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iosefa merged 1 commit into from
Oct 9, 2025
Merged

process: add skip_existing and verbose options to tile processing #39

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48 changes: 39 additions & 9 deletions pyforestscan/process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,8 @@ def _crop_dtm(dtm_path, tile_min_x, tile_min_y, tile_max_x, tile_max_y):
def process_with_tiles(ept_file, tile_size, output_path, metric, voxel_size,
voxel_height=1, buffer_size=0.1, srs=None, hag=False,
hag_dtm=False, dtm=None, bounds=None, interpolation=None, remove_outliers=False,
cover_min_height: float = 2.0, cover_k: float = 0.5) -> None:
cover_min_height: float = 2.0, cover_k: float = 0.5,
skip_existing: bool = False, verbose: bool = False) -> None:
"""
Process a large EPT point cloud by tiling, compute CHM or other metrics for each tile,
and write the results to the specified output directory.
Expand All @@ -75,6 +76,8 @@ def process_with_tiles(ept_file, tile_size, output_path, metric, voxel_size,
remove_outliers (bool, optional): Whether to remove statistical outliers before calculating metrics. Defaults to False.
cover_min_height (float, optional): Height threshold (in meters) for canopy cover (used when metric == "cover"). Defaults to 2.0.
cover_k (float, optional): Beer–Lambert extinction coefficient for canopy cover. Defaults to 0.5.
skip_existing (bool, optional): If True, skip tiles whose output file already exists. Defaults to False.
verbose (bool, optional): If True, print warnings for empty/invalid tiles and buffer adjustments. Defaults to False.

Returns:
None
Expand Down Expand Up @@ -126,7 +129,17 @@ def process_with_tiles(ept_file, tile_size, output_path, metric, voxel_size,
tile_max_y = min(max_y, tile_max_y)

if tile_max_x <= tile_min_x or tile_max_y <= tile_min_y:
print(f"Warning: Skipping tile ({i}, {j}) due to invalid spatial extent.")
if verbose:
print(f"Warning: Skipping tile ({i}, {j}) due to invalid spatial extent.")
pbar.update(1)
continue

if metric == "chm":
result_file = os.path.join(output_path, f"tile_{i}_{j}_chm.tif")
else:
result_file = os.path.join(output_path, f"tile_{i}_{j}_{metric}.tif")

if skip_existing and os.path.isfile(result_file):
pbar.update(1)
continue

Expand Down Expand Up @@ -164,7 +177,8 @@ def process_with_tiles(ept_file, tile_size, output_path, metric, voxel_size,
tile_points = tile_pipeline.arrays[0]

if tile_points.size == 0:
print(f"Warning: No data in tile ({i}, {j}). Skipping.")
if verbose:
print(f"Warning: No data in tile ({i}, {j}). Skipping.")
pbar.update(1)
continue

Expand All @@ -175,12 +189,29 @@ def process_with_tiles(ept_file, tile_size, output_path, metric, voxel_size,
chm, extent = calculate_chm(tile_points, voxel_size, interpolation=interpolation)

if buffer_pixels_x * 2 >= chm.shape[1] or buffer_pixels_y * 2 >= chm.shape[0]:
print(
f"Warning: Buffer size exceeds CHM dimensions for tile ({i}, {j}). Adjusting buffer size.")
if verbose:
print(
f"Warning: Buffer size exceeds CHM dimensions for tile ({i}, {j}). Adjusting buffer size.")
buffer_pixels_x = max(0, chm.shape[1] // 2 - 1)
buffer_pixels_y = max(0, chm.shape[0] // 2 - 1)

chm = chm[buffer_pixels_y:-buffer_pixels_y, buffer_pixels_x:-buffer_pixels_x]
# Safe crop: avoid Python's -0 slice behavior producing empty arrays.
if buffer_pixels_x < 0 or buffer_pixels_y < 0:
raise ValueError("Computed negative buffer pixels; check voxel and buffer sizes.")

start_x = buffer_pixels_x
end_x = chm.shape[1] - buffer_pixels_x if buffer_pixels_x > 0 else chm.shape[1]
start_y = buffer_pixels_y
end_y = chm.shape[0] - buffer_pixels_y if buffer_pixels_y > 0 else chm.shape[0]

# If cropping would yield an empty array due to small tiles, skip cropping
if end_x <= start_x or end_y <= start_y:
# Fall back to no buffer crop for this tile
core = chm
else:
core = chm[start_y:end_y, start_x:end_x]

chm = core

core_extent = (
tile_min_x + buffer_x,
Expand All @@ -189,7 +220,6 @@ def process_with_tiles(ept_file, tile_size, output_path, metric, voxel_size,
tile_max_y - buffer_y,
)

result_file = os.path.join(output_path, f"tile_{i}_{j}_chm.tif")
create_geotiff(chm, result_file, srs, core_extent)
elif metric in ["fhd", "pai", "cover"]:
voxels, spatial_extent = assign_voxels(tile_points, voxel_size)
Expand Down Expand Up @@ -243,11 +273,11 @@ def process_with_tiles(ept_file, tile_size, output_path, metric, voxel_size,
)

if core_extent[1] <= core_extent[0] or core_extent[3] <= core_extent[2]:
print(f"Warning: Invalid core extent for tile ({i}, {j}): {core_extent}. Skipping.")
if verbose:
print(f"Warning: Invalid core extent for tile ({i}, {j}): {core_extent}. Skipping.")
pbar.update(1)
continue

result_file = os.path.join(output_path, f"tile_{i}_{j}_{metric}.tif")
create_geotiff(result, result_file, srs, core_extent)
else:
raise ValueError(f"Unsupported metric: {metric}")
Expand Down
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