https://github.com/hectormz/napari-mat-images
A plugin for napari to load images from Matlab's .mat files
https://github.com/hectormz/napari-mat-images
napari-plugin
Last synced: about 1 month ago
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A plugin for napari to load images from Matlab's .mat files
- Host: GitHub
- URL: https://github.com/hectormz/napari-mat-images
- Owner: hectormz
- License: bsd-3-clause
- Created: 2020-03-16T23:16:03.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2021-06-30T14:02:35.000Z (almost 4 years ago)
- Last Synced: 2024-04-26T18:44:09.585Z (about 1 year ago)
- Topics: napari-plugin
- Language: Python
- Homepage:
- Size: 37.1 KB
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# napari-mat-images
[](https://pypi.org/project/napari-mat-images)
[](https://pypi.org/project/napari-mat-images)
[](https://dev.azure.com/hectormz-1/napari-mat-images/_build/latest?definitionId=1&branchName=main)
## Features
This plugin loads image variables stored in `MATLAB` `.mat` files into [napari](https://github.com/napari/napari).
It loads any variable that looks like an image.
Presently, that includes any array with more than two dimensions with size greater than 20 pixels (determined by `shape_is_image()`).
If loading a variable with 3 or more dimensions, the plugin assumes that it is a stack of images, and the dimension with greatest size is the axis of the stack.
### Loading Large Files
If loading a large `.mat` file saved in `HDF5`/`v7.3` format, chunks of the images are loaded as needed, resulting in fast initial load, but potentially slower scrolling.
Slices of the image stacks are randomly sampled to determine min/max contrast values.
## Requirements
This plugin relies on `scipy` to load small `.mat` files and `h5py` (with `dask`) to load larger `HDF5`/`v7.3` `.mat` files.
It implicitly requires `napari` for use.
## Installation
`napari-mat-images` requires [napari](https://github.com/napari/napari) to be installed, although it is not listed as a requirement for installation.
This plugin relies on plugin functionality found in `napari` version \> `0.2.12`. This can be installed via [pip](https://pypi.org/project/pip/) from [PyPI](https://pypi.org/project):
$ pip install napari>0.2.12
You can install `napari-mat-images` via [pip](https://pypi.org/project/pip/) from [PyPI](https://pypi.org/project):
$ pip install napari-mat-images
## Usage
Once installed, the plugin will be used whenever trying to load a `.mat` file.
This can be done from the `napari` GUI or commandline:
$ napari my_file.mat
## Contributing
Contributions are very welcome.
Tests can be run with [pytest](https://docs.pytest.org/en/latest/),
please ensure the coverage at least stays the same before you submit a pull request.
## License
Distributed under the terms of the [BSD-3](http://opensource.org/licenses/BSD-3-Clause) license, `napari-mat-images` is free and open source software
## Issues
If you encounter any problems, please [file an issue](https://github.com/hectormz/napari-mat-images/issues) along with a detailed description.
---
This [napari](https://github.com/napari/napari) plugin was generated with [Cookiecutter](https://github.com/audreyr/cookiecutter) along with [napari](https://github.com/napari/napari)\'s [cookiecutter-napari-plugin](https://github.com/napari/cookiecutter-napari-plugin) template.