From b5f2f0e9554f6fc313df1bb3e1e52e815295d28c Mon Sep 17 00:00:00 2001 From: tnigon <8249296+tnigon@users.noreply.github.com> Date: Fri, 26 Jan 2024 10:50:52 -0600 Subject: [PATCH 01/10] first_seed_test functions to this library --- pixels_utils/_version.py | 2 +- pixels_utils/helpers/__init__.py | 3 + pixels_utils/helpers/_helper.py | 83 ++ pixels_utils/scenes/__init__.py | 2 +- pixels_utils/scenes/_scenes.py | 92 +- poetry.lock | 1515 +++++++++++++++--------------- pyproject.toml | 4 +- 7 files changed, 942 insertions(+), 759 deletions(-) create mode 100644 pixels_utils/helpers/__init__.py create mode 100644 pixels_utils/helpers/_helper.py diff --git a/pixels_utils/_version.py b/pixels_utils/_version.py index 0a59aa1..9e0abf1 100644 --- a/pixels_utils/_version.py +++ b/pixels_utils/_version.py @@ -1,3 +1,3 @@ """Defines package version. Parsed by setup.py and imported by __init__.py.""" -__version__ = "0.4.1" +__version__ = "0.5.0" diff --git a/pixels_utils/helpers/__init__.py b/pixels_utils/helpers/__init__.py new file mode 100644 index 0000000..627be8a --- /dev/null +++ b/pixels_utils/helpers/__init__.py @@ -0,0 +1,3 @@ +from pixels_utils.helpers._helper import get_satellite_expression_as_df + +__all__ = ("get_satellite_expression_as_df",) diff --git a/pixels_utils/helpers/_helper.py b/pixels_utils/helpers/_helper.py new file mode 100644 index 0000000..88c168c --- /dev/null +++ b/pixels_utils/helpers/_helper.py @@ -0,0 +1,83 @@ +from typing import Union + +from geojson.feature import Feature +from numpy import float32 +from pandas import DataFrame, Series, concat +from rasterio import MemoryFile +from rasterio.enums import Resampling +from rasterio.sample import sample_gen + +from pixels_utils.stac_catalogs.earthsearch.v1 import EARTHSEARCH_SCENE_URL, EarthSearchCollections, Expression +from pixels_utils.titiler import TITILER_ENDPOINT +from pixels_utils.titiler.endpoints.stac import Crop, QueryParamsCrop +from pixels_utils.titiler.mask.enum_classes import Sentinel2_SCL_Group + + +def get_satellite_expression_as_df( + gdf_fields_subset: DataFrame, + scene: Series, + feature: Feature, + expression_obj: Expression, + gsd: Union[float, int], + nodata: Union[float, int], +) -> DataFrame: + """ + Retrieves image for `scene_url` via sentera.pixels.com based on `expression_obj`, then samples the NDVI value for + each centroid in `gdf_fields_subset`. + + + Returns: + DataFrame: NDVI values with "field_id" and "geom_id" join keys. + """ + query_params_crop_ndvi = QueryParamsCrop( + url=EARTHSEARCH_SCENE_URL.format(collection=EarthSearchCollections.sentinel_2_l2a.name, id=scene["id"]), + feature=feature, + gsd=gsd, + format_=".tif", + expression=expression_obj.expression, + asset_as_band=True, + nodata=nodata, + resampling=Resampling.nearest.name, + ) + crop_arable_wlist = Crop( + query_params=query_params_crop_ndvi, + clear_cache=False, + titiler_endpoint=TITILER_ENDPOINT, + mask_enum=Sentinel2_SCL_Group.ARABLE, + mask_asset="scl", + whitelist=True, + ) + data_mask, profile_mask, tags = crop_arable_wlist.to_rasterio( + **{ + "dtype": float32, + "band_names": [expression_obj.short_name], + "band_description": [expression_obj.short_name], + } + ) + + with MemoryFile() as memfile: + with memfile.open(**profile_mask) as src: # Open as DatasetWriter + src.write(data_mask) + + # Do not sort xy in sample_gen function; order must be maintained for merging to primary keys + df_data = DataFrame( + data=sample_gen( + src, + xy=list(gdf_fields_subset["geom"].apply(lambda geometry: geometry.centroid.coords[0])), + ), + # columns=["ndvi"], + columns=[expression_obj.short_name], + ) + # Remove any rows where ndvi is set to NODATA + # df_data.drop(df_data.loc[df_data["ndvi"] == nodata].index, inplace=True) + df_data.drop(df_data.loc[df_data[expression_obj.short_name] == nodata].index, inplace=True) + df_data.insert(0, "scene_id", scene["id"]) + df_data.insert(1, "datetime", scene["datetime"]) + df_data = concat( + [ + gdf_fields_subset[["site_name", "plot_id", "field_id", "geom_id"]].reset_index(drop=True), + df_data, + ], + axis=1, + ) + return df_data diff --git a/pixels_utils/scenes/__init__.py b/pixels_utils/scenes/__init__.py index 494c6d6..b279dbf 100644 --- a/pixels_utils/scenes/__init__.py +++ b/pixels_utils/scenes/__init__.py @@ -1,3 +1,3 @@ -from ._scenes import parse_nested_stac_data, request_asset_info, search_stac_scenes +from pixels_utils.scenes._scenes import parse_nested_stac_data, request_asset_info, search_stac_scenes __all__ = ("parse_nested_stac_data", "request_asset_info", "search_stac_scenes") diff --git a/pixels_utils/scenes/_scenes.py b/pixels_utils/scenes/_scenes.py index 865ea56..03ec6a7 100644 --- a/pixels_utils/scenes/_scenes.py +++ b/pixels_utils/scenes/_scenes.py @@ -1,18 +1,29 @@ import logging -from datetime import date +from datetime import date, datetime from typing import Any, Dict, Union from geo_utils.vector import geojson_to_shapely, shapely_to_geojson_geometry +from geojson.feature import Feature from joblib import Memory # type: ignore from pandas import DataFrame, Series from pystac_client import Client +from rasterio.enums import Resampling from requests import get from requests.exceptions import ConnectionError as RequestsConnectionError from retry import retry +from tqdm import tqdm from pixels_utils.scenes._utils import _validate_collections, _validate_geometry from pixels_utils.stac_catalogs.earthsearch import EARTHSEARCH_ASSET_INFO_KEY -from pixels_utils.stac_catalogs.earthsearch.v1 import EARTHSEARCH_URL, EarthSearchCollections +from pixels_utils.stac_catalogs.earthsearch.v1 import ( + EARTHSEARCH_SCENE_URL, + EARTHSEARCH_URL, + EarthSearchCollections, + Expression, +) +from pixels_utils.titiler import TITILER_ENDPOINT +from pixels_utils.titiler.endpoints.stac import QueryParamsStatistics, Statistics +from pixels_utils.titiler.mask.enum_classes import Sentinel2_SCL_Group memory = Memory("/tmp/pixels-utils-cache/", bytes_limit=2**30, verbose=0) memory.reduce_size() # Pre-emptively reduce the cache on start-up (must be done manually) @@ -148,3 +159,80 @@ def _get_stac_version(df: DataFrame) -> str: return df["assets"].apply( lambda assets: _request_asset_info(assets[EARTHSEARCH_ASSET_INFO_KEY[stac_version]]["href"]) ) + + +def filter_scenes_with_all_nodata( + df_scenes: DataFrame, + feature: Feature, + expression_obj: Expression, + gsd: Union[float, int] = 10, + nodata: Union[float, int] = -999, +) -> list: + """ + Finds the index of all scenes without any valid pixels across the extent of the field group geometry. + + Note: + The Titiler/sentera.pixels endpoint has a nuance that if all pixels within a spatial query are NODATA, then + the Statistics endpoint returns statistics values equivalent to the NODATA value set. This function finds + the index of all scenes where this is the case so they can be removed from the list of scenes to process. + + Args: + df_scenes (DataFrame): Initial list of scenes to process. + + Returns: + list: Index values of df_scenes that can safely be removed because they do not have any valid pixels. + """ + df_scene_properties = parse_nested_stac_data(df=df_scenes, column="properties") + + ind_nodata = [] + for ind in tqdm( + list(df_scenes.index), + desc="Filtering out scenes where clouds are covering the plot area", + ): + scene = df_scenes.loc[ind] + properties = df_scene_properties.loc[ind] + date = datetime.strptime(properties["datetime"].split("T")[0], "%Y-%m-%d") + # if date > datetime(2023, 5, 30): + # break + + scene_url = EARTHSEARCH_SCENE_URL.format(collection=EarthSearchCollections.sentinel_2_l2a.name, id=scene["id"]) + + query_params = QueryParamsStatistics( + url=scene_url, + feature=feature, + expression=expression_obj.expression, + asset_as_band=True, + coord_crs=None, + gsd=gsd, + nodata=nodata, + resampling=Resampling.nearest.name, + ) + + stats_arable_wlist = Statistics( + query_params=query_params, + clear_cache=False, + titiler_endpoint=TITILER_ENDPOINT, + mask_enum=Sentinel2_SCL_Group.ARABLE, + mask_asset="scl", + whitelist=True, + ) + + expression_ = list(stats_arable_wlist.response.json()["properties"]["statistics"].keys())[0] + stats = stats_arable_wlist.response.json()["properties"]["statistics"][expression_] + # if stats["mean"] == nodata: + if stats["min"] == nodata: + # Indicates at least one pixel from statistics query is set to NODATA (i.e., masked) + logging.debug( + "%s: No valid pixels available", + date.date(), + ) + ind_nodata += [ind] + + else: + logging.debug( + "%s: %s valid pixels (Mean NDVI = %s)", + date.date(), + stats["count"], + round(stats["mean"], 2), + ) + return ind_nodata diff --git a/poetry.lock b/poetry.lock index 2205b8e..999111c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. [[package]] name = "affine" @@ -43,24 +43,25 @@ docs = ["sphinx (==6.1.3)", "sphinx-mdinclude (==0.5.3)"] [[package]] name = "anyio" -version = "4.0.0" +version = "4.2.