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Delete Zarr array when finished #9

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24 changes: 19 additions & 5 deletions src/ng_slice_download/cli.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import math
import shutil
from pathlib import Path

import click
Expand Down Expand Up @@ -30,7 +31,10 @@
@click.option(
"--skip-lowres-check", is_flag=True, help="Skip the low resolution check."
)
def main(neuroglancer_url: str, output_dir: Path, skip_lowres_check: bool):
@click.option("--keep-zarr", is_flag=True, help="Keep the intermediate Zarr array.")
def main(
neuroglancer_url: str, output_dir: Path, skip_lowres_check: bool, keep_zarr: bool
):
print("Welcome to ng-slice-downloader!")

ng_state = neuroglancer.url_state.parse_url(neuroglancer_url)
Expand Down Expand Up @@ -58,6 +62,7 @@ def main(neuroglancer_url: str, output_dir: Path, skip_lowres_check: bool):
position=position,
rotation_quat=rotation_quat,
output_path=output_dir / f"ng_slice_check_{selected_layer.name}",
keep_zarr=False,
)
print()
print(
Expand Down Expand Up @@ -90,6 +95,7 @@ def main(neuroglancer_url: str, output_dir: Path, skip_lowres_check: bool):
position=position,
rotation_quat=rotation_quat,
output_path=output_dir / f"ng_slice_{selected_layer.name}",
keep_zarr=keep_zarr,
)


Expand Down Expand Up @@ -151,6 +157,7 @@ def save_image(
position: list[int],
rotation_quat: list[float],
output_path: Path,
keep_zarr: bool,
):
input_image = open_tensorstore_array(gcs_url, downsample_level=downsample_level)
print(f"Original image shape: {input_image.shape}")
Expand All @@ -168,18 +175,18 @@ def save_image(
for c, mi, ma in zip(plane.chunks, min_tile_idx, max_tile_idx, strict=True)
)

output_image_path = output_path.with_suffix(".zarr")
zarr_path = output_path.with_suffix(".zarr")
TIFF_path = output_path.with_suffix(".tiff")

if TIFF_path.exists():
yes_no_gate(f"{TIFF_path} already exists. Overwrite?", default=False)

print(f"Creating output image, shape={output_image_shape}")
print(f"Writing results to Zarr array at {output_image_path}")
print(f"Writing results to Zarr array at {zarr_path}")
print(f"TIFF image will be updated every 10 tiles at {TIFF_path}")

output_image = create_local_tensorstore_array(
path=output_image_path,
path=zarr_path,
shape=output_image_shape,
tile_shape=plane.chunks,
dtype=str(input_image.dtype.numpy_dtype),
Expand Down Expand Up @@ -232,8 +239,15 @@ def save_image(
del arr

print("Finished downloading tiles!")
print("Image saved to:", output_image_path)
print(f"Image saved to: {zarr_path}")
print("Converting to TIFF...")
arr = output_image[:].read().result()
tifffile.imwrite(TIFF_path, arr.T)

if not keep_zarr:
print(f"Deleting {zarr_path}")
shutil.rmtree(zarr_path)

print()
print("Finished! 🎉")
print("TIFF saved to:", TIFF_path)