docs+feat: decode LC Raw Data/Chromatogram Ch6, characterize Ch5's untestable grammar (#21)#22
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Nathan-D-R merged 1 commit intoJul 21, 2026
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Ch5/Ch6 share the same RC\x00\x00 segment header as the still-unsolved PDA payload, but the single giant per-channel segment turns out to have its own internal "page" framing (u16 length-prefixed/suffixed blocks of up to 256 samples) and a clean, exhaustively-verified literal/wide-token tokenization split. Cumulative-summing the decoded deltas produces a smooth, physically plausible chromatogram in every one of the 5 locally available PXD020792 files for Ch6. Ch5 shares the identical framing but is a single repeated value for its entire run in every available file, which makes its numeric grammar (delta vs. absolute-value convention) untestable from this corpus - crates/openszraw::raw::lc_chrom deliberately skips emitting it rather than guess, per the project's clean-room honesty policy. Wires Ch6 into Reader::iter_chromatograms via openmassspec-core's SpectrumSource trait, tagged with PSI-MS MS:1000811 "electromagnetic radiation chromatogram". Partially resolves Sigilweaver#21. Claude-Session: https://claude.ai/code/session_01ETdxFx6Mb8XcZqctf1AHtF
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Summary
Addresses #21 (decode the
LC Raw Data/Chromatogram Ch5/Ch6stream found while investigating #2) -Ch6is decoded and wired into the reader;Ch5is a confirmed, evidence-backed partial characterization, deliberately left undecoded.Confirmed, byte-exact (all 5 locally available
PXD020792/*.LCDfiles, both channels, 290 pages total, zero exceptions):RC\x00\x00segment (one giant segment per channel, as issue Decode LC Raw Data/Chromatogram Ch5 / Ch6 stream (found while investigating #2) #21 already noted) has internal sub-segment structure that hadn't been characterized yet: the body is a back-to-back sequence of "pages", each au16LE byte-length prefix, that many data bytes, then a matchingu16LE suffix - the same "symmetric" length-wrapper style already documented for PDA segments, just applied per-page.< 0x20is a signed 5-bit literal delta, a byte>= 0x20starts a 2-byte signed-13-bit wide delta. This(threshold=0x20, width=2)rule is the unique zero-exception result of an exhaustive(threshold, width)sweep.Corroborated, not byte-exact-proven: cumulative-summing the decoded deltas produces a smooth, physically plausible chromatogram (baseline, broad rise, stable plateau) for
Ch6in every file, clearly outperforming every alternative layout tried.Ch5- deliberately left undecoded: it shares the identical verified framing, but every sample in every available file is the same repeated token, which makes the delta-vs-absolute-value convention untestable from this corpus. Per this project's clean-room honesty policy, the reader skips emitting any channel with fewer than 2 distinct decoded values rather than guess and risk shipping a fabricated unbounded ramp.Rust implementation: new
crates/openszraw::raw::lc_chrommodule, wired intoReader'sSpectrumSource::iter_chromatograms(probing all 6 conventionalLC Raw Data/Chromatogram ChNnames generically, not hardcoded toCh5/Ch6). Records use PSI-MSMS:1000811"electromagnetic radiation chromatogram". Mirrors theiter_chromatogramswiring pattern from the sibling OpenWRaw#9.Full derivation and evidence in
docs/format/04-lcd-chromatogram-pda.md's "2026-07-21 session" section anddocs/format/06-known-limitations.md#11.Contributed by @Nabejo.
Test plan
cargo fmt --all -- --checkcargo clippy --workspace --all-targets -- -D warningscargo test --workspace(35 unit tests incl. 10 new forlc_chrom, plus 2 new corpus-conformance tests verifyingCh6decodes to a plausible trace andCh5is correctly skipped)