https://github.com/cgohlke/sdtfile

Read Becker & Hickl SDT files.

Science Score: 49.0%

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CITATION.cff file
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codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
1 of 2 committers (50.0%) from academic institutions
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Scientific vocabulary similarity
Low similarity (12.0%) to scientific vocabulary

Keywords

fluorescence-lifetime-spectroscopy fluorescence-microscopy-imaging format-reader life-sciences-image photon-counting python

Last synced: 5 months ago · JSON representation

Repository

Read Becker & Hickl SDT files.

Basic Info

Host: GitHub
Owner: cgohlke
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage: https://pypi.org/project/sdtfile
Size: 52.7 KB

Statistics

Stars: 12
Watchers: 2
Forks: 7
Open Issues: 1
Releases: 6

Topics

fluorescence-lifetime-spectroscopy fluorescence-microscopy-imaging format-reader life-sciences-image photon-counting python

Created almost 6 years ago · Last pushed 10 months ago

Metadata Files

Readme Changelog License

README.rst

..
  This file is generated by setup.py

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: 2025.5.10
:DOI: `10.5281/zenodo.10125608 `_

Quickstart
----------

Install the sdtfile package and all dependencies from the
`Python Package Index `_::

    python -m pip install -U sdtfile

See `Examples`_ for using the programming interface.

Source code and support are available on
`GitHub `_.

Requirements
------------

This revision was tested with the following requirements and dependencies
(other versions may work):

- `CPython `_ 3.10.11, 3.11.9, 3.12.10, 3.13.3 64-bit
- `NumPy `_ 2.2.5

Revisions
---------

2025.5.10

- Support Python 3.14.

2025.3.25

- Fix shape of data with routing channels.
- Drop support for Python 3.9, support Python 3.13.

2024.12.6

- Fix read MeasureInfo fields as scalars (breaking).
- Update some structure field names with BH reference (breaking).
- Parse some SetupBlock binary structures (#7).
- Include more information in str(SdtFile).
- Add subtype to FileRevision.

2024.11.24

- Update MEASURE_INFO_EXT struct to SPCM v.9.9 (breaking).

2024.5.24

- Fix docstring examples not correctly rendered on GitHub.

2024.4.24

- Support NumPy 2.

2023.9.28

- Update structs to SPCM v.9.66 (breaking).
- Shorten MEASURE_INFO struct to meas_desc_block_length.

2023.8.30

- …

Refer to the CHANGES file for older revisions.

References
----------

1. W Becker. The bh TCSPC Handbook. 9th Edition. Becker & Hickl GmbH 2021.
   pp 879.
2. SPC_data_file_structure.h header file. Part of the Becker & Hickl
   SPCM software installation.

Examples
--------

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

.. code-block:: python

    >>> sdt = SdtFile('image.sdt')
    >>> int(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 multiple data sets:

.. code-block:: python

    >>> sdt = SdtFile('fluorescein.sdt')
    >>> len(sdt.data)
    4
    >>> sdt.data[3].shape
    (1, 1024)
    >>> sdt.times[3].shape
    (1024,)
    >>> int(sdt.setup.bh_bin_hdr['soft_rev'])
    850

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

.. code-block:: python

    >>> 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,)

Owner

Name: Christoph Gohlke
Login: cgohlke
Kind: user
Location: Irvine, California

Website: https://www.cgohlke.com
Repositories: 52
Profile: https://github.com/cgohlke

GitHub Events

Total

Release event: 4
Watch event: 4
Issue comment event: 5
Push event: 4
Pull request event: 2
Fork event: 2
Create event: 4

Last Year

Release event: 4
Watch event: 4
Issue comment event: 5
Push event: 4
Pull request event: 2
Fork event: 2
Create event: 4

Committers

Last synced: over 1 year ago

All Time

Total Commits: 69
Total Committers: 2
Avg Commits per committer: 34.5
Development Distribution Score (DDS): 0.362

Past Year

Commits: 21
Committers: 1
Avg Commits per committer: 21.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Christoph Gohlke	c**e@u**u	44
Christoph Gohlke	c**e@c**m	25

Committer Domains (Top 20 + Academic)

cgohlke.com: 1 uci.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 4
Total pull requests: 3
Average time to close issues: 1 day
Average time to close pull requests: 1 day
Total issue authors: 4
Total pull request authors: 2
Average comments per issue: 3.5
Average comments per pull request: 2.33
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 1 day
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 5.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

s-weigand (1)
bhmarscheck (1)
WeiWenKevinChen (1)
Isquare1 (1)

Pull Request Authors

larsbergenholtz (2)
s-weigand (2)

Top Labels

Issue Labels

Pull Request Labels

enhancement (2)

Packages

Total packages: 3
Total downloads:
- pypi 5,182 last-month

Total dependent packages: 5
(may contain duplicates)
Total dependent repositories: 6
(may contain duplicates)
Total versions: 28
Total maintainers: 1

pypi.org: sdtfile

Read Becker & Hickl SDT files

Homepage: https://www.cgohlke.com
Documentation: https://sdtfile.readthedocs.io/
License: BSD-3-Clause
Latest release: 2025.5.10
published 10 months ago

Versions: 19
Dependent Packages: 4
Dependent Repositories: 5
Downloads: 5,166 Last month

Rankings

Dependent packages count: 2.3%

Downloads: 2.9%

Dependent repos count: 6.7%

Average: 9.1%

Forks count: 13.3%

Stargazers count: 20.3%

Maintainers (1)

cgohlke

Last synced: 6 months ago

pypi.org: napari-sdtfile

A napari plugin for reading files via sdtfile

Homepage: https://www.lfd.uci.edu/~gohlke/
Documentation: https://napari-sdtfile.readthedocs.io/
License: BSD
Latest release: 0.0.3
published about 4 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 16 Last month

Rankings

Dependent packages count: 10.0%

Forks count: 13.3%

Stargazers count: 20.3%

Dependent repos count: 21.8%

Average: 29.6%

Downloads: 82.8%

Maintainers (1)

cgohlke

Last synced: 6 months ago

conda-forge.org: sdtfile

Homepage: https://www.cgohlke.com/
License: BSD-3-Clause
Latest release: 2022.9.28
published over 3 years ago

Versions: 7
Dependent Packages: 1
Dependent Repositories: 0

Rankings

Dependent packages count: 28.8%

Dependent repos count: 34.0%

Average: 41.1%

Forks count: 46.0%

Stargazers count: 55.7%

Last synced: 6 months ago

Dependencies

setup.py pypi

numpy >=1.19.2