Adding command line interfaces and entry points

docs/workflows/README.MD

@@ -1,4 +1,49 @@
-## Workflows
+# Workflows
 The repository will handle multiple workflows and backends, some of which have specific requirements.
 
-- [pyroSAR + GAMMA](pyrosar_gamma.md)
+## Workflows
+- pyroSAR + GAMMA
+    - [Requirements](pyrosar_gamma.md)
+
+## Command line interface
+> **_NOTE:_**  At this time, pyroSAR + GAMMA is the only workflow, and the command line interfaces have not yet been generalised to other workflows.
+
+The package has a number of useful command line interfaces:
+
+### Finding the location of a scene on the NCI
+The `find-scene` command will display the location of a given scene on the NCI.
+The full path to the scene is required as the input to other commands.
+
+Example usage:
+```
+$ find-scene S1A_EW_GRDM_1SDH_20240129T091735_20240129T091828_052319_065379_0F1E
+
+/path/to/scene/S1A_EW_GRDM_1SDH_20240129T091735_20240129T091828_052319_065379_0F1E.zip
+```
+
+### Submit a workflow
+This will submit a job request to the NCI based on the job parameters and file paths in the supplied config. 
+The [default config](../../sar_antarctica/nci/configs/default.toml) will be used if no other config is provided.
+
+Example usage
+```
+$ submit-pyrosar-gamma-workflow /path/to/scene/S1A_EW_GRDM_1SDH_20240129T091735_20240129T091828_052319_065379_0F1E.zip
+```
+This will submit a job to the NCI with the default config.
+To use a different config, run the command and supply the `--config` option
+```
+--config /path/to/config.toml
+```
+
+### Run a workflow interactively
+If you are still testing a workflow, it is best to run it in an interactive session.
+While in an interactive session, you can run the workflow directly. 
+
+Example usage
+```
+$ run-pyrosar-gamma-workflow /path/to/scene/S1A_EW_GRDM_1SDH_20240129T091735_20240129T091828_052319_065379_0F1E.zip
+```
+To use a different config, run the command and supply the `--config` option
+```
+--config /path/to/config.toml
+```

pyproject.toml

@@ -21,6 +21,12 @@ version = "0.1" # TODO base this on files in proje t
 Homepage = "https://github.com/GeoscienceAustralia/sar-antarctica.git"
 # Documentation = "XXX"
 
+[project.scripts]
+find-scene = "sar_antarctica.nci.cli:find_scene_file"
+find-orbits = "sar_antarctica.nci.cli:find_orbits_for_scene"
+run-pyrosar-gamma-workflow = "sar_antarctica.nci.cli:run_pyrosar_gamma_workflow"
+submit-pyrosar-gamma-workflow = "sar_antarctica.nci.cli:submit_pyrosar_gamma_workflow"
+
 [tool.pytest.ini_options]
 testpaths = ["tests/*"]
 

