layer.edge_width = 5
layer.opacity = 0.75
layer.selected_shapes = []
# add an ellipse to the layer
ellipse = np.array([[59, 222], [110, 289], [170, 243], [119, 176]])
layer.add_shapes(ellipse,
shape_type='ellipse',
edge_width=5,
edge_color='coral',
face_color='purple',
opacity=0.75)
layer.refresh()
layer._qt_properties.setExpanded(True)
masks = layer.data.to_masks([512, 512])
masks_layer = viewer.add_image(masks.astype(float), name='masks')
masks_layer.opacity = 0.7
masks_layer.colormap = Colormap([[0.0, 0.0, 0.0, 0.0],
[1.0, 0.0, 0.0, 1.0]])
labels = layer.data.to_labels([512, 512])
labels_layer = viewer.add_labels(labels, name='labels')
labels_layer.visible = False
svg = layer.to_svg()
# To save svg file
# with open('shape.svg', 'w') as f:
# f.write(svg)
"""
Display a labels layer above of an image layer using the add_labels and
add_image APIs
"""
from skimage import data
from scipy import ndimage as ndi
from napari import ViewerApp
from napari.util import app_context
with app_context():
blobs = data.binary_blobs(length=128, volume_fraction=0.1, n_dim=3)
v = ViewerApp(blobs=blobs)
v.layers[0].colormap = 'gray'
labeled = ndi.label(blobs)[0]
label_layer = v.add_labels(labeled, name='blob ID')
add_image APIs
"""
from skimage import data
from skimage.filters import threshold_otsu
from skimage.segmentation import clear_border
from skimage.measure import label
from skimage.morphology import closing, square, remove_small_objects
from napari import ViewerApp
from napari.util import app_context
with app_context():
image = data.coins()[50:-50, 50:-50]
# apply threshold
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(4))
# remove artifacts connected to image border
cleared = remove_small_objects(clear_border(bw), 20)
# label image regions
label_image = label(cleared)
# initialise viewer with astro image
viewer = ViewerApp(coins=image, multichannel=False)
viewer.layers[0].colormap = 'gray'
# add the labels
label_layer = viewer.add_labels(label_image, name='segmentation')