Bruker 2dseq reader: ParaVision on-disk format conformance

[gdevenyi]

Parse the JCAMP-DX forms ParaVision writes (PV5.1 headers, PV360 RLE and enum arrays, strings with commas), fix frame-scaling cardinality, and derive slice count and direction from frame groups. Adds a synthetic PV360 GTest, no new external test data.

Defects fixed, per commit

• Parser: the fixed five-##/three-$$ header assumption desynchronized on PV5.1 files (two $$ lines — VisuVersion was silently consumed) and could not read ParaVision 360 files at all: @N*(value) run-length encoded arrays, $$ @vis= comments inside wrapped value blocks, commas inside <> strings (e.g. <Parameter maps T2 relaxation, bg: Otsu.>), enum values stored as sized arrays (( 1 ) + disk_normal_slice_order), and scalar struct values on the parameter line.
• Scaling: VisuCoreDataSlope/VisuCoreDataOffs may hold one value for all frames or one per frame; per-frame indexing read out of bounds when a single value was stored.
• Geometry: 2D datasets whose frame groups lack FG_SLICE (e.g. FG_ISA parameter maps) are single-slice; deriving the slice count from identical per-frame positions produced a zero slice spacing. The slice axis now follows the sign of the slice-position step along the orientation's third row, generalizing the previous coronal-only Y-component heuristic to oblique stacks.

Test results

• Existing itkBruker2dseq_PV5.1_FSE_INT16 / PV6.0_FLASH_* regression tests pass with unchanged baselines.
• New Bruker2dseqImageIO.ReadParaVision360Dataset GTest covers RLE arrays, wrapped strings with embedded commas, mid-value comments, broadcast scaling, frame-group reordering, and a reversed slice axis.
• Local sweep over 1636 public ParaVision datasets (PV5.1, PV6.0.1, PV7, PV360 3.4-3.7 studies from Zenodo, bruker2nifti_qa, MRIReco.jl, and Bruker's PV360 standard protocols): previously 677 readable, now 1631; the 5 remaining failures are zero-byte placeholder files, rejected with a clean exception. Of the 677 previously readable, 610 outputs are byte-identical; the 67 that changed are slice-axis sign corrections on oblique/coronal 2D stacks, verified against the stored VisuCorePosition progression.

AI assistance

• Tool: Claude Code
• Role: implemented the parser rewrite and geometry fixes against the Bruker ParaVision file-format specification (derived from Bruker's D01/D12 File Formats manuals and ParaVision headers), and ran the dataset sweep above.
• All code was reviewed, built, and tested locally before committing.

[gdevenyi]

This work is built on https://github.com/gdevenyi/brkraw-legacy/blob/main/FILE_FORMAT.md which was constructed using an extensive AI deep dive into publicly available Bruker datasets, the Bruker Paravision manuals over multiple versions.

[dzenanz]

@greptileai review this.

[greptile-apps]

Greptile Summary

The Bruker reader now supports ParaVision 360 parameter forms, frame scaling, and frame-derived geometry. The previously reported resource-exhaustion path was disproved: the exact oversized run-length input is rejected with an ITK exception before expansion.

Confidence Score: 5/5

No blocking failure remains.

Focused public-reader tests passed for ParaVision 360 parsing, scaling, frame ordering, geometry, and the exact oversized run-length input.

T-Rex Logs

What T-Rex did

• An earlier run of the same harness recorded the precise Bruker JCAMP-DX RLE exception text and showed no bug evidenced by execution, occurring before the expansion loop.
• Rebuilt the focused Bruker reader test target and ran an authored public-reader test that writes @2147483647*(2) into VisuCoreDataSlope before calling ImageFileReader::Update() with Bruker2dseqImageIO; the test passed after catching the expected Bruker JCAMP-DX RLE ITK exception Bruker JCAMPDX RLE count out of range: @2147483647*(2).
• Ran the focused ParaVision 360 reader test, which passed while covering parsing, scaling, frame ordering, and geometry.

_{Ran code and verified through T-Rex}

_{Reviews (2): Last reviewed commit: "BUG: Bound Bruker JCAMP-DX run-length ex..." | Re-trigger Greptile}