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Commit 975095e6 authored by Mario Chirinos's avatar Mario Chirinos
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sedema update

parent 369dd3c5
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Showing with 850 additions and 27 deletions
scripts/GI_runAnalysis.sh deleted 100755 → 0
View file @ 369dd3c5
#!/bin/sh
CSV=$1
CFG=$2
if [ ! -d "data" ]; then
mkdir data
fi
cd data
GI_createDirectories.py ../$CSV ../$CFG
for d in $(ls -d */) ; do
echo "PROCESSING " $d ...
if [ ! -f $(pwd)/"$d/scl_data.json" ]; then
GI_L2ASCL_AreaProcessing.sh $(pwd)/"$d" 0
else
echo "PASSING " $d
fi
done
scripts/GI_L2ASCL_AreaProcessing.sh → scripts/SEDEMA/GI_L2ASCL_AreaProcessing.sh
View file @ 975095e6
...@@ -19,219 +19,236 @@ echo $wkt ...@@ -19,219 +19,236 @@ echo $wkt
echo $USERDIR echo $USERDIR
cd $USERDIR cd $USERDIR
#0.- Create Shape File From WKT ##0.- Create Shape File From WKT
echo "${RED}Creating Shape file...${NC}" #echo "${RED}Creating Shape file...${NC}"
if [ -d "myshape" ]; then #if [ -d "myshape" ]; then
rm -r myshape # rm -r myshape
fi #fi
wktToShape.py $USERDIR"findProducts.json" "myshape"
#wktToShape.py $USERDIR"findProducts.json" "myshape"
#1.- Link L2A products
echo ${RED}"Linking Products..."${NC}
if [ ! -d "L2A" ]; then
mkdir L2A
fi
cd L2A
rm *
cd ..
yes yes | findProducts.py $USERDIR"findProducts.json"
##1.- Link L2A products
#echo ${RED}"Linking Products..."${NC}
#if [ ! -d "L2A" ]; then
# mkdir L2A
#fi
#cd L2A
# rm *
#cd ..
#yes yes | findProducts.py $USERDIR"findProducts.json"
#2.- Extract Images
echo ${RED}"Extracting JP2 Images..."${NC}
if [ ! -d "jp2" ]; then
mkdir jp2
fi
if [ $BYTILE -ne "0" ]; then
echo "BY TILE"
L2AProductListExtractData.sh $USERDIR"L2A/" $USERDIR"jp2/" 4 1
else ##2.- Extract Images
echo "BY DATE" #echo ${RED}"Extracting JP2 Images..."${NC}
L2AProductListExtractData.sh $USERDIR"L2A/" $USERDIR"jp2/" 4 0 #if [ ! -d "jp2" ]; then
fi # mkdir jp2
#fi
#if [ $BYTILE -ne "0" ]; then
# echo "BY TILE"
# L2AProductListExtractData.sh $USERDIR"L2A/" $USERDIR"jp2/" 4 1
#3.- Merge Images #else
echo ${RED}"\nMerging Images..."${NC} # echo "BY DATE"
if [ $BYTILE -ne "0" ]; then # L2AProductListExtractData.sh $USERDIR"L2A/" $USERDIR"jp2/" 4 0
echo "BY TILE" #fi
cd $USERDIR"jp2/"
if [ ! -d "../out" ]; then
mkdir "../out"
fi
# ls -d */ | parallel -q --jobs 1 mergeImagesByDirectory.sh $USERDIR"jp2/"{} "$wtk" 4
for i in $(ls -d */) ; do
if [ ! -d "../out/"$i ]; then
mkdir "../out/"$i
fi
mergeImagesByDirectory.sh $USERDIR"jp2/"$i ../../../out/$i "$wkt"
done ##3.- Merge Images
else #echo ${RED}"\nMerging Images..."${NC}
echo "BY DATE" #if [ $BYTILE -ne "0" ]; then
cd $USERDIR"jp2/" # echo "BY TILE"
if [ ! -d "../out" ]; then # cd $USERDIR"jp2/"
mkdir "../out" # if [ ! -d "../out" ]; then
fi # mkdir "../out"
mergeImagesByDirectory.sh $USERDIR"jp2/" $USERDIR"out/" "$wkt" 4 # fi
