Initial reformat with black

check_gamma_modules.py

@@ -7,7 +7,7 @@
 REQUIRED_LIBS_PATH = "/g/data/yp75/projects/pyrosar_processing/sar-pyrosar-nci"
 
 if os.environ.get("GAMMA_HOME", None) is None:
-    
+
     print(f"Setting GAMMA to {GAMMA_HOME_PATH}")
     os.environ["GAMMA_HOME"] = GAMMA_HOME_PATH
 
@@ -21,23 +21,39 @@
 else:
     print(os.environ.get("LD_LIBRARY_PATH"))
 
-commands_to_skip = ["coord_trans", "phase_sum", "dishgt", "SLC_cat", "ras_ratio_dB", "ptarg"]
+commands_to_skip = [
+    "coord_trans",
+    "phase_sum",
+    "dishgt",
+    "SLC_cat",
+    "ras_ratio_dB",
+    "ptarg",
+]
 
-for module in finder(GAMMA_HOME_PATH, ['[A-Z]*'], foldermode=2):
+for module in finder(GAMMA_HOME_PATH, ["[A-Z]*"], foldermode=2):
     print(module)
-    for submodule in ['bin', 'scripts']:
+    for submodule in ["bin", "scripts"]:
         print(f"{module}/{submodule}")
-        for cmd in sorted(finder(module+"/"+submodule, [r'^\w+$'], regex=True), key=lambda s: s.lower()):
+        for cmd in sorted(
+            finder(module + "/" + submodule, [r"^\w+$"], regex=True),
+            key=lambda s: s.lower(),
+        ):
             command_base = os.path.basename(cmd)
             if command_base in commands_to_skip:
                 print("    skipping " + command_base)
             else:
-                
+
                 print("  " + command_base)
-                proc = sp.Popen(cmd, stdin=sp.PIPE, stdout=sp.PIPE, stderr=sp.PIPE, universal_newlines=True)
+                proc = sp.Popen(
+                    cmd,
+                    stdin=sp.PIPE,
+                    stdout=sp.PIPE,
+                    stderr=sp.PIPE,
+                    universal_newlines=True,
+                )
                 out, err = proc.communicate()
                 out += err
-                usage = re.search('usage:.*(?=\n)', out)
+                usage = re.search("usage:.*(?=\n)", out)
                 if usage is None:
                     print("    " + err)
-        print("\n\n")
+        print("\n\n")

sar_antarctica/nci/preparation/create_config.py

@@ -7,7 +7,16 @@
 from sar_antarctica.nci.preparation.orbits import find_latest_orbit_for_scene
 from sar_antarctica.nci.preparation.dem import get_cop30_dem_for_bounds
 
-def write_file_paths(config_file: Path, scene_file: Path, orbit_file: Path, dem_file: Path, data_dir: Path, ancillary_dir="ancillary", processed_dir="processed_scene"):
+
+def write_file_paths(
+    config_file: Path,
+    scene_file: Path,
+    orbit_file: Path,
+    dem_file: Path,
+    data_dir: Path,
+    ancillary_dir="ancillary",
+    processed_dir="processed_scene",
+):
     inputs_header = "[inputs]\n"
     scene_setting = f"scene = '{str(scene_file)}'\n"
     orbit_setting = f"orbit = '{str(orbit_file)}'\n"
@@ -19,21 +28,24 @@ def write_file_paths(config_file: Path, scene_file: Path, orbit_file: Path, dem_
     processed_setting = f"processed = '{processed_dir}'\n"
 
     with open(config_file, "w") as cf:
-        cf.writelines([
-            inputs_header, 
-            scene_setting, 
-            orbit_setting,
-            dem_setting, 
-            "\n", 
-            outputs_header, 
-            data_path_setting,
-            ancillary_setting,
-            processed_setting
-        ])
-
+        cf.writelines(
+            [
+                inputs_header,
+                scene_setting,
+                orbit_setting,
+                dem_setting,
+                "\n",
+                outputs_header,
+                data_path_setting,
+                ancillary_setting,
+                processed_setting,
+            ]
+        )
+
+
 @click.command()
 @click.argument("scene_id", nargs=1)
-@click.argument('scene_config', nargs=1)
+@click.argument("scene_config", nargs=1)
 def main(scene_id: str, scene_config: str):
     print(f"Processing scene: {scene_id} \n")
 
