bmtk.utils.sonata package

Subpackages

• bmtk.utils.sonata.config package
  • Submodules
  • bmtk.utils.sonata.config.sonata_config module
  • Module contents

Submodules

bmtk.utils.sonata.column_property module

class bmtk.utils.sonata.column_property.ColumnProperty(name, dtype, dimension, nrows=0, attrs=None)

Bases: object

Representation of a column name and metadata from a hdf5 dataset, csv column, etc.

attributes

dimension

dtype

classmethod from_csv(pd_obj, name=None)

classmethod from_h5(hf_obj, name=None)

name

nrows

bmtk.utils.sonata.edge module

class bmtk.utils.sonata.edge.Edge(src_node_id, trg_node_id, source_pop, target_pop, group_id, group_props, edge_types_props)

Bases: object

dynamics_params

edge_type_id

group_id

source_node_id

source_population

target_node_id

target_population

class bmtk.utils.sonata.edge.EdgeSet(edge_ids, population)

Bases: object

next()

bmtk.utils.sonata.file module

class bmtk.utils.sonata.file.File(data_files, data_type_files, mode='r', gid_table=None, require_magic=True)

Bases: object

edges

has_edges

has_nodes

nodes

version

bmtk.utils.sonata.file_root module

class bmtk.utils.sonata.file_root.EdgesRoot(edges, edge_types, mode='r')

Bases: bmtk.utils.sonata.file_root.FileRoot

edge_types_table

get_populations(name=None, source=None, target=None)

Find all populations with matching criteria, either using the population name (which will return a list of size 0 or 1) or based on the source/target population.

To return a list of all populations just use populations() method

Parameters:

• name – (str) name of population
• source – (str or NodePopulation) returns edges with nodes coming from matching source-population
• target – (str or NodePopulation) returns edges with nodes coming from matching target-population

Returns:

A (potential empty) list of EdgePopulation objects filter by criteria.

class bmtk.utils.sonata.file_root.FileRoot(root_name, h5_files, h5_mode, csv_files)

Bases: object

Base class for both /nodes and /edges root group in h5 file

check_format()

get_population(population_name, default=None)

Return a population group object based on population’s name

population_names

populations

root_name

types_table

class bmtk.utils.sonata.file_root.NodesRoot(nodes, node_types, mode='r', gid_table=None)

Bases: bmtk.utils.sonata.file_root.FileRoot

generate_gids(file_name, gids=None, force=False)

Creates a gid <–> (node_id, population) table based on sonnet specifications.

Generating gids will take some time and so not recommend to call this during the simulation. Instead save the file to the disk and pass in h5 file during the simulation (using gid_table parameter). In fact if you’re worried about efficeny don’t use this method.

Parameters:

• file_name – Name of h5 file to save gid map to.
• gids – rule/list of gids to use
• force – set to true to overwrite existing gid map (default False).

has_gids

node_types_table

set_gid_table(gid_table, force=False)

Adds a map from a gids <–> (node_id, population) based on specification.

Parameters:

• gid_table – An h5 file/group containing map specifications
• force – Set to true to have it overwrite any exsiting gid table (default False)

bmtk.utils.sonata.group module

class bmtk.utils.sonata.group.EdgeGroup(group_id, h5_group, parent)

Bases: bmtk.utils.sonata.group.Group

build_indicies(force=False)

edge_type_ids

filter(**filter_props)

get_values(property_name, all_rows=False)

Returns all values for a group property.

Note that a row within a group may not have a corresponding node/edge, or they may have a different order or multiple node/edges may share the same group row. Setting all_rows=False will return all the values as you see if you iterated through all the population’s items. Setting all_rows=True just returns the data as a list as they appear in the dataset (will be faster).

Parameters:

• property_name – Name of dataset property/column to fetch.
• all_rows – Set false to return order in which they appear in population, false to return entire dataset

Returns:

A list of values for the given column name.

next()

src_node_ids

to_dataframe()

trg_node_ids

class bmtk.utils.sonata.group.Group(group_id, h5_group, parent)

Bases: object

A container containig a node/edge population groups.

A node or edge population will have one or more groups, each having a unique identifier. Each group shared the same columns and datatypes, thus each group is essentially a different model.

all_columns

build_indicies(force=False)

check_format()

column(column_name, group_only=False)

columns

get_dataset(column_name)

get_values(property_name, all_rows=False)

Returns all values for a group property.

Note that a row within a group may not have a corresponding node/edge, or they may have a different order or multiple node/edges may share the same group row. Setting all_rows=False will return all the values as you see if you iterated through all the population’s items. Setting all_rows=True just returns the data as a list as they appear in the dataset (will be faster).

Parameters:

• property_name – Name of dataset property/column to fetch.
• all_rows – Set false to return order in which they appear in population, false to return entire dataset

Returns:

A list of values for the given column name.

group_columns

group_id

has_dynamics_params

has_gids

parent

to_dataframe()

class bmtk.utils.sonata.group.NodeGroup(group_id, h5_group, parent)

Bases: bmtk.utils.sonata.group.Group

build_indicies(force=False)

filter(**filter_props)

Filter all nodes in the group by key=value pairs.

The filter specifications may apply to either node_type or group column properties. Currently at the moment it only supports equivlency. An intersection (and operator) is done for every different filter pair. This will produce a generator of all nodes matching the the filters.

for node in filter(pop_name=’VIp’, depth=10.0):

assert(node[‘pop_name’] == ‘VIp’ and node[‘depth’] == 10.0)

Parameters:filter_props – keys and their values to filter nodes on. Returns:A generator that produces all valid nodes within the group with matching key==value pairs.

get_values(property_name, filtered_indicies=True)

Returns all values for a group property.

