def test_cog_mem_dask(tmpdir):
pp = Path(str(tmpdir))
xx, ds = gen_test_data(pp, dask=True)
# write to memory 1
bb = write_cog(xx, ":mem:")
assert isinstance(bb, Delayed)
bb = bb.compute()
assert isinstance(bb, bytes)
path = pp / "cog1.tiff"
with open(str(path), "wb") as f:
f.write(bb)
yy = rio_slurp_xarray(path)
np.testing.assert_array_equal(yy.values, xx.values)
assert yy.geobox == xx.geobox
assert yy.nodata == xx.nodata
# write to memory 2
bb = to_cog(xx)
assert isinstance(bb, Delayed)
bb = bb.compute()
assert isinstance(bb, bytes)
path = pp / "cog2.tiff"
with open(str(path), "wb") as f:
f.write(bb)
yy = rio_slurp_xarray(path)
np.testing.assert_array_equal(yy.values, xx.values)
assert yy.geobox == xx.geobox
assert yy.nodata == xx.nodata
def add_chirps(
urls: Dict[Any, Any],
ds: xr.Dataset,
era: str,
training: bool = True,
dask_chunks: Dict[Any, Any] = {
"x": "auto",
"y": "auto"
},
) -> Optional[xr.Dataset]:
# load rainfall climatology
if era == "_S1":
chirps = rio_slurp_xarray(urls["chirps"][0])
if era == "_S2":
chirps = rio_slurp_xarray(urls["chirps"][1])
if chirps.size >= 2:
if training:
chirps = xr_reproject(chirps, ds.geobox, "bilinear")
ds["rain"] = chirps
else:
# Clip CHIRPS to ~ S2 tile boundaries so we can handle NaNs local to S2 tile
xmin, xmax = ds.x.values[0], ds.x.values[-1]
ymin, ymax = ds.y.values[0], ds.y.values[-1]
inProj = Proj("epsg:6933")
outProj = Proj("epsg:4326")
xmin, ymin = transform(inProj, outProj, xmin, ymin)
xmax, ymax = transform(inProj, outProj, xmax, ymax)
# create lat/lon indexing slices - buffer S2 bbox by 0.05deg
if (xmin < 0) & (xmax < 0):
x_slice = list(np.arange(xmin + 0.05, xmax - 0.05, -0.05))
else:
x_slice = list(np.arange(xmax - 0.05, xmin + 0.05, 0.05))
y_slice = list(np.arange(ymin - 0.05, ymax + 0.1, 0.05))
# index global chirps using buffered s2 tile bbox
chirps = assign_crs(
chirps.sel(longitude=y_slice,
latitude=x_slice,
method="nearest"))
# fill any NaNs in CHIRPS with local (s2-tile bbox) mean
chirps = chirps.fillna(chirps.mean())
chirps = xr_reproject(chirps, ds.geobox, "bilinear")
chirps = chirps.chunk(dask_chunks)
ds["rain"] = chirps
# rename bands to include era
for band in ds.data_vars:
ds = ds.rename({band: band + era})
return ds
return None
def add_chirps(ds, era, training=True, dask_chunks={'x': 'auto', 'y': 'auto'}):
# load rainfall climatology
if era == "_S1":
chirps = rio_slurp_xarray(
"s3://deafrica-input-datasets/rainfall/CHPclim_jan_jun_cumulative_rainfall.tif"
)
if era == "_S2":
chirps = rio_slurp_xarray(
"s3://deafrica-input-datasets/rainfall/CHPclim_jul_dec_cumulative_rainfall.tif"
)
if training:
chirps = xr_reproject(chirps, ds.geobox, "bilinear")
ds["rain"] = chirps
else:
# Clip CHIRPS to ~ S2 tile boundaries so we can handle NaNs local to S2 tile
xmin, xmax = ds.x.values[0], ds.x.values[-1]
ymin, ymax = ds.y.values[0], ds.y.values[-1]
inProj = Proj("epsg:6933")
outProj = Proj("epsg:4326")
xmin, ymin = transform(inProj, outProj, xmin, ymin)
xmax, ymax = transform(inProj, outProj, xmax, ymax)
# create lat/lon indexing slices - buffer S2 bbox by 0.05deg
if (xmin < 0) & (xmax < 0):
x_slice = list(np.arange(xmin + 0.05, xmax - 0.05, -0.05))
else:
x_slice = list(np.arange(xmax - 0.05, xmin + 0.05, 0.05))
if (ymin < 0) & (ymax < 0):
y_slice = list(np.arange(ymin + 0.05, ymax - 0.05, -0.05))
else:
y_slice = list(np.arange(ymin - 0.05, ymax + 0.05, 0.05))
# index global chirps using buffered s2 tile bbox
chirps = assign_crs(
chirps.sel(longitude=y_slice, latitude=x_slice, method="nearest"))
# fill any NaNs in CHIRPS with local (s2-tile bbox) mean
chirps = chirps.fillna(chirps.mean())
chirps = xr_reproject(chirps, ds.geobox, "bilinear")
chirps = chirps.chunk(dask_chunks)
ds["rain"] = chirps
#rename bands to include era
for band in ds.data_vars:
ds = ds.rename({band: band + era})
return ds
def post_processing(predicted: xr.Dataset, ) -> xr.DataArray:
"""
filter prediction results with post processing filters.
