gnssIR_api.v0

#!/bin/bash
#
echo this was the first version of the gnssIR_api script.  It will not work anymore.
echo exiting 
exit

if [ "$#" -eq 0 ]; then
  echo "----------------GREETINGS FROM KRISTINE'S REFLECTIONS API---------------------"
  echo This script runs the archive section of the https://gnss-reflections.org API.  
  echo There are three required inputs: station, year, and day of year
  echo If you have your path defined for where you install the script, type something
  echo like this, where p038 is the station name:
  echo
  echo      ./gnssIR_api p038 2019 152
  echo 
  echo but if you want to run it in the same folder you are working in:
  echo
  echo      ./gnssIR_api p038 2019 152
  echo
  echo The rest of the inputs are optional, as in:
  echo
  echo -rinex is for RINEX file uploads
  echo
  echo -e1 and -e2 for elevation angles in degrees \(defaults are 5 and 25\)
  echo 
  echo -azim1 and -azim2 are azimuth angles in degrees \(defaults are 0 and 360\)
  echo
  echo -freq can be L1, L2, L2C, L5, L1L2CL5, or L1L2. Default is L1
  echo 
  echo -amp is the minimum required amplitude
  echo
  echo -pk2noise is a qualitry control metric calculated by the peak in the periodogram divided by the average periodogram value over the RH range
  echo
  echo -h1 and -h2 are reflector height constraints in meters. Defaults are 0.5 and 7 meters 
  echo 
  echo If you would like to run multiple days, use the optional -doy_end flag \(LOOKS LIKE THIS HAS NOT BEEN IMPLEMENTED \)
  echo 
  echo Quality Control Parameters:
  echo
  echo -amp sets the periodogram peak required. The default is 8 - but it is not the right value for all receivers.
  echo -pk2noise is peak size related to background noise ratio. Four is the default and good for most snow work
  echo 
  echo The RINEX file must live in the low-rate section of the UNAVCO, SOPAC, CDDIS, 
  echo or SONEL archives. 
  echo
  echo My API creates a task queue on the site that hosts my API \(heroku\). This usually takes from 5 to 10 seconds to
  echo complete. This bash script queries the API every two seconds to see if it has completed.
  echo It saves the results \(and tells you where those are being saved\). If you would prefer a different
  echo location for your results, change the outputdir variable. The daily set of reflector height 
  echo outputs includes everything that meets certain quality control metrics.  
  echo 
  echo If you input azimuth constraints, the API will output a daily average within those 
  echo azimuths with additional QC. This is meant to make it easy for the snow/ice communities. 
  echo This option is NOT appropriate for tides, though it would be appropriate for lake monitoring.
  echo 
  echo This script does not check for all possible errors by users. Further, it is not the right place 
  echo to look for documentation on the API or for questions about what a reflector height is. For that 
  echo you need to look at the FAQ/overview section at https://gnss-reflections.org
  echo I am working on adding access to the RINEX uploader in this script, but it is not ready 
  echo for distribution as yet.
  echo 
  echo Update: May 7, 2020
  echo I have added limited RINEX upload cability.  Use -rinex and the filename.  Everything else must
  echo obey the original rules AND you can only use the frequencies allowed on the RINEX upload web app, i.e. L1, L2, or L5 
  echo If I get a chance I will add a L1L2 option.  I also still need to provide azimuth constraints.
  echo
  echo Update: August 26, 2022
  echo I have added L1L2, L1L2CL5 to frequency options
  echo the API at \https://gnss-reflections.org itself now allows up to 25 observable types in the RINEX 2.11 files.
  echo It is GPS only and only allows RH values up to 25 meters.
  echo You are further cautioned that using GPS files with 30 second sampling intervals 
  echo can be dangerous for RH \> 10 meters.
  echo 
  echo It looks like the doy_end option has not been implemented. 
  echo
  echo
  echo Happy Reflections,
  echo Kristine M. Larson
  echo https://kristinelarson.net
  echo 2022 August 26
  echo
  echo Examples:
  echo 
  echo Niwot Ridge, Colorado - L2C is in the RINEX files.  Great snow site. 
  echo   ./gnssIR_api nwot 2019 300 -freq L1L2 -h1 0.5 -h2 8 -azim1 45 -azim2 240 -e1 5 -e2 20
  echo 
  echo Phoenix, Ross Ice Shelf, Antarctica - L2C is in the RINEX files
  echo   ./gnssIR_api phnx 2019 300 -freq L1L2 -h1 0.5 -h2 8 
  echo 
  echo Lake Superior, Canada - L1 only as this site does not support modern GPS signal tracking  
  echo                 restrictions are to emphasize water reflections
  echo   ./gnssIR_api mchn 2019 205 -azim1 50 -azim2 210 -h1 2.5 -h2 8 -pk2noise 3.5
  echo 
  echo Island Park, Idaho - would be better if you had access to L2C. Ask UNAVCO about it.
  echo   ./gnssIR_api p360 2019 100  -pk2noise 3.5
  echo 
  echo 
 exit
fi
#
# define a new output directory if you like. This one assumes you will put the results in
# the directory below where you are running this code.
outputdir='./solutions'
#
# defaults for elevation angles (degrees), Reflector Heights (meters) and frequency
# h1 should never be less than 0.5
e1=5
e2=25
h1=0.5
h2=7
freq=L1
# these are defaults
pk2noise=4.0
amp=5
rinex=None
# declare these variables so they are integers
declare -i azim1=0
declare -i azim2=360
declare -i doy_end=0
declare -i doy=0
# This variable just sends output to the screen. Even if you don't set it there will be a daily
# average file created 
snow=False
#
# I am new to bash scripts - so .... 
# As long as there is at least one more argument, keep looping
declare -i k=0
while [[ $# -gt 0 ]]; do
    key="$1"
    k+=1
    #echo key is $k $key
    if [ "$k" -eq 1 ]; then
      station=$key
      shift
    elif [ "$k" -eq 2 ]; then
      year=$key
      shift
    elif [ "$k" -eq 3 ]; then
      doy=$key
      shift
    else
       case "$key" in
        # This is a flag type option. Will catch either -f or --foo
        -f|--foo)
        FOO=1
        ;;
        # This is an arg value type option. Will catch -o value or --output-file value
        -o|--output-file)
        shift # past the key and to the value
        OUTPUTFILE="$1"
        ;;
        -e1|--min-elev-file)
        shift # past the key and to the value
        e1="$1"
        ;;
        -e2|--max-elev-file)
        shift # past the key and to the value
        e2="$1"
        ;;
        -h1|--min-refl-ht)
        shift # past the key and to the value
        h1="$1"
        ;;
        -h2|--max-refl-ht)
        shift # past the key and to the value
        h2="$1"
        ;;
        -freq|--frequency)
        shift # past the key and to the value
        freq="$1"
        ;;
        -amp|--amplitude)
        shift # past the key and to the value
        amp="$1"
        ;;
        -azim1|--min-azimuth)
        shift # past the key and to the value
        azim1="$1"
        ;;
        -azim2|--max-azimuth)
        shift # past the key and to the value
        azim2="$1"
        ;;
        -doy_end|--doy_end)
        shift # past the key and to the value
        doy_end="$1"
        ;;
        -rinex |--rinex)
        shift # past the key and to the value
        rinex="$1"
        ;;
        -pk2noise |--pk2noise)
        shift # past the key and to the value
        pk2noise="$1"
        ;;
        -snow|--snow)
        shift # past the key and to the value
        snow="$1"
        ;;