@@ -52,22 +64,24 @@ def main(scene_id: str, scene_config: str):
     # Identify bounds of scene and use bounding box to build DEM
     scene = identify(str(scene_file))
     scene_bbox = scene.bbox().extent
-    scene_bounds = (scene_bbox["xmin"], scene_bbox["ymin"], scene_bbox["xmax"], scene_bbox["ymax"])
+    scene_bounds = (
+        scene_bbox["xmin"],
+        scene_bbox["ymin"],
+        scene_bbox["xmax"],
+        scene_bbox["ymax"],
+    )
 
     # Set path for dem and create
     dem_dir = data_dir / "dem"
     dem_file = dem_dir / f"{scene_id}_dem.tif"
-    _, _ = get_cop30_dem_for_bounds(bounds=scene_bounds, save_path=dem_file, ellipsoid_heights=True)
+    _, _ = get_cop30_dem_for_bounds(
+        bounds=scene_bounds, save_path=dem_file, ellipsoid_heights=True
+    )
 
     # Write to config file
-    write_file_paths(
-        config_file, 
-        scene_file, 
-        latest_poe_file, 
-        dem_file, 
-        data_dir
-    )
+    write_file_paths(config_file, scene_file, latest_poe_file, dem_file, data_dir)
+
 
 if __name__ == "__main__":
 
-    main()
+    main()

sar_antarctica/nci/preparation/create_dem_vrt.py

@@ -2,6 +2,7 @@
 from pathlib import Path
 from typing import Generator
 
+
 def find_tiles(source_dir: Path, pattern: str) -> Generator[Path, None, None]:
     """_summary_
 
@@ -24,7 +25,12 @@ def find_tiles(source_dir: Path, pattern: str) -> Generator[Path, None, None]:
 
     return tiles
 
-def build_vrt(tiles: Generator[Path, None, None] | list[Path], vrt_path: str | os.PathLike, run: bool = True):
+
+def build_vrt(
+    tiles: Generator[Path, None, None] | list[Path],
+    vrt_path: str | os.PathLike,
+    run: bool = True,
+):
     """Generic function for building a VRT from a generator of tile paths
 
     Parameters
@@ -42,11 +48,16 @@ def build_vrt(tiles: Generator[Path, None, None] | list[Path], vrt_path: str | o
         f.writelines(f"{tile}\n" for tile in tiles)
 
     if run:
-        os.system(f'gdalbuildvrt -input_file_list temp.txt {vrt_path}')
+        os.system(f"gdalbuildvrt -input_file_list temp.txt {vrt_path}")
 
         os.remove("temp.txt")
 
-def build_tileindex(tiles: Generator[Path, None, None] | list[Path], tindex_path: str | os.PathLike, run: bool = True):
+
+def build_tileindex(
+    tiles: Generator[Path, None, None] | list[Path],
+    tindex_path: str | os.PathLike,
+    run: bool = True,
+):
     """Generic function for building a tile index from a generator of tile paths
 
     Parameters
@@ -64,18 +75,18 @@ def build_tileindex(tiles: Generator[Path, None, None] | list[Path], tindex_path
         f.writelines(f"{tile}\n" for tile in tiles)
 
     if run:
-        os.system(f'gdaltindex {tindex_path} --optfile temp.txt')
+        os.system(f"gdaltindex {tindex_path} --optfile temp.txt")
 
         os.remove("temp.txt")
 
+
 def create_glo30_dem_south_vrt():
-    """Create a VRT for the Copernicus Global 30m DEM on NCI
-    """
-
+    """Create a VRT for the Copernicus Global 30m DEM on NCI"""
+
     SOURCE_DIR = Path("/g/data/v10/eoancillarydata-2/elevation/copernicus_30m_world")
     PATTERN = "Copernicus_DSM_COG_10_S??_00_????_00_DEM/*.tif"
     VRT_PATH = Path("/g/data/yp75/projects/ancillary/dem/copdem_south.vrt")
 
     tiles = find_tiles(SOURCE_DIR, PATTERN)
 
-    build_vrt(tiles, VRT_PATH)
+    build_vrt(tiles, VRT_PATH)