def test_rasterio_nodata(tmpdir):
from datacube.testutils.io import dc_read, write_gtiff
from pathlib import Path
roi = np.s_[10:20, 20:30]
xx = np.zeros((64, 64), dtype='uint8')
xx[roi] = 255
pp = Path(str(tmpdir))
mm = write_gtiff(pp/'absent_nodata.tiff', xx, nodata=None)
yy = dc_read(mm.path, gbox=mm.gbox, fallback_nodata=None)
np.testing.assert_array_equal(xx, yy)
# fallback nodata is outside source range so it shouldn't be used
yy = dc_read(mm.path, gbox=mm.gbox, fallback_nodata=-1, dst_nodata=-999, dtype='int16')
np.testing.assert_array_equal(xx.astype('int16'), yy)
# treat zeros as no-data + type conversion while reading
yy_expect = xx.copy().astype('int16')
yy_expect[xx == 0] = -999
assert set(yy_expect.ravel()) == {-999, 255}
yy = dc_read(mm.path, fallback_nodata=0, dst_nodata=-999, dtype='int16')
np.testing.assert_array_equal(yy_expect, yy)
# now check that file nodata is used instead of fallback
mm = write_gtiff(pp/'with_nodata.tiff', xx, nodata=33)
yy = dc_read(mm.path, fallback_nodata=0, dst_nodata=-999, dtype='int16')
np.testing.assert_array_equal(xx, yy)
yy = dc_read(mm.path)
np.testing.assert_array_equal(xx, yy)
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
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
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)
aa, mm = rio_slurp(mm0.path, gbox=mm0.gbox, dtype='float32')
assert aa.dtype == 'float32'
np.testing.assert_array_equal(aa, aa0.astype('float32'))
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 gen_tiff_dataset(bands,
base_folder,
prefix='',
timestamp='2018-07-19',
**kwargs):
"""
each band:
.name - string
.values - ndarray
.nodata - numeric|None
:returns: (Dataset, GeoBox)
"""
if not isinstance(bands, Sequence):
bands = (bands, )
# write arrays to disk and construct compatible measurement definitions
gbox = None
mm = []
for band in bands:
name = band.name
fname = prefix + name + '.tiff'
meta = write_gtiff(base_folder / fname,
band.values,
nodata=band.nodata,
overwrite=True,
**kwargs)
gbox = meta.gbox
mm.append(dict(name=name, path=fname, layer=1, dtype=meta.dtype))
uri = Path(base_folder / 'metadata.yaml').absolute().as_uri()
ds = mk_sample_dataset(mm, uri=uri, timestamp=timestamp)
return ds, gbox
def test_read_with_reproject(tmpdir):
from datacube.testutils import mk_test_image
from datacube.testutils.io import write_gtiff
from pathlib import Path
pp = Path(str(tmpdir))
xx = mk_test_image(128, 64, nodata=None)
assert (xx != -999).all()
tile = AlbersGS.tile_geobox((17, -40))[:64, :128]
mm = write_gtiff(pp / 'tst-read-with-reproject-128x64-int16.tif',
xx,
crs=str(tile.crs),
resolution=tile.resolution[::-1],
offset=tile.transform * (0, 0),
nodata=-999)
assert mm.gbox == tile
def _read(gbox,
resampling='nearest',
fallback_nodata=None,
dst_nodata=-999):
with RasterFileDataSource(mm.path, 1,
nodata=fallback_nodata).open() as rdr:
yy = np.full(gbox.shape, dst_nodata, dtype=rdr.dtype)
roi = read_time_slice(rdr, yy, gbox, resampling, dst_nodata)
return yy, roi
gbox = gbx.pad(mm.gbox, 10)
gbox = gbx.zoom_out(gbox, 0.873)
yy, roi = _read(gbox)
assert roi[0].start > 0 and roi[1].start > 0
assert (yy[0] == -999).all()
yy_expect, _ = rio_slurp(mm.path, gbox)
np.testing.assert_array_equal(yy, yy_expect)
gbox = gbx.zoom_out(mm.gbox[3:-3, 10:-10], 2.1)
yy, roi = _read(gbox)
assert roi_shape(roi) == gbox.shape
assert not (yy == -999).any()
gbox = GeoBox.from_geopolygon(mm.gbox.extent.to_crs(epsg3857).buffer(50),
resolution=mm.gbox.resolution)
assert gbox.extent.contains(mm.gbox.extent.to_crs(epsg3857))
assert gbox.crs != mm.gbox.crs
yy, roi = _read(gbox)
assert roi[0].start > 0 and roi[1].start > 0
assert (yy[0] == -999).all()
gbox = gbx.zoom_out(gbox, 4)
yy, roi = _read(gbox, resampling='average')
nvalid = (yy != -999).sum()
nempty = (yy == -999).sum()
assert nvalid > nempty
def test_rio_slurp_with_gbox(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.dtype.name == dtype
assert aa[10, 30] == (30 << 8) | 10
assert aa[10, 11] == nodata
aa = np.stack([aa, aa[::-1, ::-1]])
assert aa.shape == (2, h, w)
aa0 = aa.copy()
mm = write_gtiff(pp / "rio-slurp-aa.tif", aa, nodata=-999, overwrite=True)
assert mm.count == 2
