def test_view_shapes(qtbot):
"""Test adding shapes."""
np.random.seed(0)
data = 20 * np.random.random((10, 4, 2))
viewer = napari.view_shapes(data)
view = viewer.window.qt_viewer
qtbot.addWidget(view)
assert np.all(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 == 2
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 0
# Close the viewer
viewer.window.close()
"""
Display one shapes layer ontop of one image layer using the add_shapes and
add_image APIs. When the window is closed it will print the coordinates of
your shapes.
"""
import numpy as np
import napari
with napari.gui_qt():
path = [[505, 60], [402, 71], [383, 42], [251, 95], [212, 59], [131, 137],
[126, 187], [191, 204], [171, 248], [211, 260], [273, 243],
[264, 225], [430, 173], [512, 160]]
polygons = [path] + [[list(c), [10, 10]] for c in path]
shape_type = ['path'] + ['ellipse'] * len(path)
edge_colors = np.random.random((len(polygons), 4))
napari.view_shapes(polygons,
shape_type=shape_type,
edge_width=5,
opacity=1,
edge_color=edge_colors,
face_color='royalblue')
import napari
from neurom.io import swc
import numpy as np
def parse_swc(data):
break_points = [0] + list(np.nonzero(np.diff(data[:, 6]) < 0)[0]+1) + [len(data)-1]
paths = []
for i in range(len(break_points)-1):
if break_points[i+1] - break_points[i] > 2:
paths.append(data[break_points[i]:break_points[i+1], :3])
return paths
# def parse_swc_extra(data):
# break_points = [0] + list(np.nonzero(np.diff(data[:, 6]) < 0)[0]+1) + [len(data)-1]
# paths = []
# for i in range(1, len(break_points)-1):
# if break_points[i+1] - break_points[i] > 2:
# paths.append(data[[break_points[i-1], break_points[i]], :3])
# return paths
data = swc.read('data/neuromorphology/204-2-6nj.CNG.swc').data_block
paths = parse_swc(data)
# extra_paths = parse_swc_extra(data)
with napari.gui_qt():
# create an empty viewer
viewer = napari.view_shapes(paths, shape_type='path',
edge_color='blue', ndisplay=3)
# viewer.add_shapes(extra_paths, shape_type='path',
# edge_color='red')
"""
Display one 4-D image layer using the add_image API
"""
import numpy as np
import napari
# create one random polygon per "plane"
planes = np.tile(np.arange(128).reshape((128, 1, 1)), (1, 5, 1))
np.random.seed(0)
corners = np.random.uniform(0, 128, size=(128, 5, 2))
shapes = np.concatenate((planes, corners), axis=2)
base_cols = ['red', 'green', 'blue', 'white', 'yellow', 'magenta', 'cyan']
colors = np.random.choice(base_cols, size=128)
with napari.gui_qt():
viewer = napari.view_shapes(
np.array(shapes),
shape_type='polygon',
face_color=colors,
name='sliced',
)