Merge branch 'dev' of gitlab.geoint.mx:adan.salazar/GeoSentinel

config/config.json

+{
+  "PATHS": {
+    "PATH_GEOSENTINEL": "/home/david/centroGEO/repsat/GeoSentinel",
+    "PATH_NAS": "/home/david/NAS/"
+  },
+  "API_SENTINEL": {
+    "SENTINEL_USER" : "emmhp",
+    "SENTINEL_PASS" : "geoemm29"
+  }
+} 

geosentinel/APISentinel.py

@@ -94,6 +94,7 @@ class APISentinel(object):
 		os.chdir(dir)
 		#        self.api.download_all(products)
 		for p in products:
+			print(products[p]['filename'])
 			self.api.download(p)
 
 		def filterProducts(self, productList):

geosentinel/L2ASCLtoJSON.py

@@ -5,32 +5,45 @@ import osgeo.osr as osr
 import numpy as np
 import gdal
 import sys
+import os
 import json
 from collections import Counter
-sys.path.append('/home/mario/git/GeoSentinel')
+
+########### lee archivo de configuración ################
+dirname = os.path.dirname(__file__)
+configfile = os.path.join(dirname, '../config/config.json')
+
+with open(configfile, 'r') as f:
+    config = json.load(f)
+
+
+#print(config['PATHS']['PATH_GEOSENTINEL'])
+
+SENTINEL_PATH = config['PATHS']['PATH_GEOSENTINEL']
+###########################################################
+
+sys.path.append(SENTINEL_PATH)
+
 from geosentinel import rasterWkt
+CLASS_MAP = {0:0, 1:1, 2:2, 3:3, 4:4, 5:5, 6:6, 7:7, 8:8, 9:8, 10:8, 11:9}
 #-------------------------------------------------------------------------------
 def L2ASCLtoDict(filename, wkt):
 	''' 
 	L2ASCLtoDict
 	'''
+	classMap = lambda x: [ CLASS_MAP[xx] for xx in x ]
+
 	inputImage = gdal.Open(filename)
 	rows, cols, geotransform = inputImage.RasterYSize, inputImage.RasterXSize, inputImage.GetGeoTransform()
 	data = inputImage.GetRasterBand(1).ReadAsArray(0,0,cols,rows)
-#	count = Counter([])
-#	for r in data:
-#		count = count + Counter(r)
-#	sclDict = {str(k):v for k,v in dict(count).items()}
-#	print ("data")
-#	print (sclDict)
 
 	data = np.bitwise_and(data, rasterWkt.getPolygonArray(inputImage, wkt))
 	count = Counter([])
 	for r in data:
-		count = count + Counter(r)
+		count = count + Counter(classMap(r))
+
 	sclDict = {str(k):v for k,v in dict(count).items()}
-#	print ("data & POLY")
-#	print (sclDict)
+
 	return sclDict
 #-------------------------------------------------------------------------------
 def main(argv):

geosentinel/findProducts.py

@@ -4,20 +4,32 @@
 import sys, os
 import json
 
-sys.path.append('/home/mario/git/GeoSentinel')
+########### lee archivo de configuración ################
+dirname = os.path.dirname(__file__)
+configfile = os.path.join(dirname, '../config/config.json')
+
+with open(configfile, 'r') as f:
+    config = json.load(f)
+
+
+#print(config['PATHS']['PATH_GEOSENTINEL'])
+
+SENTINEL_PATH = config['PATHS']['PATH_GEOSENTINEL']
+###########################################################
+sys.path.append(SENTINEL_PATH)
+
 from geosentinel import APISentinel
 from geosentinel import polygonToBox
-
 from datetime import date 
 
-
 #def findSentinelProducts(wkt, startDate, endDate, platform, cloud):
 #	sentinel = APISentinel.APISentinel('asalazarg',  'geo135asg')
 
 #	products = sentinel.getProducts(wkt, (startDate, endDate), {"platformname":platform, "cloudcoverpercentage":"[0 TO "+str(cloud)+"]"})
 
