def test_nD_volume(qtbot):
"""Test adding nD volume."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
np.random.seed(0)
data = np.random.random((6, 10, 15, 20))
viewer.add_volume(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 == 4
assert view.dims.nsliders == 2
assert np.sum(view.dims._displayed) == 1
# Close the viewer
viewer.window.close()
"""
Displays an MRI volume
"""
from napari import Viewer, gui_qt
import numpy as np
import dask.array as da
from dask.cache import Cache
cache = Cache(2e9) # Leverage two gigabytes of memory
cache.register()
file_name = 'data/MRI/synthesized_FLASH25_pyr.zarr'
mri = np.asarray(da.from_zarr(file_name + '/' + str(3)))
mri[mri < 10] = 10
mri = mri - 10
with gui_qt():
# create an empty viewer
viewer = Viewer()
# add the mri
layer = viewer.add_volume(mri, name='mri', colormap='gray')
"""
Displays an 100GB zarr file of lattice light sheet data
"""
import numpy as np
from napari import Viewer, gui_qt
import zarr
file_name = 'data/LLSM/AOLLSM_m4_560nm-3D.zarr'
data = zarr.open(file_name, mode='r')
print(data.shape)
contrast_limits = [0, 200_000]
with gui_qt():
# create an empty viewer
viewer = Viewer()
layer = viewer.add_volume(data,
multichannel=False,
name='AOLLSM_m4_560nm',
contrast_limits=contrast_limits,
colormap='magma')