aa, mm = rio_slurp(mm.path, mm.gbox)
assert aa.shape == aa0.shape
np.testing.assert_array_equal(aa, aa0)
def test_testutils_gtif(tmpdir):
from datacube.testutils import mk_test_image
from datacube.testutils.io import write_gtiff, rio_slurp
w, h, dtype, nodata, ndw = 96, 64, 'int16', -999, 7
aa = mk_test_image(w, h, dtype, nodata, nodata_width=ndw)
bb = mk_test_image(w, h, dtype, nodata=None)
assert aa.shape == (h, w)
assert aa.dtype.name == dtype
assert aa[10, 30] == (30 << 8) | 10
assert aa[10, 11] == nodata
assert bb[10, 11] == (11 << 8) | 10
aa5 = np.stack((aa, ) * 5)
fname = pathlib.Path(str(tmpdir / "aa.tiff"))
fname5 = pathlib.Path(str(tmpdir / "aa5.tiff"))
aa_meta = write_gtiff(fname,
aa,
nodata=nodata,
blocksize=128,
resolution=(100, -100),
offset=(12300, 11100),
overwrite=True)
aa5_meta = write_gtiff(str(fname5),
aa5,
nodata=nodata,
resolution=(100, -100),
offset=(12300, 11100),
overwrite=True)
assert fname.exists()
assert fname5.exists()
assert aa_meta.gbox.shape == (h, w)
assert aa_meta.path is fname
aa_, aa_meta_ = rio_slurp(fname)
aa5_, aa5_meta_ = rio_slurp(fname5)
assert aa_meta_.path is fname
(sx, _, tx, _, sy, ty, *_) = aa5_meta_.transform
assert (tx, ty) == (12300, 11100)
assert (sx, sy) == (100, -100)
np.testing.assert_array_equal(aa, aa_)
np.testing.assert_array_equal(aa5, aa5_)
assert aa_meta_.transform == aa_meta.transform
assert aa5_meta_.transform == aa5_meta.transform
# check that overwrite is off by default
with pytest.raises(IOError):
write_gtiff(fname, aa, nodata=nodata, blocksize=128)
# check that overwrite re-writes file
write_gtiff(fname,
bb[:32, :32],
gbox=aa_meta.gbox[:32, :32],
overwrite=True)
bb_, mm = rio_slurp(fname, (32, 32))
np.testing.assert_array_equal(bb[:32, :32], bb_)
assert mm.gbox == aa_meta.gbox[:32, :32]
with pytest.raises(ValueError):
write_gtiff(fname, np.zeros((3, 4, 5, 6)))
def test_read_paste(tmpdir):
from datacube.testutils import mk_test_image
from datacube.testutils.io import write_gtiff
from pathlib import Path
pp = Path(str(tmpdir))
xx = mk_test_image(128, 64, nodata=None)
assert (xx != -999).all()
mm = write_gtiff(pp / 'tst-read-paste-128x64-int16.tif', xx, nodata=None)
def _read(gbox,
resampling='nearest',
fallback_nodata=-999,
dst_nodata=-999,
check_paste=False):
with RasterFileDataSource(mm.path, 1,
nodata=fallback_nodata).open() as rdr:
if check_paste:
# check that we are using paste
paste_ok, reason = can_paste(
compute_reproject_roi(rdr_geobox(rdr), gbox))
assert paste_ok is True, reason
yy = np.full(gbox.shape, dst_nodata, dtype=rdr.dtype)
roi = read_time_slice(rdr, yy, gbox, resampling, dst_nodata)
return yy, roi
# read native whole
yy, roi = _read(mm.gbox)
np.testing.assert_array_equal(xx, yy)
assert roi == np.s_[0:64, 0:128]
# read native whole, no nodata case
yy, roi = _read(mm.gbox, fallback_nodata=None)
np.testing.assert_array_equal(xx, yy)
assert roi == np.s_[0:64, 0:128]
# read native whole, ignoring small sub-pixel translation
yy, roi = _read(gbx.translate_pix(mm.gbox, 0.3, -0.4), fallback_nodata=-33)
np.testing.assert_array_equal(xx, yy)
assert roi == np.s_[0:64, 0:128]
# no overlap between src and dst
yy, roi = _read(gbx.translate_pix(mm.gbox, 10000, -10000))
assert roi_is_empty(roi)
# read with Y flipped
yy, roi = _read(gbx.flipy(mm.gbox))
np.testing.assert_array_equal(xx[::-1, :], yy)
assert roi == np.s_[0:64, 0:128]
# read with X flipped
yy, roi = _read(gbx.flipx(mm.gbox))
np.testing.assert_array_equal(xx[:, ::-1], yy)
assert roi == np.s_[0:64, 0:128]
# read with X and Y flipped
yy, roi = _read(gbx.flipy(gbx.flipx(mm.gbox)))
assert roi == np.s_[0:64, 0:128]
np.testing.assert_array_equal(xx[::-1, ::-1], yy[roi])
# dst is fully inside src
sroi = np.s_[10:19, 31:47]
yy, roi = _read(mm.gbox[sroi])
np.testing.assert_array_equal(xx[sroi], yy[roi])
# partial overlap
yy, roi = _read(gbx.translate_pix(mm.gbox, -3, -10))
assert roi == np.s_[10:64, 3:128]
np.testing.assert_array_equal(xx[:-10, :-3], yy[roi])
assert (yy[:10, :] == -999).all()
assert (yy[:, :3] == -999).all()
# scaling paste
yy, roi = _read(gbx.zoom_out(mm.gbox, 2), check_paste=True)
assert roi == np.s_[0:32, 0:64]
np.testing.assert_array_equal(xx[1::2, 1::2], yy)
