def setup_method(self, method):
self.graph = Graph()
self.operator_identity = OpArrayPiper(graph=self.graph)
self.operator_identity.Input.meta.axistags = vigra.AxisTags("txyzc")
self.operator_identity.Input.meta.has_mask = True
class TestOpArrayPiper7(object):
def setUp(self):
self.graph = Graph()
self.operator_identity_1 = OpArrayPiper(graph=self.graph)
self.operator_identity_2 = OpArrayPiper(graph=self.graph)
self.operator_identity_1.Input.meta.axistags = vigra.AxisTags("txyzc")
self.operator_identity_2.Input.meta.axistags = vigra.AxisTags("txyzc")
def test1(self):
# Explicitly set has_mask for the input
self.operator_identity_1.Input.meta.has_mask = True
self.operator_identity_1.Output.meta.has_mask = True
# Generate a dataset and grab chunks of it from the operator. The result should be the same as above.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
data = numpy.ma.masked_array(
data,
mask=numpy.zeros(data.shape, dtype=bool),
shrink=False
)
# Try to connect the compatible operators.
self.operator_identity_2.Input.connect(self.operator_identity_1.Output)
self.operator_identity_1.Input.setValue(data)
output = self.operator_identity_2.Output[None].wait()
assert((data == output).all())
assert(data.mask.shape == output.mask.shape)
assert((data.mask == output.mask).all())
def test2(self):
# Generate a dataset and grab chunks of it from the operator. The result should be the same as above.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
data = numpy.ma.masked_array(
data,
mask=numpy.zeros(data.shape, dtype=bool),
shrink=False
)
# Try to connect the compatible operators.
self.operator_identity_1.Input.setValue(data)
self.operator_identity_2.Input.connect(self.operator_identity_1.Output)
output = self.operator_identity_2.Output[None].wait()
assert((data == output).all())
assert(data.mask.shape == output.mask.shape)
assert((data.mask == output.mask).all())
def tearDown(self):
# Take down operators
self.operator_identity_2.Input.disconnect()
self.operator_identity_2.Output.disconnect()
self.operator_identity_2.cleanUp()
self.operator_identity_1.Input.disconnect()
self.operator_identity_1.Output.disconnect()
self.operator_identity_1.cleanUp()
def setUp(self):
self.graph = Graph()
self.operator_identity_1 = OpArrayPiper(graph=self.graph)
self.operator_identity_2 = OpArrayPiper(graph=self.graph)
self.operator_identity_1.Input.meta.axistags = vigra.AxisTags("txyzc")
self.operator_identity_2.Input.meta.axistags = vigra.AxisTags("txyzc")
def setUp(self):
self.graph = Graph()
self.operator_identity = OpArrayPiper(graph=self.graph)
self.operator_identity.Input.allow_mask = False
self.operator_identity.Output.allow_mask = False
self.operator_identity.Input.meta.axistags = vigra.AxisTags("txyzc")
def setUp(self):
self.graph = Graph()
self.operator_identity_1 = OpArrayPiper(graph=self.graph)
self.operator_identity_2 = OpArrayPiper(graph=self.graph)
self.operator_identity_1.Input.meta.axistags = vigra.AxisTags("txyzc")
self.operator_identity_2.Input.meta.axistags = vigra.AxisTags("txyzc")
class TestOpArrayPiper4(object):
def setup_method(self, method):
self.graph = Graph()
self.operator_identity = OpArrayPiper(graph=self.graph)
self.operator_identity.Input.allow_mask = False
self.operator_identity.Output.allow_mask = False
self.operator_identity.Input.meta.has_mask = False
self.operator_identity.Output.meta.has_mask = False
self.operator_identity.Input.meta.axistags = vigra.AxisTags("txyzc")
@nose.tools.raises(AllowMaskException)
def test1(self):
# Generate a random dataset and see if it we get the right masking from the operator.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
data = numpy.ma.masked_array(data, mask=numpy.zeros(data.shape, dtype=bool), shrink=False)
# Provide input read all output.
try:
self.operator_identity.Input.setValue(data)
except AssertionError as e:
raise AllowMaskException(str(e))
@nose.tools.raises(AllowMaskException)
def test2(self):
# Generate a dataset and grab chunks of it from the operator. The result should be the same as above.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
data = numpy.ma.masked_array(data, mask=numpy.zeros(data.shape, dtype=bool), shrink=False)
# Create array to store results. Don't keep original data.
output = data.copy()
output[:] = 0
output[:] = numpy.ma.nomask
# Provide input and grab chunks.
try:
self.operator_identity.Input.setValue(data)
except AssertionError as e:
raise AllowMaskException(str(e))
@nose.tools.raises(AllowMaskException)
def test3(self):
# Generate a random dataset and see if it we get the right masking from the operator.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
data = numpy.ma.masked_array(data, mask=numpy.zeros(data.shape, dtype=bool), shrink=False)
# Provide input read all output.
try:
self.operator_identity.Input.setValue(numpy.zeros_like(data))
except AssertionError as e:
raise AllowMaskException(str(e))
def teardown_method(self, method):
# Take down operators
self.operator_identity.Input.disconnect()
self.operator_identity.Output.disconnect()
self.operator_identity.cleanUp()
class TestOpArrayPiper4(object):
def setup_method(self, method):
self.graph = Graph()
self.operator_identity = OpArrayPiper(graph=self.graph)
self.operator_identity.Input.allow_mask = False
self.operator_identity.Output.allow_mask = False
self.operator_identity.Input.meta.has_mask = False
self.operator_identity.Output.meta.has_mask = False
self.operator_identity.Input.meta.axistags = vigra.AxisTags("txyzc")
def test1(self):
# Generate a random dataset and see if it we get the right masking from the operator.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
data = numpy.ma.masked_array(data, mask=numpy.zeros(data.shape, dtype=bool), shrink=False)
# Provide input read all output.
with pytest.raises(AllowMaskException):
try:
self.operator_identity.Input.setValue(data)
except AssertionError as e:
raise AllowMaskException(str(e))
def test2(self):
# Generate a dataset and grab chunks of it from the operator. The result should be the same as above.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
data = numpy.ma.masked_array(data, mask=numpy.zeros(data.shape, dtype=bool), shrink=False)
# Create array to store results. Don't keep original data.
output = data.copy()
