NASA Ocean Color

ocssw V2022
 #! /usr/bin/env python3
  
 ''' This is the aviris preprocessing script.
     Run this on the *img.hdr if it fails to run under l2gen
     or the aviris file converters.
  
     aviris_preproc <img file> <output file>
  
 R.Healy 11/1/2016 (richard.healy@nasa.gov)
  
 '''
 __version__ = '1.0.0'
  
 __author__ = 'rhealy'
  
 import argparse
 import sys, re
 import glob, os
 import numpy as np
  
 def main():
     '''Specifies command line arguments and parses command line accordingly.'''
     parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter, description='''      Read an Aviris hdr file and generate a parameter file as input to the converter if needed.
  
             ''', add_help=True)
     parser.add_argument('-ifile', nargs=1, type=str, help=' Input Aviris hdr file ')
     parser.add_argument('-ofile', nargs=1, type=str, default=('aviris_preproc.hdr'),help=' output file ')
  
     #args = parser.parse_args('-ifile /accounts/rhealy/Downloads/aviris/oci/f100828t01p00r11rdn_b/f100828t01p00r11rdn_b_sc01_ort_img.hdr -ofile blah.hdr'.split())
     #args = parser.parse_args('-ifile /glusteruser/rhealy/aviris/f940921t01p02_r06c/f940921t01p02_r06c_img.hdr -ofile blah.hdr'.split())
     #args = parser.parse_args('-ifile /glusteruser/rhealy/aviris/f000411t01p03_r04c/f000411t01p03_r04c_img.hdr'.split())
  
     args=parser.parse_args()
  
     if not args.ifile:
         parser.error("you must specify an input file")
  
     ifile = ''.join(args.ifile)
     ofile = ''.join(args.ofile)
     print("HDRFILE =",checkHdrFile(ifile,ofile))
  
  
 def checkHdrFile(ifile,ofile):
     avfields=['lines','samples','bands','interleave','rotation angle',
               'pixel size','Northing','Easting','UTM zone','wavelength','fwhm']
     musthave=['lines','samples','bands','fwhm','wavelength']
  
     avdict = {}
     avdir=os.path.dirname(ifile)
     avfile=os.path.basename(ifile)
     if avdir:
        try:
          os.chdir(avdir)
        except:
          print("Unable to change to ",avdir)
          sys.exit()
  
     for theLine in open(avfile,'r') :
         if '=' in theLine:
             fields = theLine.split('=')
             fields[0] = fields[0].strip()
             for f in avfields:
                 pattern = re.compile(f)
                 if re.search(pattern,fields[0]):
                     avdict[f] = fields[1]
                     #print(f, '=',avdict[f])
     if len(avdict) == len(avfields):
         return ifile
  
     for f in musthave:
         if f not in avdict.keys():
             print('Missing data...',f,avdict.keys())
             sys.exit()
     infofields=['pilot_st_lat','pilot_end_lat','pilot_st_long','pilot_end_long',
                 'pilot_st_time','pilot_end_time']
     infodict = {}
     infofile=''.join(glob.glob("*info"))
     if not infofile:
         print("Missing a info file")
         sys.exit()
     for theLine in open(infofile,'r'):
         if '=' in theLine:
             fields = theLine.split('=')
             fields[0] = fields[0].strip()
             for f in infofields:
                 pattern = re.compile(f)
                 if re.search(pattern,fields[0]):
                     infodict[f] = fields[1]
  
     #for info,val in infodict.items():
         #print(info," = ",val)
     if len(infodict) < len(infofields):
         print("Incomplete information in info file:",infofile)
         print("Need these fields: ",infofields)
         print("But only have: ",infodict.keys())
         sys.exit()
     if len(infodict['pilot_st_time'].split()) > 1:
         time_st = parseMinSec(infodict['pilot_st_time'])
     else:
         time_st = np.float(infodict['pilot_st_time'])
     #print("time start=",time_st)
     if len(infodict['pilot_end_time'].split()) > 1:
         time_end = parseMinSec(infodict['pilot_end_time'])
     else:
          time_end = np.float(infodict['pilot_end_time'])
  
     #print("time end=",time_end)
     if len(infodict['pilot_st_lat'].split()) > 1:
         lat_st = parseMinSec(infodict['pilot_st_lat'])
     else:
          lat_st = np.float(infodict['pilot_st_lat'])
     #print("lat_st=",lat_st)
     if len(infodict['pilot_end_lat'].split()) > 1:
         lat_end = parseMinSec(infodict['pilot_end_lat'])
     else:
         lat_end = np.float(infodict['pilot_end_lat'])
  
