Skip to content

Latest commit

 

History

History
75 lines (66 loc) · 2.79 KB

CONTRIBUTING.md

File metadata and controls

75 lines (66 loc) · 2.79 KB
Raw

Metadata and affine

Default orientation affine matrix, with origin=(0,0,0) and spacing=(1,1,1):

$$\begin{bmatrix} 1 & 0 & 0 & 0 \\\ 0 & 1 & 0 & 0 \\\ 0 & 0 & 1 & 0 \\\ 0 & 0 & 0 & 1 \end{bmatrix}$$
  • 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. 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.