nmrglue – Other skill for AI agents

nmrglue: calibrated 1D FID processing

When to use

Use for a uniformly sampled complex 1D FID whose acquisition parameters and complex

frequency convention are available. The helper produces a descending ppm spectrum,

positive peak candidates, signed region integrals, and a reproducible processing report.

It does not identify compounds or assign resonances.

The executable accepts a NumPy .npz containing exactly one complex fid array or a

canonical 1D complex time-domain NMRPipe file. NMRPipe reading is tested with a synthetic

write/read round trip, known-spectrum recovery, and a small upstream NMRPipe-generated

binary fixture. Experimental Bruker, Varian, and JEOL

imports are not verified by this suite. For those formats, first inspect the relevant

nmrglue reader and acquisition metadata. Opening a converted file does not validate the

original acquisition decoding.

Read [references/acquisition-and-validation.md](references/acquisition-and-validation.md)

for conversion boundaries, axis calibration, and quantitative limits.

Workflow

1. Preserve the raw FID. Establish spectral width in Hz, positive observation frequency

in MHz, carrier in ppm, observed nucleus, and the sign convention from the acquisition

or a known reference. Determine whether digital-filter/group-delay removal has already

occurred. Do not infer these from array length or typical instrument defaults.

2. Copy [assets/processing.json](assets/processing.json) and replace its synthetic example

values with the measured parameters and explicit processing choices. Its sign -i

means a resonance at offset f = (ppm - carrier_ppm) * observation_mhz has time

dependence exp(-2*pi*i*f*t). Select +i only for the opposite convention; the helper

conjugates it before processing. Validate with a known reference peak.

3. Choose nonnegative exponential line broadening (Hz), an even zero-filled size at

least as large as the acquired FID, first-point scaling, and phase angles.

Zero filling improves interpolation, not acquired spectral resolution.

First-point scaling 0.5 is suitable for the supplied causal synthetic example;

acquisition and prior preprocessing may require another value.

4. Run the helper, inspect the real and imaginary spectra, and revise manual phase if

needed. phase0_deg + phase1_deg * index / zero_fill_points is applied after FT;

index zero is the high-ppm edge. There is no implicit pivot or automatic phase estimate.

5. Only fit a linear baseline when explicitly supplied ppm regions are signal-free.

Set baseline to linear and add baseline_regions_ppm containing at least two

regions. Inspect residuals and broad peaks; fitting through signals biases integrals.

6. Compare peak positions with references, inspect peak candidates for artifacts, and

integrate specified regions. Report overlapped peaks as overlapped. Preserve negative

areas as diagnostic evidence of phase/baseline problems instead of taking absolute values.

Execute

Tested with Python 3.12, nmrglue 0.12, NumPy 2.5.3, and SciPy 1.18.1:

uv run --no-project --python 3.12 --with nmrglue==0.12 --with numpy==2.5.3 --with scipy==1.18.1 \
  python skills/nmrglue/scripts/process_1d.py fid.npz processing.json nmr-result

Paths assume the collection root. Adjust them when installed elsewhere. The output

directory must be new, so repeated processing keeps previous results reviewable.

For an existing 1D NMRPipe FID, add --input-format nmrpipe and supply its path in place

of fid.npz. The helper requires the canonical FDF2 direct dimension, complex quadrature,

a time-domain flag, and agreement between header and JSON spectral width, observation

frequency, and carrier. JSON settings remain explicit; a mismatch fails instead of silently

recalibrating. FDF2TDSIZE must equal the stored complex-point count, and FDF2CENTER /

FDF2ORIG must describe a canonical centered axis. Previously zero-filled, truncated,

or recentered files need a separate acquisition-aware workflow. The nucleus/complex sign

and previous digital-filter corrections still need acquisition evidence. A time-domain

flag alone does not establish an unprocessed FID.

This executable synthetic example matches the supplied settings, generates resonances

at 3 and 7 ppm in a 1:2 amplitude ratio, and does not represent an experimental sample:

import numpy as np

t = np.arange(8192) / 4000.0
fid = sum(a * np.exp(-np.pi * 2.0 * t)
          * np.exp(-2j * np.pi * (ppm - 5.0) * 400.0 * t)
          for ppm, a in [(3.0, 1.0), (7.0, 2.0)])
np.savez("fid.npz", fid=fid)

Run it with assets/processing.json as the settings argument. The repository suite

executes this signal and the CLI, checks both peak locations within 0.001 ppm, checks

integral ratio and analytic area, and checks phase and baseline recovery. The NMRPipe

round-trip test writes this FID using ng.pipe.create_dic/ng.pipe.write, reads it through

the CLI, and verifies the recovered peaks and integral ratio. Processed frequency-domain

files and conflicting calibration metadata are rejected.

The 2,176-byte upstream fixture checks complex sample order and header calibration using

a file generated by NMRPipe's simTimeND / SET tools. Those native tools were not run

in this review; this is fixture compatibility, not a live NMRPipe processing comparison.

Deliverables and interpretation

• spectrum.csv: descending ppm, real signal after baseline correction, phased imaginary

signal, and the fitted real baseline. Plot NMR with the high-ppm end on the left.

• report.json: input/settings SHA-256, package versions, all settings, acquired duration,

zero-filled digital spacing, positive peak candidates, and signed region areas.

Integrals use endpoint interpolation and trapezoidal integration along increasing ppm;

area units are arbitrary signal times ppm, independent of display direction. Regions

outside the sampled ppm axis fail rather than being silently clipped. Peak prominence

is a fraction of the largest positive real intensity; it is not a noise-derived detection

limit. Strong solvent signals can obscure weak candidates at the default threshold.

For quantitative NMR, additionally establish relaxation delay, pulse angle, saturation,

receiver behavior, internal/external reference amount, and integration uncertainty.

The helper does not calculate concentrations or correct unequal relaxation. Preserve

these limits with the result rather than converting arbitrary areas to molecule counts.

Upstream contracts

• [Processing functions](https://nmrglue.readthedocs.io/en/latest/reference/proc_base.html):

exponential apodization, zero filling, FFT, and phase operations.

• [File and axis utilities](https://nmrglue.readthedocs.io/en/latest/reference/fileiobase.html):

unit conversion uses spectral width in Hz, observation frequency in MHz, carrier in Hz.

• [NMRPipe reader/writer](https://nmrglue.readthedocs.io/en/latest/reference/pipe.html):

the validated ingestion path is a synthetic canonical 1D time-domain round trip.

• [nmrglue project](https://github.com/jjhelmus/nmrglue): upstream source and format readers.

The hosted latest documentation identified itself as 0.9-dev when checked; the actual

0.12 package APIs and numerical behavior were tested. Its proc_base.fft uses the

negative-exponent NumPy FFT followed by fftshift; NMRPipe's FT convention corresponds

to fft_positive, so do not substitute it without revisiting the FID sign and phase.

See the [v0.12 processing source](https://github.com/jjhelmus/nmrglue/blob/v0.12/nmrglue/process/proc_base.py).

Multidimensional processing, nonuniform sampling, automated assignment, and experimental vendor imports remain outside

this helper's validated scope.