spectrochempy-nmr

NMR plugin for SpectroChemPy.

This package is the home for NMR-specific readers and tools that are useful in SpectroChemPy but should not live in the core package. It currently provides a validated public 1D workflow for reading data and processing raw 1D FIDs through scp.nmr.read(...) and scp.nmr.Experiment(...). The readers also load raw 2D time-domain data and vendor-processed 2D spectra and can represent them as hypercomplex arrays; this reading/representation scope is separate from processing, which remains limited to validated 1D experiments.

Future NMR readers or processing helpers can be added here without creating a new plugin package for each vendor format. Multi-dimensional NMR processing remains under active characterization and is not currently part of the public supported processing workflow. A pseudo-2D series (a list of ordinary 1D spectra sharing a secondary coordinate, such as a relaxation series) must be distinguished from a genuine 2D experiment with two Fourier dimensions: the former follows the validated 1D processing path per spectrum.

Installation

The next release, 0.1.13, requires SpectroChemPy 1.1.0 or later (and remains restricted to SpectroChemPy versions below 2). Users who stay on SpectroChemPy 1.0.0 should keep an earlier compatible version of this plugin.

pip install spectrochempy[nmr]

For development inside the SpectroChemPy repository:

pip install -e .
pip install -e plugins/spectrochempy-nmr

Usage

import spectrochempy as scp

dataset = scp.nmr.read("path/to/1/fid")
dataset = scp.nmr.read("path/to/1/pdata/1/1r")
dataset = scp.nmr.read("path/to/experiment", expno=1, procno=1)

experiment = scp.nmr.Experiment(dataset)
spectrum = experiment.process(apodization="em", lb=2.0, size=32768)

This explicit processing example does not imply that vendor processing parameters are automatically imported and replayed from metadata. That contract remains under active characterization.

The current explicit apodization contract covers the public modes already exposed by Experiment.process(): em(lb=...), gm(lb=..., gb=...), and sp(ssb=..., pow=...).

The result of Experiment.process() also records the SpectroChemPy-owned processing trace in result.meta.nmr_processing["scp_processing"]. requested contains only the arguments explicitly provided by the user, whereas applied contains only the operations that were actually executed and the values they really consumed. This trace is attached to the result only: the source dataset is not mutated, the vendor procs profile remains purely descriptive, and phase="metadata" does not replay TopSpin PHC0/PHC1.

The NMR ppm/frequency unit context is also provided by this plugin:

from spectrochempy_nmr.units import set_nmr_context

set_nmr_context(104.3 * scp.ur.MHz)

The compatibility aliases scp.nmr.read_topspin(...) and scp.read_topspin(...) are kept for historical usage. TopSpin is a reader, so it is not exposed as dataset.read_topspin(...) or dataset.nmr.read_topspin(...).

Development

python -m pytest tests/ -v