def add_item(self, path_pro: Optional[str], path_tiff: Optional[str],
path_img: Optional[str]) -> None:
assert path_pro.endswith(".pro")
file_name = path_pro.split("\\")[-1].rstrip(".pro")
print(file_name)
b0, data = parse(path_pro)
item: Item = stac.create_item(i_id=file_name, metadata=b0)
assets: List[Asset] = [
Asset(href=path_pro, media_type="pro")
]
if path_tiff is not None:
assets.append(Asset(href=path_tiff, media_type="geotiff"))
if path_img is not None:
assets.append(Asset(href=path_img, media_type="img"))
stac.add_assets(item, assets)
catalog = self.root_catalog.get_child(str(b0["b0_common"]["satId"][0]))
if catalog is None:
extent = Extent(spatial=SpatialExtent([[-180, -90, 180, 90]]), # TODO: Реальный Extent
temporal=TemporalExtent([[
datetime.strptime("2009-01-01T00:00:00.000000", "%Y-%m-%dT%H:%M:%S.%f"),
None]]))
catalog = Collection(id=str(b0["b0_common"]["satId"][0]),
title=b0["b0_common"]["satName"][0].decode("utf-8"),
description=f"Catalog for satellite "
f"{b0['b0_common']['satName'][0].decode('utf-8')}",
extent=extent)
self.root_catalog.add_child(catalog, catalog.title)
# update_collection_extent(item, catalog)
catalog.add_item(item)
def test_asset_absolute_href(self):
item_dict = self.get_example_item_dict()
item = Item.from_dict(item_dict)
rel_asset = Asset('./data.geojson')
rel_asset.set_owner(item)
expected_href = 'http://cool-sat.com/catalog/CS3-20160503_132130_04/data.geojson'
actual_href = rel_asset.get_absolute_href()
self.assertEqual(expected_href, actual_href)
def test_asset_absolute_href(self) -> None:
item_dict = self.get_example_item_dict()
item = Item.from_dict(item_dict)
rel_asset = Asset("./data.geojson")
rel_asset.set_owner(item)
expected_href = os.path.abspath("./data.geojson")
actual_href = rel_asset.get_absolute_href()
self.assertEqual(expected_href, actual_href)
def test_asset_absolute_href_no_item_self(self) -> None:
item_dict = self.get_example_item_dict()
item = Item.from_dict(item_dict)
assert item.get_self_href() is None
rel_asset = Asset("./data.geojson")
rel_asset.set_owner(item)
actual_href = rel_asset.get_absolute_href()
self.assertEqual(None, actual_href)
def build_items(index_geom):
"""
index_geom: fioan readable file (ex, shapefile)
Build the STAC items
"""
with fiona.open(index_geom) as src:
src_crs = Proj(src.crs)
dest_crs = Proj("WGS84")
extent = box(*src.bounds)
project = Transformer.from_proj(src_crs, dest_crs)
catalog_bbox = shapely_transform(project.transform, extent)
# build spatial extent for collection
ortho_collection = GeobaseSTAC.get_child("canada_spot_orthoimages")
ortho_collection.extent.spatial = SpatialExtent(
[list(catalog_bbox.bounds)])
geobase = GeobaseSpotFTP()
count = 0
for f in src:
feature_out = f.copy()
new_coords = transform_geom(src_crs, dest_crs,
f["geometry"]["coordinates"])
feature_out["geometry"]["coordinates"] = new_coords
name = feature_out["properties"]["NAME"]
sensor = SPOT_SENSOR[name[:2]]
new_item = create_item(name, feature_out, ortho_collection)
for f in geobase.list_contents(name):
# Add data to the asset
spot_file = Asset(href=f,
title=None,
media_type="application/zip")
file_key = f[-13:-4] # image type
new_item.add_asset(file_key, spot_file)
# Add the thumbnail asset
new_item.add_asset(
key="thumbnail",
asset=Asset(
href=geobase.get_thumbnail(name),
title=None,
media_type=MediaType.JPEG,
),
)
ortho_collection.add_item(new_item)
count += 1
print(f"{count}... {new_item.id}")
def test_from_asset(self):
a1 = Asset.from_dict(self.ASSET_DICT)
with self.assertRaises(STACError):
EOAsset.from_asset(a1)
a2 = Asset.from_dict(self.EO_ASSET_DICT)
eoa = EOAsset.from_asset(a2)
self.assertIsNone(eoa.properties)
