def testFromDataset2(self):
shape = (500, 500, 500)
vol = np.zeros(shape, dtype=np.uint8)
vol = vigra.taggedView(vol, axistags="zxy")
centers = [(45, 15), (45, 350), (360, 50)]
extent = (10, 10)
shift = (1, 1)
zrange = np.arange(0, 20)
zsteps = np.arange(5, 455, 50)
for x, y in centers:
for z in zsteps:
for t in zrange:
sx = x + t * shift[0]
sy = y + t * shift[1]
vol[zsteps + t, sx - extent[0] : sx + extent[0], sy - extent[0] : sy + extent[0]] = 255
vol = vol.withAxes(*"zyx")
# step by step
op = OpLazyCC(graph=Graph())
op.Input.setValue(vol)
op.ChunkShape.setValue((64, 64, 64))
out1 = np.zeros(op.Output.meta.shape, dtype=op.Output.meta.dtype)
for z in reversed(list(range(500))):
out1[..., z : z + 1] = op.Output[..., z : z + 1].wait()
vigra.writeHDF5(out1, "/tmp/data.h5", "data")
out2 = vigra.analysis.labelVolumeWithBackground(vol)
assertEquivalentLabeling(out1.view(np.ndarray), out2.view(np.ndarray))
def testFromDataset2(self):
shape = (500, 500, 500)
vol = np.zeros(shape, dtype=np.uint8)
vol = vigra.taggedView(vol, axistags="zxy")
centers = [(45, 15), (45, 350), (360, 50)]
extent = (10, 10)
shift = (1, 1)
zrange = np.arange(0, 20)
zsteps = np.arange(5, 455, 50)
for x, y in centers:
for z in zsteps:
for t in zrange:
sx = x + t * shift[0]
sy = y + t * shift[1]
vol[zsteps + t, sx - extent[0]:sx + extent[0],
sy - extent[0]:sy + extent[0]] = 255
vol = vol.withAxes(*"zyx")
# step by step
op = OpLazyCC(graph=Graph())
op.Input.setValue(vol)
op.ChunkShape.setValue((64, 64, 64))
out1 = np.zeros(op.Output.meta.shape, dtype=op.Output.meta.dtype)
for z in reversed(list(range(500))):
out1[..., z:z + 1] = op.Output[..., z:z + 1].wait()
vigra.writeHDF5(out1, "/tmp/data.h5", "data")
out2 = vigra.analysis.labelVolumeWithBackground(vol)
assertEquivalentLabeling(out1.view(np.ndarray), out2.view(np.ndarray))
def testSingletonZ(self):
vol = np.zeros((82, 70, 1, 5, 5), dtype=np.uint8)
vol = vigra.taggedView(vol, axistags='xyzct')
blocks = np.zeros(vol.shape, dtype=np.uint8)
blocks[30:50, 40:60, :, 2:4, 3:5] = 1
blocks[30:50, 40:60, :, 2:4, 0:2] = 2
blocks[60:70, 30:40, :, :, :] = 3
vol[blocks == 1] = 255
vol[blocks == 2] = 255
vol[blocks == 3] = 255
op = OpLabelVolume(graph=Graph())
op.Method.setValue(self.method)
op.Input.setValue(vol)
out = op.Output[...].wait()
tags = op.Output.meta.getTaggedShape()
print(tags)
out = vigra.taggedView(out, axistags="".join([s for s in tags]))
for c in range(out.shape[3]):
for t in range(out.shape[4]):
print("t={}, c={}".format(t, c))
assertEquivalentLabeling(blocks[..., c, t], out[..., c, t])
def testFromDataset(self):
shape = (500, 500, 500)
vol = np.zeros(shape, dtype=np.uint8)
vol = vigra.taggedView(vol, axistags='zxy')
centers = [(45, 15), (45, 350), (360, 50)]
extent = (10, 10)
shift = (1, 1)
zrange = np.arange(0, 20)
zsteps = np.arange(5, 455, 50)
for x, y in centers:
for z in zsteps:
for t in zrange:
sx = x+t*shift[0]
sy = y+t*shift[1]
vol[zsteps + t, sx-extent[0]:sx+extent[0], sy-extent[0]:sy+extent[0]] = 255
vol = vol.withAxes(*'zyx')
