process_for_INITMIP

#!/usr/bin/env python

from __future__ import print_function
from argparse import ArgumentParser

import flo_utils as fu
import json
import netCDF4 as nc
import numpy as np
import os
import re
# import subprocess as sp
import sys
import threading

cdo='cdo'
def process_files(options):

  threads = []
  variables = options["variables"]
  files = options["FILES"]
  for ff in files:
    if not fu.check_files(["%s3"%ff], False):
      command = "/sw/rhel6-x64/nco/nco-4.5.0-gcc48/bin/ncpdq -3 -a time,y,x %s %s3"%(ff, ff)
#      print (command)
      t = threading.Thread(target=fu.qo, args=(command,))
      threads.append(t)
      t.start()
  [ x.join() for x in threads]
  threads = []
  filetimes = np.array([ nc.Dataset(x,"r").variables["time"][0] for x in files ])
  files = ["%s3"%ff for ff in files]
  durations = filetimes[1:]-filetimes[:-1]
  for n, v in variables.iteritems():
    outname = "%s_%s_%s_%s_%s.nc"%(n, "GIS", "MPIM", options["model"], options["name"])
#    fu.rm_if_exist([outname])
    for i,f in enumerate(files[1:]):
      extras=""
      if v.get("unit", False):
        extras+= " -setunit,'%s' "%v.get("unit", "NO UNIT! PANIC!")
      if v.get("divtime", False):
        extras+= " -divc,%s "%durations[i]
      if v.get("expression", False):
        extras+= " -expr,'%s=%s' "%(n, v.get("expression", "NO EXPRESSION! PANIC!"))
      if v.get("rundiff", False):
        extras = "-sub %s %s %s %s"%(extras, f, extras, files[i])
      else:
        extras += " %s "%f
      command = "%s -s -cat %s %s"%(cdo, extras, outname)
      print (command)
    #   t = threading.Thread(target=fu.qo, args=(command,))
    #   threads.append(t)
    #   t.start()
    # [ x.join() for x in threads]
    # threads = []
#      fu.qo(command)
    if v.get("standard_name", False):
      command = "ncatted -a 'standard_name,%s,o,c,%s' %s"%(n, v.get("standard_name"), outname)
      print (command)
#      fu.qo(command)



def parse_args():
  parser = ArgumentParser()
  parser.description = "Convert PISM output for INITMIP"
  parser.add_argument ("FILES", nargs="*", help='Files to process')
  parser.add_argument("-c", "--config",
                      help='''Config file (required)''', required = True)
  parser.add_argument("-v", "--verbose",
                    help='''Be verbose''', action="store_true")
  parser.add_argument("-n", "--name",
                    help="experiment name", required = True)
  parser.add_argument("-m", "--model",
                    help="model name", required = True)

  options = parser.parse_args()
  options_dict = vars(options)
  config = json.load(open(options.config))
  for x in options_dict.keys():
      if not options_dict[x] is  None :
          config[x] = options_dict[x]

  if options.verbose:
      fu.cerr(dir(options))
      fu.cerr(dir(config))
      fu.set_debug(True)

  return config

def main():
  options = parse_args()
  process_files(options)

if __name__ == "__main__":
    main()