 #	return products
-
+#productsCodes = {"L1C":"L1C","L2A":"L1C"}
+productType = {"L1C":"S2MSI1C", "L2A":"S2MSI2A"}
 def main(argv):
 
 	if len(sys.argv) != 2:
@@ -29,28 +41,72 @@ def main(argv):
 		sentinel = APISentinel.APISentinel(cfg['username'],  cfg['password'])
 
 		wkt = polygonToBox.getWKTPolygonBoundingBox(cfg['wkt'], True)
-		productList = sentinel.getProducts(wkt, (cfg['startDate'], cfg['endDate']), {"platformname":cfg['platform'], "cloudcoverpercentage":"[0 TO "+str(cfg['clouds'])+"]"}, "Contains")
+		productList = sentinel.getProducts(wkt, (cfg['startDate'], cfg['endDate']), {"producttype":productType[cfg["productLevel"]], "platformname":cfg['platform'], "cloudcoverpercentage":"[0 TO "+str(cfg['clouds'])+"]"}, "Contains")
 		if len(productList)<=0:
 			print ("No products found with 'Contains' trying with 'Intersects'")
-			productList = sentinel.getProducts(wkt, (cfg['startDate'], cfg['endDate']), {"platformname":cfg['platform'], "cloudcoverpercentage":"[0 TO "+str(cfg['clouds'])+"]"})
- 		productsCodes = {"L1C":"L1C","L2A":"L1C"}
-		fileNames = [productList[k]['filename'].replace("SAFE", "zip").replace(productsCodes[cfg['productLevel']], cfg['productLevel']) for k in productList.keys() ]
-		inDir =  cfg["productsDir"]
-		outdir =  cfg["linksDir"]
-		dirList = os.listdir(inDir)
-		
-		matchingProducts = set(fileNames).intersection(set(dirList))
-		print ( str(len(matchingProducts))+" of " + str(len(fileNames)) +" products found.")	
+			productList = sentinel.getProducts(wkt, (cfg['startDate'], cfg['endDate']), {"producttype":productType[cfg["productLevel"]], "platformname":cfg['platform'], "cloudcoverpercentage":"[0 TO "+str(cfg['clouds'])+"]"})
 
-		text =""
-		while text != "yes" and text != "no":
-			text = raw_input("Do you want to link this products to "+outdir+ " ? (yes, no)")
+#			fileNames = [productList[k]['filename'].replace("SAFE", "zip").replace(productsCodes[cfg['productLevel']], cfg['productLevel']) for k in productList.keys() ]
+		fileNames = [productList[k]['filename'].replace("SAFE", "zip") for k in productList.keys() ]
+
+		downloadDir =  cfg["productsDir"]+cfg["productLevel"]+"/"
+		dirList = os.listdir(downloadDir)
+
+		matchingProducts = set(fileNames).intersection(set(dirList))
+		print ( str(len(matchingProducts))+" of " + str(len(fileNames)) +" "+ cfg["productLevel"] + " products found.")
+#		rawDir = inDir.replace(cfg['productLevel'],productsCodes[cfg['productLevel']])
+
+ #       print(rawDir)
+
+        text =""
+        while text != "yes" and text != "no":
+			text = raw_input("Do you want to download this products to "+downloadDir+ " ? (yes, no)")
+	if text=="yes":
+           sentinel.downloadProducts(productList,downloadDir)
+
+
+	L2ADir = cfg["productsDir"]+"L2A/"
+	if cfg["productLevel"]=="L1C":
+		fileNamesL2A = [productList[k]['filename'].replace("SAFE", "zip").replace("L1C", "L2A") for k in productList.keys() ]
+		L1CDir = cfg["productsDir"]+"L1C/"
+	        linksDir=cfg["projectDir"]+"L1C/"
+		if not os.path.exists(linksDir):
+			os.mkdir(linksDir)
+                L1CDirList = os.listdir(L1CDir)
+
+		#LinkProducts
+		fileNames = [productList[k]['filename'].replace("SAFE", "zip") for k in productList.keys() ]
+		matchingProducts = set(fileNames).intersection(set(L1CDirList))
+		for f in matchingProducts:
+			print (f)
+                        print("ln -s " + L1CDir+f + " " + linksDir+f)
+
+			os.system("ln -s " + L1CDir+f + " " + linksDir+f)
+		print (str(len(matchingProducts)) + " Linked to " + linksDir)
+
+                print ( str(len(matchingProducts))+" of " + str(len(fileNames)) +" L1C products found in L2A.")
+        	text =""
+	        while text != "yes" and text != "no":
+                        text = raw_input("Do you want to convert this products and save them to "+downloadDir+ " ? (yes, no)")
+	        if text=="yes":
+			#print("L1CProductListToL2A.sh "+rawDir+" "+inDir+" 1")
+			os.system("L1CProductListToL2A.sh "+linksDir+" "+L2ADir+" 1") 
+
+        text =""
+	linksDir=cfg["projectDir"]+"L2A/"
+        while text != "yes" and text != "no":
+			text = raw_input("Do you want to link this products to "+linksDir+ " ? (yes, no)")
+
+        if text=="yes":
+			fileNames = [productList[k]['filename'].replace("SAFE", "zip").replace("L1C", "L2A") for k in productList.keys() ]
+			dirList = os.listdir(L2ADir)
+
+	                matchingProducts = set(fileNames).intersection(set(dirList))
 
