Skill: mineral spectra analysis

Use this skill when a task asks for mixed mineral Raman spectrum component prediction, spectral-library matching, Raman mixture unmixing, or a blind diagnostic report explaining which minerals are present, approximate fractions, supporting peaks, residual quality, and confidence.

This skill packages the spectra-pipeline/ workflow. Preserve the pipeline order exactly:

1. load a two-column spectrum (raman_shift,intensity)
2. align it to the reference library grid
3. apply global preprocessing exactly once: despike, denoise, baseline correction, normalize
4. save clean_spectrum.csv
5. read clean_spectrum.csv back into the loop
6. repeat on the residual: second-derivative peak detection -> peak-driven library match -> NNLS refit of all selected components -> subtract
7. stop when residual peaks vanish, correlation is too low, or residual gain is too small
8. report components, fractions, supporting peaks, residual diagnostics, and confidence
9. only if an answer key is explicitly supplied, evaluate against ground truth after the blind loop is complete

Do not read truth.json during analysis. Synthetic case generation and ground-truth evaluation are optional utilities, not part of the main inference path.

Dependencies

The OpenAI4S core remains stdlib-only, but this skill's runtime analysis needs:

python -m pip install numpy scipy pybaselines matplotlib

To build the default RRUFF library from the internet, allow network access or provide an existing local excellent_oriented.zip cache. The original prototype uses RRUFF excellent_oriented.

Default spectral database:

https://www.rruff.net/zipped_data_files/raman/excellent_oriented.zip

When build_rruff_library(dataset="excellent_oriented", cache_dir="spectra_cache") downloads the database, it stores the ZIP as:

spectra_cache/excellent_oriented.zip

If cache_dir is omitted, the skill uses ./spectra_cache/excellent_oriented.zip relative to the current working directory. You can avoid downloading by passing zip_path="/path/to/excellent_oriented.zip" explicitly.

Import

from mineral_spectra_analysis.kernel import (
    analyze_spectrum_file,
    build_rruff_library,
    default_config,
    evaluate_against_truth,
    generate_synthetic_cases,
    load_spectrum_csv,
    load_truth,
    run_blind_loop,
)

Main Workflow

For a user's own spectrum and spectral library, do not generate synthetic data. Load or build the library, then run the blind pipeline:

lib = build_rruff_library(
    dataset="excellent_oriented",
    max_minerals=120,
    cache_dir="spectra_cache",          # or pass zip_path="/path/to/excellent_oriented.zip"
)

cfg = default_config()
cfg["top_k"] = 8

result = analyze_spectrum_file(
    spectrum_csv_path="sample_spectrum.csv",
    library=lib,
    output_dir="outputs/run_sample",
    config=cfg,
    make_figures=True,
)

print(result["report_path"])
print(result["outcome"].best_result.fractions)
print(result["outcome"].best_result.diagnostics)

Outputs:

outputs/run_sample/
├── clean_spectrum.csv      # one-time preprocessed spectrum, read back by loop
├── iterations.jsonl        # residual loop trace
├── report.md               # conclusion, confidence, support peaks, config
└── figures/                # optional diagnostic plots

The report should state:

• identified components and estimated fractions
• supporting Raman peaks for each component
• number of clean-spectrum peaks
• Pearson fit correlation, residual RMSE, relative residual, explained energy
• residual peak positions and reliability (high, moderate, or low)
• the fixed config used for preprocessing, matching, and NNLS
• the iteration trace: added component, match correlation, residual, cumulative component set

Reference Library

Use build_rruff_library(...) for the RRUFF ZIP format. It mirrors the original pipeline:

• tolerant parser for RRUFF .txt files because some files contain non-data lines
• one representative spectrum per mineral
• prefer Processed files and wider grid coverage
• resample every spectrum to the common 150-1400 cm^-1 grid at 2 cm^-1 spacing
• clip negative intensity and area-normalize each reference column

For a custom library, construct a Library(grid, names, A) object where A is shape (n_grid, n_minerals) and each column is an area-normalized reference spectrum on the same grid.

Optional Evaluation

Only create synthetic cases or read answer keys when the user asks to evaluate pipeline reasonableness, benchmark a case, or reproduce the prototype.

Generate blind cases:

lib = build_rruff_library(zip_path="spectra_cache/excellent_oriented.zip", max_minerals=120)
generate_synthetic_cases(lib, out_dir="cases", n=5, seed=0, noise=0.02)

Each case contains:

caseN/
├── spectrum.csv   # observable input; safe for the blind loop
├── truth.json     # hidden answer key; evaluate only after the loop
└── input.png      # optional dirty-spectrum visualization

Evaluate after the blind loop:

analysis = analyze_spectrum_file(
    "cases/case1/spectrum.csv",
    lib,
    output_dir="outputs/run_case1",
    truth_path="cases/case1/truth.json",
)
print(analysis["evaluation"])

The analysis loop must not receive the truth dict. evaluate_against_truth(...) computes precision/recall/F1 and fraction MAE only after the loop returns.

Example Case

This skill includes a bundled case1 example copied from the prototype spectra-pipeline/cases/case1 directory:

skills/mineral_spectra_analysis/examples/case1/
├── spectrum.csv   # observable synthetic dirty Raman spectrum
├── truth.json     # hidden answer key, used only for example evaluation
└── input.png      # dirty-spectrum plot

The example's component summary is:

skills/mineral_spectra_analysis/examples/case1_components.json

It records that each mixture element is a mineral phase component from the RRUFF reference library:

• Clinoptilolite-Ca — mineral phase, true fraction 0.2509
• Bertrandite — mineral phase, true fraction 0.3027
• Diopside — mineral phase, true fraction 0.4464

The rendered example report is:

skills/mineral_spectra_analysis/examples/case1_mineral_spectra_report.md

It is regenerated from committed source data rather than hand-edited:

uv run python skills/mineral_spectra_analysis/examples/build_example.py

case1_analysis.json holds the committed blind-analysis summary and case1_components.json holds the synthetic component types and hidden fractions. Re-running the full numerical analysis from case1/spectrum.csv requires the scientific runtime dependencies and an RRUFF library cache; this small builder only regenerates the example report from committed data.

Analyst Checklist

Before submitting a conclusion:

• verify the input spectrum was aligned to the library grid
• confirm preprocessing ran once and clean_spectrum.csv was written
• inspect the loop history for weak late components or tiny residual gains
• confirm the final reconstruction overlays the clean spectrum reasonably
• treat moderate or low reliability as a warning that the library may miss a component, preprocessing may be poor, or the sample may contain phases outside the database
• do not claim experimental certainty; identify the spectral evidence and the limits of the library-driven fit