def superimpose(inm, inr):
run_subprocess(
'{otb_bin_path}/otbcli_Superimpose -inr {inr} -inm {inm} -out {out}'.
format(otb_bin_path=settings.OTB_BIN_PATH,
inr=os.path.join(RESULTS_SRC, "{}.tif".format(inr)),
inm=os.path.join(RESULTS_SRC, "{}.tif".format(inm)),
out=os.path.join(RESULTS_FEAT, "{}.tif".format(inm))))
def clip(product):
print("# Clip", product['title'])
name = '{}.SAFE'.format(product['title'])
dst_folder = os.path.join(S1_RAW_PATH, 'proc', name, 'clip')
os.makedirs(dst_folder, exist_ok=True)
vv_src = os.path.join(S1_RAW_PATH, 'proc', name, 'despeck', 'vv.tiff')
vv_dst = os.path.join(dst_folder, 'vv.tiff')
if not os.path.exists(vv_dst):
run_subprocess(
'{gdal_bin_path}/gdalwarp -of GTiff -cutline {aoi} -crop_to_cutline {src} {dst}'
.format(gdal_bin_path=settings.GDAL_BIN_PATH,
aoi=AOI_PATH,
src=vv_src,
dst=vv_dst))
vh_src = os.path.join(S1_RAW_PATH, 'proc', name, 'despeck', 'vh.tiff')
vh_dst = os.path.join(dst_folder, 'vh.tiff')
if not os.path.exists(vh_dst):
run_subprocess(
'{gdal_bin_path}/gdalwarp -of GTiff -cutline {aoi} -crop_to_cutline {src} {dst}'
.format(gdal_bin_path=settings.GDAL_BIN_PATH,
aoi=AOI_PATH,
src=vh_src,
dst=vh_dst))
def orthorectify(product):
print("# Orthorectify", product['title'])
name = '{}.SAFE'.format(product['title'])
dst_folder = os.path.join(S1_RAW_PATH, 'proc', name, 'ortho')
os.makedirs(dst_folder, exist_ok=True)
src = os.path.join(S1_RAW_PATH, 'proc', name, 'calib', 'vv.tiff')
dst = os.path.join(dst_folder, 'vv.tiff')
if not os.path.exists(dst):
run_subprocess(
'{otb_bin_path}/otbcli_OrthoRectification -io.in {src} -io.out {dst} -elev.geoid {geoid_path} -elev.dem {dem_path} -opt.gridspacing 50'
.format(otb_bin_path=settings.OTB_BIN_PATH,
src=src,
dst=dst,
geoid_path=GEOID_PATH,
dem_path=DEM_PATH))
src = os.path.join(S1_RAW_PATH, 'proc', name, 'calib', 'vh.tiff')
dst = os.path.join(dst_folder, 'vh.tiff')
if not os.path.exists(dst):
run_subprocess(
'{otb_bin_path}/otbcli_OrthoRectification -io.in {src} -io.out {dst} -elev.geoid {geoid_path} -elev.dem {dem_path} -opt.gridspacing 50'
.format(otb_bin_path=settings.OTB_BIN_PATH,
src=src,
dst=dst,
geoid_path=GEOID_PATH,
dem_path=DEM_PATH))
def classify_image():
run_subprocess(
'{otb_bin_path}/otbcli_ImageClassifier -in {input} -model {model} -out {out}'
.format(otb_bin_path=settings.OTB_BIN_PATH,
input=os.path.join(RESULTS_DIR, 'features.tif'),
model=MODEL_PATH,
out=os.path.join(RESULTS_DIR, 'cover.tif')))
def superimpose(products):
print("# Superimpose")
ref_product = products[0]
ref_name = '{}.SAFE'.format(ref_product['title'])
inr = os.path.join(S1_RAW_PATH, 'proc', ref_name, 'concatenate',
'concatenate.tiff')
dst = os.path.join(S1_RAW_PATH, 'proc', ref_name, 'concatenate',
'aligned.tiff')
if not os.path.exists(dst):
shutil.copyfile(inr, dst)
for p in products[1:]:
name = '{}.SAFE'.format(p['title'])
inm = os.path.join(S1_RAW_PATH, 'proc', name, 'concatenate',
'concatenate.tiff')
dst = os.path.join(S1_RAW_PATH, 'proc', name, 'concatenate',
'aligned.tiff')
if not os.path.exists(dst):
run_subprocess(
'{otb_bin_path}/otbcli_Superimpose -inr {inr} -inm {inm} -out {out}'
