read_hoc_file¶

single_cell_parser.reader.read_hoc_file(fname='')¶

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

This list of sections is parsed to a CellParser object using spatialgraph_to_cell().

See .hoc for more information on the hoc file format.

See also

The module singlecell_input_mapper also contains a method read_hoc_file(). A notable difference is that this method reads in axon sections, while the singlecell_input_mapper variant does not.

Parameters:¶

fname : str¶

The name of the file to be read.

Raises:¶

IOError – If the input file does not have a .hoc or .HOC suffix.

Returns:¶

A list of Edge objects.

Return type:¶

list

Example

>>> read_hoc_file(hoc_file)
[
    _Edge(
        label='Soma',
        hocLabel='soma',
        edgePts=[(1.93339, 221.367004, -450.04599), ... , (13.9619, 210.149002, -447.901001)],
        diameterList=[12.542, 13.3094, ... , 3.5997), parentID=None, parentConnect=None),
    _Edge(
        label='BasalDendrite_1_0',
        hocLabel='BasalDendrite_1_0',
        edgePts=[(6.36964, 224.735992, -452.399994), (6.34155, 222.962997, -451.906006), ...],
        diameterList=[2.04, 2.04, ... , 2.04), parentID=0, parentConnect=0.009696),
    ...
]