Simplified from production code to skip
segmentation, probability, and mode calcs
"""
dc = Datacube(app='whatever')
predict = predicted.Predictions
#--Post process masking---------------------------------------------------------------
#print(" masking with AEZ,WDPA,WOfS,slope & elevation")
# mask out classification beyond AEZ boundary
gdf = gpd.read_file('data/Southern.shp').to_crs('epsg:6933')
with HiddenPrints():
mask = xr_rasterize(gdf, predicted)
predict = predict.where(mask, 0)
# mask with WDPA
url_wdpa = "s3://deafrica-input-datasets/protected_areas/WDPA_southern.tif"
wdpa = rio_slurp_xarray(url_wdpa, gbox=predicted.geobox)
wdpa = wdpa.astype(bool)
predict = predict.where(~wdpa, 0)
#mask with WOFS
wofs = dc.load(product='wofs_ls_summary_annual',
like=predicted.geobox,
time=('2019'))
wofs = wofs.frequency > 0.2 # threshold
predict = predict.where(~wofs, 0)
#mask steep slopes
url_slope = "https://deafrica-input-datasets.s3.af-south-1.amazonaws.com/srtm_dem/srtm_africa_slope.tif"
slope = rio_slurp_xarray(url_slope, gbox=predicted.geobox)
slope = slope > 50
predict = predict.where(~slope, 0)
#mask where the elevation is above 3600m
elevation = dc.load(product='dem_srtm', like=predicted.geobox)
elevation = elevation.elevation > 3600 # threshold
predict = predict.where(~elevation.squeeze(), 0)
#set dtype
predict = predict.astype(np.int8)
return predict
def test_cog_file(tmpdir, opts):
pp = Path(str(tmpdir))
xx, ds = gen_test_data(pp)
# write to file
ff = write_cog(xx, pp / "cog.tif", **opts)
assert isinstance(ff, Path)
assert ff == pp / "cog.tif"
assert ff.exists()
yy = rio_slurp_xarray(pp / "cog.tif")
np.testing.assert_array_equal(yy.values, xx.values)
assert yy.geobox == xx.geobox
assert yy.nodata == xx.nodata
_write_cog(np.stack([xx.values, xx.values]),
xx.geobox,
pp / "cog-2-bands.tif",
overview_levels=[],
**opts)
yy, mm = rio_slurp(pp / "cog-2-bands.tif")
assert mm.gbox == xx.geobox
assert yy.shape == (2, *xx.shape)
np.testing.assert_array_equal(yy[0], xx.values)
np.testing.assert_array_equal(yy[1], xx.values)
with pytest.raises(ValueError, match="Need 2d or 3d ndarray on input"):
_write_cog(xx.values.ravel(), xx.geobox, pp / "wontwrite.tif")
# sizes that are not multiples of 16
# also check that supplying `nodata=` doesn't break things
xx_odd = xx[:23, :63]
ff = write_cog(xx_odd,
pp / "cog_odd.tif",
nodata=xx_odd.attrs["nodata"],
**opts)
assert isinstance(ff, Path)
assert ff == pp / "cog_odd.tif"
assert ff.exists()
yy = rio_slurp_xarray(pp / "cog_odd.tif")
np.testing.assert_array_equal(yy.values, xx_odd.values)
assert yy.geobox == xx_odd.geobox
assert yy.nodata == xx_odd.nodata
with pytest.warns(UserWarning):
write_cog(xx, pp / "cog_badblocksize.tif", blocksize=50)
def post_processing(
predicted: xr.Dataset,
) -> xr.DataArray:
"""
filter prediction results with post processing filters.
:param predicted: The prediction results
"""
dc = Datacube(app='whatever')
#grab predictions and proba for post process filtering
predict=predicted.Predictions
# mask out classification beyond AEZ boundary
gdf = gpd.read_file('data/Western.geojson')
with HiddenPrints():
mask = xr_rasterize(gdf, predicted)
predict = predict.where(mask,0)
# mask with WDPA
url_wdpa="s3://deafrica-input-datasets/protected_areas/WDPA_western.tif"
wdpa=rio_slurp_xarray(url_wdpa, gbox=predicted.geobox)
wdpa = wdpa.astype(bool)
predict = predict.where(~wdpa, 0)
#mask with WOFS
wofs=dc.load(product='ga_ls8c_wofs_2_summary',like=predicted.geobox)
wofs=wofs.frequency > 0.2 # threshold
predict=predict.where(~wofs, 0)
#mask steep slopes
url_slope="https://deafrica-data.s3.amazonaws.com/ancillary/dem-derivatives/cog_slope_africa.tif"
slope=rio_slurp_xarray(url_slope, gbox=predicted.geobox)
slope=slope > 35
predict=predict.where(~slope, 0)
#mask where the elevation is above 3600m
elevation=dc.load(product='dem_srtm', like=predicted.geobox)
elevation=elevation.elevation > 3600 # threshold
predict=predict.where(~elevation.squeeze(), 0)
#set dtype
predict=predict.astype(np.int8)
return predict
def test_cog_file(tmpdir):
pp = Path(str(tmpdir))
xx, ds = gen_test_data(pp)
# write to file
ff = write_cog(xx, pp / "cog.tif")
assert isinstance(ff, Path)
assert ff == pp / "cog.tif"
assert ff.exists()
yy = rio_slurp_xarray(pp / "cog.tif")
np.testing.assert_array_equal(yy.values, xx.values)
assert yy.geobox == xx.geobox
assert yy.nodata == xx.nodata
_write_cog(np.stack([xx.values, xx.values]),
xx.geobox,
pp / "cog-2-bands.tif",
overview_levels=[])
yy, mm = rio_slurp(pp / "cog-2-bands.tif")
assert mm.gbox == xx.geobox
assert yy.shape == (2, *xx.shape)
np.testing.assert_array_equal(yy[0], xx.values)
np.testing.assert_array_equal(yy[1], xx.values)
with pytest.raises(ValueError, match="Need 2d or 3d ndarray on input"):
_write_cog(xx.values.ravel(), xx.geobox, pp / "wontwrite.tif")
def test_cog_rgba(tmpdir, use_windowed_writes):
pp = Path(str(tmpdir))
xx, ds = gen_test_data(pp)
pix = np.dstack([xx.values] * 4)
rgba = xr.DataArray(pix,
attrs=xx.attrs,
dims=("y", "x", "band"),
coords=xx.coords)
assert rgba.geobox == xx.geobox
assert rgba.shape[:2] == rgba.geobox.shape
ff = write_cog(rgba,
pp / "cog.tif",
use_windowed_writes=use_windowed_writes)
yy = rio_slurp_xarray(ff)
assert yy.geobox == rgba.geobox
assert yy.shape == rgba.shape
np.testing.assert_array_equal(yy.values, rgba.values)
