tidy python

water-bodies/command-line-tools/crop/app.py

@@ -1,20 +1,21 @@
+"""Crop a STAC Item asset defined with its common band name"""
 import os
-import click
 from urllib.parse import urlparse
+import click
 from osgeo import gdal
 import pystac
 
 gdal.UseExceptions()
-settings = None
+SETTINGS = None
 
 
 def aoi2box(aoi):
-
+    """Converts an area of interest expressed as a bounding box to a list of floats"""
     return [float(c) for c in aoi.split(",")]
 
 
 def get_common_name(asset):
-
+    """Returns the common band name of a STAC Item asset"""
     if "eo:bands" in asset.to_dict().keys():
         if "common_name" in asset.to_dict()["eo:bands"][0].keys():
             return asset.to_dict()["eo:bands"][0]["common_name"]
@@ -23,9 +24,8 @@ def get_common_name(asset):
 
 
 def get_asset(item, common_name):
-
+    """Returns the asset of a STAC Item defined with its common band name"""
     for _, asset in item.get_assets().items():
-
         if not "data" in asset.to_dict()["roles"]:
             continue
 
@@ -41,20 +41,21 @@ def get_asset(item, common_name):
 
 
 def vsi_href(uri):
-
+    """Returns the VSI path of a URI"""
     parsed = urlparse(uri)
 
     if parsed.scheme.startswith("http"):
-        return "/vsicurl/{}".format(uri)
-    elif parsed.scheme.startswith("file"):
+        return f"/vsicurl/{uri}"
+    if parsed.scheme.startswith("file"):
         return uri.replace("file://", "")
-    elif parsed.scheme.startswith("s3"):
-        if settings:
-            for key, value in settings._asdict().items():
+
+    if parsed.scheme.startswith("s3"):
+        if SETTINGS:
+            for key, value in SETTINGS._asdict().items():
                 gdal.SetConfigOption(key, value)
-        return "/vsis3/{}".format(uri.strip("s3://"))
-    else:
-        return uri
+        return f"/vsis3/{uri.strip('s3://')}"
+
+    return uri
 
 
 @click.command(
@@ -86,7 +87,7 @@ def vsi_href(uri):
     required=True,
 )
 def crop(item_url, aoi, band, epsg):
-
+    """Crops a STAC Item asset defined with its common band name"""
     if os.path.isdir(item_url):
         catalog = pystac.read_file(os.path.join(item_url, "catalog.json"))
         item = next(catalog.get_items())

water-bodies/command-line-tools/norm_diff/app.py

@@ -1,15 +1,18 @@
+"""Normalized difference"""
 import click
 from osgeo import gdal
 import numpy as np
 
+gdal.UseExceptions()
 
 @click.command(
     short_help="Normalized difference",
     help="Performs a normalized difference",
 )
 @click.argument("rasters", nargs=2)
 def normalized_difference(rasters):
-
+    """Performs a normalized difference"""
+
     # Allow division by zero
     np.seterr(divide="ignore", invalid="ignore")
 
@@ -40,6 +43,5 @@ def normalized_difference(rasters):
     dst_ds = None
     ds1 = ds2 = None
 
-
 if __name__ == "__main__":
     normalized_difference()

water-bodies/command-line-tools/otsu/app.py

@@ -1,11 +1,12 @@
-from skimage.filters import threshold_otsu
+"""Command line tool to apply the Otsu threshold to a raster"""
 import click
-from osgeo import gdal
 import numpy as np
+from osgeo import gdal
+from skimage.filters import threshold_otsu
 
 
 def threshold(data):
-
+    """Returns the Otsu threshold of a numpy array"""
     return data > threshold_otsu(data[np.isfinite(data)])
 
 
@@ -15,7 +16,7 @@ def threshold(data):
 )
 @click.argument("raster", nargs=1)
 def otsu(raster):
-
+    """Applies the Otsu threshold"""
     ds = gdal.Open(raster)
 
     driver = gdal.GetDriverByName("GTiff")

water-bodies/command-line-tools/stac/app.py

@@ -1,8 +1,9 @@
+"""Creates a STAC catalog with the detected water bodies""" ""
+import os
+import shutil
 import click
 import pystac
 import rio_stac
-import shutil
-import os
 
 
 @click.command(
@@ -24,18 +25,16 @@
     multiple=True,
 )
 def to_stac(item_urls, water_bodies):
-
+    """Creates a STAC catalog with the detected water bodies"""
     cat = pystac.Catalog(id="catalog", description="water-bodies")
 
     for index, item_url in enumerate(item_urls):
-
         if os.path.isdir(item_url):
             catalog = pystac.read_file(os.path.join(item_url, "catalog.json"))
             item = next(catalog.get_items())
         else:
             item = pystac.read_file(item_url)
 
-
         water_body = water_bodies[index]
 
         os.mkdir(item.id)
@@ -58,11 +57,6 @@ def to_stac(item_urls, water_bodies):
         root_href="./", catalog_type=pystac.CatalogType.SELF_CONTAINED
     )
 
-    # for index, water_body in enumerate(water_bodies):
-    #     item = pystac.read_file(item_urls[index])
-
-    #     shutil.copy(water_body, item.id)
-
 
 if __name__ == "__main__":
     to_stac()