def generateSamples_simple(folderSample, workingDirectory, trainShape, pathWd,
featuresPath, samplesOptions, pathConf, dataField):
bindingPython = Config(file(pathConf)).GlobChain.bindingPython
dataField = Config(file(pathConf)).chain.dataField
outputPath = Config(file(pathConf)).chain.outputPath
userFeatPath = Config(file(pathConf)).chain.userFeatPath
if userFeatPath == "None": userFeatPath = None
tmpFolder = outputPath + "/TMPFOLDER"
if not os.path.exists(tmpFolder): os.mkdir(tmpFolder)
# Sensors
S2 = Sensors.Sentinel_2("", Opath(tmpFolder), pathConf, "")
L8 = Sensors.Landsat8("", Opath(tmpFolder), pathConf, "")
L5 = Sensors.Landsat5("", Opath(tmpFolder), pathConf, "")
# shutil.rmtree(tmpFolder, ignore_errors=True)
SensorsList = [S2, L8, L5]
stats = workingDirectory + "/" + trainShape.split("/")[-1].replace(
".shp", "_stats.xml")
tile = trainShape.split("/")[-1].split("_")[0]
stack = fu.getFeatStackName(pathConf)
feat = featuresPath + "/" + tile + "/Final/" + stack
if bindingPython == "True":
feat = fu.FileSearch_AND(featuresPath + "/" + tile + "/tmp/", True,
"ST_MASK")[0]
os.environ["ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS"] = "1"
cmd = "otbcli_PolygonClassStatistics -in " + feat + " -vec " + trainShape + " -out " + stats + " -field " + dataField
print cmd
os.system(cmd)
verifPolyStats(stats)
sampleSelection = workingDirectory + "/" + trainShape.split(
"/")[-1].replace(".shp", "_SampleSel.sqlite")
cmd = "otbcli_SampleSelection -out " + sampleSelection + " " + samplesOptions + " -field " + dataField + " -in " + feat + " -vec " + trainShape + " -instats " + stats
print cmd
os.system(cmd)
# if pathWd:shutil.copy(sampleSelection,folderSample)
os.environ["ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS"] = "5"
samples = workingDirectory + "/" + trainShape.split("/")[-1].replace(
".shp", "_Samples.sqlite")
if bindingPython == "True":
sampleExtr = otb.Registry.CreateApplication("SampleExtraction")
sampleExtr.SetParameterString("vec", sampleSelection)
sampleExtr.SetParameterString("field", dataField)
sampleExtr.SetParameterString("out", samples)
AllRefl = sorted(
fu.FileSearch_AND(featuresPath + "/" + tile + "/tmp/", True,
"REFL.tif"))
AllMask = sorted(
fu.FileSearch_AND(featuresPath + "/" + tile + "/tmp/", True,
"MASK.tif"))
datesInterp = sorted(
fu.FileSearch_AND(featuresPath + "/" + tile + "/tmp/", True,
"DatesInterp"))
realDates = sorted(
fu.FileSearch_AND(featuresPath + "/" + tile + "/tmp/", True,
"imagesDate"))
print AllRefl
print AllMask
print datesInterp
print realDates
# gapFill + feat
features = []
concatSensors = otb.Registry.CreateApplication("ConcatenateImages")
for refl, mask, datesInterp, realDates in zip(AllRefl, AllMask,
datesInterp, realDates):
gapFill = otb.Registry.CreateApplication(
"ImageTimeSeriesGapFilling")
nbDate = fu.getNbDateInTile(realDates)
nbReflBands = fu.getRasterNbands(refl)
comp = int(nbReflBands) / int(nbDate)
print datesInterp
if not isinstance(comp, int):
raise Exception("unvalid component by date (not integer) : " +
comp)
gapFill.SetParameterString("in", refl)
gapFill.SetParameterString("mask", mask)
gapFill.SetParameterString("comp", str(comp))
gapFill.SetParameterString("it", "linear")
gapFill.SetParameterString("id", realDates)
gapFill.SetParameterString("od", datesInterp)
gapFill.Execute()