.format(otb_bin_path=settings.OTB_BIN_PATH,
inr=inr,
inm=inm,
out=dst))
def generate_vvvh(period):
print("# Generate VV/VH band", period)
src = os.path.join(S1_RES_PATH, str(period.pk), 'median.tiff')
dst = os.path.join(S1_RES_PATH, str(period.pk), 'vv-vh.tiff')
if not os.path.exists(dst):
run_subprocess(
'{otb_bin_path}/otbcli_BandMath -il {src} -out {dst} -exp "im1b1 / im1b2"'
.format(otb_bin_path=settings.OTB_BIN_PATH, src=src, dst=dst))
def extract_haralick(name, band):
run_subprocess(
'{otb_bin_path}/otbcli_HaralickTextureExtraction -in {input} -channel {band} -texture simple -parameters.min 0 -parameters.max 0.3 -out {out}'
.format(otb_bin_path=settings.OTB_BIN_PATH,
input=os.path.join(RESULTS_FEAT, "{}.tif".format(name)),
band=band,
out=os.path.join(RESULTS_FEAT,
'haralick_{}_{}.tif'.format(name, band))))
def extract_local_stats(name, band):
run_subprocess(
'{otb_bin_path}/otbcli_LocalStatisticExtraction -in {input} -channel {band} -radius 3 -out {out}'
.format(otb_bin_path=settings.OTB_BIN_PATH,
input=os.path.join(RESULTS_FEAT, "{}.tif".format(name)),
band=band,
out=os.path.join(RESULTS_FEAT,
'local_stats_{}_{}.tif'.format(name, band))))
def concatenate_images():
current_dir = os.getcwd()
os.chdir(RESULTS_FEAT)
run_subprocess(
'{otb_bin_path}/otbcli_ConcatenateImages -il $(ls {il}) -out {out}'.
format(otb_bin_path=settings.OTB_BIN_PATH,
il=RESULTS_FEAT,
out=os.path.join(RESULTS_DIR, 'features.tif')))
os.chdir(current_dir)
def concatenate_results(period):
print("# Concatenate results", period)
median = os.path.join(S1_RES_PATH, str(period.pk), 'median.tiff')
vv_vh = os.path.join(S1_RES_PATH, str(period.pk), 'vv-vh.tiff')
dst = os.path.join(S1_RES_PATH, str(period.pk), 'concatenate.tiff')
if not os.path.exists(dst):
run_subprocess(
'{otb_bin_path}/otbcli_ConcatenateImages -il {median} {vv_vh} -out {dst}'
.format(otb_bin_path=settings.OTB_BIN_PATH,
median=median,
vv_vh=vv_vh,
dst=dst))
def clip_results(period_s):
mosaic_path = os.path.join(settings.IMAGES_PATH, 'mosaic', period_s)
tif_10m = f's2_{period_s}_10m.tif'
tif_20m = f's2_{period_s}_20m.tif'
srcs = [tif_10m, tif_20m]
for src in srcs:
run_subprocess(
'{gdal_bin_path}/gdalwarp -of GTiff -cutline {aoi} -crop_to_cutline {src} {dst}'
.format(gdal_bin_path=settings.GDAL_BIN_PATH,
aoi=AOI_UTM_PATH,
src=os.path.join(mosaic_path, src),
dst=os.path.join(RESULTS_PATH, src)))
def clip_result(period):
print("# Clip result", period)
src = os.path.join(S1_RES_PATH, str(period.pk), 'concatenate.tiff')
os.makedirs(RESULTS_PATH, exist_ok=True)
dst_name = 's1_{dfrom}_{dto}.tif'.format(
dfrom=period.date_from.strftime('%Y%m'),
dto=period.date_to.strftime('%Y%m'))
dst = os.path.join(RESULTS_PATH, dst_name)
if not os.path.exists(dst):
run_subprocess(
'{gdal_bin_path}/gdalwarp -of GTiff -cutline {aoi} -crop_to_cutline {src} {dst}'
.format(gdal_bin_path=settings.GDAL_BIN_PATH,
aoi=AOI_PATH,
src=src,
dst=dst))
def concatenate(product):
print("# Concatenate", product['title'])
name = '{}.SAFE'.format(product['title'])
dst_folder = os.path.join(S1_RAW_PATH, 'proc', name, 'concatenate')