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.0.0-py3-none-any.whl", hash = "sha256:cfdb2b588b9fc25ede96d8db56ed50848b0b649dca3dd1df0b11f683bb9e0b5f"}, - {file = "anyio-4.0.0.tar.gz", hash = "sha256:f7ed51751b2c2add651e5747c891b47e26d2a21be5d32d9311dfe9692f3e5d7a"}, + {file = "anyio-4.2.0-py3-none-any.whl", hash = "sha256:745843b39e829e108e518c489b31dc757de7d2131d53fac32bd8df268227bfee"}, + {file = "anyio-4.2.0.tar.gz", hash = "sha256:e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f"}, ] [package.dependencies] exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" +typing-extensions = {version = ">=4.1", markers = 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"cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"] [[package]] name = "babel" -version = "2.13.1" +version = "2.14.0" description = "Internationalization utilities" optional = false python-versions = ">=3.7" files = [ - {file = "Babel-2.13.1-py3-none-any.whl", hash = "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed"}, - {file = "Babel-2.13.1.tar.gz", hash = "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900"}, + {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"}, + {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"}, ] [package.extras] @@ -222,19 +224,22 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "beautifulsoup4" -version = "4.12.2" +version = "4.12.3" description = "Screen-scraping library" optional = false python-versions = 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"pixels-utils" -version = "0.4.1" +version = "0.5.0" description = "A python wrapper to [Sentera's public Titiler imagery API](https://pixels.sentera.com). The main purpose is to provide more direct access to the Pixels API via common data science libraries (like Rasterio and GeoPandas)." authors = [] exclude = ["pixels_utils/tests/data/*"] @@ -21,7 +21,7 @@ marshmallow = "^3.19.0" marshmallow-dataclass = "^8.5.14" typeguard = "^4.0.0" spyndex = "^0.5.0" -geo_utils = {git = "ssh://git@github.com/SenteraLLC/py-geo-utils.git", branch="main"} +geo_utils = {git = "ssh://git@github.com/SenteraLLC/py-geo-utils.git", branch="imgparse-ssh"} utils = {git = "ssh://git@github.com/SenteraLLC/py-utils.git", tag="v3.3.3"} python-dotenv = "^1.0.0" From 0d2483b241979c0c815c1c7bdbb35d17f262c061 Mon Sep 17 00:00:00 2001 From: tnigon <8249296+tnigon@users.noreply.github.com> Date: Fri, 26 Jan 2024 10:56:47 -0600 Subject: [PATCH 02/10] filter_scenes_with_all_nodata to init --- pixels_utils/scenes/__init__.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/pixels_utils/scenes/__init__.py b/pixels_utils/scenes/__init__.py index b279dbf..e0ae876 100644 --- a/pixels_utils/scenes/__init__.py +++ b/pixels_utils/scenes/__init__.py @@ -1,3 +1,8 @@ -from pixels_utils.scenes._scenes import parse_nested_stac_data, request_asset_info, search_stac_scenes +from pixels_utils.scenes._scenes import ( + filter_scenes_with_all_nodata, + parse_nested_stac_data, + request_asset_info, + search_stac_scenes, +) -__all__ = ("parse_nested_stac_data", "request_asset_info", "search_stac_scenes") +__all__ = ("filter_scenes_with_all_nodata", "parse_nested_stac_data", "request_asset_info", "search_stac_scenes") From d748cf71d918700517e2119cda381c0482857146 Mon Sep 17 00:00:00 2001 From: tnigon <8249296+tnigon@users.noreply.github.com> Date: Fri, 26 Jan 2024 12:36:22 -0600 Subject: [PATCH 03/10] Crop and QueryParamsCrop from root file --- pixels_utils/helpers/_helper.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixels_utils/helpers/_helper.py b/pixels_utils/helpers/_helper.py index 88c168c..2b3e4fb 100644 --- a/pixels_utils/helpers/_helper.py +++ b/pixels_utils/helpers/_helper.py @@ -9,7 +9,7 @@ from pixels_utils.stac_catalogs.earthsearch.v1 import EARTHSEARCH_SCENE_URL, EarthSearchCollections, Expression from pixels_utils.titiler import TITILER_ENDPOINT -from pixels_utils.titiler.endpoints.stac import Crop, QueryParamsCrop +from pixels_utils.titiler.endpoints.stac.crop._crop import Crop, QueryParamsCrop from pixels_utils.titiler.mask.enum_classes import Sentinel2_SCL_Group From 016c8bd469502d9d4df67c776c2794bec736e210 Mon Sep 17 00:00:00 2001 From: tnigon <8249296+tnigon@users.noreply.github.com> Date: Fri, 26 Jan 2024 12:40:14 -0600 Subject: [PATCH 04/10] Statistics and QueryParamsStatistics from root file --- pixels_utils/scenes/_scenes.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixels_utils/scenes/_scenes.py b/pixels_utils/scenes/_scenes.py index 03ec6a7..5d4a677 100644 --- a/pixels_utils/scenes/_scenes.py +++ b/pixels_utils/scenes/_scenes.py @@ -22,7 +22,7 @@ Expression, ) from pixels_utils.titiler import TITILER_ENDPOINT -from pixels_utils.titiler.endpoints.stac import QueryParamsStatistics, Statistics +from pixels_utils.titiler.endpoints.stac._statistics import QueryParamsStatistics, Statistics from pixels_utils.titiler.mask.enum_classes import Sentinel2_SCL_Group memory = Memory("/tmp/pixels-utils-cache/", bytes_limit=2**30, verbose=0) From 51abbea3ef377c608d20522397c4cb3ea41d13c1 Mon Sep 17 00:00:00 2001 From: tnigon <8249296+tnigon@users.noreply.github.com> Date: Fri, 26 Jan 2024 12:48:08 -0600 Subject: [PATCH 05/10] refactor helper funcs to avoid