## ls -d */ | parallel -q --jobs 1 mergeImagesByDirectory.sh $USERDIR"jp2/"{} "$wtk" 4
# for i in $(ls -d */) ; do
# if [ ! -d "../out/"$i ]; then
# mkdir "../out/"$i
# fi
# mergeImagesByDirectory.sh $USERDIR"jp2/"$i ../../../out/$i "$wkt"
fi # done
#else
# echo "BY DATE"
# cd $USERDIR"jp2/"
# if [ ! -d "../out" ]; then
# mkdir "../out"
# fi
# mergeImagesByDirectory.sh $USERDIR"jp2/" $USERDIR"out/" "$wkt" 4
#4.- Mask raster with shape file #fi
echo ${RED}"\nApplying Mask..."${NC}
if [ $BYTILE -ne "0" ]; then ##4.- Mask raster with shape file
echo "BY TILE" #echo ${RED}"\nApplying Mask..."${NC}
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 [ $BYTILE -ne "0" ]; then
if [ ! -e mask/$i ]; then # echo "BY TILE"
gdalwarp -cutline $USERDIR"myshape/wkt.shp" -crop_to_cutline -dstalpha $i mask/$i # cd $USERDIR"out/"
else # for d in $(ls -d */) ; do
echo "Passing " $i # cd $d
fi # if [ ! -d "mask" ]; then
done # mkdir mask
cd .. # fi
done
else # for i in $(ls *.tif) ; do
echo "BY DATE" # if [ ! -e mask/$i ]; then
cd $USERDIR"out/" # gdalwarp -cutline $USERDIR"myshape/wkt.shp" -crop_to_cutline -dstalpha $i mask/$i
if [ ! -d "mask" ]; then # else
mkdir mask # echo "Passing " $i
fi # fi
# done
# cd ..
# done
for i in $(ls *.tif) ; do #else
if [ ! -e mask/$i ]; then # echo "BY DATE"
gdalwarp -cutline ../myshape/wkt.shp -crop_to_cutline -dstalpha $i mask/$i # cd $USERDIR"out/"
else # if [ ! -d "mask" ]; then
echo "Passing " $i # mkdir mask
fi # fi
done
fi
#5.- Delete images with few data # for i in $(ls *.tif) ; do
echo ${RED}"\nDeleting Images..."${NC} # if [ ! -e mask/$i ]; then
# gdalwarp -cutline ../myshape/wkt.shp -crop_to_cutline -dstalpha $i mask/$i
# else
# echo "Passing " $i
# fi
# done
#fi
if [ $BYTILE -ne "0" ]; then ##5.- Delete images with few data
echo "BY TILE" #echo ${RED}"\nDeleting Images..."${NC}
cd $USERDIR"out/"
for i in $(ls -d */) ; do
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 {} $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_10m.tif" ../TCI/$fileprefix"_TCI_10m.tif"
done
cd $USERDIR"out/"
done
else
echo "BY DATE"
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 {} $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_10m.tif" ../TCI/$fileprefix"_TCI_10m.tif"
cd ../TCI
done
fi
#6.-Creating Thumbnails
#echo ${RED}"Creating Thumbnails"${NC}
#if [ $BYTILE -ne "0" ]; then #if [ $BYTILE -ne "0" ]; then
# echo "BY TILE" # echo "BY TILE"
# cd $USERDIR"out/" # cd $USERDIR"out/"
# for i in $(ls -d */) ; do # for i in $(ls -d */) ; do
# cd $i"mask" # cd $i"mask"
# if [ ! -d "SCL/thumbnails" ]; then # echo $i
# mkdir SCL/thumbnails # if [ ! -d "SCL" ]; then
# mkdir SCL
# fi # fi
# if [ ! -d "TCI/thumbnails" ]; then # cp *SCL_60m.tif SCL
# mkdir TCI/thumbnails # cd SCL
# ls *.tif | parallel --jobs 4 imageMissingData.py {} $USERDIR"findproducts.json" 70
# if [ ! -d "../TCI" ]; then
# mkdir ../TCI
# fi # fi
# cd TCI # for scl in $(ls *.tif)
# mogrify -format jpg -quality 100 *.tif # do
# mogrify -path ./thumbnails -resize 800x600! *.jpg # fileprefix=$(echo $scl | (cut -d"_" -f1))
# cd thumbnails # cp ../$fileprefix"_TCI_10m.tif" ../TCI/$fileprefix"_TCI_10m.tif"
# ffmpeg -pattern_type glob -i "*.jpg" -r 1 -vcodec libx264 $USERDIR"video.mp4" # done
# cd $USERDIR"out/" # cd $USERDIR"out/"
# done # done
#else #else
