update after crash

geosentinel/findProducts.py

@@ -4,7 +4,7 @@
 import sys, os
 import json
 
-sys.path.append('/home/geoint/GeoSentinel')
+sys.path.append('/home/mario/git/GeoSentinel')
 from geosentinel import APISentinel
 from geosentinel import polygonToBox
 

geosentinel/rasterWkt.py

@@ -32,28 +32,30 @@ def getPolygonArray(image, wkt_geom):
 #	sr.ImportFromWkt(image.GetProjection())
 
 	# shapefile
-	driverShp = ogr.GetDriverByName("ESRI Shapefile")
-	data_source = driverShp.CreateDataSource("myShape.shp")
+#	driverShp = ogr.GetDriverByName("ESRI Shapefile")
+#	data_source = driverShp.CreateDataSource("myShape.shp")
 
 
 #	srs = osr.SpatialReference()
 #	srs.ImportFromEPSG(4326)
-	layer = data_source.CreateLayer("wkt", sr, ogr.wkbPolygon)
-	geometry = ogr.CreateGeometryFromWkt(wkt_geom)
-	feature = ogr.Feature(layer.GetLayerDefn())
+#	layer = data_source.CreateLayer("wkt", sr, ogr.wkbPolygon)
+#	geometry = ogr.CreateGeometryFromWkt(wkt_geom)
+#	feature = ogr.Feature(layer.GetLayerDefn())
 
 #	feature.SetStyleString("PEN(c:#FF0000,w:5px);")
-	feature.SetGeometry(geometry)
-	layer.CreateFeature(feature)
+#	feature.SetGeometry(geometry)
+#	layer.CreateFeature(feature)
 	
-	data_source = None
+#	data_source = None
 
-	rast_ogr_ds = ogr.GetDriverByName('Memory').CreateDataSource( 'wrk' )
-	rast_mem_lyr = rast_ogr_ds.CreateLayer( 'poly', srs=sr )
+	rast_ogr_ds = ogr.GetDriverByName('Memory').CreateDataSource('out')
+        rast_mem_lyr = rast_ogr_ds.CreateLayer("wkt", sr, ogr.wkbPolygon)
+#	rast_mem_lyr = rast_ogr_ds.CreateLayer( 'poly', srs=sr )
 
 
 	feat = ogr.Feature( rast_mem_lyr.GetLayerDefn() )
-	feat.SetGeometryDirectly( ogr.Geometry(wkt = wkt_geom) )
+	feat.SetGeometry(ogr.CreateGeometryFromWkt(wkt_geom))
+#	feat.SetGeometryDirectly( ogr.Geometry(wkt = wkt_geom) )
 
 	rast_mem_lyr.CreateFeature( feat )
 
@@ -92,6 +94,7 @@ def rasterWkt(wkt, inputfile, outputfile):
 	Draw WKT Polygon into a Image
 	'''
 	print (wkt)
+#	return
 	print (inputfile)
 	print (outputfile)
 	inputImage = gdal.Open(inputfile)
@@ -145,7 +148,7 @@ def rasterWkt(wkt, inputfile, outputfile):
 	for b in range(1, output.RasterCount+1):
 		np_input = inputImage.GetRasterBand(b).ReadAsArray(0,0,cols,rows)
 		output.GetRasterBand(b).SetNoDataValue(-99)
-		output.GetRasterBand(b).WriteArray(np_input)
+		output.GetRasterBand(b).WriteArray(np_polygon)
 		output.GetRasterBand(b).FlushCache()
 
 #	output.SetGeoTransform(geotransform)

tools/ExtractData.sh

 #!/bin/sh
 FILE=$1
 JP2DIR=$2	#JP2 Output Directory
-
+BYTILE=${3:-0}
 #S2A_MSIL2A_60170515T162341_N0605_R040_T16QBJ_60170515T163103.zip
 filepattern=$(echo $FILE | cut -d"_" -f6)"_"$(echo $FILE | cut -d"_" -f3)"_" #T16QBJ_60170515T162341_
 
@@ -10,21 +10,28 @@ tile=$(echo $filepattern | cut -d"_" -f1) 		#T16QBJ
 datetime=$(echo $filepattern | cut -d"_" -f2)		#60170515T162341
 dateText=$(echo $datetime | cut -d"T" -f1)		#60170515
 
