mipcandy 1.1.1a0
A Candy for Medical Image Processing
Requires Python: >=3.12

# MIP Candy: A Candy for Medical Image Processing

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![poster](home/assets/poster.png)

MIP Candy is Project Neura's next-generation infrastructure framework for medical image processing. It defines a handful
of common network architectures with their corresponding training, inference, and evaluation pipelines that are
out-of-the-box ready to use. Additionally, it also provides integrations with popular frontend dashboards such as
Notion, WandB, and TensorBoard.

We provide a flexible and extensible framework for medical image processing researchers to quickly prototype their
ideas. MIP Candy takes care of all the rest, so you can focus on only the key experiment designs.

:link: [Home](https://mipcandy.projectneura.org)

:link: [Docs](https://mipcandy-docs.projectneura.org)

## Key Features

Why MIP Candy? :thinking:

<details>
<summary>Easy adaptation to fit your needs</summary>
We provide tons of easy-to-use techniques for training that seamlessly support your customized experiments.

- Sliding window
- ROI inspection
- ROI cropping to align dataset shape (100% or 33% foreground)
- Automatic padding
- ...

You only need to override one method to create a trainer for your network architecture.

```python
from typing import override

from torch import nn
from mipcandy import SegmentationTrainer


class MyTrainer(SegmentationTrainer):
    @override
    def build_network(self, example_shape: tuple[int, ...]) -> nn.Module:
        ...
```
</details>

<details>
<summary>Satisfying command-line UI design</summary>
<img src="home/assets/cli-ui.png" alt="cmd-ui"/>
</details>

<details>
<summary>Built-in 2D and 3D visualization for intuitive understanding</summary>
<img src="home/assets/visualization.png" alt="visualization"/>
</details>

<details>
<summary>High availability with interruption tolerance</summary>
Interrupted experiments can be resumed with ease.
<img src="home/assets/recovery.png" alt="recovery"/>
</details>

<details>
<summary>Support of various frontend platforms for remote monitoring</summary>

MIP Candy Supports [Notion](https://mipcandy-projectneura.notion.site), WandB, and TensorBoard.

<img src="home/assets/notion.png" alt="notion"/>
</details>

## Installation

Note that MIP Candy requires **Python >= 3.12**.

```shell
pip install "mipcandy[standard]"
```

## Quick Start

Below is a simple example of a nnU-Net style training. The batch size is set to 1 due to the varying shape of the
dataset, although you can use a `ROIDataset` to align the shapes.

```python
from typing import override

import torch
from mipcandy_bundles.unet import UNetTrainer
from torch.utils.data import DataLoader

from mipcandy import download_dataset, NNUNetDataset


class PH2(NNUNetDataset):
    @override
    def load(self, idx: int) -> tuple[torch.Tensor, torch.Tensor]:
        image, label = super().load(idx)
        return image.squeeze(0).permute(2, 0, 1), label


download_dataset("nnunet_datasets/PH2", "tutorial/datasets/PH2")
dataset, val_dataset = PH2("tutorial/datasets/PH2", device="cuda").fold()
dataloader = DataLoader(dataset, 1, shuffle=True)
val_dataloader = DataLoader(val_dataset, 1, shuffle=False)
trainer = UNetTrainer("tutorial", dataloader, val_dataloader, device="cuda")
trainer.train(1000, note="a nnU-Net style example")
```