self.assertListEqual(eoa.bands, [0])
def test_map_items_multiple_2(self):
catalog = Catalog(id='test-1', description='Test1')
item1 = Item(id='item1',
geometry=RANDOM_GEOM,
bbox=RANDOM_BBOX,
datetime=datetime.utcnow(),
properties={})
item1.add_asset('ortho', Asset(href='/some/ortho.tif'))
catalog.add_item(item1)
kitten = Catalog(id='test-kitten',
description='A cuter version of catalog')
catalog.add_child(kitten)
item2 = Item(id='item2',
geometry=RANDOM_GEOM,
bbox=RANDOM_BBOX,
datetime=datetime.utcnow(),
properties={})
item2.add_asset('ortho', Asset(href='/some/other/ortho.tif'))
kitten.add_item(item2)
def modify_item_title(item):
item.title = 'Some new title'
return item
def create_label_item(item):
# Assumes the GEOJSON labels are in the
# same location as the image
img_href = item.assets['ortho'].href
label_href = '{}.geojson'.format(os.path.splitext(img_href)[0])
label_item = Item(id='Labels',
geometry=item.geometry,
bbox=item.bbox,
datetime=datetime.utcnow(),
properties={})
label_item.ext.enable(Extensions.LABEL)
label_ext = label_item.ext.label
label_ext.apply(label_description='labels',
label_type='vector',
label_properties=['label'],
label_classes=[
LabelClasses.create(classes=['one', 'two'],
name='label')
],
label_tasks=['classification'])
label_ext.add_source(item, assets=['ortho'])
label_ext.add_geojson_labels(label_href)
return [item, label_item]
c = catalog.map_items(modify_item_title)
c = c.map_items(create_label_item)
new_catalog = c
items = new_catalog.get_all_items()
self.assertTrue(len(list(items)) == 4)
def test_asset_absolute_href(self) -> None:
item_path = TestCases.get_path("data-files/item/sample-item.json")
item_dict = self.get_example_item_dict()
item = Item.from_dict(item_dict)
item.set_self_href(item_path)
rel_asset = Asset("./data.geojson")
rel_asset.set_owner(item)
expected_href = os.path.abspath(
os.path.join(os.path.dirname(item_path), "./data.geojson"))
actual_href = rel_asset.get_absolute_href()
self.assertEqual(expected_href, actual_href)
def test_asset_absolute_href(self):
m = TestCases.get_path(
'data-files/itemcollections/sample-item-collection.json')
with open(m) as f:
item_dict = json.load(f)['features'][0]
item = Item.from_dict(item_dict)
rel_asset = Asset('./data.geojson')
rel_asset.set_owner(item)
expected_href = 'http://cool-sat.com/catalog/CS3-20160503_132130_04/data.geojson'
actual_href = rel_asset.get_absolute_href()
self.assertEqual(expected_href, actual_href)
def test_full_copy_2(self):
with TemporaryDirectory() as tmp_dir:
cat = Catalog(id='test', description='test catalog')
image_item = Item(id='Imagery',
geometry=RANDOM_GEOM,
bbox=RANDOM_BBOX,
datetime=datetime.utcnow(),
properties={})
for key in ['ortho', 'dsm']:
image_item.add_asset(
key, Asset(href='some/{}.tif'.format(key), media_type=MediaType.GEOTIFF))
label_item = LabelItem(
id='Labels',
geometry=RANDOM_GEOM,
bbox=RANDOM_BBOX,
datetime=datetime.utcnow(),
properties={},
label_description='labels',
label_type='vector',
label_properties='label',
label_classes=[LabelClasses(classes=['one', 'two'], name='label')],
label_tasks=['classification'])
label_item.add_source(image_item, assets=['ortho'])
cat.add_items([image_item, label_item])
cat.normalize_hrefs(os.path.join(tmp_dir, 'catalog-full-copy-2-source'))
cat.save(catalog_type=CatalogType.ABSOLUTE_PUBLISHED)
cat2 = cat.full_copy()
cat2.normalize_hrefs(os.path.join(tmp_dir, 'catalog-full-copy-2-dest'))
cat2.save(catalog_type=CatalogType.ABSOLUTE_PUBLISHED)
self.check_catalog(cat, 'source')
self.check_catalog(cat2, 'dest')
def data_asset(self, base: str = DEFAULT_BASE) -> Asset:
"""Returns the data asset (aka the tiff file)."""