-		if text=="yes":
 			for f in matchingProducts:
 				print (f)
-				os.system("ln -s " + inDir+f + " " + outdir+f)
-			print (str(len(matchingProducts)) + " Linked to " + outdir)
+				os.system("ln -s " + L2ADir+f + " " + linksDir+f)
+			print (str(len(matchingProducts)) + " Linked to " + linksDir)
 		
 if __name__ == "__main__":
 	main(sys.argv)

geosentinel/imageMissingData.py

@@ -5,25 +5,49 @@ import osgeo.osr as osr
 import numpy as np
 import gdal
 import sys, os
+import json
+
+########### lee archivo de configuración ################
+dirname = os.path.dirname(__file__)
+configfile = os.path.join(dirname, '../config/config.json')
+
+with open(configfile, 'r') as f:
+    config = json.load(f)
+
+
+#print(config['PATHS']['PATH_GEOSENTINEL'])
+
+SENTINEL_PATH = config['PATHS']['PATH_GEOSENTINEL']
+###########################################################
+
+sys.path.append(SENTINEL_PATH)
+
+from geosentinel import rasterWkt
 
 #-------------------------------------------------------------------------------
-def imageMissingData(filename):
+def imageMissingData(filename, wkt):
 
 	inputImage = gdal.Open(filename)
 	rows, cols, geotransform = inputImage.RasterYSize, inputImage.RasterXSize, inputImage.GetGeoTransform()
 	data = inputImage.GetRasterBand(1).ReadAsArray(0,0,cols,rows)
-	inputImage = None
+	rasterwkt = rasterWkt.getPolygonArray(inputImage, wkt)
+	data = np.bitwise_and(data, rasterwkt)
 
-	return (data>0).sum()/float((rows*cols))
+	inputImage = None
+	return (data>0).sum()/float((rasterwkt>0).sum())
 
 #-------------------------------------------------------------------------------
 def main(argv):
-	if len(sys.argv) != 3:
-		print("Usage: " + argv[0] + " <File> <%>")
+	if len(sys.argv) != 4:
+		print("Usage: " + argv[0] + " <File> <JSON> <%>")
 	else:
-		dataArea = imageMissingData(argv[1])
-		if dataArea<float(argv[2])/100.0 :
-			print ("Deleting " + argv[1] + " " + str(dataArea))
+		jsonFile=open(argv[2]).read()
+		cfg = json.loads(jsonFile)
+
+		dataArea = imageMissingData(argv[1], cfg["wkt"])
+		th = float(argv[3])/100.0
+		if dataArea<th :
+			print ("Deleting " + argv[1] + " " + str(dataArea)+" < " + str(th))
 			os.system("rm " + argv[1])
 		else:
 			print ("Keeping " + argv[1] + " " + str(dataArea))

