diff --git a/python/SoilMoistureBatchExtractAndMosaic2S2Tile.py b/python/SoilMoistureBatchExtractAndMosaic2S2Tile.py
index 70ce1666b1a8f4ee139ecc808f73a905c2688912..2db35c4ed3ac7a913e4ae75b713847897073c064 100755
--- a/python/SoilMoistureBatchExtractAndMosaic2S2Tile.py
+++ b/python/SoilMoistureBatchExtractAndMosaic2S2Tile.py
@@ -77,7 +77,7 @@ def exmos_pipeline(argsformat, mos1, mos2, ref, out):
app0.SetParameterString("interpolator","nn")
app0.SetParameterString("inr",ref)
app0.Execute()
- print("debug app0")
+
app1 = otbApplication.Registry.CreateApplication("Superimpose")
app1.SetParameterString("inm",mos2)
@@ -143,8 +143,8 @@ if __name__ == "__main__":
continue
bname = os.path.basename(file).split(".")[0]
splitbname = bname.split("_")
- acqdate = splitbname[4].split("T")[0]
- acqtime = splitbname[4].split("T")[1]
+ acqdate = splitbname[-1].split("T")[0]
+ acqtime = splitbname[-1].split("T")[1]
outfilebase = os.path.join(abspathout,"_".join(splitbname[:3])+"_"+tileid+"_"+acqdate+"T"+acqtime)
@@ -153,9 +153,6 @@ if __name__ == "__main__":
if len(l) == 2 :
- dejafait.append(indir[l[0]])
- dejafait.append(indir[l[1]])
-
in1 = os.path.join(indir[l[0]], "Sigma0_VV.img")
in2 = os.path.join(indir[l[1]], "Sigma0_VV.img")
outfile = outfilebase +"_VV.TIF"
@@ -170,7 +167,7 @@ if __name__ == "__main__":
outfile = outfilebase +"_THETA.TIF"
exmos_pipeline(args.format, in1, in2, args.inref, outfile)
-
+
dejafait.append(indir[l[0]])
dejafait.append(indir[l[1]])
diff --git a/python/SoilMoistureNdviGapfilling.py b/python/SoilMoistureNdviGapfilling.py
index 11111a57bbf9f272e0859fe9f49bba6f1790fba8..62efc928e3b95be85a898c0cc73c7ba807be3678 100755
--- a/python/SoilMoistureNdviGapfilling.py
+++ b/python/SoilMoistureNdviGapfilling.py
@@ -6,7 +6,7 @@ Created on Wed Aug 28 13:55:34 2019
@author: llozach
"""
-import os,datetime, math
+import os,datetime
import argparse
import otbApplication
@@ -27,7 +27,6 @@ def search_files(directory='.', extension='tif', resolution='NDVI'):
return images
def create_mask(ndvi,mask):
-
app1 = otbApplication.Registry.CreateApplication("BandMath")
app1.AddParameterStringList("il",ndvi)
app1.SetParameterString("out", mask)
@@ -36,96 +35,36 @@ def create_mask(ndvi,mask):
app1.ExecuteAndWriteOutput()
def concate_images(listinputimg, pixeltype, output):
- apps=[]
- for img in listinputimg:
- app0 = otbApplication.Registry.CreateApplication("Superimpose")
- app0.SetParameterString("inm", img)
- app0.SetParameterString("out", "supimp.tif")
- app0.SetParameterString("inr", listinputimg[0])
- app0.SetParameterString("interpolator", "nn")
- app0.Execute()
- apps.append(app0)
-
print('---\nConcatenation to {}...'.format(output))
appConcat = otbApplication.Registry.CreateApplication("ConcatenateImages")
- for a in apps:
- appConcat.AddImageToParameterInputImageList("il",a.GetParameterOutputImage("out"))
+ appConcat.SetParameterStringList("il", listinputimg)
appConcat.SetParameterString("out", output)
- #appConcat.SetParameterOutputImagePixelType("out", pixeltype)
+ appConcat.SetParameterOutputImagePixelType("out", pixeltype)
appConcat.Execute()
return appConcat
-
-def monthrange(start_date, end_date):
-# print("MonthRange: "+str (math.floor((end_date - start_date).days/31)))
-# for n in range(int (math.floor((end_date - start_date).days/31))+1):
-# yield start_date + datetime.timedelta(days=n*31)
-
- qannee = end_date.year - start_date.year
-
- dmois = end_date.month +12*(qannee) - start_date.month
-
- yield start_date
-
-
- anneesuiv = start_date.year
- for m in range(dmois-1):
- m+=1
- moissuiv = (start_date.month + m) % 12
- if moissuiv == 0 :
- moissuiv = 12
- if moissuiv == 1 :
- anneesuiv = anneesuiv+1
-
- yield datetime.date(anneesuiv,moissuiv,1)
- yield end_date
-
-
-def create_outputdates(listinput_date):
-# stdate = datetime.date(int(startdate[:4]),int(startdate[4:6]),1)
-# eddate = datetime.date(int(enddate[:4]),int(enddate[4:6]),15)
+def create_outputdates(startdate, enddate, listinput_date):
+ stdate = datetime.date(int(startdate[:4]),int(startdate[4:6]),15)
+ eddate = datetime.date(int(enddate[:4]),int(enddate[4:6]),15)
inst = datetime.date(int(listinput_date[0][:4]),int(listinput_date[0][4:6]),int(listinput_date[0][6:8]))
ined = datetime.date(int(listinput_date[-1][:4]),int(listinput_date[-1][4:6]),int(listinput_date[-1][6:8]))
- if inst.day > 15:
- stdate = datetime.date(inst.year,inst.month +1,1)
- else:
- stdate = datetime.date(inst.year,inst.month,15)
- if ined.day >= 15:
- eddate = datetime.date(ined.year,ined.month,15)
- else:
- eddate = datetime.date(ined.year,ined.month,1)
-
+ if (stdate < inst or eddate > ined):
+ print("Error: Output dates provided are outside the images time serie.")
