Remove GDAL's Python bindings

CHANGELOG.md

@@ -10,6 +10,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - Use [pytest](https://docs.pytest.org/) for unit testing instead of `unittest` ([#220](https://github.com/stac-utils/stactools/pull/220))
+- Signature of `stactools.core.utils.convert.cogify` ([#222](https://github.com/stac-utils/stactools/pull/222))
+
+### Removed
+
+- GDAL Python bindings dependency ([#222](https://github.com/stac-utils/stactools/pull/222))
 
 ## [0.2.5] - 2022-01-03
 

setup.cfg

@@ -31,16 +31,15 @@ packages = find_namespace:
 zip_safe = False
 include_package_data = True
 install_requires =
-    pystac[validation] ~= 1.2
+    Shapely ~= 1.7
     aiohttp ~= 3.7
     click ~= 8.0
     fsspec ~= 2021.7
-    requests ~= 2.25
-    Shapely ~= 1.7
+    lxml ~= 4.6
     pyproj ~= 3.0
+    pystac[validation] ~= 1.2
     rasterio ~= 1.2
-    lxml ~= 4.6
-    GDAL ~= 3.3.2
+    requests ~= 2.25
 
 [options.extras_require]
 all =

src/stactools/core/addraster.py

@@ -1,14 +1,16 @@
 import logging
+from typing import List
 
-from osgeo import gdal
+import numpy
 from pystac import Item
 from pystac.utils import make_absolute_href
 from pystac.extensions.raster import (DataType, Histogram, RasterBand,
                                       RasterExtension, Statistics)
+import rasterio
 
 logger = logging.getLogger(__name__)
 
-NUM_BUCKETS = 256
+BINS = 256
 
 
 def add_raster_to_item(item: Item) -> Item:
@@ -25,27 +27,29 @@ def add_raster_to_item(item: Item) -> Item:
     for asset in item.assets.values():
         if asset.roles and "data" in asset.roles:
             raster = RasterExtension.ext(asset)
-            bands = []
             href = make_absolute_href(asset.href, item.get_self_href())
-            dataset = gdal.Open(href, gdal.GA_ReadOnly)
-            for nband in range(dataset.RasterCount):
-                gdal_band = dataset.GetRasterBand(nband + 1)
-                band = RasterBand.create()
-                band.nodata = gdal_band.GetNoDataValue()
-                band.spatial_resolution = dataset.GetGeoTransform()[1]
-                band.data_type = DataType(
-                    gdal.GetDataTypeName(gdal_band.DataType).lower())
-                minimum = gdal_band.GetMinimum()
-                maximum = gdal_band.GetMaximum()
-                if not minimum or not max:
-                    minimum, maximum = gdal_band.ComputeRasterMinMax(True)
-                band.statistics = Statistics.create(minimum=minimum,
-                                                    maximum=maximum)
-                hist_data = gdal_band.GetHistogram(minimum, maximum,
-                                                   NUM_BUCKETS)
-                band.histogram = Histogram.create(NUM_BUCKETS, minimum,
-                                                  maximum, hist_data)
-                bands.append(band)
+            bands = _read_bands(href)
             if bands:
                 raster.apply(bands)
     return item
+
+
+def _read_bands(href: str) -> List[RasterBand]:
+    bands = []
+    with rasterio.open(href) as dataset:
+        for (i, index) in enumerate(dataset.indexes):
+            data = dataset.read(index, masked=True)
+            band = RasterBand.create()
+            band.nodata = dataset.nodatavals[i]
+            band.spatial_resolution = dataset.transform[0]
+            band.data_type = DataType(dataset.dtypes[i])
+            minimum = float(numpy.min(data))  # type: ignore
+            maximum = float(numpy.max(data))  # type: ignore
+            band.statistics = Statistics.create(minimum=minimum,
+                                                maximum=maximum)
+            hist_data, _ = numpy.histogram(  # type: ignore
+                data, range=(minimum, maximum), bins=BINS)
+            band.histogram = Histogram.create(BINS, minimum, maximum,
+                                              hist_data.tolist())
+            bands.append(band)
+    return bands

src/stactools/core/utils/convert.py

@@ -1,25 +1,27 @@
-from typing import List, Optional
+from typing import Dict, Any, Optional
 
-from stactools.core.utils.subprocess import call
-from stactools.core.utils import gdal_driver_is_enabled
+import rasterio
+import rasterio.shutil
+from rasterio.errors import DriverRegistrationError
 
-DEFAULT_COGIFY_ARGS = ["-co", "compress=deflate"]
+from stactools.core import utils
+
+DEFAULT_PROFILE = {
+    "compress": "deflate",
+    "driver": "COG",
+    "blocksize": 512,
+}
 
 
 def cogify(infile: str,
            outfile: str,
-           args: Optional[List[str]] = None,
-           extra_args: Optional[List[str]] = None) -> int:
+           profile: Optional[Dict[str, Any]] = None) -> None:
     """Creates a COG from a GDAL-readable file."""
-    if not gdal_driver_is_enabled("COG"):
-        raise Exception(
-            "GDAL's COG driver is not enabled. "
-            "Please make sure your GDAL version is 3.1 or greater.")
-    if args is None:
-        args = DEFAULT_COGIFY_ARGS[:]
-    args = ["gdal_translate", "-of", "COG"] + args
-    if extra_args:
-        args.extend(extra_args)
-    args.append(infile)
-    args.append(outfile)
-    return call(args)
+    if not utils.gdal_driver_is_enabled("COG"):
+        raise DriverRegistrationError(
+            "GDAL's COG driver is not enabled, make sure you're using GDAL >= 3.1"
+        )
+    destination_profile = DEFAULT_PROFILE.copy()
+    if profile:
+        destination_profile.update(profile)
+    rasterio.shutil.copy(infile, outfile, **destination_profile)

tests/cli/commands/expected/rasterbands.json

@@ -267,7 +267,7 @@
         0,
         0,
         1,
-        2
+        3
       ]
     }
   },
@@ -539,7 +539,7 @@
         2,
         7,
         7,
-        7
+        8
       ]
     }
   },
@@ -811,7 +811,7 @@
         0,
         1,
         1,
-        2
+        3
       ]
     }
   },
@@ -1083,7 +1083,7 @@
         0,
         1,
         0,
-        0
+        1
       ]
     }
   }

tests/cli/commands/test_addraster.py

@@ -39,4 +39,6 @@ def test_add_raster_to_item(self):
             asset = item.get_assets().get("analytic")
             assert asset is not None
             expected = expected_json("rasterbands.json")
-            assert expected == asset.to_dict().get("raster:bands")
+            self.maxDiff = None
+            for a, b in zip(expected, asset.to_dict().get("raster:bands")):
+                self.assertDictEqual(a, b)

tests/core/test_utils.py

@@ -26,15 +26,9 @@ def test_default(self):
                 self.assertEqual(dataset.compression,
                                  rasterio.enums.Compression.deflate)
 
-    def test_override_default(self):
-        with self.cogify(args=["-co", "compress=lzw"]) as outfile:
+    def test_profile(self):
+        with self.cogify(profile={"compress": "lzw"}) as outfile:
             self.assertTrue(os.path.exists(outfile))
             with rasterio.open(outfile) as dataset:
                 self.assertEqual(dataset.compression,
                                  rasterio.enums.Compression.lzw)
-
-    def test_extra_args(self):
-        with self.cogify(
-                extra_args=["-mo", "TIFFTAG_ARTIST=prince"]) as outfile:
-            with rasterio.open(outfile) as dataset:
-                self.assertEqual(dataset.tags()["TIFFTAG_ARTIST"], "prince")