diff --git a/README.md b/README.md index 189ee40cedbbb355878019bd14794a41ecfcc872..fbb77290b44c51d325dda1bb0603dca95cad5bc3 100644 --- a/README.md +++ b/README.md @@ -1,55 +1,37 @@ -# nd2reader +# zolfa-nd2reader -[](https://anaconda.org/conda-forge/nd2reader) -[](https://anaconda.org/conda-forge/nd2reader) -[](https://github.com/rbnvrw/nd2reader/actions/workflows/python-package.yml) ### About -`nd2reader` is a pure-Python package that reads images produced by NIS Elements 4.0+. It has only been definitively tested on NIS Elements 4.30.02 Build 1053. Support for older versions is being actively worked on. +`zolfa-nd2reader` is a pure-Python package that reads images produced by NIS Elements 4.0+. It has only been definitively tested on NIS Elements 4.30.02 Build 1053. Support for older versions is being actively worked on. The reader is written in the [pims](https://github.com/soft-matter/pims) framework, enabling easy access to multidimensional files, lazy slicing, and nice display in IPython. +This version is a fork of the project of published [here](https://github.com/Open-Science-Tools/nd2reader). + ### Documentation -The documentation is available [here](http://www.lighthacking.nl/nd2reader/). +Documentation specific to this fork is not available yet. + +The documentation of the origianl `nd2reader` project was available [here](http://www.lighthacking.nl/nd2reader/). ### Installation The package is available on PyPi. Install it using: ``` -pip install nd2reader +pip install zolfa-nd2reader ``` -If you don't already have the packages `numpy`, `pims`, `six` and `xmltodict`, they will be installed automatically if you use the `setup.py` script. -Python >= 3.5 are supported. - -#### Installation via Conda Forge +If you don't already have the packages `numpy`, `pims` and `xmltodict`, they will be installed automatically running pip. +Python >= 3.10 are supported. -Installing `nd2reader` from the `conda-forge` channel can be achieved by adding `conda-forge` to your channels with: - -``` -conda config --add channels conda-forge -``` - -Once the `conda-forge` channel has been enabled, `nd2reader` can be installed with: - -``` -conda install nd2reader -``` - -It is possible to list all of the versions of `nd2reader` available on your platform with: - -``` -conda search nd2reader --channel conda-forge -``` ### ND2s `nd2reader` follows the [pims](https://github.com/soft-matter/pims) framework. To open a file and show the first frame: ```python -from nd2reader import ND2Reader +from zolfa.nd2reader import ND2Reader import matplotlib.pyplot as plt with ND2Reader('my_directory/example.nd2') as images: @@ -58,13 +40,9 @@ with ND2Reader('my_directory/example.nd2') as images: After opening the file, all `pims` features are supported. Please refer to the [pims documentation](http://soft-matter.github.io/pims/). -#### Backwards compatibility - -Older versions of `nd2reader` do not use the `pims` framework. To provide backwards compatibility, a legacy [Nd2](http://www.lighthacking.nl/nd2reader/nd2reader.html#module-nd2reader.legacy) class is provided. - ### Contributing -If you'd like to help with the development of nd2reader or just have an idea for improvement, please see the [contributing](https://github.com/rbnvrw/nd2reader/blob/master/CONTRIBUTING.md) page +If you'd like to help with the development of nd2reader or just have an idea for improvement, please see the [contributing](https://gitlab.pasteur.fr/zolfa/zolfa-nd2reader/-/blob/master/CONTRIBUTING.md) page for more information. ### Bug Reports and Features @@ -74,6 +52,8 @@ If you get an unhandled exception, please paste the entire stack trace into the ### Acknowledgments +First fork by Ruben Verweij. + PIMS modified version by Ruben Verweij. Original version by Jim Rybarski. Support for the development of this package was partially provided by the [Finkelstein Laboratory](http://finkelsteinlab.org/).