os.makedirs(dst_folder, exist_ok=True)
vv_src = os.path.join(S1_RAW_PATH, 'proc', name, 'clip', 'vv.tiff')
vh_src = os.path.join(S1_RAW_PATH, 'proc', name, 'clip', 'vh.tiff')
dst = os.path.join(dst_folder, 'concatenate.tiff')
if not os.path.exists(dst):
run_subprocess(
'{otb_bin_path}/otbcli_ConcatenateImages -il {vv_src} {vh_src} -out {dst}'
.format(otb_bin_path=settings.OTB_BIN_PATH,
vv_src=vv_src,
vh_src=vh_src,
dst=dst))
def despeckle(product):
print("# Despeckle", product['title'])
name = '{}.SAFE'.format(product['title'])
dst_folder = os.path.join(S1_RAW_PATH, 'proc', name, 'despeck')
os.makedirs(dst_folder, exist_ok=True)
src = os.path.join(S1_RAW_PATH, 'proc', name, 'ortho', 'vv.tiff')
dst = os.path.join(dst_folder, 'vv.tiff')
if not os.path.exists(dst):
run_subprocess(
'{otb_bin_path}/otbcli_Despeckle -in {src} -out {dst}'.format(
otb_bin_path=settings.OTB_BIN_PATH, src=src, dst=dst))
src = os.path.join(S1_RAW_PATH, 'proc', name, 'ortho', 'vh.tiff')
dst = os.path.join(dst_folder, 'vh.tiff')
if not os.path.exists(dst):
run_subprocess(
'{otb_bin_path}/otbcli_Despeckle -in {src} -out {dst}'.format(
otb_bin_path=settings.OTB_BIN_PATH, src=src, dst=dst))
def calibrate(product):
print("# Calibrate", product['title'])
name = '{}.SAFE'.format(product['title'])
dst_folder = os.path.join(S1_RAW_PATH, 'proc', name, 'calib')
os.makedirs(dst_folder, exist_ok=True)
src = os.path.join(S1_RAW_PATH, name, 'measurement', '*-vv-*.tiff')
dst = os.path.join(dst_folder, 'vv.tiff')
if not os.path.exists(dst):
run_subprocess(
'{otb_bin_path}/otbcli_SARCalibration -in $(ls {src}) -out {dst}'.
format(otb_bin_path=settings.OTB_BIN_PATH, src=src, dst=dst))
src = os.path.join(S1_RAW_PATH, name, 'measurement', '*-vh-*.tiff')
dst = os.path.join(dst_folder, 'vh.tiff')
if not os.path.exists(dst):
run_subprocess(
'{otb_bin_path}/otbcli_SARCalibration -in $(ls {src}) -out {dst}'.
format(otb_bin_path=settings.OTB_BIN_PATH, src=src, dst=dst))
def concatenate_results(mosaic_name, period_s):
mosaic_path = os.path.join(settings.IMAGES_PATH, 'mosaic', period_s)
tif_10m = f's2_{period_s}_10m.tif'
tif_20m = f's2_{period_s}_20m.tif'
R10m_B02 = os.path.join(mosaic_path, '{}_R10m_B02.tif'.format(mosaic_name))
R10m_B03 = os.path.join(mosaic_path, '{}_R10m_B03.tif'.format(mosaic_name))
R10m_B04 = os.path.join(mosaic_path, '{}_R10m_B04.tif'.format(mosaic_name))
R10m_B08 = os.path.join(mosaic_path, '{}_R10m_B08.tif'.format(mosaic_name))
R10m_NDVI = os.path.join(mosaic_path,
'{}_R10m_NDVI.tif'.format(mosaic_name))
R10m_NDVI = os.path.join(mosaic_path,
'{}_R10m_NDWI.tif'.format(mosaic_name))
R10m_EVI = os.path.join(mosaic_path, '{}_R10m_EVI.tif'.format(mosaic_name))
R10m_SAVI = os.path.join(mosaic_path,
'{}_R10m_SAVI.tif'.format(mosaic_name))
src = ' '.join([
R10m_B02, R10m_B03, R10m_B04, R10m_B08, R10m_NDVI, R10m_NDVI, R10m_EVI,
R10m_SAVI
])
run_subprocess(
'{otb_bin_path}/otbcli_ConcatenateImages -il {src} -out {dst}'.format(
otb_bin_path=settings.OTB_BIN_PATH,
src=src,
dst=os.path.join(mosaic_path, tif_10m)))
R20m_B05 = os.path.join(mosaic_path, '{}_R20m_B05.tif'.format(mosaic_name))
