Sisyphe.core.sisypheImageIO

External packages/modules

ANTs, image registration, http://stnava.github.io/ANTs/

ITK, medical image processing, https://itk.org/

Numpy, scientific computing, https://numpy.org/

pydicom, DICOM library, https://pydicom.github.io/pydicom/stable/

PyQt5, Qt GUI, https://www.riverbankcomputing.com/software/pyqt/

SimpleITK, medical image processing, https://simpleitk.org/

vtk, visualization engine/3D rendering, https://vtk.org/

Sisyphe.core.sisypheImageIO.compareDataElementsBetweenDatasets(ds1: Dataset, ds2: Dataset, equality: bool = False) → Dataset

Create a dataset with DICOM fields that have the same values as the two tested datasets (ds1, ds2 parameters).

Parameters

ds1pydicom.Dataset: first dataset to compare
ds2pydicom.Dataset: second dataset to compare
equalitybool: test equality if True, difference otherwise

Returns

pydicom.Dataset: dataset

Sisyphe.core.sisypheImageIO.convertImageToAxialOrientation(img: Image) → tuple[Image, list[int]]

SimpleITK image reorientation to axial. ex. coronal to axial -> order = 0, 2, 1 (x, z, y) ex. sagittal to axial -> order = 1, 2, 0 (y, z, x)

Parameters

imgSimpleITK.Image: image to reorient

Returns

tuple[SimpleITK.Image, list[int]]

SimpleITK.Image, reoriented image
list[int] order of dimensions

Sisyphe.core.sisypheImageIO.convertSITKtoVTK(img: Image) → vtkImageData

SimpleITK image to VTK image conversion.

Parameters

imgSimpleITK.Image: image to copy

Returns

vtk.vtkImageData: image copy

Sisyphe.core.sisypheImageIO.convertVTKtoSITK(img: vtkImageData) → Image

VTK image to SimpleITK image conversion.

Parameters

imgvtk.vtkImageData: image to copy

Returns

SimpleITK.Image: image copy

Sisyphe.core.sisypheImageIO.extractDataElementValuesFromDatasets(dslist: list[FileDataset | Dataset | str], taglist: list[BaseTag]) → dict

Extract all the values of multiple dicom Tag (taglist parameter) in multiple datasets (dslist parameter).

Parameters

dslistlist[pydicom.Dataset]: list of datasets
taglistlist[pydicom.BaseTag]: list of tags

Returns

dict

key, pydicom.BaseTag
value, list of values of each pydicom.Dataset in dslist

Sisyphe.core.sisypheImageIO.flipImageToVTKDirectionConvention(img: Image) → Image

Flip sitkImage to VTK/SisypheVolume RAS+ orientation convention.

SisypheVolume is in RAS+ world coordinates convention (as MNI, Nibabel, Dipy…)

x, direction[1.0, 0.0, 0.0]: left(-) to right(+)

y, direction[0.0, 1.0, 0.0]: posterior(-) to anterior(+)

z: direction[0.0, 0.0, 1.0]: inferior(-) to superior(+)

SimpleITK/ITK is in LPS+ world coordinates convention

x right(-) to left(+), if sitkImage direction is [1.0, 0.0, 0.0] -> Flip X

y anterior (-) to posterior (+), if sitkImage direction is [0.0, 1.0, 0.0] -> Flip Y

z inferior (-) to superior (+), if sitkImage direction is [0.0, 0.0,-1.0] -> Flip Z

Parameters

imgSimpleITK.Image: image to flip

Returns

SimpleITK.Image: flipped image

Sisyphe.core.sisypheImageIO.isDicom(f: str) → bool

Test if a file is in Dicom format

Parameters

fstr: filename

Returns

bool: True if DICOM file

Sisyphe.core.sisypheImageIO.readFromBitmap(filename: str, lib: str = 'sitk') → Image

Read Bitmap file (.bmp, .jpg, .jpeg, .png, .tiff).

Parameters

filenamestr: image file name
libstr: format of returned image ‘itk’, ‘vtk’, ‘ants’ or by default ‘sitk’

Returns

SimpleITK.Image | itk.Image | vtk.ImageData | ants.core.ANTsImage: image instance

Sisyphe.core.sisypheImageIO.readFromBrainVoyagerVMR(filename: str, lib: str = 'sitk') → tuple[Image, dict]

Read BrainVoyager VMR file (.vmr).

Parameters

filenamestr: image file name
libstr: format of returned image ‘itk’, ‘vtk’, ‘ants’ or by default ‘sitk’

Returns

tuple[SimpleITK.Image | itk.Image | vtk.ImageData | ants.core.ANTsImage, dict]

image instance
dict, header of BrainVoyager VMR image format

Sisyphe.core.sisypheImageIO.readFromDicomDirectory(directory: str) → Image

Read DICOM files in a directory.

Parameters

directorystr: directory of the dicom files to convert

Returns

SimpleITK.Image: image instance

Sisyphe.core.sisypheImageIO.readFromDicomFilenames(filenames: list[str]) → Image

Read a list of DICOM files.

Parameters

filenameslist[str]: dicom filenames to convert

Returns

SimpleITK.Image: image instance

Sisyphe.core.sisypheImageIO.readFromDicomSeries(filename: list[str]) → Image

Read a list of DICOM files.

Parameters

filenamestr: one dicom filename of the series to convert

Returns

SimpleITK.Image: image instance

Sisyphe.core.sisypheImageIO.readFromFreeSurferMGH(filename: str, lib: str = 'sitk') → Image

Read FreeSurfer MGH file (.mgh, .mgz).