geosentinel/splitSCL.py

+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+import osgeo.ogr as ogr
+import osgeo.osr as osr
+import numpy as np
+import gdal
+import sys
+
+SCL_COLOR = [
+		(0,0,0,255), #NO_DATA
+		(255,0,0,255), #SATURATED_OR_DEFECTIVE
+                (64,64,64,255), #DARK_AREA_PIXELS
+                (102,51,0,255), #CLOUD_SHADOWS
+                (0,255,0,255), #VEGETATION
+		(255,255,0,255), #NOT_VEGETATED
+                (0,0,255,255), #WATER
+		(128,128,128,255), #UNCLASSIFIED
+                (192,192,192,255), #CLOUD_MEDIUM_PROBABILITY
+		(255,255,255,255), #CLOUD_HIGH_PROBABILITY
+		(102,204,255,255), #THIN_CIRRUS
+		(255,153,255,255), #SNOW
+		 ]
+CLASS_MAP = {0:0, 1:1, 2:2, 3:3, 4:4, 5:5, 6:6, 7:7, 8:8, 9:8, 10:8, 11:9}
+CLASS_GROUP = [[0], [1], [2], [3], [4], [5], [6], [7], [8,9,10], [11]]
+#-------------------------------------------------------------------------------
+def splitSCL(filename, outdir):
+	inputImage = gdal.Open(filename)
+	rows = inputImage.RasterYSize
+	cols = inputImage.RasterXSize
+	geotransform =  inputImage.GetGeoTransform()
+	projection = inputImage.GetProjection()
+
+	sr = osr.SpatialReference()
+	sr.ImportFromWkt(projection)
+	driverTiff = gdal.GetDriverByName('GTiff')
+
+#	for c in range(len(SCL_COLOR)):
+	for c in range(len(CLASS_GROUP)):
+		outputfile=outdir+filename[:-4]+"_"+str(c)+".tif"
+		output = driverTiff.Create(outputfile, cols, rows, 4, gdal.GDT_Byte)
+#		classMask  = inputImage.GetRasterBand(1).ReadAsArray(0,0,cols,rows)==c
+                classMask  = np.isin(inputImage.GetRasterBand(1).ReadAsArray(0,0,cols,rows), CLASS_GROUP[c])
+
+		for b in range(1, output.RasterCount+1):
+			output.GetRasterBand(b).SetNoDataValue(0)
+			output.GetRasterBand(b).WriteArray(classMask*SCL_COLOR[c][b-1])
+			output.GetRasterBand(b).FlushCache()
+
+		output.SetGeoTransform(geotransform)
+		output.SetProjection(projection)
+		output = None
+	inputImage = None
+
+
+#-------------------------------------------------------------------------------
+def main(argv):
+	splitSCL(argv[1], argv[2])
+
+if __name__ == "__main__":
+	main(sys.argv)
+

tools/ExtractData.sh

@@ -29,6 +29,8 @@ 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 $outDir
+#        unzip -n -j $FILE *TCI_10m.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"

tools/L1CToL2A.sh

@@ -5,10 +5,10 @@ filename=$1	#L1C Filename /home/geoint/NAS/meridaL1C_2c/S2B_MSIL1C_20181005T1631
 basename=${filename##*/} #S2B_MSIL1C_20181005T163129_N0206_R083_T16QBH_20181005T214055.zip
 #echo $filename
 #echo $basename
-Z1=$(echo $(echo $basename | cut -d "_" -f1) | cut -d "/" -f3)
-Z2=$(echo $basename | cut -d "_" -f3,4,5,6,7 | cut -d "." -f1)
+Z1=$(echo $(echo $basename | cut -d "_" -f1) | cut -d "/" -f3)  #S2B
+Z2=$(echo $basename | cut -d "_" -f3,4,5,6,7 | cut -d "." -f1)  #20181005T163129_N0206_R083_T16QBH_20181005T214055
 
-L2A=$Z1"_MSIL2A_"$Z2
+L2A=$Z1"_MSIL2A_"$Z2 #S2B_MSIL2A_20181005T163129_N0206_R083_T16QBH_20181005T214055
 #echo $L2A
 if [ ! -e  $L2A.zip ]; then
 	echo "Processing: " $filename " into " $L2A.zip

tools/L2AProductListExtractData.sh

@@ -2,10 +2,10 @@
 PRODCUTSDIR=$1	#Products Intput directory
 JP2DIR=$2	#JP2 Output Directory
 JOBS=${3:-1}
-
+BYTILE=${4:-0}
 cd $PRODCUTSDIR
 
