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fix numbering in export-as-tiff CLI #1387

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Merged
merged 4 commits into from
Oct 30, 2025
+5 −4
Merged

fix numbering in export-as-tiff CLI #1387

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55926de
fix numbering in export-as-tiff CLI
normanrz Oct 27, 2025
9592524
rename some variables
fm3 Oct 30, 2025
e1410cb
changelog
fm3 Oct 30, 2025
5c27df7
Merge branch 'master' into export-tiff-numbers
fm3 Oct 30, 2025
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1 change: 1 addition & 0 deletions webknossos/Changelog.md
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Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section

### Fixed
- Fixed test.py to parse the command line arguments correctly. [#1383](https://github.com/scalableminds/webknossos-libs/pull/1383)
- Fixed a bug in the CLI tool export_as_tiff, where filenames would not match the data z position exactly. [#1387](https://github.com/scalableminds/webknossos-libs/pull/1387)


## [2.5.0](https://github.com/scalableminds/webknossos-libs/releases/tag/v2.5.0) - 2025-10-06
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8 changes: 4 additions & 4 deletions webknossos/webknossos/cli/export_as_tiff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,12 +67,12 @@ def _slice_to_image(data_slice: np.ndarray, downsample: int = 1) -> Image.Image:
return Image.fromarray(data_slice)


def export_tiff_slice(
def export_tiff_slice_batch(
dest_path: UPath,
name: str,
tiling_size: None | tuple[int, int],
downsample: int,
start_slice_index: int,
start_slice_z_mag1: int,
view: View,
) -> None:
tiff_bbox_mag1 = view.bounding_box
Expand All @@ -97,7 +97,7 @@ def export_tiff_slice(
tiff_data = padded_tiff_data
for slice_index in range(tiff_bbox.size.z):
slice_name_number = (
tiff_bbox_mag1.topleft.z + slice_index + 1 - start_slice_index
tiff_bbox_mag1.topleft.z + slice_index * view.mag.z - start_slice_z_mag1
)
if tiling_size is None:
tiff_file_name = _make_tiff_name(name, slice_name_number)
Expand Down Expand Up @@ -165,7 +165,7 @@ def export_tiff_stack(
wait_and_ensure_success(
executor.map_to_futures(
partial(
export_tiff_slice,
export_tiff_slice_batch,
destination_path,
name,
tiling_slice_size,
Expand Down
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