"""
Annotation Setup
================


"""

import napari
from skimage import data, feature, filters, morphology

# get sample 3D image data, threshold, and find maxima
cells3d = data.cells3d()
nuclei = cells3d[:, 1]
membrane = cells3d[:, 0]

nuclei_smoothed = filters.gaussian(nuclei, sigma=4)
nuclei_thresholded = nuclei_smoothed > filters.threshold_otsu(nuclei_smoothed)
nuclei_labels = morphology.label(nuclei_thresholded)
nuclei_points = feature.peak_local_max(nuclei_smoothed, min_distance=20)

shape = [
    [29.0, 124.29706, 58.10305],
    [29.0, 120.45354, 16.251354],
    [29.0, 100.80886, 6.429018],
    [29.0, 80.310074, 6.8560762],
    [29.0, 50.416004, 24.792517],
    [29.0, 42.72896, 39.312492],
    [29.0, 46.145424, 54.68659],
    [29.0, 56.394817, 70.48774],
    [29.0, 74.33126, 83.72654],
    [29.0, 90.55947, 90.13241],
    [29.0, 105.079445, 88.42418],
    [29.0, 116.610016, 79.455956],
]

viewer = napari.Viewer()
viewer.add_image(
    membrane,
    name='membrane',
    blending='translucent_no_depth',
    colormap='orange',
    contrast_limits=(5000, 65355),
)
viewer.add_image(
    nuclei,
    name='nuclei',
    blending='additive',
    colormap='cyan',
    contrast_limits=(5000, 60000),
)
viewer.add_labels(nuclei_labels, name='nuclei labels')
viewer.add_points(
    nuclei_points,
    name='nuclei maxima',
    blending='additive',
    opacity=0.5,
)
viewer.add_shapes(
    shape,
    name='dividing cell',
    shape_type='polygon',
    blending='translucent',
    edge_color='yellow',
    face_color='#FFA50080',
)

viewer.dims.ndisplay = 3
viewer.camera.angles = (-30, 15, -35)

if __name__ == '__main__':
    napari.run()