Summary PDF parallel processing routine. Updated Changelog to v0.7.2.

cryotools · Feb 7, 2019 · 1da4932 · 1da4932
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diff --git a/doc/CHANGELOG.md b/doc/CHANGELOG.md
@@ -4,8 +4,23 @@ All notable changes to this OSARIS will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-
-## [0.7.0] - 2019-01-25	
+
+## [0.7.2] - 2019-02-07
+### Added
+- Parallel processing option for Summary PDF Module
+- Improved burst handling, now also stripping unused bursts in single slice configurations
+
+### Bugs fixed
+- Reporting in GACOS correction module
+- File downloads
+
+
+## [0.7.1] - 2019-01-28
+### Bugs fixed
+- File downloads
+
+
+## [0.7.0] - 2019-01-25
 ### Added
 - Functionality to merge multiple swaths
 - Cutting of output files to an area of interest defined by boundary box coordinates in the config file

diff --git a/modules/summary_pdf/PP-summary-pdf.sh b/modules/summary_pdf/PP-summary-pdf.sh
@@ -0,0 +1,176 @@
+#!/usr/bin/env bash
+
+start=`date +%s`
+
+config_file=$1
+work_PATH=$2
+pair_id=$3
+
+echo "Config file: $config_file"
+echo "Work path:   $work_PATH"
+echo "Pair ID:     $pair_id"
+
+source $config_file
+
+# Convert dataset configuration to arrays
+labels=( "$LABEL_1" "$LABEL_2" "$LABEL_3" "$LABEL_4" )
+directories=( "$DIRECTORY_1" "$DIRECTORY_2" "$DIRECTORY_3" "$DIRECTORY_4" )
+histeqs=( "$HIST_EQ_1" "$HIST_EQ_2" "$HIST_EQ_3" "$HIST_EQ_4" )
+cpts=( $CPT_1 $CPT_2 $CPT_3 $CPT_4 )
+ranges=( $RANGE_1 $RANGE_2 $RANGE_3 $RANGE_4 )
+show_suppls=( $SHOW_SUPPL_1 $SHOW_SUPPL_2 $SHOW_SUPPL_3 $SHOW_SUPPL_4 )
+
+dem_grd_hs="$work_PATH/Summary/hillshade.grd"
+CPDFS_dem="$work_PATH/Summary/CPDFS_dem.grd"
+CPDFS_dem_HS="$work_PATH/Summary/CPDFS_dem_HS.grd"
+
+ps_base="$work_PATH/Summary/${pair_id}-grd"	
+histeq_base="$work_PATH/Summary/${pair_id}-hiq"
+pdf_merged="$work_PATH/Summary/${pair_id}-combined.pdf"
+pdf_merged_ROT90=${pdf_merged::-4}_rot90.png
+
+
+# Set GMT parameters
+gmt gmtset MAP_FRAME_PEN          3
+gmt gmtset MAP_FRAME_WIDTH        0.1
+gmt gmtset MAP_FRAME_TYPE         plain
+gmt gmtset FONT_TITLE             Helvetica-Bold
+gmt gmtset FONT_LABEL             Helvetica-Bold 14p
+gmt gmtset PS_PAGE_ORIENTATION    landscape
+gmt gmtset PS_MEDIA               A4
+gmt gmtset FORMAT_GEO_MAP         D
+gmt gmtset MAP_DEGREE_SYMBOL      degree
+gmt gmtset PROJ_LENGTH_UNIT       cm
+
+
+
+if [ ! -f "$pdf_merged_ROT90" ]; then
+
+    GRD_FAIL=( 0 0 0 0 )
+
+    for counter in 0 1 2 3; do 
+	echo "Preparing ${labels[$counter]} ..."