return Asset(href=self._asset_href_with_extension(base, "tif"),
title=self.title,
description=self.description,
media_type=MediaType.COG,
roles=["data"])
def gpkg_asset(self, base: str = DEFAULT_BASE) -> Asset:
"""Returns the geopackage asset."""
return Asset(href=self._asset_href_with_extension(base,
"gpkg",
id_only=True),
media_type=MediaType.GEOPACKAGE,
roles=["metadata"])
def test_case_3():
root_cat = Catalog(id='test3', description='test case 3 catalog', title='test case 3 title')
image_item = Item(id='imagery-item',
geometry=RANDOM_GEOM,
bbox=RANDOM_BBOX,
datetime=datetime.utcnow(),
properties={})
image_item.add_asset('ortho', Asset(href='some/geotiff.tiff', media_type=MediaType.GEOTIFF))
overviews = [LabelOverview('label', counts=[LabelCount('one', 1), LabelCount('two', 2)])]
label_item = LabelItem(id='label-items',
geometry=RANDOM_GEOM,
bbox=RANDOM_BBOX,
datetime=datetime.utcnow(),
properties={},
label_description='ML Labels',
label_type='vector',
label_properties=['label'],
label_classes=[LabelClasses(classes=['one', 'two'], name='label')],
label_tasks=['classification'],
label_methods=['manual'],
label_overviews=overviews)
label_item.add_source(image_item, assets=['ortho'])
root_cat.add_item(image_item)
root_cat.add_item(label_item)
return root_cat
def item(href: str,
read_href_modifier: Optional[ReadHrefModifier] = None) -> Item:
"""Creates a STAC Item from the asset at the provided href.
The `read_href_modifer` argument can be used to modify the href for the
rasterio read, e.g. if you need to sign a url.
This function is intentionally minimal in its signature and capabilities. If
you need to customize your Item, do so after creation.
This function sets:
- id
- geometry
- bbox
- datetime (to the time of item creation): you'll probably want to change this
- the proj extension
- either the EPSG code or, if not available, the WKT2
- transform
- shape
- a single asset with key 'data'
- asset href
- asset roles to ['data']
In particular, the datetime and asset media type fields most likely need to be updated.
"""
id = os.path.splitext(os.path.basename(href))[0]
if read_href_modifier:
modified_href = read_href_modifier(href)
else:
modified_href = href
with rasterio.open(modified_href) as dataset:
crs = dataset.crs
proj_bbox = dataset.bounds
proj_transform = list(dataset.transform)[0:6]
proj_shape = dataset.shape
proj_geometry = shapely.geometry.mapping(shapely.geometry.box(*proj_bbox))
geometry = stactools.core.projection.reproject_geom(crs,
'EPSG:4326',
proj_geometry,
precision=6)
bbox = list(shapely.geometry.shape(geometry).bounds)
item = Item(id=id,
geometry=geometry,
bbox=bbox,
datetime=datetime.datetime.now(),
properties={})
projection = ProjectionExtension.ext(item, add_if_missing=True)
epsg = crs.to_epsg()
if epsg:
projection.epsg = epsg
else:
projection.wkt2 = crs.to_wkt('WKT2')
projection.transform = proj_transform
projection.shape = proj_shape
item.add_asset('data', Asset(href=href, roles=['data']))
return item
def process_item(self, item, source):
"""
Converts an input STAC Item's data into Zarr, returning an output STAC item
Parameters
----------
item : pystac.Item
the item that should be converted
source : harmony.message.Source
the input source defining the variables, if any, to subset from the item
Returns
-------
pystac.Item
a STAC item containing the Zarr output
"""
result = item.clone()
result.assets = {}
# Create a temporary dir for processing we may do
workdir = mkdtemp()
try:
# Get the data file
asset = next(v for k, v in item.assets.items()
if 'data' in (v.roles or []))
input_filename = download(asset.href,
workdir,
logger=self.logger,
access_token=self.message.accessToken,
cfg=self.config)