# echo "BY DATE" # echo "BY DATE"
# cd $USERDIR"out/mask/" # cd $USERDIR"out/mask/"
# if [ ! -d "SCL/thumbnails" ]; then # if [ ! -d "SCL" ]; then
# mkdir SCL/thumbnails # mkdir SCL
# fi
# if [ ! -d "TCI/thumbnails" ]; then
# mkdir TCI/thumbnails
# fi # fi
# cp *SCL_60m.tif SCL
# cd SCL
# ls *.tif | parallel --jobs 4 imageMissingData.py {} $USERDIR"findProducts.json" 70
# cd TCI # if [ ! -d "../TCI" ]; then
# mogrify -format jpg -quality 100 *.tif # mkdir ../TCI
# mogrify -path ./thumbnails -resize 10% *.jpg # fi
# for scl in $(ls *.tif)
# do
# fileprefix=$(echo $scl | (cut -d"_" -f1))
# cp ../$fileprefix"_TCI_10m.tif" ../TCI/$fileprefix"_TCI_10m.tif"
# cd ../TCI
# done
#fi #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 800x600! *.jpg
## cd thumbnails
## ffmpeg -pattern_type glob -i "*.jpg" -r 1 -vcodec libx264 $USERDIR"video.mp4"
## 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}
#if [ $BYTILE -ne "0" ]; then
# echo "BY TILE"
# cd $USERDIR"out/"
#7.-Extract SCL information # for i in $(ls -d */) ; do
echo ${RED}"Extracting SCL information..."${NC} # cd ../out/$i"mask/SCL"
# if [ ! -d "json" ]; then
# mkdir json
# fi
# 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"mask/SCL/json/" > $USERDIR$tile"_sclData.json"
# echo $tile
# echo "_sclData.json"
# cd $USERDIR"out/"
# done
#else
# echo "BY DATE"
# cd $USERDIR"out/mask/SCL/"
# if [ ! -d "json" ]; then
# mkdir json
# fi
# GI_SCLimageListToJSON.sh $USERDIR"out/mask/SCL/" $USERDIR"findProducts.json" 6
# mv *.json json
# cd json
# mergeL2ASCL_JSON.py $USERDIR"out/mask/SCL/json/" > $USERDIR"scl_data.json"
#fi
#8.-Extract SCL morphology
echo ${RED}"Extracting SCL morphology..."${NC}
if [ $BYTILE -ne "0" ]; then if [ $BYTILE -ne "0" ]; then
echo "BY TILE" echo "BY TILE"
cd $USERDIR"out/"
for i in $(ls -d */) ; do
cd ../out/$i"mask/SCL"
if [ ! -d "json" ]; then
mkdir json
fi
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"mask/SCL/json/" > $USERDIR$tile"_sclData.json"
echo $tile
echo "_sclData.json"
cd $USERDIR"out/"
done
else else
echo "BY DATE" echo "BY DATE"
cd $USERDIR"out/mask/SCL/" cd $USERDIR"out/mask/SCL/"
if [ ! -d "json" ]; then if [ ! -d "morph" ]; then
mkdir json mkdir morph
fi fi
SCLimageListToJSON.sh $USERDIR"out/mask/SCL/" $USERDIR"findProducts.json" 6 GI_SCLmorphImageListToJSON.sh $USERDIR"out/mask/SCL/" $USERDIR"findProducts.json" 6
mv *.json json mv *.json morph
cd json cd morph
mergeL2ASCL_JSON.py $USERDIR"out/mask/SCL/json/" > $USERDIR"scl_data.json" mergeL2ASCL_JSON.py $USERDIR"out/mask/SCL/morph/" > $USERDIR"scl_morph.json"
fi fi
exit exit
##8.- Split SCL ##8.- Split SCL
......
