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Better docstring, 100% coverage of rio.features

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Also change read_band() to read() in tests, pep8 corrections.
This commit is contained in:
Sean Gillies 2015-04-07 10:45:56 -06:00
parent d9347069c8
commit b5dce02abb
2 changed files with 75 additions and 31 deletions
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83
rasterio/rio/features.py
View File

@ -23,7 +23,7 @@ warnings.simplefilter('default')
# Shapes command.
@cli.command(short_help="Write the shapes of features.")
@cli.command(short_help="Write shapes extracted from bands or masks.")
@click.argument('input', type=click.Path(exists=True))
@precision_opt
@indent_opt
@ -35,12 +35,12 @@ warnings.simplefilter('default')
@geojson_type_feature_opt(True)
@geojson_type_bbox_opt(False)
@click.option('--band/--mask', default=True,
help="Extract shapes from one of the dataset bands or from "
"its nodata mask")
help="Choose to extract from a band (the default) or a mask.")
@click.option('--bidx', 'bandidx', type=int, default=None,
help="Index of the source band")
help="Index of the band or mask that is the source of shapes.")
@click.option('--sampling', type=int, default=1,
help="Inverse of the sampling fraction")
help="Inverse of the sampling fraction; "
"a value of 10 decimates.")
@click.option('--with-nodata/--without-nodata', default=False,
help="Include or do not include (the default) nodata regions.")
@click.option('--as-mask/--not-as-mask', default=False,
@ -50,8 +50,33 @@ warnings.simplefilter('default')
def shapes(
ctx, input, precision, indent, compact, projection, sequence,
use_rs, geojson_type, band, bandidx, sampling, with_nodata, as_mask):
"""Writes features of a dataset out as GeoJSON. It's intended for
use with single-band rasters and reads from the first band.
"""Extracts shapes from one band or mask of a dataset and writes
them out as GeoJSON. Unless otherwise specified, the shapes will be
transformed to WGS 84 coordinates.
The default action of this command is to extract shapes from the
first band of the input dataset. The shapes are polygons bounding
contiguous regions (or features) of the same raster value. This
command performs poorly for int16 or float type datasets.
Bands other than the first can be specified using the `--bidx`
option:
$ rio shapes --bidx 3 tests/data/RGB.byte.tif
The valid data footprint of a dataset's i-th band can be extracted
by using the `--mask` and `--bidx` options:
$ rio shapes --mask --bidx 1 tests/data/RGB.byte.tif
Omitting the `--bidx` option results in a footprint extracted from
the conjunction of all band masks. This is generally smaller than
any individual band's footprint.
A dataset band may be analyzed as though it were a binary mask with
the `--as-mask` option:
$ rio shapes --as-mask --bidx 1 tests/data/RGB.byte.tif
"""
# These import numpy, which we don't want to do unless it's needed.
import numpy
@ -96,8 +121,10 @@ def shapes(
img = src.read(bidx, img, masked=False)
transform = src.affine * Affine.scale(float(sampling))
if as_mask:
msk = img
img = None
tmp = numpy.ones_like(img, 'uint8') * 255
tmp[img == 0] = 0
img = tmp
msk = tmp
if not band or not with_nodata:
if sampling == 1:
msk = src.read_masks(bidx)
@ -106,12 +133,15 @@ def shapes(
transform = src.affine
# Decimate the mask.
else:
msk = numpy.zeros(
(src.height//sampling, src.width//sampling),
dtype=numpy.uint8)
msk_shape = src.height//sampling, src.width//sampling
if bidx is None:
msk = numpy.zeros(
(src.count,) + msk_shape, 'uint8')
else:
msk = numpy.zeros(msk_shape, 'uint8')
msk = src.read_masks(bidx, msk)
if bidx is None:
msk = numpy.logical_or.reduce(msk)
msk = numpy.logical_or.reduce(msk).astype('uint8')
transform = src.affine * Affine.scale(float(sampling))
bounds = src.bounds
@ -129,7 +159,7 @@ def shapes(
kwargs = {'transform': transform}
# Default is to exclude nodata features.
if msk is not None:
kwargs['mask'] = (msk>0)
kwargs['mask'] = msk #(msk > 0)
if img is None:
img = msk
@ -143,15 +173,17 @@ def shapes(
'type': 'Feature',
'id': str(i),
'properties': {
'val': i, 'filename': os.path.basename(src.name)},
'val': i, 'filename': os.path.basename(src.name)
},
'bbox': [min(xs), min(ys), max(xs), max(ys)],
'geometry': g }
'geometry': g
}
if not sequence:
geojson_type = 'collection'
try:
with rasterio.drivers(CPL_DEBUG=verbosity>2):
with rasterio.drivers(CPL_DEBUG=(verbosity > 2)):
write_features(
stdout, Collection(), sequence=sequence,
geojson_type=geojson_type, use_rs=use_rs,
@ -176,17 +208,19 @@ def shapes(
help='Output dataset width, height in number of pixels.')
@click.option('--res', multiple=True, type=float, default=None,
help='Output dataset resolution in units of coordinate '
'reference system. Pixels assumed to be square if this option is '
'used once, otherwise use: '
'reference system. Pixels assumed to be square if this option '
'is used once, otherwise use: '
'--res pixel_width --res pixel_height')
@click.option('--src_crs', default='EPSG:4326',
help='Source coordinate reference system. Limited to EPSG '
'codes for now. Used as output coordinate system if output does '
'not exist or --like option is not used. Default: EPSG:4326')
'codes for now. Used as output coordinate system if output '
'does not exist or --like option is not used. '
'Default: EPSG:4326')
@click.option('--all_touched', is_flag=True, default=False)
@click.option('--default_value', type=float, default=1, help='Default value '
'for rasterized pixels')
@click.option('--fill', type=float, default=0, help='Fill value for all pixels '
@click.option('--fill', type=float, default=0,
help='Fill value for allpixels '
'not overlapping features. Will be evaluated as NoData pixels '
'for output. Default: 0')
@click.option('--property', type=str, default=None, help='Property in '
@ -333,9 +367,10 @@ def rasterize(
if src_crs == 'EPSG:4326':
if (bounds[0] < -180 or bounds[2] > 180 or
bounds[1] < -80 or bounds[3] > 80):
bounds[1] < -80 or bounds[3] > 80):
raise click.BadParameter(
'Bounds are beyond the valid extent for EPSG:4326.',
"Bounds are beyond the valid extent for "
"EPSG:4326.",
ctx, param=bounds, param_hint='--bounds')
if dimensions:

