Dev

.github/workflows/update_pr_description.yml

@@ -17,16 +17,13 @@ jobs:
         uses: actions/checkout@v4
         # We need to fetch the history up to the base branch
         with:
-          fetch-depth: 0
-          ref: ${{ github.event.pull_request.head.sha }}
+          fetch-depth: 0 
 
       - name: ⚙️ Get Commit List and Format
         id: commit_list
         run: |
-          BASE_BRANCH="origin/${{ github.event.pull_request.base.ref }}"
+          COMMIT_LIST=$(git log --pretty=format:"* %s (%an, %ad)" ${{ github.event.pull_request.base.sha }}..HEAD)
 
-          COMMIT_LIST=$(git log --pretty=format:"* %s (%an, %ad)" $BASE_BRANCH..HEAD)
-
           FORMATTED_LIST="## 📦 Commits Included in this PR:\n\n${COMMIT_LIST}"
 
           echo "FORMATTED_LIST<<EOF" >> $GITHUB_ENV

README.md

@@ -1,4 +1,10 @@
 # SEN2SR Tools
+
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FMiguelPadillaR%2Fsen2sr-tools%2Fmain%2Fpyproject.toml)
+ [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+ ![Status: Active](https://img.shields.io/badge/Status-Active-00aa00.svg)
+![Code style: Ruff](https://img.shields.io/badge/code%20style-autopep8-aa0000.svg)
+
 This repository provides a list of comprehensive tools and utilities for the usage of the [SEN2SR](https://github.com/ESAOpenSR/SEN2SR.git) neural network super-resolution model, developed by the [ESAOpenSR](https://opensr.eu/) team. This model specializes in upscaling Sentinel-2's 10m/px images up to a x4 times improvement of 2.5m/px.
 
 This package implements a feature to crop a polygon directly from the SR image, useful for close-up satellite observation of agricultural states.
@@ -15,38 +21,49 @@ This package implements a feature to crop a polygon directly from the SR image,
     source venv/bin/activate   # On Windows use `venv\Scripts\activate`
     pip install -e .
     ```
-
+## Quickstart example
+The overall workflow can be run directly, since it implements a simple example in it:
+```shell
+cd sen2sr-tools
+python -m sen2sr_tools.get_sr_image
+```
+The example can also be run using commands:
+```shell
+python -m sen2sr_tools get-sr-image --latitude 42.465226 --longitude -2.292699 --start-date 2025-11-01 --end-date 2025-11-15 --geojson-path ./example.geojson
+```
+Output will be at `sen2sr_out`, where the SR and original images can be seen.
 ## Usage in Python
+All relevant methods are stored in the `get_sr_image` module.
 
 ### Get a SR image
 
-It runs the full workflow, from date and location data to super resolved image. Default `size` is 128 px, and it must be a multiple of 32. Default `bands` are Near-Infrared, Red, Blue, Green and the Scene Classification Layer, that contains cloud density information among others. Cropping a polygon from the image is optional, provided the GeoJSON filepath.
+Using `get_sr_image` runs the full workflow, from date and location data to super resolved image. Default `size` is the minimal requested 128px. Default `bands` are Near-Infrared, Red, Blue, Green and the Scene Classification Layer, that contains cloud density information among others. Cropping a polygon from the image is optional, provided the GeoJSON filepath. The final image outputs are in TIF and PNG formats, for usage and visualization respectively.
 
 ```python
 from sen2sr_tools.get_sr_image import get_sr_image
 
 lat = 37.265840
 lng = -4.593406 
-start_date = "2025-11-1"
+start_date = "2025-11-01"
 end_date = "2025-11-15"
 # bands = ["B08", "B02", "B03", "B04", "SCL"]       # Default bands
 # size = 128                                        # Default size
-# geojson_path = None                               # Default value
+# geometry = None                                   # Default value
 
 sr_filepath = get_sr_image(lat, lng, bands, start_date, end_date)
 
 print(f"SR image successfully downloaded and saved at: {sr_filepath}")
 ```
 ### Download CUBO
 
