From 881df6a9298c86a8b9b9ebdd36fc64bcaea47f4e Mon Sep 17 00:00:00 2001
From: tkiyan <48825861+tkiyan@users.noreply.github.com>
Date: Fri, 22 Mar 2019 12:48:10 +0100
Subject: [PATCH 1/7] Parallelization bug removed

When running more than 1 swath, the tmp-files of "align_cut_tops.csh" were mixed up, since up to 3 Jobs (in case of 3 activated swaths) were manipulating tmp-files. swaths are now calculated in separately directories and results for "p2p_OSARIS_no_unwrap.csh" are read out from new directories properly
---
 lib/PP-pairs.sh | 20 ++++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/lib/PP-pairs.sh b/lib/PP-pairs.sh
index acd1433..916ceca 100644
--- a/lib/PP-pairs.sh
+++ b/lib/PP-pairs.sh
@@ -39,10 +39,18 @@ job_ID=${previous_scene:15:8}--${current_scene:15:8}
 
 mkdir -pv $work_PATH/$job_ID/F$swath/raw 
 mkdir -pv $work_PATH/$job_ID/F$swath/topo 
+mkdir -pv $work_PATH/raw/$job_ID-aligned/F$swath/
 cd $work_PATH/$job_ID/F$swath/topo; ln -sf $topo_PATH/dem.grd .;
-
-cd $work_PATH/raw/$job_ID-aligned/
-
+cd $work_PATH/raw/$job_ID-aligned/F$swath/
+ln -sf $topo_PATH/dem.grd .
+ln -sf $work_PATH/raw/${previous_scene:15:8}_manifest.safe .
+ln -sf $work_PATH/raw/${current_scene:15:8}_manifest.safe .
+ln -sf $work_PATH/raw/$previous_scene.tiff .
+ln -sf $work_PATH/raw/$current_scene.tiff .
+cp -P $work_PATH/raw/$previous_scene.xml .
+cp -P $work_PATH/raw/$current_scene.xml .
+cp -P $work_PATH/raw/$previous_orbit .
+cp -P $work_PATH/raw/$current_orbit .
 
 # ALIGN SCENE PAIRS
 
@@ -74,12 +82,12 @@ $OSARIS_PATH/lib/GMTSAR-mods/align_cut_tops.csh $previous_scene $previous_orbit
 
 # INTERFEROMETRIC PROCESSING
 
-if [ ! -f $work_PATH/raw/$job_ID-aligned/a.grd ] || [ ! -f $work_PATH/raw/$job_ID-aligned/r.grd ]; then
+if [ ! -f $work_PATH/raw/$job_ID-aligned/F$swath/a.grd ] || [ ! -f $work_PATH/raw/$job_ID-aligned/F$swath/r.grd ]; then
     echo; echo "ERROR: Scene alignment failed. Aborting interferometric processing ..."; echo
 else
-
+ 
     cd $work_PATH/$job_ID/F$swath/raw/
-    ln -sf $work_PATH/raw/$job_ID-aligned/*F$swath* .
+    ln -sf $work_PATH/raw/$job_ID-aligned/F$swath/*F$swath* .
     
     cd $work_PATH/$job_ID/F$swath/
 

From 94f36c005fa6eeb046cbacdbcc67254b370bf0f7 Mon Sep 17 00:00:00 2001
From: tkiyan <48825861+tkiyan@users.noreply.github.com>
Date: Fri, 22 Mar 2019 13:03:18 +0100
Subject: [PATCH 2/7] fixed unnecessary cutting

it cutted although the aoi-flag set to 0 in the xyz.config-file. just putting a checkup with on the parameter before assample_tops might solve the Problem, but one has to think about to set it way before to speed up calculation and get rid of excessive files for this case
---
 lib/prepare-data.sh | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/lib/prepare-data.sh b/lib/prepare-data.sh
index dc6db9f..6ac7870 100755
--- a/lib/prepare-data.sh
+++ b/lib/prepare-data.sh
@@ -242,13 +242,13 @@ else
 		for((i=0;i<$stem_count;++i)); do
 		    stem_string="$stem_string ${stems_chrono[$i]}"		    
 		done
-		
-		if [ $debug -ge 1 ]; then
-		    echo; echo "Executing assemble_tops with parameters:"
-		    echo "$azimuth_min $azimuth_max $stem_string $work_PATH/preprocessing/$stem"
-		fi
-		assemble_tops $azimuth_min $azimuth_max $stem_string $work_PATH/preprocessing/$stem
-			
+		if [ $cut_to_aoi -eq 1 ]; then
+		    if [ $debug -ge 1 ]; then
+		        echo; echo "Executing assemble_tops with parameters:"
+		        echo "$azimuth_min $azimuth_max $stem_string $work_PATH/preprocessing/$stem"
+		    fi
+		    assemble_tops $azimuth_min $azimuth_max $stem_string $work_PATH/preprocessing/$stem
+		fi	
 		cd $work_PATH/preprocessing/
 
 		# Generate new PRM files for assembled tops

From 756cf627cd5d7fea8bfbdedde028ebdee688ded0 Mon Sep 17 00:00:00 2001
From: tkiyan <48825861+tkiyan@users.noreply.github.com>
Date: Fri, 22 Mar 2019 14:56:50 +0100
Subject: [PATCH 3/7] link files in case you do not want do cut

