def xr_geomedian_tmad_new(ds, **kw):
"""
Same as other one but uses reshape_yxbt instead of
reshape_for_geomedian
"""
import hdstats
def gm_tmad(arr, **kw):
"""
arr: a high dimensional numpy array where the last dimension will be reduced.
returns: a numpy array with one less dimension than input.
"""
gm = hdstats.nangeomedian_pcm(arr, **kw)
nt = kw.pop('num_threads', None)
emad = hdstats.emad_pcm(arr, gm, num_threads=nt)[:, :, np.newaxis]
smad = hdstats.smad_pcm(arr, gm, num_threads=nt)[:, :, np.newaxis]
bcmad = hdstats.bcmad_pcm(arr, gm, num_threads=nt)[:, :, np.newaxis]
return np.concatenate([gm, emad, smad, bcmad], axis=-1)
def norm_input(ds):
if isinstance(ds, xr.Dataset):
xx = reshape_yxbt(ds, yx_chunks=500)
return ds, xx, xx.data
kw.setdefault('nocheck', False)
kw.setdefault('num_threads', 1)
kw.setdefault('eps', 1e-6)
ds, xx, xx_data = norm_input(ds)
is_dask = dask.is_dask_collection(xx_data)
if is_dask:
data = da.map_blocks(lambda x: gm_tmad(x, **kw),
xx_data,
name=randomize('geomedian'),
dtype=xx_data.dtype,
chunks=xx_data.chunks[:-2] +
(xx_data.chunks[-2][0] + 3, ),
drop_axis=3)
dims = xx.dims[:-1]
cc = {k: xx.coords[k] for k in dims}
cc[dims[-1]] = np.hstack(
[xx.coords[dims[-1]].values, ['edev', 'sdev', 'bcdev']])
xx_out = xr.DataArray(data, dims=dims, coords=cc)
if ds is None:
xx_out.attrs.update(xx.attrs)
return xx_out
ds_out = xx_out.to_dataset(dim='band')
for b in ds.data_vars.keys():
src, dst = ds[b], ds_out[b]
dst.attrs.update(src.attrs)
return assign_crs(ds_out, crs=ds.geobox.crs)
def xr_geomedian_tmad(ds, axis='time', where=None, **kw):
"""
:param ds: xr.Dataset|xr.DataArray|numpy array
Other parameters:
**kwargs -- passed on to pcm.gnmpcm
maxiters : int 1000
eps : float 0.0001
num_threads: int| None None
"""
import hdstats
def gm_tmad(arr, **kw):
"""
arr: a high dimensional numpy array where the last dimension will be reduced.
returns: a numpy array with one less dimension than input.
"""
gm = hdstats.nangeomedian_pcm(arr, **kw)
nt = kw.pop('num_threads', None)
emad = hdstats.emad_pcm(arr, gm, num_threads=nt)[:,:, np.newaxis]
smad = hdstats.smad_pcm(arr, gm, num_threads=nt)[:,:, np.newaxis]
bcmad = hdstats.bcmad_pcm(arr, gm, num_threads=nt)[:,:, np.newaxis]
return np.concatenate([gm, emad, smad, bcmad], axis=-1)
def norm_input(ds, axis):
if isinstance(ds, xr.DataArray):
xx = ds
if len(xx.dims) != 4:
raise ValueError("Expect 4 dimensions on input: y,x,band,time")
if axis is not None and xx.dims[3] != axis:
raise ValueError(f"Can only reduce last dimension, expect: y,x,band,{axis}")
return None, xx, xx.data
elif isinstance(ds, xr.Dataset):
xx = reshape_for_geomedian(ds, axis)
return ds, xx, xx.data
else: # assume numpy or similar
xx_data = ds
if xx_data.ndim != 4:
raise ValueError("Expect 4 dimensions on input: y,x,band,time")
return None, None, xx_data
kw.setdefault('nocheck', False)
kw.setdefault('num_threads', 1)
kw.setdefault('eps', 1e-6)
ds, xx, xx_data = norm_input(ds, axis)
is_dask = dask.is_dask_collection(xx_data)
if where is not None:
if is_dask:
raise NotImplementedError("Dask version doesn't support output masking currently")
if where.shape != xx_data.shape[:2]:
raise ValueError("Shape for `where` parameter doesn't match")
set_nan = ~where
else:
set_nan = None
if is_dask:
if xx_data.shape[-2:] != xx_data.chunksize[-2:]:
xx_data = xx_data.rechunk(xx_data.chunksize[:2] + (-1, -1))
data = da.map_blocks(lambda x: gm_tmad(x, **kw),
xx_data,
name=randomize('geomedian'),
dtype=xx_data.dtype,
chunks=xx_data.chunks[:-2] + (xx_data.chunks[-2][0]+3,),
drop_axis=3)
else:
data = gm_tmad(xx_data, **kw)
if set_nan is not None:
data[set_nan, :] = np.nan
if xx is None:
return data
dims = xx.dims[:-1]
cc = {k: xx.coords[k] for k in dims}
cc[dims[-1]] = np.hstack([xx.coords[dims[-1]].values,['edev', 'sdev', 'bcdev']])
xx_out = xr.DataArray(data, dims=dims, coords=cc)
if ds is None:
xx_out.attrs.update(xx.attrs)
return xx_out
ds_out = xx_out.to_dataset(dim='band')
for b in ds.data_vars.keys():
src, dst = ds[b], ds_out[b]
dst.attrs.update(src.attrs)
return assign_crs(ds_out, crs=ds.geobox.crs)