Metadata-Version: 2.4
Name: warp-tm-vis
Version: 0.0.2
Summary: Visualize template matching results from WarpTools
Project-URL: homepage, https://github.com/warpem/warp-tm-vis
Project-URL: repository, https://github.com/warpem/warp-tm-vis
Author-email: Alister Burt <burt.alister@gene.com>
License: BSD-3-Clause
License-File: LICENSE
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Typing :: Typed
Requires-Python: >=3.11
Requires-Dist: mrcfile>=1.5.4
Requires-Dist: napari[pyqt5]>=0.5.6
Requires-Dist: numpy>=2.2.2
Requires-Dist: rich>=13.9.4
Requires-Dist: starfile>=0.5.11
Requires-Dist: typer>=0.15.1
Provides-Extra: dev
Requires-Dist: ipython; extra == 'dev'
Requires-Dist: mypy; extra == 'dev'
Requires-Dist: pdbpp; extra == 'dev'
Requires-Dist: pre-commit; extra == 'dev'
Requires-Dist: rich; extra == 'dev'
Requires-Dist: ruff; extra == 'dev'
Provides-Extra: test
Requires-Dist: pytest; extra == 'test'
Requires-Dist: pytest-cov; extra == 'test'
Description-Content-Type: text/markdown

# warp-tm-vis

[![License](https://img.shields.io/pypi/l/warp-tm-vis.svg?color=green)](https://github.com/warpem/warp-tm-vis/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/warp-tm-vis.svg?color=green)](https://pypi.org/project/warp-tm-vis)
[![Python Version](https://img.shields.io/pypi/pyversions/warp-tm-vis.svg?color=green)](https://python.org)
[![CI](https://github.com/warpem/warp-tm-vis/actions/workflows/ci.yml/badge.svg)](https://github.com/warpem/warp-tm-vis/actions/workflows/ci.yml)
[![codecov](https://codecov.io/gh/warpem/warp-tm-vis/branch/main/graph/badge.svg)](https://codecov.io/gh/warpem/warp-tm-vis)

Visualize template matching results from Warp

## Usage

Install [uv](https://docs.astral.sh/uv/getting-started/installation/) then run 

```shell
uvx warp-tm-vis
```

You should see the following

```txt
╭─ Options ──────────────────────────────────────────────────────────╮
│ *  --reconstruction-directory    -rdir                       PATH  │
│ *  --matching-directory          -mdir                       PATH  │
│ *  --matching-pattern            -mp                         TEXT  │
│ *  --correlation-volume-pattern  -cvp                        TEXT  │
│    --load-volumes                --no-load-volumes                 │
│    --help                                                          │
╰────────────────────────────────────────────────────────────────────╯
```

Once you've provided the necessary options, you should see a GUI window pop up

![warp-tm-vis gui screenshot](./assets/gui-screenshot.png)

Note: this is a graphical application which should be run locally, performance over ssh with XForwarding will likely be poor. 
We recommend using an ftp client like [FileZilla](https://filezilla-project.org/) to download your data if it's 
currently stored on a remote server.

## Features
- change between different tomograms
- turn on/off visualization of tomograms, correlation volumes and particle positions
- simulate thresholding results at a given cutoff

## Authorship

*warp-tm-vis* was developed by Alister Burt at Genentech, Inc. in South San Francisco, USA.