Automated swath handling initial version. Translation of InSAR proces…

…sing routines from csh to bash.

lib/GMTSAR-mods/align_cut_tops.csh

@@ -161,6 +161,7 @@ awk '{ printf("%.6f %.6f %.6f \n",$1,$3,$4) }' < offset.dat > a.xyz
 #
 #  fit a surface to the range and azimuth offsets
 #
+
 gmt blockmedian r.xyz -R0/$rmax/0/$amax -I16/8 -r -bo3d -V > rtmp.xyz
 gmt blockmedian a.xyz -R0/$rmax/0/$amax -I16/8 -r -bo3d -V > atmp.xyz
 gmt surface rtmp.xyz -bi3d -R0/$rmax/0/$amax -I16/8 -T0.3 -Grtmp.grd -N1000  -r -V &

lib/GMTSAR-mods/merge_unwrap_geocode.sh

@@ -0,0 +1,141 @@
+#/bin/csh -f
+#       $Id$
+#
+#
+#    Xiaohua(Eric) XU, July 7, 2016
+#
+# Script for merging 3 subswaths TOPS interferograms and then unwrap and geocode. 
+#
+  if ($#argv != 2) then
+    echo ""
+    echo "Usage: merge_unwrap_geocode_tops.csh inputfile config_file"
+    echo ""
+    echo "Note: Inputfiles should be as following:"
+    echo ""
+    echo "      Swath1_Path:Swath1_master.PRM:Swath1_repeat.PRM"
+    echo "      Swath2_Path:Swath2_master.PRM:Swath2_repeat.PRM"
+    echo "      Swath3_Path:Swath3_master.PRM:Swath3_repeat.PRM"
+    echo "      (Use the repeat PRM which contains the shift information.)"
+    echo "      e.g. ../F1/intf/2015016_2015030/:S1A20151012_134357_F1.PRM"
+    echo ""
+    echo "      Make sure under each path, the processed phasefilt.grd, corr.grd and mask.grd exist."
+    echo "      Also make sure the dem.grd is linked. "
+    echo ""
+    echo "      config_file is the same one used for processing."
+    echo ""
+    echo "Example: merge_unwrap_geocode_tops.csh filelist batch.config"
+    echo ""
+    exit 1
+  endif
+
+  if (-f tmp_phaselist) rm tmp_phaselist
+  if (-f tmp_corrlist) rm tmp_corrlist
+  if (-f tmp_masklist) rm tmp_masklist
+
+  if (! -f dem.grd ) then
+    echo "Please link dem.grd to current folder"
+    exit 1
+  endif
+
+  set region_cut = `grep region_cut $2 | awk '{print $3}'`
+
+  # Creating inputfiles for merging
+  foreach line (`awk '{print $0}' $1`)
+    set now_dir = `pwd`
+    set pth = `echo $line | awk -F: '{print $1}'`
+    set prm = `echo $line | awk -F: '{print $2}'`
+    set prm2 = `echo $line | awk -F: '{print $3}'`
+    cd $pth
+    set rshift = `grep rshift $prm2 | tail -1 | awk '{print $3}'`
+    set fs1 = `grep first_sample $prm | awk '{print $3}'`
+    set fs2 = `grep first_sample $prm2 | awk '{print $3}'`
+    cp $prm tmp.PRM
+    if ($fs2 > $fs1) then
+      update_PRM.csh tmp.PRM first_sample $fs2
+    endif
+    update_PRM.csh tmp.PRM rshift $rshift
+    cd $now_dir
+
+    echo $pth"tmp.PRM:"$pth"phasefilt.grd" >> tmp_phaselist
+    echo $pth"tmp.PRM:"$pth"corr.grd" >> tmp_corrlist
+    echo $pth"tmp.PRM:"$pth"mask.grd" >> tmp_masklist
+  end 
+
+  set pth = `awk -F: 'NR==1 {print $1}' $1`
+  set stem = `awk -F: 'NR==1 {print $2}' $1 | awk -F"." '{print $1}'`
+  #echo $pth $stem
+
+  echo ""
+  echo "Merging START"
+  merge_swath tmp_phaselist phasefilt.grd $stem
+  merge_swath tmp_corrlist corr.grd
+  merge_swath tmp_masklist mask.grd
+  echo "Merging END"
+  echo ""
+
+  # This step is essential, cut the DEM so it can run faster.
+  if (! -f trans.dat) then
+    set led = `grep led_file $pth$stem".PRM" | awk '{print $3}'`
+    cp $pth$led .
+    echo "Recomputing the projection LUT..."
+    gmt grd2xyz --FORMAT_FLOAT_OUT=%lf dem.grd -s | SAT_llt2rat $stem".PRM" 1 -bod > trans.dat
+  endif
+
+  # Read in parameters
+  set threshold_snaphu = `grep threshold_snaphu $2 | awk '{print $3}'`
+  set threshold_geocode = `grep threshold_geocode $2 | awk '{print $3}'`
+  set region_cut = `grep region_cut $2 | awk '{print $3}'`
+  set switch_land = `grep switch_land $2 | awk '{print $3}'`
+  set defomax = `grep defomax $2 | awk '{print $3}'`
+
+  # Unwrapping
+  if ($region_cut == "") then
+    set region_cut = `gmt grdinfo phasefilt.grd -I- | cut -c3-20`
+  endif
+  if ($threshold_snaphu != 0 ) then
+    if ($switch_land == 1) then
+      if (! -f landmask_ra.grd) then
+        landmask.csh $region_cut
+      endif
+    endif
+
+    echo ""
+    echo "SNAPHU.CSH - START"
+    echo "threshold_snaphu: $threshold_snaphu"
+    snaphu.csh $threshold_snaphu $defomax $region_cut
+    echo "SNAPHU.CSH - END"
+  else
+    echo ""
+    echo "SKIP UNWRAP PHASE"
+  endif
+
+  # Geocoding 
+  #if (-f raln.grd) rm raln.grd
+  #if (-f ralt.grd) rm ralt.grd
+
+  if ($threshold_geocode != 0) then
+    echo ""
+    echo "GEOCODE-START"
+    proj_ra2ll.csh trans.dat phasefilt.grd phasefilt_ll.grd
+    proj_ra2ll.csh trans.dat corr.grd corr_ll.grd
+    gmt makecpt -T-3.15/3.15/0.05 -Z > phase.cpt
+    set BT = `gmt grdinfo -C corr.grd | awk '{print $7}'`
+    gmt makecpt -Cgray -T0/$BT/0.05 -Z > corr.cpt
+    grd2kml.csh phasefilt_ll phase.cpt
+    grd2kml.csh corr_ll corr.cpt
+
+    if (-f unwrap.grd) then
+      gmt grdmath unwrap.grd mask.grd MUL = unwrap_mask.grd
+      proj_ra2ll.csh trans.dat unwrap.grd unwrap_ll.grd
+      proj_ra2ll.csh trans.dat unwrap_mask.grd unwrap_mask_ll.grd
+      set BT = `gmt grdinfo -C unwrap.grd | awk '{print $7}'`
+      set BL = `gmt grdinfo -C unwrap.grd | awk '{print $6}'`
+      gmt makecpt -T$BL/$BT/0.5 -Z > unwrap.cpt
+      grd2kml.csh unwrap_mask_ll unwrap.cpt
+      grd2kml.csh unwrap_ll unwrap.cpt
+    endif
+
+    echo "GEOCODE END"
+  endif 
+
+  rm tmp_phaselist tmp_corrlist tmp_masklist *.eps *.bb

