diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index a7d4d2e..a8eddc2 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -23,10 +23,11 @@ jobs: fetch-depth: 0 - name: Check linting - uses: rickstaa/action-black@v1 + uses: psf/black@stable id: action_black with: - black_args: "--check dep_tools" + options: "--check" + src: "./dep_tools" testing: runs-on: ubuntu-latest diff --git a/dep_tools/aws.py b/dep_tools/aws.py new file mode 100644 index 0000000..41d3309 --- /dev/null +++ b/dep_tools/aws.py @@ -0,0 +1,111 @@ +import json +from io import BytesIO +from pathlib import Path +from typing import IO, Union + +import boto3 +from botocore.client import BaseClient +from fiona.io import MemoryFile +from geopandas import GeoDataFrame +from odc.geo.xr import to_cog +from xarray import DataArray, Dataset + +from pystac import Item + + +def object_exists(bucket: str, key: str, client: BaseClient | None = None) -> bool: + """Check if a key exists in a bucket.""" + if client is None: + client = boto3.client("s3") + + try: + client.head_object(Bucket=bucket, Key=key) + return True + except client.exceptions.ClientError: + return False + + +def s3_dump( + data: Union[bytes, str, IO], bucket: str, key: str, client: BaseClient, **kwargs +) -> bool: + """Write data to s3 object.""" + + r = client.put_object(Bucket=bucket, Key=key, Body=data, **kwargs) + code = r["ResponseMetadata"]["HTTPStatusCode"] + return 200 <= code < 300 + + +def write_to_s3( + d: Union[DataArray, Dataset, GeoDataFrame, str], + path: Union[str, Path], + bucket: str, + overwrite: bool = True, + use_odc_writer: bool = True, + client: BaseClient | None = None, + s3_dump_kwargs=dict(), + **kwargs, +): + if client is None: + client = boto3.client("s3") + + key = str(path).lstrip("/") + + if not overwrite and object_exists(bucket, key, client): + return + + if isinstance(d, (DataArray, Dataset)): + if use_odc_writer: + if "driver" in kwargs: + del kwargs["driver"] + binary_data = to_cog(d, **kwargs) + s3_dump( + binary_data, + bucket, + key, + client, + ContentType="image/tiff", + **s3_dump_kwargs, + ) + + else: + with BytesIO() as binary_data: + d.rio.to_raster(binary_data, driver="COG", **kwargs) + binary_data.seek(0) + s3_dump( + binary_data, + bucket, + key, + client, + ContentType="image/tiff", + **s3_dump_kwargs, + ) + + elif isinstance(d, GeoDataFrame): + with MemoryFile() as buffer: + d.to_file(buffer, **kwargs) + buffer.seek(0) + s3_dump(buffer.read(), bucket, key, client, **s3_dump_kwargs) + elif isinstance(d, Item): + s3_dump( + json.dumps(d.to_dict(), indent=4), bucket, key, client, **s3_dump_kwargs + ) + elif isinstance(d, str): + s3_dump(d, bucket, key, client, **s3_dump_kwargs) + else: + raise ValueError( + "You can only write an Xarray DataArray or Dataset, Geopandas GeoDataFrame, Pystac Item, or string" + ) + + +def write_stac_s3( + item: Item, + stac_path: str, + bucket: str, + **kwargs, +) -> None: + item_string = json.dumps(item.to_dict(), indent=4) + write_to_s3( + item_string, stac_path, bucket=bucket, ContentType="application/json", **kwargs + ) + + return stac_path diff --git a/dep_tools/azure.py b/dep_tools/azure.py index a3f5537..ceb050d 100644 --- a/dep_tools/azure.py +++ b/dep_tools/azure.py @@ -1,11 +1,18 @@ +from functools import partial +import io +import json +from multiprocessing.dummy import Pool as ThreadPool import os from pathlib import Path from typing import Union, Generator -import azure.storage.blob -from azure.storage.blob import ContainerClient -from functools import partial -from multiprocessing.dummy import Pool as ThreadPool +from azure.storage.blob import ContainerClient, ContentSettings +import fiona +from geopandas import GeoDataFrame +from odc.geo.xr import to_cog +from osgeo import gdal +from pystac import Item +from xarray import DataArray, Dataset def get_container_client( @@ -23,7 +30,7 @@ def get_container_client( "'None' is not a valid value for 'credential'. Pass a valid name or set the 'AZURE_STORAGE_SAS_TOKEN' environment variable" ) - return azure.storage.blob.ContainerClient( + return ContainerClient( f"https://{storage_account}.blob.core.windows.net", container_name=container_name, credential=credential, @@ -71,3 +78,83 @@ def list_blob_container( blob_name = blob_record["name"] if blob_name.endswith(suffix): yield blob_name + + +def build_vrt( + bounds: list, + prefix: str = "", + suffix: str = "", +) -> Path: + blobs = [ + f"/vsiaz/output/{blob.name}" + for blob in get_container_client().list_blobs(name_starts_with=prefix) + if blob.name.endswith(suffix) + ] + + local_prefix = Path(prefix).stem + vrt_file = f"data/{local_prefix}.vrt" + gdal.BuildVRT(vrt_file, blobs, outputBounds=bounds) + return Path(vrt_file) + + +def write_stac_blob_storage( + item: Item, + stac_path: str, + **kwargs, +) -> str | None: + item_json = json.dumps(item.to_dict(), indent=4) + write_to_blob_storage( + item_json, + stac_path, + content_settings=ContentSettings(content_type="application/json"), + **kwargs, + ) + return stac_path + + +def write_to_blob_storage( + d: Union[DataArray, Dataset, GeoDataFrame, str], + path: Union[str, Path], + overwrite: bool = True, + use_odc_writer: bool = False, + client: ContainerClient | None = None, + **kwargs, +) -> None: + # Allowing for a shared container client, which might be + # more efficient. If not provided, get one. + if client is None: + client = get_container_client() + blob_client = client.get_blob_client(str(path)) + if not overwrite and blob_client.exists(): + return + + if isinstance(d, (DataArray, Dataset)): + if use_odc_writer: + if "driver" in kwargs: + del kwargs["driver"] + binary_data = to_cog(d, **kwargs) + blob_client.upload_blob( + binary_data, overwrite=overwrite, connection_timeout=TIMEOUT_SECONDS + ) + else: + with io.BytesIO() as buffer: + # This is needed or rioxarray doesn't know what type it is writing + if "driver" not in kwargs: + kwargs["driver"] = "COG" + d.rio.to_raster(buffer, **kwargs) + buffer.seek(0) + blob_client.upload_blob( + buffer, overwrite=overwrite, connection_timeout=TIMEOUT_SECONDS + ) + + elif isinstance(d, GeoDataFrame): + with fiona.io.MemoryFile() as buffer: + d.to_file(buffer, **kwargs) + buffer.seek(0) + blob_client.upload_blob(buffer, overwrite=overwrite) + elif isinstance(d, str): + blob_client.upload_blob(d, overwrite=overwrite, **kwargs) + else: + raise ValueError( + "You can only write an Xarray DataArray or Dataset, or Geopandas GeoDataFrame" + ) diff --git a/dep_tools/grids.py b/dep_tools/grids.py new file mode 100644 index 0000000..5229997 --- /dev/null +++ b/dep_tools/grids.py @@ -0,0 +1,91 @@ +from typing import Literal + +import antimeridian +import geopandas as gpd +from geopandas import GeoDataFrame, GeoSeries +from odc.geo import XY, BoundingBox +from odc.geo.gridspec import GridSpec +from shapely.geometry import shape + +# This EPSG code is what we're using for now +# but it's not ideal, as its not an equal area projection... +PACIFIC_EPSG = "EPSG:3832" + + +def grid( + resolution: int | float = 30, + crs=PACIFIC_EPSG, + return_type: Literal["GridSpec", "GeoSeries", "GeoDataFrame"] = "GridSpec", + intersect_with: GeoDataFrame | None = None, +) -> GridSpec | GeoSeries | GeoDataFrame: + """Returns a GridSpec or GeoSeries representing the Pacific grid, optionally + intersected with an area of interest. + + Args: + resolution: The resolution, in meters, of the output. As tiles are + defined to be 96,000 meters on each side, it should divide 96,000 + evenly. + crs: The desired crs of the output. + return_type: The return type. If intersect_with (see below) is not None, + this is ignored. + intersect_with: The output is intersected with the supplied GeoDataFrame + before returning, returning only tiles which overlap with those + features. Forces the output to be a GeoDataFrame. + """ + + if intersect_with is not None: + full_grid = _geoseries(resolution, crs) + return _intersect_grid(full_grid, intersect_with) + + return { + "GridSpec": _gridspec, + "GeoSeries": _geoseries, + "GeoDataFrame": _geodataframe, + }[return_type](resolution, crs) + + +def _intersect_grid(grid: GeoSeries, areas_of_interest): + return gpd.sjoin( + gpd.GeoDataFrame(geometry=grid), areas_of_interest.to_crs(grid.crs) + ).drop(columns=["index_right"]) + + +def _gridspec(resolution, crs=PACIFIC_EPSG): + gridspec_origin = XY(-3000000.0, -4000000.0) + + side_in_meters = 96_000 + shape = (side_in_meters / resolution, side_in_meters / resolution) + + return GridSpec( + crs=crs, + tile_shape=shape, + resolution=resolution, + origin=gridspec_origin, + ) + + +def _geodataframe(resolution, crs=PACIFIC_EPSG): + return GeoDataFrame(geometry=_geoseries(resolution, crs), crs=crs) + + +def _geoseries(resolution, crs) -> GeoSeries: + bounds = BoundingBox(120, -30, 280, 30, crs="EPSG:4326").to_crs(crs) + tiles = _gridspec(resolution, crs).tiles(bounds) + geometry, index = zip( + *[(a_tile[1].boundingbox.polygon.geom, a_tile[0]) for a_tile in tiles] + ) + + gs = gpd.GeoSeries(geometry, index, crs=PACIFIC_EPSG) + if crs != PACIFIC_EPSG: + gs = gs.to_crs(crs) + if crs == 4326: + gs = gs.apply(lambda geom: shape(antimeridian.fix_shape(geom))) + + return gs + + +# The origin is in the projected CRS. This works for Landsat. +PACIFIC_GRID_30 = grid() + +# This grid is for Sentinel-2 and has the same footprint +PACIFIC_GRID_10 = grid(resolution=10) diff --git a/dep_tools/loaders.py b/dep_tools/loaders.py index e867416..e31b815 100644 --- a/dep_tools/loaders.py +++ b/dep_tools/loaders.py @@ -1,13 +1,14 @@ from abc import ABC, abstractmethod from geopandas import GeoDataFrame -import odc.stac +from odc.geo.geobox import GeoBox +from odc.geo.geom import Geometry +from odc.stac import load as stac_load from rasterio.errors import RasterioError, RasterioIOError +import rioxarray from stackstac import stack from xarray import DataArray, Dataset, concat -from dep_tools.searchers import Searcher - class Loader(ABC): """A loader loads data.""" @@ -26,15 +27,6 @@ def load(self, items, area): pass -class SearchLoader(Loader): - def __init__(self, searcher: Searcher, loader: StacLoader): - self.searcher = searcher - self.loader = loader - - def load(self, area): - return self.loader.load(self.searcher.search(area), area) - - class OdcLoader(StacLoader): def __init__( self, @@ -47,41 +39,48 @@ def __init__( self._clip_to_area = clip_to_area self._load_as_dataset = load_as_dataset - def load(self, items, areas: GeoDataFrame) -> Dataset | DataArray: + def load(self, items, areas: GeoDataFrame | GeoBox) -> Dataset | DataArray: # If `nodata` is passed as an arg, or the stac item contains the nodata # value, xr[variable].nodata will be set on load. - xr = odc.stac.load( + + load_geometry = ( + dict(geopolygon=areas) + if isinstance(areas, GeoDataFrame) + else dict(geobox=areas) + ) + + ds = stac_load( items, - geopolygon=areas, + **load_geometry, **self._kwargs, ) - # TODO: need to handle cases where nodata is _not_ set on load. (see - # landsat qr_radsat band) - for name in xr: + for name in ds: # Since nan is more-or-less universally accepted as a nodata value, # if the dtype of a band is some sort of floating point, then recode # existing values that are equal to the value set on load to nan - if xr[name].dtype.kind == "f": + if ds[name].dtype.kind == "f": # Should I make this an option? - if "nodata" in xr[name].attrs.keys(): - xr[name] = xr[name].where(xr[name] != xr[name].nodata, float("nan")) - xr[name].attrs["nodata"] = float("nan") - # To be helpful, set the nodata so rioxarray can understand it too. - xr[name].rio.write_nodata(xr[name].nodata, inplace=True) + if "nodata" in ds[name].attrs.keys(): + ds[name] = ds[name].where(ds[name] != ds[name].nodata, float("nan")) + ds[name].attrs["nodata"] = float("nan") + # To be helpful, set the nodata for rioxarray accessor + ds[name].rio.write_nodata(ds[name].attrs.get("nodata"), inplace=True) if self._clip_to_area: - xr = xr.rio.clip( - areas.to_crs(xr.odc.crs).geometry, all_touched=True, from_disk=True - ) - # Clip loses this, so re-set. - for name in xr: - xr[name].attrs["nodata"] = xr[name].rio.nodata + if isinstance(areas, GeoBox): + raise ValueError( + "Clip not supported for GeoBox (nor should it be needed)" + ) + + geom = Geometry(areas.geometry.unary_union, crs=areas.crs) + ds = ds.odc.mask(geom) if not self._load_as_dataset: - xr = xr.to_array("band").rename("data").rio.write_crs(xr.odc.crs) + da = ds.to_array("band").rename("data").rio.write_crs(data.odc.crs) + return da - return xr + return ds class StackStacLoader(StacLoader): diff --git a/dep_tools/namers.py b/dep_tools/namers.py index b7bdaf4..2cc53c6 100644 --- a/dep_tools/namers.py +++ b/dep_tools/namers.py @@ -1,9 +1,6 @@ from abc import ABC, abstractmethod -from dataclasses import dataclass -# Should probably be renamed to AssetPath at earliest opportunity -# to avoid confusion with stac items class ItemPath(ABC): def __init__(self) -> None: pass @@ -13,18 +10,29 @@ def path(self) -> str: return "" -@dataclass -class DepItemPath(ItemPath): - sensor: str - dataset_id: str - version: str - time: str - zero_pad_numbers: bool = False - - def __post_init__(self): +class