name = generate_output_filename(asset.href, ext='.zarr')
root = self.message.stagingLocation + name
try:
store = self.s3.get_mapper(root=root, check=False, create=True)
netcdf_to_zarr(input_filename, store)
except Exception as e:
# Print the real error and convert to user-facing error that's more digestible
self.logger.error(e, exc_info=1)
filename = asset.href.split('?')[0].rstrip('/').split('/')[-1]
raise ZarrException('Could not convert file to Zarr: %s' %
(filename))
# Update the STAC record
result.assets['data'] = Asset(root,
title=name,
media_type='application/x-zarr',
roles=['data'])
# Return the STAC record
return result
finally:
# Clean up any intermediate resources
shutil.rmtree(workdir)
def test_case_3() -> Catalog:
root_cat = Catalog(id="test3",
description="test case 3 catalog",
title="test case 3 title")
image_item = Item(
id="imagery-item",
geometry=ARBITRARY_GEOM,
bbox=ARBITRARY_BBOX,
datetime=datetime.utcnow(),
properties={},
)
image_item.add_asset(
"ortho",
Asset(href="some/geotiff.tiff", media_type=MediaType.GEOTIFF))
overviews = [
LabelOverview.create(
"label",
counts=[
LabelCount.create("one", 1),
LabelCount.create("two", 2)
],
)
]
label_item = Item(
id="label-items",
geometry=ARBITRARY_GEOM,
bbox=ARBITRARY_BBOX,
datetime=datetime.utcnow(),
properties={},
)
LabelExtension.add_to(label_item)
label_ext = LabelExtension.ext(label_item)
label_ext.apply(
label_description="ML Labels",
label_type=LabelType.VECTOR,
label_properties=["label"],
label_classes=[
LabelClasses.create(classes=["one", "two"], name="label")
],
label_tasks=["classification"],
label_methods=["manual"],
label_overviews=overviews,
)
label_ext.add_source(image_item, assets=["ortho"])
root_cat.add_item(image_item)
root_cat.add_item(label_item)
return root_cat
def create_asset(self, asset):
"""
"""
desc = asset.get(self.mappings.ASSET_DESCRIPTION)
return Asset(
asset.get(self.mappings.ASSET_URL),
title=asset.get(self.mappings.ASSET_TITLE),
description=desc,
media_type=self.mappings.TYPE_DICT.get(desc),
roles=[self.mappings.ROLE_DICT.get(desc)],
)
def test_add_asset(self):
eoi_c = deepcopy(self.eoi)
a = Asset('/asset_dir/asset.json')
eoa = EOAsset('/asset_dir/eo_asset.json', bands=[0, 1])
for asset in (a, eoa):
self.assertIsNone(asset.owner)
eoi_c.add_asset('new_asset', a)
eoi_c.add_asset('new_eo_asset', eoa)
self.assertEqual(len(eoi_c.assets.items()), len(self.eoi.assets.items()) + 2)
self.assertEqual(a, eoi_c.assets['new_asset'])
self.assertEqual(eoa, eoi_c.assets['new_eo_asset'])
for asset in (a, eoa):
self.assertEqual(asset.owner, eoi_c)
def generate_cog(stac_item: Item, destination_uri: str, target_assets: List):
"""
"""
for input_layer in target_assets:
asset = stac_item.assets.get(input_layer)
result = main(asset.href, join(destination_uri, basename(asset.href)))
asset.add_asset(
"{}_cog".format(input_layer),
Asset(href=result['destination_layer'],
title=asset.title,
description=asset.description,
media_type=MediaType.COG,
roles=asset.roles,
properties=asset.properties))
return stac_item.to_dict()
def to_stac(item, in_tiff):
item_out = Item(id=item.id,
geometry=item.geometry,
bbox=item.bbox,
datetime=item.datetime,
properties=item.properties)
item_out.common_metadata.set_gsd(20)
item_out.common_metadata.set_constellation('sentinel-1')
item_out.common_metadata.set_mission('sentinel-1')
item_out.common_metadata.set_platform('sentinel-1{}'.format(item.id[2:3].lower()))
eo_item = extensions.eo.EOItemExt(item_out)
band = 'sigma_db_vv'
item_out.add_asset(key=band.lower(),
asset=Asset(href=in_tiff,
media_type=MediaType.GEOTIFF,
properties={'sar:polarizations': band.lower().split('_')[1].upper()}))
asset = eo_item.item.get_assets()[band.lower()]