23
tests/test_rio_features.py
View File

@ -157,6 +157,15 @@ def test_shapes_mask(runner):
assert result.output.count('"Feature"') == 7
def test_shapes_mask_decimated(runner):
result = runner.invoke(
features.shapes,
['tests/data/RGB.byte.tif', '--mask', '--sampling', '10'])
assert result.exit_code == 0
assert result.output.count('"FeatureCollection"') == 1
assert result.output.count('"Feature"') == 1
def test_shapes_band1_as_mask(runner):
result = runner.invoke(features.shapes,
['tests/data/RGB.byte.tif', '--band', '--bidx', '1', '--as-mask'])
@ -205,7 +214,7 @@ def test_rasterize(tmpdir, runner):
assert out.count == 1
assert out.meta['width'] == 20
assert out.meta['height'] == 10
data = out.read_band(1, masked=False)
data = out.read(1, masked=False)
assert (data == 0).sum() == 55
assert (data == 1).sum() == 145
@ -222,7 +231,7 @@ def test_rasterize(tmpdir, runner):
assert out.count == 1
assert out.meta['width'] == 40
assert out.meta['height'] == 20
data = out.read_band(1, masked=False)
data = out.read(1, masked=False)
assert (data == 0).sum() == 748
assert (data == 1).sum() == 52
@ -236,7 +245,7 @@ def test_rasterize(tmpdir, runner):
assert out.count == 1
assert out.meta['width'] == 20
assert out.meta['height'] == 10
data = out.read_band(1, masked=False)
data = out.read(1, masked=False)
assert (data == 0).sum() == 55
assert (data == 1).sum() == 145
@ -269,7 +278,7 @@ def test_rasterize_existing_output(tmpdir, runner):
with rasterio.open(output) as out:
assert out.count == 1
data = out.read_band(1, masked=False)
data = out.read(1, masked=False)
assert (data == 0).sum() == 55
assert (data == 1).sum() == 125
assert (data == 2).sum() == 20
@ -284,7 +293,7 @@ def test_rasterize_like(tmpdir, runner):
assert os.path.exists(output)
with rasterio.open(output) as out:
assert out.count == 1
data = out.read_band(1, masked=False)
data = out.read(1, masked=False)
assert (data == 0).sum() == 548576
assert (data == 1).sum() == 500000
@ -309,7 +318,7 @@ def test_rasterize_property_value(tmpdir, runner):
assert os.path.exists(output)
with rasterio.open(output) as out:
assert out.count == 1
data = out.read_band(1, masked=False)
data = out.read(1, masked=False)
assert (data == 0).sum() == 50
assert (data == 2).sum() == 25
assert (data == 3).sum() == 25
@ -323,7 +332,7 @@ def test_rasterize_property_value(tmpdir, runner):
assert os.path.exists(output)
with rasterio.open(output) as out:
assert out.count == 1
data = out.read_band(1, masked=False)
data = out.read(1, masked=False)
assert (data == 0).sum() == 55
assert (data == 15).sum() == 145