class TestObjectsSegment(TestThresholdOneLevel):
@unittest.skipIf(not haveGraphCut(), "opengm not available")
def setUp(self):
super(TestObjectsSegment, self).setUp()
self.curOperator = 2
self.usePreThreshold = True
# time axes not implemented
@unittest.expectedFailure
def testEvenFunnierAxes(self):
super(TestObjectsSegment, self).testEvenFunnierAxes()
# NoOp uses threshold value -> not meaningful for graphcut
@unittest.skip("Makes no sense with graph cut")
def testNoOp(self):
super(TestGraphCut, self).testNoOp()
oper5d.MinSize.setValue(1)
oper5d.MaxSize.setValue(vol.size)
oper5d.SingleThreshold.setValue(128)
oper5d.SmootherSigma.setValue({'x': 0.0, 'y': 0.0, 'z': 0.0})
oper5d.CurOperator.setValue(self.curOperator)
oper5d.UsePreThreshold.setValue(self.usePreThreshold)
#for i in range(vol.shape[3]):
for i in range(2, 5): # just test some sample slices (runtime :)
oper5d.Channel.setValue(i)
out5d = oper5d.Output[:].wait()
out5d[out5d > 0] = 1
numpy.testing.assert_array_equal(out5d.squeeze(), desiredResult[..., i, :])
@unittest.skipIf(not haveGraphCut(), "opengm not available")
class TestObjectsSegment(TestThresholdOneLevel):
def setUp(self):
super(TestObjectsSegment, self).setUp()
self.curOperator = 2
self.usePreThreshold = True
# time axes not implemented
@unittest.expectedFailure
def testEvenFunnierAxes(self):
super(TestObjectsSegment, self).testEvenFunnierAxes()
# NoOp uses threshold value -> not meaningful for graphcut
@unittest.skip("Makes no sense with graph cut")
def testNoOp(self):
super(TestGraphCut, self).testNoOp()
vol[0, 5:10, 5:10, 5:10, :] = np.random.rand(1, 5, 5, 5, c) * 0.39 + 0.6
vol[0, 13:18, 13:18, 13:18, :] = np.random.rand(1, 5, 5, 5, c) * 0.39 + 0.6
vol[2, 7:12, 7:12, 7:12, :] = np.random.rand(1, 5, 5, 5, c) * 0.39 + 0.6
labels[0, 5:10, 5:10, 5:10, :] = 1
labels[0, 13:18, 13:18, 13:18, :] = 2
labels[2, 7:12, 7:12, 7:12, :] = 1
# convert to the thresholding operators internal axes order
fullVolume = vigra.taggedView(vol, axistags='tzyxc')
fullLabels = vigra.taggedView(labels, axistags='tzyxc')
return (fullVolume, fullLabels)
if haveGraphCut():
from ilastik.applets.thresholdTwoLevels.opGraphcutSegment import OpObjectsSegment, OpGraphCut
class TestOpGraphCut(unittest.TestCase):
def setUp(self):
self.tinyVolume, self.labels = getTinyTestVolume()
def testComplete(self):
graph = Graph()
op = OpGraphCut(graph=graph)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(self.tinyVolume)
op.Prediction.connect(piper.Output)
out = op.CachedOutput[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
vol[0, 5:10, 5:10, 5:10, :] = np.random.rand(1, 5, 5, 5, c) * 0.39 + 0.6
vol[0, 13:18, 13:18, 13:18, :] = np.random.rand(1, 5, 5, 5, c) * 0.39 + 0.6
vol[2, 7:12, 7:12, 7:12, :] = np.random.rand(1, 5, 5, 5, c) * 0.39 + 0.6
labels[0, 5:10, 5:10, 5:10, :] = 1
labels[0, 13:18, 13:18, 13:18, :] = 2
labels[2, 7:12, 7:12, 7:12, :] = 1
# convert to the thresholding operators internal axes order
fullVolume = vigra.taggedView(vol, axistags="tzyxc")
fullLabels = vigra.taggedView(labels, axistags="tzyxc")
return (fullVolume, fullLabels)
if haveGraphCut():
from ilastik.applets.thresholdTwoLevels.opGraphcutSegment import OpObjectsSegment, OpGraphCut
@pytest.mark.skipif(not haveGraphCut(), reason="GraphCut not available")
class TestOpGraphCut(unittest.TestCase):
def setUp(self):
self.tinyVolume, self.labels = getTinyTestVolume()
def testComplete(self):
graph = Graph()
op = OpGraphCut(graph=graph)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(self.tinyVolume)
op.Prediction.connect(piper.Output)
# workflows and plugins which are not covered under the GNU
# General Public License.
#
# See the LICENSE file for details. License information is also available
# on the ilastik web site at:
# http://ilastik.org/license.html
##############################################################################
import unittest
import numpy as np
import vigra
from ilastik.applets.thresholdTwoLevels.opGraphcutSegment import haveGraphCut
have_opengm = haveGraphCut()
from numpy.testing.utils import assert_array_equal, assert_array_almost_equal, assert_array_less
from nose import SkipTest
from lazyflow.graph import Graph
from lazyflow.operators.opArrayPiper import OpArrayPiper
if have_opengm:
from ilastik.applets.thresholdTwoLevels.opGraphcutSegment import OpObjectsSegment, OpGraphCut
def getTestVolume():
t, c = 3, 2
shape = (t, 120, 100, 90, c)
vol = np.zeros(shape, dtype=np.float32)
