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A python package that converts SpikeGadgets rec files in the Frank lab directory format to more useable binaries with the same directory format.

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rec_to_binaries

rec_to_binaries is a python package that converts SpikeGadgets rec files in the Frank lab directory format to more useable binaries with the same directory format. The binaries are more useable because the data in the rec files has been broken out into separate categories.

The package wraps C++ functions provided by SpikeGadgets in order to put everything into the correct directory structure. It extracts rec files in the /raw folder to binaries to the /preprocessing folder.

The binaries are separated out into:

  • analog
  • DIO
  • LFP
  • mda (for mountainSort spike sorting)
  • spikes (for trodes spike sorting)
  • time

Installation

  1. Download SpikeGadgets and install (https://bitbucket.org/mkarlsso/trodes/downloads/)
  2. Add SpikeGadgets to path (assuming the SpikeGadgets is in the default location)
export PATH="$HOME/SpikeGadgets/:$PATH"
  1. Download and install miniconda (https://docs.conda.io/en/latest/miniconda.html) if conda isn't installed.
  2. Install rec_to_binaries package into a conda environment
conda install -c franklab rec_to_binaries

Usage

import logging
from rec_to_binaries import extract_trodes_rec_file

logging.basicConfig(level='INFO', format='%(asctime)s %(message)s',
                    datefmt='%d-%b-%y %H:%M:%S')

data_dir = 'test_data/'
animal = 'lotus'

extract_trodes_rec_file(data_dir, animal, parallel_instances=4)

Common Issues

  • Problem: rec_to_binaries is not finding my files. Solution: Data is not in the correct file structure. See below for the expected format.
  • Problem: rec_to_binaries can't find a function. Solution: Make sure you have Trodes installed and on your path.
  • Problem: rec_to_binaries won't import. Solution: If you used conda then make sure the environment you installed rec_to_binaries in is activated.

Example file structure (in folder test_data/)

Before running extract_trodes_rec_file

.
|-- lotus
|   |
|   `-- raw
|       `-- 20190902
|           |-- 20190902_lotus_06_r3.1.h264
|           |-- 20190902_lotus_06_r3.1.trackgeometry
|           |-- 20190902_lotus_06_r3.1.videoPositionTracking
|           |-- 20190902_lotus_06_r3.1.videoTimeStamps
|           |-- 20190902_lotus_06_r3.1.videoTimeStamps.cameraHWSync
|           |-- 20190902_lotus_06_r3.rec
|           `-- 20190902_lotus_06_r3.stateScriptLog
`-- README.md