output[:] = 0
output[:] = numpy.ma.nomask
# Provide input and grab chunks.
with pytest.raises(AllowMaskException):
try:
self.operator_identity.Input.setValue(data)
except AssertionError as e:
raise AllowMaskException(str(e))
def test3(self):
# Generate a random dataset and see if it we get the right masking from the operator.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
data = numpy.ma.masked_array(data, mask=numpy.zeros(data.shape, dtype=bool), shrink=False)
# Provide input read all output.
with pytest.raises(AllowMaskException):
try:
self.operator_identity.Input.setValue(numpy.zeros_like(data))
except AssertionError as e:
raise AllowMaskException(str(e))
def teardown_method(self, method):
# Take down operators
self.operator_identity.Input.disconnect()
self.operator_identity.Output.disconnect()
self.operator_identity.cleanUp()
def setUp(self):
self.graph = Graph()
self.operator_border = OpMaskArray(graph=self.graph)
self.operator_identity = OpArrayPiper(graph=self.graph)
self.operator_border.InputArray.meta.axistags = vigra.AxisTags("txyzc")
self.operator_identity.Input.connect(self.operator_border.Output)
class TestOpArrayPiper(object):
def setup_method(self, method):
self.graph = Graph()
self.operator_identity = OpArrayPiper(graph=self.graph)
self.operator_identity.Input.meta.axistags = vigra.AxisTags("txyzc")
def test1(self):
# Generate a random dataset and see if it we get the right masking from the operator.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
# Provide input read all output.
self.operator_identity.Input.setValue(data)
output = self.operator_identity.Output[None].wait()
assert (data == output).all()
def test2(self):
# Generate a dataset and grab chunks of it from the operator. The result should be the same as above.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
# Create array to store results. Don't keep original data.
output = data.copy()
output[:] = 0
# Provide input and grab chunks.
self.operator_identity.Input.setValue(data)
output[:2] = self.operator_identity.Output[:2].wait()
output[2:] = self.operator_identity.Output[2:].wait()
assert (data == output).all()
def test3(self):
# Generate a random dataset and see if it we get the right masking from the operator.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
# Provide input read all output.
self.operator_identity.Input.setValue(numpy.zeros_like(data))
output = self.operator_identity.Output[None].wait()
assert (output == 0).all()
# Try setInSlot
data_shape_roi = roiFromShape(data.shape)
data_shape_slice = roiToSlice(*data_shape_roi)
self.operator_identity.Input[data_shape_slice] = data
output = self.operator_identity.Output[None].wait()
assert (data == output).all()
def teardown_method(self, method):
# Take down operators
self.operator_identity.Input.disconnect()
self.operator_identity.Output.disconnect()
self.operator_identity.cleanUp()
class TestOpArrayPiper(object):
def setUp(self):
self.graph = Graph()
self.operator_identity = OpArrayPiper(graph=self.graph)
self.operator_identity.Input.meta.axistags = vigra.AxisTags("txyzc")
def test1(self):
# Generate a random dataset and see if it we get the right masking from the operator.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
# Provide input read all output.
self.operator_identity.Input.setValue(data)
output = self.operator_identity.Output[None].wait()
assert((data == output).all())
def test2(self):
# Generate a dataset and grab chunks of it from the operator. The result should be the same as above.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
# Create array to store results. Don't keep original data.
output = data.copy()
output[:] = 0
# Provide input and grab chunks.
self.operator_identity.Input.setValue(data)
output[:2] = self.operator_identity.Output[:2].wait()
output[2:] = self.operator_identity.Output[2:].wait()
assert((data == output).all())
def test3(self):
# Generate a random dataset and see if it we get the right masking from the operator.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
# Provide input read all output.
self.operator_identity.Input.setValue(numpy.zeros_like(data))
output = self.operator_identity.Output[None].wait()
assert((output == 0).all())
# Try setInSlot
data_shape_roi = roiFromShape(data.shape)
data_shape_slice = roiToSlice(*data_shape_roi)
self.operator_identity.Input[data_shape_slice] = data
output = self.operator_identity.Output[None].wait()
assert((data == output).all())
def tearDown(self):
# Take down operators
self.operator_identity.Input.disconnect()
self.operator_identity.Output.disconnect()
self.operator_identity.cleanUp()
def setup_method(self, method):
self.graph = Graph()
self.operator_identity_1 = OpArrayPiper(graph=self.graph)
self.operator_identity_2 = OpArrayPiper(graph=self.graph)
self.operator_identity_2.Input.allow_mask = False
self.operator_identity_2.Output.allow_mask = False
self.operator_identity_1.Input.meta.axistags = vigra.AxisTags("txyzc")
self.operator_identity_2.Input.meta.axistags = vigra.AxisTags("txyzc")
def setup_method(self, method):
self.graph = Graph()
self.operator_identity_1 = OpArrayPiper(graph=self.graph)
self.operator_identity_2 = OpArrayPiper(graph=self.graph)
self.operator_identity_2.Input.allow_mask = False
self.operator_identity_2.Output.allow_mask = False
self.operator_identity_1.Input.meta.axistags = vigra.AxisTags("txyzc")
self.operator_identity_2.Input.meta.axistags = vigra.AxisTags("txyzc")
class TestOpArrayPiper7(object):
def setup_method(self, method):
self.graph = Graph()
self.operator_identity_1 = OpArrayPiper(graph=self.graph)
self.operator_identity_2 = OpArrayPiper(graph=self.graph)
self.operator_identity_1.Input.meta.axistags = vigra.AxisTags("txyzc")
self.operator_identity_2.Input.meta.axistags = vigra.AxisTags("txyzc")
def test1(self):
# Explicitly set has_mask for the input
self.operator_identity_1.Input.meta.has_mask = True
self.operator_identity_1.Output.meta.has_mask = True
# Generate a dataset and grab chunks of it from the operator. The result should be the same as above.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
data = numpy.ma.masked_array(data,
mask=numpy.zeros(data.shape, dtype=bool),
shrink=False)
# Try to connect the compatible operators.
self.operator_identity_2.Input.connect(self.operator_identity_1.Output)
self.operator_identity_1.Input.setValue(data)
output = self.operator_identity_2.Output[None].wait()
assert (data == output).all()
assert data.mask.shape == output.mask.shape
assert (data.mask == output.mask).all()
def test2(self):
# Generate a dataset and grab chunks of it from the operator. The result should be the same as above.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
data = numpy.ma.masked_array(data,
mask=numpy.zeros(data.shape, dtype=bool),
shrink=False)
