mvpa2.datasets.cosmo.CosmoSearchlight¶

class mvpa2.datasets.cosmo.CosmoSearchlight(datameasure, nbrhood, add_center_fa=False, results_postproc_fx=None, results_backend='native', results_fx=None, tmp_prefix='tmpsl', nblocks=None, **kwargs)¶

Implement a standard Searchlight measure, but with a separate postprocessing step that involves setting feature (.fa) and dataset (.a) attributes after the searchlight call has been made.

A typical use case is in combination with a neighborhood from CoSMoMVPA, either from a .mat matlab file or through a CosmoQueryEngine

Notes

Available conditional attributes:

calling_time+: Time (in seconds) it took to call the node
null_prob+: None
null_t: None
raw_results: Computed results before invoking postproc. Stored only if postproc is not None.
roi_center_ids+: Center ID for all generated ROIs.
roi_feature_ids: Feature IDs for all generated ROIs.
roi_sizes: Number of features in each ROI.
trained_dataset: The dataset it has been trained on
trained_nsamples+: Number of samples it has been trained on
trained_targets+: Set of unique targets (or any other space) it has been trained on (if present in the dataset trained on)
training_time+: Time (in seconds) it took to train the learner

(Conditional attributes enabled by default suffixed with +)

Attributes

`add_center_fa`
`auto_train`	Whether the Learner performs automatic trainingwhen called untrained.
`datameasure`
`descr`	Description of the object if any
`force_train`	Whether the Learner enforces training upon every call.
`null_dist`	Return Null Distribution estimator
`pass_attr`	Which attributes of the dataset or self.ca to pass into result dataset upon call
`postproc`	Node to perform post-processing of results
`queryengine`
`roi_ids`
`space`	Processing space name of this node

Methods

`__call__`(ds)
`generate`(ds)	Yield processing results.
`get_postproc`()	Returns the post-processing node or None.
`get_space`()	Query the processing space name of this node.
`reset`()
`set_postproc`(node)	Assigns a post-processing node
`set_space`(name)	Set the processing space name of this node.
`train`(ds)	The default implementation calls `_pretrain()`, `_train()`, and finally `_posttrain()`.
`untrain`()	Reverts changes in the state of this node caused by previous training

Parameters:

datameasure : callable

Any object that takes a Dataset and returns some measure when called.

nbrhood : str or dict or CosmoQueryEngine

Defines the neighborhood for each feature. A str indicates the filename of a matlab .mat file with a neighborhood generated by CoSMoMVPA. A dict indicates the result of such a neighborhood when loaded by loadmat. A CosmoQueryEngine indicates such a neighborhood as a QueryEngineInterface object

add_center_fa : bool or str

If True or a string, each searchlight ROI dataset will have a boolean vector as a feature attribute that indicates the feature that is the seed (e.g. sphere center) for the respective ROI. If True, the attribute is named ‘roi_seed’, the provided string is used as the name otherwise.

results_postproc_fx : callable

Called with all the results computed in a block for possible post-processing which needs to be done in parallel instead of serial aggregation in results_fx.

results_backend : (‘native’, ‘hdf5’), optional

Specifies the way results are provided back from a processing block in case of nproc > 1. ‘native’ is pickling/unpickling of results by pprocess, while ‘hdf5’ would use h5save/h5load functionality. ‘hdf5’ might be more time and memory efficient in some cases.

results_fx : callable, optional

Function to process/combine results of each searchlight block run. By default it would simply append them all into the list. It receives as keyword arguments sl, dataset, roi_ids, and results (iterable of lists). It is the one to take care of assigning roi_* ca’s

tmp_prefix : str, optional

If specified – serves as a prefix for temporary files storage if results_backend == ‘hdf5’. Thus can specify the directory to use (trailing file path separator is not added automagically).

nblocks : None or int

Into how many blocks to split the computation (could be larger than nproc). If None – nproc is used.

enable_ca : None or list of str

Names of the conditional attributes which should be enabled in addition to the default ones

disable_ca : None or list of str

Names of the conditional attributes which should be disabled

preallocate_output : bool, optional

If set, the output of each computation block will be pre-allocated. This can speed up computations if the datameasure returns a large number of samples and there are many features for which the datameasure is computed. The user should verify the correct assignment of sample attributes and feature attributes, since no hstacking is performed within each computing block.

queryengine : QueryEngine

Engine to use to discover the “neighborhood” of each feature. See QueryEngine.

roi_ids : None or list(int) or str

List of query engine ids (e.g., feature ids, not coordinates, in case of IndexQueryEngine; and node_indices in case of SurfaceQueryEngine) that shall serve as ROI seeds (e.g., sphere centers). Alternatively, this can be the name of a feature attribute of the input dataset, whose non-zero values determine the feature ids (be careful to use it only with IndexQueryEngine). By default all query engine ids will be used.

nproc : None or int

How many processes to use for computation. Requires pprocess external module. If None – all available cores will be used.

null_dist : instance of distribution estimator

The estimated distribution is used to assign a probability for a certain value of the computed measure.

auto_train : bool

Flag whether the learner will automatically train itself on the input dataset when called untrained.

force_train : bool

Flag whether the learner will enforce training on the input dataset upon every call.

space : str, optional

Name of the ‘processing space’. The actual meaning of this argument heavily depends on the sub-class implementation. In general, this is a trigger that tells the node to compute and store information about the input data that is “interesting” in the context of the corresponding processing in the output dataset.

pass_attr : str, list of str|tuple, optional

Additional attributes to pass on to an output dataset. Attributes can be taken from all three attribute collections of an input dataset (sa, fa, a – see Dataset.get_attr()), or from the collection of conditional attributes (ca) of a node instance. Corresponding collection name prefixes should be used to identify attributes, e.g. ‘ca.null_prob’ for the conditional attribute ‘null_prob’, or ‘fa.stats’ for the feature attribute stats. In addition to a plain attribute identifier it is possible to use a tuple to trigger more complex operations. The first tuple element is the attribute identifier, as described before. The second element is the name of the target attribute collection (sa, fa, or a). The third element is the axis number of a multidimensional array that shall be swapped with the current first axis. The fourth element is a new name that shall be used for an attribute in the output dataset. Example: (‘ca.null_prob’, ‘fa’, 1, ‘pvalues’) will take the conditional attribute ‘null_prob’ and store it as a feature attribute ‘pvalues’, while swapping the first and second axes. Simplified instructions can be given by leaving out consecutive tuple elements starting from the end.

postproc : Node instance, optional

Node to perform post-processing of results. This node is applied in __call__() to perform a final processing step on the to be result dataset. If None, nothing is done.

descr : str

Description of the instance

Attributes

`add_center_fa`
`auto_train`	Whether the Learner performs automatic trainingwhen called untrained.
`datameasure`
`descr`	Description of the object if any
`force_train`	Whether the Learner enforces training upon every call.
`null_dist`	Return Null Distribution estimator
`pass_attr`	Which attributes of the dataset or self.ca to pass into result dataset upon call
`postproc`	Node to perform post-processing of results
`queryengine`
`roi_ids`
`space`	Processing space name of this node

Methods

`__call__`(ds)
`generate`(ds)	Yield processing results.
`get_postproc`()	Returns the post-processing node or None.
`get_space`()	Query the processing space name of this node.
`reset`()
`set_postproc`(node)	Assigns a post-processing node
`set_space`(name)	Set the processing space name of this node.
`train`(ds)	The default implementation calls `_pretrain()`, `_train()`, and finally `_posttrain()`.
`untrain`()	Reverts changes in the state of this node caused by previous training