def test_label():
"""Test plotting of label."""
_set_backend()
subject_id = "fsaverage"
hemi = "lh"
surf = "inflated"
brain = Brain(subject_id, hemi, surf)
brain.add_label("BA1")
brain.add_label("BA1", color="blue", scalar_thresh=.5)
subj_dir = utils._get_subjects_dir()
label_file = pjoin(subj_dir, subject_id, "label", "%s.MT.label" % hemi)
brain.add_label(label_file)
brain.add_label("BA44", borders=True)
brain.add_label("BA6", alpha=.7)
brain.show_view("medial")
brain.add_label("V1", color="steelblue", alpha=.6)
brain.add_label("V2", color="#FF6347", alpha=.6)
brain.add_label("entorhinal", color=(.2, 1, .5), alpha=.6)
brain.set_surf('white')
# remove labels
brain.remove_labels('V1')
assert_in('V2', brain.labels_dict)
assert_not_in('V1', brain.labels_dict)
brain.remove_labels()
assert_not_in('V2', brain.labels_dict)
brain.close()
def test_annot():
"""Test plotting of annot."""
_set_backend()
annots = ['aparc', 'aparc.a2005s']
borders = [True, False, 2]
alphas = [1, 0.5]
brain = Brain(*std_args)
view = get_view(brain)
for a, b, p in zip(annots, borders, alphas):
brain.add_annotation(a, b, p, opacity=0.8)
check_view(brain, view)
brain.set_surf('white')
with pytest.raises(ValueError):
brain.add_annotation('aparc', borders=-1)
subj_dir = utils._get_subjects_dir()
annot_path = pjoin(subj_dir, subject_id, 'label', 'lh.aparc.a2009s.annot')
labels, ctab, names = nib.freesurfer.read_annot(annot_path)
brain.add_annotation((labels, ctab))
brain.add_annotation('aparc', color="red", remove_existing=True)
surf = brain.annot["surface"]
ctab = surf.module_manager.scalar_lut_manager.lut.table
for color in ctab:
assert color[:3] == (255, 0, 0)
brain.close()
def test_label():
"""Test plotting of label."""
_set_backend()
subject_id = "fsaverage"
hemi = "lh"
surf = "inflated"
brain = Brain(subject_id, hemi, surf)
view = get_view(brain)
extra, subj_dir = _get_extra()
brain.add_label("BA1" + extra)
check_view(brain, view)
brain.add_label("BA1" + extra, color="blue", scalar_thresh=.5)
label_file = pjoin(subj_dir, subject_id, "label",
"%s.MT%s.label" % (hemi, extra))
brain.add_label(label_file)
brain.add_label("BA44" + extra, borders=True)
brain.add_label("BA6" + extra, alpha=.7)
brain.show_view("medial")
brain.add_label("V1" + extra, color="steelblue", alpha=.6)
brain.add_label("V2" + extra, color="#FF6347", alpha=.6)
brain.add_label("entorhinal" + extra, color=(.2, 1, .5), alpha=.6)
brain.set_surf('white')
brain.show_view(dict(elevation=40, distance=430), distance=430)
with pytest.raises(ValueError, match='!='):
brain.show_view(dict(elevation=40, distance=430), distance=431)
# remove labels
brain.remove_labels('V1' + extra)
assert 'V2' + extra in brain.labels_dict
assert 'V1' + extra not in brain.labels_dict
brain.remove_labels()
assert 'V2' + extra not in brain.labels_dict
brain.close()
def test_meg_inverse():
"""Test plotting of MEG inverse solution."""