# Try to connect the compatible operators.
self.operator_identity_1.Input.setValue(data)
self.operator_identity_2.Input.connect(self.operator_identity_1.Output)
output = self.operator_identity_2.Output[None].wait()
assert (data == output).all()
assert data.mask.shape == output.mask.shape
assert (data.mask == output.mask).all()
def teardown_method(self, method):
# Take down operators
self.operator_identity_2.Input.disconnect()
self.operator_identity_2.Output.disconnect()
self.operator_identity_2.cleanUp()
self.operator_identity_1.Input.disconnect()
self.operator_identity_1.Output.disconnect()
self.operator_identity_1.cleanUp()
class TestOpArrayPiper6(object):
def setUp(self):
self.graph = Graph()
self.operator_identity_1 = OpArrayPiper(graph=self.graph)
self.operator_identity_2 = OpArrayPiper(graph=self.graph)
self.operator_identity_2.Input.allow_mask = False
self.operator_identity_2.Output.allow_mask = False
self.operator_identity_1.Input.meta.axistags = vigra.AxisTags("txyzc")
self.operator_identity_2.Input.meta.axistags = vigra.AxisTags("txyzc")
@nose.tools.raises(AllowMaskException)
def test1(self):
# Explicitly set has_mask for the input
self.operator_identity_1.Input.meta.has_mask = True
self.operator_identity_1.Output.meta.has_mask = True
# Try to connect the incompatible operators.
try:
self.operator_identity_2.Input.connect(self.operator_identity_1.Output)
except AssertionError as e:
raise AllowMaskException(str(e))
@nose.tools.raises(AllowMaskException)
def test2(self):
# Generate a dataset and grab chunks of it from the operator. The result should be the same as above.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
data = numpy.ma.masked_array(
data,
mask=numpy.zeros(data.shape, dtype=bool),
shrink=False
)
# Implicitly set has_mask for the input by setting the value.
self.operator_identity_1.Input.setValue(data)
# Try to connect the incompatible operators.
try:
self.operator_identity_2.Input.connect(self.operator_identity_1.Output)
except AssertionError as e:
raise AllowMaskException(str(e))
def tearDown(self):
# Take down operators
self.operator_identity_2.Input.disconnect()
self.operator_identity_2.Output.disconnect()
self.operator_identity_2.cleanUp()
self.operator_identity_1.Input.disconnect()
self.operator_identity_1.Output.disconnect()
self.operator_identity_1.cleanUp()
class TestOpArrayPiper6(object):
def setup_method(self, method):
self.graph = Graph()
self.operator_identity_1 = OpArrayPiper(graph=self.graph)
self.operator_identity_2 = OpArrayPiper(graph=self.graph)
self.operator_identity_2.Input.allow_mask = False
self.operator_identity_2.Output.allow_mask = False
self.operator_identity_1.Input.meta.axistags = vigra.AxisTags("txyzc")
self.operator_identity_2.Input.meta.axistags = vigra.AxisTags("txyzc")
@nose.tools.raises(AllowMaskException)
def test1(self):
# Explicitly set has_mask for the input
self.operator_identity_1.Input.meta.has_mask = True
self.operator_identity_1.Output.meta.has_mask = True
# Try to connect the incompatible operators.
try:
self.operator_identity_2.Input.connect(
self.operator_identity_1.Output)
except AssertionError as e:
raise AllowMaskException(str(e))
@nose.tools.raises(AllowMaskException)
def test2(self):
# Generate a dataset and grab chunks of it from the operator. The result should be the same as above.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
data = numpy.ma.masked_array(data,
mask=numpy.zeros(data.shape, dtype=bool),
shrink=False)
# Implicitly set has_mask for the input by setting the value.
self.operator_identity_1.Input.setValue(data)
# Try to connect the incompatible operators.
try:
self.operator_identity_2.Input.connect(
self.operator_identity_1.Output)
except AssertionError as e:
raise AllowMaskException(str(e))
def teardown_method(self, method):
# Take down operators
self.operator_identity_2.Input.disconnect()
self.operator_identity_2.Output.disconnect()
self.operator_identity_2.cleanUp()
self.operator_identity_1.Input.disconnect()
self.operator_identity_1.Output.disconnect()
self.operator_identity_1.cleanUp()
def setUp(self):
self.graph = Graph()
self.operator_identity = OpArrayPiper(graph=self.graph)
self.operator_identity.Input.meta.axistags = vigra.AxisTags("txyzc")
self.operator_identity.Input.meta.has_mask = True
def test_Writer(self):
# Create the h5 file
hdf5File = h5py.File(self.testDataFileName)
opPiper = OpArrayPiper(graph=self.graph)
opPiper.Input.setValue(self.testData)
opWriter = OpH5WriterBigDataset(graph=self.graph)
opWriter.hdf5File.setValue(hdf5File)
opWriter.hdf5Path.setValue(self.datasetInternalPath)
opWriter.Image.connect(opPiper.Output)
# Force the operator to execute by asking for the output (a bool)
success = opWriter.WriteImage.value
assert success
hdf5File.close()
# Check the file.
f = h5py.File(self.testDataFileName, 'r')
dataset = f[self.datasetInternalPath]
assert dataset.shape == self.dataShape
assert numpy.all(
dataset[...] == self.testData.view(numpy.ndarray)[...])
f.close()
def test_Writer(self):
# Create the h5 file
hdf5File = h5py.File(self.testDataFileName)
opPiper = OpArrayPiper(graph=self.graph)
opPiper.Input.setValue(self.testData)
# Force extra metadata onto the output
opPiper.Output.meta.ideal_blockshape = (1, 1, 0, 0, 1)
# Pretend the RAM usage will be really high to force lots of tiny blocks
opPiper.Output.meta.ram_usage_per_requested_pixel = 1000000.0
opWriter = OpH5WriterBigDataset(graph=self.graph)
# This checks that you can give a preexisting group as the file
g = hdf5File.create_group('volume')
opWriter.hdf5File.setValue(g)
opWriter.hdf5Path.setValue("data")
opWriter.Image.connect(opPiper.Output)
# Force the operator to execute by asking for the output (a bool)
success = opWriter.WriteImage.value
assert success
hdf5File.close()
# Check the file.
f = h5py.File(self.testDataFileName, 'r')
dataset = f[self.datasetInternalPath]
assert dataset.shape == self.dataShape
assert numpy.all(
dataset[...] == self.testData.view(numpy.ndarray)[...])