# all at once
op = OpLazyCC(graph=Graph())
op.Input.setValue(vol)
op.ChunkShape.setValue((64, 64, 64))
out1 = op.Output[...].wait()
out2 = vigra.analysis.labelVolumeWithBackground(vol)
assertEquivalentLabeling(out1.view(np.ndarray), out2.view(np.ndarray))
def testFromDataset(self):
shape = (500, 500, 500)
vol = np.zeros(shape, dtype=np.uint8)
vol = vigra.taggedView(vol, axistags='zxy')
centers = [(45, 15), (45, 350), (360, 50)]
extent = (10, 10)
shift = (1, 1)
zrange = np.arange(0, 20)
zsteps = np.arange(5, 455, 50)
for x, y in centers:
for z in zsteps:
for t in zrange:
sx = x+t*shift[0]
sy = y+t*shift[1]
vol[zsteps + t, sx-extent[0]:sx+extent[0], sy-extent[0]:sy+extent[0]] = 255
vol = vol.withAxes(*'xyz')
# all at once
op = OpLazyCC(graph=Graph())
op.Input.setValue(vol)
op.ChunkShape.setValue((64, 64, 64))
out1 = op.Output[...].wait()
out2 = vigra.analysis.labelVolumeWithBackground(vol)
assertEquivalentLabeling(out1.view(np.ndarray), out2.view(np.ndarray))
def testCorrectLabeling(self):
vol = np.zeros((1000, 100, 10))
vol = vol.astype(np.uint8)
vol = vigra.taggedView(vol, axistags="zyx")
vol[20:40, 10:30, 2:4] = 1
op = OpLazyCC(graph=Graph())
op.Input.setValue(vol)
op.ChunkShape.setValue((100, 10, 10))
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
assertEquivalentLabeling(vol, out)
def testCorrectLabeling(self):
vol = np.zeros((1000, 100, 10))
vol = vol.astype(np.uint8)
vol = vigra.taggedView(vol, axistags="zyx")
vol[20:40, 10:30, 2:4] = 1
op = OpLazyCC(graph=Graph())
op.Input.setValue(vol)
op.ChunkShape.setValue((100, 10, 10))
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
assertEquivalentLabeling(vol, out)
def testCorrectLabeling(self):
vol = np.zeros((1000, 100, 10))
vol = vol.astype(np.uint8)
vol = vigra.taggedView(vol, axistags="xyz")
vol[20:40, 10:30, 2:4] = 1
op = OpLabelVolume(graph=Graph())
op.Method.setValue(self.method)
op.Input.setValue(vol)
out = op.Output[...].wait()
tags = op.Output.meta.getTaggedShape()
out = vigra.taggedView(out, axistags="".join([s for s in tags]))
assertEquivalentLabeling(vol, out)
def testCorrectLabeling(self):
vol = np.zeros((1000, 100, 10))
vol = vol.astype(np.uint8)
vol = vigra.taggedView(vol, axistags='xyz')
vol[20:40, 10:30, 2:4] = 1
op = OpLabelVolume(graph=Graph())
op.Method.setValue(self.method)
op.Input.setValue(vol)
out = op.Output[...].wait()
tags = op.Output.meta.getTaggedShape()
out = vigra.taggedView(out, axistags="".join([s for s in tags]))
assertEquivalentLabeling(vol, out)
def testSingletonZ(self):
vol = np.zeros((1, 70, 82), dtype=np.uint8)
vol = vigra.taggedView(vol, axistags="zyx")
blocks = np.zeros(vol.shape, dtype=np.uint8)
blocks[:, 30:50, 40:60] = 1
blocks[:, 60:70, 30:40] = 3
blocks = vigra.taggedView(blocks, axistags="zyx")
vol[blocks > 0] = 255
op = OpLazyCC(graph=Graph())
op.ChunkShape.setValue((1, 25, 30))
op.Input.setValue(vol)
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
np.set_printoptions(threshold=sys.maxsize, linewidth=200)
assertEquivalentLabeling(blocks, out)
def testSingletonZ(self):