-It serves the requested bands' data directly. It uses the date range to get cloudless (<=1%) images. The `crs` can be provided (i.e, "EPSG:32630"), but it can also be automatically calculated from the `lat` and `lon` arguments. If no requested data was found within the date range, it retries with by expanding it backwards in time.
+Running `download_sentinel_cubo` serves the requested bands' data directly. It uses the date range to get cloudless (<=1%) images. The `crs` can be provided (i.e, "EPSG:32630"), but it can also be automatically calculated from the `lat` and `lon` arguments. If no requested data is found within the date range, it retries with by expanding it backwards in time. The CUBO data is provided as a `Dask.array`.
 
 ```python
 from sen2sr_tools.get_sr_image import download_sentinel_cubo
 
 lat = 37.265840
 lng = -4.593406 
-start_date = "2025-11-1"
+start_date = "2025-11-01"
 end_date = "2025-11-15"
 # crs = None                                   # Default CRS
 # bands = ["B08", "B02", "B03", "B04", "SCL"]  # Default bands
@@ -55,22 +72,38 @@ end_date = "2025-11-15"
 # max_retries = 3                              # Default retries
 # retry_days_shift = 15                        # Default shift
 
-cloudless_image_data_array, sample_date = download_sentinel_cubo(lat, lon, start_date, end_date):
+cloudless_cubo_data_array, sample_date = download_sentinel_cubo(lat, lon, start_date, end_date)
+
+print(f"CUBO data summary:\n\n{cloudless_cubo_data_array.coords}")
+
+# If you need the array as NumPy
+# cubo_np_array = (cloudless_cubo_data_array.astype("float32") / 10_000).compute()
 ```
+
 ### Crop parcel from image
 
-It crops the polygon from the given TIF file and returns the cropped image as PNG.
+The `crop_parcel_from_tif` method crops the polygon from the given TIF file and returns the cropped image output and metadata.
 
 ```python
-from sen2sr_tools.get_sr_image import crop_png_from_tif
+import json
+import geopandas as gpd
+from sen2sr_tools.get_sr_image import crop_parcel_from_tif
 
-raster_path = "path/to/file.tif"
-geojson_path = "path/to/polygon.geojson"
-date = "2025-11-1"
+gdf = gpd.read_file(geometry)
 
-out_png_path = crop_png_from_tif(raster_path, geojson_path, date)
-
-print(f"Polygon successfully cropped and saved at: {out_png_path}")
+raster_path = "path/to/file.tif"
+geometry = {
+    "type": "Polygon",
+    "coordinates": [[
+        [-2.29544172799985, 42.46242962302221],[-2.292531924994703, 42.46538599420777],
+        [-2.292180580738519, 42.463584097818824], [-2.286733836169323, 42.464620125420105],
+        [-2.29544172799985, 42.46242962302221]
+    ]], 
+    "CRS": "epsg:4258"}
+
+out_image, out_meta = crop_parcel_from_tif(raster_path, geojson_path)
+
+print(f"Polygon successfully cropped!")
 ```
 
 ## Attribution and License

pyproject.toml

@@ -8,6 +8,16 @@ authors = [
 license = "MIT"
 readme = "README.md"
 requires-python = ">=3.10"
+classifiers = [
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Development Status :: 1 - Planning",
+    "License :: OSI Approved :: MIT License",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: GIS",
+    "Topic :: Scientific/Engineering :: SR",
+    "Topic :: Utilities"
+]
 dependencies = [
     "cubo",
     "mlstac",
@@ -19,14 +29,17 @@ dependencies = [
     "structlog",
     "xarray",
     "pillow",
+    "matplotlib",
     "opencv-python (>=4.11, <4.12)",
     "numpy (>=1.9, <2.0.0)"
 ]
 
 [project.urls]
-"Homepage" = "https://github.com/KhaosResearch/sigpac-tools"
-"Bug Tracker" = "https://github.com/KhaosResearch/sigpac-tools/issues"
+"Homepage" = "https://github.com/MiguelPadillaR/sen2sr-tools"
+"Bug Tracker" = "https://github.com/MiguelPadillaR/sen2sr-tools/issues"
 
+[project.optional-dependencies]
+dev = ["autopep8", "pytest"]
 
 [build-system]
 requires = ["poetry-core>=2.0.0,<3.0.0"]

sen2sr_tools/__main__.py

@@ -6,6 +6,11 @@
 
 logger = structlog.get_logger()
 