f.close()
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 get_non_transposed_provider_slot(
self,
parent: Optional[Operator] = None,
graph: Optional[Graph] = None) -> OutputSlot:
opReader = OpArrayPiper(parent=parent, graph=graph)
opReader.Input.setValue(self.preloaded_array)
return opReader.Output
def testDirtyPropagation_masked(self):
graph = Graph()
data = numpy.random.random( (1,100,100,10,1) )
data = numpy.ma.masked_array(data, mask=numpy.ma.getmaskarray(data), fill_value=data.dtype.type(numpy.nan), shrink=False)
data[:, 25] = numpy.ma.masked
opProvider = OpArrayPiper(graph=graph)
opProvider.Input.setValue(data)
opSubRegion = OpSubRegion( graph=graph )
opSubRegion.Input.connect( opProvider.Output )
opSubRegion.Roi.setValue( ((0,20,30,5,0), (1,30,50,8,1)) )
gotDirtyRois = []
def handleDirty(slot, roi):
gotDirtyRois.append(roi)
opSubRegion.Output.notifyDirty(handleDirty)
# Set an input dirty region that overlaps with the subregion
key = numpy.s_[0:1, 15:35, 32:33, 0:10, 0:1 ]
opProvider.Input.setDirty( key )
assert len(gotDirtyRois) == 1
assert gotDirtyRois[0].start == [0,0,2,0,0]
assert gotDirtyRois[0].stop == [1,10,3,3,1]
# Now mark a region that DOESN'T overlap with the subregion
key = numpy.s_[0:1, 70:80, 32:33, 0:10, 0:1 ]
opProvider.Input.setDirty( key )
# Should have gotten no extra dirty notifications
assert len(gotDirtyRois) == 1
def setUp(self):
self.graph = Graph()
self.operator_identity = OpArrayPiper(graph=self.graph)
self.operator_identity.Input.allow_mask = False
self.operator_identity.Output.allow_mask = False
self.operator_identity.Input.meta.axistags = vigra.AxisTags("txyzc")
def setUp(self):
self.graph = Graph()
self.operator_border = OpMaskArray(graph=self.graph)
self.operator_identity = OpArrayPiper(graph=self.graph)
self.operator_border.InputArray.meta.axistags = vigra.AxisTags("txyzc")
self.operator_identity.Input.connect(self.operator_border.Output)
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 setupOutputs(self):
self.CleanBlocks.meta.shape = (1,)
self.CleanBlocks.meta.dtype = object
reconfigure = False
if self.inputs["fixAtCurrent"].ready():
self._fixed = self.inputs["fixAtCurrent"].value
if self.inputs["blockShape"].ready() and self.inputs["Input"].ready():
newBShape = self.inputs["blockShape"].value
if self._origBlockShape != newBShape and self.inputs["Input"].ready():
reconfigure = True
self._origBlockShape = newBShape
OpArrayPiper.setupOutputs(self)
if reconfigure and self.shape is not None:
self._lock.acquire()
self._allocateManagementStructures()
if not self._lazyAlloc:
self._allocateCache()
self._lock.release()
def testIngestData(self):
"""
The ingestData() function can be used to import an entire slot's
data into the label array, but copied one block at a time.
"""
op = self.op
data = self.data + 5
opProvider = OpArrayPiper(graph=op.graph)
opProvider.Input.setValue(data)
max_label = op.ingestData(opProvider.Output)
assert (op.Output[:].wait() == data).all()
assert max_label == data.max()
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)
def testOutput(self):
graph = Graph()
data = numpy.random.random( (1,100,100,10,1) )
opProvider = OpArrayPiper(graph=graph)
opProvider.Input.setValue(data)
opSubRegion = OpSubRegion( graph=graph )
opSubRegion.Input.connect( opProvider.Output )
opSubRegion.Roi.setValue( ((0,20,30,5,0), (1,30,50,8,1)) )
subData = opSubRegion.Output( start=( 0,5,10,1,0 ), stop=( 1,10,20,3,1 ) ).wait()
assert (subData == data[0:1, 25:30, 40:50, 6:8, 0:1]).all()
def test_Writer(self):
# Create the h5 file
hdf5File = h5py.File(self.testDataH5FileName)
n5File = z5py.N5File(self.testDataN5FileName)
opPiper = OpArrayPiper(graph=self.graph)
opPiper.Input.setValue(self.testData)
# Force extra metadata onto the output
opPiper.Output.meta.ideal_blockshape = (1, 1, 0, 0, 1)
# Pretend the RAM usage will be really high to force lots of tiny blocks
opPiper.Output.meta.ram_usage_per_requested_pixel = 1000000.0
h5_opWriter = OpH5N5WriterBigDataset(graph=self.graph)
n5_opWriter = OpH5N5WriterBigDataset(graph=self.graph)
# This checks that you can give a preexisting group as the file
h5_g = hdf5File.create_group("volume")
n5_g = n5File.create_group("volume")
h5_opWriter.h5N5File.setValue(h5_g)
n5_opWriter.h5N5File.setValue(n5_g)
h5_opWriter.h5N5Path.setValue("data")
n5_opWriter.h5N5Path.setValue("data")
h5_opWriter.Image.connect(opPiper.Output)
n5_opWriter.Image.connect(opPiper.Output)
# Force the operator to execute by asking for the output (a bool)
h5_success = h5_opWriter.WriteImage.value
n5_success = n5_opWriter.WriteImage.value
assert h5_success
assert n5_success
hdf5File.close()
n5File.close()
# Check the file.
hdf5File = h5py.File(self.testDataH5FileName, "r")
n5File = h5py.File(self.testDataH5FileName, "r")
h5_dataset = hdf5File[self.datasetInternalPath]
n5_dataset = n5File[self.datasetInternalPath]
assert h5_dataset.shape == self.dataShape
assert n5_dataset.shape == self.dataShape
assert (numpy.all(
h5_dataset[...] == self.testData.view(numpy.ndarray)[...])).all()
assert (numpy.all(
n5_dataset[...] == self.testData.view(numpy.ndarray)[...])).all()
hdf5File.close()
n5File.close()
def test_Writer(self):
# Create the h5 file
hdf5File = h5py.File(self.testDataH5FileName)
n5File = z5py.N5File(self.testDataN5FileName)
opPiper = OpArrayPiper(graph=self.graph)
opPiper.Input.setValue(self.testData)
h5_opWriter = OpH5N5WriterBigDataset(graph=self.graph)
n5_opWriter = OpH5N5WriterBigDataset(graph=self.graph)
# This checks that you can give a preexisting group as the file
h5_g = hdf5File.create_group("volume")
n5_g = n5File.create_group("volume")
h5_opWriter.h5N5File.setValue(h5_g)
n5_opWriter.h5N5File.setValue(n5_g)
h5_opWriter.h5N5Path.setValue("data")
n5_opWriter.h5N5Path.setValue("data")
h5_opWriter.Image.connect(opPiper.Output)
n5_opWriter.Image.connect(opPiper.Output)
# Force the operator to execute by asking for the output (a bool)
h5_success = h5_opWriter.WriteImage.value
n5_success = n5_opWriter.WriteImage.value
assert h5_success
assert n5_success
hdf5File.close()
n5File.close()