description = '{} for polarization channel {}{}'.format(band.lower().split('_')[0].title(),
band.lower().split('_')[1].upper(),
' in {}'.format(band.lower().split('_')[2]) if len(band.lower().split('_')) == 3 else '')
stac_band = extensions.eo.Band.create(name=band.lower(),
common_name=band.lower(),
description=description)
#bands.append(stac_band)
eo_item.set_bands([stac_band], asset=asset)
#eo_item.set_bands(bands)
#eo_item.apply(bands)
return item_out
def collection_add_sentinel_chips(collection,
uri_list,
sentinel_version,
debug=False):
""" Add sentinel images to a collection """
if debug:
uri_list = list(uri_list)[:10]
for uri in uri_list:
if not uri.endswith(".tif"):
continue
item_id = os.path.basename(uri).split(".")[0]
country, event_id, *_ = item_id.split("_")
params = {}
params["id"] = item_id
params["collection"] = collection
params["properties"] = {
"country": country,
"event_id": event_id,
}
params["bbox"] = get_chip_bbox(uri, country, event_id)
params["geometry"] = box(*params["bbox"]).__geo_interface__
params["datetime"] = image_date_for_country(sentinel_version, country)
# Create Tiff Item
item = Item(**params)
asset = Asset(href=uri,
title="GeoTiff",
media_type="image/tiff; application=geotiff")
item.add_asset(key="image", asset=asset)
SENTINEL_CHIP_ITEM_CACHE[sentinel_version.upper()][chip_cache_id(
country, event_id)] = item
collection.add_item(item)
print("Collection {}: Added STAC Item {}".format(
collection.id, item.id))
def label_collection_add_items(
collection,
root_catalog,
uri_list,
links_func,
label_description,
label_type,
label_classes=None,
label_tasks=None,
debug=False,
):
""" Add uri_list tif uris to collection as LabelItems
root_catalog is the top level node in the STAC Catalog where the chips labeled by these tifs
can be found. Required to correctly setup Links to the source chips.
links_func is a method with the following signature:
def links_func(root_catalog: Catalog,
label_item: LabelItem,
country: str,
event_id: int): [Link]
This method should construct a list of links that map the label_item to the STAC objects in
the root_catalog that label_item is derived from. Assumes for now that the asset referenced
uses the key "labels"
The label_ arguments will be passed down to each LabelItem in the collection
"""
if debug:
uri_list = list(uri_list)[:10]
for uri in uri_list:
if not uri.endswith(".tif"):
continue
item_id = os.path.basename(uri).split(".")[0]
country, event_id, *_ = item_id.split("_")
params = {}
params["id"] = item_id
params["collection"] = collection
params["datetime"] = image_date_for_country("s1", country)
params["stac_extensions"] = [Extensions.LABEL]
params["properties"] = {
"country": country,
"event_id": event_id,
}
params["bbox"] = get_chip_bbox(uri, country, event_id)
params["geometry"] = box(*params["bbox"]).__geo_interface__
label_ext_params = {}
if isinstance(label_classes, list):
label_ext_params["label_classes"] = label_classes
else:
label_ext_params["label_classes"] = []
label_ext_params["label_description"] = label_description
if label_tasks is not None:
label_ext_params["label_tasks"] = label_tasks
label_ext_params["label_type"] = label_type
item = Item(**params)
item.ext.label.apply(**label_ext_params)
# Add Asset
asset = Asset(href=uri,
title="GeoTiff",
media_type="image/tiff; application=geotiff")
item.add_asset(key="labels", asset=asset)
item.links = links_func(root_catalog, item, country, event_id)
collection.add_item(item)
print("Collection {}: Added STAC Item {}".format(
collection.id, item.id))
def main(ctx, input_reference, s_expression, cbn):
dump(ctx)
item = get_item(os.path.join(input_reference, "catalog.json"))
logging.info(f"Processing {item.id}")