scripts/SEDEMA/GI_L2ASCLtoJSON.py 0 → 100755
View file @ 975095e6
#!/usr/bin/python
# -*- coding: utf-8 -*-
import osgeo.ogr as ogr
import osgeo.osr as osr
import numpy as np
import gdal
import sys
import os
import json
from collections import Counter
#from collections import OrderedDict
########### 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, wktsub):
'''
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)
data1 = np.bitwise_and(data, rasterWkt.getPolygonArray(inputImage, wkt))
count1 = Counter([])
for r in data:
count1 = count1+ Counter(classMap(r))
sclDict1 = {str(k):v for k,v in dict(count1).items()}
if wktsub!="":
data2 = np.bitwise_and(data1, np.invert(rasterWkt.getPolygonArray(inputImage, wktsub)))
count2 = Counter([])
for r in data2:
count2 = count2 + Counter(classMap(r))
sclDict2 = {str(k):v for k,v in dict(count2).items()}
else:
sclDict2=sclDict1
return {"areaTotal":sclDict1, "areaNoConservacion":sclDict2}
#-------------------------------------------------------------------------------
def main(argv):
if len(sys.argv) != 3:
print("Usage: " + argv[0] + "<JSON SCL> <JSON Cfg>")
else:
jsonFile=open(argv[2]).read()
cfg = json.loads(jsonFile)
dataDict = L2ASCLtoDict(argv[1], cfg['wkt'], cfg["wkt2"])
print(json.dumps(dataDict, sort_keys=True))
#-------------------------------------------------------------------------------
if __name__ == "__main__":
main(sys.argv)
scripts/SEDEMA/GI_SCLimageListToJSON.sh 0 → 100755
View file @ 975095e6
#!/bin/sh
DIR=$1
CGF=$2
JOBS=${3:-1}
cd $DIR
ls *.tif | parallel --jobs $JOBS 'GI_L2ASCLtoJSON.py '{} $2 ' > $(echo '{}' | cut -d"." -f1).json'
scripts/SEDEMA/GI_SCLmorphImageListToJSON.sh 0 → 100755
View file @ 975095e6
#!/bin/sh
DIR=$1
CGF=$2
JOBS=${3:-1}
cd $DIR
ls *.tif | parallel --jobs $JOBS 'GI_getComponentsMorphology.py '{} $2 ' > $(echo '{}' | cut -d"." -f1).json'
scripts/GI_createDirectories.py → scripts/SEDEMA/GI_createDirectories.py
View file @ 975095e6
...@@ -14,16 +14,17 @@ def createDirectories(datafile, cfgfile, level1="CVE_ENT", level2="CVE_MUN"): ...@@ -14,16 +14,17 @@ def createDirectories(datafile, cfgfile, level1="CVE_ENT", level2="CVE_MUN"):
data = csv.DictReader(csvfile, delimiter=',') data = csv.DictReader(csvfile, delimiter=',')
for row in data: for row in data:
mun = row[level1] mun = row[level2]
ent = row[level2] ent = row[level1]
dirname = ent+mun dirname = ent.zfill(2)+"-"+mun.zfill(3)
print(ent) print(ent)
# for k in cfg.keys(): # for k in cfg.keys():
# p[k]=cfg[k] # p[k]=cfg[k]
print(os.getcwd()) print(os.getcwd())
cfg["projectDir"]=os.getcwd()+"/"+dirname+"/" cfg["projectDir"]=os.getcwd()+"/"+dirname+"/"
cfg["endDate"]=datetime.datetime.now().strftime("%Y%m%d") # cfg["endDate"]=datetime.datetime.now().strftime("%Y%m%d")
cfg["wkt"]=row["WKT"] cfg["wkt"]=row["WKT"]
cfg["wkt2"]=row["WKT2"]
if not os.path.exists(dirname): if not os.path.exists(dirname):
os.mkdir(dirname) os.mkdir(dirname)
with open(dirname+'/findProducts.json', 'w') as outfile: with open(dirname+'/findProducts.json', 'w') as outfile:
...@@ -31,11 +32,14 @@ def createDirectories(datafile, cfgfile, level1="CVE_ENT", level2="CVE_MUN"): ...@@ -31,11 +32,14 @@ def createDirectories(datafile, cfgfile, level1="CVE_ENT", level2="CVE_MUN"):
#=============================================================================== #===============================================================================
def main(argv): def main(argv):
if len(sys.argv) != 3: if len(sys.argv) != 3 and len(sys.argv) != 5:
print(len(sys.argv)) print(len(sys.argv))
print ("Usage: "+argv[0] + " <csv> <cfg>") print ("Usage: "+argv[0] + " <csv> <cfg>")
else: elif(len(sys.argv) == 3 ):
createDirectories(argv[1], argv[2]) createDirectories(argv[1], argv[2])
else:
createDirectories(argv[1], argv[2], argv[3], argv[4])
if __name__ == "__main__": if __name__ == "__main__":
......