vol = np.zeros((1, 70, 82), dtype=np.uint8)
vol = vigra.taggedView(vol, axistags="zyx")
blocks = np.zeros(vol.shape, dtype=np.uint8)
blocks[:, 30:50, 40:60] = 1
blocks[:, 60:70, 30:40] = 3
blocks = vigra.taggedView(blocks, axistags="zyx")
vol[blocks > 0] = 255
op = OpLazyCC(graph=Graph())
op.ChunkShape.setValue((1, 25, 30))
op.Input.setValue(vol)
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
np.set_printoptions(threshold=np.nan, linewidth=200)
assertEquivalentLabeling(blocks, out)
def testSingletonZ(self):
vol = np.zeros((82, 70, 1), dtype=np.uint8)
vol = vigra.taggedView(vol, axistags='xyz')
blocks = np.zeros(vol.shape, dtype=np.uint8)
blocks[30:50, 40:60, :] = 1
blocks[60:70, 30:40, :] = 3
blocks = vigra.taggedView(blocks, axistags='xyz')
vol[blocks > 0] = 255
op = OpLazyCC(graph=Graph())
op.ChunkShape.setValue((30, 25, 1))
op.Input.setValue(vol)
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
np.set_printoptions(threshold=np.nan, linewidth=200)
print(out[..., 0])
print(blocks[..., 0])
assertEquivalentLabeling(blocks, out)
def testDtypeUint16(self):
vol = np.zeros((82, 70, 75, 5, 5), dtype=np.uint16)
vol = vigra.taggedView(vol, axistags="xyzct")
blocks = np.zeros(vol.shape, dtype=np.uint8)
blocks[30:50, 40:60, 50:70, 2:4, 3:5] = 1
blocks[30:50, 40:60, 50:70, 2:4, 0:2] = 2
blocks[60:70, 30:40, 10:33, :, :] = 3
vol[blocks == 1] = 255
vol[blocks == 2] = 255
vol[blocks == 3] = 255
op = OpLabelVolume(graph=Graph())
op.Method.setValue(self.method)
op.Input.setValue(vol)
out = op.Output[...].wait()
tags = op.Output.meta.getTaggedShape()
out = vigra.taggedView(out, axistags="".join([s for s in tags]))
for c in range(out.shape[3]):
for t in range(out.shape[4]):
assertEquivalentLabeling(blocks[..., c, t], out[..., c, t])
def testBackground(self):
vol = np.zeros((1000, 100, 10))
vol = vol.astype(np.uint8)
vol = vigra.taggedView(vol, axistags='xyz')
vol[20:40, 10:30, 2:4] = 1
op = OpLabelVolume(graph=Graph())
op.Method.setValue(self.method)
op.Background.setValue(1)
op.Input.setValue(vol)
out = op.Output[...].wait()
tags = op.Output.meta.getTaggedShape()
out = vigra.taggedView(out, axistags="".join([s for s in tags]))
assert np.all(out[20:40, 10:30, 2:4] == 0)
assertEquivalentLabeling(1-vol, out)
vol = vol.withAxes(*'xyzct')
vol = np.concatenate(3*(vol,), axis=3)
vol = np.concatenate(4*(vol,), axis=4)
vol = vigra.taggedView(vol, axistags='xyzct')
assert len(vol.shape) == 5
assert vol.shape[3] == 3
assert vol.shape[4] == 4
#op = OpLabelVolume(graph=Graph())
op.Method.setValue(self.method)
bg = np.asarray([[1, 0, 1, 0],
[0, 1, 0, 1],
[1, 0, 0, 1]], dtype=np.uint8)
bg = vigra.taggedView(bg, axistags='ct')
assert len(bg.shape) == 2
assert bg.shape[0] == 3
assert bg.shape[1] == 4
op.Background.setValue(bg)
op.Input.setValue(vol)
for c in range(bg.shape[0]):
for t in range(bg.shape[1]):
out = op.Output[..., c, t].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
if bg[c, t]:
assertEquivalentLabeling(1-vol[..., c, t], out.squeeze())
else:
assertEquivalentLabeling(vol[..., c, t], out.squeeze())
