mcmodels.core.Mask

class mcmodels.core.Mask(reference_space, structure_ids=None, hemisphere_id=None)

Object for masking the grid data from allensdk.

This object is useful for masking grid data as well as reshaping/filling ‘masked’ arrays to be the shape of the annotation (CCF) from allensdk. Also, this object is useful for determining the location or structure id of a given voxel from the voxel-voxel connectivity matrix.

Parameters:

voxel_model_cache : VoxelModelCache object

This supplies the interface for pulling cached reference space, annotation, and structure tree objects.

structure_ids : array-like, optional, shape (n_structure_ids,)

AllenSDK CCF Annotation structure ids to be included in the model

Hemisphere : int

hemisphere id to be included in the projection in the model.

• 1, left hemisphere
• 2, right hemisphere
• 3, both hemispheres

Examples

>>> from mcmodels.core import Mask, VoxelModelCache
>>> cache = VoxelModelCache()
>>> mask = Mask.from_cache(cache)
>>> # what shape will a masked volume be
>>> mask.masked_shape
(448962,)

Attributes:

reference_space : reference_space object

see allensdk.reference_space

Methods

fill_volume_where_masked(self, X, fill[, …])	Fills a data volume where mask is valid.
from_cache(cache, \*\*kwargs)	Parameters:
get_flattened_voxel_index(self, voxel_idx)	Return the index of a givel voxel in the flattened mask.
get_key(self[, structure_ids, hemisphere_id])	Returns flattened annotation key.
get_structure_flattened_mask(self[, …])	Masks a structure_mask or union of structure_masks.
get_structure_indices(self[, structure_ids, …])	Returns the indices of a masked structure_mask or union of structure_masks.
map_masked_to_annotation(self, y)	Maps a masked vector y back to annotation volume.
mask_volume(self, X)	Masks a given volume.

__init__(self, reference_space, structure_ids=None, hemisphere_id=None)

Methods

__init__(self, reference_space[, …])
fill_volume_where_masked(self, X, fill[, …])	Fills a data volume where mask is valid.
from_cache(cache, \*\*kwargs)	Parameters:
get_flattened_voxel_index(self, voxel_idx)	Return the index of a givel voxel in the flattened mask.
get_key(self[, structure_ids, hemisphere_id])	Returns flattened annotation key.
get_structure_flattened_mask(self[, …])	Masks a structure_mask or union of structure_masks.
get_structure_indices(self[, structure_ids, …])	Returns the indices of a masked structure_mask or union of structure_masks.
map_masked_to_annotation(self, y)	Maps a masked vector y back to annotation volume.
mask_volume(self, X)	Masks a given volume.

assigned_structures

List of resolved structures in annotation

coordinates

Returns coordinates inside mask.

fill_volume_where_masked(self, X, fill, inplace=True)

Fills a data volume where mask is valid.

Parameters:

X : array, shape (x_ccf, y_ccf, z_ccf)

Array to be filled where mask is valid.

fill : int or array, shape=(masked_shape)

Fill value or array.

inplace : boolean

If True, X is filled in place, else a copy is returned.

Returns:

array - shape (x_ccf, y_ccf, z_ccf)

Filled array.

classmethod from_cache(cache, **kwargs)

Parameters:

cache : caching object

MCC or RSC or VMC

get_flattened_voxel_index(self, voxel_idx)

Return the index of a givel voxel in the flattened mask.

Parameters:

voxel_idx : array

coordinates of voxel of which the flattened index position is wanted

Returns:

int

idx of voxel_idx in flattened mask

get_key(self, structure_ids=None, hemisphere_id=None)

Returns flattened annotation key.

Useful in performing structure specific computations on the voxel-voxel array.

Parameters:

structure_ids : list, optional (default=None)

Ids of structures which to include in the key. If None, the structure_ids used to make the Mask object will be used.

hemisphere_id : int, optional (default=None)

Hemisphere to include in the key. If None, the hemisphere used to mask the Mask object will be used.

Returns:

key = array, shape (masked_shape,), type np.int

Key mapping an element in a masked data volume to its structure id in the annotation. Each element in key is a structure_id.

get_structure_flattened_mask(self, structure_ids=None, hemisphere_id=None)

Masks a structure_mask or union of structure_masks.

Parameters:

structure_ids : array-like, optional (default = None)

A list of structure ids with which to construct a structure union mask. If None, the object’s structure_ids are used.

hemisphere_id : int, optional (default = None)

The hemisphere to which the structure union mask will be additionally masked to. If None, the object’s hemisphere_id is used.

Returns:

array - shape (masked_shape)

Masked structure union mask.

get_structure_indices(self, structure_ids=None, hemisphere_id=None)

Returns the indices of a masked structure_mask or union of structure_masks.

Parameters:

structure_ids : array-like, optional (default = None)

A list of structure ids with which to construct a structure union mask. If None, the object’s structure_ids are used.

hemisphere_id : int, optional (default = None)

The hemisphere to which the structure union mask will be additionally masked to. If None, the object’s hemisphere_id is used.

Returns:

array - shape (masked_nonzero,)

The indices of the masked structure union mask that are nonzero

map_masked_to_annotation(self, y)

Maps a masked vector y back to annotation volume.

Parameters:

y : array, shape (masked_shape)

Array to be mapped into where mask is valid.

Returns:

y_volume : shape (x_ccf, y_ccf, z_ccf)

Array same shape as annotation, filled with input parameter y where mask is valid

mask

Boolean mask defining ‘interesting’ voxels.

mask_volume(self, X)

Masks a given volume.

Parameters:

X - array, shape (x_ccf, y_ccf, z_ccf)

Data volume to be masked. Must be same shape as self.reference_space.annotation.shape

Returns:

array - shape (masked_shape)

Masked data volume.

masked_shape

Shape a data volume would become after masking.