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eyurtsev / fcsparser

A python parser for reading fcs files supporting FCS 2.0, 3.0, 3.1
MIT License
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$PnE based rescaling is not heeded #16

Open xiamaz opened 6 years ago

xiamaz commented 6 years ago

According to the FCS 3.1 specification (and probably older ones, too), logarithmic data channels can be saved in linearized form with $PnE specifying the logarithmic range and minimal value.

Currently the library does not transform these values into logarithmic form for later transformations.

eyurtsev commented 6 years ago

Feel free to file a PR if you know how to fix this

My only concern would be to provide the user with enough information to know that a transformation has been applied to the data

bpteague commented 6 years ago

Hi @xiamaz - for what it's worth, I've just implemented this functionality in my project, cytoflow, which builds on fcsparser. It's a pretty straightforward transformation to do once you've sucked the data in with fcsparser -- see commit bpteague/cytoflow@039f9aba1664fe274cd8613c342edc2a9602c7f1 for details.