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Merge pull request #7 from ymaan4/skipRFI_opts
New Skip-RFI-excision options, a little bit better documentation and other minor changes
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| * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA | ||
| * | ||
| */ | ||
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| #!/bin/bash | ||
| #======================================================================= | ||
| # Crude parallelization of RFIClean for processing GMRT data files. | ||
| # | ||
| # Yogesh Maan, Dec. 2019 | ||
| #======================================================================= | ||
| # | ||
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| #------------------------------------------------------------------------------ | ||
| 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=$6 | ||
| #------------------------------------------------------------------------------ | ||
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| rtag=${outfile%*.fil} # tag for part-files | ||
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| ##------------------------------- | ||
| ## 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 $gminfo_file` | ||
| ##------------------------------- | ||
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| # deduce number of blocks to be processed in each part | ||
| fsize=$(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, $block ---" | ||
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| echo "Starting parallel-RFIClean processing at: " | ||
| date | ||
| echo "" | ||
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| ##-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= | ||
| # prepare and execute the commands for all parts | ||
| mkdir -p RFIClean_ps | ||
| combine_cmd="cat " | ||
| remove_cmd="rm " | ||
| count=0 | ||
| for (( c=1; c<=$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 $cmd | ||
| done | ||
| wait | ||
| ##-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= | ||
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| # Now combine all parts and then remove the parts | ||
| combine_cmd="${combine_cmd} >> ${outfile}" | ||
| #echo $combine_cmd | ||
| #echo $remove_cmd | ||
| cmd="$combine_cmd && $remove_cmd" | ||
| echo $cmd | ||
| eval $cmd | ||
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| echo "Finished parallel-RFIClean processing at: " | ||
| date | ||
| echo "" | ||
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| exit 0 | ||
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