def test_extract_from_array():
"""Extract subdata from array."""
in_tile = BufferedTilePyramid("geodetic", metatiling=4).tile(5, 5, 5)
shape = (in_tile.shape[0] // 2, in_tile.shape[1])
data = ma.masked_array(np.concatenate([np.ones(shape),
np.ones(shape) * 2]))
# intersecting at top
out_tile = BufferedTilePyramid("geodetic").tile(5, 20, 20)
out_array = extract_from_array(in_raster=data,
in_affine=in_tile.affine,
out_tile=out_tile)
assert isinstance(out_array, np.ndarray)
assert np.all(np.where(out_array == 1, True, False))
# intersecting at bottom
out_tile = BufferedTilePyramid("geodetic").tile(5, 22, 20)
out_array = extract_from_array(in_raster=data,
in_affine=in_tile.affine,
out_tile=out_tile)
assert isinstance(out_array, np.ndarray)
assert np.all(np.where(out_array == 2, True, False))
# not intersecting
out_tile = BufferedTilePyramid("geodetic").tile(5, 15, 20)
with pytest.raises(ValueError):
out_array = extract_from_array(in_raster=data,
in_affine=in_tile.affine,
out_tile=out_tile)
def read(self, **kwargs):
"""
Read existing output data from a previous run.
Returns
-------
process output : NumPy array (raster) or feature iterator (vector)
"""
if self.tile.pixelbuffer > self.config.output.pixelbuffer:
output_tiles = list(
self.config.output_pyramid.tiles_from_bounds(
self.tile.bounds, self.tile.zoom))
else:
output_tiles = self.config.output_pyramid.intersecting(self.tile)
if self.config.output.METADATA["data_type"] == "raster":
return raster.extract_from_array(in_raster=raster.create_mosaic([
(output_tile, self.config.output.read(output_tile))
for output_tile in output_tiles
]),
out_tile=self.tile)
elif self.config.output.METADATA["data_type"] == "vector":
return list(
chain.from_iterable([
self.config.output.read(output_tile)
for output_tile in output_tiles
]))
def write(self, process_tile, data):
"""
Write data from process tiles into GeoTIFF file(s).
Parameters
----------
process_tile : ``BufferedTile``
must be member of process ``TilePyramid``
"""
data = prepare_array(data,
masked=True,
nodata=self.output_params["nodata"],
dtype=self.profile(process_tile)["dtype"])
if data.mask.all():
logger.debug("data empty, nothing to write")
else:
# Convert from process_tile to output_tiles and write
for tile in self.pyramid.intersecting(process_tile):
out_tile = BufferedTile(tile, self.pixelbuffer)
write_window = from_bounds(
*out_tile.bounds,
transform=self.rio_file.transform,
height=self.rio_file.height,
width=self.rio_file.width).round_lengths(
pixel_precision=0).round_offsets(pixel_precision=0)
if _window_in_out_file(write_window, self.rio_file):
logger.debug("write data to window: %s", write_window)
self.rio_file.write(
extract_from_array(in_raster=data,
in_affine=process_tile.affine,
out_tile=out_tile)
if process_tile != out_tile else data,
window=write_window,
)
def _read_existing_output(self, tile, output_tiles):
if self.config.output.METADATA["data_type"] == "raster":
mosaic, affine = raster.create_mosaic([
(output_tile, self.read(output_tile))
for output_tile in output_tiles
])
return raster.extract_from_array(mosaic, affine, tile)
elif self.config.output.METADATA["data_type"] == "vector":
return list(
chain.from_iterable(
[self.read(output_tile) for output_tile in output_tiles]))
def _extract(self, in_tile=None, in_data=None, out_tile=None):
"""Extract data from tile."""
if self.config.output.METADATA["data_type"] == "raster":
return raster.extract_from_array(in_raster=raster.prepare_array(
in_data,
nodata=self.config.output.nodata,
dtype=self.config.output.output_params["dtype"]),
in_affine=in_tile.affine,
out_tile=out_tile)
elif self.config.output.METADATA["data_type"] == "vector":
return [
feature for feature in in_data
if shape(feature["geometry"]).intersects(out_tile.bbox)
]
def extract_subset(self, input_data_tiles=None, out_tile=None):
"""
Extract subset from multiple tiles.
input_data_tiles : list of (``Tile``, process data) tuples
out_tile : ``Tile``
Returns
-------
NumPy array or list of features.
"""
if self.METADATA["data_type"] == "raster":
mosaic = create_mosaic(input_data_tiles)
return extract_from_array(in_raster=prepare_array(
mosaic.data,
nodata=self.output_params["nodata"],
dtype=self.output_params["dtype"]),
in_affine=mosaic.affine,
out_tile=out_tile)
elif self.METADATA["data_type"] == "vector":
return [
feature for feature in list(
chain.from_iterable(
[features for _, features in input_data_tiles]))
if shape(feature["geometry"]).intersects(out_tile.bbox)
]