with pytest.raises(ValueError):
_write_cog(
rgba.values[1:, :, :],
rgba.geobox,
":mem:",
use_windowed_writes=use_windowed_writes,
)
def gm_mads_two_seasons_production(ds1, ds2):
"""
Feature layer function for production run of
eastern crop-mask
"""
def fun(ds, era):
# normalise SR and edev bands
for band in ds.data_vars:
if band not in ["sdev", "bcdev"]:
ds[band] = ds[band] / 10000
gm_mads = calculate_indices(
ds,
index=["NDVI", "LAI", "MNDWI"],
drop=False,
normalise=False,
collection="s2",
)
gm_mads["sdev"] = -np.log(gm_mads["sdev"])
gm_mads["bcdev"] = -np.log(gm_mads["bcdev"])
gm_mads["edev"] = -np.log(gm_mads["edev"])
# rainfall climatology
if era == "_S1":
chirps = assign_crs(
xr.open_rasterio(
"/g/data/CHIRPS/cumulative_alltime/CHPclim_jan_jun_cumulative_rainfall.nc"
),
crs="epsg:4326",
)
if era == "_S2":
chirps = assign_crs(
xr.open_rasterio(
"/g/data/CHIRPS/cumulative_alltime/CHPclim_jul_dec_cumulative_rainfall.nc"
),
crs="epsg:4326",
)
chirps = xr_reproject(chirps, ds.geobox, "bilinear")
gm_mads["rain"] = chirps
for band in gm_mads.data_vars:
gm_mads = gm_mads.rename({band: band + era})
return gm_mads
epoch1 = fun(ds1, era="_S1")
epoch2 = fun(ds2, era="_S2")
# slope
url_slope = "https://deafrica-data.s3.amazonaws.com/ancillary/dem-derivatives/cog_slope_africa.tif"
slope = rio_slurp_xarray(url_slope, gbox=ds1.geobox)
slope = slope.to_dataset(name="slope")
result = xr.merge([epoch1, epoch2, slope], compat="override")
result = result.astype(np.float32)
return result.squeeze()
def gm_mads_two_seasons_training(query):
#connect to the datacube
dc = datacube.Datacube(app='feature_layers')
#load S2 geomedian
ds = dc.load(product='gm_s2_semiannual', **query)
# load the data
dss = {"S1": ds.isel(time=0), "S2": ds.isel(time=1)}
#create features
epoch1 = common_ops(dss["S1"], era="_S1")
epoch1 = add_chirps(epoch1, era='_S1')
epoch2 = common_ops(dss["S2"], era="_S2")
epoch2 = add_chirps(epoch2, era='_S2')
# add slope
url_slope = "https://deafrica-input-datasets.s3.af-south-1.amazonaws.com/srtm_dem/srtm_africa_slope.tif"
slope = rio_slurp_xarray(url_slope, gbox=ds.geobox)
slope = slope.to_dataset(name="slope")
result = xr.merge([epoch1, epoch2, slope], compat="override")
return result.astype(np.float32).squeeze()
def gm_mads_two_seasons_predict(ds):
dc = datacube.Datacube(app="training")
ds = ds / 10000
ds1 = ds.sel(time=slice("2019-01", "2019-06"))
ds2 = ds.sel(time=slice("2019-07", "2019-12"))
def fun(ds, era):
# geomedian and tmads
# gm_mads = xr_geomedian_tmad(ds)
gm_mads = xr_geomedian_tmad_new(ds).compute()
gm_mads = calculate_indices(
gm_mads,
index=["NDVI", "LAI", "MNDWI"],
drop=False,
normalise=False,
collection="s2",
)
gm_mads["sdev"] = -np.log(gm_mads["sdev"])
gm_mads["bcdev"] = -np.log(gm_mads["bcdev"])
gm_mads["edev"] = -np.log(gm_mads["edev"])
gm_mads = gm_mads.chunk({"x": 2000, "y": 2000})
# rainfall climatology
if era == "_S1":
chirps = assign_crs(
xr.open_rasterio(
"/g/data/CHIRPS/cumulative_alltime/CHPclim_jan_jun_cumulative_rainfall.nc"
),
crs="epsg:4326",
)
if era == "_S2":
chirps = assign_crs(
xr.open_rasterio(
"/g/data/CHIRPS/cumulative_alltime/CHPclim_jul_dec_cumulative_rainfall.nc"
),
crs="epsg:4326",
)
chirps = xr_reproject(chirps, ds.geobox, "bilinear")
chirps = chirps.chunk({"x": 2000, "y": 2000})
gm_mads["rain"] = chirps
for band in gm_mads.data_vars:
gm_mads = gm_mads.rename({band: band + era})
return gm_mads
epoch1 = fun(ds1, era="_S1")
epoch2 = fun(ds2, era="_S2")
# slope
url_slope = "https://deafrica-data.s3.amazonaws.com/ancillary/dem-derivatives/cog_slope_africa.tif"
slope = rio_slurp_xarray(url_slope, gbox=ds.geobox)
slope = slope.to_dataset(name="slope").chunk({"x": 2000, "y": 2000})
result = xr.merge([epoch1, epoch2, slope], compat="override")
return result.squeeze()
def gm_mads_two_seasons_prediction(
datasets,
geobox,
measurements: List[str],
urls: Dict[Any, Any],
dask_chunks: Dict[str, Any] = {
"x": -1,
"y": -1
},
) -> Optional[xr.Dataset]:
"""
Feature layer function for production run of
eastern crop-mask. Similar to the training function
but data is loaded internally, CHIRPS is reprojected differently,
and dask chunks are used.
"""
ds = load_with_native_transform(
datasets,
geobox=geobox,
native_transform=lambda x: drop_nan_nodata(x),
bands=measurements,
chunks=dask_chunks,
resampling="bilinear",
)
dss = {
"S1": ds.isel(spec=0).drop(["spatial_ref", "spec"]),
"S2": ds.isel(spec=1).drop(["spatial_ref", "spec"]),
}
# create features
epoch1 = common_ops(dss["S1"], era="_S1")
epoch1 = add_chirps(urls,
epoch1,
era="_S1",
training=False,
dask_chunks=dask_chunks)
epoch2 = common_ops(dss["S2"], era="_S2")
epoch2 = add_chirps(urls,
epoch2,
era="_S2",
training=False,
dask_chunks=dask_chunks)
if (not epoch1) or (not epoch2):
return None
# add slope
url_slope = urls["slope"]
slope = rio_slurp_xarray(url_slope, gbox=ds.geobox)
slope = slope.to_dataset(name="slope").chunk(dask_chunks)
result = xr.merge([epoch1, epoch2, slope], compat="override")
result = result.astype(np.float32)
return result.squeeze()
def gm_mads_two_seasons_prediction(geobox, dask_chunks):
"""
Feature layer function for production run of
eastern crop-mask. Similar to the training function
but data is loaded internally, CHIRPS is reprojected differently,
and dask chunks are used.