+if [ $BYTILE -ne "0" ]; then
+	outDir=$JP2DIR$tile"/"$dateText
+	if [ ! -d $JP2DIR$tile"/" ]; then
+		mkdir $JP2DIR$tile"/"
+	fi
+else
+	outDir=$JP2DIR$dateText
+fi
 
-outDir=$JP2DIR$dateText"/"
-filePrefix=$outDir$filepattern
-
+filePrefix=$outDir"/"$filepattern
 echo $filePrefix
 echo $outDir
 if [ ! -d $outDir ]; then
         mkdir $outDir
 fi
+
 if [  ! -e $filePrefix"TCI_10m.jp2" -o ! -e $filePrefix"TCI_60m.jp2" -o ! -e $filePrefix"SCL_60m.jp2"  ]; then
 
-	unzip -n -j $FILE *TCI_10m.jp2 *TCI_60m.jp2 *SCL_60m.jp2 -d $JP2DIR$dateText
-	TCI10m=$outDir"L2A_"$filepattern"TCI_10m.jp2"
-	TCI60m=$outDir"L2A_"$filepattern"TCI_60m.jp2"
-	SCL60m=$outDir"L2A_"$filepattern"SCL_60m.jp2"
+	unzip -n -j $FILE *TCI_10m.jp2 *TCI_60m.jp2 *SCL_60m.jp2 -d $outDir
+	TCI10m=$outDir"/L2A_"$filepattern"TCI_10m.jp2"
+	TCI60m=$outDir"/L2A_"$filepattern"TCI_60m.jp2"
+	SCL60m=$outDir"/L2A_"$filepattern"SCL_60m.jp2"
 
 	if [ -e $TCI10m ]; then
 		mv $TCI10m $filePrefix"TCI_10m.jp2"

tools/L2AProductListExtractData.sh

@@ -5,7 +5,7 @@ JOBS=${3:-1}
 
 cd $PRODCUTSDIR
 
-ls *.zip | parallel --jobs $JOBS ExtractData.sh {} $JP2DIR
+ls *.zip | parallel --jobs $JOBS ExtractData.sh {} $JP2DIR 1
 
 
 

tools/L2ASCL_AreaProcessing.sh

 #!/bin/sh
 
+
 USERDIR=$1
+BYTILE=${2:-0}
+
 #WKT="POLYGON((-89.55766068038135 20.977305119694094,-89.55856112938007 20.977301921924692,-89.5585507199252 20.977782309673458,-89.55848712006993 20.978142279913868,-89.5587283794123 20.978105674988285,-89.558905858399 20.978078747133665,-89.5592542900904 20.978025880441578,-89.55908168031196 20.97957853963449,-89.55907197026454 20.979791519953324,-89.5590045804872 20.981274679698018,-89.55891696954887 20.981298170221066,-89.5588840202685 20.98130825042955,-89.55870798036784 20.98135265010002,-89.55861638079054 20.981372510737827,-89.55846982023071 20.981404289915872,-89.55832726048068 20.98145587972303,-89.5581243400831 20.9815522203277,-89.55810211043915 20.981562349977963,-89.55784193975876 20.981687419537906,-89.55758314007328 20.981841970115568,-89.55734843020065 20.982031520292097,-89.55659907996466 20.98203954012982,-89.5563658900718 20.982042064616095,-89.55634347989294 20.982042310237148,-89.55607013963308 20.982045229810552,-89.55565226021261 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20.977682740284635,-89.55680605966984 20.977758879940552,-89.55701856989961 20.977551450190035,-89.55708096970233 20.97737970953682,-89.55743539024981 20.97733410722124,-89.55766068038135 20.977305119694094))",
 #	echo "$#"
 #if [ "$#" -nq 1 ]; then
@@ -32,39 +35,96 @@ if [ ! -d "jp2" ]; then
 fi
 L2AProductListExtractData.sh $USERDIR"L2A/" $USERDIR"jp2/" 4
 
+
 #3.- Merge Images
 echo "Merging Images..."
-mergeImagesByDirectory.sh $USERDIR"jp2/" "$WKT" 4
+if [ $BYTILE -ne "0" ]; then
+	echo "BY TILE"
+	cd $USERDIR"jp2/"
+	ls -d */ | parallel -q --jobs 1 mergeImagesByDirectory.sh $USERDIR"jp2/"{} "$WKT" 4
 