-ls *.zip | parallel --jobs $JOBS ExtractData.sh {} $JP2DIR 1
+ls *.zip | parallel --jobs $JOBS ExtractData.sh {} $JP2DIR $BYTILE
 
 
 

tools/L2AProductListToL3A.sh

+#!/bin/sh
+#Convert L2A Products to L3A using L2AtoL3C Process
+
+DATE=$1
+TILE=$2
+INDIR=$3
+OUTDIR=$4
+
+cd $INDIR
+for f in $(ls | egrep $DATE.{21}$TILE)
+	echo $f
+done

tools/L2ASCL_AreaProcessing.sh

@@ -8,6 +8,8 @@ BYTILE=${2:-0}
 
 #	exit
 #fi
+echo "Starting Process..."
+echo $USERDIR"findProducts.json"
 wkt=$(getJSONparameter.py $USERDIR"findProducts.json" wkt)
 RED='\033[0;31m'
 NC='\033[0m' # No Color
@@ -17,27 +19,39 @@ echo $wkt
 echo $USERDIR
 cd $USERDIR
 
+#0.- Create Shape File From WKT
+echo "${RED}Creating Shape file...${NC}"
+rm -r myshape
+wktToShape.py "$wkt" "myshape"
+
+
 #1.- Link L2A products 
-echo "Linking Products..."
+echo ${RED}"Linking Products..."${NC}
 if [ ! -d "L2A" ]; then
 	mkdir L2A
 fi
 cd L2A
 	rm *
 cd ..
-echo yes | findProducts.py $USERDIR"findProducts.json"
+yes yes | findProducts.py $USERDIR"findProducts.json"
 
 
 #2.- Extract Images
-echo "Extracting JP2 Images..."
+echo ${RED}"Extracting JP2 Images..."${NC}
 if [ ! -d "jp2" ]; then
 	mkdir jp2
 fi
-L2AProductListExtractData.sh $USERDIR"L2A/" $USERDIR"jp2/" 4
+if [ $BYTILE -ne "0" ]; then
+        echo "BY TILE"
+	L2AProductListExtractData.sh $USERDIR"L2A/" $USERDIR"jp2/" 4 1
 
+else
+        echo "BY DATE"
+	L2AProductListExtractData.sh $USERDIR"L2A/" $USERDIR"jp2/" 4 0
+fi
 
 #3.- Merge Images
-echo "Merging Images..."
+echo ${RED}"\nMerging Images..."${NC}
 if [ $BYTILE -ne "0" ]; then
 	echo "BY TILE"
 	cd $USERDIR"jp2/"
@@ -49,51 +63,92 @@ if [ $BYTILE -ne "0" ]; then
 		if [ ! -d "../out/"$i ]; then
 			mkdir "../out/"$i
 		fi
-		"mergeImagesByDirectory.sh" $USERDIR"jp2/"$i ../../../out/$i "$wkt"
+		mergeImagesByDirectory.sh $USERDIR"jp2/"$i ../../../out/$i "$wkt"
 
 	done
 else
 	echo "BY DATE"
-#	mergeImagesByDirectory.sh $USERDIR"jp2/" "$wtk" 4
+        cd $USERDIR"jp2/"
+        if [ ! -d "../out" ]; then
+                mkdir "../out"
+        fi
+        mergeImagesByDirectory.sh $USERDIR"jp2/" $USERDIR"out/" "$wkt" 4
+
 fi
 
