phconvert
Convert Beker&Hickl, PicoQuant and other formats to Photon-HDF5
Science Score: 36.0%
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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 -
○DOI references
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○Academic publication links
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✓Committers with academic emails
3 of 8 committers (37.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.8%) to scientific vocabulary
Repository
Convert Beker&Hickl, PicoQuant and other formats to Photon-HDF5
Basic Info
- Host: GitHub
- Owner: Photon-HDF5
- License: other
- Language: Python
- Default Branch: master
- Homepage: http://photon-hdf5.github.io/phconvert
- Size: 809 KB
Statistics
- Stars: 16
- Watchers: 6
- Forks: 13
- Open Issues: 11
- Releases: 26
Metadata Files
README.md
phconvert
phconvert is a python 2 & 3 library that helps writing valid Photon-HDF5 files, a file format for time stamp-based single-molecule spectroscopy. Additionally, phconvert can convert to Photon-HDF5 all the common binary formats used in solution-based single-molecule spectroscopy. These includes PicoQuant's .HT3/.PT3/.PTU/.T3R, Becker & Hickl's .SPC/.SET and the .SM format used by WeissLab and others for µs-ALEX smFRET.
For questions or issues running this software please use the Photon-HDF5 Google Group or open an issue on GitHub.
What's new
Nov. 2018: Phconvert 0.9 released, see the release notes.
Quick-start: Converting files to Photon-HDF5
Converting one of the supported files formats to Photon-HDF5 does not require being able to program in python. All you need is running the "notebook" corresponding to the file format you want to convert from, and follow the instructions therein.
For demonstration purposes, we provide a demo service to run the notebooks online without any installation. With this online service, you can convert data files up to 35MB to Photon-HDF5. To launch the demo click on the following button (see also instructions):
To execute the phconvert notebooks on your machine, you need to install the Jupyter Notebook App first. A quick-start guide on installing and running the Jupyter Notebook App is available here:
Next, you need to install the phconvert library with the following command
(type it in Terminal on OS X or Linux, or in the cmd prompt on Windows):
conda install -c conda-forge phconvert
Finally, you can download one of the provided notebooks and run it on your machine.
Simply, download the
phconvert zip,
which contains all the notebooks in the notebooks subfolder.
For questions or issues:
- Open an GitHub issue or
- Ask a question on the Photon-HDF5 Google Group.
Project details
What's inside?
phconvert repository contains a python package (library) and a set of notebooks (online viewer). Each notebook can convert a different format to Photon-HDF5 using the phconvert library.
If you have a file format that is not yet supported, please open an new Issue. We are willing add support for as many file formats as possible!
Why phconvert?
When writing Photon-HDF5 files, phconvert saves you time and protects you against common errors that risk to make the file not a valid Photon-HDF5. Also a description is automatically added to each Photon-HDF5 field. The descriptions are extracted from a JSON file which contains the list Photon-HDF5 field names, types, and descriptions.
See also Writing Photon-HDF5 files in the Photon-HDF5 reference documentation.
Read Photon-HDF5 files
In case you just want to read Photon-HDF5 files you don't need to use phconvert. Photon-HDF5 files can be directly opened with a standard HDF5 viewer HDFView.
See also Reading Photon-HDF5 files in the Photon-HDF5 reference documentation.
Installation
The recommended way to install phconvert is using conda:
conda install -c conda-forge phconvert
If you don't have conda installed, please install the free python distribution Anaconda choosing the python 3 version. Starting from version 0.9, the aging python 2.7 is not supported anymore.
Alternatively, you can install phconvert in any python installation using PIP:
pip install phconvert
In this latter case, make sure that numpy and pytables are installed.
See also:
Dependencies
- python 3.4 or greater (3.6+ recommended)
- numpy >=1.9
- pytables >=3.1
- numba (optional) for faster PicoQuant files decoding
Note when installing via
condaall the dependencies are automatically installed.
The phconvert library documentation (for developers)
The phconvert API documentation can be found on ReadTheDocs:
License
phconvert is released under the open source MIT license.
