def test_arraylike(self, sj_fixture):
Views = imglyb.util.Views
shape = (3, 5)
data = np.arange(np.prod(shape)).reshape(shape)
block_size = (2, 2)
img, _ = imglyb.as_cell_img(data,
block_size,
access_type='native',
cache=1)
cursor = Views.flatIterable(img).cursor()
expected = 0
while cursor.hasNext():
assert expected == cursor.next().get()
expected += 1
BdvFunctions = imglyb.util.BdvFunctions
BdvOptions = imglyb.util.BdvOptions
VolatileTypeMatcher = autoclass('bdv.util.volatiles.VolatileTypeMatcher')
VolatileViews = autoclass('bdv.util.volatiles.VolatileViews')
block_size = (30, ) * 3
file = h5py.File(path, 'r')
ds = file['volumes/raw']
data = da.from_array(ds, chunks=block_size)
sigma = (0.1, 1.0, 1.0)
smoothed = ndfilters.gaussian_filter(data, sigma=sigma)
img1, s1 = imglyb.as_cell_img(ds,
block_size,
cache=100,
access_type='native',
chunk_as_array=identity)
img2, s2 = imglyb.as_cell_img(smoothed,
block_size,
cache=100,
access_type='native',
chunk_as_array=compute)
try:
vimg1 = VolatileViews.wrapAsVolatile(img1)
vimg2 = VolatileViews.wrapAsVolatile(img2)
except JavaException as e:
print(e.classname)
print(e.innermessage)
if e.stacktrace:
for s in e.stacktrace:
BdvFunctions = imglyb.util.BdvFunctions
BdvOptions = imglyb.util.BdvOptions
VolatileTypeMatcher = autoclass('bdv.util.volatiles.VolatileTypeMatcher')
VolatileViews = autoclass('bdv.util.volatiles.VolatileViews')
shape = (150, 100, 125)
block_size = (32, ) * 3
data1 = da.random.randint(0,
256,
size=shape,
chunks=block_size,
dtype=np.uint8)
img1, s1 = imglyb.as_cell_img(data1,
block_size,
access_type='native',
chunk_as_array=lambda x: x.compute(),
cache=100)
data2 = da.random.randint(0,
256,
size=shape,
chunks=block_size,
dtype=np.uint8)
img2, s2 = imglyb.as_cell_img(data2,
block_size,
access_type='native',
chunk_as_array=lambda x: x.compute(),
cache=100)
try:
vimg1 = VolatileViews.wrapAsVolatile(img1)
vimg2 = VolatileViews.wrapAsVolatile(img2)
scyjava_config.add_endpoints('sc.fiji:bigdataviewer-vistools:1.0.0-beta-18')
import imglyb
from jnius import autoclass, JavaException
path = '/home/hanslovskyp/Downloads/sample_A_padded_20160501.hdf'
BdvFunctions = imglyb.util.BdvFunctions
VolatileTypeMatcher = autoclass('bdv.util.volatiles.VolatileTypeMatcher')
VolatileViews = autoclass('bdv.util.volatiles.VolatileViews')
file = h5py.File(path, 'r')
ds = file['volumes/raw']
block_size = (32, ) * 3
img, _ = imglyb.as_cell_img(ds, block_size, access_type='array', cache=10000)
try:
vimg = VolatileViews.wrapAsVolatile(img)
except JavaException as e:
print(e.classname)
print(e.innermessage)
if e.stacktrace:
for s in e.stacktrace:
print(s)
raise e
bdv = BdvFunctions.show(vimg, 'raw')
def runUntilBdvDoesNotShow():
panel = bdv.getBdvHandle().getViewerPanel()
import scyjava_config
scyjava_config.add_endpoints('sc.fiji:bigdataviewer-vistools:1.0.0-beta-18')
import imglyb
import numpy as np
from jnius import cast
Views = imglyb.util.Views
shape = (3, 5)
data = np.arange(np.prod(shape)).reshape(shape)
block_size = (2, 2)
img, _ = imglyb.as_cell_img(data, block_size, access_type='native', cache=1)
print(data)
print(img.toString())
cursor = Views.flatIterable(img).cursor()
print('Cell Img')
while cursor.hasNext():
print(cursor.next().toString())
print()
print('ndarray')
for d in data.flat:
print(d)
print(data)
print()
print('cells')
cursor = cast('net.imglib2.IterableInterval', img.getCells()).cursor()