Include bash script for GMRT data

.gitignore

@@ -52,7 +52,7 @@ Mkfile.old
 dkms.conf
 
 ##bin/rficlean.flags  # include this in the package as an example
-bin/crp_rficlean_gm.sh
+#bin/crp_rficlean_gm.sh
 bin/rficlean
 bin/read_n_make_plot
 src/read_n_make_plot.c

bin/crp_rficlean_gm.sh

@@ -0,0 +1,98 @@
+#!/bin/bash
+#=======================================================================
+#  Crude parallelization of RFIClean for processing GMRT data files.
+#
+#           Yogesh Maan, Dec. 2019
+#=======================================================================
+#
+
+
+
+#------------------------------------------------------------------------------
+if [ $# -lt 6 ] ; then
+ echo "========================================================================================"
+ echo " Usage: "
+ echo " crp_rficlean_gm.sh  <out_filename>  <flag-file>  <N_parallel>  <in_filename>  <gm_info>  <extra-flag>" 
+ echo " "
+ echo "========================================================================================"
+ exit 0
+fi
+outfile=$1
+flagfile=$2
+Np=$3
+infile=$4
+gminfo_file=$5
+extra_flag=$6
+#------------------------------------------------------------------------------
+
+rtag=${outfile%*.fil}  # tag for part-files
+
+##-------------------------------
+## read flags from the flag-file
+block=`sed -n 1p $flagfile`
+flag=`sed -n 2p $flagfile`
+#echo "block-size: $block"
+#echo "flag:   '$flag'"
+## read nchan from the gm-info-file
+nchans=`sed -n 4p $gminfo_file`
+##-------------------------------
+
+
+# deduce number of blocks to be processed in each part
+fsize=$(stat -cL%s "$infile")
+nsamples=`echo "scale=0; $fsize/(2*$nchans)" | bc`    ## gmrt data --> 2 bytes/sample
+Nb=`echo "scale=0; $nsamples/($Np*$block) + 1" | bc`
+#echo "nsamples, Nblocks: $nsamples, $Nb, $Np, $block ---"
+
+
+echo "Starting parallel-RFIClean processing at: "
+date
+echo ""
+
+##-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
+# prepare and execute the commands for all parts
+mkdir -p RFIClean_ps
+combine_cmd="cat "
+remove_cmd="rm  "
+count=0
+for (( c=1; c<=$Np; c++ )); do
+  bst=$(($count*$Nb + 1))
+  count=$((count+1))
+  #echo $count
+  tempout=${rtag}_part${count}.fil
+  psfile=${rtag}_part${count}.ps
+  pdffile=${rtag}_part${count}.pdf
+  #-------------------------------------
+  if [ $count -eq 1 ]; then
+    cmd="/home/ymaan/bin/rficlean -t $block $flag -o  $outfile -ps RFIClean_ps/$psfile  $infile -bst $bst -nbl $Nb -gm $gminfo_file $extra_flag  && ps2pdf  RFIClean_ps/$psfile RFIClean_ps/$pdffile  &&  rm RFIClean_ps/$psfile &"
+  elif [ $count -eq $Np ]; then
+    combine_cmd="${combine_cmd} ${tempout}"
+    remove_cmd="${remove_cmd} ${tempout}"
+    cmd="/home/ymaan/bin/rficlean -t $block $flag -o  $tempout -ps RFIClean_ps/$psfile  $infile -bst $bst -headerless -gm $gminfo_file $extra_flag  && ps2pdf  RFIClean_ps/$psfile RFIClean_ps/$pdffile  &&  rm RFIClean_ps/$psfile &"
+  else
+    combine_cmd="${combine_cmd} ${tempout}"
+    remove_cmd="${remove_cmd} ${tempout}"
+    cmd="/home/ymaan/bin/rficlean -t $block $flag -o  $tempout -ps RFIClean_ps/$psfile  $infile -bst $bst -nbl $Nb -headerless -gm $gminfo_file $extra_flag  && ps2pdf  RFIClean_ps/$psfile RFIClean_ps/$pdffile  &&  rm RFIClean_ps/$psfile &"
+  fi
+  echo $cmd
+  eval $cmd
+done
+wait
+##-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
+
+
+# Now combine all parts and then remove the parts
+combine_cmd="${combine_cmd} >> ${outfile}"
+#echo $combine_cmd
+#echo $remove_cmd
+cmd="$combine_cmd && $remove_cmd"
+echo $cmd
+eval $cmd
+
+
+echo "Finished parallel-RFIClean processing at: "
+date
+echo ""
+
+exit 0
+