Contributing
As with other Photon-HDF5 subprojects, we encourage contributions in any form, from simple suggestions, typo fix to the addition of new features. Please use GitHub by opening Issues or sending Pull Requests.
All the contributors will be acknowledged in this website, and will included as authors in the next software-paper publication.
For more details see our contribution policy.
Authors & Contributors
List of contributors:
- Antonino Ingargiola (@tritemio)
- Ted Laurence (@talaurence)
- Marco Lamperti (@lampo808)
- Xavier Michalet (@smXplorer)
- Anders Barth (@AndersBarth)
- Biswajit Pradhan (@biswajitSM) <biswajitp145 AT gmail.com.
- Sébastien Weber (@seb5g)
- David Palmer (@dmopalmer)
We thank also @ncodina for providing PTU files and helping in testing the PTU decoder in phconvert.
Acknowledgements
This work was supported by NIH Grant R01-GM95904.
Release 0.9 was supported by Prof. Eitan Lerner.
Owner
- Name: Photon-HDF5
- Login: Photon-HDF5
- Kind: organization
- Website: http://photon-hdf5.org/
- Repositories: 6
- Profile: https://github.com/Photon-HDF5
The open file format for timestamp-based single-molecule spectroscopy.
GitHub Events
Total
- Issue comment event: 8
- Push event: 2
- Pull request event: 1
- Create event: 1
Last Year
- Issue comment event: 8
- Push event: 2
- Pull request event: 1
- Create event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Antonino Ingargiola | t****o@g****m | 528 |
| Biswajit Pradhan | b****5@g****m | 5 |
| smXplorer | m****t@c****u | 3 |
| seb5g | s****r@g****m | 2 |
| AndersBarth | a****h@g****m | 1 |
| David Palmer | p****r@l****v | 1 |
| m_lamperti | m****o@g****m | 1 |
| talaurence | l****2@l****v | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 36
- Total pull requests: 26
- Average time to close issues: 4 months
- Average time to close pull requests: 6 months
- Total issue authors: 20
- Total pull request authors: 10
- Average comments per issue: 4.39
- Average comments per pull request: 2.27
- Merged pull requests: 20
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 9.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- tritemio (12)
- ncodina (3)
- AndersBarth (2)
- jrivers96 (2)
- smXplorer (2)
- Mattyboi123 (1)
- nzijlstra (1)
- Tomkaehst (1)
- snizzleorg (1)
- mayeshh (1)
- talaurence (1)
- lampo808 (1)
- dmopalmer (1)
- tomjensen2 (1)
- MaraHenschel (1)
Pull Request Authors
- tritemio (9)
- jacrossley (4)
- harripd (4)
- ramenbytes (4)
- seb5g (3)
- lampo808 (2)
- biswajitSM (2)
- talaurence (2)
- dmopalmer (1)
- AndersBarth (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 3,865 last-month
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Total dependent packages: 2
(may contain duplicates) -
Total dependent repositories: 6
(may contain duplicates) - Total versions: 27
- Total maintainers: 2
pypi.org: phconvert
Convert Beker&Hickl, PicoQuant and other formats to Photon-HDF5.
- Homepage: http://photon-hdf5.github.io/phconvert/
- Documentation: https://phconvert.readthedocs.io/en/latest/
- License: The MIT License (MIT) Copyright (c) 2015-2016 The Regents of the University of California, Antonino Ingargiola and contributors. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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Latest release: 0.9.1
published about 2 years ago
Rankings
conda-forge.org: phconvert
*phconvert* is a python 3 library that helps writing valid Photon-HDF5 <http://photon-hdf5.org/> files, a file format for time stamp-based single-molecule spectroscopy. Additionally, phconvert can convert all the common binary formats used in in single-molecule spectroscopy (e.g. PicoQuant .HT3, Becker & Hickl .SPC/.SET) to Photon-HDF5.
- Homepage: http://photon-hdf5.github.io/phconvert
- License: MIT
-
Latest release: 0.8.2
published almost 4 years ago
Rankings
Dependencies
- actions/checkout v4 composite
- conda-incubator/setup-miniconda v3 composite
- importlib_resources python_version<="3.10"
- numpy >=1.19
- tables *