# In addition, as a special exception, the copyright holders of
# ilastik give you permission to combine ilastik with applets,
# workflows and plugins which are not covered under the GNU
# General Public License.
#
# See the LICENSE file for details. License information is also available
# on the ilastik web site at:
# http://ilastik.org/license.html
##############################################################################
import unittest
import numpy as np
import vigra
from ilastik.applets.thresholdTwoLevels.opGraphcutSegment import haveGraphCut
have_opengm = haveGraphCut()
from numpy.testing.utils import assert_array_equal,\
assert_array_almost_equal, assert_array_less
from nose import SkipTest
from lazyflow.graph import Graph
from lazyflow.operators.opArrayPiper import OpArrayPiper
if have_opengm:
from ilastik.applets.thresholdTwoLevels.opGraphcutSegment\
import OpObjectsSegment, OpGraphCut
def getTestVolume():
t, c = 3, 2
oper5d.MinSize.setValue(1)
oper5d.MaxSize.setValue(vol.size)
oper5d.SingleThreshold.setValue(128)
oper5d.SmootherSigma.setValue({'x': 0.0, 'y': 0.0, 'z': 0.0})
oper5d.CurOperator.setValue(self.curOperator)
oper5d.UsePreThreshold.setValue(self.usePreThreshold)
#for i in range(vol.shape[3]):
for i in range(2, 5): # just test some sample slices (runtime :)
oper5d.Channel.setValue(i)
out5d = oper5d.Output[:].wait()
out5d[out5d > 0] = 1
numpy.testing.assert_array_equal(out5d.squeeze(), desiredResult[..., i, :])
@unittest.skipIf(not haveGraphCut(), "opengm not available")
class TestObjectsSegment(TestThresholdOneLevel):
def setUp(self):
super(TestObjectsSegment, self).setUp()
self.curOperator = 2
self.usePreThreshold = True
# time axes not implemented
@unittest.expectedFailure
def testEvenFunnierAxes(self):
super(TestObjectsSegment, self).testEvenFunnierAxes()
# NoOp uses threshold value -> not meaningful for graphcut
@unittest.skip("Makes no sense with graph cut")
def testNoOp(self):
super(TestGraphCut, self).testNoOp()
vol[0, 5:10, 5:10, 5:10, :] = np.random.rand(1, 5, 5, 5, c)*0.39+0.6
vol[0, 13:18, 13:18, 13:18, :] = np.random.rand(1, 5, 5, 5, c)*0.39+0.6
vol[2, 7:12, 7:12, 7:12, :] = np.random.rand(1, 5, 5, 5, c)*0.39+0.6
labels[0, 5:10, 5:10, 5:10, :] = 1
labels[0, 13:18, 13:18, 13:18, :] = 2
labels[2, 7:12, 7:12, 7:12, :] = 1
# convert to the thresholding operators internal axes order
fullVolume = vigra.taggedView(vol, axistags='tzyxc')
fullLabels = vigra.taggedView(labels, axistags='tzyxc')
return (fullVolume, fullLabels)
if haveGraphCut():
from ilastik.applets.thresholdTwoLevels.opGraphcutSegment import OpObjectsSegment, OpGraphCut
@pytest.mark.skipif(not haveGraphCut(), reason="GraphCut not available")
class TestOpGraphCut(unittest.TestCase):
def setUp(self):
self.tinyVolume, self.labels = getTinyTestVolume()
def testComplete(self):
graph = Graph()
op = OpGraphCut(graph=graph)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(self.tinyVolume)
op.Prediction.connect(piper.Output)
class TestGraphCut(TestObjectsSegment):
@unittest.skipIf(not haveGraphCut(), "opengm not available")
def setUp(self):
super(TestGraphCut, self).setUp()
self.usePreThreshold = False
vol[0, 5:10, 5:10, 5:10, :] = np.random.rand(1, 5, 5, 5, c)*0.39+0.6
vol[0, 13:18, 13:18, 13:18, :] = np.random.rand(1, 5, 5, 5, c)*0.39+0.6
vol[2, 7:12, 7:12, 7:12, :] = np.random.rand(1, 5, 5, 5, c)*0.39+0.6
labels[0, 5:10, 5:10, 5:10, :] = 1
labels[0, 13:18, 13:18, 13:18, :] = 2
labels[2, 7:12, 7:12, 7:12, :] = 1
# convert to the thresholding operators internal axes order
fullVolume = vigra.taggedView(vol, axistags='tzyxc')
fullLabels = vigra.taggedView(labels, axistags='tzyxc')
return (fullVolume, fullLabels)
if haveGraphCut():
from ilastik.applets.thresholdTwoLevels.opGraphcutSegment import OpObjectsSegment, OpGraphCut
class TestOpGraphCut(unittest.TestCase):
def setUp(self):
self.tinyVolume, self.labels = getTinyTestVolume()
def testComplete(self):
graph = Graph()
op = OpGraphCut(graph=graph)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(self.tinyVolume)
op.Prediction.connect(piper.Output)
out = op.CachedOutput[...].wait()