semvec/pypi-packages huggingface dataset:
parody-py 0.0.6
Python package to process data from PARODY-JA4.3 dynamo simulations.
License: MIT

# paropy

Python package to process data from PARODY-JA4.3 dynamo simulations.

## Getting Started

### Prerequisites
- [Python](https://www.python.org/)

### Installing
Conda:
```
conda install -c jnywong parody_py
```

Pip:
```
pip install parody_py
```

Git:

Find the Git repo [here](https://github.com/jnywong/nondim-slurry).

### Example script: diagnostics

Sample scripts can be found within the module package `paropy/scripts`.

1. Open `paropy/scripts/diagnostics.py`

2. Set path to simulation data by setting

```
run_ID = <run_ID> # PARODY simulation tag
directory = <path_to_data>
```

3. Run `paropy/scripts/diagnostics.py`

4. Admire the output:

![](https://raw.githubusercontent.com/jnywong/parody_py/master/docs/diag1_test.png)

![](https://raw.githubusercontent.com/jnywong/parody_py/master/docs/diag2_test.png)

### Example script: meridional snapshots

1. Open `paropy/scripts/meridional_snapshot.py`

2. Set path to simulation data by setting

```
run_ID = <run_ID> # PARODY simulation tag
directory = <path_to_data>
```

3. Specify timestamp of snapshot by setting `timestamp`

4. Run `paropy/scripts/meridional_snapshot.py`

5. Admire the output:

![](https://raw.githubusercontent.com/jnywong/parody_py/master/docs/merid_test.png)

### Example script: surface snapshots

1. Open `paropy/scripts/surface_snapshot.py`

2. Set path to simulation data by setting

```
run_ID = <run_ID> # PARODY simulation tag
directory = <path_to_data>
```

3. Specify timestamp of snapshot by setting `timestamp`

4. Run `paropy/scripts/surface_snapshot.py`

5. Admire the output:

![](https://raw.githubusercontent.com/jnywong/parody_py/master/docs/surface_test.png)

## Links

* [PyPI](https://pypi.org/project/parody_py/)
* [Anaconda Cloud](https://anaconda.org/jnywong/parody_py)

## Authors

* [**Jenny Wong**](https://jnywong.github.io/) - *Institut de Physique du Globe de Paris - Institut des Sciences de la Terre*

## License

This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details

## Acknowledgments

* Del Duca Foundation
* ERC SEIC

:tada:
napari-cellfinder 0.2.1
Visualise cellfinder results with napari
License: MIT
Requires Python: >=3.6

# napari-cellfinder

[![License](https://img.shields.io/pypi/l/napari-cellfinder.svg?color=green)](https://github.com/napari/napari-cellfinder/raw/master/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/napari-cellfinder.svg?color=green)](https://pypi.org/project/napari-cellfinder)
[![Python Version](https://img.shields.io/pypi/pyversions/napari-cellfinder.svg?color=green)](https://python.org)
[![tests](https://github.com/adamltyson/napari-cellfinder/workflows/tests/badge.svg)](https://github.com/adamltyson/napari-cellfinder/actions)
[![codecov](https://codecov.io/gh/adamltyson/napari-cellfinder/branch/master/graph/badge.svg)](https://codecov.io/gh/adamltyson/napari-cellfinder)

Visualise cellfinder results with napari


----------------------------------


## Installation

You can install `napari-cellfinder` via [pip]:

    pip install napari-cellfinder

## Usage
* Open napari (however you normally do it, but typically just type `napari` into your terminal)
* Load your raw data (drag and drop the data directories into napari, one at a time)
* Drag and drop your cellfinder output directory into napari.

The plugin will then load your detected cells (in yellow) and the rejected cell 
candidates (in blue). If you carried out registration, then these results will be 
overlaid (similarly to the [napari-brainreg] plugin, but transformed to the 
coordinate space of your raw data).

![load_data](https://raw.githubusercontent.com/brainglobe/napari-cellfinder/master/resources/load_data.gif)
**Loading raw data**

![load_data](https://raw.githubusercontent.com/brainglobe/napari-cellfinder/master/resources/load_results.gif)
**Loading cellfinder results**

## Contributing

Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.

## License

Distributed under the terms of the [MIT] license,
"napari-cellfinder" is free and open source software

## Issues

If you encounter any problems, please [file an issue] along with a detailed description.

[napari-brainreg]: https://github.com/brainglobe/napari-brainreg
[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
[file an issue]: https://github.com/adamltyson/napari-cellfinder/issues
[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/