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phy format

This is an early draft.

  • Root directory: /home/user/spikesorting/20160101/
  • All paths below are relative to this directory.

Raw data

API

Looking at the traces in the terminal:

phy traces 20160101_1.ns5
phy traces 20160101_2.dat --n-channels=128 --dtype=int16 --sample-rate=20000

Looking at the traces in IPython:

import phy.io
import phy.plot as plt

traces = phy.io.read_traces(['20160101_1.ns5', '20160101_2.dat'])
plt.plot_traces(traces)
plt.show()

File structure

/20160101_1.ns5
/20160101_2.dat
/metadata.json
[/params.prm]

/main/0/params.json  # refers to basename of dat files
/main/0/clusters.json  # metadata about JSON
/main/0/spike_times.npy
/main/0/spike_clusters.npy
/main/0/mean_waveforms.npy
/main/0/raw_0.ns5  # symlinks to ../20160101_1.ns5...
/main/0/raw_1.dat

/test/0/...

Data arrays

  • An array is either:

    • a JSON array,
    • or an object with a path attribute.

  • The path refers to a file

  • The path is relative to the phy directory.

  • Every array is defined by one file

  • The file extension defines the format for the array

  • Supported formats: txt, npy, ns5, Neo formats http://neo.readthedocs.org/en/latest/io.html...

  • New tar format: first archived file is format.ini with comment with link to description, array description, then one or several flat binary files

    • array description in ini: dtype, shape, labels

API

  • TODO: how the user specifies the parameters/probe (PRM? PRB)? Where these files should be stored? Should the parameters be imported in the JSON? => duplication problem. Any traces/spike detection/clustering parameter should be stored in a single file.

_read_array(path)
_write_array(path, array)


exp = Experiment(metadata_path=None, metadata_dict=None, base_dir=None)

exp.base_dir  # the path (absolute or relative) to the root.
              # all relative paths are made relative to the base dir

exp.metadata  # the JSON dictionary
exp.read_metadata(alias_or_path)  # return a dict
exp.write_metadata(alias_or_path, metadata)  # update the current metadata
                                             # dict and save it

exp._resolve_alias(alias)  # return a relative path
exp.read_array(alias_or_path)  # return an array
exp.write_array(alias_or_path, array)

Examples
exp.read_array('0/spike_times')
exp.read_array('0/spike_times')