        *)
        # Do whatever you want with extra options
        echo "Unknown option '$key'"
        ;;
    esac
    # Shift after checking all the cases to get the next option
    shift
  fi
done

echo rinex is $rinex

ok=0
if [ "$freq" == "L1" ] || [ "$freq" == "L2" ] ; then
  ok=1
  echo You have chosen a legal frequency, $freq
elif [ "$freq" == "L5" ] ; then
  ok=1
  echo You have chosen a legal frequency, $freq
elif  [ "$freq" == "L1L2" ] || [ "$freq" == "L2C" ] || [ "$freq" == "L1L2CL5" ]; then
  ok=1
  echo You have chosen a legal frequency, $freq
fi

if [ $ok -eq 0 ]; then 
    echo $freq illegal frequency input, exiting
    exit
fi
# check doy
if [ $doy -gt 0 ] && [ $doy -lt 367 ]; then
   echo This is a legal day of year
else
   echo This is an illegal day of year.
   exit
fi
# check year
if [ $year -ge 2000 ] && [ $year -lt 2025 ]; then
    echo This is a legal year although the year you chose might be in the future
else 
    echo This is an illegal year.
    exit
fi

# check h2 
if [ $h2 -gt 25 ] ; then
    echo The max reflector height you have chosen is too big for the API.
    echo It must be less than 25 meters. For a typical unobstructed site the 
    echo reflector height minimum should be 0.5 meters.  For other sites you 
    echo might restrict the choices to eliminate soil, e.g. you want to only
    echo see water reflections.
    exit
fi
# make sure the output directories are there
if [ ! -e "${outputdir}" ]; then
    echo "making output directory "
    mkdir "${outputdir}"
fi

# make sure the output directories are there
if [ ! -e "${outputdir}/${station}" ]; then
    echo "making station output directory "
    mkdir "${outputdir}/$station"
fi

if [ ! -e "${outputdir}/${station}/${year}" ]; then
    echo "making station year output directory "
    mkdir "${outputdir}/${station}/${year}"
fi


# if not set, have doy_end be the same of doy, 
if [ $doy_end -eq 0 ]; then
   doy_end=$doy
fi

# output for daily averages
comboFile=${outputdir}/${station}_RH_all.csv
echo Combination File $comboFile
echo Day of Year End is $doy_end
echo Look for solutions in the $outputdir directory