_set_backend()
brain = Brain(*std_args)
stc_fname = os.path.join(data_dir, 'meg_source_estimate-lh.stc')
stc = io.read_stc(stc_fname)
vertices = stc['vertices']
colormap = 'hot'
data = stc['data']
data_full = (brain.geo['lh'].nn[vertices][..., np.newaxis] *
data[:, np.newaxis])
time = np.linspace(stc['tmin'], stc['tmin'] + data.shape[1] * stc['tstep'],
data.shape[1], endpoint=False)
def time_label(t):
return 'time=%0.2f ms' % (1e3 * t)
for use_data in (data, data_full):
brain.add_data(use_data, colormap=colormap, vertices=vertices,
smoothing_steps=1, time=time, time_label=time_label)
brain.scale_data_colormap(fmin=13, fmid=18, fmax=22, transparent=True)
assert_equal(brain.data_dict['lh']['time_idx'], 0)
brain.set_time(.1)
assert_equal(brain.data_dict['lh']['time_idx'], 2)
# viewer = TimeViewer(brain)
# multiple data layers
assert_raises(ValueError, brain.add_data, data, vertices=vertices,
time=time[:-1])
brain.add_data(data, colormap=colormap, vertices=vertices,
smoothing_steps=1, time=time, time_label=time_label,
initial_time=.09)
assert_equal(brain.data_dict['lh']['time_idx'], 1)
data_dicts = brain._data_dicts['lh']
assert_equal(len(data_dicts), 3)
assert_equal(data_dicts[0]['time_idx'], 1)
assert_equal(data_dicts[1]['time_idx'], 1)
# shift time in both layers
brain.set_data_time_index(0)
assert_equal(data_dicts[0]['time_idx'], 0)
assert_equal(data_dicts[1]['time_idx'], 0)
brain.set_data_smoothing_steps(2)
# add second data-layer without time axis
brain.add_data(data[:, 1], colormap=colormap, vertices=vertices,
smoothing_steps=2)
brain.set_data_time_index(2)
assert_equal(len(data_dicts), 4)
# change surface
brain.set_surf('white')
# remove all layers
brain.remove_data()
assert_equal(brain._data_dicts['lh'], [])
brain.close()
def test_meg_inverse():
"""Test plotting of MEG inverse solution."""
_set_backend()
brain = Brain(*std_args)
stc_fname = os.path.join(data_dir, 'meg_source_estimate-lh.stc')
stc = io.read_stc(stc_fname)
vertices = stc['vertices']
colormap = 'hot'
data = stc['data']
data_full = (brain.geo['lh'].nn[vertices][..., np.newaxis] *
data[:, np.newaxis])
time = np.linspace(stc['tmin'], stc['tmin'] + data.shape[1] * stc['tstep'],
data.shape[1], endpoint=False)
def time_label(t):
return 'time=%0.2f ms' % (1e3 * t)
for use_data in (data, data_full):
brain.add_data(use_data, colormap=colormap, vertices=vertices,
smoothing_steps=1, time=time, time_label=time_label)
brain.scale_data_colormap(fmin=13, fmid=18, fmax=22, transparent=True)
assert brain.data_dict['lh']['time_idx'] == 0
brain.set_time(.1)
assert brain.data_dict['lh']['time_idx'] == 2
# viewer = TimeViewer(brain)
# multiple data layers
pytest.raises(ValueError, brain.add_data, data, vertices=vertices,
time=time[:-1])
brain.add_data(data, colormap=colormap, vertices=vertices,
smoothing_steps=1, time=time, time_label=time_label,
initial_time=.09)
assert brain.data_dict['lh']['time_idx'] == 1
data_dicts = brain._data_dicts['lh']
assert len(data_dicts) == 3
assert data_dicts[0]['time_idx'] == 1
assert data_dicts[1]['time_idx'] == 1
# shift time in both layers
brain.set_data_time_index(0)
assert data_dicts[0]['time_idx'] == 0
assert data_dicts[1]['time_idx'] == 0
brain.set_data_smoothing_steps(2)
# add second data-layer without time axis
brain.add_data(data[:, 1], colormap=colormap, vertices=vertices,
smoothing_steps=2)
brain.set_data_time_index(2)
assert len(data_dicts) == 4
# change surface
brain.set_surf('white')
# remove all layers
brain.remove_data()
assert brain._data_dicts['lh'] == []
brain.close()
def test_label():
"""Test plotting of label."""