+class VerboseArgumentParser(argparse.ArgumentParser):
+    def error(self, message):
+        raise RuntimeError(f"Argument error: {message}")
+
+
 # --- Helper to load dynamic logic and run command ---
 
 def run_command(command_name: str, args: argparse.Namespace):
@@ -18,27 +23,29 @@ def run_command(command_name: str, args: argparse.Namespace):
             crop_png_from_tif,
         )
     except ImportError:
-        logger.error(f"Could not import logic from sen2sr_tools.get_sr_image. Ensure the package is installed in editable mode.")
+        logger.error(f"Could not import logic from sen2sr_tools.get-sr-image. Ensure the package is installed in editable mode.")
         sys.exit(1)
 
     # Dispatch logic based on command
-    if command_name == "get_sr_image":
+    if command_name == "get-sr-image":
         logger.info("Starting Super Resolution task", 
                     latitude=args.latitude, longitude=args.longitude, 
-                    start_date=args.start_date, end_date=args.end_date)
-
+                    start_date=args.start_date, end_date=args.end_date,
+                    geometry=args.geometry
+        )
         result = get_sr_image(
             lat=args.latitude, 
             lon=args.longitude, 
             bands=args.bands, 
             start_date=args.start_date, 
             end_date=args.end_date, 
-            size=args.size
+            size=args.size,
+            geometry=args.geometry
         )
         logger.info(f"✅ Get SR Image task completed. Result (filepath):\n{result}")
         return result
 
-    elif command_name == "download_cubo":
+    elif command_name == "download-cubo":
         logger.info("Starting Sentinel-2 Cubo download", start_date=args.start_date, end_date=args.end_date)
 
         # Note: The download function returns two values, we'll only print the path/date for CLI feedback
@@ -53,9 +60,9 @@ def run_command(command_name: str, args: argparse.Namespace):
             cloud_threshold=args.cloud_threshold
         )
         logger.info(f"✅ Download successful for acquisition date: {date}")
-        return date
+        return data, date
 
-    elif command_name == "crop_parcel":
+    elif command_name == "crop-polygon":
         logger.info("Starting parcel cropping.", tif_path=args.raster_path)
 
         # Note: The crop function needs a `date` string as the second argument,
@@ -65,52 +72,56 @@ def run_command(command_name: str, args: argparse.Namespace):
 
         out_path = crop_png_from_tif(
             raster_path=args.raster_path, 
+            geometry=args.geometry, 
             date=args.acquisition_date
         )
         logger.info(f"✅ Cropping successful. Output path: {out_path}")
         return out_path
-
-
+
 # --- Argument Parser Setup ---
 
 def get_parser():
-    parser = argparse.ArgumentParser(description="SEN2SR Tools: Command Line Interface for Sentinel-2 Super Resolution.")
+    parser = VerboseArgumentParser(description="SEN2SR Tools: Command Line Interface for Sentinel-2 Super Resolution.")
 
     subparsers = parser.add_subparsers(
         dest="command", help="Available commands")
     subparsers.required = True
 
     # =========================================================================
-    # 1. get_sr_image (Main Function)
+    # 1. get-sr-image (Main Function)
     # =========================================================================
     get_sr_image_parser = subparsers.add_parser(
-        "get_sr_image", help="Get SR image from downloaded Sentinel's imagery data and load up SEN2SR model to Super-Resolve it."
+        "get-sr-image", help="Get SR image from downloaded Sentinel's imagery data and load up SEN2SR model to Super-Resolve it."
     )
     get_sr_image_parser.add_argument(
         "--latitude", type=float, help="Latitude coordinate component (e.g., 37.265840).", required=True, metavar="FLOAT",
     )
     get_sr_image_parser.add_argument(
         "--longitude", type=float, help="Longitude coordinate component (e.g., -4.593406).", required=True, metavar="FLOAT",
     )
-    get_sr_image_parser.add_argument(
-        "--bands", nargs='+', default=["B08", "B02", "B03", "B04", "SCL"], 
-        help="Image bands to retrieve (space-separated, e.g., B08 B02 B03 B04 SCL).", required=False, metavar="STR [...]",
-    )
     get_sr_image_parser.add_argument(
         "--start-date", type=str, help="Initial date in search range in ISO format (yyyy-mm-dd).", required=True, metavar="STR",
     )
     get_sr_image_parser.add_argument(
         "--end-date", type=str, help="Final date in search range in ISO format (yyyy-mm-dd).", required=True, metavar="STR",
     )
+    get_sr_image_parser.add_argument(
+        "--bands", nargs='+', default=["B08", "B02", "B03", "B04", "SCL"], 
+        help="Image bands to retrieve (space-separated, e.g., B08 B02 B03 B04 SCL).", required=False,
+    )
     get_sr_image_parser.add_argument(
         "--size", type=int, default=128, help="Size of the image tile in pixels (e.g., 128 for 128x128).", required=False, metavar="INT",
     )
+    get_sr_image_parser.add_argument(
+        "--geojson-path", type=str, default="", help="GeoJSON to crop SR image filepath. If none is provided, it downloads the image in sizexsize", metavar="STR",
+    )
+
 