sar_antarctica/nci/cli.py

@@ -0,0 +1,174 @@
+import click
+from pathlib import Path
+import tomli
+
+from sar_antarctica.nci.filesystem import get_orbits_nci
+from sar_antarctica.nci.submission.pyrosar_gamma.prepare_input import (
+    get_orbit_and_dem,
+)
+from sar_antarctica.nci.preparation.orbits import (
+    filter_orbits_to_cover_time_window,
+)
+from sar_antarctica.nci.preparation.scenes import (
+    parse_scene_file_sensor,
+    parse_scene_file_dates,
+    find_scene_file_from_id,
+)
+from sar_antarctica.nci.processing.pyroSAR.pyrosar_geocode import (
+    run_pyrosar_gamma_geocode,
+)
+from sar_antarctica.nci.submission.pyrosar_gamma.submit_job import submit_job
+
+
+@click.command()
+@click.argument("scene_name", type=str)
+def find_scene_file(scene_name):
+    scene_file = find_scene_file_from_id(scene_name)
+
+    click.echo(scene_file)
+
+
+DEFAULT_CONFIGURATION = Path(__file__).resolve().parent / "configs/default.toml"
+
+
+def configure(ctx, param, filename):
+    with open(filename, "rb") as f:
+        configuration_dictionary = tomli.load(f)
+    ctx.default_map = configuration_dictionary
+
+
+@click.command()
+@click.argument(
+    "scene",
+    type=click.Path(exists=True, dir_okay=False, path_type=Path),
+)
+@click.option(
+    "-c",
+    "--config",
+    type=click.Path(dir_okay=False),
+    default=DEFAULT_CONFIGURATION,
+    callback=configure,
+    is_eager=True,
+    expose_value=False,
+    help="Read option defaults from the specified .toml file",
+    show_default=True,
+)
+@click.option("--spacing", type=int)
+@click.option("--scaling", type=click.Choice(["linear", "db"]))
+@click.option("--ncpu", type=str, default="4")
+@click.option("--mem", type=str, default="32")
+@click.option("--queue", type=str, default="normal")
+@click.option("--project", type=str, default="u46")
+@click.option("--walltime", type=str, default="02:00:00")
+@click.option(
+    "--output-dir",
+    type=click.Path(exists=True, file_okay=False, path_type=Path),
+    default="/g/data/yp75/projects/sar-antractica-processing/pyrosar_gamma/",
+)
+def submit_pyrosar_gamma_workflow(
+    scene, spacing, scaling, ncpu, mem, queue, project, walltime, output_dir
+):
+
+    pbs_parameters = {
+        "ncpu": ncpu,
+        "mem": mem,
+        "queue": queue,
+        "project": project,
+        "walltime": walltime,
+    }
+
+    log_dir = output_dir / "submission/logs"
+    log_dir.mkdir(parents=True, exist_ok=True)
+
+    submit_job(scene, spacing, scaling, pbs_parameters, log_dir)
+
+
+@click.command()
+@click.argument(
+    "scene",
+    type=click.Path(exists=True, dir_okay=False, path_type=Path),
+)
+@click.option(
+    "-c",
+    "--config",
+    type=click.Path(dir_okay=False),
+    default=DEFAULT_CONFIGURATION,
+    callback=configure,
+    is_eager=True,
+    expose_value=False,
+    help="Read option defaults from the specified .toml file",
+    show_default=True,
+)
+@click.option("--spacing", type=int)
+@click.option("--scaling", type=click.Choice(["linear", "db"]))
+@click.option(
+    "--orbit-dir", type=click.Path(exists=True, file_okay=False, path_type=Path)
+)
+@click.option("--orbit-type", type=click.Choice(["POE", "RES", "either"]))
+@click.option(
+    "--output-dir",
+    type=click.Path(exists=True, file_okay=False, path_type=Path),
+    default="/g/data/yp75/projects/sar-antractica-processing/pyrosar_gamma/",
+)
+@click.option(
+    "--gamma-lib-dir",
+    type=click.Path(exists=True, file_okay=False, path_type=Path),
+    default="/g/data/dg9/GAMMA/GAMMA_SOFTWARE-20230712",
+)
+@click.option(
+    "--gamma-env-var",
+    type=str,
+    default="/g/data/yp75/projects/pyrosar_processing/sar-pyrosar-nci:/apps/fftw3/3.3.10/lib:/apps/gdal/3.6.4/lib64",
+)
+def run_pyrosar_gamma_workflow(
+    scene,
+    spacing,
+    scaling,
+    orbit_dir,
+    orbit_type,
+    output_dir,
+    gamma_lib_dir,
+    gamma_env_var,
+):
+
+    click.echo("Preparing orbit and DEM")
+    dem_output_dir = output_dir / "data/dem"
+
+    orbit, dem = get_orbit_and_dem(scene, dem_output_dir, orbit_dir, orbit_type)
+
+    click.echo(f"    Identified orbit: {orbit}")
+    click.echo(f"    Identified DEM: {dem}")
+
+    click.echo("Running processing")
+    print(scene, spacing, scaling, output_dir, gamma_lib_dir, gamma_env_var)
+    run_pyrosar_gamma_geocode(
+        scene=scene,
+        orbit=orbit,
+        dem=dem,
+        output=output_dir,
+        gamma_library=gamma_lib_dir,
+        gamma_env=gamma_env_var,
+        geocode_spacing=spacing,
+        geocode_scaling=scaling,
+    )
+
+
+@click.command()
+@click.argument("scene")
+def find_orbits_for_scene(scene: str):
+    sensor = parse_scene_file_sensor(scene)
+    start_time, stop_time = parse_scene_file_dates(scene)
+
+    poe_paths = get_orbits_nci("POE", sensor)
+    relevent_poe_paths = filter_orbits_to_cover_time_window(
+        poe_paths, start_time, stop_time
+    )
+    for orbit in relevent_poe_paths:
+        print(orbit["orbit"])
+
+    res_paths = get_orbits_nci("RES", sensor)
+    relevant_res_paths = filter_orbits_to_cover_time_window(
+        res_paths, start_time, stop_time
+    )
+    for orbit in relevant_res_paths:
+        print(orbit["orbit"])

