PTU2BIN

Copyright (c) 2021 Christian R. Halaszovich (See LICENSE.txt for licensing information.)

Introduction

Tools to convert PicoQuant PTU files (as written by e.g. PicoQuant's SymPhoTime 64) to BIN files or IgorPro binary wave files (IBW) containing pre-histogrammed data.

This works for T3-mode FLIM data. The file must have been recorded in "Image" mode, "Point" or "Line" modes are not supported.

It has only been tested with TimeHarp260P and PicoHarp data so far. Feel free to get in touch with me if you need additional formats supported. Support for T2 mode is planned.

There are two tools provided:

• PTU2BIN - This is the conversion tool that is used to convert individual PTU files. (The original file is preserved, of course.) Additionally, some useful metadata is extracted from the PTU file.

• convertPTUs.py - A Python script that batch-converts all .ptu files in the current directory and its sub-directories using PTU2BIN. By default the output from PTU2BIN is written to individual text files. There is a command-line switch to send the output of PTU2BIN to the terminal instead.

BUILDING

Only the PTU2BIN executable needs to be build. The python script can be used "as is". Only standard C++17 is used, so building should work on most systems. Instructions for Windows and Linux are provided.

External dependencies: cxxopts.hpp (available at https://github.com/jarro2783/cxxopts.git). A copy of this file has been placed in the "PTU2BIN/external/" directory. PTU2BIN was build using version 2.2.1 of cxxopts, newer versions might contain breaking changes.

The build process uses cmake. You will need a C++ compiler installed. To install from scratch, first clone the repository:

git clone https://github.com/ChrisHal/PTU2BIN.git

Create the build directory:

mkdir PTU2BIN_build

The build directory should sit in parallel to the repository directory "PTU2BIN". Change to the build directory:

cd PTU2BIN_build

Execute these commands (for "Release" type build):
cmake -DCMAKE_BUILD_TYPE=Release ../PTU2BIN
cmake --build . --config Release

INSTALLATION

Make sure that Python3.7 (or higher) is installed on your system.

The executables will be installed in the default path ('/usr/local/bin' on Unix-like systems, e.g. Linux and Mac OS X, on Windows 'bin' in the users home directory). You should make sure that this directory is included in your PATH.

Use this command (executed in the build directory):

windows: cmake --install .

Linux, Mac OS X etc.: sudo cmake --install .

USAGE

Batch-Processing

To convert all files in current directory and subdirectories:

Windows: Double-click convertPTUs.py -> all PTU files that are found in sub-directories, starting from the location of convertPTUs.py will be converted.

Alternatively, if you installed in your PATH, you can use the method described in the next paragraph.

Linux and unixoids (and also Windows): In terminal, change to the directory where the PTU files to be converted reside. Start the conversion using the command convertPTUs.py.

By default, the output of the conversion tool for each converted <name>.ptu file will be written to a <name>.txt file. Use option -d to direct this output to the terminal.

To learn about additional features, execute

convertPTUs.py -h

Converting individual files

All OSs: It is assumed that PTU2BIN is installed in your path.

To convert a single file:

PTU2BIN <infile> <outfile> [<channel #>]

<infile> must be in PTU format.

If <outfile> has extension .ibw, an Igor binary file is written, otherwise a BIN file.

The created file will contain data from one individual detector channel or the sum of data from all channels. For historical reasons, channel # 2 is evaluated by default. This can be overwritten by giving the number of the desired channel as the 3rd argument. Numbers <=0 indicate that all channels should be used, i.e. the photon counts of all channels will be summed together.

To learn about additional options:

PTU2BIN --help