GenericItemPath(ItemPath): + def __init__( + self, + sensor: str, + dataset_id: str, + version: str, + time: str, + prefix: str = "dep", + zero_pad_numbers: bool = False, + ): + self.sensor = sensor + self.dataset_id = dataset_id + self.version = version + self.time = time + self.prefix = prefix + self.zero_pad_numbers = zero_pad_numbers self.version = self.version.replace(".", "-") - self._folder_prefix = f"dep_{self.sensor}_{self.dataset_id}/{self.version}" - self.item_prefix = f"dep_{self.sensor}_{self.dataset_id.replace('/','_')}" + self._folder_prefix = ( + f"{self.prefix}_{self.sensor}_{self.dataset_id}/{self.version}" + ) + self.item_prefix = ( + f"{self.prefix}_{self.sensor}_{self.dataset_id.replace('/','_')}" + ) def _format_item_id( self, item_id: list[str | int] | tuple[str | int] | str, join_str="/" @@ -65,10 +73,35 @@ def log_path(self) -> str: return f"{self._folder_prefix}/logs/{self.item_prefix}_{self.time}_log.csv" +class DepItemPath(GenericItemPath): + pass + + +class S3ItemPath(GenericItemPath): + def __init__( + self, + bucket: str, + sensor: str, + dataset_id: str, + version: str, + time: str, + prefix: str = "dep", + zero_pad_numbers: bool = False, + ): + super().__init__( + sensor=sensor, + dataset_id=dataset_id, + version=version, + time=time, + prefix=prefix, + zero_pad_numbers=zero_pad_numbers, + ) + self.bucket = bucket + + class LocalPath(DepItemPath): - def __init__(self, local_folder: str, **kwargs): - # Need to create an abc for DepItemPath and drop this + def __init__(self, local_folder: str, prefix: str = "dep", **kwargs): super().__init__(**kwargs) self._folder_prefix = ( - f"{local_folder}/dep_{self.sensor}_{self.dataset_id}/{self.version}" + f"{local_folder}/{prefix}_{self.sensor}_{self.dataset_id}/{self.version}" ) diff --git a/dep_tools/s2_utils.py b/dep_tools/s2_utils.py index 2d38817..fcf1bef 100644 --- a/dep_tools/s2_utils.py +++ b/dep_tools/s2_utils.py @@ -27,10 +27,12 @@ def mask_clouds( for field in [CLOUD_SHADOWS, CLOUD_HIGH_PROBABILITY]: bitmask |= 1 << field + scl = "scl" if "scl" in xr else "SCL" + try: - cloud_mask = xr.sel(band="SCL").astype("uint16") & bitmask != 0 + cloud_mask = xr.sel(band=scl).astype("uint16") & bitmask != 0 except KeyError: - cloud_mask = xr.SCL.astype("uint16") & bitmask != 0 + cloud_mask = xr[scl].astype("uint16") & bitmask != 0 if filters is not None: cloud_mask = mask_cleanup(cloud_mask, filters) diff --git a/dep_tools/searchers.py b/dep_tools/searchers.py index 9387e46..e6f00b5 100644 --- a/dep_tools/searchers.py +++ b/dep_tools/searchers.py @@ -1,17 +1,14 @@ -from abc import ABC, abstractmethod import warnings +from abc import ABC, abstractmethod from geopandas import GeoDataFrame, read_file +from odc.geo.geobox import GeoBox from pystac import ItemCollection -import pystac_client +from pystac_client import Client from dep_tools.exceptions import EmptyCollectionError from dep_tools.landsat_utils import items_in_pathrows, pathrows_in_area -from dep_tools.utils import ( - fix_bad_epsgs, - remove_bad_items, - search_across_180, -) +from dep_tools.utils import fix_bad_epsgs, remove_bad_items, search_across_180 class Searcher(ABC): @@ -47,15 +44,15 @@ class PystacSearcher(Searcher): def __init__( self, - client: pystac_client.Client | None = None, + catalog: str, raise_empty_collection_error: bool = True, **kwargs, ): - self._client = client + self._client = Client.open(catalog) self._raise_errors = raise_empty_collection_error self._kwargs = kwargs - def search(self, area: GeoDataFrame) -> ItemCollection: + def search(self, area: GeoDataFrame | GeoBox) -> ItemCollection: """Search for stac items within the bounds of the corresponding area. Args: @@ -102,20 +99,21 @@ class LandsatPystacSearcher(PystacSearcher): def __init__( self, - client: pystac_client.Client | None = None, + catalog: str = "https://planetarycomputer.microsoft.com/api/stac/v1/", + collections: list[str] | None = ["landsat-c2-l2"], raise_empty_collection_error: bool = True, search_intersecting_pathrows: bool = False, - exclude_platforms: list | None = None, + exclude_platforms: list[str] | None = None, only_tier_one: bool = False, fall_back_to_tier_two: bool = False, **kwargs, ): super().__init__( - client=client, + catalog=catalog, raise_empty_collection_error=raise_empty_collection_error, **kwargs, ) - self._kwargs["collections"] = ["landsat-c2-l2"] + self._kwargs["collections"] = collections self._search_intersecting_pathrows = search_intersecting_pathrows self._exclude_platforms = exclude_platforms self._only_tier_one = only_tier_one @@ -125,10 +123,12 @@ def __init__( # we might look to combine. if "query" in self._kwargs.keys(): warnings.warn( - "`query` argument being ignored. To send a query directly, use `PystacSearcher`." + "Portions of `query` argument may be replaced. To specify the full query directly, use `PystacSearcher`." ) + query = kwargs.pop("query") + else: + query = {} - query = {} if self._exclude_platforms is not None: landsat_platforms = ["landsat-5", "landsat-7", "landsat-8", "landsat-9"] query["platform"] = { diff --git a/dep_tools/stac_utils.py b/dep_tools/stac_utils.py index 2175813..7e343a7 100644 --- a/dep_tools/stac_utils.py +++ b/dep_tools/stac_utils.py @@ -1,67 +1,102 @@ -import datetime +from datetime import datetime import json +from pathlib import Path import numpy as np -from pystac import Item +from pandas import DataFrame +from pystac import Asset, Item, MediaType from rio_stac.stac import create_stac_item from urlpath import URL from xarray import DataArray, Dataset -from azure.storage.blob import ContentSettings -from .utils import write_to_blob_storage, write_to_local_storage +from .aws import object_exists +from .namers import DepItemPath, S3ItemPath +from .processors import Processor -def write_stac( - xr: DataArray | Dataset, - path: str, - stac_url, - writer=write_to_blob_storage, - **kwargs, -) -> None: - item = _get_stac_item(xr, path, **kwargs) - item_json = json.dumps(item.to_dict(), indent=4) - writer( - item_json, - stac_url, - content_settings=ContentSettings(content_type="application/json"), - ) - - return stac_url - - -def write_stac_local(xr: DataArray | Dataset, path: str, stac_url, **kwargs): - write_stac( - xr, path, stac_url, writer=write_to_local_storage, remote=False, **kwargs - ) - - -write_stac_blob_storage = write_stac +class StacCreator(Processor): + def __init__( + self, + itempath: DepItemPath, + remote: bool = True, + collection_url_root: str = "https://stac.staging.digitalearthpacific.org/collections", + **kwargs, + ): + self._itempath = itempath + self._remote = remote + self._collection_url_root = collection_url_root + self._kwargs = kwargs + + def process( + self, + data: DataArray | Dataset, + item_id: str, + ) -> Item | str: + return get_stac_item( + itempath=self._itempath, + item_id=item_id, + data=data, + remote=self._remote, + collection_url_root=self._collection_url_root, + **self._kwargs, + ) -def _get_stac_item( - xr: DataArray | Dataset, - path: str, - collection: str, +def get_stac_item( + itempath: DepItemPath, + item_id: str, + data: DataArray | Dataset, remote: bool = True, + collection_url_root: str = "https://stac.staging.digitalearthpacific.org/collections", **kwargs, -) -> Item: - az_prefix = URL("https://deppcpublicstorage.blob.core.windows.net/output") - blob_url = az_prefix / path if remote else path +) -> Item | str: + prefix = Path("./") + # Remote means not local + # TODO: neaten local file writing up + if remote: + # Or, isinstance(itempath, S3ItemPath) + if hasattr(itempath, "bucket"): + # Writing to S3 + prefix = URL(f"s3://{getattr(itempath,'bucket')}") + else: + # Default to Azure + prefix = URL("https://deppcpublicstorage.blob.core.windows.net/output") + properties = {} - if "stac_properties" in xr.attrs: + if "stac_properties" in data.attrs: properties = ( - json.loads(xr.attrs["stac_properties"].replace("'", '"')) - if isinstance(xr.attrs["stac_properties"], str) - else xr.attrs["stac_properties"] + json.loads(data.attrs["stac_properties"].replace("'", '"')) + if isinstance(data.attrs["stac_properties"], str) + else data.attrs["stac_properties"] ) - collection_url = ( - f"https://stac.staging.digitalearthpacific.org/collections/{collection}" - ) - return create_stac_item( - str(blob_url), - asset_roles=["data"], + paths = [itempath.path(item_id, variable) for variable in data] + + assets = { + variable: Asset( + media_type=MediaType.COG, + href=str(prefix / path), + roles=["data"], + ) + for variable, path in zip(data, paths) + } + stac_id = itempath.basename(item_id) + collection = itempath.item_prefix + collection_url = f"{collection_url_root}/{collection}" + + input_datetime = properties.get("datetime", None) + if input_datetime is not None: + format_string = ( + "%Y-%m-%dT%H:%M:%S.%fZ" if "." in input_datetime else "%Y-%m-%dT%H:%M:%SZ" + ) + input_datetime = datetime.strptime(input_datetime, format_string) + + item = create_stac_item( + str(prefix / paths[0]), + id=stac_id, + input_datetime=input_datetime, + assets=assets, with_proj=True, properties=properties, collection_url=collection_url, @@ -69,6 +104,32 @@ def _get_stac_item( **kwargs, ) + stac_url = str(prefix / itempath.stac_path(item_id)) + item.set_self_href(stac_url) + + return item + + +def write_stac_local(item: Item, stac_path: str) -> None: + with open(stac_path, "w") as f: + json.dump(item.to_dict(), f, indent=4) + + +def existing_stac_items(possible_ids: list, itempath: S3ItemPath) -> list: + """Returns only those ids which have an existing stac item.""" + return [ + id + for id in possible_ids + if object_exists(itempath.bucket, itempath.stac_path(id)) + ] + + +def remove_items_with_existing_stac(grid: DataFrame, itempath: S3ItemPath) -> DataFrame: + """Filter a dataframe to only include items which don't have an existing stac output. + The dataframe must have an index which corresponds to ids for the given itempath. + """ + return grid[~grid.index.isin(existing_stac_items(list(grid.index), itempath))] + def set_stac_properties( input_xr: DataArray | Dataset, output_xr: DataArray | Dataset @@ -94,9 +155,7 @@ def set_stac_properties( start_datetime=start_datetime, datetime=start_datetime, end_datetime=end_datetime, - created=np.datetime_as_string( - np.datetime64(datetime.datetime.now()), timezone="UTC" - ), + created=np.datetime_as_string(np.datetime64(datetime.now()), timezone="UTC"), ) return output_xr diff --git a/dep_tools/task.py b/dep_tools/task.py index 5b437fe..e075a6f 100644 --- a/dep_tools/task.py +++ b/dep_tools/task.py @@ -4,17 +4,20 @@ from geopandas import GeoDataFrame from .exceptions import EmptyCollectionError, NoOutputError -from .loaders import Loader -from .processors import Processor -from .writers import Writer +from .loaders import Loader, StacLoader +from .processors import Processor, XrPostProcessor +from .namers import S3ItemPath +from .searchers import Searcher +from .stac_utils import set_stac_properties, StacCreator +from .writers import Writer, AwsDsCogWriter, AwsStacWriter -task_id = str +TaskID = str class Task(ABC): def __init__( self, - task_id: task_id, + task_id: TaskID, loader: Loader, processor: Processor, writer: Writer, @@ -34,7 +37,7 @@ def run(self): class AreaTask(Task): def __init__( self, - id: task_id, + id: TaskID, area: GeoDataFrame, loader: Loader, processor: Processor, @@ -55,16 +58,100 @@ def run(self): return paths +class StacTask(AreaTask): + def __init__( + self, + id: TaskID, + area: GeoDataFrame, + searcher: Searcher, + loader: StacLoader, + processor: Processor, + writer: Writer, + post_processor: Processor | None = None, + stac_creator: StacCreator | None = None, + stac_writer: Writer | None = None, + logger: Logger = getLogger(), + ): + """Implementation of a typical DEP product pipeline as a series of + generic operations. For a defined location (identified by an id and + a spatial region), search for and then load appropriate input data, + process that data to create an output, optionally post-process that + output to prep for writing, then write. Also allows for + optional creation and writing of a stac item document. + """ + super().__init__(id, area, loader, processor, writer, logger) + self.id = id + self.searcher = searcher + self.post_processor = post_processor + self.stac_creator = stac_creator + self.stac_writer = stac_writer + + def run(self): + items = self.searcher.search(self.area) + input_data = self.loader.load(items, self.area) + + processor_kwargs = ( + dict(area=self.area) if self.processor.send_area_to_processor else dict() + ) + + output_data = set_stac_properties( + input_data, self.processor.process(input_data, **processor_kwargs) + ) + + if self.post_processor is not None: + output_data = self.post_processor.process(output_data) + + paths = self.writer.write(output_data, self.id) + + if self.stac_creator is not None and self.stac_writer is not None: + stac_item = self.stac_creator.process(output_data, self.id) + self.stac_writer.write(stac_item, self.id) + + return paths + + +class AwsStacTask(StacTask): + def __init__( + self, + itempath: S3ItemPath, + id: TaskID, + area, + searcher: Searcher, + loader: StacLoader, + processor: Processor, + post_processor: Processor | None = XrPostProcessor(), + logger: Logger = getLogger(), + **kwargs, + ): + """A StacTask with typical parameters to write to s3 storage.""" + writer = kwargs.pop("writer", AwsDsCogWriter(itempath)) + stac_creator = kwargs.pop("stac_creator", StacCreator(itempath)) + stac_writer = kwargs.pop("stac_writer", AwsStacWriter(itempath)) + super().