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gen_toy.py
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281 lines (256 loc) · 17.6 KB
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from pathlib import Path
import numpy as np
import pandas as pd
import geopandas as gpd
import rasterio
from rasterio.windows import Window, bounds
from skmap.io import read_rasters, save_rasters
from skmap.mapper import SpaceTimeOverlay
from skmap.misc import ttprint
DEFAULT = {
'static_rasters': [
'https://s3.eu-central-1.wasabisys.com/eumap/dtm/dtm_elev.lowestmode_gedi.eml_mf_30m_0..0cm_2000..2018_eumap_epsg3035_v0.3.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/dtm/dtm_slope.percent_gedi.eml_m_30m_0..0cm_2000..2018_eumap_epsg3035_v0.3.tif'
],
'ndvi_rasters': [
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2014.12.02..2015.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2015.03.21..2015.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2015.06.25..2015.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2015.09.13..2015.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2015.12.02..2016.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2016.03.21..2016.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2016.06.25..2016.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2016.09.13..2016.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2016.12.02..2017.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2017.03.21..2017.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2017.06.25..2017.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2017.09.13..2017.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2017.12.02..2018.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2018.03.21..2018.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2018.06.25..2018.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2018.09.13..2018.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2018.12.02..2019.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2019.03.21..2019.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2019.06.25..2019.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2019.09.13..2019.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2019.12.02..2020.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2020.03.21..2020.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2020.06.25..2020.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_ndvi_landsat.glad.ard_p50_30m_0..0cm_2020.09.13..2020.12.01_eumap_epsg3035_v1.1.tif'
],
'swir1_rasters': [
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2014.12.02..2015.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2015.03.21..2015.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2015.06.25..2015.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2015.09.13..2015.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2015.12.02..2016.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2016.03.21..2016.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2016.06.25..2016.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2016.09.13..2016.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2016.12.02..2017.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2017.03.21..2017.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2017.06.25..2017.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2017.09.13..2017.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2017.12.02..2018.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2018.03.21..2018.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2018.06.25..2018.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2018.09.13..2018.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2018.12.02..2019.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2019.03.21..2019.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2019.06.25..2019.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2019.09.13..2019.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2019.12.02..2020.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2020.03.21..2020.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2020.06.25..2020.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_swir1_landsat.glad.ard_p50_30m_0..0cm_2020.09.13..2020.12.01_eumap_epsg3035_v1.1.tif'
],
'qa_ndvi_rasters': [
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2014.12.02..2015.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2015.03.21..2015.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2015.06.25..2015.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2015.09.13..2015.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2015.12.02..2016.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2016.03.21..2016.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2016.06.25..2016.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2016.09.13..2016.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2016.12.02..2017.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2017.03.21..2017.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2017.06.25..2017.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2017.09.13..2017.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2017.12.02..2018.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2018.03.21..2018.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2018.06.25..2018.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2018.09.13..2018.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2018.12.02..2019.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2019.03.21..2019.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2019.06.25..2019.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2019.09.13..2019.12.01_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2019.12.02..2020.03.20_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2020.03.21..2020.06.24_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2020.06.25..2020.09.12_eumap_epsg3035_v1.1.tif',
