Electrodes mapping #92
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luiztauffer
commented
Jun 8, 2020
luiztauffer
commented
- maps electrodes ids for each trace
- fix Cannot save bad channels #89
Codecov Report
@@ Coverage Diff @@
## master #92 +/- ##
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- Coverage 19.12% 19.12% -0.01%
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Files 25 25
Lines 5584 5580 -4
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- Hits 1068 1067 -1
+ Misses 4516 4513 -3
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ecogvis/functions/nwb_copy_file.py
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| @@ -266,10 +266,10 @@ def copy_obj(obj_old, nwb_old, nwb_new): | |||
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| # ElectricalSeries -------------------------------------------------------- | |||
| if type(obj_old) is ElectricalSeries: | |||
| nChannels = len(obj_old.electrodes.table['x'].data) | |||
| elecs_region = nwb_new.electrodes.create_region( | |||
| region = list(obj_old.electrodes.to_dataframe().index) | |||
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Here you are converting to a dataframe, which will work but is unnecessarily costly if all you want is the ids in the region. It is more efficient to first get the ids from the table, and then index them by the data field of the ElectricalSeries.electrodes.data. See the eventual fix for similar code in SpikeInterface:
https://github.com/SpikeInterface/spikeextractors/pull/401/files
ecogvis/functions/subFunctions.py
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| self.nChTotal = self.source.data.shape[1] # total number of channels | ||
| self.allChannels = np.arange(0, self.nChTotal) # array with all channels | ||
| self.all_channels_ids = list(self.source.electrodes.to_dataframe().index) # all channels ids | ||
| self.n_channels_total = len(self.all_channels_ids) # total number of channels |
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Similar issue here. See:
https://github.com/SpikeInterface/spikeextractors/pull/401/files
Also, I don't the "all_channel_ids" is an appropriate name here because we are intentionally excluding the channels that are not associated with the ElectricalSeries, so maybe electrical_series_channel_ids would be better
- remove unused button save bad channels
- change channel index in copy