__init__( + id=id, + area=area, + searcher=searcher, + loader=loader, + processor=processor, + post_processor=post_processor, + writer=writer, + stac_creator=stac_creator, + stac_writer=stac_writer, + logger=logger, + **kwargs, + ) + + class ErrorCategoryAreaTask(AreaTask): def run(self): try: input_data = self.loader.load(self.area) except EmptyCollectionError as e: - self.logger.info([self.id, "no items for areas"]) + self.logger.error([self.id, "no items for areas"]) raise e except Exception as e: - self.logger.info([self.id, "load error", e]) + self.logger.error([self.id, "load error", e]) raise e processor_kwargs = ( @@ -73,11 +160,11 @@ def run(self): try: output_data = self.processor.process(input_data, **processor_kwargs) except Exception as e: - self.logger.info([self.id, "processor error", e]) + self.logger.error([self.id, "processor error", e]) raise e if output_data is None: - self.logger.info([self.id, "no output from processor"]) + self.logger.error([self.id, "no output from processor"]) raise NoOutputError() try: paths = self.writer.write(output_data, self.id) @@ -90,41 +177,32 @@ def run(self): return paths -class MultiAreaTask(ABC): +class MultiAreaTask: def __init__( self, - ids: list[task_id], + ids: list[TaskID], areas: GeoDataFrame, + logger, task_class: type[AreaTask], - loader: Loader, - processor: Processor, - writer: Writer, - logger: Logger = getLogger(), fail_on_error: bool = True, + **kwargs, ): self.ids = ids self.areas = areas - self.loader = loader - self.processor = processor - self.writer = writer - self.logger = logger self.task_class = task_class self.fail_on_error = fail_on_error + self.logger = logger + self._kwargs = kwargs def run(self): for id in self.ids: try: - self.task_class( - id, - self.areas.loc[[id]], - self.loader, - self.processor, - self.writer, - self.logger, - ).run() + paths = self.task_class(id, self.areas.loc[[id]], **self._kwargs).run() + self.logger.info([id, "complete", paths]) except Exception as e: if self.fail_on_error: raise e + self.logger.error([id, "error", [], e]) continue diff --git a/dep_tools/utils.py b/dep_tools/utils.py index 75374c6..cb7e70b 100644 --- a/dep_tools/utils.py +++ b/dep_tools/utils.py @@ -1,31 +1,46 @@ -import io +from logging import INFO, Formatter, Logger, StreamHandler, getLogger from pathlib import Path from typing import Dict, List, Union -import fiona +from antimeridian import bbox as antimeridian_bbox +from antimeridian import ( + fix_multi_polygon, + fix_polygon, + fix_line_string, + fix_multi_line_string, +) +from geopandas import GeoDataFrame import numpy as np +from odc.geo.geobox import GeoBox as GeoBox +from odc.geo.xr import write_cog import planetary_computer -import pystac_client -import rasterio -import rioxarray -import xarray as xr -from azure.storage.blob import ContainerClient -from dask.distributed import Client, Lock -from geocube.api.core import make_geocube -from geopandas import GeoDataFrame -from odc.geo.xr import to_cog, write_cog -from osgeo import gdal from pystac import ItemCollection +import pystac_client from retry import retry -from shapely.geometry import LineString, MultiLineString +from shapely.geometry import LineString, MultiLineString, GeometryCollection from xarray import DataArray, Dataset -from .azure import get_container_client - # Set the timeout to five minutes, which is an extremely long time TIMEOUT_SECONDS = 60 * 5 +def get_logger(prefix: str, name: str) -> Logger: + """Set up a simple logger""" + console = StreamHandler() + time_format = "%Y-%m-%d %H:%M:%S" + console.setFormatter( + Formatter( + fmt=f"%(asctime)s %(levelname)s ({prefix}): %(message)s", + datefmt=time_format, + ) + ) + + log = getLogger(name) + log.addHandler(console) + log.setLevel(INFO) + return log + + def shift_negative_longitudes( geometry: Union[LineString, MultiLineString] ) -> Union[LineString, MultiLineString]: @@ -49,28 +64,21 @@ def shift_negative_longitudes( BBOX = list[float] -def bbox_across_180(region: GeoDataFrame) -> BBOX | tuple[BBOX, BBOX]: - # Previously we just used region.to_crs(4326).total_bounds but if the geom - # is split right at the antimeridian (see landsat pathrow 073072), output - # will have zero width (since min and max will be -180 and 180) - # So get the bounds for all geoms in region, remove the 180s and calculate - # the min and max values ourselves - region_ll = GeoDataFrame(region.to_crs(4326)) - x_values = ( - region_ll.explode(index_parts=True).bounds.minx.tolist() - + region_ll.explode(index_parts=True).bounds.maxx.tolist() - ) - # Possible we just do a direct compare, we shall see if this causes issues - # with locations _really close_ to 180 but not touching it - tolerance = 1e-5 - x_values = [i for i in x_values if abs(180 - abs(i)) > tolerance] - - y_values = ( - region_ll.explode(index_parts=True).bounds.miny.tolist() - + region_ll.explode(index_parts=True).bounds.maxy.tolist() - ) - - bbox = [min(x_values), min(y_values), max(x_values), max(y_values)] +def bbox_across_180(region: GeoDataFrame | GeoBox) -> BBOX | tuple[BBOX, BBOX]: + if isinstance(region, GeoBox): + geometry = region.geographic_extent.geom + else: + geometry = region.to_crs(4326).geometry.make_valid().explode() + geometry = geometry[ + geometry.geom_type.isin(["Polygon", "MultiPolygon"]) + ].unary_union + + geometry = _fix_geometry(geometry) + bbox = antimeridian_bbox(geometry) + # Sometimes they still come through with the negative value first, see + # https://github.com/gadomski/antimeridian/issues/134 + if bbox[0] < 0 and bbox[2] > 0: + bbox[0], bbox[2] = bbox[2], bbox[0] # Now fix some coord issues # If the lower left X coordinate is greater than 180 it needs to shift @@ -81,28 +89,48 @@ def bbox_across_180(region: GeoDataFrame) -> BBOX | tuple[BBOX, BBOX]: if bbox[2] > 180: bbox[2] = bbox[2] - 360 - # These are Pacific specific tests! - bbox_crosses_antimeridian = (bbox[0] < 0 and bbox[2] > 0) or ( + # These are Pacific specific tests, meaning e.g. we know that these aren't + # areas that are crossing 0 longitude. + bbox_crosses_antimeridian = (bbox[0] > 0 and bbox[2] < 0) or ( bbox[0] < 180 and bbox[2] > 180 ) + if bbox_crosses_antimeridian: # Split into two bboxes across