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JCAMP-DX file reader

Project description

# jcamp

## Overview

A set of Python utilities for reading [JCAMP-DX](http://www.jcamp-dx.org/) files.

The following features are supported:

  • JCAMP-DX are parsed

  • x values are normalized to wavelength values (in microns)

  • y values are interpreted (optional)

A few example datasets are provided.

## Installation

You can download and install the latest version of this software from the Python package index ([PyPI](https://pypi.org/)) as follows:

`shell pip install --upgrade jcamp `

## Parsing a file

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.

If the input is a compound file, then the returned dictionary will contain a children field. This field is an array of dictionaries that each represent a block.

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.

## Using jcamp for web queries

In order to use jcamp for online queries rather than static text files, we can use the following procedure with the requests package:

`python response = requests.get(something) content = response.content.splitlines() content = [line.decode("utf-8") for line in content] data_dict = jcamp_read(content) `

## Contributing

Your contributions and hints are welcome.

See [CONTRIBUTING.md](CONTRIBUTING.md) for details.

## License

jcamp is licensed under the MIT License - see the [LICENSE.txt](./LICENSE.txt) file for details

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