"""
dc = datacube.Datacube(app="prediction")
# load the data
measurements = [
"blue",
"green",
"red",
"nir",
"swir_1",
"swir_2",
"red_edge_1",
"red_edge_2",
"red_edge_3",
"bcdev",
"edev",
"sdev",
]
ds = dc.load(product="gm_s2_semiannual",
time="2019",
measurements=measurements,
like=geobox,
dask_chunks=dask_chunks,
resampling='bilinear')
dss = {"S1": ds.isel(time=0), "S2": ds.isel(time=1)}
#create features
epoch1 = common_ops(dss["S1"], era="_S1")
epoch1 = add_chirps(epoch1,
era='_S1',
training=False,
dask_chunks=dask_chunks)
epoch2 = common_ops(dss["S2"], era="_S2")
epoch2 = add_chirps(epoch2,
era='_S2',
training=False,
dask_chunks=dask_chunks)
# add slope
url_slope = "https://deafrica-input-datasets.s3.af-south-1.amazonaws.com/srtm_dem/srtm_africa_slope.tif"
slope = rio_slurp_xarray(url_slope, gbox=ds.geobox)
slope = slope.to_dataset(name="slope").chunk(dask_chunks)
result = xr.merge([epoch1, epoch2, slope], compat="override")
result = result.astype(np.float32)
return result.squeeze()
def annual_gm_mads_evi_training(ds):
dc = datacube.Datacube(app='training')
# grab gm+tmads
gm_mads=dc.load(product='ga_s2_gm',time='2019',like=ds.geobox,
measurements=['red', 'blue', 'green', 'nir',
'swir_1', 'swir_2', 'red_edge_1',
'red_edge_2', 'red_edge_3', 'SMAD',
'BCMAD','EMAD'])
gm_mads['SMAD'] = -np.log(gm_mads['SMAD'])
gm_mads['BCMAD'] = -np.log(gm_mads['BCMAD'])
gm_mads['EMAD'] = -np.log(gm_mads['EMAD']/10000)
#calculate band indices on gm
gm_mads = calculate_indices(gm_mads,
index=['EVI','LAI','MNDWI'],
drop=False,
collection='s2')
#normalise spectral GM bands 0-1
for band in gm_mads.data_vars:
if band not in ['SMAD', 'BCMAD','EMAD', 'EVI', 'LAI', 'MNDWI']:
gm_mads[band] = gm_mads[band] / 10000
#calculate EVI on annual timeseries
evi = calculate_indices(ds,index=['EVI'], drop=True, normalise=True, collection='s2')
# EVI stats
gm_mads['evi_std'] = evi.EVI.std(dim='time')
gm_mads['evi_10'] = evi.EVI.quantile(0.1, dim='time')
gm_mads['evi_25'] = evi.EVI.quantile(0.25, dim='time')
gm_mads['evi_75'] = evi.EVI.quantile(0.75, dim='time')
gm_mads['evi_90'] = evi.EVI.quantile(0.9, dim='time')
gm_mads['evi_range'] = gm_mads['evi_90'] - gm_mads['evi_10']
#rainfall climatology
chirps_S1 = xr_reproject(assign_crs(xr.open_rasterio('/g/data/CHIRPS/cumulative_alltime/CHPclim_jan_jun_cumulative_rainfall.nc'),
crs='epsg:4326'), ds.geobox,"bilinear")
chirps_S2 = xr_reproject(assign_crs(xr.open_rasterio('/g/data/CHIRPS/cumulative_alltime/CHPclim_jul_dec_cumulative_rainfall.nc'),
crs='epsg:4326'), ds.geobox,"bilinear")
gm_mads['rain_S1'] = chirps_S1
gm_mads['rain_S2'] = chirps_S2
#slope
url_slope = "https://deafrica-data.s3.amazonaws.com/ancillary/dem-derivatives/cog_slope_africa.tif"
slope = rio_slurp_xarray(url_slope, gbox=ds.geobox)
slope = slope.to_dataset(name='slope')#.chunk({'x':2000,'y':2000})
result = xr.merge([gm_mads,slope],compat='override')
return result.squeeze()
def gm_mads_two_seasons_predict(ds):
dc = datacube.Datacube(app='training')
ds = ds / 10_000
ds1 = ds.sel(time=slice('2019-01', '2019-06'))
ds2 = ds.sel(time=slice('2019-07', '2019-12'))
def fun(ds, era):
#geomedian and tmads
#gm_mads = xr_geomedian_tmad(ds)
gm_mads = xr_geomedian_tmad_new(ds).compute()
gm_mads = calculate_indices(gm_mads,
index=['NDVI', 'LAI', 'MNDWI'],
drop=False,
normalise=False,
collection='s2')
gm_mads['sdev'] = -np.log(gm_mads['sdev'])
gm_mads['bcdev'] = -np.log(gm_mads['bcdev'])
gm_mads['edev'] = -np.log(gm_mads['edev'])
gm_mads = gm_mads.chunk({'x': 2000, 'y': 2000})
#rainfall climatology
if era == '_S1':
chirps = assign_crs(xr.open_rasterio(
'/g/data/CHIRPS/cumulative_alltime/CHPclim_jan_jun_cumulative_rainfall.nc'
),
crs='epsg:4326')
if era == '_S2':
chirps = assign_crs(xr.open_rasterio(
'/g/data/CHIRPS/cumulative_alltime/CHPclim_jul_dec_cumulative_rainfall.nc'
),
crs='epsg:4326')
chirps = xr_reproject(chirps, ds.geobox, "bilinear")
chirps = chirps.chunk({'x': 2000, 'y': 2000})
gm_mads['rain'] = chirps
for band in gm_mads.data_vars:
gm_mads = gm_mads.rename({band: band + era})
return gm_mads
epoch1 = fun(ds1, era='_S1')
epoch2 = fun(ds2, era='_S2')
#slope
url_slope = "https://deafrica-data.s3.amazonaws.com/ancillary/dem-derivatives/cog_slope_africa.tif"
slope = rio_slurp_xarray(url_slope, gbox=ds.geobox)
slope = slope.to_dataset(name='slope').chunk({'x': 2000, 'y': 2000})
result = xr.merge([epoch1, epoch2, slope], compat='override')
return result.squeeze()
def test_cog_mem(tmpdir, shape):
pp = Path(str(tmpdir))
xx, ds = gen_test_data(pp, shape=shape)
# write to memory 1
bb = write_cog(xx, ":mem:")
assert isinstance(bb, bytes)
path = pp / "cog1.tiff"
with open(str(path), "wb") as f:
f.write(bb)
yy = rio_slurp_xarray(path)
np.testing.assert_array_equal(yy.values, xx.values)
assert yy.geobox == xx.geobox
assert yy.nodata == xx.nodata
# write to memory 2
bb = to_cog(xx)
assert isinstance(bb, bytes)
path = pp / "cog2.tiff"
with open(str(path), "wb") as f:
f.write(bb)
yy = rio_slurp_xarray(path)
np.testing.assert_array_equal(yy.values, xx.values)
assert yy.geobox == xx.geobox
assert yy.nodata == xx.nodata
# write to memory 3 -- no overviews
bb = to_cog(xx, overview_levels=[])
assert isinstance(bb, bytes)
path = pp / "cog3.tiff"
with open(str(path), "wb") as f:
f.write(bb)
yy = rio_slurp_xarray(path)
np.testing.assert_array_equal(yy.values, xx.values)
assert yy.geobox == xx.geobox
assert yy.nodata == xx.nodata
def merge_tile_ds(
x: int,
y: int,
config: FeaturePathConfig,
geobox_dict: Dict[Tuple, GeoBox],
gm_ds: Optional[xr.Dataset] = None,
) -> Tuple[str, GeoBox, xr.Dataset]:
"""
overall all tile tifs and additional features merged here,
the xarray dataset, 3 extra indi:withces, integration of rainfall, slope with gm_ds
:param gm_ds:
:param x: tile index x
:param y: time inde y
:param config: FeaturePathConfig containing the model path and product info`et al.
:param geobox_dict: geobox will calculate the tile geometry from the tile index
:return: subfolder path and the xarray dataset of the features
"""
# this folder naming x, y will change
subfld = "x{x:+04d}/y{y:+04d}".format(x=x, y=y)
P6M_tifs: Dict = get_tifs_paths(config.TIF_path, subfld)
geobox = geobox_dict[(x, y)]
seasoned_ds = {}
for k, tifs in P6M_tifs.items():
era = "_S1" if "2019-01--P6M" in k else "_S2"
if not gm_ds:
# no prepare base ds
base_ds = merge_tifs_into_ds(k,
tifs,
rename_dict=config.rename_dict)
else:
