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OpenReadout

trace

trace returns the samples and statistics of one sweep of a sampled signal: electrophysiology, chromatography detector traces, NMR FIDs and spectra, IR, Raman and UV-Vis spectra, qPCR curves and other 1-D data.

openreadout trace [OPTIONS] [FILE]...

info lists a file’s traces under traces[], with their sweeps, channels, units and sample rate.

Flags

  • --json: print the JSON wrapper instead of text.
  • --trace N: trace index. Default 0 (in a batch table, every trace).
  • --sweep N: sweep (episode or segment) index. Default 0 (in a batch table, every sweep).
  • --channel N: channel index. Repeatable. Default: all channels.
  • --first N: first sample of the window, zero-based within the sweep. Default 0.
  • --count N: window length in samples. Default: to the end of the sweep.
  • --x-range A:B: a window on the trace’s own axis instead of --first/--count: cm⁻¹, nm, ppm, or a chromatogram’s retention time. Seconds for signals without an axis.
  • --max-samples N: samples returned per channel, at most 100000. Default 1000. The statistics always cover the whole window.
  • --process: NMR: read FIDs as spectra processed by OpenReadout.
  • --process-phase MODE, --process-lb HZ, --process-size N, --process-baseline MODE: processing settings. See analyze nmr-peaks.

Several files, a directory or a glob give one table with a row per file, trace, sweep and channel. trace takes the flags in Several inputs and the batch table flags.

Examples

Terminal window
$ openreadout trace synthetic-timeseries.nwb --trace 2 --channel 0
synthetic-timeseries.nwb (nwb): trace 2 sweep 0/1  samples 0..1000 of 1000  2000 Hz
  ch0 voltage[0]       volts  min -0.205000  max 0.184610  mean -0.010195  std 0.112583
      max at sample 857 = 1.928500 s
      first: -0.205000, -0.202270, -0.199540

The wavenumber of the strongest band of an IR spectrum, and the statistics of one band:

Terminal window
openreadout trace sample.0 --only /channels/0/stats/argmax_axis_value
openreadout trace sample.0 --x-range 1000:1100

Reading the positions

  • argmin and argmax are sample indices counted from the start of the sweep, not the window.
  • argmax_time_s gives the position on the trace’s clock. For a chromatogram this is the retention time, which can be negative when acquisition started before injection.
  • argmax_axis_value gives the position on the trace’s axis (ppm, cm⁻¹, nm, minutes), so no arithmetic is needed.
  • Files without traces (images, FCS) exit 6. An index out of range exits 2.

Domain walkthroughs: Electrophysiology, NMR.

JSON

trace, batch table.

Run openreadout trace --help for the full help of your installed version.