# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
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# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
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"""Module for morphology SWC data loading.
Data is unpacked into a 2-dimensional raw data block:
[X, Y, Z, R, TYPE, ID, PARENT_ID]
SWC format:
[ID, TYPE, X, Y, Z, R, PARENT_ID]
There is one such row per measured point.
"""
import numpy as np
from .datawrapper import DataWrapper
ID, TYPE, X, Y, Z, R, P = range(7)
[docs]def read(filename, data_wrapper=DataWrapper):
"""Read an SWC file and return a tuple of data, format."""
data = np.loadtxt(filename)
if len(np.shape(data)) == 1:
data = np.reshape(data, (1, -1))
# Setting all type ids > 4 to 5 (custom section type): issue #735
data[:, TYPE] = np.clip(data[:, TYPE], a_min=None, a_max=5)
return data_wrapper(data[:, [X, Y, Z, R, TYPE, ID, P]], 'SWC', None)