def testMargin(self):
graph = Graph()
vol = np.zeros((100, 110, 10), dtype=np.float32)
# draw a big plus sign
vol[50:70, :, :] = 1.0
vol[:, 60:80, :] = 1.0
vol = vigra.taggedView(vol, axistags="zyx").withAxes(*"tzyxc")
labels = np.zeros((100, 110, 10), dtype=np.uint32)
labels[45:75, 55:85, 3:4] = 1
labels = vigra.taggedView(labels, axistags="zyx").withAxes(*"tzyxc")
op = OpObjectsSegment(graph=graph)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(vol)
op.Prediction.connect(piper.Output)
op.LabelImage.setValue(labels)
# without margin
op.MarginZYX.setValue(np.asarray((0, 0, 0)))
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
out = out.withAxes(*"zyx")
vol = vol.withAxes(*"zyx")
assert_array_equal(out[50:70, 60:80, 3] > 0,
vol[50:70, 60:80, 3] > 0.5)
assert np.all(out[:45, ...] == 0)
# with margin
op.MarginZYX.setValue(np.asarray((5, 5, 0)))
out = op.Output[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
out = out.withAxes(*"zyx")
assert_array_equal(out[45:75, 55:85, 3] > 0,
vol[45:75, 55:85, 3] > 0.5)
assert np.all(out[:40, ...] == 0)
def testBB(self):
graph = Graph()
op = OpObjectsSegment(graph=graph)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(self.vol)
op.Prediction.connect(piper.Output)
op.LabelImage.setValue(self.labels)
bbox = op.BoundingBoxes[0, ..., 0].wait()
assert isinstance(bbox, dict)
def testFaulty(self):
vec = vigra.taggedView(np.zeros((500, ), dtype=np.float32),
axistags=vigra.defaultAxistags('x'))
graph = Graph()
op = OpObjectsSegment(graph=graph)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(vec)
with self.assertRaises(AssertionError):
op.Prediction.connect(piper.Output)
op.LabelImage.connect(piper.Output)
def testComplete(self):
graph = Graph()
op = OpObjectsSegment(graph=graph)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(self.vol)
op.Prediction.connect(piper.Output)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(self.labels)
op.LabelImage.connect(piper.Output)
# get whole volume
out = op.CachedOutput[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
# check whether no new blocks introduced
mask = np.where(self.labels > 0, 0, 1)
masked = out * mask
assert_array_equal(masked, 0 * masked)
# check whether the interior was labeled 1
assert np.all(out[:, 22:38, 22:38, 22:38, :] > 0)
assert np.all(out[:, 62:78, 62:78, 62:78, :] > 0)
