import rasterio
from click import secho
from eodatasets3 import wagl
from eodatasets3.ui import PathPath
DEFAULT_MATURITY = wagl.ProductMaturity.stable
@click.command(help=__doc__)
@click.option(
"--level1",
help="Optional path to the input level1 metadata doc "
"(otherwise it will be loaded from the level1 path in the HDF5)",
required=False,
type=PathPath(exists=True, readable=True, dir_okay=False, file_okay=True),
)
@click.option(
"--output",
help="Put the output package into this directory",
required=True,
type=PathPath(exists=True, writable=True, dir_okay=True, file_okay=False),
)
@click.option(
"-p",
"--product",
"products",
help="Package only the given products (can specify multiple times)",
type=click.Choice(wagl.POSSIBLE_PRODUCTS, case_sensitive=False),
multiple=True,
)
"""
items = []
def _find(name, obj):
if obj.attrs.get("CLASS") == dataset_class:
items.append(name)
h5_obj.visititems(_find)
return items
RES_GROUP_PATH = re.compile(r"(.*/RES-GROUP-\d+)/")
@click.command(help=__doc__)
@click.argument("input", type=PathPath(dir_okay=False, readable=True))
@click.option("--factor", type=int, default=100)
@click.option("--anti-alias/--no-anti-alias", is_flag=True, default=False)
def downsample(input: Path, factor: int, anti_alias: bool):
# Fail early if h5repack cli command is not available.
from sh import h5repack, gdal_translate
granule_name = find_a_granule_name(input)
fmask_image = input.with_name(f"{granule_name}.fmask.img")
nbar_size = None
with h5py.File(input) as f:
image_paths = find_h5_paths(f, "IMAGE")
for i, image_path in enumerate(image_paths):
old_image: Optional[h5py.Dataset] = f[image_path]
blockxsize=block_size_x,
blockysize=block_size_y,
tiled=True,
)
with output_fp.open(**profile) as output_dataset:
output_dataset.write(array, 1)
# Copy gdal metadata
output_dataset.update_tags(**input_image.tags())
output_dataset.update_tags(1, **input_image.tags(1))
@click.command(help=__doc__)
@click.option(
"--output-base",
type=PathPath(file_okay=False, writable=True),
help="The base output directory "
"(default to same dir as input if --clean-inputs).",
)
@click.option("--zlevel",
type=click.IntRange(0, 9),
default=5,
help="Deflate compression level.")
@click.option("--block-size",
type=int,
default=512,
help="Compression block size (both x and y)")
@click.option(
"--clean-inputs/--no-clean-inputs",
default=False,
help="Delete originals after repackaging",
# relative_to_dataset_location=True,
# )
path_file = os.path.join(ds_path, file_location)
p.write_measurement(band_aliases[usgs_band_id], path_file)
p.add_accessory_file("metadata:landsat_mtl", Path(mtl_filename))
return p.done()
@click.command(help=__doc__)
@click.option(
"--output-base",
help="Write output into this directory instead of with the dataset",
required=True,
type=PathPath(exists=True, writable=True, dir_okay=True, file_okay=False),
)
@click.option(
"--producer",
help="Organisation that produced the data: probably either 'ga.gov.au' or 'usgs.gov'.",
required=False,
default="usgs.gov",
)
@click.argument(
"datasets", type=PathPath(exists=True, readable=True, writable=False), nargs=-1
)
@click.option(
"--newer-than",
type=serialise.ClickDatetime(),
default=None,
help="Only prepare files newer than this date",
"non_epsg",
f"Prefer an EPSG code to a WKT when possible. (Can change CRS to 'epsg:{wkt_crs.to_epsg()}')",
)
def _has_some_geo(dataset):
return dataset.geometry is not None or dataset.grids or dataset.crs
@click.command(help=__doc__ + """
Paths can be both product and dataset
documents, but each product must come before
its datasets to be matched against it.
""")
@click.version_option()
@click.argument("paths", nargs=-1, type=PathPath(exists=True, readable=True))
@click.option(
"--warnings-as-errors",
"-W",
"strict_warnings",
is_flag=True,
help="Fail if any warnings are produced",
)
@click.option(
"--thorough",
is_flag=True,
help=
"Attempt to read the data/measurements, and check their properties match",
)
@click.option(
"--expect-extra-measurements/--warn-extra-measurements",
def stats(self) -> Dict:
"""Get stats about the lookup table"""
self.open()
res = self._db.execute("""
select
count(*) as total,
count(distinct region_code) as unique_regions
--- count(distinct (lat1, lon1, lat2, lon2)) as unique_areas
from regions
""").fetchone()
return res
@click.group("s2_regions", help=__doc__)
@click.option("--db", default=DEFAULT_DB, type=PathPath())
@click.pass_context
def cli(ctx, db: Path):
ctx.obj = RegionLookup(db)
@cli.command("create", help="Recreate the database")
@click.option("--scan-path", default=None, type=PathPath(exists=True))
@click.option("-f", "paths_file", default=None, type=PathPath(exists=True))
@pass_obj
def cli_create(db: RegionLookup, scan_path: Path, paths_file: Path):
if scan_path is None and paths_file is None:
echo("Nothing specified. Scanning default NCI location.")
scan_path = NCI_L1C_LOCATION
if scan_path is not None:
name=SENTINEL_MSI_BAND_ALIASES[path.stem.replace(
"B", "")],
)
p.add_accessory_file("metadata:product_info", product_info_path)
p.add_accessory_file("metadata:sinergise_metadata",
metadata_xml_path)
return p.done()
else:
raise NotImplementedError("Unknown input file type?")
@click.command(help=__doc__)
@click.option(
"--dataset",
type=PathPath(),
required=True,
help="Path to ESA zipped dataset or Sinergise dataset directory",
)
@click.option(
"--dataset-document",
type=PathPath(),
required=True,
help="Location to output the L1C dataset document (yaml)",
)
def main(
dataset: Path,
dataset_document: Path,
):
uuid, path = prepare_and_write(
from eodatasets3.model import DatasetDoc
from eodatasets3.ui import PathPath
@click.command(help=__doc__)
@click.option("-v", "--verbose", is_flag=True)
@click.option("--stac-base-url", "-u", help="Base URL of the STAC file")
@click.option("--explorer-base-url", "-e", help="Base URL of the ODC Explorer")
@click.option(
"--validate/--no-validate",
default=False,
help="Validate output STAC Item against online schemas",
)
@click.argument(
"odc_metadata_files",
type=PathPath(exists=True, readable=True, writable=False),
nargs=-1,
)
def run(
verbose: bool,
odc_metadata_files: Iterable[Path],
stac_base_url: str,
explorer_base_url: str,
validate: bool,
):
for input_metadata in odc_metadata_files:
dataset = serialise.from_path(input_metadata)
name = input_metadata.stem.replace(".odc-metadata", "")
output_path = input_metadata.with_name(f"{name}.stac-item.json")