_set_backend()
subject_id = "fsaverage"
hemi = "lh"
surf = "inflated"
brain = Brain(subject_id, hemi, surf)
brain.add_label("BA1")
brain.add_label("BA1", color="blue", scalar_thresh=.5)
subj_dir = utils._get_subjects_dir()
label_file = pjoin(subj_dir, subject_id,
"label", "%s.MT.label" % hemi)
brain.add_label(label_file)
brain.add_label("BA44", borders=True)
brain.add_label("BA6", alpha=.7)
brain.show_view("medial")
brain.add_label("V1", color="steelblue", alpha=.6)
brain.add_label("V2", color="#FF6347", alpha=.6)
brain.add_label("entorhinal", color=(.2, 1, .5), alpha=.6)
brain.set_surf('white')
# remove labels
brain.remove_labels('V1')
assert_in('V2', brain.labels_dict)
assert_not_in('V1', brain.labels_dict)
brain.remove_labels()
assert_not_in('V2', brain.labels_dict)
brain.close()
def test_label():
"""Test plotting of label."""
_set_backend()
subject_id = "fsaverage"
hemi = "lh"
surf = "inflated"
brain = Brain(subject_id, hemi, surf)
view = get_view(brain)
extra, subj_dir = _get_extra()
brain.add_label("BA1" + extra)
check_view(brain, view)
brain.add_label("BA1" + extra, color="blue", scalar_thresh=.5)
label_file = pjoin(subj_dir, subject_id,
"label", "%s.MT%s.label" % (hemi, extra))
brain.add_label(label_file)
brain.add_label("BA44" + extra, borders=True)
brain.add_label("BA6" + extra, alpha=.7)
brain.show_view("medial")
brain.add_label("V1" + extra, color="steelblue", alpha=.6)
brain.add_label("V2" + extra, color="#FF6347", alpha=.6)
brain.add_label("entorhinal" + extra, color=(.2, 1, .5), alpha=.6)
brain.set_surf('white')
brain.show_view(dict(elevation=40, distance=430), distance=430)
with pytest.raises(ValueError, match='!='):
brain.show_view(dict(elevation=40, distance=430), distance=431)
# remove labels
brain.remove_labels('V1' + extra)
assert 'V2' + extra in brain.labels_dict
assert 'V1' + extra not in brain.labels_dict
brain.remove_labels()
assert 'V2' + extra not in brain.labels_dict
brain.close()
def test_data():
"""Test plotting of data."""
_set_backend()
brain = Brain(*std_args)
mri_file = pjoin(data_dir, 'resting_corr.nii.gz')
reg_file = pjoin(data_dir, 'register.dat')
surf_data = io.project_volume_data(mri_file, "lh", reg_file)
brain.add_data(surf_data, -.7, .7, colormap="jet", alpha=.7)
brain.set_surf('white')
brain.add_data([], vertices=np.array([], int))
brain.close()
def test_data():
"""Test plotting of data."""
_set_backend()
brain = Brain(*std_args)
mri_file = pjoin(data_dir, 'resting_corr.nii.gz')
reg_file = pjoin(data_dir, 'register.dat')
surf_data = io.project_volume_data(mri_file, "lh", reg_file)
brain.add_data(surf_data, -.7, .7, colormap="jet", alpha=.7)
brain.set_surf('white')
brain.add_data([], vertices=np.array([], int))
brain.close()
def test_annot():
"""Test plotting of annot."""
_set_backend()
annots = ['aparc', 'aparc.a2005s']
borders = [True, False, 2]
alphas = [1, 0.5]
brain = Brain(*std_args)
for a, b, p in zip(annots, borders, alphas):
brain.add_annotation(a, b, p)
brain.set_surf('white')
assert_raises(ValueError, brain.add_annotation, 'aparc', borders=-1)
subj_dir = utils._get_subjects_dir()
annot_path = pjoin(subj_dir, subject_id, 'label', 'lh.aparc.a2009s.annot')
labels, ctab, names = nib.freesurfer.read_annot(annot_path)
brain.add_annotation((labels, ctab))
brain.close()
def test_annot():
"""Test plotting of annot."""
