linumpy.stack_alignment.io#

CSV loading and cumulative shift computation.

Functions#

load_shifts_csv(shifts_path)

Load shifts CSV and build cumulative shift lookup.

build_cumulative_shifts(shifts_df, selected_slice_ids, ...)

Build cumulative pixel shifts for selected slices.

Module Contents#

linumpy.stack_alignment.io.load_shifts_csv(shifts_path)[source]#

Load shifts CSV and build cumulative shift lookup.

The shifts file contains pairwise shifts: fixed_id -> moving_id in mm. Accumulates these to get absolute positions from the first slice.

Parameters:

shifts_path (str or Path) – Path to CSV file with columns: fixed_id, moving_id, x_shift_mm, y_shift_mm

Returns:

  • cumsum (dict) – Mapping from slice_id to (cumulative_dx_mm, cumulative_dy_mm)

  • all_ids (list) – Sorted list of all slice IDs

Return type:

tuple[dict, list]

linumpy.stack_alignment.io.build_cumulative_shifts(shifts_df, selected_slice_ids, resolution, center_drift=True)[source]#

Build cumulative pixel shifts for selected slices.

Handles skipped slices by accumulating intermediate steps. Converts mm shifts to pixels using the provided resolution.

Parameters:

  • shifts_df (pd.DataFrame) – DataFrame with columns: fixed_id, moving_id, x_shift_mm, y_shift_mm

  • selected_slice_ids (list) – Sorted list of slice IDs to process.

  • resolution (tuple) – Resolution (res_z, res_y, res_x) from read_omezarr; auto-detects mm vs µm.

  • center_drift (bool) – If True, center cumulative drift around the middle slice.

Returns:

Mapping from slice_id to (cumulative_dx_px, cumulative_dy_px).

Return type:

dict