# Metadata and affine

Default orientation affine matrix, with origin=(0,0,0) and spacing=(1,1,1):
```math
\begin{bmatrix}
1 & 0 & 0 & 0 \\
0 & 1 & 0 & 0 \\
0 & 0 & 1 & 0 \\
0 & 0 & 0 & 1
\end{bmatrix}
```
- 48 possible orientations for 3d image

# Comparison between IO backends
Key features, pros & cons:
## ITK
- The engine behind ITK-SNAP
- Presents the most comprehensive formats support
- Originally written in C++ - wrapped with swig to python. Consequently, itk python code is unnatural/not pythonic and hard to understand
- Uses itk world coordinates for origin and directions. Default orientation: RAI
- Dicom file: can save only UChar - unsigned int 8, good for segmentations. int16/float are not supported
- Derived: SimpleITK (sitk), allows saving dicom folder

## NiBabel
- Pythonic nifti package
- Contains reorientation handling
- Packs metadata into affine matrix
- Uses nifti world coordinates for affine and orientation. Default orientation: RAS+ = LPI

## Pydicom
- Pythonic dicom package
- Relatively easy access to tags
- Supports modifying dicom single file pixel data and saving it - dicom2dicom
- No reorientation support. Can use nibabel: [ornt_transform and apply_orientation](https://nipy.org/nibabel/reference/nibabel.orientations.html#ornt-transform). Get original orientation with itk
- Derived: dicom_numpy for combining slices - dicom folder, high level

## Performance
- Nifti segmentation: 
	1. itk
	2. nib
- Nifti image (dense):
	1. nib
	2. itk

## Functionality
### Conversion
| input/output | nifti         | dicom folder  | dicom file    |
| :---         | :-----------: | :-----------: | :-----------: |
| nifti        | v        | v        | v        |
| dicom folder | v        | v        | v        |
| dicom file   | v        | v        | v        |

### Backends
| IO engine                | ITK | NiBabel | Pydicom           |
|--------------------------|-----|---------|-------------------|
| nifti support            | v   | v       | x                 |
| dicom support            | v   | x       | v                 |
| single dicom file reader | v   | x       | v                 |
| single dicom file writer | v   | x       | v                 |
| reorientation            | v   | v       | x                 |
| metadata                 | v   | v       | v                 |
| saving dicom int16       |     | x       | v - with template |
| saving dicom uint8       | v   | x       |                   |
| pythonic                 | x   | v       | v                 |
| high level               | x   | v       | x                 |

# Tests
- (add dataset sources)

# Distribution
Build the whl file with the following command (in the cmd/terminal): 
```
(<env-name>) C:\...\medio>python setup.py sdist bdist_wheel
```
Make sure you are in the project's root - where the setup.py file is located.