# gapFill.SetParameterString("out","/ptmp/vincenta/tmp/TestGapFill.tif")
# gapFill.ExecuteAndWriteOutput()
# pause = raw_input("Pause1")
# featExtr = otb.Registry.CreateApplication("iota2FeatureExtraction")
# featExtr.SetParameterInputImage("in",gapFill.GetParameterOutputImage("out"))
# featExtr.SetParameterString("comp",str(comp))
# for currentSensor in SensorsList:
# if currentSensor.name in refl:
# red = str(currentSensor.bands["BANDS"]["red"])
# nir = str(currentSensor.bands["BANDS"]["NIR"])
# swir = str(currentSensor.bands["BANDS"]["SWIR"])
# featExtr.SetParameterString("red",red)
# featExtr.SetParameterString("nir",nir)
# featExtr.SetParameterString("swir",swir)
# featExtr.SetParameterString("ram","256")
# featExtr.Execute()
# features.append(featExtr)
concatSensors.AddImageToParameterInputImageList(
"il", gapFill.GetParameterOutputImage("out"))
features.append(gapFill)
# sensors Concatenation + sampleExtraction
sampleExtr = otb.Registry.CreateApplication("SampleExtraction")
sampleExtr.SetParameterString("ram", "1024")
sampleExtr.SetParameterString("vec", sampleSelection)
sampleExtr.SetParameterString("field", dataField)
sampleExtr.SetParameterString("out", samples)
if len(AllRefl) > 1:
concatSensors.Execute()
allFeatures = concatSensors.GetParameterOutputImage("out")
else:
allFeatures = features[0].GetParameterOutputImage("out")
if userFeatPath:
print "Add user features"
userFeat_arbo = Config(file(pathConf)).userFeat.arbo
userFeat_pattern = (Config(
file(pathConf)).userFeat.patterns).split(",")
concatFeatures = otb.Registry.CreateApplication(
"ConcatenateImages")
userFeatures = fu.getUserFeatInTile(userFeatPath, tile,
userFeat_arbo,
userFeat_pattern)
concatFeatures.SetParameterStringList("il", userFeatures)
concatFeatures.Execute()
concatAllFeatures = otb.Registry.CreateApplication(
"ConcatenateImages")
concatAllFeatures.AddImageToParameterInputImageList(
"il", allFeatures)
concatAllFeatures.AddImageToParameterInputImageList(
"il", concatFeatures.GetParameterOutputImage("out"))
concatAllFeatures.Execute()
allFeatures = concatAllFeatures.GetParameterOutputImage("out")
sampleExtr.SetParameterInputImage("in", allFeatures)
sampleExtr.ExecuteAndWriteOutput()
# cmd = "otbcli_SampleExtraction -field "+dataField+" -out "+samples+" -vec "+sampleSelection+" -in /ptmp/vincenta/tmp/TestGapFill.tif"
# print cmd
# pause = raw_input("Pause")
# os.system(cmd)
else:
cmd = "otbcli_SampleExtraction -field " + dataField + " -out " + samples + " -vec " + sampleSelection + " -in " + feat
print cmd
os.system(cmd)
if pathWd:
shutil.copy(
samples, folderSample + "/" +
trainShape.split("/")[-1].replace(".shp", "_Samples.sqlite"))
os.remove(sampleSelection)
os.remove(stats)
def launchClassification(tempFolderSerie, Classifmask, model, stats,
outputClassif, confmap, pathWd, pathConf, pixType):
outputClassif = outputClassif.replace(".tif", "_TMP.tif")
confmap = confmap.replace(".tif", "_TMP.tif")
os.environ["ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS"] = "5"
featuresPath = Config(file(pathConf)).chain.featuresPath
outputPath = Config(file(pathConf)).chain.outputPath
tile = outputClassif.split("/")[-1].split("_")[1]
userFeatPath = Config(file(pathConf)).chain.userFeatPath
if userFeatPath == "None": userFeatPath = None
AllRefl = sorted(
fu.FileSearch_AND(featuresPath + "/" + tile + "/tmp/", True,
"REFL.tif"))
AllMask = sorted(
fu.FileSearch_AND(featuresPath + "/" + tile + "/tmp/", True,
"MASK.tif"))
datesInterp = sorted(
fu.FileSearch_AND(featuresPath + "/" + tile + "/tmp/", True,
"DatesInterp"))
realDates = sorted(
fu.FileSearch_AND(featuresPath + "/" + tile + "/tmp/", True,
"imagesDate"))
tmpFolder = outputPath + "/TMPFOLDER_" + tile
if not os.path.exists(tmpFolder):
os.mkdir(tmpFolder)
# Sensors
S2 = Sensors.Sentinel_2("", Opath(tmpFolder), pathConf, "")
L8 = Sensors.Landsat8("", Opath(tmpFolder), pathConf, "")
L5 = Sensors.Landsat5("", Opath(tmpFolder), pathConf, "")
# shutil.rmtree(tmpFolder, ignore_errors=True)
SensorsList = [S2, L8, L5]
# gapFill + feat
features = []