'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_qa_landsat.glad.ard_f_30m_0..0cm_2020.09.13..2020.12.01_eumap_epsg3035_v1.1.tif'
],
'window': Window(col_off=104020, row_off=74740, width=256, height=256),
'n_samples': 256,
'start_year': 2015,
'end_year': 2020,
'lc_raster': 'https://s3.eu-central-1.wasabisys.com/eumap/lcv/lcv_landcover.hcl_lucas.corine.eml_f_30m_0..0cm_{year}_eumap_epsg3035_v0.2.tif',
'lc_label_remap': {
'1': 'Continuous urban fabric',
'2': 'Discontinuous urban fabric',
'3': 'Industrial or commercial units',
'4': 'Road and rail networks and associated land',
'5': 'Port areas',
'6': 'Airports',
'7': 'Mineral extraction sites',
'8': 'Dump sites',
'9': 'Construction sites',
'10': 'Green urban areas',
'11': 'Sport and leisure facilities',
'12': 'Non-irrigated arable land',
'13': 'Permanently irrigated land',
'14': 'Rice fields',
'15': 'Vineyards',
'16': 'Fruit trees and berry plantations',
'17': 'Olive groves',
'18': 'Pastures',
'19': 'Annual crops associated with permanent crops',
'20': 'Complex cultivation patterns',
'21': 'Land principally occupied by agriculture, with significant areas of natural vegetation',
'22': 'Agro-forestry areas',
'23': 'Broad-leaved forest',
'24': 'Coniferous forest',
'25': 'Mixed forest',
'26': 'Natural grasslands',
'27': 'Moors and heathland',
'28': 'Sclerophyllous vegetation',
'29': 'Transitional woodland-shrub',
'30': 'Beaches, dunes, sands',
'31': 'Bare rocks',
'32': 'Sparsely vegetated areas',
'33': 'Burnt areas',
'34': 'Glaciers and perpetual snow',
'35': 'Inland marshes',
'36': 'Peat bogs',
'37': 'Salt marshes',
'38': 'Salines',
'39': 'Intertidal flats',
'40': 'Water courses',
'41': 'Water bodies',
'42': 'Coastal lagoons',
'43': 'Estuaries',
'48': 'Sea and ocean'
},
'lc_code_remap': {
'1': '111',
'2': '112',
'3': '121',
'4': '122',
'5': '123',
'6': '124',
'7': '131',
'8': '132',
'9': '133',
'10': '141',
'11': '142',
'12': '211',
'13': '212',
'14': '213',
'15': '221',
'16': '222',
'17': '223',
'18': '231',
'19': '241',
'20': '242',
'21': '243',
'22': '244',
'23': '311',
'24': '312',
'25': '313',
'26': '321',
'27': '322',
'28': '323',
'29': '324',
'30': '331',
'31': '332',
'32': '333',
'33': '334',
'34': '335',
'35': '411',
'36': '412',
'37': '421',
'38': '422',
'39': '423',
'40': '511',
'41': '512',
'42': '521',
'43': '522',
'48': '523'
},
'static_outdir': Path('skmap/data/toy/static'),
'ndvi_outdir': Path('skmap/data/toy/ndvi'),
'swir1_outdir': Path('skmap/data/toy/swir1'),
'samples_outdir': Path('skmap/data/toy/samples')
}
def _out_rasters(raster_files, basedir = 'data'):
out_files = []
for f in [
Path(basedir).joinpath(Path(f).name.replace('lcv_','')
.replace('dtm_','')
.replace('v0.2','v20230720')
.replace('2000..2018','20000101_20181231')
.replace('0..0cm','s')
.replace('..','_')
.replace('eumap','nl')
.replace('v1.1','v20230720')
.replace('epsg','epsg.')
.replace('glad.','')
.replace('ard','ard1')
)
for f in raster_files
]:
dt1 = str(f).split('_')[5]
dt2 = str(f).split('_')[6]
out_files.append((str(f).replace(dt1,dt1.replace('.','')).replace(dt2,dt2.replace('.',''))))
return out_files
def gen_dataset(start_year, end_year, static_rasters, swir1_rasters, ndvi_rasters, qa_ndvi_rasters, window, n_samples,
lc_raster, lc_label_remap, lc_code_remap, static_outdir, swir1_outdir, ndvi_outdir, samples_outdir):
ds = rasterio.open(ndvi_rasters[0])
ttprint("Reading static rasters")
static_data = read_rasters(raster_files=static_rasters, window=window)
ttprint("Reading temporal rasters")
swir1_data = read_rasters(raster_files=swir1_rasters, window=window)
ndvi_data = read_rasters(raster_files=ndvi_rasters, window=window)
ndvi_data = np.where(ndvi_data < 100, 100, ndvi_data) - 100
qa_data = read_rasters(raster_files=qa_ndvi_rasters, window=window)
qa_mask = ~np.isnan(qa_data)
ttprint("Saving static rasters")
save_rasters(static_rasters[0], _out_rasters(static_rasters, static_outdir), static_data, window=window)
ttprint("Saving temporal rasters")
save_rasters(swir1_rasters[0], _out_rasters(swir1_rasters, swir1_outdir), swir1_data, window=window, nodata = 255)
save_rasters(ndvi_rasters[0], _out_rasters(ndvi_rasters, ndvi_outdir.joinpath('filled')), ndvi_data, window=window, nodata = 255)
ndvi_data[qa_mask] = np.nan
save_rasters(ndvi_rasters[0], _out_rasters(ndvi_rasters, ndvi_outdir.joinpath('gappy')), ndvi_data, window=window, nodata = 255)
ttprint("Generating random LC samples")
x_min, y_min, x_max, y_max = bounds(window, ds.transform)
x = np.random.uniform(x_min, x_max, n_samples)
y = np.random.uniform(y_min, y_max, n_samples)
years = np.random.randint(start_year, end_year+1, n_samples)
samples = gpd.GeoDataFrame(
data={'date': pd.to_datetime(years, format='%Y')},
geometry=gpd.GeoSeries(gpd.points_from_xy(x, y, crs=ds.crs))
)
ttprint("Running spacetime overlay")
spt_overlay = SpaceTimeOverlay(samples, 'date', [ lc_raster ])
samples_overlaid = spt_overlay.run()
rename_col = {}
rename_col[samples_overlaid.columns[-1]] = 'target'
samples_overlaid = samples_overlaid.drop(columns=['overlay_id']) \
.rename(columns=rename_col)
samples_overlaid['target'] = samples_overlaid['target'].astype('int')
samples_overlaid['label'] = samples_overlaid['target'].astype('int').astype('str').replace(lc_label_remap)
samples_overlaid['code'] = samples_overlaid['target'].astype('int').astype('str').replace(lc_code_remap)
ttprint("Saving land-cover samples")
samples_outdir.mkdir(parents=True, exist_ok=True)
samples_overlaid[['date','label','code','target','geometry']].to_file(samples_outdir.joinpath('samples.gpkg'))
gen_dataset(**DEFAULT)