+#4.- Mask raster with shape file
+echo ${RED}"\nApplying Mask..."${NC}
 
-#4.- Delete images with few data
-echo "Deleting Images..."
 if [ $BYTILE -ne "0" ]; then
         echo "BY TILE"
-        cd $USERDIR"jp2/"
+        cd $USERDIR"out/"
+        for d in $(ls -d */) ; do
+		cd $d
+	        if [ ! -d "mask" ]; then
+        	        mkdir mask
+        	fi
+
+	        for i in $(ls *.tif) ; do
+        	        if [  ! -e mask/$i ]; then
+                	        gdalwarp -cutline  $USERDIR"myshape/wkt.shp" -crop_to_cutline -dstalpha $i mask/$i
+	                else
+        	                echo "Passing " $i
+                	fi
+	        done
+		cd ..
+        done
+
+else
+        echo "BY DATE"
+	cd $USERDIR"out/"
+	if [ ! -d "mask" ]; then
+        	mkdir mask
+	fi
+
+        for i in $(ls *.tif) ; do
+		if [  ! -e mask/$i ]; then
+			gdalwarp -cutline ../myshape/wkt.shp -crop_to_cutline -dstalpha $i mask/$i
+		else
+			echo "Passing " $i
+		fi
+	done
+fi
+
+#5.- Delete images with few data
+echo ${RED}"\nDeleting Images..."${NC}
+
+if [ $BYTILE -ne "0" ]; then
+        echo "BY TILE"
+        cd $USERDIR"out/"
 	for i in $(ls -d */) ; do
-		cd ../out/$i
+		cd $i"mask"
 			echo $i
 	        if [ ! -d "SCL" ]; then
         	        mkdir SCL
         	fi
         	cp *SCL_60m.tif SCL
         	cd SCL
-	       	ls *.tif | parallel --jobs 4 imageMissingData.py {} 50
+	       	ls *.tif | parallel --jobs 4 imageMissingData.py {} $USERDIR"findproducts.json" 70
 	        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/$fileprefix"_TCI_60m.tif"
+                	cp ../$fileprefix"_TCI_10m.tif" ../TCI/$fileprefix"_TCI_10m.tif"
         	done
-		cd ../TCI
-		mogrify -format jpg -quality 100 *.tif
+	        cd $USERDIR"out/"
 
-	        cd $USERDIR"jp2/"
 	done
 else
         echo "BY DATE"
-	cd jp2/merge_out/
+        cd $USERDIR"out/mask/"
 	if [ ! -d "SCL" ]; then
         	mkdir SCL
 	fi
 	cp *SCL_60m.tif SCL
 	cd SCL
-	ls *.tif | parallel --jobs 4 imageMissingData.py {} 50
+	ls *.tif | parallel --jobs 4 imageMissingData.py {} $USERDIR"findproducts.json" 70
 
 	if [ ! -d "../TCI" ]; then
         	mkdir ../TCI
@@ -102,39 +157,162 @@ else
 	do
         	fileprefix=$(echo $scl | (cut -d"_" -f1))
 	        cp ../$fileprefix"_TCI_10m.tif" ../TCI/$fileprefix"_TCI_10m.tif"
+                cd ../TCI
 	done
-	cd ../TCI
-	echo "mogrify -format jpg -quality 100 *.tif"
-	mogrify -format jpg -quality 100 *.tif
 fi
+#6.-Creating Thumbnails
+echo ${RED}"Creating Thumbnails"${NC}
+if [ $BYTILE -ne "0" ]; then
+        echo "BY TILE"
+        cd $USERDIR"out/"
+	for i in $(ls -d */) ; do
+                cd $i"mask"
+		if [ ! -d "SCL/thumbnails" ]; then
+			mkdir SCL/thumbnails
+	        fi
+        	if [ ! -d "TCI/thumbnails" ]; then
+                	mkdir TCI/thumbnails
+	        fi
+	        cd TCI
+        	mogrify -format jpg -quality 100 *.tif
+	        mogrify -path ./thumbnails -resize 10%  *.jpg
+		cd $USERDIR"out/"
+	done
+else
+        echo "BY DATE"
+        cd $USERDIR"out/mask/"
+        if [ ! -d "SCL/thumbnails" ]; then
+                mkdir SCL/thumbnails
+        fi
+        if [ ! -d "TCI/thumbnails" ]; then
+                mkdir TCI/thumbnails
+        fi
+
+	cd TCI
+        mogrify -format jpg -quality 100 *.tif
+	mogrify -path ./thumbnails -resize 10%  *.jpg
+
+fi
+
+
+#7.-Extract SCL information
+echo ${RED}"Extracting SCL information..."${NC}
 
