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AllenInstitute / drcme

Dimensionality-reduction and classification for morphology and electrophysiology
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Feature vector key discrepancy #19

Open blogeman opened 3 years ago

blogeman commented 3 years ago

One of the inputs to this package is a "feature vector" file generated by the package IPFX using its "run_feature_vector_extraction" script. The types of data generated from IPFX must match the key values listed in the spca_params.json input.

As of IPFX v 1.0 the names of the datasets have changed from what is listed in drcme/config/default_spca_params.json. Below are the discrepancies Capture : Shown in yellow are the dataset keys with the same name while blue indicates a discrepancy in the name. I think I've got them matched up correctly and after getting confirmation I can submit a pull request with the names changed to match the ipfx output.

gouwens commented 3 years ago

Thanks for identifying the issue. It looks correct apart from inst_freq - that should match up with the old spiking_inst_freq. The data set inst_freq_norm is actually calculated by DRCME rather than IPFX (since it's directly calculated from inst_freq in the H5 file). And subthresh_depol_norm doesn't have a pre-existing entry in that default parameters file.

blogeman commented 3 years ago

Oh that makes more sense now, thanks for clarifying. I've submitted a pull request to change the 3 key names that don't match.