+ exit
+ if (stdate >= eddate):
+ print("Error: Output dates provided are not valid.")
+ exit
exformat = "%Y%m%d"
- print("Start date: "+stdate.strftime(exformat))
- print("End date: "+eddate.strftime(exformat))
-
outputdates=[]
- #outputdates.append(stdate.strftime(exformat))
+ outputdates.append(stdate.strftime(exformat))
procd = stdate
- for dstep in monthrange(stdate, eddate):
- procd = dstep
- if dstep == stdate:
- if stdate.day == 1:
- outputdates.append(procd.strftime(exformat))
- procd = datetime.date(dstep.year,dstep.month,15)
- outputdates.append(procd.strftime(exformat))
- else:
- outputdates.append(procd.strftime(exformat))
- elif dstep == eddate:
- if eddate.day == 1:
- outputdates.append(procd.strftime(exformat))
- else:
- procd = datetime.date(dstep.year,dstep.month,1)
- outputdates.append(procd.strftime(exformat))
- procd = datetime.date(dstep.year,dstep.month,15)
- outputdates.append(procd.strftime(exformat))
- else:
- procd = datetime.date(dstep.year,dstep.month,1)
- outputdates.append(procd.strftime(exformat))
- procd = datetime.date(dstep.year,dstep.month,15)
- outputdates.append(procd.strftime(exformat))
+ dstep = datetime.timedelta(weeks=4)
+ while procd < eddate:
+ procd = procd + dstep
+ procd = datetime.date(procd.year,procd.month,15)
+ outputdates.append(procd.strftime(exformat))
return outputdates
@@ -138,6 +77,8 @@ if __name__ == "__main__":
""")
parser.add_argument('-ndvidir', action='store', required=True, help='Directory containing time serie NDVI to be gapfilled')
+ parser.add_argument('-startdate', action='store', required=True, help='Start date for output gapfilled NDVIs (first date in input must be before), ex. 201809')
+ parser.add_argument('-enddate', action='store', required=True, help='End date for output gapfilled NDVIs (last date in input must be after), ex. 201908')
parser.add_argument('-outmaskdir', action='store', required=True, help='Output directory for NDVIs mask used for gapfilling')
parser.add_argument('-interpolation', choices=['linear', 'spline'], default='linear', required=False, help='Interpolation mode for OTB ImageTimeSeriesGapFilling')
parser.add_argument('-outdir', action='store', required=True, help='Output directory for time serie gapfilled NDVIs image')
@@ -167,7 +108,7 @@ if __name__ == "__main__":
listinput_img = [row[1] for row in parameters]
listinput_mask = [row[2] for row in parameters]
- listoutput_date = create_outputdates(listinput_date)
+ listoutput_date = create_outputdates(args.startdate, args.enddate, listinput_date)
inputdatesfile = os.path.join(args.ndvidir,"InputDates.txt")
outputdatesfile = os.path.join(args.ndvidir,"OutputDates.txt")
@@ -183,44 +124,10 @@ if __name__ == "__main__":
# Concatenate
print("Concatenate NDVI files : ")
[print(" "+nm) for nm in listinput_img]
- #appConcatImg = concate_images(listinput_img, otbApplication.ImagePixelType_uint8, "tempimg.tif")
- apps=[]
- for img in listinput_img:
- app0 = otbApplication.Registry.CreateApplication("Superimpose")
- app0.SetParameterString("inm", img)
- app0.SetParameterString("out", "supimp.tif")
- app0.SetParameterString("inr", listinput_img[0])
- app0.SetParameterString("interpolator", "nn")
- app0.Execute()
- apps.append(app0)
- appConcatImg = otbApplication.Registry.CreateApplication("ConcatenateImages")
- for a in apps:
- appConcatImg.AddImageToParameterInputImageList("il",a.GetParameterOutputImage("out"))
-# appConcatImg.SetParameterStringList("il", listinput_img)
- appConcatImg.SetParameterString("out", "tempimg.tif")
- appConcatImg.Execute()
+ appConcatImg = concate_images(listinput_img, otbApplication.ImagePixelType_uint8, "tempimg.tif")
print("Concatenate MASK files : ")
[print(" "+nm) for nm in listinput_mask]
- #appConcatMask = concate_images(listinput_mask, otbApplication.ImagePixelType_uint8, "tempmask.tif")