lib/GMTSAR-mods/p2p_OSARIS_no_unwrap.csh

@@ -278,16 +278,18 @@ set OSARIS_PATH = $4
       if ($shift_topo == 1) then
         ln -s ../../topo/topo_shift.grd .
         intf.csh $ref.PRM $rep.PRM -topo topo_shift.grd  
-        filter.csh $ref.PRM $rep.PRM $filter $dec 
+        # filter.csh $ref.PRM $rep.PRM $filter $dec 
       else 
         ln -s ../../topo/topo_ra.grd . 
         intf.csh $ref.PRM $rep.PRM -topo topo_ra.grd 
-        filter.csh $ref.PRM $rep.PRM $filter $dec 
+        # filter.csh $ref.PRM $rep.PRM $filter $dec 
       endif
     else
       intf.csh $ref.PRM $rep.PRM
-      filter.csh $ref.PRM $rep.PRM $filter $dec 
+      # filter.csh $ref.PRM $rep.PRM $filter $dec 
     endif
+    filter.csh $ref.PRM $rep.PRM $filter $dec 
+    cp -u *gauss* ../../../
     cd ../..
     echo "INTF.CSH, FILTER.CSH - END"
   endif

lib/GMTSAR-mods/single-swath-unwrap-geocode.csh

@@ -0,0 +1,69 @@
+
+################################
+# 5 - start from unwrap phase  #
+################################
+
+  if ($stage <= 5 ) then
+    if ($threshold_snaphu != 0 ) then
+      cd intf
+      set ref_id  = `grep SC_clock_start ../SLC/$master.PRM | awk '{printf("%d",int($3))}' `
+      set rep_id  = `grep SC_clock_start ../SLC/$slave.PRM | awk '{printf("%d",int($3))}' `
+      cd $ref_id"_"$rep_id
+      if ((! $?region_cut) || ($region_cut == "")) then
+        set region_cut = `grdinfo phase.grd -I- | cut -c3-20`
+      endif
+
+#
+# landmask
+#
+      if ($switch_land == 1) then
+        cd ../../topo
+        if (! -f landmask_ra.grd) then
+          landmask.csh $region_cut
+        endif
+        cd ../intf
+        cd $ref_id"_"$rep_id
+        ln -s ../../topo/landmask_ra.grd .
+      endif
+
+      echo " "
+      echo "SNAPHU.CSH - START"
+      echo "threshold_snaphu: $threshold_snaphu"
+
+      $OSARIS_PATH/lib/GMTSAR-mods/snaphu_OSARIS.csh $threshold_snaphu $defomax $region_cut
+
+      echo "SNAPHU.CSH - END"
+      cd ../..
+    else 
+      echo ""
+      echo "SKIP UNWRAP PHASE"
+    endif
+  endif
+
+###########################
+# 6 - start from geocode  #
+###########################
+
+    if ($stage <= 6) then
+    cd intf
+    set ref_id  = `grep SC_clock_start ../SLC/$master.PRM | awk '{printf("%d",int($3))}' `
+    set rep_id  = `grep SC_clock_start ../SLC/$slave.PRM | awk '{printf("%d",int($3))}' `
+    cd $ref_id"_"$rep_id
+    echo " "
+    echo "GEOCODE.CSH - START"
+    rm raln.grd ralt.grd
+    if ($topo_phase == 1) then
+      rm trans.dat
+      ln -s  ../../topo/trans.dat . 
+      echo "threshold_geocode: $threshold_geocode"
+      $OSARIS_PATH/lib/GMTSAR-mods/geocode_OSARIS.csh $threshold_geocode
+    else 
+      echo "topo_ra is needed to geocode"
+      exit 1
+    endif
+    echo "GEOCODE.CSH - END"
+    cd ../..
+  endif
+
+# end
+