How to use the morphio.RawDataError function in morphio

To help you get started, we’ve selected a few morphio examples, based on popular ways it is used in public projects.

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github BlueBrain / MorphIO / tests / test_1_swc.py View on Github external
def test_repeated_id():
    _test_swc_exception('''# A simple neuron with a repeated id
                       1 1 0 0 1 0.5 -1
                       2 3 0 0 2 0.5 1
                       3 3 0 0 3 0.5 2
                       4 3 0 0 4 0.5 3
                       4 3 0 0 4 0.5 3 # <-- repeated id
                       5 3 0 0 5 0.5 4
                       ''',
                        RawDataError,
                        'Repeated ID: 4\nID already appears here:',
                        ':6:warning')
github BlueBrain / MorphIO / tests / test_8_all_morphologies.py View on Github external
from nose.tools import ok_, nottest
import subprocess

from morphio import Morphology, SomaError, RawDataError, MorphioError
from morphio.mut import Morphology as MutMorphology


bad_files = {'MorphologyRepository/Vincent Delattre/vd100714C/vd100714C_idA.ASC': SomaError,
             'MorphologyRepository/Vincent Delattre/vd100714B/vd100714B_idB.ASC': RawDataError,
             'MorphologyRepository/Shruti Muralidhar/sm100614a2/sm100614a2.ASC': RawDataError,
             'MorphologyRepository/Rodrigo Perin/rp120607_P_1-2/rp120607_P_1-2_idE.ASC': SomaError,
             'MorphologyRepository/Shruti Muralidhar/sm080904a1-6/._sm080904a1.asc': SomaError,
             'MorphologyRepository/Rodrigo Perin/rp110616_C1/rp110616_C1_idB.ASC': SomaError,

             'MorphologyRepository/Thomas Berger/tkb070202a2/tkb070202a2_ch0_cc2_n_tb_100x_3.asc': RawDataError,
             'MorphologyRepository/Thomas Berger/tkb061122a2/tkb061122a2_ch1_ct_n_rm_100x_1.asc': RawDataError,
             'MorphologyRepository/Thomas Berger/tkb051201b1/tkb051201b1_ch7_ct_n_es_100x_1.asc': RawDataError,

             'MorphologyRepository/Thomas Berger/tkb060123a2/tkb060123a2_ch2_ct_x_db_60x_2.asc': RawDataError,
             'MorphologyRepository/Cristina Radaelli/cr161021_A/cr161021_A_idB.ASC': RawDataError,
             'MorphologyRepository/Cristina Radaelli/cr161027_A/cr161027_A_idA.ASC': SomaError,
             'MorphologyRepository/Olivier Gschwend/og060829a1-4/og060829a1-4_idB.asc': RawDataError,
             'MorphologyRepository/Ani Gupta/C271097A/C271097A-I4.asc': RawDataError,
             'MorphologyRepository/Ani Gupta/C030397A/C030397A-P3.asc': RawDataError,
             'MorphologyRepository/Ani Gupta/C310897B/C310897B-P3.asc': RawDataError,
github BlueBrain / MorphIO / tests / test_2_neurolucida.py View on Github external
def test_unfinished_file():
    _test_asc_exception('''
                     ((Dendrite)
                      (3 -4 0 2)
                      (3 -6 0 2)
                      (3 -8 0 2)
                      (3 -10 0 2)
                      (
                        (3 -10 0 2)
                        (0 -10 0 2)
                        (-3 -10 0 2)
                        |
                     ''',
                        RawDataError,
                        "Hit end of file while consuming a neurite",
                        ":12:error")
github BlueBrain / MorphIO / tests / test_1_swc.py View on Github external
def test_cyclic():
    _test_swc_exception("""1 1  0  0 0 1. -1
                           2 3  0  0 0 1.  1
                           3 3  0  5 0 1.  2
                           4 3 -5  5 0 0.  3
                           5 3  6  5 0 0.  3
                           6 2  0  0 0 1.  6  # <-- cyclic point
                           7 2  0 -4 0 1.  6
                           8 2  6 -4 0 0.  7
                           9 2 -5 -4 0 0.  7""",
                        RawDataError,
                        'Parent ID can not be itself',
                        ':6:error')
github BlueBrain / MorphIO / tests / test_3_h5.py View on Github external
def test_wrong_section_type():
    assert_raises(RawDataError, Morphology, os.path.join(H5V1_PATH, 'simple-broken-section-type.h5'))
github BlueBrain / MorphIO / tests / test_2_neurolucida.py View on Github external
def test_unknown_token():
    _test_asc_exception('''
                   ("CellBody"
                   (Color Red)
                   (CellBody)
                   (1 1 0 1 S1)
                   (Z 1 0 1 S2) ; <-- Z is a BAD token
                   (-1 -1 0 2 S3)
                   )''',
                        RawDataError,
                        "Unexpected token: Z",
                        ":6:error")