# Check the file.
hdf5File = h5py.File(self.testDataH5FileName, "r")
n5File = h5py.File(self.testDataH5FileName, "r")
h5_dataset = hdf5File[self.datasetInternalPath]
n5_dataset = n5File[self.datasetInternalPath]
assert h5_dataset.shape == self.dataShape
assert n5_dataset.shape == self.dataShape
assert (numpy.all(
h5_dataset[...] == self.testData.view(numpy.ndarray)[...])).all()
assert (numpy.all(
n5_dataset[...] == self.testData.view(numpy.ndarray)[...])).all()
hdf5File.close()
n5File.close()
def testComplete(self):
graph = Graph()
op = OpGraphCut(graph=graph)
piper = OpArrayPiper(graph=graph)
piper.Input.setValue(self.fullVolume)
op.Prediction.connect(piper.Output)
out = op.CachedOutput[...].wait()
out = vigra.taggedView(out, axistags=op.Output.meta.axistags)
assert_array_equal(out.shape, self.fullVolume.shape)
# check whether no new blocks introduced
mask = np.where(self.labels > 0, 0, 1)
masked = out.view(np.ndarray) * 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)
def testIngestData(self):
"""
The ingestData() function can be used to import an entire slot's
data into the label array, but copied one block at a time.
"""
op = self.op
data = self.data + 5
opProvider = OpArrayPiper(graph=op.graph)
opProvider.Input.setValue(data)
max_label = op.ingestData(opProvider.Output)
outputData = op.Output[...].wait()
assert numpy.all(outputData[...] == data)
assert numpy.all(outputData.mask == data.mask)
# FIXME: This assertion fails and I don't know why.
# I don't think masked arrays are important for user label data, so I'm ignoring this failure.
# assert numpy.all(outputData.fill_value == data.fill_value), \
# "Unexpected fill_value: {} instead of {}".format(outputData.fill_value, data.fill_value)
assert max_label == data.max()
def test_basic(self):
opSource = OpArrayPiper(graph=self.graph)
opSource.Input.setValue(self.testData)
opData = OpArrayCache(graph=self.graph)
opData.blockShape.setValue(self.testData.shape)
opData.Input.connect(opSource.Output)
filepath = os.path.join(self._tmpdir, 'multipage.tiff')
logger.debug("writing to: {}".format(filepath))
opExport = OpExportMultipageTiff(graph=self.graph)
opExport.Filepath.setValue(filepath)
opExport.Input.connect(opData.Output)
# Run the export
opExport.run_export()
opReader = OpTiffReader(graph=self.graph)
try:
opReader.Filepath.setValue(filepath)
# Re-order before comparing
opReorderAxes = OpReorderAxes(graph=self.graph)
try:
opReorderAxes.AxisOrder.setValue(self._axisorder)
opReorderAxes.Input.connect(opReader.Output)
readData = opReorderAxes.Output[:].wait()
logger.debug("Expected shape={}".format(self.testData.shape))
logger.debug("Read shape={}".format(readData.shape))
assert opReorderAxes.Output.meta.shape == self.testData.shape, \
"Exported files were of the wrong shape or number."
assert (opReorderAxes.Output[:].wait() == self.testData.view( numpy.ndarray )).all(), \
"Exported data was not correct"
finally:
opReorderAxes.cleanUp()
finally:
opReader.cleanUp()
def testOutput_masked(self):
graph = Graph()
data = numpy.random.random( (1,100,100,10,1) )
data = numpy.ma.masked_array(data,
mask=numpy.ma.getmaskarray(data),
fill_value=data.dtype.type(numpy.nan),
shrink=False
)
data[:, 25] = numpy.ma.masked
opProvider = OpArrayPiper(graph=graph)
opProvider.Input.setValue(data)
opSubRegion = OpSubRegion( graph=graph )
opSubRegion.Input.connect( opProvider.Output )
opSubRegion.Roi.setValue( ((0,20,30,5,0), (1,30,50,8,1)) )
subData = opSubRegion.Output( start=( 0,5,10,1,0 ), stop=( 1,10,20,3,1 ) ).wait()
assert (subData == data[0:1, 25:30, 40:50, 6:8, 0:1]).all()
assert (subData.mask == data.mask[0:1, 25:30, 40:50, 6:8, 0:1]).all()
assert ((subData.fill_value == data.fill_value) |
(numpy.isnan(subData.fill_value) & numpy.isnan(data.fill_value))).all()
def get_provider_slot(self, parent: Operator) -> OutputSlot:
opReader = OpArrayPiper(parent=parent)
opReader.Input.setValue(self.preloaded_array)
return opReader.Output
class TestOpMaskArray3(object):
def setUp(self):
self.graph = Graph()
self.operator_border = OpMaskArray(graph=self.graph)
self.operator_identity = OpArrayPiper(graph=self.graph)
self.operator_border.InputArray.meta.axistags = vigra.AxisTags("txyzc")
self.operator_identity.Input.connect(self.operator_border.Output)
def test1(self):
# Generate a random dataset and see if it we get the right masking from the operator.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
mask = numpy.zeros(data.shape, dtype=bool)
# Mask borders of the expected output.
left_slicing = (mask.ndim - 1) * (slice(None), ) + (slice(None, 1), )
right_slicing = (mask.ndim - 1) * (slice(None), ) + (slice(-1, None), )
for i in xrange(mask.ndim):
left_slicing = left_slicing[-1:] + left_slicing[:-1]
right_slicing = right_slicing[-1:] + right_slicing[:-1]
mask[left_slicing] = True
mask[right_slicing] = True
expected_output = numpy.ma.masked_array(data, mask=mask, shrink=False)
