# MedImgKit
A comprehensive toolkit for medical image processing, providing utilities for DICOM, NIfTI, and other medical image formats with seamless multi-format I/O operations.
## Features
- **DICOM Support**: Read, anonymize, and manipulate DICOM files
- **NIfTI Support**: Work with neuroimaging data in NIfTI format
- **Multi-format I/O**: Unified interface for reading various image formats
- **Anonymization**: DICOM anonymization following DICOM standards
- **Coordinate Conversion**: Convert between pixel and patient coordinates
- **Multi-frame Assembly**: Combine multiple DICOM files into multi-frame volumes
## Installation
### From PyPI
```bash
pip install medimgkit
```
### From Source
```bash
pip install git+https://github.com/SonanceAI/medimgkit
```
## Quick Start
### DICOM Operations
```python
import medimgkit as mik
import pydicom
# Read and normalize DICOM image
ds = pydicom.dcmread('path/to/dicom.dcm')
image_array = mik.load_image_normalized(ds)
# Anonymize DICOM
anonymized_ds = mik.anonymize_dicom(ds)
# Convert pixel coordinates to patient coordinates
patient_coords = mik.pixel_to_patient(ds, pixel_x=100, pixel_y=150)
```
### NIfTI Operations
```python
import nibabel as nib
import medimgkit as mik
# Load NIfTI file
nifti_data = nib.load('path/to/image.nii.gz')
# Get a specific slice
slice_image = mik.get_slice(nifti_data, slice_index=50, slice_axis=2)
# Convert world coordinates to slice index
slice_idx, axis = mik.line_to_slice_index(nifti_data, point1, point2)
```
### Multi-format Reading
```python
import medimgkit as mik
# Read any supported format
image_array = mik.read_array_normalized('path/to/image.dcm')
image_array = mik.read_array_normalized('path/to/image.nii.gz')
image_array = mik.read_array_normalized('path/to/image.png')
```
## API Reference
### DICOM Utils (`medimgkit.dicom_utils`)
#### Core Functions
- `load_image_normalized(dicom, index=None)`: Load and normalize DICOM pixel data
- `anonymize_dicom(ds, retain_codes=[], copy=False, token_mapper=None)`: Anonymize DICOM following standards
- `assemble_dicoms(files_path, return_as_IO=False)`: Combine multiple DICOMs into multi-frame
- `is_dicom(f)`: Check if file is a DICOM
#### Coordinate Conversion
- `pixel_to_patient(ds, pixel_x, pixel_y, slice_index=None)`: Convert pixel to patient coordinates
- `get_image_position(ds, slice_index=None)`: Get image position in patient coordinates
- `get_pixel_spacing(ds, slice_index)`: Get pixel spacing information
#### Anatomical Analysis
- `determine_anatomical_plane_from_dicom(ds, slice_axis, alignment_threshold=0.95)`: Determine anatomical plane
### NIfTI Utils (`medimgkit.nifti_utils`)
#### Slice Operations
- `get_slice(data, slice_index, slice_axis)`: Extract 2D slice from 3D volume
- `get_slice_from_line(data, world_point1, world_point2)`: Get slice defined by line
- `slice_location_to_slice_index(data, slice_location, slice_axis)`: Convert location to index
#### Coordinate Conversion
- `line_to_slice_index(data, world_point1=None, world_point2=None, coplanar_vector=None)`: Convert line to slice
- `axis_name_to_axis_index(data, axis_name)`: Convert axis name to index
#### Utilities
- `is_nifti_file(file_path)`: Check if file is NIfTI format
### I/O Utils (`medimgkit.io_utils`)
#### Reading Functions
- `read_array_normalized(file_path, index=None, return_metainfo=False, use_magic=False)`: Universal image reader
- `read_image(file_path)`: Read standard image formats (PNG, JPEG)
- `read_nifti(file_path, mimetype=None)`: Read NIfTI files
- `read_video(file_path, index=None)`: Read video files
## Supported Formats
- **DICOM**: .dcm, .dicom (and files without extension)
- **NIfTI**: .nii, .nii.gz
- **Images**: .png, .jpg, .jpeg
- **Video**: .mp4, .avi, .mov, .mkv
- **NumPy**: .npy
## Development
### Running Tests
```bash
pytest
```
## License
MIT License - see LICENSE file for details.