     # =========================================================================
     # 2. download_cubo (Helper Function)
     # =========================================================================
     download_cubo_parser = subparsers.add_parser(
-        "download_cubo", help="Download raw Sentinel-2 imagery data using Cubo and filter for cloudless data."
+        "download-cubo", help="Download raw Sentinel-2 imagery data using Cubo and filter for cloudless data."
     )
     # Re-use common arguments
     download_cubo_parser.add_argument(
@@ -119,15 +130,15 @@ def get_parser():
     download_cubo_parser.add_argument(
         "--longitude", type=float, help="Longitude coordinate component.", required=True, metavar="FLOAT",
     )
-    download_cubo_parser.add_argument(
-        "--bands", nargs='+', default=["B08", "B02", "B03", "B04", "SCL"], help="Image bands to retrieve.", metavar="STR [...]",
-    )
     download_cubo_parser.add_argument(
         "--start-date", type=str, help="Initial date in search range (yyyy-mm-dd).", required=True, metavar="STR",
     )
     download_cubo_parser.add_argument(
         "--end-date", type=str, help="Final date in search range (yyyy-mm-dd).", required=True, metavar="STR",
     )
+    download_cubo_parser.add_argument(
+        "--bands", nargs='+', default=["B08", "B02", "B03", "B04", "SCL"], help="Image bands to retrieve.",
+    )
     download_cubo_parser.add_argument(
         "--size", type=int, default=128, help="Size of the image tile in pixels.", metavar="INT",
     )
@@ -139,15 +150,15 @@ def get_parser():
         "--cloud-threshold", type=float, default=0.01, help="Max percentage of cloud density tolerated (0.0 to 1.0).", metavar="FLOAT",
     )
     download_cubo_parser.add_argument(
-        "--polygon-path", type=str, default="", help="GeoJSON to crop SR image filepath. If none is provided, it downloads the image in sizexsize", metavar="STR",
+        "--geojson-path", type=str, default="", help="GeoJSON to crop SR image filepath. If none is provided, it downloads the image in sizexsize", metavar="STR",
     )
 
 
     # =========================================================================
     # 3. crop_parcel (Helper Function)
     # =========================================================================
     crop_parcel_parser = subparsers.add_parser(
-        "crop_parcel", help="Crops a parcel from a Super-Resolved TIF using a local GeoJSON file."
+        "crop-polygon", help="Crops a parcel from a Super-Resolved TIF using a local GeoJSON file."
     )
     crop_parcel_parser.add_argument(
         "--raster-path", type=Path, help="Path to the uncropped SR TIF image.", required=True, metavar="PATH",
@@ -161,13 +172,16 @@ def get_parser():
         "--acquisition-date", type=str, help="Acquisition date (yyyy-mm-dd) used to name the output file.", required=True, metavar="STR",
     )
 
+    return parser
 
 def main():
     args = get_parser().parse_args() 
 
     # Run the command
-    run_command(args.command, args)
+    result = run_command(args.command, args)
 
+    logger.info(f"RESULT:")
+    logger.info(f"{result}")
 
 if __name__ == "__main__":
-    main()
+    main()

sen2sr_tools/constants.py

@@ -5,7 +5,9 @@
 
 CURR_SCRIPT_DIR = Path.Path(os.path.dirname(os.path.abspath(__file__)))
 
-MODEL_DIR = str(CURR_SCRIPT_DIR / "model")
+MODEL_DIR = CURR_SCRIPT_DIR / "model"
+RGBN_MODEL_DIR = str(MODEL_DIR / "SEN2SRLite_RGBN")
+MAIN_MODEL_DIR = str(MODEL_DIR / "SEN2SRLite")
 SEN2SR_SR_DIR = CURR_SCRIPT_DIR / "sen2sr_out"
 PNG_DIR = SEN2SR_SR_DIR / "png"
 TIF_DIR = SEN2SR_SR_DIR / "tif"