PerkinElmer Spectrum / IR

Status: Supported (scoped) · Vendor: PerkinElmer · Extensions: .sp (.fsm imaging out of v1 scope)

PerkinElmer’s Spectrum and Spotlight software write the PEPE block container. nirs4all-formats reads the .sp single-spectrum flavour of that container; the .fsm Spotlight imaging flavour shares the family magic but is intentionally left out of the v1 scope.

Instruments & software

Produced by PerkinElmer Spectrum software across the FT-IR / FT-NIR ranges and by Spotlight imaging systems. The committed .sp fixture comes from the specio project.

File structure

A PEPE magic at offset 0, a fixed description field, then a root block (id 120) whose payload is a recursive sequence of typed little-endian blocks. Each block has a 6-byte header (id + signed payload length); container blocks nest further block sequences. Data-bearing blocks are tagged: f64 pair (0x751d), single f64 (0x751b), i32 (0x752b), string (0x7523) and f64 array (0x7516). The ordinate array, axis bounds, step and point count are read from their specific block ids and tags.

Newer Spectrum 10 FT-MIR exports append one or more trailing top-level blocks after the DataSet root block (e.g. a CustomColumn audit/history block, ~187 bytes). These siblings are tolerated: the reader records them structurally and keeps reading from the canonical root block, so the spectral data is unaffected.

What nirs4all-formats extracts

• Signals — one SpectralRecord per file with the f64 ordinate array. The signal type is inferred from the signal label, and falls back to absorbance when the signal unit is A.

• Axis — generated from the typed first_x / step / point_count blocks (with last_x used to infer the step when needed). The axis kind follows the declared unit: wavenumber (cm-1), wavelength (nm / um), otherwise index.

• Metadata — description, signal min/max, x-step and point count, plus string blocks for sample id, instrument, instrument serial, software, detector, source type, beam splitter, apodization, measurement / processing / ordinate modes, accessory, ratio mode and scan date when present.

• Provenance & warnings — a perkin_elmer_reverse_engineered_blocks warning, source file and SHA-256. Files that carry trailing top-level blocks after the root also raise perkin_elmer_reverse_engineered_trailing_blocks (the audit block is recorded structurally but its content is not surfaced).

Variants & support status

Variant	Status	Notes
.sp Spectrum single spectrum	Supported	Typed block table, f64 ordinate array, rich instrument metadata.
FT-MIR .sp (Spectrum 10, trailing audit blocks)	Supported	Same single-spectrum path; trailing top-level audit/CustomColumn blocks after the root are tolerated as siblings and flagged with perkin_elmer_reverse_engineered_trailing_blocks.
.fsm Spotlight imaging	Detected / refused	Recognised by the PEPE magic and .fsm extension, then refused with a clear unsupported-imaging error rather than misread as a 1D spectrum.
PE NIR / Lambda variants	Planned	Need sample-backed validation.

Limitations & known gaps

• .fsm Spotlight imaging is deliberately out of scope for v1; an image cube is never interpreted as a single spectrum.

• The committed .sp fixture carries a footer whose scan range disagrees with the typed axis blocks; the reader treats the typed blocks as canonical and leaves the footer text for future reverse-engineering. Likewise, the trailing top-level audit/CustomColumn blocks of Spectrum 10 FT-MIR exports are recorded structurally only — their content is left for future reverse-engineering and flagged with perkin_elmer_reverse_engineered_trailing_blocks.

• Malformed input yields clean errors, never a panic: a negative point count is rejected and container-block recursion is depth-capped.

• PE NIR / Lambda variants are not yet sample-backed. A future split of .sp from .fsm would let the .sp scope be promoted on its own.

Reference readers

specio reads the same .sp container and is the practical cross-check for this format.

Samples & validation

The real specio fixture samples/perkin_elmer/spectra.sp (1 record, cm-1, 3301 points, absorbance with unit A) is golden-backed and exercised by a direct semantic test. The synthetic fixture samples/perkin_elmer/synthetic_trailing.sp carries a trailing top-level block after the root and is golden-backed to lock in the trailing-block tolerance. The probe reports perkin-elmer-sp at Confidence::Definite, and perkin-elmer-fsm (also Definite) for the recognised-but-refused imaging variant.

The local-only FT-MIR corpus under samples_local/perkin_elmer/ (31 .sp with paired cm-1;Absorbance CSV exports, private, licence TBD) was validated: every .sp parses to a descending cm-1 axis (4000→450, 3551 points) and matches its paired CSV to export precision (~5e-5).