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Merged
joshua-gould merged 3 commits into from
May 11, 2026
Merged

stitch-single-file-input #115

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fc3745b
handle single nd2 file input
joshua-gould May 11, 2026
5923624
handle single nd2 file input
joshua-gould May 11, 2026
63c8875
handle single nd2 file input
joshua-gould May 11, 2026
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11 changes: 9 additions & 2 deletions scallops/stitch/_stitch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -242,7 +242,11 @@ def _single_stitch(
np.sum(stitch_position_coords - center, axis=1) ** 2
)

stitch_positions_df["source"] = original_filepaths
stitch_positions_df["source"] = (
original_filepaths * len(stitch_positions_df)
if len(original_filepaths) == 1
else original_filepaths
)
if fileattrs is not None:
stitch_positions_df["source_metadata"] = fileattrs
stitch_positions_df["tile"] = np.arange(len(stitch_positions_df))
Expand Down Expand Up @@ -286,7 +290,10 @@ def _single_stitch(

# replace source with local source
stitch_positions_df_local = stitch_positions_df.copy()
stitch_positions_df_local["source"] = filepaths
stitch_positions_df_local["source"] = (
filepaths * len(stitch_positions_df_local) if len(filepaths) == 1 else filepaths
)

logger.info(f"Saving report to {other_output_path}{image_key}.pdf.")
_qc_report(
path=f"{other_output_path}{image_key}.pdf",
Expand Down