circular imports --- pixels_utils/helpers/__init__.py | 7 ++- pixels_utils/helpers/_helper.py | 83 +++++++++++++++++++++++++++- pixels_utils/scenes/__init__.py | 9 +--- pixels_utils/scenes/_scenes.py | 92 +------------------------------- 4 files changed, 91 insertions(+), 100 deletions(-) diff --git a/pixels_utils/helpers/__init__.py b/pixels_utils/helpers/__init__.py index 627be8a..0dae426 100644 --- a/pixels_utils/helpers/__init__.py +++ b/pixels_utils/helpers/__init__.py @@ -1,3 +1,6 @@ -from pixels_utils.helpers._helper import get_satellite_expression_as_df +from pixels_utils.helpers._helper import filter_scenes_with_all_nodata, get_satellite_expression_as_df -__all__ = ("get_satellite_expression_as_df",) +__all__ = ( + "filter_scenes_with_all_nodata", + "get_satellite_expression_as_df", +) diff --git a/pixels_utils/helpers/_helper.py b/pixels_utils/helpers/_helper.py index 2b3e4fb..193bdbc 100644 --- a/pixels_utils/helpers/_helper.py +++ b/pixels_utils/helpers/_helper.py @@ -1,3 +1,5 @@ +import logging +from datetime import datetime from typing import Union from geojson.feature import Feature @@ -6,13 +8,92 @@ from rasterio import MemoryFile from rasterio.enums import Resampling from rasterio.sample import sample_gen +from tqdm import tqdm +from pixels_utils.scenes import parse_nested_stac_data from pixels_utils.stac_catalogs.earthsearch.v1 import EARTHSEARCH_SCENE_URL, EarthSearchCollections, Expression from pixels_utils.titiler import TITILER_ENDPOINT -from pixels_utils.titiler.endpoints.stac.crop._crop import Crop, QueryParamsCrop +from pixels_utils.titiler.endpoints.stac import Crop, QueryParamsCrop, QueryParamsStatistics, Statistics from pixels_utils.titiler.mask.enum_classes import Sentinel2_SCL_Group +def filter_scenes_with_all_nodata( + df_scenes: DataFrame, + feature: Feature, + expression_obj: Expression, + gsd: Union[float, int] = 10, + nodata: Union[float, int] = -999, +) -> list: + """ + Finds the index of all scenes without any valid pixels across the extent of the field group geometry. + + Note: + The Titiler/sentera.pixels endpoint has a nuance that if all pixels within a spatial query are NODATA, then + the Statistics endpoint returns statistics values equivalent to the NODATA value set. This function finds + the index of all scenes where this is the case so they can be removed from the list of scenes to process. + + Args: + df_scenes (DataFrame): Initial list of scenes to process. + + Returns: + list: Index values of df_scenes that can safely be removed because they do not have any valid pixels. + """ + df_scene_properties = parse_nested_stac_data(df=df_scenes, column="properties") + + ind_nodata = [] + for ind in tqdm( + list(df_scenes.index), + desc="Filtering out scenes where clouds are covering the plot area", + ): + scene = df_scenes.loc[ind] + properties = df_scene_properties.loc[ind] + date = datetime.strptime(properties["datetime"].split("T")[0], "%Y-%m-%d") + # if date > datetime(2023, 5, 30): + # break + + scene_url = EARTHSEARCH_SCENE_URL.format(collection=EarthSearchCollections.sentinel_2_l2a.name, id=scene["id"]) + + query_params = QueryParamsStatistics( + url=scene_url, + feature=feature, + expression=expression_obj.expression, + asset_as_band=True, + coord_crs=None, + gsd=gsd, + nodata=nodata, + resampling=Resampling.nearest.name, + ) + + stats_arable_wlist = Statistics( + query_params=query_params, + clear_cache=False, + titiler_endpoint=TITILER_ENDPOINT, + mask_enum=Sentinel2_SCL_Group.ARABLE, + mask_asset="scl", + whitelist=True, + ) + + expression_ = list(stats_arable_wlist.response.json()["properties"]["statistics"].keys())[0] + stats = stats_arable_wlist.response.json()["properties"]["statistics"][expression_] + # if stats["mean"] == nodata: + if stats["min"] == nodata: + # Indicates at least one pixel from statistics query is set to NODATA (i.e., masked) + logging.debug( + "%s: No valid pixels available", + date.date(), + ) + ind_nodata += [ind] + + else: + logging.debug( + "%s: %s valid pixels (Mean NDVI = %s)", + date.date(), + stats["count"], + round(stats["mean"], 2), + ) + return ind_nodata + + def get_satellite_expression_as_df( gdf_fields_subset: DataFrame, scene: Series, diff --git a/pixels_utils/scenes/__init__.py b/pixels_utils/scenes/__init__.py index e0ae876..b279dbf 100644 --- a/pixels_utils/scenes/__init__.py +++ b/pixels_utils/scenes/__init__.py @@ -1,8 +1,3 @@ -from pixels_utils.scenes._scenes import ( - filter_scenes_with_all_nodata, - parse_nested_stac_data, - request_asset_info, - search_stac_scenes, -) +from pixels_utils.scenes._scenes import parse_nested_stac_data, request_asset_info, search_stac_scenes -__all__ = ("filter_scenes_with_all_nodata", "parse_nested_stac_data", "request_asset_info", "search_stac_scenes") +__all__ = ("parse_nested_stac_data", "request_asset_info", "search_stac_scenes") diff --git a/pixels_utils/scenes/_scenes.py b/pixels_utils/scenes/_scenes.py index 5d4a677..865ea56 100644 --- a/pixels_utils/scenes/_scenes.py +++ b/pixels_utils/scenes/_scenes.py @@ -1,29 +1,18 @@ import logging -from datetime import date, datetime +from datetime import date from typing import Any, Dict, Union from geo_utils.vector import geojson_to_shapely, shapely_to_geojson_geometry -from geojson.feature import Feature from joblib import Memory # type: ignore from pandas import DataFrame, Series from pystac_client import Client -from rasterio.enums import Resampling from requests import get from requests.exceptions import ConnectionError as RequestsConnectionError from retry import retry -from tqdm import tqdm from pixels_utils.scenes._utils import _validate_collections, _validate_geometry from pixels_utils.stac_catalogs.earthsearch import EARTHSEARCH_ASSET_INFO_KEY -from pixels_utils.stac_catalogs.earthsearch.v1 import ( - EARTHSEARCH_SCENE_URL, - EARTHSEARCH_URL, - EarthSearchCollections, - Expression, -) -from pixels_utils.titiler import TITILER_ENDPOINT -from pixels_utils.titiler.endpoints.stac._statistics import QueryParamsStatistics, Statistics -from pixels_utils.titiler.mask.enum_classes import Sentinel2_SCL_Group +from pixels_utils.stac_catalogs.earthsearch.v1 import EARTHSEARCH_URL, EarthSearchCollections memory = Memory("/tmp/pixels-utils-cache/", bytes_limit=2**30, verbose=0) memory.reduce_size() # Pre-emptively reduce the cache on start-up (must be done manually) @@ -159,80 +148,3 @@ def _get_stac_version(df: DataFrame) -> str: return df["assets"].apply( lambda assets: _request_asset_info(assets[EARTHSEARCH_ASSET_INFO_KEY[stac_version]]["href"]) ) - - -def filter_scenes_with_all_nodata( - df_scenes: DataFrame, - feature: Feature, - expression_obj: Expression, - gsd: Union[float, int] = 10, - nodata: Union[float, int] = -999, -) -> list: - """ - Finds the index of all scenes without any valid pixels across the extent of the field group geometry. - - Note: - The Titiler/sentera.pixels endpoint has a nuance that if all pixels within a spatial query are NODATA, then - the Statistics endpoint returns statistics values equivalent to the NODATA value set. This function finds - the index of all scenes where this is the case so they can be removed from the list of scenes to process. - - Args: - df_scenes (DataFrame): Initial list of scenes to process. - - Returns: - list: Index values of df_scenes that can safely be removed because they do not have any valid pixels. - """ - df_scene_properties = parse_nested_stac_data(df=df_scenes, column="properties") - - ind_nodata = [] - for ind in tqdm( - list(df_scenes.index), - desc="Filtering out scenes where clouds are covering the plot area", - ): - scene = df_scenes.loc[ind] - properties = df_scene_properties.loc[ind] - date = datetime.strptime(properties["datetime"].split("T")[0], "%Y-%m-%d") - # if date > datetime(2023, 5, 30): - # break - - scene_url = EARTHSEARCH_SCENE_URL.format(collection=EarthSearchCollections.sentinel_2_l2a.name, id=scene["id"]) - - query_params = QueryParamsStatistics( - url=scene_url, - feature=feature, - expression=expression_obj.expression, - asset_as_band=True, - coord_crs=None, - gsd=gsd, - nodata=nodata, - resampling=Resampling.nearest.name, - ) - - stats_arable_wlist = Statistics( - query_params=query_params, - clear_cache=False, - titiler_endpoint=TITILER_ENDPOINT, - mask_enum=Sentinel2_SCL_Group.ARABLE, - mask_asset="scl", - whitelist=True, - ) - - expression_ = list(stats_arable_wlist.response.json()["properties"]["statistics"].keys())[0] - stats = stats_arable_wlist.response.json()["properties"]["statistics"][expression_] - # if stats["mean"] == nodata: - if stats["min"] == nodata: - # Indicates at least one pixel from statistics query is set to NODATA (i.e., masked) - logging.debug( - "%s: No valid pixels available", - date.date(), - ) - ind_nodata += [ind] - - else: - logging.debug( - "%s: %s valid pixels (Mean NDVI = %s)", - date.date(), - stats["count"], - round(stats["mean"], 2), - ) - return ind_nodata From c0d3f16ec9872c5ddc502b096effa193d3c1cdb6 Mon Sep 17 00:00:00 2001 From: tnigon <8249296+tnigon@users.noreply.github.com> Date: Fri, 26 Jan 2024 16:59:52 -0600 Subject: [PATCH 06/10] get_satellite_expression_as_df() make more flexible --- pixels_utils/helpers/_helper.