def test_add_surface(qtbot):
"""Test adding 3D surface."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
np.random.seed(0)
vertices = np.random.random((10, 3))
faces = np.random.randint(10, size=(6, 3))
values = np.random.random(10)
data = (vertices, faces, values)
viewer.add_surface(data)
assert np.all(
[np.all(vd == d) for vd, d in zip(viewer.layers[0].data, data)]
)
assert len(viewer.layers) == 1
assert view.layers.vbox_layout.count() == 2 * len(viewer.layers) + 2
assert viewer.dims.ndim == 3
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 1
# Switch to 3D rendering mode and back to 2D rendering mode
viewer.dims.ndisplay = 3
assert viewer.dims.ndisplay == 3
viewer.dims.ndisplay = 2
assert viewer.dims.ndisplay == 2
# Close the viewer
viewer.window.close()
def test_data_change_ndisplay_surface(qtbot):
"""Test change data calls for surface layer with ndisplay change."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
np.random.seed(0)
vertices = np.random.random((10, 3))
faces = np.random.randint(10, size=(6, 3))
values = np.random.random(10)
data = (vertices, faces, values)
layer = viewer.add_surface(data)
visual = view.layer_to_visual[layer]
@patch.object(visual, '_on_data_change', wraps=visual._on_data_change)
def test_ndisplay_change(mocked_method, ndisplay=3):
viewer.dims.ndisplay = ndisplay
mocked_method.assert_called_once()
# Switch to 3D rendering mode and back to 2D rendering mode
test_ndisplay_change(ndisplay=3)
test_ndisplay_change(ndisplay=2)
# Close the viewer
viewer.window.close()
def test_changing_display_surface(qtbot):
"""Test adding 3D surface and changing its display."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
np.random.seed(0)
vertices = np.random.random((10, 3))
faces = np.random.randint(10, size=(6, 3))
values = np.random.random(10)
data = (vertices, faces, values)
viewer.add_surface(data)
assert np.all(
[np.all(vd == d) for vd, d in zip(viewer.layers[0].data, data)])
assert len(viewer.layers) == 1
assert view.layers.vbox_layout.count() == 2 * len(viewer.layers) + 2
assert viewer.dims.ndim == 3
assert view.dims.nsliders == viewer.dims.ndim
# Check display is currently 2D with one slider
assert viewer.layers[0]._data_view.shape[1] == 2
assert np.sum(view.dims._displayed_sliders) == 1
# Make display 3D
viewer.dims.ndisplay = 3
assert viewer.layers[0]._data_view.shape[1] == 3
assert np.sum(view.dims._displayed_sliders) == 0
# Make display 2D again
viewer.dims.ndisplay = 2
assert viewer.layers[0]._data_view.shape[1] == 2
assert np.sum(view.dims._displayed_sliders) == 1
# Iterate over all values in first dimension
len_slider = viewer.dims.range[0]
for s in len_slider:
viewer.dims.set_point(0, s)
# Close the viewer
viewer.window.close()
from vispy.color import Colormap
first = int((128 * 2) - np.round(255 * (1. - 0.90)))
second = (256 - first)
colors2 = plt.cm.viridis(np.linspace(0.1, .98, first))
colors3 = plt.cm.YlOrBr(np.linspace(0.25, 1, second))
cols = np.vstack((colors2, colors3))
mymap = Colormap(cols)
base_path = 'data-njs/CBIG/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/FreeSurfer5.3/fsaverage6/'
lh_pial = surface.load_surf_mesh(base_path + 'surf/lh.pial')
lh_curv = surface.load_surf_data(base_path + 'surf/lh.curv')
lg400_atlas = surface.load_surf_data(
base_path + 'label/lh.Schaefer2018_400Parcels_7Networks_order.annot')
u, idx = np.unique(lg400_atlas, return_inverse=True)
ed = np.loadtxt('data-njs/mri/LG400_Med.txt')
ed_lh = ed[:200]
X = np.insert(ed_lh, 0, 0, axis=0)
values = X[idx]
with gui_qt():
# create an empty viewer
viewer = Viewer(ndisplay=3)
# add the mri
layer = viewer.add_surface((lh_pial[0], lh_pial[1], lh_curv), name='base')
layer = viewer.add_surface((lh_pial[0], lh_pial[1], values),
name='gradient',
colormap={'mymap': mymap},
opacity=0.8)