try:
os.mkdir(item.id)
except FileExistsError:
pass
cbn = cbn.replace(' ', '-')
result = os.path.join(item.id, f"{cbn}.tif")
logging.info(f"Apply {s_expression} to {item.id}")
apply_s_expression(item=item, s_expression=s_expression, out_tif=result)
logging.info("STAC")
item_out = Item(
id=item.id,
geometry=item.geometry,
bbox=item.bbox,
datetime=item.datetime,
properties=item.properties,
stac_extensions=item.stac_extensions,
)
eo_item = extensions.eo.EOItemExt(item_out)
asset_properties = dict()
asset_properties["s-expression"] = s_expression
asset = Asset(
href=os.path.basename(result),
media_type=MediaType.COG,
roles=["data"],
properties=asset_properties,
)
eo_bands = [
extensions.eo.Band.create(
name=cbn.lower(),
common_name=cbn.lower(),
description=f"{cbn.lower()} ({s_expression})",
)
]
eo_item.set_bands(eo_bands, asset=asset)
item_out.add_asset(key=cbn.lower(), asset=asset)
logging.info("STAC")
cat = Catalog(id="catalog", description="s-expression")
cat.add_items([item_out])
cat.normalize_and_save(root_href="./",
catalog_type=CatalogType.SELF_CONTAINED)
logging.info("Done!")
def burned(pre_item, post_item, ndvi_threshold, ndwi_threshold):
items = {}
items["pre-event"] = pre_item
items["post-event"] = post_item
veg_indices = {}
scl = {}
for key, item in items.items():
stack(
item=item,
bands=["B04", "B08", "B11", "SCL"],
target_res=10,
output_name=f"{key}.tif",
)
ndvi, ndwi = indices(f"{key}.tif")
veg_indices[key] = {"ndvi": ndvi, "ndwi": ndwi}
scl[key] = get_scl(f"{key}.tif")
if key in ["pre-event"]:
geotransform, georef = get_geo(f"{key}.tif")
os.remove(f"{key}.tif")
conditions = (
(veg_indices["post-event"]["ndwi"] - veg_indices["pre-event"]["ndwi"])
> float(ndwi_threshold)
) & (
(veg_indices["post-event"]["ndvi"] - veg_indices["pre-event"]["ndvi"])
> float(ndvi_threshold)
) & (
scl["pre-event"] == 4
) | (
scl["post-event"] == 4
)
height = scl["pre-event"].shape[1]
width = scl["pre-event"].shape[0]
burned = np.zeros((height, width), dtype=np.uint8)
burned[conditions] = 1
# free memory
for key, _ in items.items():
for indice, _ in veg_indices.items():
veg_indices[key][indice] = None
burned[
np.where(
(scl["pre-event"] == 0)
| (scl["post-event"] == 0)
| (scl["pre-event"] == 1)
| (scl["post-event"] == 1)
| (scl["pre-event"] == 5)
| (scl["post-event"] == 5)
| (scl["pre-event"] == 6)
| (scl["post-event"] == 6)
| (scl["pre-event"] == 7)
| (scl["post-event"] == 7)
| (scl["pre-event"] == 8)
| (scl["post-event"] == 8)
| (scl["pre-event"] == 9)
| (scl["post-event"] == 9)
)
] = 2
output_name = "BURNED_AREA_{}".format(
"_".join(
[s2_item.datetime.strftime("%Y%m%d") for key, s2_item in items.items()]
)
)
item_id = "burned-area"
write_tif(
burned,
os.path.join(item_id, f"{output_name}.tif"),
width,
height,
geotransform,
georef,
)
item = Item(
id=item_id,
geometry=items["pre-event"].geometry,
bbox=items["pre-event"].bbox,
datetime=items["pre-event"].datetime,
properties={},
)
item.add_asset(
key="data",
asset=Asset(
href=os.path.join(".", f"{output_name}.tif"),
media_type=MediaType.COG,
title="Burned area analysis from Sentinel-2",
),
)
return item
if running_start_dt > start_dt:
running_start_dt = start_dt
else:
running_start_dt = start_dt
if running_end_dt:
if running_end_dt < end_dt:
running_end_dt = end_dt
else:
running_end_dt = end_dt
fid = feature["id"]
binary_asset = Asset(
href="{}-usfimr.wkb".format(fid),
description="well known binary representation",
media_type="application/wkb",
)
text_asset = Asset(
href="{}-usfimr.wkt".format(fid),
description="well known text representation",
media_type="application/wkt",
)
json_asset = Asset(
href="{}-usfimr.geojson".format(fid),
description="geojson representation",
