def test_nD_pyramid(qtbot):
"""Test adding nD image pyramid."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
shapes = [(8, 40, 20), (4, 20, 10), (4, 10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
viewer.add_pyramid(data)
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 == 3
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 1
# Flip dims order displayed
viewer.dims.order = [0, 2, 1]
assert viewer.dims.order == [0, 2, 1]
# Flip dims order including non-displayed
viewer.dims.order = [1, 0, 2]
assert viewer.dims.order == [1, 0, 2]
# Close the viewer
viewer.window.close()
def test_pyramid_dytpes(qtbot, dtype):
"""Test different dtype pyramids."""
np.random.seed(0)
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
# add dtype pyramid data
data = [
np.random.randint(20, size=(30, 40)).astype(dtype),
np.random.randint(20, size=(15, 20)).astype(dtype),
]
viewer.add_pyramid(data)
assert np.all(viewer.layers[0].data == data)
# Close the viewer
viewer.window.close()
def test_add_pyramid(qtbot):
"""Test adding image pyramid."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
viewer.add_pyramid(data)
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()
"""
Displays the allen brain reference atlas at 10 um resolution
"""
from napari import Viewer, gui_qt
import dask.array as da
from dask.cache import Cache
import numpy as np
cache = Cache(2e9) # Leverage two gigabytes of memory
cache.register()
base = da.random.randint(0, 255, (100, 2000, 5000), dtype='uint8')
pyramid = [base]
image = pyramid[0]
for i in range(4):
image = da.coarsen(np.mean, image, {0: 1, 1: 2, 2: 2}, trim_excess=True)
pyramid.append(image)
print('pyramid level shapes: ', [p.shape for p in pyramid])
with gui_qt():
# create an empty viewer
viewer = Viewer()
# layer = viewer.add_image(base, name='base')
layer = viewer.add_pyramid(pyramid, name='pyramid')
"""
Dynamically load irregularly shapes images of ants and bees
"""
import numpy as np
import dask.array as da
from dask.cache import Cache
from napari import Viewer, gui_qt
cache = Cache(2e9) # Leverage two gigabytes of memory
cache.register()
base_name = 'data-njs/ndcn/keiser/slides/'
slide_name = 'NA4009-02_AB'
pyramid = [
da.from_zarr(base_name + slide_name + '.zarr/' + str(i)) for i in range(8)
]
print([p.shape[:2] for p in pyramid])
with gui_qt():
# create an empty viewer
viewer = Viewer()
# add the images
layer = viewer.add_pyramid(pyramid,
name=slide_name,
contrast_limits=[0, 255])