-#5.-Extract SCL information
-echo "Extracting SCL information..."
-cd $USERDIR"jp2/"
 if [ $BYTILE -ne "0" ]; then
         echo "BY TILE"
+	cd $USERDIR"out/"
+
         for i in $(ls -d */) ; do
-	        cd ../out/$i"SCL"
+	        cd ../out/$i"mask/SCL"
 	        if [ ! -d "json" ]; then
         	        mkdir json
 	        fi
-        	SCLimageListToJSON.sh $USERDIR"out/"$i"SCL/" $USERDIR"findProducts.json" 6
+        	SCLimageListToJSON.sh $USERDIR"out/"$i"mask/SCL/" $USERDIR"findProducts.json" 6
 	        mv *.json json
         	cd json
 		tile=$(echo $i | cut -d "/" -f1)
-	        mergeL2ASCL_JSON.py $USERDIR"out/"$i"SCL/json/" > $USERDIR$tile"_sclData.json"
-		cd $USERDIR"jp2/"
+	        mergeL2ASCL_JSON.py $USERDIR"out/"$i"mask/SCL/json/" > $USERDIR$tile"_sclData.json"
+		echo $tile
+		echo "_sclData.json"
+		cd $USERDIR"out/"
 	done
 else
         echo "BY DATE"
-	cd $USERDIR/jp2/merge_out/SCL
+	cd $USERDIR"out/mask/SCL/"
 	if [ ! -d "json" ]; then
         	mkdir json
 	fi
-	SCLimageListToJSON.sh $USERDIR"jp2/merge_out/SCL/" $USERDIR"findProducts.json" 6
+	SCLimageListToJSON.sh $USERDIR"out/mask/SCL/" $USERDIR"findProducts.json" 6
 	mv *.json json
 	cd json
-	mergeL2ASCL_JSON.py $USERDIR"jp2/merge_out/SCL/json/" > $USERDIR"scl_data.json"
+	mergeL2ASCL_JSON.py $USERDIR"out/mask/SCL/json/" > $USERDIR"scl_data.json"
 fi
+
+#8.- Split SCL
+echo ${RED}"Spliting SCL image..."${NC}
+if [ $BYTILE -ne "0" ]; then
+        echo "BY TILE"
+
+else
+        echo "BY DATE"
+        cd $USERDIR"out/mask/SCL/"
+        if [ ! -d "split" ]; then
+		mkdir split
+	fi
+
+	
+        for f in $(ls  *.tif) ; do
+		echo $f
+		splitSCL.py $f split/
+	done
+fi
+
+#9.-Create Tiles
+echo ${RED}"Creating Tiles..."${NC}
+if [ $BYTILE -ne "0" ]; then
+        echo "BY TILE"
+        cd $USERDIR"out/"
+        for d in $(ls -d */) ; do
+		cd $d"mask/TCI/"
+
+        	if [ ! -d "tiles" ]; then
+                	mkdir tiles
+	        fi
+
+	        for i in $(ls  *.tif) ;
+        	do
+                	cd tiles
+	                gdal2tiles.py ../$i
+        	        cd ..
+	        done
+        	cd $USERDIR"out/"
+		cd $d"mask/SCL/"
+                if [ ! -d "tiles" ]; then
+                        mkdir tiles
+                fi
+
+                for i in $(ls  *.tif) ;
+                do
+                        cd tiles
+                        gdal2tiles.py ../$i
+                        cd ..
+                done
+                cd $USERDIR"out/"
+
+        done
+else
+        echo "BY DATE"
+        cd $USERDIR"out/mask/TCI/"
+        if [ ! -d "tiles" ]; then
+                mkdir tiles
+        fi
+	for i in $(ls  *.tif) ;
+	do
+		cd tiles
+		gdal2tiles.py --zoom="10-15" ../$i
+		cd ..
+	done
+
+        cd $USERDIR"out/mask/SCL/split/"
+        if [ ! -d "tiles" ]; then
+                mkdir tiles
+        fi
+        for i in $(ls  *.tif) ;
+        do
+                cd tiles
+                gdal2tiles.py --zoom="10-15" ../$i
+                cd ..
+        done
+
+	
+fi
+
+exit
+#9.-Create ZIP file
+echo "Compresing Files in " $USERDIR "..."
+cd $USERDIR
+zip -r myzip . --exclude *.json --exclude *.zip --exclude *thumbnails* --exclude *.tif -x ./jp2\* ./L2A\* \*\*/\*/SCL/\*^C
+echo "END"
+
 #mv *SCL_60m.tif json
 #cd json