Note that a row within a group may not have a corresponding node/edge, or they may have a different order or multiple node/edges may share the same group row. Setting all_rows=False will return all the values as you see if you iterated through all the population’s items. Setting all_rows=True just returns the data as a list as they appear in the dataset (will be faster).

Parameters:

• property_name – Name of dataset property/column to fetch.
• all_rows – Set false to return order in which they appear in population, false to return entire dataset

Returns:

A list of values for the given column name.

gids

node_ids

node_type_ids

to_dataframe()

bmtk.utils.sonata.node module

class bmtk.utils.sonata.node.Node(node_id, pop_name, node_type_id, node_types_props, group_id, group_props, dynamics_params, gid=None)

Bases: object

dynamics_params

gid

group_id

group_props

node_id

node_type_id

node_type_properties

population_name

class bmtk.utils.sonata.node.NodeSet(node_indicies, population, **parameters)

Bases: object

get_properties(property_name)

gids

next()

node_ids

node_type_ids

bmtk.utils.sonata.population module

class bmtk.utils.sonata.population.EdgePopulation(pop_name, pop_group, edge_types_tables)

Bases: bmtk.utils.sonata.population.Population

build_indicies()

edge_types_table

filter(**filter_props)

get_row(index)

get_source(source_node_id)

static get_source_population(pop_group_h5)

get_sources(source_node_ids)

get_target(target_node_id)

static get_target_population(pop_group_h5)

get_targets(target_node_ids)

group_id_column

group_index_column

group_indicies(group_id, build_cache=False, as_list=False)

Returns a list of all the population row index that maps onto the given group.

Used for iterating or searching within a Group

Parameters:

• group_id – id of a given group
• build_cache – Will cache indicies for all groups. Will be faster if making multiple calls but requires more memory (default False)

Returns:

A (possibly empty) list of row indicies (non-contiguous, but unique)

next()

source_population

target_population

to_dataframe()

Convert Population to dataframe

type_ids_column

class bmtk.utils.sonata.population.NodePopulation(pop_name, pop_group, node_types_tables)

Bases: bmtk.utils.sonata.population.Population

add_gids(gid_map_df, force=False)

filter(**filter_props)

get_gid(gid)

get_node_id(node_id)

get_row(row_indx)

get_rows(row_indicies)

Returns a set of all nodes based on list of row indicies.

Warning: currently due to the use of h5py, the list must be ordered and cannot contain duplicates.

Parameters:row_indicies – A list of row indicies Returns:An iterable NodeSet of nodes in the specified indicies

gids

group_id_column

group_index_column

has_gids

igids(row_indicies)

index_column_name

inode_ids(row_indicies)

inode_type_ids(row_indicies)

next()

node_ids

node_types_table

to_dataframe(index_by_id=True)

Convert Population to dataframe

type_ids_column

class bmtk.utils.sonata.population.Population(pop_name, pop_group, types_table)

Bases: object

get_group(group_id)

group_id_column

group_id_ds

group_ids

List of all group_ids belonging to population

group_index_column

group_index_ds

group_indicies(group_id, build_cache=False)

Returns a list of all the population row index that maps onto the given group.

Used for iterating or searching within a Group

Parameters:

• group_id – id of a given group
• build_cache – Will cache indicies for all groups. Will be faster if making multiple calls but requires more memory (default False)

Returns:

A (possibly empty) list of row indicies (non-contiguous, but unique)

groups

Returns a list of sonata.Group objects

igroup_ids(row_indicies)

igroup_indicies(row_indicies)

name

name of current population

to_dataframe()

Convert Population to dataframe

type_ids

type_ids_column

types_table

bmtk.utils.sonata.types_table module

class bmtk.utils.sonata.types_table.EdgeTypesTable(parent=None)

Bases: bmtk.utils.sonata.types_table.TypesTable

edge_type_ids

index_column_name

class bmtk.utils.sonata.types_table.NodeTypesTable(parent=None)

Bases: bmtk.utils.sonata.types_table.TypesTable

index_column_name

node_type_ids

class bmtk.utils.sonata.types_table.TypesTable(parent=None)

Bases: object

add_table(nt_df)

column(column_name)

columns

find(column_key, column_val, silent=False)

Returns a list of type_ids that contain column property column_key==column_val

Parameters:

• column_key – Name of column to search
• column_val – Value of column to select for
• silent – Set to true to prevent KeyError if column_key doesn’t exist (default=False)

Returns:

A (potentially empty) list of type_ids

index_column_name

next()

to_dataframe(cache=False)

type_ids

bmtk.utils.sonata.types_table.remove_nans(types_dict)

Convert nan values to None in type row (dict)

bmtk.utils.sonata.utils module

bmtk.utils.sonata.utils.add_hdf5_magic(hdf5_handle)

bmtk.utils.sonata.utils.add_hdf5_version(hdf5_handle)

bmtk.utils.sonata.utils.check_magic(hdf5_file)

Check the magic attribute exists according to the sonata format

bmtk.utils.sonata.utils.get_attribute_h5(h5obj, attribut_name, default=None)

bmtk.utils.sonata.utils.get_node_ids(nodes_path, population)

bmtk.utils.sonata.utils.get_version(hdf5_file)

bmtk.utils.sonata.utils.listify(files)

bmtk.utils.sonata.utils.load_csv(csvfile)

bmtk.utils.sonata.utils.load_h5(h5file, mode='r')

Module contents