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[MRG+1] fix elp reading #3690

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Merged
merged 2 commits into from
Oct 25, 2016
Merged

[MRG+1] fix elp reading #3690

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52b4f64
fix elp reading
jona-sassenhagen Oct 24, 2016
e88455b
montage test now runs on 4 channels
jona-sassenhagen Oct 24, 2016
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2 changes: 1 addition & 1 deletion mne/channels/montage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -266,7 +266,7 @@ def read_montage(kind, ch_names=None, path=None, unit='m', transform=False):
az = np.deg2rad(np.array([90. - h if a >= 0. else -90. - h
for h, a in zip(horiz, az)]))
pol = radius * np.pi
pos = _sph_to_cart(np.array([np.ones(len(az)) * 85., az, pol])).T
pos = _sph_to_cart(np.array([np.ones(len(az)) * 85., az, pol]).T)
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This looks like the right change. Can you add a test? You're right that we need one...

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I'm surprised current tests didn't catch it ...

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Maybe the array was 3x3, and the output values (which would have been very broken) never checked. Or maybe the lines were never tested?

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I think all of these channel position readers are tested at the same time, so if it's a problem with one, it's possibly a problem with all.

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Can you look into it?

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Good call Eric:

        'EEG\t      F3\t -62.027\t -50.053\t      85\n'
        'EEG\t      Fz\t  45.608\t      90\t      85\n'
        'EEG\t      F4\t   62.01\t  50.103\t      85\n',

I'll go for it.

elif ext == '.hpts':
# MNE-C specified format for generic digitizer data
dtype = [('type', 'S8'), ('name', 'S8'),
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26 changes: 16 additions & 10 deletions mne/channels/tests/test_montage.py
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Expand Up @@ -43,28 +43,34 @@ def test_montage():
# no pep8
input_str = [
'FidNz 0.00000 10.56381 -2.05108\nFidT9 -7.82694 0.45386 -3.76056\n'
'very_very_very_long_name 7.82694 0.45386 -3.76056',
'very_very_very_long_name 7.82694 0.45386 -3.76056\nDmy 7.0 0.0 1.0',
'// MatLab Sphere coordinates [degrees] Cartesian coordinates\n' # noqa: E501
'// Label Theta Phi Radius X Y Z off sphere surface\n' # noqa: E501
'E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011\n' # noqa: E501
'E2 44.600 -0.880 1.000 0.7119 0.7021 -0.0154 0.00000000000000000\n' # noqa: E501
'E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000', # noqa: E501
'E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000\n' # noqa: E501
'E4 52.700 12.000 1.000 0.7084 0.7504 0.1508 0.00000000000000000', # noqa: E501; dummy line
'# ASA electrode file\nReferenceLabel avg\nUnitPosition mm\n'
'NumberPositions= 68\nPositions\n-86.0761 -19.9897 -47.9860\n'
'85.7939 -20.0093 -48.0310\n0.0083 86.8110 -39.9830\n'
'Labels\nLPA\nRPA\nNz\n',
'85 -20 -48\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
'# ASA electrode file\nReferenceLabel avg\nUnitPosition m\n'
'NumberPositions= 68\nPositions\n-.0860761 -.0199897 -.0479860\n'
'.0857939 -.0200093 -.0480310\n.0000083 .00868110 -.0399830\n'
'Labels\nLPA\nRPA\nNz\n',
'.08 -.02 -.04\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
'Site Theta Phi\nFp1 -92 -72\nFp2 92 72\n'
'very_very_very_long_name -60 -51\n',
'very_very_very_long_name -60 -51\n'
'dummy -60 -52\n',
'346\n'
'EEG\t F3\t -62.027\t -50.053\t 85\n'
'EEG\t Fz\t 45.608\t 90\t 85\n'
'EEG\t F4\t 62.01\t 50.103\t 85\n',
'eeg Fp1 -95.0 -31.0 -3.0\neeg AF7 -81 -59 -3\neeg AF3 -87 -41 28\n'
'EEG\t F4\t 62.01\t 50.103\t 85\n'
'EEG\t FCz\t 68.01\t 58.103\t 85\n',
'eeg Fp1 -95.0 -3. -3.\neeg AF7 -1 -1 -3\neeg A3 -2 -2 2\neeg A 0 0 0'
]

kinds = ['test.sfp', 'test.csd', 'test_mm.elc', 'test_m.elc', 'test.txt',
'test.elp', 'test.hpts']
for kind, text in zip(kinds, input_str):
Expand All @@ -74,9 +80,9 @@ def test_montage():
montage = read_montage(fname)
if ".sfp" in kind or ".txt" in kind:
assert_true('very_very_very_long_name' in montage.ch_names)
assert_equal(len(montage.ch_names), 3)
assert_equal(len(montage.ch_names), 4)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (3, 3))
assert_equal(montage.pos.shape, (4, 3))
assert_equal(montage.kind, op.splitext(kind)[0])
if kind.endswith('csd'):
dtype = [('label', 'S4'), ('theta', 'f8'), ('phi', 'f8'),
Expand All @@ -87,7 +93,7 @@ def test_montage():
except TypeError:
table = np.loadtxt(fname, skiprows=2, dtype=dtype)
pos2 = np.c_[table['x'], table['y'], table['z']]
assert_array_almost_equal(pos2, montage.pos, 4)
assert_array_almost_equal(pos2[:-1, :], montage.pos[:-1, :], 4)
if kind.endswith('elc'):
# Make sure points are reasonable distance from geometric centroid
centroid = np.sum(montage.pos, axis=0) / montage.pos.shape[0]
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