tools/L2AtoL3AbyDateTile.sh

+#!/bin/sh
+#Convert L2A Products to L3A using L2AProductListToL3A Process
+
+DATE=$1
+TILE=$2
+INDIR=$3
+OUTDIR=$4
+
+cd $INDIR
+for f in $(ls | egrep $DATE.{21}$TILE) ; do
+	TMPDIR=MSIL3A_$DATE"_"$TILE"/"
+	cd $OUTDIR
+
+        if [ ! -d $TMPDIR"L2A/TCI/" ]; then
+                mkdir -p $TMPDIR"L2A/TCI/"
+        fi
+
+        if [ ! -d $TMPDIR"L2A/SCL/" ]; then
+                mkdir -p $TMPDIR"L2A/SCL/"
+        fi
+
+
+	JP2DIR=$TMPDIR"GRANULE/L3A_"$TILE"_"$DATE"/IMG_DATA/R60m/" 
+        if [ ! -d $JP2DIR ]; then
+                mkdir -p $JP2DIR
+        fi
+
+	cd .. 
+	ln -s $INDIR$f $OUTDIR$TMPDIR"L2A/"$f
+	unzip -n -j $OUTDIR$TMPDIR"L2A/"$f *TCI_60m.jp2 -d $OUTDIR$TMPDIR"L2A/TCI/"
+        unzip -n -j $OUTDIR$TMPDIR"L2A/"$f *SCL_60m.jp2 -d $OUTDIR$TMPDIR"L2A/SCL/"
+
+
+	echo $f
+done
+
+
+cd $OUTDIR$TMPDIR"L2A/"
+L2AtoL3A.py $OUTDIR$TMPDIR"L2A/"

tools/mergeImages.sh

 #!/bin/sh
-INDIR=$1	#Output filename
-OUTDIR=$2	#Output filename
-POLYGON=$3	#Crop Window
+INDIR=$1	#Directory with images to merge
+OUTDIR=$2	#Output directory
+POLYGON=$3	#Crop Window (minX, maxX, minY, maxY)
 DIRNAME=$(echo $INDIR | cut -d"/" -f1)
 echo "INDIR:" $INDIR
 echo "OUTDIR:" $OUTDIR
@@ -22,7 +22,7 @@ echo $DIRNAME
 for f in $(ls);  do echo ${f}; done;
 #exit
 ##------------------------------------------------------------------------------
-MERGEDIMAGE=$DIRNAME"_TCI_60m_merged.tif"
+MERGEDIMAGE=$DIRNAME"_TCI_10m_merged.tif"
 if [  ! -e $MERGEDIMAGE  ]; then
 	echo "gdal_merge.py -o "$MERGEDIMAGE $(ls *TCI_10m.jp2)
 	gdal_merge.py -o $MERGEDIMAGE $(ls *TCI_10m.jp2)
@@ -30,7 +30,7 @@ else
 	echo PASSING $MERGEDIMAGE FOUND
 fi
 
-CROPEDIMAGE=$OUTDIR$DIRNAME"_TCI_60m.tif"
+CROPEDIMAGE=$OUTDIR$DIRNAME"_TCI_10m.tif"
 if [  ! -e $CROPEDIMAGE  ]; then
 	gdal_translate -projwin $BOX -projwin_srs WGS84 -ot Byte -of GTiff $MERGEDIMAGE $CROPEDIMAGE
 else

tools/mergeImagesByDirectory.sh

@@ -7,6 +7,8 @@ DIRNAME=$(echo $JP2DIR | cut -d"/" -f1)
 #echo "POLYGON"
 #echo $POLYGON
 BOX=$(polygonToBox.py "$POLYGON")
+echo "Polygon BOX"
+echo $BOX
 if [ "$#" -le 1 ]; then
 	echo "Usage " $0 " <Parent Directory with subdirectories> <POLYGON> [jobs]" 
 	exit