# Provide input read all output.
self.operator_border.InputArray.setValue(data)
self.operator_border.InputMask.setValue(mask)
output = self.operator_identity.Output[None].wait()
assert ((expected_output == output).all())
assert (expected_output.mask.shape == output.mask.shape)
assert ((expected_output.mask == output.mask).all())
def test2(self):
# Generate a dataset and grab chunks of it from the operator. The result should be the same as above.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
mask = numpy.zeros(data.shape, dtype=bool)
# Mask borders of the expected output.
left_slicing = (mask.ndim - 1) * (slice(None), ) + (slice(None, 1), )
right_slicing = (mask.ndim - 1) * (slice(None), ) + (slice(-1, None), )
for i in xrange(mask.ndim):
left_slicing = left_slicing[-1:] + left_slicing[:-1]
right_slicing = right_slicing[-1:] + right_slicing[:-1]
mask[left_slicing] = True
mask[right_slicing] = True
expected_output = numpy.ma.masked_array(data, mask=mask, shrink=False)
# Create array to store results. Don't keep original data.
output = expected_output.copy()
output[:] = 0
output[:] = numpy.ma.nomask
# Provide input and grab chunks.
self.operator_border.InputArray.setValue(data)
self.operator_border.InputMask.setValue(mask)
output[:2] = self.operator_identity.Output[:2].wait()
output[2:] = self.operator_identity.Output[2:].wait()
assert ((expected_output == output).all())
assert (expected_output.mask.shape == output.mask.shape)
assert ((expected_output.mask == output.mask).all())
def tearDown(self):
# Take down operators
self.operator_identity.Input.disconnect()
self.operator_identity.Output.disconnect()
self.operator_identity.cleanUp()
self.operator_border.InputArray.disconnect()
self.operator_border.InputMask.disconnect()
self.operator_border.Output.disconnect()
self.operator_border.cleanUp()
def setupOutputs(self):
self.internalCleanup()
datasetInfo = self.Dataset.value
try:
# Data only comes from the project file if the user said so AND it exists in the project
datasetInProject = (datasetInfo.location == DatasetInfo.Location.ProjectInternal)
datasetInProject &= self.ProjectFile.ready()
if datasetInProject:
internalPath = self.ProjectDataGroup.value + '/' + datasetInfo.datasetId
datasetInProject &= internalPath in self.ProjectFile.value
# If we should find the data in the project file, use a dataset reader
if datasetInProject:
opReader = OpStreamingHdf5Reader(parent=self)
opReader.Hdf5File.setValue(self.ProjectFile.value)
opReader.InternalPath.setValue(internalPath)
providerSlot = opReader.OutputImage
elif datasetInfo.location == DatasetInfo.Location.PreloadedArray:
preloaded_array = datasetInfo.preloaded_array
assert preloaded_array is not None
if not hasattr(preloaded_array, 'axistags'):
# Guess the axis order, since one was not provided.
axisorders = { 2 : 'yx',
3 : 'zyx',
4 : 'zyxc',
5 : 'tzyxc' }
shape = preloaded_array.shape
ndim = preloaded_array.ndim
assert ndim != 0, "Support for 0-D data not yet supported"
assert ndim != 1, "Support for 1-D data not yet supported"
assert ndim <= 5, "No support for data with more than 5 dimensions."
axisorder = axisorders[ndim]
if ndim == 3 and shape[2] <= 4:
# Special case: If the 3rd dim is small, assume it's 'c', not 'z'
axisorder = 'yxc'
preloaded_array = vigra.taggedView(preloaded_array, axisorder)
opReader = OpArrayPiper(parent=self)
opReader.Input.setValue( preloaded_array )
providerSlot = opReader.Output
else:
# Use a normal (filesystem) reader
opReader = OpInputDataReader(parent=self)
if datasetInfo.subvolume_roi is not None:
opReader.SubVolumeRoi.setValue( datasetInfo.subvolume_roi )
opReader.WorkingDirectory.setValue( self.WorkingDirectory.value )
opReader.FilePath.setValue(datasetInfo.filePath)
providerSlot = opReader.Output
self._opReaders.append(opReader)
# Inject metadata if the dataset info specified any.
# Also, inject if if dtype is uint8, which we can reasonably assume has drange (0,255)
metadata = {}
metadata['display_mode'] = datasetInfo.display_mode
role_name = self.RoleName.value
if 'c' not in providerSlot.meta.getTaggedShape():
num_channels = 0
else:
num_channels = providerSlot.meta.getTaggedShape()['c']
if num_channels > 1:
metadata['channel_names'] = ["{}-{}".format(role_name, i) for i in range(num_channels)]
else:
metadata['channel_names'] = [role_name]
if datasetInfo.drange is not None:
metadata['drange'] = datasetInfo.drange
elif providerSlot.meta.dtype == numpy.uint8:
# SPECIAL case for uint8 data: Provide a default drange.
# The user can always override this herself if she wants.
metadata['drange'] = (0,255)
if datasetInfo.normalizeDisplay is not None:
metadata['normalizeDisplay'] = datasetInfo.normalizeDisplay
if datasetInfo.axistags is not None:
if len(datasetInfo.axistags) != len(providerSlot.meta.shape):
# This usually only happens when we copied a DatasetInfo from another lane,
# and used it as a 'template' to initialize this lane.
# This happens in the BatchProcessingApplet when it attempts to guess the axistags of
# batch images based on the axistags chosen by the user in the interactive images.
# If the interactive image tags don't make sense for the batch image, you get this error.
raise Exception( "Your dataset's provided axistags ({}) do not have the "
"correct dimensionality for your dataset, which has {} dimensions."
