pyptu 2023.1

Load PicoQuant PTU files.

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title: README author: Jan-Michael Rye

Synopsis

Read PicoQuand PTU files. The code follows the same parsing logic as the Python demo provided by PicoQuant but is up to 40 times faster due to the use of vectorized operations using Numpy arrays.

Links

• Source code
• Online documentation
• PyPI package

Usage

Python API

The data in the file is parsed into the following objects which are set as attributes of the parser:

• headers - A dict mapping header fields to their values.
• markers - A Pandas DataFrame where each row is a record index with an index, a time tag and a marker.
• overflows - A Pandas DataFrame where each row is a record with a record index and an overflow values.
• photons.csv - A Pandas DataFrame where each row is a record with a record index, a channel, a time tag, a resolved time tag (using the global resolution value), and a dtime value.

from pyptu import PTUParser

# A path to a PTU file.
path = /tmp/example.ptu

# Instantiate the parser.
parser = PTUParser(path)

# Load the data.
parser.load()

# The PTU header data.
headers = parser.headers

# The Pandas DataFrame of photon data.
photons = parser.photons

# The Pandas DataFrame of marker data.
markers = parser.markers

# The Pandas DataFrame of overflow values.
overflows = parser.overflows

Command-Line

The package installs the pyptu command-line tool that can be used to convert the data in a PTU file to JSON and CSV files. It accepts the path to a PTU file and an output directory.

# Extract the PTU data to files in an output directory.
pyptu example.ptu output_directory

The output directory will contain the following files:

• header.json - A JSON file with the headers described above.
• markers.csv - A CSV file containing the markers DataFrame.
• overflows.csv - A CSV file containing the overflows DataFrame.
• photons.csv - A CSV containing the photons DataFrame.

Help Message

$ pyptu -h
usage: pyptu [-h] path dir

Extract PTU data to standard files.

positional arguments:
  path        A path to a PTU file.
  dir         A path to an output directory.

options:
  -h, --help  show this help message and exit