def noInSituDataAvailable() :
global validation_polygons
#Data Smoothing for Reflectances (Step 16)
executeStep("DataSmoothing for Reflectances", "otbcli", "DataSmoothing", buildFolder,"-ts", tocr, "-mask", mask, "-dates", dates, "-lambda", lmbd, "-sts",rtocr_smooth, "-outdays", outdays_smooth, skip=fromstep>16, rmfiles=[] if keepfiles else [rtocr])
#Features when no insitu data is available (Step 17)
executeStep("FeaturesWithoutInsitu", "otbcli", "FeaturesWithoutInsitu", buildFolder, "-ts", rtocr_smooth, "-dates", outdays_smooth , "-sf", spectral_features, skip=fromstep>17, rmfiles=[] if keepfiles else [rtocr_smooth])
# Image Statistics (Step 18)
executeStep("ComputeImagesStatistics", "otbcli_ComputeImagesStatistics", "-il", spectral_features, "-out", statistics_noinsitu, skip=fromstep>18)
# Reference Map preparation (Step 19 and 20)
with open(shape_proj, 'r') as file:
shape_wkt = "ESRI::" + file.read()
executeStep("gdalwarp for cropping Reference map", "gdalwarp", "-dstnodata", "0", "-overwrite", "-cutline", shape, "-crop_to_cutline", reference, cropped_reference, skip=fromstep>19)
executeStep("gdalwarp for reprojecting Reference map", "gdalwarp", "-dstnodata", "0", "-overwrite", "-t_srs", shape_wkt, cropped_reference, reprojected_reference, skip=fromstep>19, rmfiles=[] if keepfiles else [cropped_reference])
executeStep("gdalwarp for resampling Reference map", "gdalwarp", "-dstnodata", "0", "-overwrite", "-tr", pixsize, pixsize, "-cutline", shape, "-crop_to_cutline", reprojected_reference, crop_reference, skip=fromstep>20, rmfiles=[] if keepfiles else [reprojected_reference])
# Erosion (Step 21)
executeStep("Erosion", "otbcli", "Erosion", buildFolder,"-in", crop_reference, "-out", eroded_reference, "-radius", erode_radius, skip=fromstep>21, rmfiles=[] if keepfiles else [crop_reference])
# Trimming (Step 22)
executeStep("Trimming", "otbcli", "Trimming", buildFolder,"-feat", spectral_features, "-ref", eroded_reference, "-out", trimmed_reference_raster, "-alpha", alpha, "-nbsamples", "0", "-seed", random_seed, skip=fromstep>22, rmfiles=[] if keepfiles else [eroded_reference])
#Train Image Classifier (Step 23)
executeStep("TrainImagesClassifierNew", "otbcli", "TrainImagesClassifierNew", buildFolder, "-io.il", spectral_features,"-io.rs",trimmed_reference_raster,"-nodatalabel", "-10000", "-io.imstat", statistics_noinsitu, "-rand", random_seed, "-sample.bm", "0", "-io.confmatout", confmatout,"-io.out",model,"-sample.mt", nbtrsample,"-sample.mv","4000","-sample.vtr",sample_ratio,"-classifier","rf", "-classifier.rf.nbtrees",rfnbtrees,"-classifier.rf.min",rfmin,"-classifier.rf.max",rfmax, skip=fromstep>23)
#Image Classifier (Step 24)
executeStep("ImageClassifier", "otbcli_ImageClassifier", "-in", spectral_features,"-imstat",statistics_noinsitu,"-model", model, "-out", raw_crop_mask_uncompressed, skip=fromstep>24, rmfiles=[] if keepfiles else [spectral_features])
return
confusion_matrix_validation=os.path.join(args.outdir, "crop-mask-confusion-matrix-validation.csv")
quality_metrics=os.path.join(args.outdir, "crop-mask-quality-metrics.txt")
xml_validation_metrics=os.path.join(args.outdir, "crop-mask-validation-metrics.xml")
keepfiles = args.keepfiles
fromstep = args.fromstep
if not os.path.exists(args.outdir):
os.makedirs(args.outdir)
globalStart = datetime.datetime.now()
try:
# Bands Extractor (Step 1)
executeStep("BandsExtractor", "otbcli", "BandsExtractor", buildFolder,"-mission",mission,"-out",rawtocr,"-mask",rawmask, "-outdate", dates, "-shape", shape, "-pixsize", pixsize,"-merge", "false", "-il", *indesc, skip=fromstep>1)
# gdalwarp (Step 2 and 3)
executeStep("gdalwarp for reflectances", "gdalwarp", "-multi", "-wm", "2048", "-dstnodata", "\"-10000\"", "-overwrite", "-cutline", shape, "-crop_to_cutline", rawtocr, tocr, skip=fromstep>2, rmfiles=[] if keepfiles else [rawtocr])
executeStep("gdalwarp for masks", "gdalwarp", "-multi", "-wm", "2048", "-dstnodata", "\"-10000\"", "-overwrite", "-cutline", shape, "-crop_to_cutline", rawmask, mask, skip=fromstep>3, rmfiles=[] if keepfiles else [rawmask])
# Select either inSitu or noInSitu branches
if reference_polygons != "" :
# Temporal Resampling (Step 4)
executeStep("TemporalResampling", "otbcli", "TemporalResampling", buildFolder, "-tocr", tocr, "-mask", mask, "-ind", dates, "-sp", "SENTINEL", "5", "SPOT", "5", "LANDSAT", "16", "-rtocr", rtocr, "-outdays", outdays, "-mode", trm, "-merge", "1", skip=fromstep>4, rmfiles=[] if keepfiles else [tocr, mask])
# Feature Extraction with insitu (Step 5)
executeStep("FeatureExtraction", "otbcli", "FeatureExtraction", buildFolder, "-rtocr", rtocr, "-ndvi", ndvi, "-ndwi", ndwi, "-brightness", brightness, skip=fromstep>5, rmfiles=[] if keepfiles else [rtocr])
#Perform insitu specific steps.