+	echo "Searching for files in ${directories[$counter]}"
+	cpt_files[$counter]="$work_PATH/Summary/grd_${counter}_color.cpt"
+	cd ${directories[$counter]}
+	ls_result=$( ls ${pair_id}*.grd )
+	echo "Found file $ls_result"
+	if [ -f $ls_result ]; then		    	    
+	    GRD[$counter]="${directories[$counter]}/$ls_result"
+	    echo "${labels[$counter]} file found: ${GRD[$counter]}"		
+
+	    echo "histeqs $counter : ${histeqs[$counter]}"
+
+	    if [ ${histeqs[$counter]} -eq "1" ]; then
+		if [ ! -f ${histeq_base}-$counter.grd ]; then
+    		    echo; echo "Calculate histogram equalization for ${GRD[$counter]}"
+    		    gmt grdhisteq ${GRD[$counter]} -G${histeq_base}-$counter.grd -N -V
+    		    gmt grd2cpt -E15 ${histeq_base}-$counter.grd -C${cpts[$counter]} -V > $work_PATH/Summary/grd_${counter}.cpt
+		else
+		    echo; echo "${labels[$counter]} histogram exists, skipping ..."; echo
+		fi
+	    fi
+	else
+	    echo "No ${labels[$counter]} file found"
+	    GRD_FAIL[$counter]=1
+	    GRD_MESSAGE[$counter]="No ${labels[$counter]} file"
+	fi
+    done
+
+
+
+    cd $work_PATH/Summary
+
+    SCALE=18  
+    XSTEPS=0.5
+    YSTEPS=0.5	
+
+    if [ ! -e $pdf_merged ]; then
+	for counter in 0 1 2 3; do
+    	    if [ ! -e ${ps_base}-$counter.ps ]; then
+		echo; echo "Creating ${labels[$counter]} in ${ps_base}-$counter.ps"		
+		TITLE="${labels[$counter]} {master_date}"			
+		if [ ! "${GRD_FAIL[$counter]}" -eq 1 ]; then
+		    if [ ${histeqs[$counter]} -eq 1 ]; then
+			echo; echo "${labels[$counter]}: ${histeq_base}-$counter.grd"; echo
+			gmt grdimage ${histeq_base}-$counter.grd  \
+			    -C$work_PATH/Summary/grd_${counter}.cpt -R$AOI_REGION -JM$SCALE -B+t"$TITLE" -Q \
+			    -Bx$XSTEPS -By$YSTEPS -V -K -Yc -Xc > ${ps_base}-$counter.ps
+		    else
+			gmt grdimage ${GRD[$counter]}  \
+			    -C${cpt_files[$counter]} -R$AOI_REGION -JM$SCALE -B+t"$TITLE" -Q \
+			    -Bx$XSTEPS -By$YSTEPS -V -K -Yc -Xc > ${ps_base}-$counter.ps
+		    fi
+
+		    if [ ${show_suppls[$counter]} -eq 1 ]; then
+			for vector_file in ${vector_files[@]}; do
+			    style_name=${vector_file}_style
+			    vector_style=$( echo "${!style_name}" | tr -d "'" )
+			    gmt psxy $vector_style -JM$SCALE -R$AOI_REGION ${!vector_file::-4}.gmt -O -K -V >> ${ps_base}-$counter.ps			    				
+			done
+		    fi
+		else			
+		    gmt grdimage $CPDFS_dem_HS -C#ffffff,#eeeeee \
+			-R$AOI_REGION -JM$SCALE -B+t"${GRD_MESSAGE[$counter]}" -Q -Bx$XSTEPS -By$YSTEPS -V -K -Yc -Xc > ${ps_base}-$counter.ps
+
+
+		    if [ $page_orientation -eq 1 ]; then
+			convert -density $resolution -fill red -pointsize 18 -gravity center \
+			    -trim -verbose label:"${GRD_MESSAGE[$counter]}" \
+			    ${ps_base}-$counter.ps -quality 100  ${ps_base}-$counter.ps
+		    else
+			convert -rotate 90 -density $resolution -fill red -pointsize 18 -gravity center \
+			    -trim -verbose label:"${GRD_MESSAGE[$counter]}" \
+			    ${ps_base}-$counter.ps -quality 100  ${ps_base}-$counter.ps
+		    fi
+		fi
+
+		if [ $page_orientation -eq 1 ]; then
+		    convert -verbose -density $resolution -trim  ${ps_base}-$counter.ps -quality 100 ${ps_base}-$counter.png
+		else
+		    convert -verbose -rotate 90 -density $resolution -trim  ${ps_base}-$counter.ps -quality 100 ${ps_base}-$counter.png
+		fi
+	    else
+		echo; echo "${labels[$counter]} in ${ps_base}-$counter.ps exists, skipping ..."
+    	    fi
+	done
+
+
+    	echo "Merging PS into $pdf_merged_ROT90"
+	take_diff=$(( ($(date --date="$slave_date" +%s) - $(date --date="$master_date" +%s) )/(60*60*24) ))
+	if [ "$page_orientation" -eq 1 ]; then
+    	    montage ${ps_base}-0.png ${ps_base}-1.png ${ps_base}-2.png ${ps_base}-3.png  \
+		-rotate 90 -geometry +100+150 -density $resolution -title "${pair_id} (${take_diff} days)" \
+		-quality 100 -tile 4x1 -mode concatenate -verbose $pdf_merged_ROT90
+	else
+	    montage -tile 1x4 -geometry +20+30 \
+		${ps_base}-0.png ${ps_base}-1.png ${ps_base}-2.png ${ps_base}-3.png  \
+		-title "${pair_id} (${take_diff} days)" \
+		-density $resolution -quality 100 -mode concatenate -verbose $pdf_merged_ROT90
+	fi
+
+
+	if [ "$clean_up" -ge 1 ]; then
+    	    rm ${ps_base}_*.ps 
+	    rm ${ps_base}_*.png
+	fi
+
+	if [ "${histeq_base}-$counter.grd" != "$CPDFS_dem_HS" ]; then
+	    rm ${histeq_base}-*.grd
+	fi
+    fi
+else
+    echo "File $pdf_merged_ROT90 exists, skipping ..."
+fi
+
+
+if [ -f $pdf_merged_ROT90 ]; then status_SUMMARY=1; else status_SUMMARY=0; fi
+
+end=`date +%s`
+runtime=$((end-start))
+
+echo "${pair_id:0:8} ${pair_id:10:8} $SLURM_JOB_ID $runtime $status_SUMMARY" >> $output_PATH/Reports/PP-SUMMARY-stats.tmp
+
+printf 'Processing finished in %02dd %02dh:%02dm:%02ds\n' $(($runtime/86400)) $(($runtime%86400/3600)) $(($runtime%3600/60)) $(($runtime%60))
+
+