DOC: Clarify Align Sections (List) row order and shift direction

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需要修改的文本位于 src/Plugins/SimplnxCore/docs/AlignSectionsListFilter.md 的文件导入和 shift 格式部分。它应描述的行为见于 AlignSectionsList.cpp（行处理与累加）和 src/simplnx/Utilities/AlignSections.cpp（切片映射、源坐标查找、零填充）。完成的标准是：文档说明第 r 行映射到切片 Z-1-r，第 0 行是固定为 [0, 0] 的锚点条目，且存储的正 X 或 Y 偏移会使内容向坐标减小的方向移动，并附带带索引的示例。

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documentation

Summary

Clarify the row order, fixed slice, and shift direction in the Align Sections (List) documentation. The file-import instructions say that slices must be ordered "bottom to top", but do not define the corresponding Z indices. The relative/cumulative descriptions also leave the reference slice and sign convention implicit. These details are needed to prepare external shifts or interpret shifts saved by an alignment filter.

At simplnx commit fe6c4a15e5a5bffef2523f52cec01be33b1e62a9, the existing behavior is:

  • For Z slices, shift-array row r corresponds to local slice z = Z - 1 - r.
  • Slice z = Z - 1 stays fixed. Row zero is an unused anchor entry in both input modes; use [0, 0] for it.
  • Relative mode accumulates rows starting at row 1: C[0] = [0, 0] and C[r] = C[r-1] + R[r]. Cumulative mode reads C[r] directly for rows 1 through Z-1.
  • For cumulative shift (sx, sy) in row r, the transfer is out[z, y, x] = in[z, y + sy, x + sx], with zero fill where the source coordinate is outside the slice. Thus a positive stored X shift moves image content toward decreasing X; the same convention applies to Y.

The row handling and accumulation and slice mapping, source-coordinate lookup, and zero fill define this behavior. The documentation to clarify is AlignSectionsListFilter.md.

For a concrete example, a native Small IN100 run on a 128 x 128 x 8 crop produced the following rows. Z indices are local to the crop; shift pairs are (X, Y) in cells.

Row Target Z Saved MI Slice Indices Relative shift Cumulative shift
0 7, fixed [0, 0], placeholder [0, 0] [0, 0]
1 6 [6, 7] [0, 0] [0, 0]
2 5 [5, 6] [-1, 0] [-1, 0]
3 4 [4, 5] [0, -1] [-1, -1]
4 3 [3, 4] [-1, 0] [-2, -1]
5 2 [2, 3] [-1, 0] [-3, -1]
6 1 [1, 2] [-1, 0] [-4, -1]
7 0 [0, 1] [-1, 0] [-5, -1]

The row-zero Slice Indices value is a placeholder, not an instruction to shift slice zero. Slice Indices is explanatory output from Mutual Information; Align Sections (List) consumes the selected two-component shifts array.

On Windows, the 17-step native pipeline passed preflight and execution, and 76 independent checks passed. Replaying both shift formats matched the native Mutual Information output exactly for Quats, Phases, Mask, FeatureIds, and IPFColors. The checks confirmed the fixed highest-Z slice, coordinate transfer, and zero-filled borders. They establish the transfer convention, not the physical accuracy or optimality of the estimated alignment.

Please document these existing conventions in the shift-format and file-import instructions, including an indexed example that makes the fixed row and shift sign explicit.

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