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/pixels_utils/helpers/_helper.py b/pixels_utils/helpers/_helper.py index 193bdbc..e98ca82 100644 --- a/pixels_utils/helpers/_helper.py +++ b/pixels_utils/helpers/_helper.py @@ -144,7 +144,11 @@ def get_satellite_expression_as_df( df_data = DataFrame( data=sample_gen( src, - xy=list(gdf_fields_subset["geom"].apply(lambda geometry: geometry.centroid.coords[0])), + xy=list( + gdf_fields_subset[gdf_fields_subset.geometry.name].apply( + lambda geometry: geometry.centroid.coords[0] + ) + ), ), # columns=["ndvi"], columns=[expression_obj.short_name], @@ -156,7 +160,7 @@ def get_satellite_expression_as_df( df_data.insert(1, "datetime", scene["datetime"]) df_data = concat( [ - gdf_fields_subset[["site_name", "plot_id", "field_id", "geom_id"]].reset_index(drop=True), + gdf_fields_subset.reset_index(drop=True), df_data, ], axis=1, From 40e2139b2f45baa898c463c8e03e23368207e128 Mon Sep 17 00:00:00 2001 From: tnigon <8249296+tnigon@users.noreply.github.com> Date: Sat, 27 Jan 2024 12:13:55 -0600 Subject: [PATCH 07/10] _generate_experession_override() --- pixels_utils/stac_catalogs/earthsearch/v1.py | 79 +++++++++++++++----- 1 file changed, 62 insertions(+), 17 deletions(-) diff --git a/pixels_utils/stac_catalogs/earthsearch/v1.py b/pixels_utils/stac_catalogs/earthsearch/v1.py index 34a28cd..ba381d7 100644 --- a/pixels_utils/stac_catalogs/earthsearch/v1.py +++ b/pixels_utils/stac_catalogs/earthsearch/v1.py @@ -31,6 +31,14 @@ def _version(self): return "v1" +def _generate_experession_override(expression: str, assets: list[str], assets_override: list[str]) -> str: + """Return expression_override with assets replaced by assets_override.""" + expression_override = expression + for asset_common, asset_collection in zip(assets, assets_override): + expression_override = expression_override.replace(asset_common, asset_collection) + return expression_override + + def expression_from_collection( collection: EarthSearchCollections = EarthSearchCollections.sentinel_2_l2a, spectral_index: str = "NDVI" ) -> Expression: @@ -49,21 +57,57 @@ def expression_from_collection( Returns: Expression: The tailored Expression object. """ - assert collection._version == "v1", ( - f"The `collection` and `expression_from_collection()` function versions do not match ({collection._version} vs " - f'v1). Ensure both the "{collection}" and expression_from_collection() function are imported from the same ' - "version of `pixels_utils.stac_catalogs.earthsearch`." - ) + if collection._version != "v1": + raise AssertionError( + f"The `collection` and `expression_from_collection()` function versions do not match ({collection._version} vs " + f'v1). Ensure both the "{collection}" and expression_from_collection() function are imported from the same ' + "version of `pixels_utils.stac_catalogs.earthsearch`." + ) stac_collection_url = EARTHSEARCH_COLLECTION_URL.format(collection=collection.name) stac_metadata = STACMetaData(collection_url=stac_collection_url) # TODO: stac_metadata.parse_asset_bands("eo:bands", return_dataframe=True) for support of EarthSearch v0 - assert set(Expression(spyndex_object=spyndex_indices[spectral_index]).assets).issubset( - set(stac_metadata.asset_names) - ), f'Assets for spectral index "{spectral_index}" are not available in collection "{collection}".' - assert ( - spectral_index in spyndex_indices.keys() - ), f"{spectral_index} is not a valid spectral index (must be available via spyndex.indices)." - return Expression(spyndex_object=spyndex_indices["NDVI"]) + + # get list of `name` values where `common_name` matches spectral_index + assets_ = Expression(spyndex_object=spyndex_indices[spectral_index]).assets + expression_str_ = Expression(spyndex_object=spyndex_indices[spectral_index]).expression + + df_collection_assets = stac_metadata.parse_asset_bands("eo:bands", return_dataframe=True) + df_expr_assets_ = df_collection_assets[df_collection_assets["common_name"].isin(assets_)][ + ["name", "common_name"] + ].drop_duplicates(subset="common_name") + + # Check if all `common_names` match `names` (i.e., collection_names) + if any([row["name"] != row["common_name"] for _, row in df_expr_assets_.iterrows()]): + # Raise error if collection does not have assets available + for asset in assets_: + if asset not in df_expr_assets_["common_name"].values: + raise ValueError( + f'"{asset}" is required for spectral index "{spectral_index}", but is not a valid asset (i.e., ' + f'"common_name") in collection "{collection}".