_set_backend()
annots = ['aparc', 'aparc.a2005s']
borders = [True, False, 2]
alphas = [1, 0.5]
brain = Brain(*std_args)
for a, b, p in zip(annots, borders, alphas):
brain.add_annotation(a, b, p)
brain.set_surf('white')
assert_raises(ValueError, brain.add_annotation, 'aparc', borders=-1)
subj_dir = utils._get_subjects_dir()
annot_path = pjoin(subj_dir, subject_id, 'label', 'lh.aparc.a2009s.annot')
labels, ctab, names = nib.freesurfer.read_annot(annot_path)
brain.add_annotation((labels, ctab))
brain.close()
def test_overlay():
"""Test plotting of overlay."""
_set_backend()
# basic overlay support
overlay_file = pjoin(data_dir, "lh.sig.nii.gz")
brain = Brain(*std_args)
brain.add_overlay(overlay_file)
brain.overlays["sig"].remove()
brain.add_overlay(overlay_file, min=5, max=20, sign="pos")
sig1 = io.read_scalar_data(pjoin(data_dir, "lh.sig.nii.gz"))
sig2 = io.read_scalar_data(pjoin(data_dir, "lh.alt_sig.nii.gz"))
# two-sided overlay
brain.add_overlay(sig1, 4, 30, name="two-sided")
overlay = brain.overlays_dict.pop('two-sided')[0]
assert_array_equal(overlay.pos_bar.data_range, [4, 30])
assert_array_equal(overlay.neg_bar.data_range, [-30, -4])
assert_equal(overlay.pos_bar.reverse_lut, True)
assert_equal(overlay.neg_bar.reverse_lut, False)
overlay.remove()
thresh = 4
sig1[sig1 < thresh] = 0
sig2[sig2 < thresh] = 0
conjunct = np.min(np.vstack((sig1, sig2)), axis=0)
brain.add_overlay(sig1, 4, 30, name="sig1")
brain.overlays["sig1"].pos_bar.lut_mode = "Reds"
brain.overlays["sig1"].pos_bar.visible = False
brain.add_overlay(sig2, 4, 30, name="sig2")
brain.overlays["sig2"].pos_bar.lut_mode = "Blues"
brain.overlays["sig2"].pos_bar.visible = False
brain.add_overlay(conjunct, 4, 30, name="conjunct")
brain.overlays["conjunct"].pos_bar.lut_mode = "Purples"
brain.overlays["conjunct"].pos_bar.visible = False
brain.set_surf('white')
brain.close()
def test_overlay():
"""Test plotting of overlay."""
_set_backend()
# basic overlay support
overlay_file = pjoin(data_dir, "lh.sig.nii.gz")
brain = Brain(*std_args)
brain.add_overlay(overlay_file)
brain.overlays["sig"].remove()
brain.add_overlay(overlay_file, min=5, max=20, sign="pos")
sig1 = io.read_scalar_data(pjoin(data_dir, "lh.sig.nii.gz"))
sig2 = io.read_scalar_data(pjoin(data_dir, "lh.alt_sig.nii.gz"))
# two-sided overlay
brain.add_overlay(sig1, 4, 30, name="two-sided")
overlay = brain.overlays_dict.pop('two-sided')[0]
assert_array_equal(overlay.pos_bar.data_range, [4, 30])
assert_array_equal(overlay.neg_bar.data_range, [-30, -4])
assert_equal(overlay.pos_bar.reverse_lut, True)
assert_equal(overlay.neg_bar.reverse_lut, False)
overlay.remove()
thresh = 4
sig1[sig1 < thresh] = 0
sig2[sig2 < thresh] = 0
conjunct = np.min(np.vstack((sig1, sig2)), axis=0)
brain.add_overlay(sig1, 4, 30, name="sig1")
brain.overlays["sig1"].pos_bar.lut_mode = "Reds"
brain.overlays["sig1"].pos_bar.visible = False
brain.add_overlay(sig2, 4, 30, name="sig2")
brain.overlays["sig2"].pos_bar.lut_mode = "Blues"
brain.overlays["sig2"].pos_bar.visible = False
brain.add_overlay(conjunct, 4, 30, name="conjunct")
brain.overlays["conjunct"].pos_bar.lut_mode = "Purples"
brain.overlays["conjunct"].pos_bar.visible = False
brain.set_surf('white')
brain.close()