Parameters

filenamestr: image file name
libstr: format of returned image ‘itk’, ‘vtk’, ‘ants’ or by default ‘sitk’

Returns

SimpleITK.Image | itk.Image | vtk.ImageData | ants.core.ANTsImage: image instance

Sisyphe.core.sisypheImageIO.readFromMINC(filename: str, lib: str = 'sitk') → Image

Read MINC file (.mnc).

Parameters

filenamestr: image file name
libstr: format of returned image ‘itk’, ‘vtk’, ‘ants’ or by default ‘sitk’

Returns

SimpleITK.Image | itk.Image | vtk.ImageData | ants.core.ANTsImage: image instance

Sisyphe.core.sisypheImageIO.readFromNIFTI(filename: str, lib: str = 'sitk') → Image

Read Nifti file (.nii, .hdr, .img, .nia, .nii.gz, .img.gz).

Parameters

filenamestr: image file name
libstr: format of returned image ‘itk’, ‘vtk’, ‘ants’ or by default ‘sitk’

Returns

SimpleITK.Image | itk.Image | vtk.ImageData | ants.core.ANTsImage: image instance

Sisyphe.core.sisypheImageIO.readFromNRRD(filename: str, lib: str = 'sitk') → Image

Read NRRD file (.nrrd, .nhdr).

Parameters

filenamestr: image file name
libstr: format of returned image ‘itk’, ‘vtk’, ‘ants’ or by default ‘sitk’

Returns

SimpleITK.Image | itk.Image | vtk.ImageData | ants.core.ANTsImage: image instance

Sisyphe.core.sisypheImageIO.readFromNumpy(filename: str, defaultshape: bool = True, lib: str = 'sitk') → Image

Read Numpy file (.npy).

Parameters

filenamestr: image file name
defaultshapebool: shape (z, y, x) if True, (x, y, z) if False
libstr: format of returned image ‘itk’, ‘vtk’, ‘ants’ or by default ‘sitk’

Returns

SimpleITK.Image | itk.Image | vtk.ImageData | ants.core.ANTsImage: image instance

Sisyphe.core.sisypheImageIO.readFromSisyphe(filename: str, lib: str = 'sitk') → tuple[Image, dict]

Read Sisyphe file (.vol).

Parameters

filenamestr: image file name
libstr: format of returned image ‘itk’, ‘vtk’, ‘ants’ or by default ‘sitk’

Returns

tuple[SimpleITK.Image | itk.Image | vtk.ImageData | ants.core.ANTsImage, dict]

image instance
dict, header of Sisyphe image format

Sisyphe.core.sisypheImageIO.readFromSisypheROI(filename: str, lib: str = 'sitk') → tuple[list[Image], dict]

Read sitkImage.

Parameters

filenamestr: ROI file name
libstr: format of returned image ‘itk’, ‘vtk’, ‘ants’ or by default ‘sitk’

Returns

tuple[SimpleITK.Image, dict]

image instance
dict, header of Sisyphe ROI image format, key = string of field, value of field

Sisyphe.core.sisypheImageIO.readFromVTK(filename: str, lib: str = 'sitk') → Image

Read VTK file (.vtk, .vti).

Parameters

filenamestr: image file name
libstr: format of returned image ‘itk’, ‘vtk’, ‘ants’ or by default ‘sitk’

Returns

SimpleITK.Image | itk.Image | vtk.ImageData | ants.core.ANTsImage: image instance

Sisyphe.core.sisypheImageIO.readImage(filename: str, lib: str = 'sitk') → Image | tuple[Image, dict]

Read image from Nifti, Nrrd, Minc, VTK, Numpy, old Sisyphe, or Bitmap format. Format is detectied from filename extension. Instance returned can be SimpleITK.Image | itk.Image | vtk.ImageData | ants.core.ANTsImage.

Parameters

filenamestr: image file name
libstr: format of returned image ‘itk’, ‘vtk’, ‘ants’ or by default ‘sitk’

Returns

SimpleITK.Image | itk.Image | vtk.ImageData | ants.core.ANTsImage: image instance

Sisyphe.core.sisypheImageIO.writeToJSON(img: Image, filename: str) → None

Write SimpleITK image to disk with JSON format (.json)

Parameters

imgSimpleITK.Image: image to save
filenamestr: file save name

Sisyphe.core.sisypheImageIO.writeToMINC(img: Image, filename: str) → None

Write SimpleITK image to disk with MINC format (.mnc).

Parameters

imgSimpleITK.Image: image to save
filenamestr: file save name

Sisyphe.core.sisypheImageIO.writeToNIFTI(img: Image, filename: str, compression: bool = False) → None

Write SimpleITK image to disk with NIFTI format (.nii, .hdr, .img, .nia, .nii.gz, .img.gz).

Parameters

imgSimpleITK.Image: image to save
filenamestr: file save name
compressionbool: write compressed format nii.gz if True, default is False

Sisyphe.core.sisypheImageIO.writeToNRRD(img: Image, filename: str) → None

Write SimpleITK image to disk with NRRD format (.nrrd, .nhdr).

Parameters

imgSimpleITK.Image: image to save
filenamestr: file save name

Sisyphe.core.sisypheImageIO.writeToNumpy(img: Image, filename: str) → None

Write SimpleITK image to disk with Numpy format (.npy)

Parameters

imgSimpleITK.Image: image to save
filenamestr: file save name

Sisyphe.core.sisypheImageIO.writeToVTK(img: Image, filename: str) → None

Write SimpleITK image to disk with VTK format (.vtk)

Parameters

imgSimpleITK.Image: image to save
filenamestr: file save name