'''
Convert a bunch of GDAL readable grids to a NetCDF Time Series.
Here we read a bunch of files that have names like:
/usgs/data0/prism/1890-1899/us_tmin_1895.01
/usgs/data0/prism/1890-1899/us_tmin_1895.02
...
/usgs/data0/prism/1890-1899/us_tmin_1895.12
'''
import numpy as np
import datetime as dt
import os
import gdal
import netCDF4
import re
ds = gdal.Open('/usgs/data0/prism/1890-1899/us_tmin_1895.01')
a = ds.ReadAsArray()
nlat,nlon = np.shape(a)
b = ds.GetGeoTransform() #bbox, interval
lon = np.arange(nlon)*b[1]+b[0]
lat = np.arange(nlat)*b[5]+b[3]
basedate = dt.datetime(1858,11,17,0,0,0)
cd /usgs/data2/notebook
/usgs/data2/notebook
# create NetCDF file
nco = netCDF4.Dataset('time_series.nc','w',clobber=True)
# chunking is optional, but can improve access a lot:
# (see: http://www.unidata.ucar.edu/blogs/developer/entry/chunking_data_choosing_shapes)
chunk_lon=16
chunk_lat=16
chunk_time=12
# create dimensions, variables and attributes:
nco.createDimension('lon',nlon)
nco.createDimension('lat',nlat)
nco.createDimension('time',None)
timeo = nco.createVariable('time','f4',('time'))
timeo.units = 'days since 1858-11-17 00:00:00'
timeo.standard_name = 'time'
lono = nco.createVariable('lon','f4',('lon'))
lono.units = 'degrees_east'
lono.standard_name = 'longitude'
lato = nco.createVariable('lat','f4',('lat'))
lato.units = 'degrees_north'
lato.standard_name = 'latitude'
# create container variable for CRS: lon/lat WGS84 datum
crso = nco.createVariable('crs','i4')
csro.long_name = 'Lon/Lat Coords in WGS84'
crso.grid_mapping_name='latitude_longitude'
crso.longitude_of_prime_meridian = 0.0
crso.semi_major_axis = 6378137.0
crso.inverse_flattening = 298.257223563
# create short integer variable for temperature data, with chunking
tmno = nco.createVariable('tmn', 'i2', ('time', 'lat', 'lon'),
zlib=True,chunksizes=[chunk_time,chunk_lat,chunk_lon],fill_value=-9999)
tmno.units = 'degC'
tmno.scale_factor = 0.01
tmno.add_offset = 0.00
tmno.long_name = 'minimum monthly temperature'
tmno.standard_name = 'air_temperature'
tmno.grid_mapping = 'crs'
tmno.set_auto_maskandscale(False)
nco.Conventions='CF-1.6'
#write lon,lat
lono[:]=lon
lato[:]=lat
pat = re.compile('us_tmin_[0-9]{4}\.[0-9]{2}')
itime=0
#step through data, writing time and data to NetCDF
for root, dirs, files in os.walk('/usgs/data0/prism/1890-1899/'):
dirs.sort()
files.sort()
for f in files:
if re.match(pat,f):
# read the time values by parsing the filename
year=int(f[8:12])
mon=int(f[13:15])
date=dt.datetime(year,mon,1,0,0,0)
print(date)
dtime=(date-basedate).total_seconds()/86400.
timeo[itime]=dtime
# min temp
tmn_path = os.path.join(root,f)
print(tmn_path)
tmn=gdal.Open(tmn_path)
a=tmn.ReadAsArray() #data
tmno[itime,:,:]=a
itime=itime+1
nco.close()
1895-01-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1895.01 1895-02-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1895.02 1895-03-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1895.03 1895-04-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1895.04 1895-05-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1895.05 1895-06-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1895.06 1895-07-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1895.07 1895-08-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1895.08 1895-09-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1895.09 1895-10-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1895.10 1895-11-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1895.11 1895-12-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1895.12 1896-01-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1896.01 1896-02-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1896.02 1896-03-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1896.03 1896-04-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1896.04 1896-05-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1896.05 1896-06-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1896.06 1896-07-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1896.07 1896-08-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1896.08 1896-09-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1896.09 1896-10-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1896.10 1896-11-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1896.11 1896-12-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1896.12 1897-01-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1897.01 1897-02-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1897.02 1897-03-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1897.03 1897-04-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1897.04 1897-05-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1897.05 1897-06-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1897.06 1897-07-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1897.07 1897-08-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1897.08 1897-09-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1897.09 1897-10-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1897.10 1897-11-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1897.11 1897-12-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1897.12 1898-01-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1898.01 1898-02-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1898.02 1898-03-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1898.03 1898-04-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1898.04 1898-05-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1898.05 1898-06-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1898.06 1898-07-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1898.07 1898-08-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1898.08 1898-09-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1898.09 1898-10-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1898.10 1898-11-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1898.11 1898-12-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1898.12 1899-01-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1899.01 1899-02-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1899.02 1899-03-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1899.03 1899-04-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1899.04 1899-05-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1899.05 1899-06-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1899.06 1899-07-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1899.07 1899-08-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1899.08 1899-09-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1899.09 1899-10-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1899.10 1899-11-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1899.11 1899-12-01 00:00:00 /usgs/data0/prism/1890-1899/us_tmin_1899.12