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from TimeSeries.s2sen2cor import *
import planetary_computer as PC
from pystac_client import Client
import rasterio.mask
from Common.geotools import get_query_bbox
from pyproj import Transformer as T
from shapely.geometry import Polygon
from datetime import *
import geopandas as gpd
from scipy.interpolate import interp1d
def fetch(shp, dt, output_fld, auth=None, band_list=None):
bbox, i_bbox, shp_srs = get_query_bbox(shp, return_all=True)
if auth is not None:
os.environ['PC_SDK_SUBSCRIPTION_KEY'] = auth
api = Client.open('https://planetarycomputer.microsoft.com/api/stac/v1', modifier=PC.sign_inplace)
res = api.search(collections="sentinel-2-l2a", bbox=bbox, datetime=dt)
lst = ['B02','B03','B04','B05','B06','B07','B08','B8A','B11','B12','SCL']
if band_list is not None:
lst = band_list
prg = tqdm.tqdm(total=len(res.item_collection()) * len(lst), desc="Fetching from Planetary")
for item in res.items():
with rasterio.open(item.assets['B02'].href) as ds:
img_srs = ds.crs.to_epsg()
if shp_srs == img_srs:
o_bbox = [20 * round(x / 20) for x in i_bbox]
else:
tr = T.from_crs(shp_srs, img_srs, always_xy=True)
x_min, y_min = tr.transform(i_bbox[0], i_bbox[1])
x_max, y_max = tr.transform(i_bbox[2], i_bbox[3])
o_bbox = [20 * round(x / 20) for x in [x_min, y_min, x_max, y_max]]
ofn = os.path.join(output_fld, '/'.join(item.assets[a].get_absolute_href().split('?')[0].split('/')[10:]))
os.makedirs(os.path.dirname(ofn),exist_ok=True)
with rasterio.open(item.assets[a].href) as img:
out_img, out_geot = rasterio.mask.mask(img,
[Polygon.from_bounds(o_bbox[0], o_bbox[1],
o_bbox[2], o_bbox[3])],
crop=True)
out_meta = img.meta
out_meta.update({"driver": "GTiff",
"height": out_img.shape[1],
"width": out_img.shape[2],
"transform": out_geot})
with rasterio.open(ofn, "w", **out_meta) as dest:
dest.write(out_img)
prg.update()
prg.close()
if band_list is None:
return S2PlaneteryPipeline(output_fld)
else:
warnings.warn("Queried for a non-default band list. Skipping pipeline setup.")
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return ofiles
def split_dt_monthly(dt):
sdt, edt = [datetime.strptime(x,'%Y-%m-%d') for x in dt.split('/')]
dts = [sdt]
cdt = sdt
while cdt < edt:
cdt += timedelta(weeks=4)
dts.append(cdt)
if dts[-1] > edt:
dts = dts[:-1]
if dts[-1] < edt:
dts.append(edt+timedelta(1))
out = []
for i in range(len(dts)-1):
out.append(datetime.strftime(dts[i], '%Y-%m-%d') + '/' + datetime.strftime(dts[i+1]-timedelta(1), '%Y-%m-%d'))
return out
def sample(shp, dt, band_list, field_name, temp_dir = '/tmp', strategy='all', auth = None):
fd = dt.split('/')[0]
fd = datetime.strptime(fd,'%Y-%m-%d')
ed = fd + timedelta(5)
ndt = datetime.strftime(fd, '%Y-%m-%d') + '/' + datetime.strftime(ed, '%Y-%m-%d')
#fn = fetch(shp, ndt, temp_dir, band_list=[band_list[0]])
fn = ['/work/temp/S2B_MSIL2A_20210104T103329_N0212_R108_T30PVT_20210121T134941.SAFE/GRANULE/L2A_T30PVT_A020011_20210104T104033/IMG_DATA/R10m/T30PVT_20210104T103329_B04_10m.tif',
'/work/temp/S2B_MSIL2A_20210104T103329_N0212_R108_T30PUT_20210105T133826.SAFE/GRANULE/L2A_T30PUT_A020011_20210104T104033/IMG_DATA/R10m/T30PUT_20210104T103329_B04_10m.tif']
mos = otb.Registry.CreateApplication('Mosaic')
mos.SetParameterStringList('il', fn)
mos.Execute()
sts = otb.Registry.CreateApplication('PolygonClassStatistics')