media_type="application/geo+json",
)
serializable_convex_hull = mapping(shapely_geom.convex_hull)
item = Item(fid, serializable_convex_hull, bbox_list, start_dt,
deepcopy(props))
start_time = datetime.fromisoformat(time_range["from"][:-1])
end_time = datetime.fromisoformat(time_range["to"][:-1])
temporal_extent = TemporalExtent(intervals=[[start_time, end_time]])
stac_items = []
for group_id, image_group in imagery_grouped:
# assemble assets so that they might be grouped (without duplication) in items
assets = []
for image in image_group:
s3_path = "s3://" + image.bucket_name + "/" + image.key
# The extents should be the same, so whichever one is checked last should be fine
with rio.open(s3_path) as img:
bounds = img.bounds
assets.append(Asset(s3_path))
if aggregate_bounds is None:
aggregate_bounds = bounds
else:
aggregate_bounds = rio.coords.BoundingBox(
min(bounds.left, aggregate_bounds.left),
min(bounds.bottom, aggregate_bounds.bottom),
max(bounds.right, aggregate_bounds.right),
max(bounds.top, aggregate_bounds.top),
)
item_spatial_extent = SpatialExtent(
[[bounds.bottom, bounds.left, bounds.top, bounds.right]])
item_extent = Extent(item_spatial_extent, temporal_extent)
image_item = Item(
def process_item(self, item, source):
"""
Processes a single input item. Services that are not aggregating multiple input files
should prefer to implement this method rather than #invoke
This example copies its input to the output, marking "dpi" and "variables" message
attributes as having been processed
Parameters
----------
item : pystac.Item
the item that should be processed
source : harmony.message.Source
the input source defining the variables, if any, to subset from the item
Returns
-------
pystac.Item
a STAC catalog whose metadata and assets describe the service output
"""
result = item.clone()
result.assets = {}
# Create a temporary dir for processing we may do
workdir = mkdtemp()
try:
# Get the data file
asset = next(v for k, v in item.assets.items()
if 'data' in (v.roles or []))
input_filename = download(asset.href,
workdir,
logger=self.logger,
access_token=self.message.accessToken)
# Mark any fields the service processes so later services do not repeat work
dpi = self.message.format.process('dpi')
# Variable subsetting
variables = source.process('variables')
# Do the work here!
var_names = [v.name for v in variables]
print('Processing item %s, DPI=%d, vars=[%s]' %
(item.id, dpi, ', '.join(var_names)))
working_filename = os.path.join(workdir, 'tmp.txt')
shutil.copyfile(input_filename, working_filename)
# Stage the output file with a conventional filename
output_filename = generate_output_filename(asset.href,
ext=None,
variable_subset=None,
is_regridded=False,
is_subsetted=False)
url = stage(working_filename,
output_filename,
'text/plain',
location=self.message.stagingLocation,
logger=self.logger)
# Update the STAC record
result.assets['data'] = Asset(url,
title=output_filename,
media_type='text/plain',
roles=['data'])
# Other metadata updates may be appropriate, such as result.bbox and result.geometry
# if a spatial subset was performed
# Return the STAC record
return result
finally:
# Clean up any intermediate resources
shutil.rmtree(workdir)
def metadata_asset(self, base: str = DEFAULT_BASE) -> Asset:
"""Returns the data asset (aka the tiff file)."""
return Asset(href=self._asset_href_with_extension(base, "xml"),
media_type=MediaType.XML,
roles=["metadata"])
def thumbnail_asset(self, base: str = DEFAULT_BASE) -> Asset:
"""Returns the thumbnail asset."""
return Asset(href=self._asset_href_with_extension(base, "jpg"),
media_type=MediaType.JPEG,
roles=["thumbnail"])
def example_asset(self) -> Asset:
return Asset.from_dict(self.asset_dict)
