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182 changes: 1 addition & 181 deletions docs/contributing.md
Original file line number Diff line number Diff line change
Expand Up @@ -35,130 +35,6 @@ Thank you for your interest in contributing to ITKIT! This guide will help you g

This ensures code is automatically formatted and checked before commits.

## Development Workflow

### Code Style

ITKIT follows these code style guidelines:

- **Python version:** >= 3.10
- **Formatter:** Black with 150 character line length
- **Import sorting:** isort with black profile
- **Type hints:** Encouraged for public APIs
- **Docstrings:** Follow NumPy/Google style

### Running Tests

ITKIT uses pytest for testing:

```bash
# Run all tests
pytest

# Run specific test file
pytest tests/test_io.py

# Run tests with specific marker
pytest -m torch # Only PyTorch tests
pytest -m itk_process # Only ITK processing tests

# Run with coverage
pytest --cov=itkit
```

Available test markers:

- `gui`: GUI tests (requires Qt)
- `itk_process`: ITK preprocessing script tests
- `mm`: MMEngine runner tests
- `torch`: PyTorch-dependent tests

### Code Formatting

Format your code before committing:

```bash
# Format with black
black itkit/

# Sort imports
isort itkit/

# Or use pre-commit to run all checks
pre-commit run --all-files
```

### Type Checking

Run type checkers:

```bash
# Pyright
pyright

# Mypy
mypy itkit/
```

## Contribution Guidelines

### Reporting Issues

When reporting bugs or requesting features:

1. **Search existing issues** first to avoid duplicates
2. **Use issue templates** if available
3. **Provide clear description** with:
- Expected behavior
- Actual behavior
- Steps to reproduce
- Environment details (OS, Python version, ITKIT version)
- Sample code or data if applicable

### Submitting Pull Requests

1. **Create a new branch** for your feature/fix:

```bash
git checkout -b feature/my-new-feature
```

2. **Make your changes** following code style guidelines

3. **Add tests** for new functionality

4. **Update documentation** if needed

5. **Run tests** to ensure nothing breaks:

```bash
pytest
```

6. **Commit your changes** with clear messages:

```bash
git commit -m "Add feature: description of feature"
```

7. **Push to your fork:**

```bash
git push origin feature/my-new-feature
```

8. **Create a Pull Request** on GitHub

### Pull Request Checklist

- [ ] Code follows ITKIT style guidelines
- [ ] Tests added for new functionality
- [ ] All tests pass
- [ ] Documentation updated
- [ ] Commit messages are clear
- [ ] PR description explains changes
- [ ] No unnecessary files included

## What to Contribute

### Areas for Contribution
Expand Down Expand Up @@ -249,64 +125,8 @@ To add a new preprocessing command:
4. Add tests in `tests/`
5. Support common flags (`--mp`, `--help`)

## Release Process

ITKIT follows a specific release policy:

### Release Branches

- Stable releases managed on branches: `v1`, `v2`, `v3`, etc.
- Development occurs on feature branches
- Only merges to release branches trigger releases

### Release Triggers

- Any PR merged into a release branch automatically triggers a new release
- Releases are typically minor version updates (v3.1, v3.2, etc.)
- Tagged accordingly

### Version Numbering

ITKIT uses semantic versioning: `MAJOR.MINOR.PATCH`

- **MAJOR:** Breaking changes
- **MINOR:** New features (backwards compatible)
- **PATCH:** Bug fixes (backwards compatible)

## Communication

### Getting Help
## Getting Help

- **Issues:** Use GitHub Issues for bug reports and feature requests
- **Email:** Contact maintainer at [312065559@qq.com](mailto:312065559@qq.com)
- **Discussions:** Use GitHub Discussions for questions

### Community Guidelines

- Be respectful and constructive
- Help others when you can
- Follow the code of conduct
- Give credit where due
- Focus on what's best for the project

## License

By contributing to ITKIT, you agree that your contributions will be licensed under the MIT License.

## Recognition

Contributors are recognized in:

- GitHub contributors list
- Release notes
- CITATION file (for significant contributions)

## Questions?

If you have any questions about contributing, feel free to:

- Open an issue with the "question" label
- Contact the maintainer via email
- Start a discussion on GitHub

Thank you for making ITKIT better!
67 changes: 3 additions & 64 deletions docs/datasets.md
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Expand Up @@ -209,68 +209,7 @@ For each supported dataset, you can find conversion scripts at: `itkit/dataset/<

---

## Dataset Categories

### By Modality

**CT Datasets:**

- AbdomenCT-1K
- CT-ORG
- CTSpine1K
- FLARE 2022/2023
- ImageTBAD
- KiTS23
- LUNA16
- TotalSegmentator
- LiTS

