SPCSpectra

A module for working with .SPC files in Julia. SPC is a binary data format to store a variety of spectral data, developed by Galactic Industries Corporation in the '90s. Popularly used Thermo Fisher/Scientific software GRAMS/AI. Also used by others including Ocean Optics, Jobin Yvon Horiba. Can store a variety of spectrum including FT-IR, UV-VIS, X-ray Diffraction, Mass Spectroscopy, NMR, Raman and Fluorescence spectra.

The SPC file format can store either single or multiple y-values, and the x-values can either be given explicitly or even spaced x-values can be generated based on initial and final points as well as number of points. In addition the format can store various log data and parameters, as well as various information such as axis labels and scan type.

NOTE: This file is still in beta state and has not been fully tested.

Acknowledgement

This package is highly inspired the python package spc by rohanisaac.

Features

Extracts header information
Store x and y data of all traces into a vector data. Single traces can be addressed by spc.data[1] (, spc.data[2], spc.data[3], ...)
Attempts to interpret x-, y-, and z-labels, as well as experiment type
Store z values of multifiles into a vector zdata

Currently only file version 0x4b is supported. Data output is not yet implemented.

Installation

julia> ]

pkg> add SPCSpectra

Usage

using SPCSpectra

datadir = joinpath(pkgdir(SPCSpectra), "test", "data")
filenames = filter(endswith(r"\.spc"i), readdir(datadir; join=true))

spc = SPC(filenames[1])

# Plotting

using PlotlyBase
plotspc(spc::SPC) = plotspc(spc.data)
plotspc(data) = Plot([scatter(x = s[1], y = s[2]) for s in data])

plotspc(spc)

Accessing data

In contrast to the original spc python package, all data elements contain both x and y values. This is not a waste of storage as x arrays are stored by reference.

The following fields are currently supported.

metadata	variable
x-label	spc.xlabel
y-label	spc.ylabel
z-label	spc.zlabel
Timestamp	spc.timestamp
Experiment type	spc.experimenttype
Log dictionary	spc.param_dict
Log (remaining)	spc.params

File versions supported

File versions are given by the second bit in the file. Currently the library supports the following fversn bytes.

fversn	Description	Support
0x4B	New format (LSB)	Good
0x4C	New format (MSB)	None
0x4D	Old format	None
0xCF	SHIMADZU format	None

Notes

Used format specification from Universal Data Format Specification [1], [2]
Loads entire file into memory
Data uses variable naming as in SPC.H

Todo

support of other format versions
data output / conversion
integration of plot functions

References

[1] "SPC file format", Wikipedia (https://en.wikipedia.org/wiki/SPC_file_format)
[2] "Universal Data Format Specification" (PDF). (https://ensembles-eu.metoffice.gov.uk/met-res/aries/technical/GSPC_UDF.PDF)

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