Two speedups (opengeos#262)

* Two speedups

- allow the sample window size to be set from samgeo.generate. Fewer,
  larger windows take less time as long as you have the memory.
- Skip any sample windows which are 100% nodata, with the option to set
  lower thresholds.

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: sdtaylor

samgeo/common.py

@@ -1122,6 +1122,8 @@ def tiff_to_tiff(
     func,
     data_to_rgb=chw_to_hwc,
     sample_size=(512, 512),
+    sample_nodata_threshold=1.0,
+    nodata_value=None,
     sample_resize=None,
     bound=128,
     foreground=True,
@@ -1132,6 +1134,9 @@ def tiff_to_tiff(
     with rasterio.open(src_fp) as src:
         profile = src.profile
 
+        if nodata_value is None:
+            nodata_values = profile.get("nodata", None)
+
         # Computer blocks
         rh, rw = profile["height"], profile["width"]
         sh, sw = sample_size
@@ -1154,6 +1159,11 @@ def tiff_to_tiff(
             for b in tqdm(sample_grid):
                 # Read each tile from the source
                 r = read_block(src, **b)
+
+                if nodata_value is not None:
+                    if (r == nodata_value).mean() >= sample_nodata_threshold:
+                        continue
+
                 # Extract the first 3 channels as RGB
                 uint8_rgb_in = data_to_rgb(r)
                 orig_size = uint8_rgb_in.shape[:2]

samgeo/samgeo.py

@@ -152,6 +152,9 @@ def generate(
         output=None,
         foreground=True,
         batch=False,
+        batch_sample_size=(512, 512),
+        batch_nodata_threshold=1.0,
+        nodata_value=None,
         erosion_kernel=None,
         mask_multiplier=255,
         unique=True,
@@ -164,6 +167,12 @@ def generate(
             output (str, optional): The path to the output image. Defaults to None.
             foreground (bool, optional): Whether to generate the foreground mask. Defaults to True.
             batch (bool, optional): Whether to generate masks for a batch of image tiles. Defaults to False.
+            batch_sample_size (tuple, optional): When batch=True, the size of the sample window when iterating over rasters.
+            batch_nodata_threshold (float,optional): Batch samples with a fraction of nodata pixels above this threshold will
+                not be used to generate a mask. The default, 1.0, will skip samples with 100% nodata values. This is useful
+                when rasters have large areas of nodata values which can be skipped.
+            nodata_value (int, optional): Nodata value to use in checking batch_nodata_threshold. The default, None,
+                will use the nodata value in the raster metadata if present.
             erosion_kernel (tuple, optional): The erosion kernel for filtering object masks and extract borders.
                 Such as (3, 3) or (5, 5). Set to None to disable it. Defaults to None.
             mask_multiplier (int, optional): The mask multiplier for the output mask, which is usually a binary mask [0, 1].
@@ -190,6 +199,9 @@ def generate(
                     output,
                     self,
                     foreground=foreground,
+                    sample_size=batch_sample_size,
+                    sample_nodata_threshold=batch_nodata_threshold,
+                    nodata_value=nodata_value,
                     erosion_kernel=erosion_kernel,
                     mask_multiplier=mask_multiplier,
                     **kwargs,