resolved merge conflicts

.dockerignore

@@ -1,5 +1,6 @@
 *
 !hls_vi/
 !tests/
+tests/fixtures/
 !setup.py
 !tox.ini

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# See https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/test.yml

@@ -0,0 +1,14 @@
+name: Test
+
+on: [push, workflow_dispatch]
+
+jobs:
+  tox_in_docker:
+    runs-on: ubuntu-20.04
+
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v4
+
+      - name: Run tests in Docker container
+        run: make test

Dockerfile

@@ -12,8 +12,8 @@ RUN : \
     python3-venv \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* \
-    && pip3 install --no-cache --upgrade pip setuptools \
-    && pip3 install --no-cache rasterio==1.1.3 tox tox-venv --no-binary rasterio \
+    && pip3 install --no-cache-dir --upgrade pip setuptools \
+    && pip3 install --no-cache-dir rasterio==1.1.3 tox tox-venv --no-binary rasterio \
     && :
 
 WORKDIR /hls_vi

Makefile

@@ -0,0 +1,7 @@
+.PHONY = build test
+
+build:
+	docker compose build
+
+test:
+	docker compose run --build tox

README.md

@@ -38,5 +38,5 @@ where:
 You can run tests using Docker:
 
 ```bash
-docker compose run --build tox
+make test
 ```

compose.yaml

@@ -1,3 +1,5 @@
 services:
   tox:
     build: .
+    volumes:
+      - ${PWD}/tests/fixtures:/hls_vi/tests/fixtures

hls_vi/generate_indices.py

@@ -3,14 +3,14 @@
 import getopt
 import os
 import re
+import shutil
 import sys
 from datetime import datetime, timezone
 from enum import Enum, unique
 from pathlib import Path
 from typing import Callable, Mapping, Optional, SupportsFloat, Tuple, Type
 from typing_extensions import TypeAlias
 
-import matplotlib.pyplot as plt
 import numpy as np
 import rasterio
 import rasterio.crs
@@ -261,10 +261,6 @@ def write_granule_index(
             _FillValue=data.fill_value,
         )
 
-    # Create browse image using NDVI
-    if index == Index.NDVI:
-        plt.imsave(str(output_path.with_suffix(".jpeg")), data, dpi=300, cmap="gray")
-
 
 def evi(data: BandData) -> np.ma.masked_array:
     b, r, nir = data[Band.B], data[Band.R], data[Band.NIR]
@@ -345,7 +341,7 @@ def __init__(self, long_name: str, scale_factor: SupportsFloat = 0.0001) -> None
 
     def __call__(self, data: BandData) -> np.ma.masked_array:
         scaled_index = self.compute_index(data) / self.scale_factor
-        return np.ma.round(scaled_index).astype(np.int16)
+        return np.ma.round(scaled_index, decimals=4).astype(np.int16)
 
 
 def parse_args() -> Tuple[Path, Path, str]:
@@ -379,9 +375,20 @@ def parse_args() -> Tuple[Path, Path, str]:
     return Path(input_dir), Path(output_dir), id_str
 
 
+def generate_vi_granule(input_dir: Path, output_dir: Path, id_str: str) -> Granule:
+    granule = read_granule_bands(input_dir, id_str)
+    write_granule_indices(output_dir, granule)
+    shutil.copy(
+        input_dir / f"{granule.id_}.jpg",
+        output_dir / f"{str(granule.id_).replace('HLS', 'HLS-VI')}.jpg",
+    )
+
+    return granule
+
+
 def main():
     input_dir, output_dir, id_str = parse_args()
-    write_granule_indices(output_dir, read_granule_bands(input_dir, id_str))
+    generate_vi_granule(input_dir, output_dir, id_str)
 
 
 if __name__ == "__main__":

hls_vi/generate_metadata.py

@@ -38,8 +38,19 @@ def generate_metadata(input_dir: Path, output_dir: Path):
     tree.find("InsertTime").text = formatted_date
     tree.find("LastUpdate").text = formatted_date
 
