Tools for reading PicoQuant file formats.
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README.md

libpicoquant

libpicoquant provides command-line interfaces to various formats used by PicoQuant TCSPC hardware. It is intended to provide a generic interface to these formats which is compatible with other analysis code (e.g. photon_correlation).

Hardware and measurement modes supported

HydraHarp

  • v1: hhd, ht2, ht3
  • v2: hhd, ht2, ht3

PicoHarp

  • v2: phd, pt2, pt3

TimeHarp

  • v3: thd, t3r
  • v5: thd
  • v6: thd, t3r

Overview

The picoquant command uses the binary header for the data file to determine the hardware identity, version, measurement mode, and any other relevant metadata. Using these metadata, it outputs the photon arrival or other data in a common format. Measurement modes currently supported:

  • Histogramming: also known as lifetime data, this is a histogram of counts per time bin, accumulated by integrating for some amount of time during a measurement
  • t2: the absolute arrival time of each detection event during a measurment. Often used for CW excitation
  • t3: the absolute arrival pulse and relative arrival time for each detection event durin a measurement. Used with pulsed excitation.

These measurements vary in their resolution and implementation across hardware, but in picoquant the data types are normalized. On the command line the output is comma-delimited records of the following formats:

  • histograming: detection channel, time bin (left edge), time bin (right edge), counts
  • t2: detection channel, arrival time
  • t3: detection channel, arrival pulse, arrival time

Usage

The most typical way to interact with the library is the picoquant command:

picoquant --file-in "data.phd"

This outputs the data contained in data.phd, with one record per line.

To view all of the metadata in INI-style format:

picoquant --file-in "data.phd" --header-only

Or just some:

picoquant --file-in "data.phd" --resolution-only

For any supported file format, simply change "data.phd" to your own file. picoquant is intelligent enough to find the correct decoder, or to tell you the format is not supported.

Further information

See the man page for fuller documentation of picoquant.

Contact

Let me know if you end up using this code. There are some internal quirks that should be smoothed out in order to make integration simpler (these updates are currently on the back burner), and I am happy to help or provide guidance.