concatSensors = otb.Registry.CreateApplication("ConcatenateImages")
for refl, mask, datesInterp, realDates in zip(AllRefl, AllMask,
datesInterp, realDates):
gapFill = otb.Registry.CreateApplication("ImageTimeSeriesGapFilling")
nbDate = fu.getNbDateInTile(realDates)
nbReflBands = fu.getRasterNbands(refl)
comp = int(nbReflBands) / int(nbDate)
if not isinstance(comp, int):
raise Exception("unvalid component by date (not integer) : " +
comp)
gapFill.SetParameterString("in", refl)
gapFill.SetParameterString("mask", mask)
gapFill.SetParameterString("comp", str(comp))
gapFill.SetParameterString("it", "linear")
gapFill.SetParameterString("id", realDates)
gapFill.SetParameterString("od", datesInterp)
# gapFill.SetParameterString("ram","1024")
gapFill.Execute()
# featExtr = otb.Registry.CreateApplication("iota2FeatureExtraction")
# featExtr.SetParameterInputImage("in",gapFill.GetParameterOutputImage("out"))
# featExtr.SetParameterString("comp",str(comp))
# for currentSensor in SensorsList:
# if currentSensor.name in refl:
# red = str(currentSensor.bands["BANDS"]["red"])
# nir = str(currentSensor.bands["BANDS"]["NIR"])
# swir = str(currentSensor.bands["BANDS"]["SWIR"])
# featExtr.SetParameterString("red",red)
# featExtr.SetParameterString("nir",nir)
# featExtr.SetParameterString("swir",swir)
# featExtr.Execute()
# features.append(featExtr)
concatSensors.AddImageToParameterInputImageList(
"il", gapFill.GetParameterOutputImage("out"))
features.append(gapFill)
classifier = otb.Registry.CreateApplication("ImageClassifier")
classifier.SetParameterString("mask", Classifmask)
if stats: classifier.SetParameterString("imstat", stats)
classifier.SetParameterString("out", outputClassif)
classifier.SetParameterString("model", model)
classifier.SetParameterString("confmap", confmap)
classifier.SetParameterString("ram", "512")
print "AllRefl"
print AllRefl
# if len(AllRefl) >1:
# concatSensors.Execute()
# classifier.SetParameterInputImage("in",concatSensors.GetParameterOutputImage("out"))
# else:
# classifier.SetParameterInputImage("in",features[0].GetParameterOutputImage("out"))
# classifier.ExecuteAndWriteOutput()
if len(AllRefl) > 1:
concatSensors.Execute()
allFeatures = concatSensors.GetParameterOutputImage("out")
else:
allFeatures = features[0].GetParameterOutputImage("out")
if userFeatPath:
print "Add user features"
userFeat_arbo = Config(file(pathConf)).userFeat.arbo
userFeat_pattern = (Config(
file(pathConf)).userFeat.patterns).split(",")
concatFeatures = otb.Registry.CreateApplication("ConcatenateImages")
userFeatures = fu.getUserFeatInTile(userFeatPath, tile, userFeat_arbo,
userFeat_pattern)
concatFeatures.SetParameterStringList("il", userFeatures)
concatFeatures.Execute()
concatAllFeatures = otb.Registry.CreateApplication("ConcatenateImages")
concatAllFeatures.AddImageToParameterInputImageList("il", allFeatures)
concatAllFeatures.AddImageToParameterInputImageList(
"il", concatFeatures.GetParameterOutputImage("out"))
concatAllFeatures.Execute()
allFeatures = concatAllFeatures.GetParameterOutputImage("out")
classifier.SetParameterInputImage("in", allFeatures)
classifier.ExecuteAndWriteOutput()
expr = "im2b1>=1?im1b1:0"
cmd = 'otbcli_BandMath -il ' + outputClassif + ' ' + Classifmask + ' -out ' + outputClassif.replace(
"_TMP.tif", ".tif") + ' -exp "' + expr + '"'
print cmd
os.system(cmd)
cmd = 'otbcli_BandMath -il ' + confmap + ' ' + Classifmask + ' -out ' + confmap.replace(
"_TMP.tif", ".tif") + ' -exp "' + expr + '"'
print cmd
os.system(cmd)
if pathWd:
shutil.copy(outputClassif.replace("_TMP.tif", ".tif"),
outputPath + "/classif")
if pathWd:
shutil.copy(confmap.replace("_TMP.tif", ".tif"),
outputPath + "/classif")
os.remove(outputClassif)
os.remove(confmap)
