sdtfile 2020.12.10

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

Organization:

Laboratory for Fluorescence Dynamics. University of California, Irvine

License:

BSD 3-Clause

Version:

2020.12.10

Requirements

• CPython >= 3.7

• Numpy 1.15

Revisions

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.

Notes

The API is not stable yet and might change between revisions.

This module has been tested with a limited number of files only.

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,)