asldro.containers package

Submodules

asldro.containers.image module

Classes for image encapsulation Used to create a standard interface for ND images which can be instantiated with either NIFTI files or using numpy arrays

class asldro.containers.image.BaseImageContainer(data_domain: str = 'SPATIAL_DOMAIN', image_type=None, metadata=None, **kwargs)

Bases: abc.ABC

An abstract (interface) for an ND image. Defines a set of accessors :param data_domain: defines the data domain as SPATIAL_DOMAIN or INVERSE_DOMAIN (default is SPATIAL_DOMAIN) :param image_type: the image type. Must be one of: - REAL_IMAGE_TYPE - IMAGINARY_IMAGE_TYPE - MAGNITUDE_IMAGE_TYPE - PHASE_IMAGE_TYPE - COMPLEX_IMAGE_TYPE if this is not specified, it will be set to REAL_IMAGE_TYPE for scalar image dtypes and COMPLEX_IMAGE_TYPE for complex dtypes :param metadata: a metadata dictionary which is associated with the image data. This might contain, for example, timing parameters associated with the image acquisition.

abstract property affine

Return a 4x4 numpy array with the image affine transformation

abstract as_nifti() → asldro.containers.image.NiftiImageContainer

Return the image container as a NiftiImageContainer. If the container is already a NiftiImageContainer, return self

abstract as_numpy() → asldro.containers.image.NumpyImageContainer

Return the image container as a NumpyImageContainer. If the container is already a NumpyImageContainer, return self

clone() → asldro.containers.image.BaseImageContainer

Makes a deep copy of all member variables in a new ImageContainer

abstract property has_nifti

Returns True if the image has an associated nifti container

abstract property image

Return the image data as a numpy array

property metadata

Get the metadata

abstract property shape

Returns the shape of the image [x, y, z, t, etc]

abstract property space_units

Uses the NIFTI header xyzt_units to extract the space units. Returns one of: ‘meter’ ‘mm’ ‘micron’

abstract property time_step_seconds

Return the time step in seconds

abstract property time_units

Uses the NIFTI header xyzt_units to extract the time units. Returns one of: ‘sec’ ‘msec’ ‘usec’

abstract property voxel_size_mm

Returns the voxel size in mm

class asldro.containers.image.NiftiImageContainer(nifti_img: Union[nibabel.Nifti1Image, nibabel.Nifti2Image] = None, **kwargs)

Bases: asldro.containers.image.BaseImageContainer

A container for an ND image. Must be initialised with a nibabel Nifti1Image or Nifti2Image

property affine

Return a 4x4 numpy array with the image affine transformation

as_nifti() → asldro.containers.image.NiftiImageContainer

Returns self

as_numpy() → asldro.containers.image.NumpyImageContainer

Return the NiftiImageContainer as a NumpyImageContainer.

property has_nifti

Returns True if the image has an associated nifti container

property header

Returns the NIFTI header if initialised from a NIFTI file, othewise returns None

property image

Return the image data as a numpy array. Returns data in the type it is created (i.e. won’t convert to float64 as .get_fdata() will)

property nifti_type

Return the type of NIFTI data contained here (nib.Nifti1Image or nib.Nifti2Image)

property shape

Returns the shape of the image [x, y, z, t, etc]

property space_units

Uses the NIFTI header xyzt_units to extract the space units. Returns one of: ‘meter’ ‘mm’ ‘micron’

property time_step_seconds

Return the time step in seconds

property time_units

Uses the NIFTI header xyzt_units to extract the time units. Returns one of: ‘sec’ ‘msec’ ‘usec’

property voxel_size_mm

Returns the voxel size in mm

class asldro.containers.image.NumpyImageContainer(image: numpy.ndarray, affine: numpy.ndarray = numpy.eye, space_units: str = 'mm', time_units: str = 'sec', voxel_size=numpy.array, time_step=1.0, **kwargs)

Bases: asldro.containers.image.BaseImageContainer

A container for an ND image. Must be initialised with a a numpy array and some associated metadata.

property affine

Return a 4x4 numpy array with the image affine transformation

as_nifti() → asldro.containers.image.NiftiImageContainer

Return the NumpyImageContainer as a NiftiImageContainer.

as_numpy() → asldro.containers.image.NumpyImageContainer

Returns self

property has_nifti

Returns True if the image has an associated nifti container

property header

Returns the NIFTI header if initialised from a NIFTI file, othewise returns None

property image

Return the image data as a numpy array

property shape

Returns the shape of the image [x, y, z, t, etc]

property space_units

Uses the NIFTI header xyzt_units to extract the space units. Returns one of: ‘meter’ ‘mm’ ‘micron’

property time_step_seconds

Return the time step in seconds

property time_units

Uses the NIFTI header xyzt_units to extract the time units. Returns one of: ‘sec’ ‘msec’ ‘usec’

property voxel_size_mm

Returns the voxel size in mm

Module contents