I was made aware the other day that some people are still confused about Index Channels in iolite and what masking does. So I thought I'd start a discussion about it.
Here is a definition of both from a paper we're writing at the moment:
A data reduction scheme begins by assigning an `index channel'. The index channel in this instance is simply a channel that is measured in all files, and thus will have a complete associated time array c.f. channels that appear in a subset of files that will have gaps in their associated time arrays (there is no requisite in iolite that all channels appear in all data files). The intermediate and output channels and splines calculated by the DRS are interpolated onto the time array of the index channel. Optionally, a 'mask' can also be created which, depending on the chosen 'mask' method, can either be via the 'on' periods recorded in the laser log file, or in the absence of a laser log file, the 'cutoff' method can be chosen where results are masked during time intervals where the index channel drops below the chosen threshold. Masking helps avoid the noisy ratios associated with baseline intervals that overwhelm the vertical scale when plotting time-series.
It's a pretty short explanation, but if you have any questions, please feel free to post below.