\nValid "common_names":\n' + f'{df_collection_assets["common_name"].values}' + ) + # Set assets_override and expression_override based on available `name` values for the collection. + assets_override = [ + df_expr_assets_[df_expr_assets_["common_name"] == asset]["name"].values[0] for asset in assets_ + ] + expression_override = _generate_experession_override(expression_str_, assets_, assets_override) + else: + assets_override, expression_override = None, None + + expression = Expression( + spyndex_object=spyndex_indices[spectral_index], + assets_override=assets_override, + expression_override=expression_override, + ) + + if not set(expression.assets).issubset(set(stac_metadata.asset_names)): + raise AssertionError( + f'Assets for spectral index "{spectral_index}" are not available in collection "{collection}".' + ) + if spectral_index not in spyndex_indices.keys(): + raise AssertionError(f"{spectral_index} is not a valid spectral index (must be available via spyndex.indices).") + + return expression def expressions_from_collection( @@ -79,11 +123,12 @@ def expressions_from_collection( Returns: Expressions: The Expressions object containing all available spectral indices for the given collection. """ - assert collection._version == "v1", ( - f"The `collection` and `expression_from_collection()` function versions do not match ({collection._version} vs " - f'v1). Ensure both the "{collection}" and expression_from_collection() function are imported from the same ' - "version of `pixels_utils.stac_catalogs.earthsearch`." - ) + if collection._version != "v1": + raise AssertionError( + f"The `collection` and `expression_from_collection()` function versions do not match ({collection._version} vs " + f'v1). Ensure both the "{collection}" and expression_from_collection() function are imported from the same ' + "version of `pixels_utils.stac_catalogs.earthsearch`." + ) # Get list of assets in collection and filter spyndex_bands by collection assets stac_collection_url = EARTHSEARCH_COLLECTION_URL.format(collection=collection.name) stac_metadata = STACMetaData(collection_url=stac_collection_url) From 44e24cc3954025c2764f2cf053438bd68149ac57 Mon Sep 17 00:00:00 2001 From: tnigon <8249296+tnigon@users.noreply.github.com> Date: Sat, 27 Jan 2024 12:26:27 -0600 Subject: [PATCH 08/10] move spyndex_indices check to top of expression_from_collection() --- pixels_utils/stac_catalogs/earthsearch/v1.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/pixels_utils/stac_catalogs/earthsearch/v1.py b/pixels_utils/stac_catalogs/earthsearch/v1.py index ba381d7..12ec01a 100644 --- a/pixels_utils/stac_catalogs/earthsearch/v1.py +++ b/pixels_utils/stac_catalogs/earthsearch/v1.py @@ -57,6 +57,8 @@ def expression_from_collection( Returns: Expression: The tailored Expression object. """ + if spectral_index not in spyndex_indices.keys(): + raise AssertionError(f"{spectral_index} is not a valid spectral index (must be available via spyndex.indices).") if collection._version != "v1": raise AssertionError( f"The `collection` and `expression_from_collection()` function versions do not match ({collection._version} vs " @@ -104,9 +106,6 @@ def expression_from_collection( raise AssertionError( f'Assets for spectral index "{spectral_index}" are not available in collection "{collection}".' ) - if spectral_index not in spyndex_indices.keys(): - raise AssertionError(f"{spectral_index} is not a valid spectral index (must be available via spyndex.indices).") - return expression From dbc5e55cc2cb319961becde603e24918276832cd Mon Sep 17 00:00:00 2001 From: tnigon <8249296+tnigon@users.noreply.github.com> Date: Mon, 29 Jan 2024 12:08:26 -0600 Subject: [PATCH 09/10] update deps --- .pre-commit-config.yaml | 6 +++--- poetry.lock | 36 ++++++++++++++++++------------------ 2 files changed, 21 insertions(+), 21 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 60e4a4c..b705ea0 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,15 +1,15 @@ repos: - repo: https://github.com/pycqa/isort - rev: 5.12.0 + rev: 5.13.2 hooks: - id: isort name: isort (python) - repo: https://github.com/ambv/black - rev: 23.11.0 + rev: 24.1.1 hooks: - id: black - repo: https://github.com/pycqa/flake8 - rev: '6.1.0' + rev: '7.0.0' hooks: - id: flake8 exclude: (tests|doc) diff --git a/poetry.lock b/poetry.lock index 999111c..68a34b5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -690,13 +690,13 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"] [[package]] name = "dask" -version = "2024.1.0" +version = "2024.1.1" description = "Parallel PyData with Task Scheduling" optional = false python-versions = ">=3.9" files = [ - {file = "dask-2024.1.0-py3-none-any.whl", hash = "sha256:717102ef7c309297291095a0061d374f3b72e11ce4e1115ab9faff940e274b4b"}, - {file = "dask-2024.1.0.tar.gz", hash = "sha256:f24fdc7a07e59a1403bf6903e6d8dc15ed6f8607d3311b4f00f88d8a2ac63e49"}, + {file = "dask-2024.1.1-py3-none-any.whl", hash = "sha256:860ce2797905095beff0187c214840b80c77d752dcb9098a8283e3655a762bf5"}, + {file = "dask-2024.1.1.tar.gz", hash = "sha256:d0dc92e81ce68594a0a0ce23ba33f4d648f2c2f4217ab9b79068b7ecfb0416c7"}, ] [package.dependencies] @@ -714,7 +714,7 @@ array = ["numpy (>=1.21)"] complete = ["dask[array,dataframe,diagnostics,distributed]", "lz4 (>=4.3.2)", "pyarrow (>=7.0)", "pyarrow-hotfix"] dataframe = ["dask[array]", "pandas (>=1.3)"] diagnostics = ["bokeh (>=2.4.2)", "jinja2 (>=2.10.3)"] -distributed = ["distributed (==2024.1.0)"] +distributed = ["distributed (==2024.1.1)"] test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout", "pytest-xdist"] [[package]] @@ -2917,13 +2917,13 @@ numpy = [ [[package]] name = "overrides" -version = "7.6.0" +version = "7.7.0" description = "A decorator to automatically detect mismatch when overriding a method." optional = false python-versions = ">=3.6" files = [ - {file = "overrides-7.6.0-py3-none-any.whl", hash = "sha256:c36e6635519ea9c5b043b65c36d4b886aee8bd45b7d4681d2a6df0898df4b654"}, - {file = "overrides-7.6.0.tar.gz", hash = "sha256:01e15bbbf15b766f0675c275baa1878bd1c7dc9bc7b9ee13e677cdba93dc1bd9"}, + {file = "overrides-7.7.0-py3-none-any.whl", hash = "sha256:c7ed9d062f78b8e4c1a7b70bd8796b35ead4d9f510227ef9c5dc7626c60d7e49"}, + {file = "overrides-7.7.0.tar.gz", hash = "sha256:55158fa3d93b98cc75299b1e67078ad9003ca27945c76162c1c0766d6f91820a"}, ] [[package]] @@ -3548,13 +3548,13 @@ validation = ["jsonschema (>=4.5.1)"] [[package]] name = "pytest" -version = "7.4.4" +version = "8.0.0" description = "pytest: simple powerful testing with Python" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "pytest-7.4.4-py3-none-any.whl", hash = "sha256:b090cdf5ed60bf4c45261be03239c2c1c22df034fbffe691abe93cd80cea01d8"}, - {file = "pytest-7.4.4.tar.gz", hash = "sha256:2cf0005922c6ace4a3e2ec8b4080eb0d9753fdc93107415332f50ce9e7994280"}, + {file = "pytest-8.0.0-py3-none-any.whl", hash = "sha256:50fb9cbe836c3f20f0dfa99c565201fb75dc54c8d76373cd1bde06b06657bdb6"}, + {file = "pytest-8.0.0.tar.gz", hash = "sha256:249b1b0864530ba251b7438274c4d251c58d868edaaec8762893ad4a0d71c36c"}, ] [package.dependencies] @@ -3562,7 +3562,7 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""} exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} iniconfig = "*" packaging = "*" -pluggy = ">=0.12,<2.0" +pluggy = ">=1.3.0,<2.0" tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} [package.extras] @@ -3641,13 +3641,13 @@ files = [ [[package]] name = "pytz" -version = "2023.3.post1" +version = "2023.4" description = "World timezone definitions, modern and historical" optional = false python-versions = "*" files = [ - {file = "pytz-2023.3.post1-py2.py3-none-any.whl", hash = "sha256:ce42d816b81b68506614c11e8937d3aa9e41007ceb50bfdcb0749b921bf646c7"}, - {file = "pytz-2023.3.post1.tar.gz", hash = "sha256:7b4fddbeb94a1eba4b557da24f19fdf9db575192544270a9101d8509f9f43d7b"}, + {file = "pytz-2023.4-py2.py3-none-any.whl", hash = "sha256:f90ef520d95e7c46951105338d918664ebfd6f1d995bd7d153127ce90efafa6a"}, + {file = "pytz-2023.4.tar.gz", hash = "sha256:31d4583c4ed539cd037956140d695e42c033a19e984bfce9964a3f7d59bc2b40"}, ] [[package]] @@ -3893,13 +3893,13 @@ test = ["boto3 (>=1.2.4)", "hypothesis", "packaging", "pytest (>=2.8.2)", "pytes [[package]] name = "referencing" -version = "0.32.1" +version = "0.33.0" description = "JSON Referencing + Python" optional = false python-versions = ">=3.8" files = [ - {file = "referencing-0.32.1-py3-none-any.whl", hash = "sha256:7e4dc12271d8e15612bfe35792f5ea1c40970dadf8624602e33db2758f7ee554"}, - {file = "referencing-0.32.1.tar.gz", hash = "sha256:3c57da0513e9563eb7e203ebe9bb3a1b509b042016433bd1e45a2853466c3dd3"}, + {file = "referencing-0.33.0-py3-none-any.whl", hash = "sha256:39240f2ecc770258f28b642dd47fd74bc8b02484de54e1882b74b35ebd779bd5"}, + {file = "referencing-0.33.0.tar.gz", hash = "sha256:c775fedf74bc0f9189c2a3be1c12fd03e8c23f4d371dce795df44e06c5b412f7"}, ] [package.dependencies] From eff44b1749b1e89eddf6ce167ed889a1f41f9a2d Mon Sep 17 00:00:00 2001 From: tnigon <8249296+tnigon@users.noreply.github.com> Date: Mon, 29 Jan 2024 12:16:33 -0600 Subject: [PATCH 10/10] formatting --- pixels_utils/titiler/endpoints/stac/crop/_crop.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixels_utils/titiler/endpoints/stac/crop/_crop.py b/pixels_utils/titiler/endpoints/stac/crop/_crop.py index 2affd3d..d592416 100644 --- a/pixels_utils/titiler/endpoints/stac/crop/_crop.py +++ b/pixels_utils/titiler/endpoints/stac/crop/_crop.py @@ -359,7 +359,7 @@ def to_rasterio(self, **kwargs) -> Tuple[ArrayLike, Profile, Dict]: # TODO: Consider validating kwargs before passing to parse_crop_response() data_mask, profile_mask, tags = parse_crop_response( r=self.response, - **kwargs + **kwargs, # **{"dtype": float32, "band_names": [collection_ndvi.short_name], "band_description": [collection_ndvi.short_name]}, ) return data_mask, profile_mask, tags