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JCAMP-DX file reader

Project description

A set of Python utilities for reading JCAMP-DX files.

The JCAMP_reader() function takes a filename as input, and returns a dictionary containing the data found in the file. Specifically, the keys contained in the dictionary are: (1) the field names found in the file’s header, with values being int- or float-type if the corresponding field is a numerical type, or a string-type otherwise. (2) two arrays x and y, giving the scaled values of the data points (scaled according to the xfactor and yfactor fields in the header, if they exist. The units of x and y are whatever are indicated in the header fields xunits and yunits, if these exist.

The JCAMP_calc_xsec() function is intended to takes as input the result of the JCAMP_reader() function and to convert the x data to wavelength in microns, and the y data to cross-section in units of m^2 for gas concentration of 1ppm at standard atmospheric pressure and temperature, across a path length of 1 meter. The JCAMP_calc_xsec() function takes as input the data dictionary jcamp_dict, and manipulates that dictionary directly without having a separate return value. Changes to the dictionary may including adding the fields:

wavelengths: the array of wavelength values (in microns) for each data point
wavenumbers: the array of wavenumber values (in cm^-1) for each data point
xsec: the array of cross-section values (in units of m^2 at 1ppm.m)

and modifying the fields:

xunits: micron
yunits: m^2 at 1ppm.m

The optional arguments wavemin, wavemax are used if the user wishes to truncate the data to only a desired spectral range. For example, setting wavemin=8.0 and wavemax=12.0 means that the returned data arrays will only contain data corresponding to those wavlengths. If the skip_nonquant optional input argument is used, then any input spectrum that does not have the complete path_length and partial_pressure fields in its dictionary will be passed without modification. (That is, no conversion to quantitative cross-section will be attempted.) If this option is set to True, then if the code finds missing data, it will attempt to generate a quantitative cross-section by guessing the missing values. Based upon NIST’s infrared database, typical values for guessing here are partial_pressure = 150.0 mmHg and path length = 0.1 m.

You can view a notebook demo in the doc folder to see how you can produce a series of plots showing spectra.

jcamp files

The repository comes with four folders containing JCAMP-format files: infrared_spectra/, mass_spectra/, raman_spectra/, and uvvis_spectra. These were downloaded from freely-available internet databases, and can be used as example format files.

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