Batch Processing

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Batch Processing

All of the previous steps can be automated using the proc_data fuction located in the gcmstools.general module.

In : from gcmstools.general import proc_data

This function only has two required arguments: 1) the path to the folder that contains all of the GCMS files and 2) the name of the HDF data file that you’d like to generate. In this example, our data is in the folder “data” and our processed data file is called “data.h5”.

In : proc_data('data/', 'data.h5')
... # Lots of stuff will get printed at this point.

The proc_data function accepts numerous keyword arguments to allow some process control.

Complete Processing Command

A complete version of this processing command might look like the following.

In : proc_data('data/', 'data.h5', filetype='aia', reffile='ref_spects.txt',
        fittype='nnls', calfile='calibration.csv', multiproc=True)
### Lot's of stuff gets printed

The HDF file “data.h5” contains all of your data. See the Data Storage, Calibration and Concentration Determination, and Appendix B for more information on how to view and plot these data.

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