---
 lib/prepare-data.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/prepare-data.sh b/lib/prepare-data.sh
index 6ac7870..add2529 100755
--- a/lib/prepare-data.sh
+++ b/lib/prepare-data.sh
@@ -195,6 +195,10 @@ else
 		   
 		    ln -sf $work_PATH/orig/${files_chrono[$i]}/measurement/${stem}.tiff .
 		    ln -sf $work_PATH/orig/${files_chrono[$i]}/annotation/${stem}.xml .
+		    cd $work_PATH/preprocessing/
+		    ln -sf $work_PATH/orig/${files_chrono[$i]}/measurement/${stem}.tiff .
+		    ln -sf $work_PATH/orig/${files_chrono[$i]}/annotation/${stem}.xml .
+		    cd $work_PATH/preprocessing/raw
 		    make_s1a_tops ${stem}.xml ${stem}.tiff ${stem} 0
 		    scene_prefix="${stem:15:8}_${stem:24:6}_F${swath}"
 		    prefixes+=($scene_prefix)

From 46d4dbf3715b79f127f990e41728fc85e6d43ea7 Mon Sep 17 00:00:00 2001
From: tkiyan <48825861+tkiyan@users.noreply.github.com>
Date: Fri, 22 Mar 2019 16:52:11 +0100
Subject: [PATCH 4/7] Update displacement.sh

---
 modules/displacement/displacement.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/displacement/displacement.sh b/modules/displacement/displacement.sh
index e2813ba..66d87ac 100644
--- a/modules/displacement/displacement.sh
+++ b/modules/displacement/displacement.sh
@@ -46,8 +46,8 @@ else
     
     if [ -z "$unwrapped_intf_PATH" ]; then
 	echo "No path to unwrapped interferograms specified in ${module_name}.config"
-	echo "Trying default path $output_PATH/Pairs-forward/Interferograms-unwrapped ..."
-	unwrapped_intf_PATH="$output_PATH/Pairs-forward/Interferograms-unwrapped"
+	echo "Trying default path $output_PATH/Interf-unwrpd ..."
+	unwrapped_intf_PATH="$output_PATH/Interf-unwrpd"
     fi
 
     if [ ! -d "$unwrapped_intf_PATH" ]; then

From 61d61719f5f0e9647904bf5bb14584abebffdad5 Mon Sep 17 00:00:00 2001
From: tkiyan <48825861+tkiyan@users.noreply.github.com>
Date: Fri, 22 Mar 2019 16:53:24 +0100
Subject: [PATCH 5/7] Update align_cut_tops.csh

---
 lib/GMTSAR-mods/align_cut_tops.csh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/GMTSAR-mods/align_cut_tops.csh b/lib/GMTSAR-mods/align_cut_tops.csh
index 36f0ec1..7208f52 100755
--- a/lib/GMTSAR-mods/align_cut_tops.csh
+++ b/lib/GMTSAR-mods/align_cut_tops.csh
@@ -73,10 +73,10 @@ echo $spre
 
 # Copy LED and PRM file created at preprocessing stage
 pwd
-cp ../../preprocessing/$mpre".PRM" .
-cp ../../preprocessing/$mpre".LED" .
-cp ../../preprocessing/$spre".PRM" .
-cp ../../preprocessing/$spre".LED" .
+cp ../../../preprocessing/$mpre".PRM" .
+cp ../../../preprocessing/$mpre".LED" .
+cp ../../../preprocessing/$spre".PRM" .
+cp ../../../preprocessing/$spre".LED" .
 
 # cp $mpre".LED" $1".LED"
 # cp $spre".LED" $3".LED"

From 346579e492ec03f23171e9d7cfdae82edf48fec4 Mon Sep 17 00:00:00 2001
From: tkiyan <48825861+tkiyan@users.noreply.github.com>
Date: Fri, 22 Mar 2019 16:55:52 +0100
Subject: [PATCH 6/7] Update p2p_OSARIS_no_unwrap.csh

---
 lib/GMTSAR-mods/p2p_OSARIS_no_unwrap.csh | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/lib/GMTSAR-mods/p2p_OSARIS_no_unwrap.csh b/lib/GMTSAR-mods/p2p_OSARIS_no_unwrap.csh
index 105edad..8b667d1 100755
--- a/lib/GMTSAR-mods/p2p_OSARIS_no_unwrap.csh
+++ b/lib/GMTSAR-mods/p2p_OSARIS_no_unwrap.csh
@@ -278,15 +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
+	cp -u *gauss* ../../../
       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
+	cp -u *gauss* ../../../
       endif
     else
       intf.csh $ref.PRM $rep.PRM
-      filter.csh $ref.PRM $rep.PRM $filter $dec 
+      filter.csh $ref.PRM $rep.PRM $filter $dec
+      cp -u *gauss* ../../../
     endif
     cd ../..
     echo "INTF.CSH, FILTER.CSH - END"

From 02b313f958a0718061a05c1f7a27e09f0318d7a9 Mon Sep 17 00:00:00 2001
From: tkiyan <48825861+tkiyan@users.noreply.github.com>
Date: Fri, 22 Mar 2019 20:36:29 +0100
Subject: [PATCH 7/7] Update displacement.sh

---
 modules/displacement/displacement.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/displacement/displacement.sh b/modules/displacement/displacement.sh
index 66d87ac..e2813ba 100644
--- a/modules/displacement/displacement.sh
+++ b/modules/displacement/displacement.sh
@@ -46,8 +46,8 @@ else
     
     if [ -z "$unwrapped_intf_PATH" ]; then
 	echo "No path to unwrapped interferograms specified in ${module_name}.config"
-	echo "Trying default path $output_PATH/Interf-unwrpd ..."
-	unwrapped_intf_PATH="$output_PATH/Interf-unwrpd"
+	echo "Trying default path $output_PATH/Pairs-forward/Interferograms-unwrapped ..."
+	unwrapped_intf_PATH="$output_PATH/Pairs-forward/Interferograms-unwrapped"
     fi
 
     if [ ! -d "$unwrapped_intf_PATH" ]; then