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()