the antimeridian - xmax_ll, ymin_ll = bbox[0], bbox[1] - xmin_ll, ymax_ll = bbox[2], bbox[3] + xmin, ymin = bbox[0], bbox[1] + xmax, ymax = bbox[2], bbox[3] - xmax_ll = xmax_ll - 360 if xmax_ll > 180 else xmax_ll - - left_bbox = BBOX([xmin_ll, ymin_ll, 180, ymax_ll]) - right_bbox = BBOX([-180, ymin_ll, xmax_ll, ymax_ll]) + xmax = xmax - 360 if xmax > 180 else xmax + left_bbox = BBOX([xmin, ymin, 180, ymax]) + right_bbox = BBOX([-180, ymin, xmax, ymax]) return (left_bbox, right_bbox) else: return BBOX(bbox) +def _fix_geometry(geometry): + if isinstance(geometry, GeometryCollection): + return GeometryCollection( + [_fix_geometry(a_geometry) for a_geometry in geometry.geoms] + ) + match geometry.geom_type: + case "Polygon": + geometry = fix_polygon(geometry) + case "MultiPolygon": + geometry = fix_multi_polygon(geometry) + case "LineString": + geometry = fix_line_string(geometry) + case "MultiLineString": + geometry = fix_multi_line_string(geometry) + case _: + raise ValueError(f"Unsupported geometry type: {geometry.type}") + return geometry + + # retry is for search timeouts which occasionally occur @retry(tries=5, delay=1) def search_across_180( - region: GeoDataFrame, client: pystac_client.Client | None = None, **kwargs + region: GeoDataFrame | GeoBox, client: pystac_client.Client | None = None, **kwargs ) -> ItemCollection: """ region: A GeoDataFrame. @@ -118,10 +146,15 @@ def search_across_180( bbox = bbox_across_180(region) if isinstance(bbox, tuple): - return ItemCollection( - list(client.search(bbox=bbox[0], **kwargs).items()) - + list(client.search(bbox=bbox[1], **kwargs).items()) - ) + first_result = list(client.search(bbox=bbox[0], **kwargs).items()) + first_ids = [item.id for item in first_result] + + second_result = list(client.search(bbox=bbox[1], **kwargs).items()) + unique_second_result = [ + item for item in second_result if item.id not in first_ids + ] + + return ItemCollection(first_result + unique_second_result) else: return client.search(bbox=bbox, **kwargs).item_collection() @@ -187,55 +220,6 @@ def write_to_local_storage( ) -def write_to_blob_storage( - d: Union[DataArray, Dataset, GeoDataFrame, str], - path: Union[str, Path], - overwrite: bool = True, - use_odc_writer: bool = False, - client: ContainerClient | None = None, - **kwargs, -) -> None: - # Allowing for a shared container client, which might be - # more efficient. If not provided, get one. - if client is None: - client = get_container_client() - blob_client = client.get_blob_client(str(path)) - if not overwrite and blob_client.exists(): - return - - if isinstance(d, (DataArray, Dataset)): - if use_odc_writer: - if "driver" in kwargs: - del kwargs["driver"] - binary_data = to_cog(d, **kwargs) - blob_client.upload_blob( - binary_data, overwrite=overwrite, connection_timeout=TIMEOUT_SECONDS - ) - else: - with io.BytesIO() as buffer: - # This is needed or rioxarray doesn't know what type it is - # writing - if not "driver" in kwargs: - kwargs["driver"] = "COG" - d.rio.to_raster(buffer, **kwargs) - buffer.seek(0) - blob_client.upload_blob( - buffer, overwrite=overwrite, connection_timeout=TIMEOUT_SECONDS - ) - - elif isinstance(d, GeoDataFrame): - with fiona.io.MemoryFile() as buffer: - d.to_file(buffer, **kwargs) - buffer.seek(0) - blob_client.upload_blob(buffer, overwrite=overwrite) - elif isinstance(d, str): - blob_client.upload_blob(d, overwrite=overwrite, **kwargs) - else: - raise ValueError( - "You can only write an Xarray DataArray or Dataset, or Geopandas GeoDataFrame" - ) - - def scale_to_int16( xr: Union[DataArray, Dataset], output_multiplier: int, @@ -254,93 +238,33 @@ def scale_da(da: DataArray): return ( da.where(da.notnull(), output_nodata) .astype("int16") - .rio.write_nodata(output_nodata) + .rio.write_nodata(output_nodata) # for rioxarray + .assign_attrs(nodata=output_nodata) # for odc ) if isinstance(xr, Dataset): for var in xr: xr[var] = scale_da(xr[var]) - xr[var].rio.write_nodata(output_nodata, inplace=True) + # Assuming this needs to be redone? + xr[var].rio.write_nodata(output_nodata, inplace=True).assign_attrs( + nodata=output_nodata + ) else: xr = scale_da(xr) return xr -def raster_bounds(raster_path: Path) -> List: - """Returns the bounds for a raster file at the given path""" - with rasterio.open(raster_path) as t: - return list(t.bounds) - - -def gpdf_bounds(gpdf: GeoDataFrame) -> List[float]: - """Returns the bounds for the give GeoDataFrame, and makes sure - it doesn't cross the antimeridian.""" - bbox = gpdf.to_crs("EPSG:4326").total_bounds - # Or the opposite! - bbox_crosses_antimeridian = bbox[0] < 0 and bbox[2] > 0 - if bbox_crosses_antimeridian: - # This may be overkill, but nothing else was really working - bbox[0] = -179.9999999999 - bbox[2] = 179.9999999999 - return bbox - - -def build_vrt( - bounds: List, - prefix: str = "", - suffix: str = "", -) -> Path: - blobs = [ - f"/vsiaz/output/{blob.name}" - for blob in get_container_client().list_blobs(name_starts_with=prefix) - if blob.name.endswith(suffix) - ] - - local_prefix = Path(prefix).stem - vrt_file = f"data/{local_prefix}.vrt" - gdal.BuildVRT(vrt_file, blobs, outputBounds=bounds) - return Path(vrt_file) - - -def _local_prefix(prefix: str) -> str: - return Path(prefix).stem - - -def _mosaic_file(prefix: str) -> str: - return f"data/{_local_prefix(prefix)}.tif" - - -def mosaic_scenes( - prefix: str, - bounds: List, - client: Client, - scale_factor: float = None, - overwrite: bool = True, -) -> None: - mosaic_file = _mosaic_file(prefix) - if not Path(mosaic_file).is_file() or overwrite: - vrt_file = build_vrt(prefix, bounds) - rioxarray.open_rasterio(vrt_file, chunks=True).rio.to_raster( - mosaic_file, - compress="LZW", - lock=Lock("rio", client=client), - ) - - if scale_factor is not None: - with rasterio.open(mosaic_file, "r+") as dst: - dst.scales = (scale_factor,) - - def fix_bad_epsgs(item_collection: ItemCollection) -> None: - """Repairs soLC08_L2SP_101055_20220612_20220617_02_T2me band epsg codes in stac items loaded from the Planetary + """Repairs some band epsg codes in stac items loaded from the Planetary Computer stac catalog""" # ** modifies in place ** # See https://github.com/microsoft/PlanetaryComputer/discussions/113 # Will get fixed at some point and we can remove this for item in item_collection: - epsg = str(item.properties["proj:epsg"]) - item.properties["proj:epsg"] = int(f"{epsg[0:3]}{int(epsg[3:]):02d}") + if item.collection_id == "landsat-c2-l2": + epsg = str(item.properties["proj:epsg"]) + item.properties["proj:epsg"] = int(f"{epsg[0:3]}{int(epsg[3:]):02d}") def