scripts/SEDEMA/GI_getComponentsMorphology.py 0 → 100755
View file @ 975095e6
#!/usr/bin/python3
# -*- coding: utf-8 -*-
import sys
import os
import json
import csv
import gdal
import numpy as np
import osgeo.ogr as ogr, osr
sys.path.append("/home/geoint/GeoSentinel")
from geosentinel import rasterWkt
from skimage import measure
AREAm = 60*60 #m²
AREAkm = AREAm/1000000#km²
DISTANCE = 60#m
#===============================================================================
def getComponentsMorphology(image_filename, wkt, wktsub):
inputImage = gdal.Open(image_filename)
rows, cols, geotransform = inputImage.RasterYSize, inputImage.RasterXSize, inputImage.GetGeoTransform()
data = inputImage.GetRasterBand(1).ReadAsArray(0,0,cols,rows)
data1 = np.bitwise_and(data, rasterWkt.getPolygonArray(inputImage, wkt))
if wktsub!="":
data2 = np.bitwise_and(data1, np.invert(rasterWkt.getPolygonArray(inputImage, wktsub)))
else:
data2 = data1
geometry = ogr.CreateGeometryFromWkt(wkt)
inSpatialRef = osr.SpatialReference()
inSpatialRef.ImportFromEPSG(4326)
outSpatialRef = osr.SpatialReference()
outSpatialRef.ImportFromEPSG(32514)
coordTrans = osr.CoordinateTransformation(inSpatialRef, outSpatialRef)
geometry.Transform(coordTrans)
wktArea = geometry.GetArea()
classDict={}
for i in range(12):
myDict = dict()
dataC = data2==i
myDict["area_tot"]=wktArea/1000000
myDict["area_verde_tot"] = np.count_nonzero(dataC)
if myDict["area_verde_tot"]==0.0:
continue
myDict["area_verde_tot"]=myDict["area_verde_tot"]*AREAkm
components_labels = measure.label(dataC)
myDict["nAreas"] = int( np.max(components_labels))
properties = measure.regionprops(components_labels)
myDict["gf1"] = 1 / (myDict["area_verde_tot"]/myDict["nAreas"])
# myDict["gf2"]
myDict["gdv"]=myDict["area_verde_tot"]/myDict["area_tot"]
myDict["vp"]=myDict["area_verde_tot"]
myDict["tp"]=myDict["area_verde_tot"]/myDict["nAreas"]
myDict["fp"]=sum([ p["perimeter"]/p["area"] for p in properties])/myDict["nAreas"]
myDict["alp"]=sum([ 0 if p["minor_axis_length"]==0 else p["major_axis_length"]/p["minor_axis_length"] for p in properties])/myDict["nAreas"]
classDict[str(i)]=myDict
# print(myDict)
# print(classDict)
return classDict
#===============================================================================
def main(argv):
if len(sys.argv) != 3:
print (argv[0] + " <image.tif> <cfg.json>")
else:
with open(argv[2]) as jsonFile:
cfg = json.load(jsonFile)
dataDict = getComponentsMorphology(argv[1], cfg["wkt"], cfg["wkt2"])
print(json.dumps(dataDict, sort_keys=True))
if __name__ == "__main__":
main(sys.argv)
scripts/SEDEMA/GI_getComponentsMorphology_csv.py 0 → 100755
View file @ 975095e6
#!/usr/bin/python3
# -*- coding: utf-8 -*-
import sys
import os
import json
import csv
import gdal
import numpy as np
import osgeo.ogr as ogr, osr
sys.path.append("/home/mchc/git/GeoSentinel")
from geosentinel import rasterWkt
from skimage import measure
AREAm = 60*60 #m²
AREAkm = AREAm/1000000#km²
DISTANCE = 60#m
#===============================================================================
def getComponentsMorphology(image_filename, wktlist):