After running extract_trodes_rec_file

.
|-- lotus
|   |-- preprocessing
|   |   `-- 20190902
|   |       |-- 20190902_lotus_06_r3.1.pos
|   |       |   |-- 20190902_lotus_06_r3.1.pos_cameraHWFrameCount.dat
|   |       |   |-- 20190902_lotus_06_r3.1.pos_online.dat
|   |       |   `-- 20190902_lotus_06_r3.1.pos_timestamps.dat
|   |       |-- 20190902_lotus_06_r3.analog
|   |       |   |-- 20190902_lotus_06_r3.analog_AccelX.dat
|   |       |   |-- 20190902_lotus_06_r3.analog_AccelY.dat
|   |       |   |-- 20190902_lotus_06_r3.analog_AccelZ.dat
|   |       |   |-- 20190902_lotus_06_r3.analog_GyroX.dat
|   |       |   |-- 20190902_lotus_06_r3.analog_GyroY.dat
|   |       |   |-- 20190902_lotus_06_r3.analog_GyroZ.dat
|   |       |   |-- 20190902_lotus_06_r3.analog_MagX.dat
|   |       |   |-- 20190902_lotus_06_r3.analog_MagY.dat
|   |       |   |-- 20190902_lotus_06_r3.analog_MagZ.dat
|   |       |   |-- 20190902_lotus_06_r3.exportanalog.log
|   |       |   `-- 20190902_lotus_06_r3.timestamps.dat
|   |       |-- 20190902_lotus_06_r3.DIO
|   |       |   |-- 20190902_lotus_06_r3.dio_Din10.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din11.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din12.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din13.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din14.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din15.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din16.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din17.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din18.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din19.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din1.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din20.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din21.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din22.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din23.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din24.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din25.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din26.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din27.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din28.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din29.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din2.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din30.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din31.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din32.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din3.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din4.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din5.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din6.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din7.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din8.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Din9.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout10.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout11.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout12.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout13.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout14.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout15.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout16.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout17.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout18.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout19.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout1.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout20.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout21.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout22.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout23.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout24.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout25.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout26.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout27.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout28.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout29.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout2.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout30.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout31.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout32.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout3.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout4.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout5.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout6.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout7.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout8.dat
|   |       |   |-- 20190902_lotus_06_r3.dio_Dout9.dat
|   |       |   `-- 20190902_lotus_06_r3.exportdio.log
|   |       |-- 20190902_lotus_06_r3.LFP
|   |       |   |-- 20190902_lotus_06_r3.exportLFP.log
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt10ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt11ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt12ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt13ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt14ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt15ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt16ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt17ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt18ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt19ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt1ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt20ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt21ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt22ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt23ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt24ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt25ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt26ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt27ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt28ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt29ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt2ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt30ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt31ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt32ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt3ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt4ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt5ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt6ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt7ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt8ch1.dat
|   |       |   |-- 20190902_lotus_06_r3.LFP_nt9ch1.dat
|   |       |   `-- 20190902_lotus_06_r3.timestamps.dat
|   |       |-- 20190902_lotus_06_r3.mda
|   |       |   |-- 20190902_lotus_06_r3.exportmda.log
|   |       |   |-- 20190902_lotus_06_r3.nt10.mda
|   |       |   |-- 20190902_lotus_06_r3.nt11.mda
|   |       |   |-- 20190902_lotus_06_r3.nt12.mda
|   |       |   |-- 20190902_lotus_06_r3.nt13.mda
|   |       |   |-- 20190902_lotus_06_r3.nt14.mda
|   |       |   |-- 20190902_lotus_06_r3.nt15.mda
|   |       |   |-- 20190902_lotus_06_r3.nt16.mda
|   |       |   |-- 20190902_lotus_06_r3.nt17.mda
|   |       |   |-- 20190902_lotus_06_r3.nt18.mda
|   |       |   |-- 20190902_lotus_06_r3.nt19.mda
|   |       |   |-- 20190902_lotus_06_r3.nt1.mda
|   |       |   |-- 20190902_lotus_06_r3.nt20.mda
|   |       |   |-- 20190902_lotus_06_r3.nt21.mda
|   |       |   |-- 20190902_lotus_06_r3.nt22.mda
|   |       |   |-- 20190902_lotus_06_r3.nt23.mda
|   |       |   |-- 20190902_lotus_06_r3.nt24.mda
|   |       |   |-- 20190902_lotus_06_r3.nt25.mda
|   |       |   |-- 20190902_lotus_06_r3.nt26.mda
|   |       |   |-- 20190902_lotus_06_r3.nt27.mda
|   |       |   |-- 20190902_lotus_06_r3.nt28.mda
|   |       |   |-- 20190902_lotus_06_r3.nt29.mda
|   |       |   |-- 20190902_lotus_06_r3.nt2.mda
|   |       |   |-- 20190902_lotus_06_r3.nt30.mda
|   |       |   |-- 20190902_lotus_06_r3.nt31.mda
|   |       |   |-- 20190902_lotus_06_r3.nt32.mda
|   |       |   |-- 20190902_lotus_06_r3.nt3.mda
|   |       |   |-- 20190902_lotus_06_r3.nt4.mda
|   |       |   |-- 20190902_lotus_06_r3.nt5.mda
|   |       |   |-- 20190902_lotus_06_r3.nt6.mda
|   |       |   |-- 20190902_lotus_06_r3.nt7.mda
|   |       |   |-- 20190902_lotus_06_r3.nt8.mda
|   |       |   |-- 20190902_lotus_06_r3.nt9.mda
|   |       |   `-- 20190902_lotus_06_r3.timestamps.mda
|   |       |-- 20190902_lotus_06_r3.mountain
|   |       |-- 20190902_lotus_06_r3.spikes
|   |       |   |-- 20190902_lotus_06_r3.exportspikes.log
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt10.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt11.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt12.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt13.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt14.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt15.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt16.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt17.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt18.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt19.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt1.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt20.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt21.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt22.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt23.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt24.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt25.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt26.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt27.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt28.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt29.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt2.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt30.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt31.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt32.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt3.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt4.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt5.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt6.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt7.dat
|   |       |   |-- 20190902_lotus_06_r3.spikes_nt8.dat
|   |       |   `-- 20190902_lotus_06_r3.spikes_nt9.dat
|   |       `-- 20190902_lotus_06_r3.time
|   |           |-- 20190902_lotus_06_r3.continuoustime.dat
|   |           |-- 20190902_lotus_06_r3.exporttime.log
|   |           `-- 20190902_lotus_06_r3.time.dat
|   `-- raw
|       `-- 20190902
|           |-- 20190902_lotus_06_r3.1.h264
|           |-- 20190902_lotus_06_r3.1.trackgeometry
|           |-- 20190902_lotus_06_r3.1.videoPositionTracking
|           |-- 20190902_lotus_06_r3.1.videoTimeStamps
|           |-- 20190902_lotus_06_r3.1.videoTimeStamps.cameraHWSync
|           |-- 20190902_lotus_06_r3.rec
|           `-- 20190902_lotus_06_r3.stateScriptLog
`-- README.md

About

A python package that converts SpikeGadgets rec files in the Frank lab directory format to more useable binaries with the same directory format.

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v0.7.5 Latest
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