base_ds = gm_ds
# TODO: to validate the 6month geomedia is down scaled already.
base_ds = down_scale_gm_band(base_ds)
seasoned_ds[era] = complete_gm_mads(base_ds, geobox, era)
slope = (rio_slurp_xarray(
config.url_slope,
gbox=geobox).drop("spatial_ref").to_dataset(name="slope"))
return (
subfld,
geobox,
xr.merge([seasoned_ds["_S1"], seasoned_ds["_S2"], slope],
compat="override").chunk({
"x": -1,
"y": -1
}),
)
def test_cog_file_dask(tmpdir):
pp = Path(str(tmpdir))
xx, ds = gen_test_data(pp, dask=True)
assert dask.is_dask_collection(xx)
path = pp / "cog.tif"
ff = write_cog(xx, path, overview_levels=[2, 4])
assert isinstance(ff, Delayed)
assert path.exists() is False
assert ff.compute() == path
assert path.exists()
yy = rio_slurp_xarray(pp / "cog.tif")
np.testing.assert_array_equal(yy.values, xx.values)
assert yy.geobox == xx.geobox
assert yy.nodata == xx.nodata
def test_cog_rgba(tmpdir):
pp = Path(str(tmpdir))
xx, ds = gen_test_data(pp)
pix = np.dstack([xx.values] * 4)
rgba = xr.DataArray(pix,
attrs=xx.attrs,
dims=('y', 'x', 'band'),
coords=xx.coords)
assert(rgba.geobox == xx.geobox)
assert(rgba.shape[:2] == rgba.geobox.shape)
ff = write_cog(rgba, pp / "cog.tif")
yy = rio_slurp_xarray(ff)
assert(yy.geobox == rgba.geobox)
assert(yy.shape == rgba.shape)
np.testing.assert_array_equal(yy.values, rgba.values)
with pytest.raises(ValueError):
_write_cog(rgba.values[1:, :, :], rgba.geobox, ':mem:')
def gm_mads_evi_rainfall(ds):
"""
6 monthly and annual
gm + mads
evi stats (10, 50, 90 percentile, range, std)
rainfall actual stats (min, mean, max, range, std) from monthly data
rainfall clim stats (min, mean, max, range, std) from monthly data
"""
dc = datacube.Datacube(app='training')
ds = ds / 10000
ds = ds.rename({'nir_1':'nir_wide', 'nir_2':'nir'})
ds1 = ds.sel(time=slice('2019-01', '2019-06'))
ds2 = ds.sel(time=slice('2019-07', '2019-12'))
chirps = []
chpclim = []
for m in range(1,13):
chirps.append(xr_reproject(assign_crs(xr.open_rasterio(f'/g/data/CHIRPS/monthly_2019/chirps-v2.0.2019.{m:02d}.tif').squeeze().expand_dims({'time':[m]}), crs='epsg:4326'),
ds.geobox, "bilinear"))
chpclim.append(rio_slurp_xarray(f'https://deafrica-data-dev.s3.amazonaws.com/product-dev/deafrica_chpclim_50n_50s_{m:02d}.tif', gbox=ds.geobox,
resapling='bilinear').expand_dims({'time':[m]}))
chirps = xr.concat(chirps, dim='time')
chpclim = xr.concat(chpclim, dim='time')
def fun(ds, chirps, chpclim, era):
ds = calculate_indices(ds,
index=['EVI'],
drop=False,
normalise=False,
collection='s2')
#geomedian and tmads
gm_mads = xr_geomedian_tmad(ds)
gm_mads = calculate_indices(gm_mads,
index=['EVI','NDVI','LAI','MNDWI'],
drop=False,
normalise=False,
collection='s2')
gm_mads['sdev'] = -np.log(gm_mads['sdev'])
gm_mads['bcdev'] = -np.log(gm_mads['bcdev'])
gm_mads['edev'] = -np.log(gm_mads['edev'])
# EVI stats
gm_mads['evi_10'] = ds.EVI.quantile(0.1, dim='time')
gm_mads['evi_50'] = ds.EVI.quantile(0.5, dim='time')
gm_mads['evi_90'] = ds.EVI.quantile(0.9, dim='time')
gm_mads['evi_range'] = gm_mads['evi_90'] - gm_mads['evi_10']
gm_mads['evi_std'] = ds.EVI.std(dim='time')
# rainfall actual
gm_mads['rain_min'] = chirps.min(dim='time')
gm_mads['rain_mean'] = chirps.mean(dim='time')
gm_mads['rain_max'] = chirps.max(dim='time')
gm_mads['rain_range'] = gm_mads['rain_max'] - gm_mads['rain_min']
gm_mads['rain_std'] = chirps.std(dim='time')
# rainfall climatology
gm_mads['rainclim_min'] = chpclim.min(dim='time')
gm_mads['rainclim_mean'] = chpclim.mean(dim='time')
gm_mads['rainclim_max'] = chpclim.max(dim='time')
gm_mads['rainclim_range'] = gm_mads['rainclim_max'] - gm_mads['rainclim_min']
gm_mads['rainclim_std'] = chpclim.std(dim='time')
for band in gm_mads.data_vars:
gm_mads = gm_mads.rename({band:band+era})
return gm_mads
epoch0 = fun(ds, chirps, chpclim, era='_S0')
time, month = slice('2019-01', '2019-06'), slice(1, 6)
epoch1 = fun(ds.sel(time=time), chirps.sel(time=month), chpclim.sel(time=month), era='_S1')
time, month = slice('2019-07', '2019-12'), slice(7, 12)
epoch2 = fun(ds.sel(time=time), chirps.sel(time=month), chpclim.sel(time=month), era='_S2')
#slope
url_slope = "https://deafrica-data.s3.amazonaws.com/ancillary/dem-derivatives/cog_slope_africa.tif"
slope = rio_slurp_xarray(url_slope, gbox=ds.geobox)
slope = slope.to_dataset(name='slope')
result = xr.merge([epoch0,
epoch1,
epoch2,
slope],compat='override')
return result.squeeze()
def test_rio_slurp(tmpdir):
w, h, dtype, nodata, ndw = 96, 64, 'int16', -999, 7
pp = Path(str(tmpdir))
aa = mk_test_image(w, h, dtype, nodata, nodata_width=ndw)
assert aa.shape == (h, w)
assert aa.dtype.name == dtype
assert aa[10, 30] == (30 << 8) | 10
assert aa[10, 11] == nodata
aa0 = aa.copy()
mm0 = write_gtiff(pp / "rio-slurp-aa.tif", aa, nodata=-999, overwrite=True)
mm00 = write_gtiff(pp / "rio-slurp-aa-missing-nodata.tif",
aa,
nodata=None,
overwrite=True)
aa, mm = rio_slurp(mm0.path)
np.testing.assert_array_equal(aa, aa0)
assert mm.gbox == mm0.gbox
assert aa.shape == mm.gbox.shape
xx = rio_slurp_xarray(mm0.path)
assert mm.gbox == xx.geobox
np.testing.assert_array_equal(xx.values, aa0)
aa, mm = rio_slurp(mm0.path, aa0.shape)
np.testing.assert_array_equal(aa, aa0)
assert aa.shape == mm.gbox.shape
assert mm.gbox is mm.src_gbox
xx = rio_slurp_xarray(mm0.path, aa0.shape)
assert mm.gbox == xx.geobox
np.testing.assert_array_equal(xx.values, aa0)
aa, mm = rio_slurp(mm0.path, (3, 7))
assert aa.shape == (3, 7)
assert aa.shape == mm.gbox.shape
assert mm.gbox != mm.src_gbox
assert mm.src_gbox == mm0.gbox
assert mm.gbox.extent == mm0.gbox.extent
aa, mm = rio_slurp(mm0.path, aa0.shape)
np.testing.assert_array_equal(aa, aa0)
assert aa.shape == mm.gbox.shape
aa, mm = rio_slurp(mm0.path, mm0.gbox, resampling='nearest')
np.testing.assert_array_equal(aa, aa0)
xx = rio_slurp_xarray(mm0.path, mm0.gbox)
assert mm.gbox == xx.geobox
np.testing.assert_array_equal(xx.values, aa0)
aa, mm = rio_slurp(mm0.path, gbox=mm0.gbox, dtype='float32')
assert aa.dtype == 'float32'
np.testing.assert_array_equal(aa, aa0.astype('float32'))
xx = rio_slurp_xarray(mm0.path, gbox=mm0.gbox)
assert mm.gbox == xx.geobox
assert mm.nodata == xx.nodata
np.testing.assert_array_equal(xx.values, aa0)
aa, mm = rio_slurp(mm0.path, mm0.gbox, dst_nodata=-33)
np.testing.assert_array_equal(aa == -33, aa0 == -999)
aa, mm = rio_slurp(mm00.path, mm00.gbox, dst_nodata=None)
np.testing.assert_array_equal(aa, aa0)
def post_processing(predicted):
"""
filter prediction results with post processing filters.