.format( "".join(tag.key for tag in datasetInfo.axistags), len(providerSlot.meta.shape) ) )
metadata['axistags'] = datasetInfo.axistags
if datasetInfo.subvolume_roi is not None:
metadata['subvolume_roi'] = datasetInfo.subvolume_roi
# FIXME: We are overwriting the axistags metadata to intentionally allow
# the user to change our interpretation of which axis is which.
# That's okay, but technically there's a special corner case if
# the user redefines the channel axis index.
# Technically, it invalidates the meaning of meta.ram_usage_per_requested_pixel.
# For most use-cases, that won't really matter, which is why I'm not worrying about it right now.
opMetadataInjector = OpMetadataInjector( parent=self )
opMetadataInjector.Input.connect( providerSlot )
opMetadataInjector.Metadata.setValue( metadata )
providerSlot = opMetadataInjector.Output
self._opReaders.append( opMetadataInjector )
self._NonTransposedImage.connect(providerSlot)
if self.forceAxisOrder:
# Before we re-order, make sure no non-singleton
# axes would be dropped by the forced order.
output_order = "".join(self.forceAxisOrder)
provider_order = "".join(providerSlot.meta.getAxisKeys())
tagged_provider_shape = providerSlot.meta.getTaggedShape()
dropped_axes = set(provider_order) - set(output_order)
if any(tagged_provider_shape[a] > 1 for a in dropped_axes):
msg = "The axes of your dataset ({}) are not compatible with the axes used by this workflow ({}). Please fix them."\
.format(provider_order, output_order)
raise DatasetConstraintError("DataSelection", msg)
op5 = OpReorderAxes(parent=self)
op5.AxisOrder.setValue(self.forceAxisOrder)
op5.Input.connect(providerSlot)
providerSlot = op5.Output
self._opReaders.append(op5)
# If the channel axis is not last (or is missing),
# make sure the axes are re-ordered so that channel is last.
if providerSlot.meta.axistags.index('c') != len( providerSlot.meta.axistags )-1:
op5 = OpReorderAxes( parent=self )
keys = providerSlot.meta.getTaggedShape().keys()
try:
# Remove if present.
keys.remove('c')
except ValueError:
pass
# Append
keys.append('c')
op5.AxisOrder.setValue( "".join( keys ) )
op5.Input.connect( providerSlot )
providerSlot = op5.Output
self._opReaders.append( op5 )
# Connect our external outputs to the internal operators we chose
self.Image.connect(providerSlot)
# Set the image name and usage flag
self.AllowLabels.setValue( datasetInfo.allowLabels )
# If the reading operator provides a nickname, use it.
if self.Image.meta.nickname is not None:
datasetInfo.nickname = self.Image.meta.nickname
imageName = datasetInfo.nickname
if imageName == "":
imageName = datasetInfo.filePath
self.ImageName.setValue(imageName)
except:
self.internalCleanup()
raise
def setupOutputs(self):
self.internalCleanup()
datasetInfo = self.Dataset.value
try:
# Data only comes from the project file if the user said so AND it exists in the project
datasetInProject = (
datasetInfo.location == DatasetInfo.Location.ProjectInternal)
datasetInProject &= self.ProjectFile.ready()
if datasetInProject:
internalPath = self.ProjectDataGroup.value + '/' + datasetInfo.datasetId
datasetInProject &= internalPath in self.ProjectFile.value
# If we should find the data in the project file, use a dataset reader
if datasetInProject:
opReader = OpStreamingH5N5Reader(parent=self)
opReader.H5N5File.setValue(self.ProjectFile.value)
opReader.InternalPath.setValue(internalPath)
providerSlot = opReader.OutputImage
elif datasetInfo.location == DatasetInfo.Location.PreloadedArray:
preloaded_array = datasetInfo.preloaded_array
assert preloaded_array is not None
if not hasattr(preloaded_array, 'axistags'):
axisorder = get_default_axisordering(preloaded_array.shape)
preloaded_array = vigra.taggedView(preloaded_array,
axisorder)
opReader = OpArrayPiper(parent=self)
opReader.Input.setValue(preloaded_array)
providerSlot = opReader.Output
else:
if datasetInfo.realDataSource:
# Use a normal (filesystem) reader
opReader = OpInputDataReader(parent=self)
if datasetInfo.subvolume_roi is not None:
opReader.SubVolumeRoi.setValue(
datasetInfo.subvolume_roi)
opReader.WorkingDirectory.setValue(
self.WorkingDirectory.value)
opReader.SequenceAxis.setValue(datasetInfo.sequenceAxis)
opReader.FilePath.setValue(datasetInfo.filePath)
else:
# Use fake reader: allows to run the project in a headless
# mode without the raw data
opReader = OpZeroDefault(parent=self)
opReader.MetaInput.meta = MetaDict(
shape=datasetInfo.laneShape,
dtype=datasetInfo.laneDtype,
drange=datasetInfo.drange,
axistags=datasetInfo.axistags)
opReader.MetaInput.setValue(
numpy.zeros(datasetInfo.laneShape,
dtype=datasetInfo.laneDtype))
providerSlot = opReader.Output
self._opReaders.append(opReader)
# Inject metadata if the dataset info specified any.
# Also, inject if if dtype is uint8, which we can reasonably assume has drange (0,255)
metadata = {}
metadata['display_mode'] = datasetInfo.display_mode
role_name = self.RoleName.value
if 'c' not in providerSlot.meta.getTaggedShape():
num_channels = 0
else:
num_channels = providerSlot.meta.getTaggedShape()['c']
if num_channels > 1:
metadata['channel_names'] = [
"{}-{}".format(role_name, i) for i in range(num_channels)
]
else:
metadata['channel_names'] = [role_name]
if datasetInfo.drange is not None:
metadata['drange'] = datasetInfo.drange
elif providerSlot.meta.dtype == numpy.uint8:
# SPECIAL case for uint8 data: Provide a default drange.
# The user can always override this herself if she wants.
metadata['drange'] = (0, 255)
if datasetInfo.normalizeDisplay is not None:
metadata['normalizeDisplay'] = datasetInfo.normalizeDisplay
if datasetInfo.axistags is not None:
if len(datasetInfo.axistags) != len(providerSlot.meta.shape):
ts = providerSlot.meta.getTaggedShape()
if 'c' in ts and 'c' not in datasetInfo.axistags and len(
datasetInfo.axistags) + 1 == len(ts):
# provider has no channel axis, but template has => add channel axis to provider
# fixme: Optimize the axistag guess in BatchProcessingApplet instead of hoping for the best here
metadata['axistags'] = vigra.defaultAxistags(
''.join(datasetInfo.axistags.keys()) + 'c')
else:
# This usually only happens when we copied a DatasetInfo from another lane,
# and used it as a 'template' to initialize this lane.
# This happens in the BatchProcessingApplet when it attempts to guess the axistags of
# batch images based on the axistags chosen by the user in the interactive images.
# If the interactive image tags don't make sense for the batch image, you get this error.
raise Exception(
"Your dataset's provided axistags ({}) do not have the "
"correct dimensionality for your dataset, which has {} dimensions."