**MRI Datasets:**

- BraTS 2024

**Multi-Modal:**

- TCGA

### By Anatomical Region

**Abdomen:**

- AbdomenCT-1K
- FLARE 2022/2023
- LiTS

**Brain:**

- BraTS 2024
- CT-ORG (brain)

**Thorax:**

- LUNA16
- CT-ORG (lungs)

**Kidney:**

- KiTS23
- CT-ORG (kidneys)

**Cardiovascular:**

- ImageTBAD

**Spine:**

- CTSpine1K

**Whole Body:**

- TotalSegmentator

## Using Conversion Scripts

### Example: Converting AbdomenCT-1K
## Example: Converting AbdomenCT-1K

```bash
# Navigate to dataset conversion directory
Expand All @@ -282,12 +221,12 @@ python convert_official.py \
--output /path/to/itkit/format
```

### General Workflow
## General Workflow

1. **Download official dataset** from the source
2. **Locate conversion script** in `itkit/dataset/<dataset_name>/`
3. **Run conversion script** with appropriate paths
4. **Verify structure** matches ITKIT format (image/ and label/ folders)
4. **Verify structure** matches ITKIT format (`image/` and `label/` folders)
5. **Use with ITKIT tools** for preprocessing and training

## Custom Dataset Preparation
Expand Down
33 changes: 1 addition & 32 deletions docs/index.md
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Expand Up @@ -9,12 +9,10 @@ Welcome to the ITKIT documentation! ITKIT is a user-friendly toolkit built on `S
### Getting Started

- **[Installation Guide](installation.md)** - Install ITKIT and its dependencies
- **[Quick Start](quickstart.md)** - Get started with basic usage and examples
- **[Dataset Structure](dataset_structure.md)** - Understand the required dataset format

### Processing Tools

- **[Overview](preprocessing.md)** - General notes and best practices
- **[itk_check](itk_check.md)** - Image checking and validation
- **[itk_resample](itk_resample.md)** - Resampling to target spacing/size
- **[itk_orient](itk_orient.md)** - Image re-orientation
Expand Down Expand Up @@ -51,18 +49,12 @@ Welcome to the ITKIT documentation! ITKIT is a user-friendly toolkit built on `S

### Community

- **[Contributing Guide](contributing.md)** - How to contribute to ITKIT
- **[Contributing Guide](contributing.md)**
- Development setup
- Code style guidelines
- Submission process
- Release policy

- **[FAQ & Troubleshooting](faq.md)** - Common issues and solutions
- Installation problems
- Usage questions
- Performance tips
- Framework integration issues

## 🚀 Key Features

- **🔧 Feasible Operations**: Simple command-line interface for complex ITK operations
Expand All @@ -73,29 +65,6 @@ Welcome to the ITKIT documentation! ITKIT is a user-friendly toolkit built on `S
- **⚡ High Performance**: Multiprocessing support for faster preprocessing
- **🎨 Flexible**: Works with multiple file formats (MHA, NIfTI, NRRD, DICOM)

## 🎯 Quick Navigation

**New to ITKIT?**

1. Start with [Installation Guide](installation.md)
2. Follow the [Quick Start](quickstart.md) tutorial
3. Learn about [Dataset Structure](dataset_structure.md)

**Ready to preprocess data?**

- See [Processing Tools](preprocessing.md) for command documentation and overview.
- Use the GUI: `pip install "itkit[gui]"` then `itkit-app`

**Building models?**

- Explore [Framework Integration](framework_integration.md)
- Check available [Models](models.md)

**Need help?**

- Check [FAQ & Troubleshooting](faq.md)
- See [Contributing Guide](contributing.md) to report issues

## 📝 Citation

If you use ITKIT in your research, please cite:
Expand Down
22 changes: 0 additions & 22 deletions docs/installation.md
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Expand Up @@ -129,25 +129,3 @@ python -c "import itkit; print(itkit.__version__)"
itk_check --help
itk_resample --help
```

## Troubleshooting

### Import Errors

If you encounter import errors, ensure all dependencies are installed:

```bash
pip install itkit --force-reinstall
```

### GUI DPI Issues

If the GUI's DPI is not optimal, specify the `QT_SCALE_FACTOR` environment variable:

```bash
QT_SCALE_FACTOR=2 itkit-app
```

### PyTorch Compatibility

For GPU support with PyTorch-based features, install PyTorch separately following the [official PyTorch installation guide](https://pytorch.org/get-started/locally/).
2 changes: 1 addition & 1 deletion docs/models.md
Original file line number Diff line number Diff line change
Expand Up @@ -183,7 +183,7 @@ from itkit.models import DA_TransUNet

# Model config in your experiment config file
model = dict(
type='DA_TransUNet',
type=DA_TransUNet,
in_channels=1,
num_classes=3,
# ... other parameters
Expand Down
19 changes: 0 additions & 19 deletions docs/preprocessing.md

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