-    # TODO: Find out what the Collection ID should be
-    tree.find("Collection/DataSetId").text = "Update HLS-VI New Collection ID String"
+    dataset_id = tree.find("Collection/DataSetId")
+    dataset_id.text = (
+        "HLS Operational Land Imager Vegetation Indices Daily Global 30 m V2.0"
+        if "L30" in metadata_path.name
+        else "HLS Sentinel-2 Multi-spectral Instrument Vegetation Indices Daily Global 30 m V2.0"  # noqa: E501
+    )
+    set_additional_attribute(
+        tree.find("AdditionalAttributes"),
+        "IDENTIFIER_PRODUCT_DOI",
+        "10.5067/HLS/HLSL30_VI.002"
+        if "L30" in metadata_path.name
+        else "10.5067/HLS/HLSS30_VI.002",
+    )
 
     data_granule = tree.find("DataGranule")
     data_granule.remove(data_granule.find("DataGranuleSizeInBytes"))
@@ -57,6 +68,24 @@ def generate_metadata(input_dir: Path, output_dir: Path):
     )
 
 
+def set_additional_attribute(attrs: ET.Element, name: str, value: str):
+    attr = attrs.find(f'./AdditionalAttribute[Name="{name}"]')
+
+    if attr is not None:
+        attr.find(".//Value").text = value
+    else:
+        attr = ET.Element("AdditionalAttribute")
+        attr_name = ET.Element("Name")
+        attr_name.text = name
+        attr_values = ET.Element("Values")
+        attr_value = ET.Element("Value")
+        attr_value.text = value
+        attr_values.append(attr_value)
+        attr.append(attr_name)
+        attr.append(attr_values)
+        attrs.append(attr)
+
+
 def parse_args() -> Tuple[Path, Path]:
     short_options = "i:o:"
     long_options = ["instrument=", "inputdir=", "outputdir="]

setup.py

@@ -6,7 +6,6 @@
     packages=["hls_vi"],
     install_requires=[
         "dataclasses",
-        "matplotlib",
         "numpy~=1.19.0",
         "rasterio",
         "typing-extensions",
@@ -16,6 +15,7 @@
         "console_scripts": [
             "vi_generate_indices=hls_vi.generate_indices:main",
             "vi_generate_metadata=hls_vi.generate_metadata:main",
+            "vi_generate_stac_items=hls_vi.generate_stac_items:main"
         ],
     },
 )

tests/fixtures/HLS-VI.L30.T06WVS.2024120T211159.v2.0.cmr.xml

@@ -4,7 +4,7 @@
   <InsertTime>2024-05-08T21:25:20.907010Z</InsertTime>
   <LastUpdate>2024-05-08T21:25:20.907443Z</LastUpdate>
   <Collection>
-    <DataSetId>Update HLS-VI New Collection ID String</DataSetId>
+    <DataSetId>HLS Operational Land Imager Vegetation Indices Daily Global 30 m V2.0</DataSetId>
   </Collection>
   <DataGranule>
     <ProducerGranuleId>HLS-VI.L30.T06WVS.2024120T211159</ProducerGranuleId>
@@ -231,7 +231,7 @@
     <AdditionalAttribute>
       <Name>IDENTIFIER_PRODUCT_DOI</Name>
       <Values>
-        <Value>10.5067/HLS/HLSL30.002</Value>
+        <Value>10.5067/HLS/HLSL30_VI.002</Value>
       </Values>
     </AdditionalAttribute>
     <AdditionalAttribute>

tests/fixtures/HLS-VI.S30.T13RCN.2024128T173909.v2.0.cmr.xml

@@ -4,7 +4,7 @@
   <InsertTime>2024-05-09T20:08:04.550553Z</InsertTime>
   <LastUpdate>2024-05-09T20:08:04.550572Z</LastUpdate>
   <Collection>
-    <DataSetId>Update HLS-VI New Collection ID String</DataSetId>
+    <DataSetId>HLS Sentinel-2 Multi-spectral Instrument Vegetation Indices Daily Global 30 m V2.0</DataSetId>
   </Collection>
   <DataGranule>
     <ProducerGranuleId>HLS-VI.S30.T13RCN.2024128T173909</ProducerGranuleId>
@@ -293,7 +293,7 @@
     <AdditionalAttribute>
       <Name>IDENTIFIER_PRODUCT_DOI</Name>
       <Values>
-        <Value>10.5067/HLS/HLSS30.002</Value>
+        <Value>10.5067/HLS/HLSS30_VI.002</Value>
       </Values>
     </AdditionalAttribute>
     <AdditionalAttribute>
@@ -309,13 +309,5 @@
   </OnlineResources>
   <DataFormat>Cloud Optimized GeoTIFF (COG)</DataFormat>
   <AssociatedBrowseImageUrls>
-    <ProviderBrowseUrl>
-      <URL>https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-public/HLSS30.020/HLS.S30.T13RCN.2024128T173909.v2.0/HLS.S30.T13RCN.2024128T173909.v2.0.jpg</URL>
-      <Description>Download HLS.S30.T13RCN.2024128T173909.v2.0.jpg</Description>
-    </ProviderBrowseUrl>
-    <ProviderBrowseUrl>
-      <URL>s3://lp-prod-public/HLSS30.020/HLS.S30.T13RCN.2024128T173909.v2.0/HLS.S30.T13RCN.2024128T173909.v2.0.jpg</URL>
-      <Description>This link provides direct download access via S3 to the granule</Description>
-    </ProviderBrowseUrl>
   </AssociatedBrowseImageUrls>
 </Granule>