inputImage = gdal.Open(image_filename)
rows, cols, geotransform = inputImage.RasterYSize, inputImage.RasterXSize, inputImage.GetGeoTransform()
data = inputImage.GetRasterBand(1).ReadAsArray(0,0,cols,rows)
areaList = []
for key, value in wktlist.items():
print(key)
dataMask = np.bitwise_and(data, rasterWkt.getPolygonArray(inputImage, value))
geometry = ogr.CreateGeometryFromWkt(value)
inSpatialRef = osr.SpatialReference()
inSpatialRef.ImportFromEPSG(4326)
outSpatialRef = osr.SpatialReference()
outSpatialRef.ImportFromEPSG(32514)
coordTrans = osr.CoordinateTransformation(inSpatialRef, outSpatialRef)
geometry.Transform(coordTrans)
wktArea = geometry.GetArea()
print(key, wktArea/1000000)
myDict = dict()
myDict["clave"] = key
dataC = dataMask!=0#==i
myDict["area_tot"]=wktArea/1000000
myDict["area_verde_tot"] = np.count_nonzero(dataC)
if myDict["area_verde_tot"]==0.0:
continue
myDict["area_verde_tot"]=myDict["area_verde_tot"]*AREAkm
components_labels = measure.label(dataC)
myDict["nAreas"] = int( np.max(components_labels))
properties = measure.regionprops(components_labels)
myDict["gf1"] = 1 / (myDict["area_verde_tot"]/myDict["nAreas"])
## myDict["gf2"]
myDict["gdv"]=myDict["area_verde_tot"]/myDict["area_tot"]
myDict["vp"]=myDict["area_verde_tot"]
myDict["tp"]=myDict["area_verde_tot"]/myDict["nAreas"]
myDict["fp"]=sum([ p["perimeter"]/p["area"] for p in properties])/myDict["nAreas"]
## print("axis", [ p["minor_axis_length"] for p in properties])
myDict["alp"]=sum([ 0 if p["minor_axis_length"]==0 else p["major_axis_length"]/p["minor_axis_length"] for p in properties])/myDict["nAreas"]
# classDict[str(i)]=myDict
areaList.append(myDict)
print(myDict)
with open('morphology.csv', 'w', newline='') as csvfile:
writer = csv.DictWriter(csvfile, fieldnames=areaList[0].keys())
writer.writeheader()
for i in areaList:
writer.writerow(i)
## print(classDict)
# return classDict
#===============================================================================
def main(argv):
if len(sys.argv) != 3:
print ("Usage: " + argv[0] + " <reference_image.tif> <wkt_list.csv>")
else:
with open(argv[2]) as csvfile:
reader = csv.DictReader(csvfile)
areasDic = { row["CVEGEO"]:row["WKT"] for row in reader}
dataDict = getComponentsMorphology(argv[1], areasDic)
if __name__ == "__main__":
main(sys.argv)
scripts/GI_getMinMax.py → scripts/SEDEMA/GI_getMinMax.py
View file @ 975095e6
...@@ -8,32 +8,58 @@ import csv ...@@ -8,32 +8,58 @@ import csv
def getMinMax(clase): def getMinMax(clase):
polylist = [] polylist = []
morphList = []
for item in os.listdir("."): for item in os.listdir("."):
if os.path.isdir(item): if os.path.isdir(item):
print(item) print(item)
with open(os.getcwd()+"/"+item+"/scl_data.json") as json_file: with open(os.getcwd()+"/"+item+"/scl_data.json") as json_file:
dataSCL = json.load(json_file) dataSCL = json.load(json_file)
with open(os.getcwd()+"/"+item+"/scl_morph.json") as json_file:
dataMorph = json.load(json_file)
with open(os.getcwd()+"/"+item+"/findProducts.json") as json_file: with open(os.getcwd()+"/"+item+"/findProducts.json") as json_file:
