single_cell_parserreader

reader

Read and parse .hoc, .syn, .con, and .am files.

Deprecated since version This: module additionally provides readers for Synapse activation and Presynaptic spike times files. However, as these formats are now dataframes, they are saved with a pandas or dask dumpers in databases. They can still be explicitly read using Python’s open() and read() capabilities, but this is not recommended, or efficient.

See also:

data_base.IO.LoaderDumper for dask and pandas related IO.

Functions

read_hoc_file(fname)

Reads a hoc file and returns a list of Edge objects.

read_scalar_field(fname)

Read AMIRA scalar fields.

read_synapse_realization(fname)

Read a .syn file and returns a dictionary of synapse locations.

read_pruned_synapse_realization(fname)

Read in a .syn and returns a dictionary of synapse locations and whether they are pruned or not.

read_functional_realization_map(fname)

Read in a .con file and return a dictionary of functional connections.

read_synapse_activation_file(fname)

Reads list of all functional synapses and their activation times.

read_complete_synapse_activation_file(fname)

Reads list of all functional synapses and their activation times.

read_spike_times_file(fname)

Reads all trials and spike times within these trials.

read_synapse_weight_file(fname)

Reads list of all anatomical synapses and their maximum conductance values.

read_landmark_file(landmarkFilename)

Read an AMIRA landmark file