sts.SetParameterInputImage('in', mos.GetParameterOutputImage('out'))
sts.SetParameterString('vec', shp)
sts.SetParameterString('field', field_name)
sts.SetParameterString('out', os.path.join(temp_dir, 'stats.xml'))
sts.ExecuteAndWriteOutput()
stats_fn = os.path.join(temp_dir, 'stats.xml')
samples_fn = os.path.join(temp_dir, 'samples.sqlite')
mos = otb.Registry.CreateApplication('Mosaic')
mos.SetParameterStringList('il', fn)
mos.Execute()
smp = otb.Registry.CreateApplication('SampleSelection')
smp.SetParameterInputImage('in', mos.GetParameterOutputImage('out'))
smp.SetParameterString('vec', shp)
smp.SetParameterString('instats', stats_fn)
smp.SetParameterString('field', field_name)
if isinstance(strategy, str):
smp.SetParameterString('strategy', strategy)
elif isinstance(strategy, int):
smp.SetParameterString('strategy','constant')
smp.SetParameterInt('strategy.constant.nb', strategy)
smp.SetParameterString('out', samples_fn)
smp.ExecuteAndWriteOutput()
ds = gpd.read_file(samples_fn)
coords = list(zip(list(ds.geometry.x),list(ds.geometry.y)))
bbox, _, _ = get_query_bbox(shp, return_all=True)
if auth is not None:
os.environ['PC_SDK_SUBSCRIPTION_KEY'] = auth
all_arr = []
dates = []
for dti in split_dt_monthly(dt):
api = Client.open('https://planetarycomputer.microsoft.com/api/stac/v1', modifier=PC.sign_inplace)
res = api.search(collections="sentinel-2-l2a", bbox=bbox, datetime=dti, sortby='datetime')
found = res.item_collection()
if 'SCL' not in band_list:
band_list.append('SCL')
arr = {x : np.empty((ds.shape[0],len(found))) for x in band_list}
i = 0
prg = tqdm.tqdm(total=len(found), desc="Sampling from Planetary on period {}".format(dti))
for item in found:
dates.append(item.datetime)
for band in band_list:
with rasterio.open(item.assets[band].href) as src:
arr[band][:,i] = np.array([x for x in src.sample(coords)]).flatten()
i += 1
prg.update()
prg.close()
api = None
all_arr.append(arr)
days = np.array([(x-dates[0]).days for x in dates])
final_arr = {}
for b in band_list:
final_arr[b] = np.hstack([x[b] for x in all_arr])
band_list.remove('SCL')
final_arr['SCL'] = np.invert(np.isin(final_arr['SCL'],[0,1,3,8,9,10]))
for i in tqdm.tqdm(range(ds.shape[0]), desc="Interpolating time series"):
x = days[final_arr['SCL'][i,:]]
for b in band_list:
y = final_arr[b][i,final_arr['SCL'][i,:]]
f = interp1d(x,y, fill_value='extrapolate')
final_arr[b][i,:] = f(days)
_, ii = np.unique(days, return_index=True)
for b in band_list:
final_arr[b] = final_arr[b][:,ii]
#[os.remove(x) for x in fn]
os.remove(stats_fn)
os.remove(samples_fn)
return final_arr, dates[ii], list(ds[field_name.lower()])
class S2PlanetaryTilePipeline(S2Sen2CorTilePipeline):
PTRN_10m = ['GRANULE/*/IMG_DATA/R10m/*_B02_10m.tif',
'GRANULE/*/IMG_DATA/R10m/*_B03_10m.tif',
'GRANULE/*/IMG_DATA/R10m/*_B04_10m.tif',
'GRANULE/*/IMG_DATA/R10m/*_B08_10m.tif']
PTRN_20m = ['GRANULE/*/IMG_DATA/R20m/*_B05_20m.tif',
'GRANULE/*/IMG_DATA/R20m/*_B06_20m.tif',
'GRANULE/*/IMG_DATA/R20m/*_B07_20m.tif',
'GRANULE/*/IMG_DATA/R20m/*_B8A_20m.tif',
'GRANULE/*/IMG_DATA/R20m/*_B11_20m.tif',
'GRANULE/*/IMG_DATA/R20m/*_B12_20m.tif']
PTRN_msk = ['GRANULE/*/IMG_DATA/R20m/*_SCL_20m.tif']
PTRN_ful = PTRN_10m[0:3] + PTRN_20m[0:3] + [PTRN_10m[3]] + PTRN_20m[3:]
class S2PlaneteryPipeline(S2Sen2CorPipeline):
S2TilePipeline = S2PlanetaryTilePipeline
_check = S2TilePipeline._check
_tile_id = S2TilePipeline._tile_id