tests/fixtures/HLS.S30.T13RCN.2024128T173909.v2.0/HLS.S30.T13RCN.2024128T173909.v2.0.cmr.xml

@@ -310,13 +310,5 @@
   </OnlineResources>
   <DataFormat>Cloud Optimized GeoTIFF (COG)</DataFormat>
   <AssociatedBrowseImageUrls>
-    <ProviderBrowseUrl>
-      <URL>https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-public/HLSS30.020/HLS.S30.T13RCN.2024128T173909.v2.0/HLS.S30.T13RCN.2024128T173909.v2.0.jpg</URL>
-      <Description>Download HLS.S30.T13RCN.2024128T173909.v2.0.jpg</Description>
-    </ProviderBrowseUrl>
-    <ProviderBrowseUrl>
-      <URL>s3://lp-prod-public/HLSS30.020/HLS.S30.T13RCN.2024128T173909.v2.0/HLS.S30.T13RCN.2024128T173909.v2.0.jpg</URL>
-      <Description>This link provides direct download access via S3 to the granule</Description>
-    </ProviderBrowseUrl>
   </AssociatedBrowseImageUrls>
 </Granule>

tests/fixtures/test_output.json

@@ -15,7 +15,7 @@
     "proj:epsg": 32606,
     "view:sun_azimuth": 168.41547441,
     "view:azimuth": 179.72857034,
-    "sci:doi": "10.5067/HLS/HLSL30.002",
+    "sci:doi": "10.5067/HLS/HLSL30_VI.002",
     "datetime": "2024-05-08T16:25:12.736230Z"
   },
   "geometry": {
@@ -38,7 +38,7 @@
       "href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-public/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0_stac.json",
       "type": "application/json"
     },
-    { "rel": "cite-as", "href": "https://doi.org/10.5067/HLS/HLSL30.002" }
+    { "rel": "cite-as", "href": "https://doi.org/10.5067/HLS/HLSL30_VI.002" }
   ],
   "assets": {
     "NDVI": {

