def mask(geotiff, geojson, clean=False, filled=False, **kwargs):
"""Mask geotiff with geojson features.
Arguments:
geotiff: A GeoTiff
geojson: Path to a GeoJSON Feature or Feature Collection
clean: bool: To delete input file after processing
filled: bool: To fill masked areas with nodata value, or if not,
to return a masked image.
**kwargs: Further options to pass to rasterio.mask.mask(), e.g.:
nodata: Override nodata value. Defaults to value for geotiff, or 0.
invert: bool: To mask the areas _inside_ the vector shapes.
Returns: Path to the masked geotiff.
"""
with rasterio.open(geotiff) as dataset:
profile = dataset.profile.copy()
epsg_code = profile['crs']['init'].split('epsg:')[-1]
geoms = geojsonio.load_geometries(geojson)
geoms = [projections.project_geojson_geom(g, epsg_code) for g in geoms]
masked, _ = rasterio.mask.mask(dataset, geoms, filled=filled, **kwargs)
outpath = geotiff.split('.tif')[0] + '-masked.tif'
with rasterio.open(outpath, 'w', **profile) as of:
of.write(masked)
if not filled:
gdalmask = (~masked.mask)[0]
of.write_mask(gdalmask)
if clean:
os.remove(geotiff)
return outpath
def resolve(vrtfile, **kwargs):
"""Convert vrtfile to tif while resolving bands and geographic bounds.
Arguments:
vrtfile: A file output by gdalbuildvrt
kwargs (optional):
bandlist: Ordered list of output bands
geojson: A geojson feature or feature collection expressing
a crop region
Outputs a geotiff; returns the filename.
"""
tiffile = vrtfile.split('.vrt')[0] + '.tif'
commands = ['gdal_translate', vrtfile, tiffile, '-co', 'COMPRESS=LZW']
bandlist = kwargs.get('bandlist')
if bandlist:
dressed_bands = np.asarray([('-b', str(b)) for b in bandlist])
commands += [*dressed_bands.flatten()]
if len(bandlist) == 3:
commands += ['-colorinterp', 'red,green,blue']
geojson = kwargs.get('geojson')
if geojson:
bbox = geobox.bbox_from_geometries(geojsonio.load_geometries(geojson))
gdal_bounds = [str(bbox.bounds[n]) for n in (0, 3, 2, 1)]
commands += ['-projwin_srs', 'EPSG:4326', '-projwin', *gdal_bounds]
subprocess.call(commands)
os.remove(vrtfile)
return tiffile
def crop(geotiff, geojson, outpath):
"""Crop geotiff to bounding box of geojson and save to outpath."""
bbox = geobox.bbox_from_geometries(geojsonio.load_geometries(geojson))
gdal_bounds = [str(bbox.bounds[n]) for n in (0, 3, 2, 1)]
commands = [
'gdal_translate', geotiff, outpath, '-projwin_srs', 'EPSG:4326',
'-projwin', *gdal_bounds
]
subprocess.call(commands)
return outpath
def burn(geojson, geotiff):
"""Burn features in geojson into a container defined by existing geotiff."""
with rasterio.open(geotiff) as f:
profile = f.profile.copy()
epsg_code = profile['crs']['init'].split('epsg:')[-1]
shape = (profile['height'], profile['width'])
pixel_max = pixel_limits.get_max(profile['dtype'])
geoms = geojsonio.load_geometries(geojson)
geoms = [projections.project_geojson_geom(g, epsg_code) for g in geoms]
raster = rasterio.features.rasterize(((geom, pixel_max) for geom in geoms),
out_shape=shape,
transform=profile['transform'])
raster = raster.reshape((1,) + shape)
profile.update({'count': 1})
rasterfile = '.'.join(geojson.split('.')[:-1]) + '-burned.tif'
with rasterio.open(rasterfile, 'w', **profile) as f:
f.write(raster)
return rasterfile
'--indices',
type=str,
nargs='+',
choices=INDICES,
default=INDICES,
help='Indices to compute, from {}. Defaults to all.'.format(INDICES))
parser.add_argument(
'-g',
'--geojson',
type=str,
help='Geojson file expressing area of interest for optional crop.')
parser.add_argument(
'-d',
'--image_dir',
type=str,
default='',
help='Directory containing image band files. Defaults to pwd.')
args = parser.parse_args()
geoms = geojsonio.load_geometries(args.geojson) if args.geojson else []
bounds = geobox.bbox_from_geometries(geoms).bounds if geoms else []
base = os.path.join(args.image_dir, '*band?')
paths = [glob.glob(base + ext) for ext in ['.tif', '.TIF']]
paths = [p for sublist in paths for p in sublist]
grouped = reduce_landsat.partition(paths, args.bandlist)
for prefix, grouped_paths in grouped.items():
for index in args.indices:
build_index(prefix, grouped_paths, bounds, index)