sdtfile 2022.9.28

Read Becker & Hickl SDT files

Sdtfile is a Python library to read SDT files produced by Becker & Hickl SPCM software. SDT files contain time correlated single photon counting instrumentation parameters and measurement data. Currently only the “Setup & Data”, “DLL Data”, and “FCS Data” formats are supported.

Becker & Hickl GmbH is a manufacturer of equipment for photon counting.

Author:

Christoph Gohlke

License:

BSD 3-Clause

Version:

2022.9.28

Requirements

This release has been tested with the following requirements and dependencies (other versions may work):

• CPython 3.8.10, 3.9.13, 3.10.7, 3.11.0rc2

• Numpy 1.22.4

Revisions

2022.9.28

• Convert docstrings to Google style with Sphinx directives.

2022.2.2

• Add type hints.

• Drop support for Python 3.7 and numpy < 1.19 (NEP29).

2021.11.18

• Fix reading FLIM files created by Prairie View software (#5).

2021.3.21

• Add sdt2dat script.

2020.12.10

• Fix shape of non-square frames.

2020.8.3

• Fix integer overflow (#3).

• Support os.PathLike file names.

2020.1.1

• Fix reading MCS_BLOCK data.

• Remove support for Python 2.7 and 3.5.

• Update copyright.

2019.7.28

• Fix reading compressed, multi-channel data.

2018.9.22

• Use str, not bytes for ASCII data.

2018.8.29

• Move module into sdtfile package.

2018.2.7

• Bug fixes.

2016.3.30

• Support revision 15 files and compression.

2015.1.29

• Read SPC DLL data files.

2014.9.5

• Fix reading multiple MEASURE_INFO records.

References

1. W Becker. The bh TCSPC Handbook. Third Edition. Becker & Hickl GmbH 2008. pp 401.

2. SPC_data_file_structure.h header file. Part of the Becker & Hickl SPCM software.

Examples

Read image and metadata from a “SPC Setup & Data File”:

>>> sdt = SdtFile('image.sdt')
>>> sdt.header.revision
588
>>> sdt.info.id[1:-1]
'SPC Setup & Data File'
>>> int(sdt.measure_info[0].scan_x)
128
>>> len(sdt.data)
1
>>> sdt.data[0].shape
(128, 128, 256)
>>> sdt.times[0].shape
(256,)

Read data and metadata from a “SPC Setup & Data File” with mutliple data sets:

>>> sdt = SdtFile('fluorescein.sdt')
>>> len(sdt.data)
4
>>> sdt.data[3].shape
(1, 1024)
>>> sdt.times[3].shape
(1024,)

Read image data from a “SPC FCS Data File” as numpy array:

>>> sdt = SdtFile('fcs.sdt')
>>> sdt.info.id[1:-1]
'SPC FCS Data File'
>>> len(sdt.data)
1
>>> sdt.data[0].shape
(512, 512, 256)
>>> sdt.times[0].shape
(256,)