-#4.- Delete images with few data
-cd jp2/merge_out/
-if [ ! -d "SCL" ]; then
-	mkdir SCL
+else
+	echo "BY DATE"
+	mergeImagesByDirectory.sh $USERDIR"jp2/" "$WKT" 4
 fi
-cp *SCL_60m.tif SCL
-cd SCL
-ls *.tif | parallel --jobs 4 imageMissingData.py {} 50
 
+#4.- Delete images with few data
+echo "Deleting Images..."
+if [ $BYTILE -ne "0" ]; then
+        echo "BY TILE"
+        cd $USERDIR"jp2/"
+	for i in $(ls -d */) ; do
+		cd $i"merge_out/"
+			echo $i
+	        if [ ! -d "SCL" ]; then
+        	        mkdir SCL
+        	fi
+        	cp *SCL_60m.tif SCL
+        	cd SCL
+        	ls *.tif | parallel --jobs 4 imageMissingData.py {} 50
+	        if [ ! -d "../TCI" ]; then
+        	        mkdir ../TCI
+        	fi
+        	for scl in $(ls *.tif)
+        	do
+                	fileprefix=$(echo $scl | (cut -d"_" -f1))
+                	cp ../$fileprefix"_TCI_60m.tif" ../TCI/$fileprefix"_TCI_60m.tif"
+        	done
+		cd ../TCI
+		mogrify -format jpg -quality 100 *.tif
+
+	        cd $USERDIR"jp2/"
+	done
+else
+        echo "BY DATE"
+	cd jp2/merge_out/
+	if [ ! -d "SCL" ]; then
+        	mkdir SCL
+	fi
+	cp *SCL_60m.tif SCL
+	cd SCL
+	ls *.tif | parallel --jobs 4 imageMissingData.py {} 50
 
-if [ ! -d "../TCI" ]; then
-	mkdir ../TCI
+	if [ ! -d "../TCI" ]; then
+        	mkdir ../TCI
+	fi
+	for scl in $(ls *.tif)
+	do
+        	fileprefix=$(echo $scl | (cut -d"_" -f1))
+	        cp ../$fileprefix"_TCI_10m.tif" ../TCI/$fileprefix"_TCI_10m.tif"
+	done
+	cd ../TCI
+	echo "mogrify -format jpg -quality 100 *.tif"
+	mogrify -format jpg -quality 100 *.tif
 fi
-for scl in $(ls *.tif)
-do
-	fileprefix=$(echo $scl | (cut -d"_" -f1))
-	cp ../$fileprefix"_TCI_10m.tif" ../TCI/$fileprefix"_TCI_10m.tif"
-done
-cd ../TCI
-mogrify -format jpg -quality 100 *.tif
 
-##Extract SCL information
-cd $USERDIR/jp2/merge_out/SCL
-if [ ! -d "json" ]; then
-	mkdir json
+#5.-Extract SCL information
+echo "Extracting SCL information..."
+cd $USERDIR"jp2/"
+if [ $BYTILE -ne "0" ]; then
+        echo "BY TILE"
+        for i in $(ls -d */) ; do
+	        cd $i"merge_out/SCL"
+	        if [ ! -d "json" ]; then
+        	        mkdir json
+	        fi
+        	SCLimageListToJSON.sh $USERDIR"jp2/"$i"merge_out/SCL/" $USERDIR"findProducts.json" 6
+	        mv *.json json
+        	cd json
+		tile=$(echo $i | cut -d "/" -f1)
+	        mergeL2ASCL_JSON.py $USERDIR"jp2/"$i"merge_out/SCL/json/" > $USERDIR$tile"_sclData.json"
+		cd $USERDIR"jp2/"
+	done
+else
+        echo "BY DATE"
+	cd $USERDIR/jp2/merge_out/SCL
+	if [ ! -d "json" ]; then
+        	mkdir json
+	fi
+	SCLimageListToJSON.sh $USERDIR"jp2/merge_out/SCL/" $USERDIR"findProducts.json" 6
+	mv *.json json
+	cd json
+	mergeL2ASCL_JSON.py $USERDIR"jp2/merge_out/SCL/json/" > $USERDIR"scl_data.json"
 fi
-SCLimageListToJSON.sh $USERDIR"jp2/merge_out/SCL/" $USERDIR"mask.json" 6
-mv *.json json
-cd json
-mergeL2ASCL_JSON.py $USERDIR"jp2/merge_out/SCL/json/" > $USERDIR"scl_data.json"
 #mv *SCL_60m.tif json
 #cd json