:param predicted: The prediction results
"""
dc = Datacube(app='whatever')
# grab predictions and proba for post process filtering
predict = predicted.Predictions
# proba = predicted.Probabilities
# proba = proba.where(predict == 1, 100 - proba) # crop proba only
# #------image seg and filtering -------------
# # write out ndvi for image seg
# ndvi = assign_crs(predicted[["NDVI_S1", "NDVI_S2"]],
# crs=predicted.geobox.crs)
# # call function with dask delayed
# filtered = image_segmentation(ndvi, predict)
# # convert delayed object to dask array
# filtered = dask.array.from_delayed(filtered.squeeze(),
# shape=predict.shape,
# dtype=np.int8)
# # convert dask array to xr.Datarray
# filtered = xr.DataArray(filtered,
# coords=predict.coords,
# attrs=predict.attrs)
# --Post process masking------------------------------------------------
# merge back together for masking
ds = xr.Dataset({"mask":
predict}) #, "prob": proba, "filtered": filtered})
# mask out classification beyond AEZ boundary
gdf = gpd.read_file(
'https://github.com/digitalearthafrica/crop-mask/blob/main/testing/eastern_cropmask/data/Eastern.geojson?raw=true'
)
with HiddenPrints():
mask = xr_rasterize(gdf, predicted)
mask = mask.chunk({})
ds = ds.where(mask, 0)
# mask with WDPA
wdpa = rio_slurp_xarray(
"s3://deafrica-input-datasets/protected_areas/WDPA_eastern.tif",
gbox=predicted.geobox)
wdpa = wdpa.chunk({})
wdpa = wdpa.astype(bool)
ds = ds.where(~wdpa, 0)
# mask with WOFS
wofs = dc.load(product="ga_ls8c_wofs_2_summary",
like=predicted.geobox,
dask_chunks={})
wofs = wofs.frequency > 0.2 # threshold
ds = ds.where(~wofs, 0)
# mask steep slopes
slope = rio_slurp_xarray(
'https://deafrica-data.s3.amazonaws.com/ancillary/dem-derivatives/cog_slope_africa.tif',
gbox=predicted.geobox)
slope = slope.chunk({})
slope = slope > 35
ds = ds.where(~slope, 0)
# mask where the elevation is above 3600m
elevation = dc.load(product="dem_srtm",
like=predicted.geobox,
dask_chunks={})
elevation = elevation.elevation > 3600 # threshold
ds = ds.where(~elevation.squeeze(), 0)
return ds.squeeze()
def gm_mads_two_seasons_production(x, y):
"""
Feature layer function for production run of
eastern crop-mask
"""
rename_dict = {
"B02": "blue",
"B03": "green",
"B04": "red",
"B05": "red_edge_1",
"B06": "red_edge_2",
"B07": "red_edge_3",
"B08": "nir",
"B8A": "nir_narrow",
"B11": "swir_1",
"B12": "swir_2",
"BCMAD": "bcdev",
"EMAD": "edev",
"SMAD": "sdev",
}
training_features = [
"red_S1",
"blue_S1",
"green_S1",
"nir_S1",
"swir_1_S1",
"swir_2_S1",
"red_edge_1_S1",
"red_edge_2_S1",
"red_edge_3_S1",
"edev_S1",
"sdev_S1",
"bcdev_S1",
"NDVI_S1",
"LAI_S1",
"MNDWI_S1",
"rain_S1",
"red_S2",
"blue_S2",
"green_S2",
"nir_S2",
"swir_1_S2",
"swir_2_S2",
"red_edge_1_S2",
"red_edge_2_S2",
"red_edge_3_S2",
"edev_S2",
"sdev_S2",
"bcdev_S2",
"NDVI_S2",
"LAI_S2",
"MNDWI_S2",
"rain_S2",
"slope",
]
DATA_PATH = "/g/data/u23/data/"
TIF_path = osp.join(DATA_PATH, "tifs20")
subfld = "x{x:+04d}/y{y:+04d}/".format(x=x, y=y)
P6M_tifs = get_tifs_paths(TIF_path, subfld)
seasoned_ds = {}
for k, tifs in P6M_tifs.items():
era = "_S1" if "2019-01--P6M" in k else "_S2"
base_ds = merge_tifs_into_ds(k, tifs, rename_dict=rename_dict)
seasoned_ds[era] = base_ds
#convert from bands to features
epoch1 = features(seasoned_ds['_S1'], era='_S1')
epoch2 = features(seasoned_ds['_S2'], era='_S2')
#append slope
url_slope = "https://deafrica-data.s3.amazonaws.com/ancillary/dem-derivatives/cog_slope_africa.tif"
slope = rio_slurp_xarray(url_slope, epoch2.geobox)
slope = slope.to_dataset(name='slope')
#merge everything
result = xr.merge([epoch1, epoch2, slope], compat='override')
#order the features correctly
result = result[training_features]
result = result.astype(np.float32)
return result.squeeze()
def gm_mads_two_seasons(geobox):
"""
Feature layer function for production run of
eastern crop-mask
"""
dc = datacube.Datacube(app="prediction")
# load the data
measurements = [
"blue",
"green",
"red",
"nir",
"swir_1",
"swir_2",
"red_edge_1",
"red_edge_2",
"red_edge_3",
"bcdev",
"edev",
"sdev",
]
ds1 = dc.load(
product="ga_s2_gm", time="2019", measurements=measurements, like=geobox
)
ds2 = dc.load(
product="ga_s2_gm", time="2019", measurements=measurements, like=geobox
)
dss = {"S1": ds1, "S2": ds2}
def fun(ds, era):
# normalise SR and edev bands
for band in ds.data_vars:
if band not in ["sdev", "bcdev"]:
ds[band] = ds[band] / 10000
gm_mads = calculate_indices(
ds,
index=["NDVI", "LAI", "MNDWI"],
drop=False,
normalise=False,
collection="s2",
)
gm_mads["sdev"] = -np.log(gm_mads["sdev"])
gm_mads["bcdev"] = -np.log(gm_mads["bcdev"])
gm_mads["edev"] = -np.log(gm_mads["edev"])
# rainfall climatology
if era == "_S1":
chirps = assign_crs(
xr.open_rasterio(
"/g/data/CHIRPS/cumulative_alltime/CHPclim_jan_jun_cumulative_rainfall.nc"
),
crs="epsg:4326",
)
if era == "_S2":
chirps = assign_crs(
xr.open_rasterio(
