# simpleITK-Snap

**Repository Path**: E3D/simpleITK-Snap

## Basic Information

- **Project Name**: simpleITK-Snap
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2022-02-10
- **Last Updated**: 2022-02-10

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

<div align="center">
  <img width="700px" src="logo.png">
  <br/>
  <img src="https://img.shields.io/badge/Version-0.1.2--alpha-brightgreen">
</div>


## Overview
SimpleITKSnap is a 3D-image visualization tool. SimpleITKSnap is developed to bridge the gap between 3D-image process
programming and its visualization. Comparing to the existing method, SimpleITKSnap have these advantage:

<img src="demoCode.png" height="270px"></a>  <img src="demo.gif" height="270px">

1. Matplotlib-style display: ```SimpleITKSnap.imshow(yourArray)```. 
You don't need to save your processed result to disk, open ITK-SNAP, find the file and load it again.
2. Extension-based design, meet your visualization demand by writing your own extension. 
The extension development requires minimal code and is super easy to √evelop.


## Install
First, clone this repo to your local environment:

```bash
git clone https://github.com/JamesQFreeman/simpleITK-Snap.git
```

Then use pip to install the dependency package:

```bash
pip install -r requirements.txt
```

Then you are ready to go!

## Usage

### In-place Mode
You can open 3D image in python code.
```python
import SimpleITKSnap as sis
from SimpleITKSnap.Extension import histogram
array = np.arange(0,256*256*256).reshape(256,256,256)
sis.imshow(array, histogram)
```

### Application Mode
Let's see an example of a brain CT image:
To open an image, simply type:
```bash
python simpleITK-Snap -f YourFile.nii.gz
```

![A CTA image opened in simpleITK-Snap](./demo.gif)

## Extension
You can develop your own extension in two ways:
- Matplotlib-style:
```python
@pltExtension
def yourExtension(array3d:ndarray, x:int, y:int, z:int) -> str:
    plt.whateverYouWant()
    return "Extention display test at {}, {}, {}".format(x,y,z)
```

- Array-style:
```python
@imgExtension
def yourExtention(array3d:ndarray, x:int, y:int, z:int) -> Tuple[ndarray,str]:
    processed_2d_image = whateverYouWant()
    return processed_2d_image, "Extention display test at {}, {}, {}".format(x,y,z)
```

## Dependency & Compatibility

SimpleITKSnap is based on:
- python3
- SimpleITK
- numpy
- opencv-python
- PyQt5

Compatibility Test Status:

|       | Windows 10  | OS X | Linux |
|-------|-------------|------|-------|
| Build | ![Build Status](https://img.shields.io/badge/Build-Pass-green) | ![Build Status](https://img.shields.io/badge/Build-Pass-green) | ![Build Status](https://img.shields.io/badge/Build-Pass-green) |
| PyPI  |                                                                | ![Build Status](https://img.shields.io/badge/Build-Pass-green) |                                                                |

## Coming Soon
#### release 0.1.3
- Acceleration using `lru_cache`.
#### release 0.1.4
- Package the project to a `.wheel`
#### release 0.1.5
- Add jupyter notebook support.

## Developer
This project is started by JamesQFreeman(wsheng@sjtu.edu.cn) and supported by SJTU MIC lab.