def inSituDataAvailable() :
#Features when insitu data is available (Step 6 or 7 or 8)
executeStep("FeaturesWithInsitu", "otbcli", "FeaturesWithInsitu", buildFolder,"-ndvi",ndvi,"-ndwi",ndwi,"-brightness",brightness,"-dates",outdays,"-window", window,"-bm", "true", "-out",features, skip=fromstep>6, rmfiles=[] if keepfiles else [ndwi, brightness])
# Image Statistics (Step 9)
executeStep("ComputeImagesStatistics", "otbcli_ComputeImagesStatistics", "-il", features,"-out",statistics, skip=fromstep>9)
# ogr2ogr Reproject insitu data (Step 10)
with open(shape_proj, 'r') as file:
shape_wkt = "ESRI::" + file.read()
executeStep("ogr2ogr", "ogr2ogr", "-t_srs", shape_wkt,"-progress","-overwrite",reference_polygons_reproject, reference_polygons, skip=fromstep>10)
# ogr2ogr Crop insitu data (Step 11)
executeStep("ogr2ogr", "ogr2ogr", "-clipsrc", shape,"-progress","-overwrite",reference_polygons_clip, reference_polygons_reproject, skip=fromstep>11)
# Sample Selection (Step 12)
executeStep("SampleSelection", "otbcli","SampleSelection", buildFolder, "-ref",reference_polygons_clip,"-ratio", sample_ratio, "-seed", random_seed, "-tp", training_polygons, "-vp", validation_polygons,"-nofilter","true", skip=fromstep>12)
#Train Image Classifier (Step 13)
executeStep("TrainImagesClassifier", "otbcli_TrainImagesClassifier", "-io.il",
features,"-io.vd",training_polygons,"-io.imstat", statistics, "-rand", random_seed,
"-sample.bm", "0", "-sample.vtr", "0.5", "-io.confmatout",
confmatout,"-io.out",model,"-sample.mt", "4000","-sample.mv","-1","-sample.vfn","CROP","-classifier","rf", "-classifier.rf.nbtrees",rfnbtrees,"-classifier.rf.min",rfmin,"-classifier.rf.max",rfmax, skip=fromstep>13)
#Image Classifier (Step 14)
executeStep("ImageClassifier", "otbcli_ImageClassifier", "-in", features,"-imstat",statistics,"-model", model, "-out", raw_crop_mask_uncompressed, skip=fromstep>14, rmfiles=[] if keepfiles else [features])
return;
confusion_matrix_validation=os.path.join(args.outdir, "confusion-matrix-validation.csv")
quality_metrics=os.path.join(args.outdir, "quality-metrics.txt")
xml_validation_metrics=os.path.join(args.outdir, "validation-metrics.xml")
keepfiles = args.keepfiles
fromstep = args.fromstep
if not os.path.exists(args.outdir):
os.makedirs(args.outdir)
globalStart = datetime.datetime.now()
try:
# Bands Extractor (Step 1)
executeStep("BandsExtractor", "otbcli", "BandsExtractor", buildFolder,"-mission",mission,"-out",rawtocr,"-mask",rawmask,"-outdate", dates, "-shape", shape, "-pixsize", pixsize, "-il", *indesc, skip=fromstep>1)
# gdalwarp (Step 2 and 3)
executeStep("gdalwarp for reflectances", "gdalwarp", "-multi", "-wm", "2048", "-dstnodata", "\"-10000\"", "-overwrite", "-cutline", shape, "-crop_to_cutline", rawtocr, tocr, skip=fromstep>2, rmfiles=[] if keepfiles else [rawtocr])
executeStep("gdalwarp for masks", "gdalwarp", "-multi", "-wm", "2048", "-dstnodata", "\"-10000\"", "-overwrite", "-cutline", shape, "-crop_to_cutline", rawmask, mask, skip=fromstep>3, rmfiles=[] if keepfiles else [rawmask])
# Temporal Resampling (Step 4)
executeStep("TemporalResampling", "otbcli", "TemporalResampling", buildFolder, "-tocr", tocr, "-mask", mask, "-ind", dates, "-sp", "SENTINEL", "5", "SPOT", "5", "LANDSAT", "16", "-rtocr", rtocr, "-mode", trm, skip=fromstep>4, rmfiles=[] if keepfiles else [tocr, mask])
# Feature Extraction (Step 5)
executeStep("FeatureExtraction", "otbcli", "FeatureExtraction", buildFolder, "-rtocr", rtocr, "-fts", fts, skip=fromstep>5, rmfiles=[] if keepfiles else [rtocr])
# ogr2ogr Reproject insitu data (Step 6)
with open(shape_proj, 'r') as file:
shape_wkt = "ESRI::" + file.read()