sar_antarctica/nci/configs/EW.toml

@@ -0,0 +1,12 @@
+spacing = 40
+scaling = "linear"
+ncpu = "4"
+mem = "64"
+queue = "normal"
+project = "u46"
+walltime = "02:00:00"
+orbit_dir = "/g/data/fj7/Copernicus/Sentinel-1/"
+orbit_type = "POE"
+output_dir = "/g/data/yp75/projects/sar-antractica-processing/pyrosar_gamma/"
+gamma_lib_dir = "/g/data/dg9/GAMMA/GAMMA_SOFTWARE-20230712"
+gamma_env_var = "/g/data/yp75/projects/pyrosar_processing/sar-pyrosar-nci:/apps/fftw3/3.3.10/lib:/apps/gdal/3.6.4/lib64"

sar_antarctica/nci/configs/IW.toml

@@ -0,0 +1,12 @@
+spacing = 10
+scaling = "linear"
+ncpu = "4"
+mem = "128"
+queue = "normal"
+project = "u46"
+walltime = "02:00:00"
+orbit_dir = "/g/data/fj7/Copernicus/Sentinel-1/"
+orbit_type = "POE"
+output_dir = "/g/data/yp75/projects/sar-antractica-processing/pyrosar_gamma_IW/"
+gamma_lib_dir = "/g/data/dg9/GAMMA/GAMMA_SOFTWARE-20230712"
+gamma_env_var = "/g/data/yp75/projects/pyrosar_processing/sar-pyrosar-nci:/apps/fftw3/3.3.10/lib:/apps/gdal/3.6.4/lib64"

sar_antarctica/nci/configs/default.toml

@@ -0,0 +1,12 @@
+spacing = 40
+scaling = "linear"
+ncpu = "4"
+mem = "32"
+queue = "normal"
+project = "u46"
+walltime = "02:00:00"
+orbit_dir = "/g/data/fj7/Copernicus/Sentinel-1/"
+orbit_type = "POE"
+output_dir = "/g/data/yp75/projects/sar-antractica-processing/pyrosar_gamma/"
+gamma_lib_dir = "/g/data/dg9/GAMMA/GAMMA_SOFTWARE-20230712"
+gamma_env_var = "/g/data/yp75/projects/pyrosar_processing/sar-pyrosar-nci:/apps/fftw3/3.3.10/lib:/apps/gdal/3.6.4/lib64"

sar_antarctica/nci/filesystem.py

@@ -1,9 +1,14 @@
 from pathlib import Path
 
 from sar_antarctica.nci.preparation.orbits import find_orbits
+from sar_antarctica.nci.preparation.dem import get_cop30_dem_for_bounds
 
 
-def get_orbits_nci(orbit_type: str | None, sensor: str) -> list[Path]:
+def get_orbits_nci(
+    orbit_type: str | None,
+    sensor: str,
+    nci_orbit_dir: Path = Path("/g/data/fj7/Copernicus/Sentinel-1/"),
+) -> list[Path]:
     """For a given orbit type and sensor, compile the relevant orbit files
 
     Parameters
@@ -12,7 +17,8 @@ def get_orbits_nci(orbit_type: str | None, sensor: str) -> list[Path]:
         One of 'POE', 'RES', or None. If None, both POE and RES orbits will be included
     sensor : str
         Sensor (e.g. S1A or S1B) to search. Typically extracted from the scene ID
-
+    nci_orbit_dir : Path, optional
+        The path containing orbit files on the NCI, by default Path("/g/data/fj7/Copernicus/Sentinel-1/")
     Returns
     -------
     list[Path]
@@ -25,7 +31,6 @@ def get_orbits_nci(orbit_type: str | None, sensor: str) -> list[Path]:
     """
 
     # Constants for NCI
-    S1_DIR = Path("/g/data/fj7/Copernicus/Sentinel-1/")
     POE_DIR = "POEORB"
     RES_DIR = "RESORB"
 
@@ -39,9 +44,22 @@ def get_orbits_nci(orbit_type: str | None, sensor: str) -> list[Path]:
         raise ValueError("orbit_type must be one of 'POE', 'RES', or None")
 
     nci_orbit_directories = [
-        S1_DIR / orbit_dir / sensor for orbit_dir in orbit_type_directories
+        nci_orbit_dir / orbit_dir / sensor for orbit_dir in orbit_type_directories
     ]
 
     orbits = find_orbits(nci_orbit_directories)
 
     return orbits
+
+
+def get_dem_nci(
+    scene: Path, scene_bounds: tuple[float, float, float, float], output_dir: Path
+) -> Path:
+    if not output_dir.exists():
+        output_dir.mkdir(parents=True, exist_ok=True)
+    dem_file = output_dir / f"{scene.stem}.tif"
+
+    if not dem_file.exists():
+        _, _ = get_cop30_dem_for_bounds(scene_bounds, dem_file, ellipsoid_heights=True)
+
+    return dem_file