# name for the script that calls the API
scriptname=xit.${year}.${station}
# name for the temporary output
dailyname=test.${year}.${station}
while [ $doy -le $doy_end ] ; do

echo CHOICES THAT WILL BE SENT TO THE GNSS-IR API
echo Station $station
echo Year $year
echo Day of Year $doy 
echo Elevation Angle choices $e1 $e2 
echo Azimuth Angle choices $azim1 $azim2
echo Reflector Height restrictions $h1 $h2 
echo Frequency choice $freq	
echo Amplitude $amp
echo Peak to Noise $pk2noise
echo End day of year $doy_end

# calculate string doy with exactly three characters
  cdoy=$( printf '%03d' $doy )

# make a script to run the webapp
  rm -f ${scriptname}
  if [ $rinex = None ];  then
     echo Archive section 
  else
     echo Uploading RINEX
     rm -f out.txt xit 
     curl -F "file=@${rinex}" -F "azim1=${azim1}" -F "azim2=${azim2}" -F "freq=${freq}" -F "h1=${h1}" -F "h2=${h2}" -F "e1=${e1}" -F "e2=${e2}" -F "pk2noise=${pk2noise}" -F "amp=${amp}" "http://trywithgps2.herokuapp.com/api" > out.txt
     var=`grep Numerical out.txt | wc -l`
     echo $var
     if [ $var -lt 1 ]; then
        echo Nothing came back from the app. This usually means you have uploaded an illegal RINEX file
        echo or used an illegal RINEX filename. Right now I do not return detailed information if you are
        echo accessing the API via this bash script.  Rules on RINEX files and their naming conventions
	echo The allowed frequencies are slightly different from the archive section, so check that as well.
	echo Exiting
	exit
     fi
     echo \# > xit
     cat out.txt | grep Numerical | awk '{print "curl https://gnss-reflections.org/"substr($2,7,26) }' >> xit
     cat xit
     chmod +x xit
     ./xit > ${dailyname}
     # print to screen
     cat ${dailyname}
     echo Now moving daily results to ${station}_${year}_${cdoy}.txt in the output directory
     mv -f ${dailyname}  ${outputdir}/${station}/${year}/${station}_${year}_${cdoy}.txt
     rm -f ${comboFile}
     echo \# https://gnss-reflections.org > ${comboFile}
     echo \# Year,DayOfYear,ReflectorHeight\(m\),Month,Day,RHsigma  >> ${comboFile}
     cat ${outputdir}/${station}/????/*.txt | grep DailyAverage | awk '{print $3"," $4"," $5"," $6"," $7",0"}' >> ${comboFile}
     exit
  fi
  echo \# > ${scriptname}
  curl "http://gnss-reflections.org/api?station=${station}&year=${year}&doy=${doy}&freq=${freq}&amp=${amp}&h1=${h1}&h2=${h2}&e1=${e1}&e2=${e2}&pk2noise=${pk2noise}&azim1=${azim1}&azim2=${azim2}" \
	| grep results2 | awk '{print "curl http://gnss-reflections.org/"substr($6,2,45)}' >> ${scriptname}

# make the script executable
  chmod +x ${scriptname}

  finished=false
# check heroku for the results for 36 seconds and then give up
  x=36
  while [ "$finished" = false ]
  do
    echo checking job status every two seconds. 
    sleep 2
    x=$(( $x - 2 ))
    if [ $x -eq 0 ]; then
      finished=true
      echo time has run out, exiting
    fi
    rm -f ${dailyname}
    ./${scriptname} > ${dailyname}
    var=`grep "still running" ${dailyname} | wc -l`
    if [ $var -eq 0 ]; then
      finished=true
      echo the job has finished
      var2=`grep "No Results" ${dailyname}  | wc -l`
      if [ $var2 -eq 1 ]; then
	   echo ""
         echo Not saving the result file
         echo This could mean the RINEX file for station ${station} does not exist at any of the archives. 
      else
	 #  print results to the screen for the given day
         cat ${dailyname}
         echo moving daily results to ${station}_${year}_${cdoy}.txt in the output directory
         mv -f ${dailyname}  ${outputdir}/${station}/${year}/${station}_${year}_${cdoy}.txt
         rm -f ${comboFile}
	 echo \# https://gnss-reflections.org > ${comboFile}
	 echo \# Year,DayOfYear,ReflectorHeight\(m\),Month,Day,RHsigma  >> ${comboFile}
         cat ${outputdir}/${station}/????/*.txt | grep DailyAverage | awk '{print $3"," $4"," $5"," $6"," $7",0"}' >> ${comboFile}
      fi
    fi
  done
  doy+=1
# end of doy while loop
done
echo Daily averages are stored here: ${comboFile}
echo Output directory ${outputdir}
# clean up
rm -f ${scriptname}