"/g/data/CHIRPS/cumulative_alltime/CHPclim_jul_dec_cumulative_rainfall.nc"
),
crs="epsg:4326",
)
# Clip CHIRPS to ~ S2 tile boundaries so we can handle NaNs local to S2 tile
xmin, xmax = ds.x.values[0], ds.x.values[-1]
ymin, ymax = ds.y.values[0], ds.y.values[-1]
inProj = Proj("epsg:6933")
outProj = Proj("epsg:4326")
xmin, ymin = transform(inProj, outProj, xmin, ymin)
xmax, ymax = transform(inProj, outProj, xmax, ymax)
# create lat/lon indexing slices - buffer S2 bbox by 0.05deg
if (xmin < 0) & (xmax < 0):
x_slice = list(np.arange(xmin + 0.05, xmax - 0.05, -0.05))
else:
x_slice = list(np.arange(xmax - 0.05, xmin + 0.05, 0.05))
if (ymin < 0) & (ymax < 0):
y_slice = list(np.arange(ymin + 0.05, ymax - 0.05, -0.05))
else:
y_slice = list(np.arange(ymin - 0.05, ymax + 0.05, 0.05))
# index global chirps using buffered s2 tile bbox
chirps = assign_crs(chirps.sel(x=y_slice, y=x_slice, method="nearest"))
# fill any NaNs in CHIRPS with local (s2-tile bbox) mean
chirps = chirps.fillna(chirps.mean())
chirps = xr_reproject(chirps, ds.geobox, "bilinear")
gm_mads["rain"] = chirps
for band in gm_mads.data_vars:
gm_mads = gm_mads.rename({band: band + era})
return gm_mads
epoch1 = fun(dss["S1"], era="_S1")
epoch2 = fun(dss["S1"], era="_S2")
# slope
url_slope = "https://deafrica-data.s3.amazonaws.com/ancillary/dem-derivatives/cog_slope_africa.tif"
slope = rio_slurp_xarray(url_slope, gbox=ds1.geobox)
slope = slope.to_dataset(name="slope")
result = xr.merge([epoch1, epoch2, slope], compat="override")
result = result.astype(np.float32)
return result.squeeze()
def annual_gm_mads_evi_training(ds):
dc = datacube.Datacube(app="training")
# grab gm+tmads
gm_mads = dc.load(
product="ga_s2_gm",
time="2019",
like=ds.geobox,
measurements=[
"red",
"blue",
"green",
"nir",
"swir_1",
"swir_2",
"red_edge_1",
"red_edge_2",
"red_edge_3",
"SMAD",
"BCMAD",
"EMAD",
],
)
gm_mads["SMAD"] = -np.log(gm_mads["SMAD"])
gm_mads["BCMAD"] = -np.log(gm_mads["BCMAD"])
gm_mads["EMAD"] = -np.log(gm_mads["EMAD"] / 10000)
# calculate band indices on gm
gm_mads = calculate_indices(
gm_mads, index=["EVI", "LAI", "MNDWI"], drop=False, collection="s2"
)
# normalise spectral GM bands 0-1
for band in gm_mads.data_vars:
if band not in ["SMAD", "BCMAD", "EMAD", "EVI", "LAI", "MNDWI"]:
gm_mads[band] = gm_mads[band] / 10000
# calculate EVI on annual timeseries
evi = calculate_indices(
ds, index=["EVI"], drop=True, normalise=True, collection="s2"
)
# EVI stats
gm_mads["evi_std"] = evi.EVI.std(dim="time")
gm_mads["evi_10"] = evi.EVI.quantile(0.1, dim="time")
gm_mads["evi_25"] = evi.EVI.quantile(0.25, dim="time")
gm_mads["evi_75"] = evi.EVI.quantile(0.75, dim="time")
gm_mads["evi_90"] = evi.EVI.quantile(0.9, dim="time")
gm_mads["evi_range"] = gm_mads["evi_90"] - gm_mads["evi_10"]
# rainfall climatology
chirps_S1 = xr_reproject(
assign_crs(
xr.open_rasterio(
"/g/data/CHIRPS/cumulative_alltime/CHPclim_jan_jun_cumulative_rainfall.nc"
),
crs="epsg:4326",
),
ds.geobox,
"bilinear",
)
chirps_S2 = xr_reproject(
assign_crs(
xr.open_rasterio(
"/g/data/CHIRPS/cumulative_alltime/CHPclim_jul_dec_cumulative_rainfall.nc"
),
crs="epsg:4326",
),
ds.geobox,
"bilinear",
)
gm_mads["rain_S1"] = chirps_S1
gm_mads["rain_S2"] = chirps_S2
# slope
url_slope = "https://deafrica-data.s3.amazonaws.com/ancillary/dem-derivatives/cog_slope_africa.tif"
slope = rio_slurp_xarray(url_slope, gbox=ds.geobox)
slope = slope.to_dataset(name="slope") # .chunk({'x':2000,'y':2000})
result = xr.merge([gm_mads, slope], compat="override")
return result.squeeze()
def gm_mads_evi_rainfall(ds):
"""
6 monthly and annual
gm + mads
evi stats (10, 50, 90 percentile, range, std)
rainfall actual stats (min, mean, max, range, std) from monthly data
rainfall clim stats (min, mean, max, range, std) from monthly data
"""
dc = datacube.Datacube(app="training")
ds = ds / 10000
ds = ds.rename({"nir_1": "nir_wide", "nir_2": "nir"})
ds1 = ds.sel(time=slice("2019-01", "2019-06"))
ds2 = ds.sel(time=slice("2019-07", "2019-12"))
chirps = []
chpclim = []
for m in range(1, 13):
chirps.append(
xr_reproject(
assign_crs(
xr.open_rasterio(
f"/g/data/CHIRPS/monthly_2019/chirps-v2.0.2019.{m:02d}.tif"
)
.squeeze()
.expand_dims({"time": [m]}),
crs="epsg:4326",
),
ds.geobox,
"bilinear",
)
)
chpclim.append(
rio_slurp_xarray(
f"https://deafrica-data-dev.s3.amazonaws.com/product-dev/deafrica_chpclim_50n_50s_{m:02d}.tif",
gbox=ds.geobox,
resapling="bilinear",
).expand_dims({"time": [m]})
)
chirps = xr.concat(chirps, dim="time")
chpclim = xr.concat(chpclim, dim="time")
def fun(ds, chirps, chpclim, era):
ds = calculate_indices(
ds, index=["EVI"], drop=False, normalise=False, collection="s2"
)
# geomedian and tmads
gm_mads = xr_geomedian_tmad(ds)
gm_mads = calculate_indices(
gm_mads,
index=["EVI", "NDVI", "LAI", "MNDWI"],
drop=False,
normalise=False,
collection="s2",
)
gm_mads["sdev"] = -np.log(gm_mads["sdev"])