tests/fixtures/unit_test_output.json

@@ -1 +1 @@
-{"type": "Feature", "stac_version": "1.0.0", "id": "HLS-VI.L30.T06WVS.2024120T211159.v2.0", "properties": {"start_datetime": "2024-05-08T16:25:12.736230Z", "end_datetime": "2024-05-08T16:25:12.736230Z", "platform": "landsat-8", "instruments": ["oli"], "eo:cloud_cover": 6.0, "proj:transform": [30.0, 0.0, 399960.0, 0.0, -30.0, 7200000.0, 0.0, 0.0, 1.0], "proj:shape": [3660, 3660], "proj:epsg": 32606, "view:sun_azimuth": 168.41547441, "view:azimuth": 179.72857034, "sci:doi": "10.5067/HLS/HLSL30.002", "datetime": "2024-05-08T16:25:12.736230Z"}, "geometry": {"type": "MultiPolygon", "coordinates": [[[[-149.114568, 64.909135], [-146.793616, 64.923996], [-146.800894, 63.938713], [-149.040061, 63.924491], [-149.114568, 64.909135]]]]}, "links": [{"rel": "self", "href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-public/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0_stac.json", "type": "application/json"}, {"rel": "cite-as", "href": "https://doi.org/10.5067/HLS/HLSL30.002"}], "assets": {"NDVI": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.NDVI.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "NDVI", "common_name": "NDVI"}], "roles": ["data"]}, "EVI": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.EVI.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "EVI", "common_name": "EVI"}], "roles": ["data"]}, "MSAVI": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.MSAVI.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "MSAVI", "common_name": "MSAVI"}], "roles": ["data"]}, "NBR": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.NBR.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "NBR", "common_name": "NBR"}], "roles": ["data"]}, "NBR2": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.NBR2.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "NBR2", "common_name": "NBR2"}], "roles": ["data"]}, "NDMI": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.NDMI.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "NDMI", "common_name": "NDMI"}], "roles": ["data"]}, "NDWI": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.NDWI.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "NDWI", "common_name": "NDWI"}], "roles": ["data"]}, "SAVI": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.SAVI.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "SAVI", "common_name": "SAVI"}], "roles": ["data"]}, "TVI": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.TVI.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "TVI", "common_name": "TVI"}], "roles": ["data"]}, "thumbnail": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-public/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.jpg", "type": "image/jpeg", "roles": ["thumbnail"]}}, "bbox": [-149.114568, 63.924491, -146.793616, 64.923996], "stac_extensions": ["https://stac-extensions.github.io/eo/v1.1.0/schema.json", "https://stac-extensions.github.io/projection/v1.1.0/schema.json", "https://stac-extensions.github.io/view/v1.0.0/schema.json", "https://stac-extensions.github.io/scientific/v1.0.0/schema.json"]}
+{"type": "Feature", "stac_version": "1.0.0", "id": "HLS-VI.L30.T06WVS.2024120T211159.v2.0", "properties": {"start_datetime": "2024-05-08T16:25:12.736230Z", "end_datetime": "2024-05-08T16:25:12.736230Z", "platform": "landsat-8", "instruments": ["oli"], "eo:cloud_cover": 6.0, "proj:transform": [30.0, 0.0, 399960.0, 0.0, -30.0, 7200000.0, 0.0, 0.0, 1.0], "proj:shape": [3660, 3660], "proj:epsg": 32606, "view:sun_azimuth": 168.41547441, "view:azimuth": 179.72857034, "sci:doi": "10.5067/HLS/HLSL30_VI.002", "datetime": "2024-05-08T16:25:12.736230Z"}, "geometry": {"type": "MultiPolygon", "coordinates": [[[[-149.114568, 64.909135], [-146.793616, 64.923996], [-146.800894, 63.938713], [-149.040061, 63.924491], [-149.114568, 64.909135]]]]}, "links": [{"rel": "self", "href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-public/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0_stac.json", "type": "application/json"}, {"rel": "cite-as", "href": "https://doi.org/10.5067/HLS/HLSL30_VI.002"}], "assets": {"NDVI": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.NDVI.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "NDVI", "common_name": "NDVI"}], "roles": ["data"]}, "EVI": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.EVI.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "EVI", "common_name": "EVI"}], "roles": ["data"]}, "MSAVI": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.MSAVI.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "MSAVI", "common_name": "MSAVI"}], "roles": ["data"]}, "NBR": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.NBR.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "NBR", "common_name": "NBR"}], "roles": ["data"]}, "NBR2": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.NBR2.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "NBR2", "common_name": "NBR2"}], "roles": ["data"]}, "NDMI": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.NDMI.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "NDMI", "common_name": "NDMI"}], "roles": ["data"]}, "NDWI": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.NDWI.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "NDWI", "common_name": "NDWI"}], "roles": ["data"]}, "SAVI": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.SAVI.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "SAVI", "common_name": "SAVI"}], "roles": ["data"]}, "TVI": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.TVI.tif", "type": "image/tiff; application=geotiff; profile=cloud-optimized", "eo:bands": [{"name": "TVI", "common_name": "TVI"}], "roles": ["data"]}, "thumbnail": {"href": "https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-public/HLSL30.020/HLS-VI.L30.T06WVS.2024120T211159.v2.0/HLS-VI.L30.T06WVS.2024120T211159.v2.0.jpg", "type": "image/jpeg", "roles": ["thumbnail"]}}, "bbox": [-149.114568, 63.924491, -146.793616, 64.923996], "stac_extensions": ["https://stac-extensions.github.io/eo/v1.1.0/schema.json", "https://stac-extensions.github.io/projection/v1.1.0/schema.json", "https://stac-extensions.github.io/view/v1.0.0/schema.json", "https://stac-extensions.github.io/scientific/v1.0.0/schema.json"]}