- appsm=[]
- for img in listinput_mask:
- app0 = otbApplication.Registry.CreateApplication("Superimpose")
- app0.SetParameterString("inm", img)
- app0.SetParameterString("out", "supimp.tif")
- app0.SetParameterString("inr", listinput_img[0])
- app0.SetParameterString("interpolator", "nn")
- app0.Execute()
- appsm.append(app0)
- appConcatMask = otbApplication.Registry.CreateApplication("ConcatenateImages")
- for a in appsm:
- appConcatMask.AddImageToParameterInputImageList("il",a.GetParameterOutputImage("out"))
-# appConcatMask.SetParameterStringList("il", listinput_mask)
- appConcatMask.SetParameterString("out", "tempmask.tif")
- appConcatMask.Execute()
-
-
-
-
+ appConcatMask = concate_images(listinput_mask, otbApplication.ImagePixelType_uint8, "tempmask.tif")
# Gapfill
print("Gapfilled NDVIs from input dates in "+inputdatesfile+" : ")
diff --git a/python/SoilMoisturePipeline.py b/python/SoilMoisturePipeline.py
index e30d2925c78612da57cc526a454653f834516b62..8fdf527360f96fcc3f457ca8d985fcefe9f1d836 100755
--- a/python/SoilMoisturePipeline.py
+++ b/python/SoilMoisturePipeline.py
@@ -733,10 +733,6 @@ if __name__ == "__main__":
print("Error: Exception on sarmode")
exit
- if os.path.exists(output):
- print(output+" already exists! Passing...")
- continue
-
print("using: \n"+sarvv+" \n"+sarth+" \n"+ndvi+" \n"+output)
short_pipeline(normalize_proj_and_extend())
@@ -744,8 +740,8 @@ if __name__ == "__main__":
elif args.pipeline == 'stack' :
if not os.path.isdir(args.ndvidir):
- print("erreur "+args.ndvidir+" n'est pas un dossier")
- exit
+ print("erreur "+args.ndvidir+" n'est pas un dossier")
+ exit
ndvis=[]
ndvis=search_files(args.ndvidir)
diff --git a/tools/docker/esa-snap/Dockerfile b/tools/docker/esa-snap/Dockerfile
index 5380353b8605d84fb8e91bce393f11e13fbcd224..f198f73b71b404fb96a6fe0d0d857f0645678efb 100755
--- a/tools/docker/esa-snap/Dockerfile
+++ b/tools/docker/esa-snap/Dockerfile
@@ -25,7 +25,7 @@ RUN export uid=1001 gid=1001 && \
# Download Snap + Sen2Cor
# ----------------------------------------------------------------------------
RUN cd /home/lozach/esa-snap \
- && wget http://step.esa.int/downloads/7.0/installers/esa-snap_sentinel_unix_7_0.sh \
+ && wget http://step.esa.int/downloads/6.0/installers/esa-snap_sentinel_unix_6_0.sh \
&& wget http://step.esa.int/thirdparties/sen2cor/2.8.0/Sen2Cor-02.08.00-Linux64.run
# ----------------------------------------------------------------------------
@@ -33,9 +33,9 @@ RUN cd /home/lozach/esa-snap \
# ----------------------------------------------------------------------------
RUN cd /home/lozach/esa-snap \
&& chown -R lozach:lozach /home/lozach \
- && chmod +x esa-snap_sentinel_unix_7_0.sh \
+ && chmod +x esa-snap_sentinel_unix_6_0.sh \
&& chmod +x Sen2Cor-02.08.00-Linux64.run \
- && echo "\n\n/home/lozach/esa-snap/snap\n\nn\n\nn\n" | sudo -u lozach ./esa-snap_sentinel_unix_7_0.sh \
+ && echo "\n\n/home/lozach/esa-snap/snap\n\nn\n\nn\n" | sudo -u lozach ./esa-snap_sentinel_unix_6_0.sh \
&& sudo -u lozach ./Sen2Cor-02.08.00-Linux64.run
diff --git a/tools/docker/otbtf-soilmoisture-withuser/Dockerfile b/tools/docker/otbtf-soilmoisture-withuser/Dockerfile
index c9b42a069819530d59247ce51d29b7dbf4890f13..7f174a9d59e835b5d3248f457a8c1ef1134410a2 100755
--- a/tools/docker/otbtf-soilmoisture-withuser/Dockerfile
+++ b/tools/docker/otbtf-soilmoisture-withuser/Dockerfile
@@ -1,4 +1,4 @@
-FROM mdl4eo/otbtf1.6
+FROM mdl4eo/otbtf1.6:nouser
MAINTAINER Loic Lozach <loic.lozach[at]irstea[dot]fr>
@@ -12,7 +12,6 @@ RUN cd /work/otb/otb/Modules/Remote \
&& cd /work/otb/build/OTB/build \
&& cmake /work/otb/otb \
-DModule_AgriSoilMoisture=ON \
- -DModule_OTBTemporalGapFilling=ON \
&& cd /work/otb/build/ \
&& make -j $(grep -c ^processor /proc/cpuinfo)