Source code for neuron_morphology.marker

import csv
import neuron_morphology.constants as constants
from neuron_morphology.validation.result import InvalidMarkerFile
from neuron_morphology.validation.result import MarkerValidationError


class Marker(dict):
    """ Simple dictionary class for handling reconstruction marker objects. """

    def __init__(self, *args, **kwargs):
        super(Marker, self).__init__(*args, **kwargs)

        self['original_x'] = self['x']
        self['original_y'] = self['y']
        self['original_z'] = self['z']

        # marker file x,y,z coordinates are offset by a single image-space pixel
        self['x'] -= constants.SPACING[0]
        self['y'] -= constants.SPACING[1]
        self['z'] -= constants.SPACING[2]


def read_marker_file(file_name):
    """ read in a marker file and return a list of dictionaries """

    with open(file_name, 'r') as f:
        rows = csv.DictReader((r for r in f if not r.startswith('#')), fieldnames=['x', 'y', 'z', 'radius', 'shape',
                                                                                   'name', 'comment', 'color_r',
                                                                                   'color_g', 'color_b'])

        markers = []

        for r in rows:
            try:
                markers.append(Marker({'x': float(r['x']),
                                       'y': float(r['y']),
                                       'z': float(r['z']),
                                       'name': int(r['name'])}))

            except ValueError:
                message = "Failed to parse row. One of (x, y, z, name) is missing or invalid"
                raise InvalidMarkerFile([MarkerValidationError(message, r, "Error")])

        return markers