## Contributing
1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Submit a pull request
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"description": "# MedImgKit\n\nA comprehensive toolkit for medical image processing, providing utilities for DICOM, NIfTI, and other medical image formats with seamless multi-format I/O operations.\n\n## Features\n\n- **DICOM Support**: Read, anonymize, and manipulate DICOM files\n- **NIfTI Support**: Work with neuroimaging data in NIfTI format\n- **Multi-format I/O**: Unified interface for reading various image formats\n- **Anonymization**: DICOM anonymization following DICOM standards\n- **Coordinate Conversion**: Convert between pixel and patient coordinates\n- **Multi-frame Assembly**: Combine multiple DICOM files into multi-frame volumes\n\n## Installation\n\n### From PyPI\n```bash\npip install medimgkit\n```\n\n### From Source\n```bash\npip install git+https://github.com/SonanceAI/medimgkit\n```\n\n## Quick Start\n\n### DICOM Operations\n```python\nimport medimgkit as mik\nimport pydicom\n\n# Read and normalize DICOM image\nds = pydicom.dcmread('path/to/dicom.dcm')\nimage_array = mik.load_image_normalized(ds)\n\n# Anonymize DICOM\nanonymized_ds = mik.anonymize_dicom(ds)\n\n# Convert pixel coordinates to patient coordinates\npatient_coords = mik.pixel_to_patient(ds, pixel_x=100, pixel_y=150)\n```\n\n### NIfTI Operations\n```python\nimport nibabel as nib\nimport medimgkit as mik\n\n# Load NIfTI file\nnifti_data = nib.load('path/to/image.nii.gz')\n\n# Get a specific slice\nslice_image = mik.get_slice(nifti_data, slice_index=50, slice_axis=2)\n\n# Convert world coordinates to slice index\nslice_idx, axis = mik.line_to_slice_index(nifti_data, point1, point2)\n```\n\n### Multi-format Reading\n```python\nimport medimgkit as mik\n\n# Read any supported format\nimage_array = mik.read_array_normalized('path/to/image.dcm')\nimage_array = mik.read_array_normalized('path/to/image.nii.gz')\nimage_array = mik.read_array_normalized('path/to/image.png')\n```\n\n## API Reference\n\n### DICOM Utils (`medimgkit.dicom_utils`)\n\n#### Core Functions\n- `load_image_normalized(dicom, index=None)`: Load and normalize DICOM pixel data\n- `anonymize_dicom(ds, retain_codes=[], copy=False, token_mapper=None)`: Anonymize DICOM following standards\n- `assemble_dicoms(files_path, return_as_IO=False)`: Combine multiple DICOMs into multi-frame\n- `is_dicom(f)`: Check if file is a DICOM\n\n#### Coordinate Conversion\n- `pixel_to_patient(ds, pixel_x, pixel_y, slice_index=None)`: Convert pixel to patient coordinates\n- `get_image_position(ds, slice_index=None)`: Get image position in patient coordinates\n- `get_pixel_spacing(ds, slice_index)`: Get pixel spacing information\n\n#### Anatomical Analysis\n- `determine_anatomical_plane_from_dicom(ds, slice_axis, alignment_threshold=0.95)`: Determine anatomical plane\n\n### NIfTI Utils (`medimgkit.nifti_utils`)\n\n#### Slice Operations\n- `get_slice(data, slice_index, slice_axis)`: Extract 2D slice from 3D volume\n- `get_slice_from_line(data, world_point1, world_point2)`: Get slice defined by line\n- `slice_location_to_slice_index(data, slice_location, slice_axis)`: Convert location to index\n\n#### Coordinate Conversion\n- `line_to_slice_index(data, world_point1=None, world_point2=None, coplanar_vector=None)`: Convert line to slice\n- `axis_name_to_axis_index(data, axis_name)`: Convert axis name to index\n\n#### Utilities\n- `is_nifti_file(file_path)`: Check if file is NIfTI format\n\n### I/O Utils (`medimgkit.io_utils`)\n\n#### Reading Functions\n- `read_array_normalized(file_path, index=None, return_metainfo=False, use_magic=False)`: Universal image reader\n- `read_image(file_path)`: Read standard image formats (PNG, JPEG)\n- `read_nifti(file_path, mimetype=None)`: Read NIfTI files\n- `read_video(file_path, index=None)`: Read video files\n\n## Supported Formats\n\n- **DICOM**: .dcm, .dicom (and files without extension)\n- **NIfTI**: .nii, .nii.gz\n- **Images**: .png, .jpg, .jpeg\n- **Video**: .mp4, .avi, .mov, .mkv\n- **NumPy**: .npy\n\n## Development\n\n### Running Tests\n```bash\npytest\n```\n## License\n\nMIT License - see LICENSE file for details.\n\n## Contributing\n\n1. Fork the repository\n2. Create a feature branch\n3. Make your changes\n4. Submit a pull request\n",
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