     #print("lat_end=",lat_end)
     if len(infodict['pilot_st_long'].split()) > 1:
         lon_st = parseMinSec(infodict['pilot_st_long'])
     else:
         lon_st = np.float(infodict['pilot_st_long'])
  
     #print("lon_st=",lon_st)
     if len(infodict['pilot_st_long'].split()) > 1:
         lon_end = parseMinSec(infodict['pilot_end_long'])
     else:
         lon_end = np.float(infodict['pilot_end_long'])
     #print("lon_end=",lon_end)
  
     sign_lat = np.sign(lat_st)
     sign_lon = np.sign(lon_st)
  
     navfile=''.join(glob.glob("*nav"))
     #print("navfile <<",navfile,">>")
     if not navfile:
         print("Missing a navigation file")
         sys.exit()
  
     navout = ofile.split(".")[0]+"_nav.txt"
     fnavout = open(navout,"w")
  
     fnav = open(navfile,'r')
     line = fnav.readline()
     fnav.close()
     if len(line.split()) == 3:
         alt,lat,lon = line.split()
         # correct the sign in the nav file
         if np.sign(np.float(lat)) == sign_lat:
             sign_lat = 1.0
         if np.sign(np.float(lon)) == sign_lon:
             sign_lon = 1.0
  
         time_ar = np.arange(time_st,time_end,(time_end-time_st)/np.float(avdict['lines']))
         for theLine, avtime in zip(open(navfile,'r'), time_ar):
             alt,lat,lon = theLine.split()
             fnavout.write("{:.8f} {:.4f} {:.4f} {:.4f}\n".format(avtime,np.float(alt),sign_lat*np.float(lat),sign_lon*np.float(lon)))
     else:
         for theLine in open(navfile,'r'):
             nav_data = theLine.split()
             stime_ar = nav_data[3].split(':')
             avtime = np.float(stime_ar[1])+np.float(stime_ar[2])/60.+np.float(stime_ar[3])/3600.
             alt = nav_data[20]
             lat = nav_data[4]
             lon = nav_data[5]
             fnavout.write("{:.8f} {:.4f} {:.4f} {:.4f}\n".format(avtime,np.float(alt)/1000.,np.float(lat),np.float(lon)))
  
     fnavout.close()
     fhdr = open(ofile,"w")
     fhdr.write('AVIRIS_PREPROC_HDR\n')
     fhdr.write("hdrfile = {}\n".format(avfile))
     fhdr.write("navfile = {}\n".format(navout))
     gainfile=''.join(glob.glob("*gain"))
     if gainfile:
         fhdr.write("gainfile = {}\n".format(gainfile))
     imgfile=''.join(glob.glob("*img"))
     if imgfile:
         fhdr.write("imgfile = {}\n".format(imgfile))
     else:
         print("WARNING!! No img file\n")
         print("It is extremely likely the aviris reader will not work unless you add imgfile=the_name_of_the_img_file \n")
         print("into the file ",ofile)
  
     fhdr.close()
     return ofile
  
 def parseMinSec(timeFld):
     time_stamp =timeFld.split()
     if len(time_stamp) < 3:
         time_stamp = timeFld.split()
         if len(time_stamp) < 3:
             print("Can't parse Time Field: ",timeFld)
             sys.exit()
     shr = ''.join(time_stamp[0].split(':'))
     smin = ''.join(time_stamp[1].split(':'))
     ssec = ''.join(time_stamp[2].split(':'))
     #print("hr={},min={},sec={}".format(shr,smin,ssec))
     hr = np.float(shr)
     return hr+np.sign(hr)*(np.float(smin)+np.float(ssec)/60)/60
  
 def ParseCommandLine(args):
     '''Specifies command line arguments and parses command line accordingly.'''
     parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter, description='''      Read an Aviris hdr file and generate a parameter file as input to the converter if needed.
  
             ''', add_help=True)
     parser.add_argument('-ifile', nargs=1, type=str, help=' Aviris hdr file ')
     args = parser.parse_args('-ifile=/accounts/rhealy/Downloads/aviris/oci/f100828t01p00r11rdn_b/f100828t01p00r11rdn_b_sc01_ort_img.hdr'.split())
  
     parsedArgs = parser.parse_args(args)
     return parsedArgs
  
  
 if __name__ == '__main__': main()
avirispreproc.main
def main()
Definition: avirispreproc.py:21
avirispreproc.parseMinSec
def parseMinSec(timeFld)
Definition: avirispreproc.py:187
avirispreproc.ParseCommandLine
def ParseCommandLine(args)
Definition: avirispreproc.py:201
void print(std::ostream &stream, const char *format)
Definition: PrintDebug.hpp:38
avirispreproc.checkHdrFile
def checkHdrFile(ifile, ofile)
Definition: avirispreproc.py:43