remove_bad_items(item_collection: ItemCollection) -> ItemCollection: diff --git a/dep_tools/writers.py b/dep_tools/writers.py index ccb6380..de946be 100644 --- a/dep_tools/writers.py +++ b/dep_tools/writers.py @@ -3,134 +3,29 @@ from functools import partial from typing import Callable, Hashable, List -import numpy as np -from pystac import Asset -from urlpath import URL from xarray import Dataset -from .azure import blob_exists -from .namers import DepItemPath -from .processors import Processor, XrPostProcessor -from .stac_utils import write_stac_blob_storage, write_stac_local -from .utils import write_to_blob_storage, write_to_local_storage +from .aws import write_to_s3, write_stac_s3 +from .namers import DepItemPath, S3ItemPath +from .utils import write_to_local_storage class Writer(ABC): + """The base abstract class for writing.""" + @abstractmethod - def write(self, data, item_id) -> str: + def write(self, data, item_id) -> str | list[str]: pass -class DepWriter(Writer): - def __init__( - self, - itempath: DepItemPath, - pre_processor: Processor, - cog_writer: Writer, - stac_writer: Writer | None, - ): - self._itempath = itempath - self._pre_processor = pre_processor - self._cog_writer = cog_writer - self._stac_writer = stac_writer - - def _stac_exists(self, item_id): - return blob_exists(self._itempath.stac_path(item_id)) - - def _all_paths(self, ds: Dataset, item_id: str): - # Only problem here is if xr has variables that aren't in the stac - # so maybe we need to read stac? - paths = [self._itempath.path(item_id, variable) for variable in ds] - paths.append(self._itempath.stac_path(item_id)) - return paths - - def write(self, xr, item_id): - if self._stac_exists(item_id): - return self._all_paths(xr, item_id) - output = self._pre_processor.process(xr) - self._cog_writer.write(output, item_id) - if self._stac_writer is not None: - self._stac_writer.write(output, item_id) - - -class DsWriter(DepWriter): - def __init__( - self, - itempath: DepItemPath, - convert_to_int16: bool = True, - output_value_multiplier: int = 10000, - scale_int16s: bool = False, - output_nodata: int = -32767, - extra_attrs: dict = {}, - write_function: Callable = write_to_blob_storage, - write_multithreaded: bool = True, - write_stac: bool = True, - write_stac_function=write_stac_blob_storage, - load_before_write: bool = False, - **kwargs - ): - pre_processor = XrPostProcessor( - convert_to_int16, - output_value_multiplier, - scale_int16s, - output_nodata, - extra_attrs, - ) - cog_writer = DsCogWriter( - itempath, write_multithreaded, load_before_write, write_function, **kwargs - ) - stac_writer = StacWriter(itempath, write_stac_function) if write_stac else None - super().__init__(itempath, pre_processor, cog_writer, stac_writer) - - -class StacWriter(Writer): - def __init__( - self, - itempath: DepItemPath, - write_stac_function: Callable = write_stac_blob_storage, - ): - self._itempath = itempath - self._write_stac_function = write_stac_function - - def write(self, ds: Dataset, item_id): - paths = [self._itempath.path(item_id, variable) for variable in ds] - assets = { - variable: Asset( - media_type="image/tiff; application=geotiff; profile=cloud-optimized", - href=str( - URL("https://deppcpublicstorage.blob.core.windows.net/output") - / path - ), - roles=["data"], - ) - for variable, path in zip(ds, paths) - } - stac_id = self._itempath.basename(item_id) - collection = self._itempath.item_prefix - # has to be a datetime datetime object - datetime = np.datetime64(ds.attrs["stac_properties"]["datetime"]).item() - stac_path = self._write_stac_function( - ds, - paths[0], - stac_url=self._itempath.path(item_id, ext=".stac-item.json"), - input_datetime=datetime, - assets=assets, - collection=collection, - id=stac_id, - ) - paths.append(stac_path) - - return paths - - class DsCogWriter(Writer): def __init__( self, itempath: DepItemPath, write_multithreaded: bool = False, load_before_write: bool = False, - write_function: Callable = write_to_blob_storage, - **kwargs + write_function: Callable = write_to_s3, + **kwargs, ): self._itempath = itempath self._write_multithreaded = write_multithreaded @@ -169,14 +64,73 @@ def get_write_partial(variable: Hashable) -> Callable: return paths -class LocalDsCogWriter(DsWriter): +class AwsDsCogWriter(DsCogWriter): + def __init__( + self, + itempath: S3ItemPath, + write_multithreaded: bool = False, + load_before_write: bool = False, + write_function: Callable = write_to_s3, + **kwargs, + ): + super().__init__( + itempath=itempath, + write_multithreaded=write_multithreaded, + load_before_write=load_before_write, + write_function=write_function, + bucket=itempath.bucket, + **kwargs, + ) + + +class LocalDsCogWriter(DsCogWriter): def __init__(self, **kwargs): super().__init__( write_function=write_to_local_storage, - write_stac_function=write_stac_local, **kwargs, ) -class AzureDsWriter(DsWriter): - pass +class StacWriter(Writer): + def __init__( + self, + itempath: DepItemPath, + write_stac_function: Callable = write_stac_s3, + **kwargs, + ): + self._itempath = itempath + self._write_stac_function = write_stac_function + self._kwargs = kwargs + + def write(self, item, item_id) -> str: + stac_path = self._itempath.stac_path(item_id) + self._write_stac_function(item, stac_path, **self._kwargs) + + return item.self_href + + +class AwsStacWriter(StacWriter): + def __init__( + self, + itempath: S3ItemPath, + **kwargs, + ): + super().__init__( + itempath=itempath, + write_stac_function=write_to_s3, + bucket=itempath.bucket, + **kwargs, + ) + + +class LocalStacWriter(StacWriter): + def __init__( + self, + itempath: S3ItemPath, + **kwargs, + ): + super().