R20m_B06 = os.path.join(mosaic_path, '{}_R20m_B06.tif'.format(mosaic_name))
R20m_B07 = os.path.join(mosaic_path, '{}_R20m_B07.tif'.format(mosaic_name))
R20m_B8A = os.path.join(mosaic_path, '{}_R20m_B8A.tif'.format(mosaic_name))
R20m_B11 = os.path.join(mosaic_path, '{}_R20m_B11.tif'.format(mosaic_name))
R20m_B12 = os.path.join(mosaic_path, '{}_R20m_B12.tif'.format(mosaic_name))
src = ' '.join(
[R20m_B05, R20m_B06, R20m_B07, R20m_B8A, R20m_B11, R20m_B12])
run_subprocess(
'{otb_bin_path}/otbcli_ConcatenateImages -il {src} -out {dst}'.format(
otb_bin_path=settings.OTB_BIN_PATH,
src=src,
dst=os.path.join(mosaic_path, tif_20m)))
def generate_vegetation_indexes(mosaic_name, period_s):
mosaic_path = os.path.join(settings.IMAGES_PATH, 'mosaic', period_s)
nir = os.path.join(mosaic_path, '{}_R10m_NIR.vrt'.format(mosaic_name))
rgb = os.path.join(mosaic_path, '{}_R10m_RGB.vrt'.format(mosaic_name))
#ndiv
dst = os.path.join(mosaic_path, '{}_R10m_NDVI.tif'.format(mosaic_name))
exp = '(im1b1 - im2b1) / (im1b1 + im2b1)'
run_subprocess(
'{otb_bin_path}/otbcli_BandMath -il {nir} {rgb} -out {dst} -exp "{exp}"'
.format(otb_bin_path=settings.OTB_BIN_PATH,
nir=nir,
rgb=rgb,
dst=dst,
exp=exp))
#ndwi
dst = os.path.join(mosaic_path, '{}_R10m_NDWI.tif'.format(mosaic_name))
exp = '(im1b1 - im2b2) / (im1b1 + im2b2)'
run_subprocess(
'{otb_bin_path}/otbcli_BandMath -il {nir} {rgb} -out {dst} -exp "{exp}"'
.format(otb_bin_path=settings.OTB_BIN_PATH,
nir=nir,
rgb=rgb,
dst=dst,
exp=exp))
#evi
dst = os.path.join(mosaic_path, '{}_R10m_EVI.tif'.format(mosaic_name))
exp = '(2.5 * ((im1b1 - im2b1) / (im1b1 + 6 * im2b1 - 7.5 * im2b3 + 1)))'
run_subprocess(
'{otb_bin_path}/otbcli_BandMath -il {nir} {rgb} -out {dst} -exp "{exp}"'
.format(otb_bin_path=settings.OTB_BIN_PATH,
nir=nir,
rgb=rgb,
dst=dst,
exp=exp))
#savi
dst = os.path.join(mosaic_path, '{}_R10m_SAVI.tif'.format(mosaic_name))
exp = '((im1b1 - im2b1) * 1.5 / (im1b1 + im2b1 + 0.5))'
run_subprocess(
'{otb_bin_path}/otbcli_BandMath -il {nir} {rgb} -out {dst} -exp "{exp}"'
.format(otb_bin_path=settings.OTB_BIN_PATH,
nir=nir,
rgb=rgb,
dst=dst,
exp=exp))
unzip(p, delete_zip=False)
# Build mosaic
mosaic_dir = os.path.join(proc_scene_dir, 'mosaic')
os.makedirs(mosaic_dir, exist_ok=True)
# FIXME: Read bounds from EXTENT_UTM_PATH
xmin, ymin, xmax, ymax = [
261215.0000000000000000, 8620583.0000000000000000,
323691.8790999995544553, 8719912.0846999995410442
]
cmd = f"python3 {settings.S2M_CLI_PATH}/mosaic.py " \
f"-te {xmin} {ymin} {xmax} {ymax} " \
f"-e 32718 -res 10 -v " \
f"-p {settings.S2M_NUM_JOBS} " \
f"-o {mosaic_dir} {raw_dir}"
run_subprocess(cmd)
# Get mosaic band rasters
mosaic_rgb_paths = [
glob(os.path.join(mosaic_dir, f'*_{band}.tif'))
for band in ['B04', 'B03', 'B02']
]
mosaic_rgb_paths = [p[0] for p in mosaic_rgb_paths if p]
logger.info("RGB paths: %s", mosaic_rgb_paths)
# Use gdalbuildvrt to concatenate RGB bands from mosaic
vrt_path = os.path.join(mosaic_dir, 'tci.vrt')
cmd = f"gdalbuildvrt -separate {vrt_path} {' '.join(mosaic_rgb_paths)}"
run_subprocess(cmd)
# Clip to extent and rescale virtual raster
