neurolang.frontend.deterministic_frontend module¶

class neurolang.frontend.deterministic_frontend.ExplicitVBR(voxels, affine_matrix, image_dim=None, prebuild_tree=False)¶

Bases: VolumetricBrainRegion

Attributes:

aabb_tree
bounding_box
center
width

Methods

`to_ijk`(affine)	return ijk voxels coordinates corresponding to the affine matrix transform
`to_xyz`([affine])	return world coordinates of the region corresponding to the affine matrix transform

build_tree
from_spatial_image_label
generate_bounding_box
remove_empty_bounding_boxes
spatial_image
to_explicit_vbr
to_ijk_set
to_xyz_set

property aabb_tree¶

property bounding_box¶

build_tree()¶

generate_bounding_box(voxels_ijk)¶

spatial_image(out=None, value=1)¶

to_ijk(affine)¶: return ijk voxels coordinates corresponding to the affine matrix transform

to_xyz(affine=None)¶: return world coordinates of the region corresponding to the affine matrix transform

class neurolang.frontend.deterministic_frontend.ExplicitVBROverlay(voxels, affine_matrix, overlay, image_dim=None, prebuild_tree=False)¶

Bases: ExplicitVBR

Attributes:

aabb_tree
bounding_box
center
width

Methods

`to_ijk`(affine)	return ijk voxels coordinates corresponding to the affine matrix transform
`to_xyz`([affine])	return world coordinates of the region corresponding to the affine matrix transform

build_tree
from_spatial_image_label
generate_bounding_box
remove_empty_bounding_boxes
spatial_image
to_explicit_vbr
to_ijk_set
to_xyz_set

spatial_image(out=None, background_value=0)¶

class neurolang.frontend.deterministic_frontend.NeurolangDL(program_ir=None)¶

Bases: QueryBuilderDatalog

Deterministic Datalog Frontend for Neurolang. QueryBuilderDatalog with a RegionFrontendDatalogSolver program intermediate representation

Attributes:

current_program: Returns the list of expressions that have currently been
environment: Dynamic context that can be used to create symbols to write a Datalog program.
functions: Returns the list of symbols corresponding to callables
region_names: Returns the list of symbol names with Region type
region_set_names: Returns the list of symbol names with set_type
scope: Dynamic context that can be used to create symbols to write a Datalog program.
symbol_table: Projector to the program_ir’s symbol_table
symbols: Iterator through the symbol’s names
types: Returns a list of the types of the symbols currently

Methods

`add_atlas_set`(name, atlas_labels, spatial_image)	Creates an atlas set: 1- for each region specified by a label and name in atlas_labels, creates associated ExplicitVBR and symbols Tuple[region_name: str, Region] 2- groups regions in an AbstractSet[Tuple[str, Region]] symbol with specified name
`add_constraint`(antecedent, consequent)	Creates an right implication of the consequent by the antecedent and adds the rule to the current program: antecedent -> consequent
`add_region`(region[, name])	Adds region fe.Symbol to symbol_table
`add_region_set`(region_set[, name])	Creates an AbstractSet fe.Symbol containing the elements specified in the iterable with a List[Tuple[Region]] format
`add_symbol`(value[, name, type_])	Creates a symbol with given value and adds it to the current symbol_table.
`add_tuple_set`(iterable[, type_, name])	Creates an AbstractSet fe.Symbol containing the elements specified in the iterable with a List[Tuple[Any, ...]] format (see examples).
`all`(quantified_variable, body)	Universal predicate on the body.
`create_region`(spatial_image[, label, ...])	Creates an ExplicitVBR out of the voxels of a dense spatial_image with specified label
`del_symbol`(name)	Deletes the symbol with parameter name from the symbol_table
`execute_datalog_program`(code)	Execute a Datalog program in classical syntax.
`exists`(quantified_variable, body)	Existential predicate on the body.
`get_symbol`(symbol_name)	Retrieves symbol via its name, either providing a fe.Expression with the correct name or the name itself
`load_neurosynth_mni_peaks_reported`(data_dir)	Load the coordinates for the peaks reported by studies in the Neurosynth dataset.
`load_neurosynth_study_ids`(data_dir[, name, ...])	Load all study ids (PMIDs) that are part of the Neurosynth database.
`load_neurosynth_term_study_associations`(data_dir)	Load TF-IDF values for each (term, study) association within the Neurosynth database.
`make_implicit_regions_explicit`(affine, dim)	Raises NotImplementedError for now
`new_region_symbol`([name])	Returns symbol with type Region
`new_symbol`([type_, name])	Creates a symbol and associated expression, optionally specifying it's type and/or name
`predicate_parameter_names`(predicate_name)	Get the names of the parameters for the given predicate
`query`(*args)	Performs an inferential query on the database.
`reset_program`()	Clears current symbol table
`solve_all`()	Returns a dictionary of "predicate_name": "Content" for all elements in the solution of the Datalog program.
`sphere`(center, radius[, name])	Creates a Region symbol associated with the spherical volume described by its center and volume

magic_sets_rewrite_program

class neurolang.frontend.deterministic_frontend.Symbol(query_builder: QueryBuilderBase, symbol_name: str)¶

Bases: Expression

A Symbol represents an atomic Expression. Its is the most recurrent element of queries

Attributes:

expression: Projects to symbol property
neurolang_symbol: Returns backend symbol
symbol: Returns backend symbol from symbol_table
type: Returns expression’s type
value: If any, returns value corresponding to the symbol

Methods

`__call__`(args, *kwargs)	Returns a FunctionApplication expression, applied to the args cast as Constant if not Symbol or Expression *kwargs are ignored
`help`()	Returns help based on Expression's subclass

property expression: Symbol¶: Projects to symbol property

property neurolang_symbol: Symbol¶: Returns backend symbol

property symbol: Symbol¶: Returns backend symbol from symbol_table

property value: Any¶

If any, returns value corresponding to the symbol

Returns:

Any: see description

Raises:

ValueError: if Symbol doesn’t have a python value