__init__( + itempath=itempath, + write_stac_function=write_to_local_storage, + **kwargs, + ) diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 8c668a9..0000000 --- a/poetry.lock +++ /dev/null @@ -1,4036 +0,0 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. - 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-[metadata] -lock-version = "2.0" -python-versions = "^3.8" -content-hash = "877476bd6c72d4b5fdd5bdb3412e89544ae0b3cd31f284d947062125da18020e" diff --git a/poetry.toml b/poetry.toml deleted file mode 100644 index 6ee81a0..0000000 --- a/poetry.toml +++ /dev/null @@ -1,2 +0,0 @@ -[installer] -no-binary = ["gdal", "rasterio"] diff --git a/pyproject.toml b/pyproject.toml index 3d21a10..0c2eba4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,47 +1,16 @@ -[tool.poetry] +[build-system] +requires = ["setuptools"] +build-backend = "setuptools.build_meta" + +[project] +dynamic = ["dependencies"] +license = {file = "LICENSE"} name = "dep-tools" +requires-python = ">=3.10" version = "0.2.0" -description = "" -authors = ["Jesse Anderson "] -license = "MIT" -packages = [{include = "dep_tools"}] -include = ["*.gpkg"] - -[tool.poetry.dependencies] -python = "^3.8" -azure-storage-blob = "*" -geopandas = "*" -dask = {extras = ["complete"], version = "*"} -dask-gateway = "*" -geocube = "*" -gdal = "*" -pystac-client = "*" -planetary-computer = "*" -rioxarray = "*" -stackstac = "*" -retry = "*" -tqdm = "*" -urlpath = "^1.2.0" -xarray = "*" -rio-stac = "^0.8.0" -odc-stac = "*" -odc-algo = "*" -fiona = "^1.9.6" - -[tool.poetry.group.dev] -optional = true -[tool.poetry.group.test] -optional = true +[tool.setuptools] +packages = ["dep_tools"] -[tool.poetry.group.dev.dependencies] -black = "^23.1.0" -pylint = "^2.17.1" -mypy = "^1.1.1" - -[tool.poetry.group.test.dependencies] -pytest = "^7.4.0" - -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" +[tool.setuptools.dynamic] +dependencies = { file = ["requirements.txt"] } diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..d39813c --- /dev/null +++ b/requirements.txt @@ -0,0 +1,20 @@ +antimeridian +azure-storage-blob +boto3 +dask[complete] +dask-gateway +fiona +gdal +geocube +geopandas +odc-stac +odc-algo +pystac-client +planetary-computer +rioxarray +rio-stac>=0.8.0 +stackstac +retry +tqdm +urlpath>=1.2.0 +xarray diff --git a/tests/data/dep_spysat_wofs/1-0-0/12/34/2021-01-01/dep_spysat_wofs_12_34_2021-01-01_wofs.tif b/tests/data/dep_spysat_wofs/1-0-0/12/34/2021-01-01/dep_spysat_wofs_12_34_2021-01-01_wofs.tif new file mode 100644 index 0000000..f2bdf9b Binary files /dev/null and b/tests/data/dep_spysat_wofs/1-0-0/12/34/2021-01-01/dep_spysat_wofs_12_34_2021-01-01_wofs.tif differ diff --git a/tests/test_aws.py b/tests/test_aws.py new file mode 100644 index 0000000..da0cab4 --- /dev/null +++ b/tests/test_aws.py @@ -0,0 +1,12 @@ +from geopandas import GeoDataFrame +from shapely import box + +from dep_tools.aws import write_to_s3, object_exists + + +# def test_write_to_s3_kwargs(): +# bucket = "dep-public-staging" +# key = "test.gpkg" +# d = GeoDataFrame(geometry=[box(-170, 0, -169, 1)]) +# write_to_s3(d, path=key, bucket=bucket, driver="GPKG") +# assert object_exists(bucket, key) diff --git a/tests/test_depwriter.py b/tests/test_depwriter.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/test_dswriter.py b/tests/test_dswriter.py new file mode 100644 index 0000000..d05a9a2 --- /dev/null +++ b/tests/test_dswriter.py @@ -0,0 +1,10 @@ +# from dep_tools.writers import DsWriter +# from dep_tools.namers import DepItemPath +# +# +# def test_kwargs(): +# itempath = DepItemPath( +# sensor="spc_sat", dataset_id="clear_waters", version="1.0", time="1901" +# ) +# writer = DsWriter(itempath=itempath, bucket="dep_bucket") +# assert isinstance(writer, DsWriter) diff --git a/tests/test_get_stac_item.py b/tests/test_get_stac_item.py index 1b0a79c..491ea00 100644 --- a/tests/test_get_stac_item.py +++ b/tests/test_get_stac_item.py @@ -1,25 +1,40 @@ import rioxarray -from dep_tools.stac_utils import _get_stac_item +from dep_tools.namers import LocalPath +from dep_tools.stac_utils import StacCreator +from dep_tools.writers import StacWriter +from dep_tools.stac_utils import get_stac_item +from pathlib import Path import pytest -TEST_ITEM_URL = "https://deppcpublicstorage.blob.core.windows.net/output/dep_ls_wofs/0-0-2/TV/001/2021/dep_ls_wofs_TV_001_2021_mean.tif" +DATA_DIR = Path(__file__).parent / "data" @pytest.fixture def stac_item(): - test_path = "dep_ls_wofs/0-0-2/TV/001/2021/dep_ls_wofs_TV_001_2021_mean.tif" - test_xr = rioxarray.open_rasterio(TEST_ITEM_URL, chunks=True) - item = _get_stac_item(test_xr, test_path, collection="dep_ls_wofs") + itempath = LocalPath( + str(DATA_DIR), + sensor="spysat", + dataset_id="wofs", + version="1.0.0", + time="2021-01-01", + ) + tif = itempath.path("12,34", asset_name="wofs") + test_xr = rioxarray.open_rasterio(tif).to_dataset(name="wofs") + item = get_stac_item( + itempath=itempath, + item_id="12,34", + data=test_xr, + remote=False, + ) + return item def test_get_stac_item_properties(stac_item): properties = stac_item.properties keys = [ - "start_datetime", - "end_datetime", "proj:epsg", "proj:geometry", "proj:bbox", @@ -31,8 +46,11 @@ def test_get_stac_item_properties(stac_item): def test_get_stac_item_collection_id(stac_item): - assert stac_item.collection_id == "dep_ls_wofs" + assert stac_item.collection_id == "dep_spysat_wofs" def test_stac_asset_href_is_valid(stac_item): - assert stac_item.assets["asset"].href == TEST_ITEM_URL + assert stac_item.assets["wofs"].href == str( + DATA_DIR + / "dep_spysat_wofs/1-0-0/12/34/2021-01-01/dep_spysat_wofs_12_34_2021-01-01_wofs.tif" + ) diff --git a/tests/test_landsat_mspc_stac_search_fixes.py b/tests/test_landsat_mspc_stac_search_fixes.py index 90662be..e891dad 100644 --- a/tests/test_landsat_mspc_stac_search_fixes.py +++ b/tests/test_landsat_mspc_stac_search_fixes.py @@ -1,6 +1,4 @@ -from re import search import geopandas as gpd -from pystac_client import Client import pytest from shapely.geometry import box diff --git a/tests/test_searchers.py b/tests/test_searchers.py index 3e0ceb6..b0f347c 100644 --- a/tests/test_searchers.py +++ b/tests/test_searchers.py @@ -1,8 +1,10 @@ import geopandas as gpd +import odc.stac from pystac import ItemCollection -from pystac_client import Client +import planetary_computer as pc import pytest from shapely.geometry import box +from xarray import Dataset from dep_tools.searchers import PystacSearcher, LandsatPystacSearcher @@ -18,12 +20,14 @@ def area() -> gpd.GeoDataFrame: @pytest.fixture -def mspc_client(): - return Client.open("https://planetarycomputer.microsoft.com/api/stac/v1") +def mspc_catalog(): + return "https://planetarycomputer.microsoft.com/api/stac/v1" -def test_PystacSearcher(area): - s = PystacSearcher(collections=["landsat-c2-l2"], datetime="2007") +def test_PystacSearcher(area, mspc_catalog): + s = PystacSearcher( + catalog=mspc_catalog, collections=["landsat-c2-l2"], datetime="2007" + ) items = s.search(area) assert isinstance(items, ItemCollection) @@ -34,3 +38,12 @@ def test_PystacSearcher(area): def test_LandsatPystacSearcher_exclude_platforms(area): s = LandsatPystacSearcher(exclude_platforms=["landsat-7"]) s.search(area) + + +def test_unsigned_search(area, mspc_catalog): + s = PystacSearcher( + catalog=mspc_catalog, collections=["landsat-c2-l2"], datetime="2007" + ) + items = s.search(area) + ds = odc.stac.load([items[0]], patch_url=pc.sign, chunks=dict(x=2048, y=2048)) + assert isinstance(ds, Dataset)