schnitzer-lab / EXTRACT-public

EXTRACT is a tractable and robust automated cell extraction tool for calcium imaging, which extracts the activities of cells as time series from both one-photon and two-photon calcium imaging movies.
MIT License
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inconsistencies b/w docs and code #32

Closed sg-s closed 1 year ago

sg-s commented 1 year ago

in this file, we find the following:

trace_output_option: EXTRACT has two options for trace output: 'raw' and 'nonneg'. 'nonneg' outputs only the signal portion of the trace, consistent with the fundamental assumptions of EXTRACT. 'raw' outputs signal + noise. Default: 'nonneg'.

However, when we look at the default config, we find:

>> config = get_defaults([]);
>> config.trace_output_option
ans =
    'baseline_adjusted'

which is not referred to in the docs

fatihdinc commented 1 year ago

Thanks! I am in the process of re-writing the full documentation, and will add a user manual soon.