mvpa2.datasets.cosmo.CosmoQueryEngine¶
-
class
mvpa2.datasets.cosmo.
CosmoQueryEngine
(mapping, a=None, fa=None)¶ queryengine for neighborhoods defined in CoSMoMVPA. This class behaves like a normal QueryEngine, and its use is intended with a searchlight. It differs in that it contains the dataset (.a) and feature (.fa) attributes for the output of a searchlight. This is implemented by the method set_output_dataset_attributes. Although the standard Searchlight can be used with this function, using CosmoSearchlight automatically calls this method so that the dataset attributes for the output are properly set.
Attributes
a
Returns: fa
Returns: ids
Returns: Methods
__call__
(\*\*kwargs)from_mat
(neighbors[, a, fa, origin])Create CosmoQueryEngine from mat struct query
(\*\*kwargs)query_byid
(id)Returns set_output_dataset_attributes
(ds)Set attributes to output dataset (e.g. train
(dataset)This method does nothing untrain
()This method does nothing Parameters: mapping: dict
mapping from center ids (int) to array of feature ids (numpy array of datatype int)
a: None or dict or ArrayCollectable
dataset attributes to be used for the output of a Searchlight
fa: None or dict or ArrayCollectable
dataset attributes to be used for the output of a Searchlight
Attributes
a
Returns: fa
Returns: ids
Returns: Methods
__call__
(\*\*kwargs)from_mat
(neighbors[, a, fa, origin])Create CosmoQueryEngine from mat struct query
(\*\*kwargs)query_byid
(id)Returns set_output_dataset_attributes
(ds)Set attributes to output dataset (e.g. train
(dataset)This method does nothing untrain
()This method does nothing -
a
¶ Returns: a : DatasetAttributesCollection
Dataset attributes for the output dataset from using this instance
-
fa
¶ Returns: fa : FeatureAttributesCollection
Feature attributes for the output dataset from using this instance. It has as many elements as self.ids
-
classmethod
from_mat
(neighbors, a=None, fa=None, origin=None)¶ Create CosmoQueryEngine from mat struct
Parameters: neighbors: numpy.object
Object from scipy’s matload; must have been a Px1 cell with in each cell a vector with indices of neighboring features in base 1. Typically this is from a CoSMoMVPA neighborhood struct.
a: None or dict or ArrayCollectable
dataset attributes to be used for the output of a Searchlight
fa: None or dict or ArrayCollectable
dataset attributes to be used for the output of a Searchlight
origin:
Optional contents of .a and .fa of dataset indexed by neighbors; its content is ignored
Notes
Empty elements are ignored. Future implementations may store the origin element, and check that its contents agrees with a dataset when this instances trains on it.
-
ids
¶ Returns: keys: npndarray
vector with feature indices that can be used as keys
-
query
(**kwargs)¶
-
query_byid
(id)¶ - fids : np.ndarray
- vector with feature indices of neighbors of the feature indexed by id
-
set_output_dataset_attributes
(ds)¶ Set attributes to output dataset (e.g. after running a searchlight)
Parameters: ds : Dataset
dataset with ds.fa.center_ids containing the center id of each feature
Returns
ds_copy : Dataset
copy of ds, but with feature (.fa) and dataset (.a) attributes provided to the contstructor of this instance. The .fa and .a from the input ds are removed first.
-
train
(dataset)¶ This method does nothing
-
untrain
()¶ This method does nothing
-