Phantom#

class snake.core.phantom.static.Phantom(name, masks, labels, props)[source]#

Bases: object

A Phantom consist of a list of tissue mask and parameters for those tissues.

Methods

`__init__`
`add_tissue`	Add a tissue to the phantom.
`from_brainweb`	Get the Brainweb Phantom.
`from_guerin_kern`	Get the Guerin-Kern Phantom.
`from_mrd_dataset`	Load the phantom from a mrd dataset.
`from_shared_memory`	Give access the tissue masks and properties in shared memory.
`from_shepp_logan`	Get the Shepp-Logan Phantom.
`in_shared_memory`	Add a copy of the phantom in shared memory.
`to_mrd_dataset`	Add the phantom as an image to the dataset.

Attributes

`anat_shape`	Get the shape of the base volume.
`n_tissues`	Get the number of tissues.
`name`
`masks`
`labels`
`props`

Parameters:

name (str)
masks (ndarray[Any, dtype[float32]])
labels (ndarray[Any, dtype[bytes_]])
props (ndarray[Any, dtype[float32]])

add_tissue(tissue_name, mask, props, phantom_name=None)[source]#

Add a tissue to the phantom. Creates a new Phantom object.

Parameters:

tissue_name (str)
mask (ndarray[Any, dtype[float32]])
props (ndarray[Any, dtype[float32]])
phantom_name (str | None)

Return type:

Phantom

classmethod from_brainweb(sub_id, sim_conf, tissue_file=TissueFile.tissue_1T5, tissue_select=None, tissue_ignore=None)[source]#

Get the Brainweb Phantom.

Parameters:

sub_id (int)
sim_conf (SimConfig)
tissue_file (str | TissueFile)
tissue_select (list[str] | None)
tissue_ignore (list[str] | None)

Return type:

Phantom

classmethod from_shepp_logan(resolution)[source]#

Get the Shepp-Logan Phantom.

Parameters:: resolution (tuple[int])
Return type:: Phantom

classmethod from_guerin_kern(resolution)[source]#

Get the Guerin-Kern Phantom.

Parameters:: resolution (tuple[int])
Return type:: Phantom

classmethod from_mrd_dataset(dataset, imnum=0)[source]#

Load the phantom from a mrd dataset.

Parameters:

dataset (Dataset | PathLike)
imnum (int)

Return type:

Phantom

to_mrd_dataset(dataset, sim_conf, imnum=0)[source]#

Add the phantom as an image to the dataset.

Parameters:

dataset (Dataset)
sim_conf (SimConfig)
imnum (int)

Return type:

Dataset

classmethod from_shared_memory(name, mask_prop, properties_prop, label_prop)[source]#

Give access the tissue masks and properties in shared memory.

Parameters:

name (str)
mask_prop (ArrayProps)
properties_prop (ArrayProps)
label_prop (ArrayProps)

Return type:

Generator[Phantom, None, None]

in_shared_memory(manager)[source]#

Add a copy of the phantom in shared memory.

Parameters:: manager (SharedMemoryManager)
Return type:: tuple[tuple[str, ArrayProps, ArrayProps, ArrayProps], tuple[SharedMemory, SharedMemory, SharedMemory]]

property anat_shape: tuple[int, ...]#: Get the shape of the base volume.

property n_tissues: int#: Get the number of tissues.

Phantom

Contents

Phantom#