def load_population_data(self, population):
"""Load node properties from SONATA Nodes.
Args:
population (str): a population name .
Returns:
pandas.DataFrame with node properties (zero-based index).
"""
nodes = self.storage.open_population(population)
categoricals = nodes.enumeration_names
node_count = nodes.size
result = pd.DataFrame(index=np.arange(node_count))
_all = libsonata.Selection([(0, node_count)])
for attr in sorted(nodes.attribute_names):
if attr in categoricals:
enumeration = np.asarray(nodes.get_enumeration(attr, _all))
values = np.asarray(nodes.enumeration_values(attr))
# if the size of `values` is large enough compared to `enumeration`, not using
# categorical reduces the memory usage.
if values.shape[0] < 0.5 * enumeration.shape[0]:
result[attr] = pd.Categorical.from_codes(enumeration,
categories=values)
else:
result[attr] = values[enumeration]
else:
result[attr] = nodes.get_attribute(attr, _all)
for attr in sorted(
utils.add_dynamic_prefix(nodes.dynamics_attribute_names)):
result[attr] = nodes.get_dynamics_attribute(
attr.split(DYNAMICS_PREFIX)[1], _all)
return result
def properties(self, edge_ids, properties):
"""
Edge properties as pandas DataFrame.
Args:
edge_ids: array-like of edge IDs
properties: edge property name | list of edge property names
Returns:
Pandas Series indexed by edge IDs if `properties` is scalar;
Pandas DataFrame indexed by edge IDs if `properties` is list.
"""
selection = libsonata.Selection(edge_ids)
return self._get(selection, properties)
def _load_population(h5_filepath, csv_filepath, population):
"""
Load node properties from SONATA Nodes.
Returns:
pandas.DataFrame with node properties (zero-based index).
"""
nodes = libsonata.NodePopulation(h5_filepath, csv_filepath or '', population)
node_count = nodes.size
result = pd.DataFrame(index=np.arange(node_count))
_all = libsonata.Selection([(0, node_count)])
for prop in sorted(nodes.attribute_names):
result[prop] = nodes.get_attribute(prop, _all)
return result
def properties(self, edge_ids, properties):
"""Edge properties as pandas DataFrame.
Args:
edge_ids (array-like): array-like of edge IDs
properties (str/list): an edge property name or a list of edge property names
Returns:
pandas.Series/pandas.DataFrame:
A pandas Series indexed by edge IDs if ``properties`` is scalar.
A pandas DataFrame indexed by edge IDs if ``properties`` is list.
Notes:
The EdgePopulation.property_names function will give you all the usable properties
for the `properties` argument.
"""
selection = libsonata.Selection(edge_ids)
return self._get(selection, properties)