Batch scripts updated and gridding script completed.

fdbesanto2 · Mar 23, 2019 · 46ccee5 · 46ccee5
1 parent 7b38a11
commit 46ccee5
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diff --git a/.batchBiomass.bash.swp b/.batchBiomass.bash.swp
diff --git a/batchBiomass.bash b/batchBiomass.bash
@@ -0,0 +1,69 @@
+#!/bin/bash -f
+
+
+#################
+# Batch process #
+# GEDI data     #
+#################
+
+
+# defaults
+output="allBiomass.txt"
+bin="/geos/netdata/avtrain/data/3d/active_sensing/week10/active_sensing"
+
+# Read the command line
+while [[ $# -gt 0 ]]
+do
+key="$1"
+  case $key in
+    -inDir)
+      inDir="$2"
+      shift;shift 
+      ;;
+    -output)
+      output="$2"
+      shift;shift
+      ;;
+    -help)
+      echo " "
+      echo "Batch processing of GEDI biomass"
+      echo " "
+      echo "-inDir name;       directory name to process all HDF5 files within"
+      echo "-output name;      output filename"
+      echo " "
+      exit
+      ;;
+    *)
+      echo $"Unrecognised option: $key"
+      exit 1
+  esac
+done  # command line reader
+
+
+# if a directory specified, read directory
+list="/tmp/gedoToProcess.$$.txt"
+pushd $inDir/
+ls -l|grep ".metric.txt"|gawk '{printf("%s/%s\n",dir,$NF)}' dir="$inDir" > $list
+popd
+
+# clear old output
+if [ -e $output ];then
+  rm $output
+fi
+
+# loop over input files
+temp="/tmp/workSpace.biomass.$$.txt"
+while read inName; do
+
+  python3 $bin/predictBiomass.py --input $inName --outpout $temp
+  cat $temp >> $output
+
+  if [ -e $temp ];then
+    rm $temp
+  fi
+done  < $list
+
+if [ -e $list ];then
+  rm $list
+fi
+
diff --git a/batchProcess.bash b/batchProcess.bash
@@ -76,7 +76,7 @@ key="$1"
       echo "-inDir name;                  directory name to process all HDF5 files within"
       echo "-input name;                  input filename for single file"
       echo "-outRoot name;                output filename root"
-      echo "-bound minX minY maxX maxY;   define bounds"
+      echo "-bounds minX minY maxX maxY;  define bounds"
       echo " "
       echo "### Denoising options ###" 
       echo "-varScale nStdev;             number of standard deviations to use for noise threshold"

diff --git a/gridBiomass.py b/gridBiomass.py
@@ -0,0 +1,94 @@
+
+'''
+Grids biomass estimates
+'''
+
+#############################################
+import numpy as np
+import argparse
+import scipy.stats as stats
+
+
+#############################################
+
+class gediBiomass(object):
+  '''Class to hold GEDI biomass estimates'''
+
+  #################################
+
+  def __init__(self,filename):
+    '''Read footprint level file'''
+    self.lon,self.lat,self.agbd=np.loadtxt=np.loadtxt(filename,usecols=(0,1,2),unpack=True, dtype=float,comments='#')
+
+
+  #################################
+
+  def gridAGBDmean(self,res,outName):
+    '''Grid AGBD estimates by simple mean'''
+    # determine number of cells
+    minX=np.min(self.lon)
+    maxX=np.max(self.lon)
+    minY=np.min(self.lat)
+    maxY=np.max(self.lat)
+    nX=int((maxX-minX)/res+1)
+    nY=int((maxY-minY)/res+1)
+    # grid up
+    meanAGBD,x0,y0,binnumber=stats.binned_statistic_2d(self.lon,self.lat,values=self.agbd,statistic='mean',bins=[np.arange(nX), np.arange(nY)])
+    # write header
+    f=open(outName,'w')
+    noData=-9999
+    header="NCOLS"+str(nX)+"\n"
+    header=header+"NROWS"+str(nY)+"\n"
+    header=header+"XLLCENTER"+str(minX)+"\n"
+    header=header+"YLLCENTER"+str(minY)+"\n"
+    header=header+"CELLSIZE"+str(res)+"\n"
+    header=header+"NODATA_VALUE"+str(noData)+"\n"
+    f.write(header)
+    # remove nan
+    meanAGBD[np.isnan(meanAGBD)]=noData
+    # write data
+    for j in range(nY-1,-1,-1):
+      line=""
+      for x in meanAGBD[j]:
+        line=line+str(x)+" "
+      line=line+"\n"
+      f.write(line)
+    f.close()
+    print("Written to",outName)
+
+
+# end of gediBiomass
+#############################################
+
+
+###########################################
+# read the command line
+
+def gediCommands():
+  '''
+  Read commandline arguments
+  '''
+  p = argparse.ArgumentParser(description=("Writes out properties of GEDI waveform files"))
+  p.add_argument("--input",dest="inName",type=str,help=("Input GEDI metric filename"))
+  p.add_argument("--output",dest="output",type=str,default='test.asc',help=("Output graph filename"))
+  p.add_argument("--res",dest="res",type=float,default=100,help=("Output resolution"))
+  cmdargs = p.parse_args()
+  return cmdargs
+
+
+###########################################
+# the main block
+
+if __name__ == '__main__':
+  # read the command line
+  cmdargs=gediCommands()
+  inName=cmdargs.inName
+  output=cmdargs.output
+  res=cmdargs.res
+
+  # read data
+  agbd=gediBiomass(inName)
+
+  # grid data and write output
+  agbd.gridAGBDmean(res,output)
+