gm_mads["bcdev"] = -np.log(gm_mads["bcdev"])
gm_mads["edev"] = -np.log(gm_mads["edev"])
# EVI stats
gm_mads["evi_10"] = ds.EVI.quantile(0.1, dim="time")
gm_mads["evi_50"] = ds.EVI.quantile(0.5, dim="time")
gm_mads["evi_90"] = ds.EVI.quantile(0.9, dim="time")
gm_mads["evi_range"] = gm_mads["evi_90"] - gm_mads["evi_10"]
gm_mads["evi_std"] = ds.EVI.std(dim="time")
# rainfall actual
gm_mads["rain_min"] = chirps.min(dim="time")
gm_mads["rain_mean"] = chirps.mean(dim="time")
gm_mads["rain_max"] = chirps.max(dim="time")
gm_mads["rain_range"] = gm_mads["rain_max"] - gm_mads["rain_min"]
gm_mads["rain_std"] = chirps.std(dim="time")
# rainfall climatology
gm_mads["rainclim_min"] = chpclim.min(dim="time")
gm_mads["rainclim_mean"] = chpclim.mean(dim="time")
gm_mads["rainclim_max"] = chpclim.max(dim="time")
gm_mads["rainclim_range"] = gm_mads["rainclim_max"] - gm_mads["rainclim_min"]
gm_mads["rainclim_std"] = chpclim.std(dim="time")
for band in gm_mads.data_vars:
gm_mads = gm_mads.rename({band: band + era})
return gm_mads
epoch0 = fun(ds, chirps, chpclim, era="_S0")
time, month = slice("2019-01", "2019-06"), slice(1, 6)
epoch1 = fun(
ds.sel(time=time), chirps.sel(time=month), chpclim.sel(time=month), era="_S1"
)
time, month = slice("2019-07", "2019-12"), slice(7, 12)
epoch2 = fun(
ds.sel(time=time), chirps.sel(time=month), chpclim.sel(time=month), era="_S2"
)
# slope
url_slope = "https://deafrica-data.s3.amazonaws.com/ancillary/dem-derivatives/cog_slope_africa.tif"
slope = rio_slurp_xarray(url_slope, gbox=ds.geobox)
slope = slope.to_dataset(name="slope")
result = xr.merge([epoch0, epoch1, epoch2, slope], compat="override")
return result.squeeze()
def post_processing(
predicted: xr.Dataset, urls: Dict[str, Any]
) -> Tuple[xr.DataArray, xr.DataArray, xr.DataArray]:
"""
Run the delayed post_processing functions, then create a lazy
xr.Dataset to satisfy odc-stats
"""
dc = Datacube(app="whatever")
# grab predictions and proba for post process filtering
predict = predicted.Predictions
proba = predicted.Probabilities
proba = proba.where(predict == 1, 100 - proba) # crop proba only
# ------image seg and filtering -------------
# write out ndvi for image seg
ndvi = assign_crs(predicted[["NDVI_S1", "NDVI_S2"]], crs=predicted.geobox.crs)
# call function with dask delayed
filtered = image_segmentation(ndvi, predict)
# convert delayed object to dask array
filtered = dask.array.from_delayed(
filtered.squeeze(), shape=predict.shape, dtype=np.uint8
)
# convert dask array to xr.Datarray
filtered = xr.DataArray(filtered, coords=predict.coords, attrs=predict.attrs)
# --Post process masking----------------------------------------
# merge back together for masking
ds = xr.Dataset({"mask": predict, "prob": proba, "filtered": filtered})
# mask out classification beyond AEZ boundary
gdf = gpd.read_file(urls["aez"])
with HiddenPrints():
mask = xr_rasterize(gdf, predicted)
mask = mask.chunk({})
ds = ds.where(mask, 0)
# mask with WDPA
wdpa = rio_slurp_xarray(urls["wdpa"], gbox=predicted.geobox)
wdpa = wdpa.chunk({})
wdpa = wdpa.astype(bool)
ds = ds.where(~wdpa, 0)
# mask with WOFS
wofs=dc.load(product='wofs_ls_summary_annual',
like=predicted.geobox,
dask_chunks={},
time=('2019'))
wofs=wofs.frequency > 0.20 # threshold
ds=ds.where(~wofs, 0)
# mask steep slopes
slope = rio_slurp_xarray(urls["slope"], gbox=predicted.geobox)
slope = slope.chunk({})
slope = slope > 50
ds = ds.where(~slope, 0)
# mask where the elevation is above 3600m
elevation = dc.load(product="dem_srtm", like=predicted.geobox, dask_chunks={})
elevation = elevation.elevation > 3600 # threshold
ds = ds.where(~elevation.squeeze(), 0)
return ds.squeeze()
# from sklearn.impute import SimpleImputer
#dc = datacube.Datacube(config='/home/547/sc0554/datacube.conf', env='lccs_dev')
#query = {'time': ('2015-01-01', '2015-12-31')}
#query['crs'] = 'EPSG:3577'
#data = dc.load(product='fc_percentile_albers_annual', measurements='PV_PC_90', **query)
data = xr.open_rasterio(
'/g/data/r78/LCCS_Aberystwyth/urban_tests/test_sites_peter/perth_2015_gm.tif'
)
data = assign_crs(data, crs='epsg:3577')
# quickshift expects multiband images with bands in the last dimension
data = data.transpose()
fname = '/g/data/r78/LCCS_Aberystwyth/continental_run_april2020/2015/lccs_2015_L4_0.5.0.tif'
LCCS = rio_slurp_xarray(fname, gbox=data.geobox)
LCCS = LCCS.isel(band=0)
print("LCCS shape", LCCS.shape)
meta_d = LCCS.copy() ##.squeeze().drop('time')
seg = felzenszwalb(LCCS.data.transpose())
#seg = quickshift(LCCS.data.transpose(), kernel_size=3, convert2lab=False, max_dist=10, ratio=0.5)
print('seg shape', seg.shape)
data_seg_med = scipy.ndimage.median(input=LCCS.data.transpose(),
labels=seg,
index=seg)
#data_seg_med = data_seg_med.squeeze("time").drop("time")
print("seg_med shape", data_seg_med.shape)
out = xr.DataArray(data=data_seg_med.transpose(),
dims=meta_d.dims,
coords=meta_d.coords,
attrs=meta_d.attrs)