dataWKT = json.load(json_file) dataWKT = json.load(json_file)
wkt = dataWKT["wkt"] wkt = dataWKT["wkt"]
values = []
for k, v in dataSCL.items():
values.append(v[clase])
minval = min(values)
maxval = max(values)
polylist.append({"clave": item, "wkt":wkt, "min":minval, "max":maxval}) polyDict = {"clave": item, "wkt":wkt}
cDict = {k:v["areaTotal"][clase] for k, v in dataSCL.items() }
maxkey = max(cDict, key=cDict.get )
maxval = dataSCL[maxkey]["areaTotal"][clase]
polyDict["areaTotal"] = maxval
cDict = {k:v["areaNoConservacion"][clase] for k, v in dataSCL.items() if clase in v["areaNoConservacion"]}
if len(cDict) >0 and clase in dataSCL[maxkey]["areaNoConservacion"]:
maxkey = max(cDict, key=cDict.get )
maxval = dataSCL[maxkey]["areaNoConservacion"][clase]
else:
maxval=0
polyDict["areaNoConservacion"] = maxval
polylist.append(polyDict)
tmpDict = dataMorph[maxkey][clase]
tmpDict["wkt"] = wkt
tmpDict["clave"]=item
morphList.append(dataMorph[maxkey][clase])
with open('minmax_'+clase+'.csv', 'w') as outfile: with open('minmax_'+clase+'.csv', 'w') as outfile:
writer = csv.DictWriter(outfile, fieldnames=polylist[0].keys()) writer = csv.DictWriter(outfile, fieldnames=polylist[0].keys())
writer.writeheader() writer.writeheader()
for item in polylist: for item in polylist:
writer.writerow(item) writer.writerow(item)
# json.dump(polylist, outfile)
with open('morphology_'+clase+'.csv', 'w') as outfile:
writer = csv.DictWriter(outfile, fieldnames=morphList[0].keys())
writer.writeheader()
for item in morphList:
writer.writerow(item)
#=============================================================================== #===============================================================================
def main(argv): def main(argv):
......
scripts/SEDEMA/GI_rasterShp.py 0 → 100755
View file @ 975095e6
#!/usr/bin/python
# -*- coding: utf-8 -*-
#"POLYGON((-89.65513229370117 21.048938357786966,-89.62852478027342 21.047816903874505,-89.6261215209961 21.03339745836918,-89.6465492248535 21.022822311328852,-89.65873718261717 21.039325621609095,-89.65513229370117 21.048938357786966))"
import osgeo.ogr as ogr
import osgeo.osr as osr
import numpy as np
import gdal
import sys
from collections import Counter
#-------------------------------------------------------------------------------
def getPolygonArray(image, shp_filename):
rows = image.RasterYSize
cols = image.RasterXSize
geotransform = image.GetGeoTransform()
projection = image.GetProjection()
sr = osr.SpatialReference(wkt=projection)
sr4326 = osr.SpatialReference()
sr4326.ImportFromEPSG(4326)
driverMEM = gdal.GetDriverByName('MEM')
driverMemory = ogr.GetDriverByName('Memory')
driverTiff = gdal.GetDriverByName('GTiff')
driverShape = ogr.GetDriverByName("ESRI Shapefile")
#RASTER
target_ds = driverMEM.Create('raster.tif', cols, rows, 1, gdal.GDT_Byte) #MEM
target_ds.GetRasterBand(1).SetNoDataValue(0)
target_ds.GetRasterBand(1).WriteArray(np.zeros((rows, cols), dtype=np.uint8))
target_ds.SetProjection(projection)
target_ds.SetGeoTransform(geotransform)
target_ds.GetRasterBand(1).FlushCache()
#VECTOR
dataSource = driverShape.Open(shp_filename, 0)
