brainiak.searchlight package¶
Distributed Searchlight
Submodules¶
brainiak.searchlight.searchlight module¶

class
brainiak.searchlight.searchlight.
Ball
(rad)¶ Bases:
brainiak.searchlight.searchlight.Shape
Searchlight shape which is a ball inscribed in a cube of size (2*rad+1,2*rad+1,2*rad+1). Any location in the cube which has a Euclidean distance of equal to or less than rad from the center point is set to True.
 Parameters
rad (radius, in voxels, of the sphere inscribed in the) – searchlight cube, not counting the center voxel

class
brainiak.searchlight.searchlight.
Cube
(rad)¶ Bases:
brainiak.searchlight.searchlight.Shape
Searchlight shape which is a cube of size (2*rad+1,2*rad+1,2*rad+1)
 Parameters
rad (radius, in voxels, of the sphere inscribed in the) – searchlight cube, not counting the center voxel

class
brainiak.searchlight.searchlight.
Diamond
(rad)¶ Bases:
brainiak.searchlight.searchlight.Shape
Searchlight shape which is a diamond inscribed in a cube of size (2*rad+1,2*rad+1,2*rad+1). Any location in the cube which has a Manhattan distance of equal to or less than rad from the center point is set to True.
 Parameters
rad (radius, in voxels, of the sphere inscribed in the) – searchlight cube, not counting the center voxel

class
brainiak.searchlight.searchlight.
Searchlight
(sl_rad=1, max_blk_edge=10, shape=<class 'brainiak.searchlight.searchlight.Cube'>, min_active_voxels_proportion=0)¶ Bases:
object
Distributed Searchlight
Run a userdefined function over each voxel in a multisubject dataset.
Optionally, users can define a block function which runs over larger portions of the volume called blocks.
 Parameters
sl_rad (radius, in voxels, of the sphere inscribed in the) – searchlight cube, not counting the center voxel
max_blk_edge (max edge length, in voxels, of the 3D block) –
shape (brainiak.searchlight.searchlight.Shape indicating the) –
in voxels of the searchlight region (shape) –
min_active_voxels_proportion (float) – If a searchlight region does not have more than this minimum proportion of active voxels in the mask, it is not processed by the searchlight function. The mask used for the test is the intersection of the global (brain) mask and the
Shape
mask. The seed (central) voxel of the searchlight region is taken into consideration.

broadcast
(bcast_var)¶ Distribute data to processes
 Parameters
bcast_var (shared data which is broadcast to all processes) –

distribute
(subjects, mask)¶ Distribute data to MPI ranks
 Parameters
subjects (list of 4D arrays containing data for one or more subjects.) –
Each entry of the list must be present on at most one rank, and the other ranks contain a “None” at this list location.
For example, for 3 ranks you may lay out the data in the following manner:
Rank 0: [Subj0, None, None] Rank 1: [None, Subj1, None] Rank 2: [None, None, Subj2]
Or alternatively, you may lay out the data in this manner:
Rank 0: [Subj0, Subj1, Subj2] Rank 1: [None, None, None] Rank 2: [None, None, None]
mask (3D array with "True" entries at active vertices) –

run_block_function
(block_fn, extra_block_fn_params=None, pool_size=None)¶ Perform a function for each block in a volume.
 Parameters
block_fn –
Parameters
 data: list of 4D arrays containing subset of subject data,
which is padded with sl_rad voxels.
mask: 3D array containing subset of mask data
sl_rad: radius, in voxels, of the sphere inscribed in the cube
bcast_var: shared data which is broadcast to all processes
extra_params: extra parameters
 extra_block_fn_params: tuple
Extra parameters to pass to the block function
 pool_size: int
Maximum number of processes running the block function in parallel. If None, number of available hardware threads, considering cpusets restrictions.

run_searchlight
(voxel_fn, pool_size=None)¶ Perform a function at each voxel which is set to True in the userprovided mask. The mask passed to the searchlight function will be further masked by the userprovided searchlight shape.
 Parameters
voxel_fn –
Must be serializeable using pickle.
Parameters
subj: list of 4D arrays containing subset of subject data
mask: 3D array containing subset of mask data
sl_rad: radius, in voxels, of the sphere inscribed in the cube
bcast_var: shared data which is broadcast to all processes
 Returns
A volume which is the same size as the mask, however a number of voxels
equal to the searchlight radius has been removed from each border of
the volume. This volume contains the values returned from the
searchlight function at each voxel which was set to True in the mask,
and None elsewhere.

class
brainiak.searchlight.searchlight.
Shape
(rad)¶ Bases:
object
Searchlight shape which is contained in a cube sized (2*rad+1,2*rad+1,2*rad+1)

mask_
¶ which is set to True within the boundaries of the desired shape
 Type
a 3D boolean numpy array of size (2*rad+1,2*rad+1,2*rad+1)
 Parameters
rad (radius, in voxels, of the sphere inscribed in the) – searchlight cube, not counting the center voxel
