latitude',type=float)
parser.add_argument('latmax',help='Maximum latitude',type=float)
parser.add_argument('lonmin',help='Minimum longitude',type=float)
parser.add_argument('lonmax',help='Maximum longitude',type=float)
# Parse the arguments
args=parser.parse_args()
return args.infile, \
args.outfile, \
args.latmin, \
args.latmax, \
args.lonmin, \
args.lonmax, \
args.inmissing, \
args.outmissing, \
args.lat_binsize, \
args.lon_binsize
################################################################################
################################################################################
#
# Main function
#
################################################################################
################################################################################
if __name__=='__main__':
# Call the class
e=extract()
infile, outfile, latmin, latmax, lonmin, lonmax, in_mv, out_mv, lat_binsize, lon_binsize = e.parse_input()
# '/users/eow/edwcom/data/HWSD/hwsd.bil', '/users/eow/edwcom/data/HWSD/test.nc', \
# 20., 90., -180., 180., 0.0, -9999.0, 5, 5
# Open input file
print "Read input file: %s"%infile
# Get header information
hfile=infile[:-4]+'.hdr'
print "Header in file: %s"%hfile
hdr={}
for lin in open(hfile,'r').readlines():
name,value = lin.strip().split()
if name=='BYTEORDER' or name=='LAYOUT':
hdr[name]=value
else:
hdr[name]=int(value)
# The grid definition
gfile=infile[:-4]+'.blw'
print "Grid definition in file: %s"%hfile
dlon,rot1,rot2,dlat,lon0,lat0=[float(f.strip()) for f in open(gfile,'r').readlines() ]
# Set up grid
# These will be the CENTRES of the grid squares
lon=np.arange(lon0,lon0+(hdr['NCOLS']*dlon),dlon)
lonrange=[lon[0]-(dlon/2),lon[-1]+(dlon/2)]
lat=np.arange(lat0,lat0+(hdr['NROWS']*dlat),dlat)
latrange=[lat[-1]+(dlat/2),lat[0]-(dlat/2)]
# finally read the input data
indata=np.fromfile(infile,dtype='int16').reshape([hdr['NROWS'],hdr['NCOLS']]).astype(float)
# mask where data=missing value
if in_mv!=None:
indata=np.ma.masked_equal(indata,in_mv)
# Cut down to what we need
xmin=np.argmin(np.abs(lon-lonmin))
if lon[xmin]<lonmin:
xmin+=1
xmax=np.argmin(np.abs(lon-lonmax))
if lon[xmax]>lonmax:
xmax-=1
ymin=np.argmin(np.abs(lat-latmax))
if lat[ymin]>latmax:
ymin-=1
ymax=np.argmin(np.abs(lat-latmin))
if lat[ymax]<latmin:
ymax-=1
###################################################################
# ECP MOD
# If rebinning ensure dimensions are multiples of bins,
# extend nort/east where neccessary
if (lat_binsize!=None)&(lon_binsize!=None):
xmax=((np.ceil(float(xmax-xmin)/lon_binsize))*lon_binsize)+xmin
ymax=((np.ceil(float(ymax-ymin)/lat_binsize))*lat_binsize)+ymin
###################################################################
outdata=indata[ymin:ymax,xmin:xmax]
outlat=lat[ymin:ymax]
outlon=lon[xmin:xmax]
del indata
del lat
del lon
#outdataindx=np.ma.masked_equal(np.ones_like(outdata)*in_mv,in_mv)
#j=1
#for i in np.unique(outdata):
#outdataindx[np.where(outdata==i)]=j
#j+=1
#plt.imshow(outdata.data)
#plt.colorbar()
#plt.grid(True)
#plt.savefig('/users/eow/edwcom/test_plots/HWSD_fullres.png')
###################################################################
# ECP Modification:
# regrid to new latitude/longitude grid if required
if (lat_binsize!=None)&(lon_binsize!=None):
nlats = len(outlat)
nlons = len(outlon)
tempdata=outdata.reshape([nlats/lat_binsize,lat_binsize,\
nlons/lon_binsize,lon_binsize])
tempdata=tempdata.transpose(0,2,1,3)
tempdata=tempdata.reshape( (nlats/lat_binsize), (nlons/lon_binsize), (lat_binsize*lon_binsize) )
mode=stats.mode(tempdata.data,axis=2)[0]
del outdata
del tempdata
outdata=np.ma.masked_equal(mode,0).reshape( (nlats/lat_binsize), (nlons/lon_binsize) )
del mode
outlat=np.array(np.median(outlat.reshape(nlats/lat_binsize,lat_binsize),axis=1))
outlon=np.array(np.median(outlon.reshape(nlons/lon_binsize,lon_binsize),axis=1))
# plt.imshow(outdata.data)
# plt.colorbar()
# plt.grid(True)
# plt.savefig('/users/eow/edwcom/test_plots/HWSD_rebinned.png')
###################################################################
# Output file
print "Opening output file: %s"%outfile
outf=nc.Dataset(outfile,'w')
outf.createDimension('lon',len(outlon))
outf.createVariable('lon','double',('lon',))
outf.variables['lon'][:]=outlon[:]
outf.variables['lon'].setncattr('long_name','longitude')
outf.variables['lon'].setncattr('units','degrees east')
outf.createDimension('lat',len(outlat))
outf.createVariable('lat','double',('lat',))
outf.variables['lat'][:]=outlat[:]
outf.variables['lat'].setncattr('long_name','latitude')
outf.variables['lat'].setncattr('units','degrees north')
outf.createDimension('time',1)
outf.createVariable('time','int32',('time',))
outf.variables['time'][:]=0
outf.variables['time'].setncattr('long_name','Seconds since 1900-01-01')
outf.variables['time'].setncattr('units','seconds')
outvar=outf.createVariable('mu','double',('time','lat','lon'),fill_value=out_mv)
outvar[0,:]=outdata[:]
outvar.long_name='mapping unit'
outvar.units='none'
user=getpass.getuser()
now=dt.datetime.now().strftime('%d-%m-%Y')
outf.title='Mapping unit extracted from %s on %s by %s'%(infile,now,user)
outf.close()