# Check to see if shapefile is found.
if dataSource is None:
print('Could not open', shp_filename)
else:
print('Opened %s', shp_filename)
layer = dataSource.GetLayer()
featureCount = layer.GetFeatureCount()
print("Number of features in", shp_filename, featureCount)
# rast_ogr_ds = driverMemory.CreateDataSource( 'myshape.shp' )
# rast_mem_lyr = rast_ogr_ds.CreateLayer( 'POLYGON', sr4326, ogr.wkbPolygon)
# feat = ogr.Feature( rast_mem_lyr.GetLayerDefn() )
# feat.SetGeometry( ogr.CreateGeometryFromWkt(wkt_geom) )
# rast_mem_lyr.CreateFeature( feat )
err = gdal.RasterizeLayer(target_ds, [1], layer, burn_values=[255])
if err != 0:
print(err)
gdaltest.post_reason( 'got non-zero result code from RasterizeLayer' )
return 'fail'
target_ds.GetRasterBand(1).FlushCache()
np_polygon = target_ds.GetRasterBand(1).ReadAsArray(0,0,cols,rows)
count = Counter([])
# for r in np_polygon:
# count = count + Counter(r)
# colorDict = {str(k):v for k,v in dict(count).items()}
# print(colorDict)
target_ds = None
return np_polygon
#-------------------------------------------------------------------------------
def rasterWkt(shpfile, tifffile, outputfile):
'''
Draw WKT Polygon into a Image
'''
inputImage = gdal.Open(tifffile)
rows = inputImage.RasterYSize
cols = inputImage.RasterXSize
geotransform = inputImage.GetGeoTransform()
projection = inputImage.GetProjection()
sr = osr.SpatialReference()
sr.ImportFromWkt(projection)
driverTiff = gdal.GetDriverByName('GTiff')
output = driverTiff.Create(outputfile, cols, rows, inputImage.RasterCount, gdal.GDT_Byte)
np_polygon = getPolygonArray(inputImage, shpfile)
for b in range(1, output.RasterCount+1):
np_input = inputImage.GetRasterBand(b).ReadAsArray(0,0,cols,rows)
output.GetRasterBand(b).SetNoDataValue(0)
output.GetRasterBand(b).WriteArray(np_polygon)#np.bitwise_and(np_polygon, np_input))
output.GetRasterBand(b).FlushCache()
output.SetGeoTransform(geotransform)
output.SetProjection(projection)
#Close files
polygonRaster = None
output = None
inputImage = None
def main(argv):
rasterWkt(argv[1], argv[2], argv[3])
if __name__ == "__main__":
main(sys.argv)
scripts/greenIndexAnalisis.py 0 → 100755
View file @ 975095e6
#!/usr/bin/python3
# -*- coding: utf-8 -*-
import sys
import os
import csv
import json
from datetime import date, datetime
sys.path.append("/home/mchc/git/GeoSentinel")
from geosentinel import findProducts
csv.field_size_limit(sys.maxsize)
#===============================================================================
def greenIndexAnalisis(csvfile, cfg):
today = date.today()
startDate = datetime.strptime(cfg["startDate"], '%Y%m%d')
regionList = {}
with open(csvfile) as csvfile:
reader = csv.DictReader(csvfile)
for row in reader:
regionList[row["CVE_ENT"]] = row["WKT"]
os.chdir(cfg["projectDir"])
if not os.path.isdir(cfg["productLevel"]):
os.mkdir(cfg["productLevel"])
if not os.path.isdir("out"):
os.mkdir("out")
os.chdir("out")
for y in range(today.year, startDate.year-1, -1):
year = str(y)
if not os.path.isdir(year):
os.mkdir(year)
os.chdir(year)
for key, value in regionList.items():
settings = cfg
settings["wkt"]=value
settings["endDate"]= date.today().strftime("%Y%m%d")
findProducts.findSentinelProducts(settings)
#===============================================================================
def main(argv):
if len(argv) != 3:
print ("Usage: " + argv[0] + "<regionList.csv> <settings.json>")
else:
with open(argv[2]) as json_file:
cfg = json.load(json_file)
greenIndexAnalisis(argv[1], cfg)
if __name__ == "__main__":
main(sys.argv)
scripts/runAnalisis.sh 0 → 100644
View file @ 975095e6
#!/bin/sh
greenIndexAnalisis.py data/00ent.csv data/settings.json
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