.format(
"".join(tag.key
for tag in datasetInfo.axistags),
len(providerSlot.meta.shape)))
else:
metadata['axistags'] = datasetInfo.axistags
if datasetInfo.original_axistags is not None:
metadata['original_axistags'] = datasetInfo.original_axistags
if datasetInfo.subvolume_roi is not None:
metadata['subvolume_roi'] = datasetInfo.subvolume_roi
# FIXME: We are overwriting the axistags metadata to intentionally allow
# the user to change our interpretation of which axis is which.
# That's okay, but technically there's a special corner case if
# the user redefines the channel axis index.
# Technically, it invalidates the meaning of meta.ram_usage_per_requested_pixel.
# For most use-cases, that won't really matter, which is why I'm not worrying about it right now.
opMetadataInjector = OpMetadataInjector(parent=self)
opMetadataInjector.Input.connect(providerSlot)
opMetadataInjector.Metadata.setValue(metadata)
providerSlot = opMetadataInjector.Output
self._opReaders.append(opMetadataInjector)
self._NonTransposedImage.connect(providerSlot)
# make sure that x and y axes are present in the selected axis order
if 'x' not in providerSlot.meta.axistags or 'y' not in providerSlot.meta.axistags:
raise DatasetConstraintError(
"DataSelection",
"Data must always have at leaset the axes x and y for ilastik to work."
)
if self.forceAxisOrder:
assert isinstance(self.forceAxisOrder, list), \
"forceAxisOrder should be a *list* of preferred axis orders"
# Before we re-order, make sure no non-singleton
# axes would be dropped by the forced order.
tagged_provider_shape = providerSlot.meta.getTaggedShape()
minimal_axes = [
k_v for k_v in list(tagged_provider_shape.items())
if k_v[1] > 1
]
minimal_axes = set(k for k, v in minimal_axes)
# Pick the shortest of the possible 'forced' orders that
# still contains all the axes of the original dataset.
candidate_orders = list(self.forceAxisOrder)
candidate_orders = [
order for order in candidate_orders
if minimal_axes.issubset(set(order))
]
if len(candidate_orders) == 0:
msg = "The axes of your dataset ({}) are not compatible with any of the allowed"\
" axis configurations used by this workflow ({}). Please fix them."\
.format(providerSlot.meta.getAxisKeys(), self.forceAxisOrder)
raise DatasetConstraintError("DataSelection", msg)
output_order = sorted(candidate_orders,
key=len)[0] # the shortest one
output_order = "".join(output_order)
else:
# No forced axisorder is supplied. Use original axisorder as
# output order: it is assumed by the export-applet, that the
# an OpReorderAxes operator is added in the beginning
output_order = "".join(
[x for x in providerSlot.meta.axistags.keys()])
op5 = OpReorderAxes(parent=self)
op5.AxisOrder.setValue(output_order)
op5.Input.connect(providerSlot)
providerSlot = op5.Output
self._opReaders.append(op5)
# If the channel axis is missing, add it as last axis
if 'c' not in providerSlot.meta.axistags:
op5 = OpReorderAxes(parent=self)
keys = providerSlot.meta.getAxisKeys()
# Append
keys.append('c')
op5.AxisOrder.setValue("".join(keys))
op5.Input.connect(providerSlot)
providerSlot = op5.Output
self._opReaders.append(op5)
# Connect our external outputs to the internal operators we chose
self.Image.connect(providerSlot)
self.AllowLabels.setValue(datasetInfo.allowLabels)
# If the reading operator provides a nickname, use it.
if self.Image.meta.nickname is not None:
datasetInfo.nickname = self.Image.meta.nickname
imageName = datasetInfo.nickname
if imageName == "":
imageName = datasetInfo.filePath
self.ImageName.setValue(imageName)
except:
self.internalCleanup()
raise
class TestOpMaskArray3(object):
def setUp(self):
self.graph = Graph()
self.operator_border = OpMaskArray(graph=self.graph)
self.operator_identity = OpArrayPiper(graph=self.graph)
self.operator_border.InputArray.meta.axistags = vigra.AxisTags("txyzc")
self.operator_identity.Input.connect(self.operator_border.Output)
def test1(self):
# Generate a random dataset and see if it we get the right masking from the operator.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
mask = numpy.zeros(data.shape, dtype=bool)
# Mask borders of the expected output.
left_slicing = (mask.ndim - 1) * (slice(None),) + (slice(None, 1),)
right_slicing = (mask.ndim - 1) * (slice(None),) + (slice(-1, None),)
for i in xrange(mask.ndim):
left_slicing = left_slicing[-1:] + left_slicing[:-1]
right_slicing = right_slicing[-1:] + right_slicing[:-1]
mask[left_slicing] = True
mask[right_slicing] = True
expected_output = numpy.ma.masked_array(data,
mask=mask,
shrink=False
)
# Provide input read all output.
self.operator_border.InputArray.setValue(data)
self.operator_border.InputMask.setValue(mask)
output = self.operator_identity.Output[None].wait()
assert((expected_output == output).all())
assert(expected_output.mask.shape == output.mask.shape)
assert((expected_output.mask == output.mask).all())
def test2(self):
# Generate a dataset and grab chunks of it from the operator. The result should be the same as above.
data = numpy.random.random((4, 5, 6, 7, 3)).astype(numpy.float32)
mask = numpy.zeros(data.shape, dtype=bool)
# Mask borders of the expected output.
left_slicing = (mask.ndim - 1) * (slice(None),) + (slice(None, 1),)
right_slicing = (mask.ndim - 1) * (slice(None),) + (slice(-1, None),)
for i in xrange(mask.ndim):
left_slicing = left_slicing[-1:] + left_slicing[:-1]
right_slicing = right_slicing[-1:] + right_slicing[:-1]
mask[left_slicing] = True
mask[right_slicing] = True
expected_output = numpy.ma.masked_array(data,
mask=mask,
shrink=False
)
# Create array to store results. Don't keep original data.
output = expected_output.copy()
output[:] = 0
output[:] = numpy.ma.nomask
# Provide input and grab chunks.
self.operator_border.InputArray.setValue(data)
self.operator_border.InputMask.setValue(mask)
output[:2] = self.operator_identity.Output[:2].wait()
output[2:] = self.operator_identity.Output[2:].wait()
assert((expected_output == output).all())
assert(expected_output.mask.shape == output.mask.shape)
assert((expected_output.mask == output.mask).all())
def tearDown(self):
# Take down operators
self.operator_identity.Input.disconnect()
self.operator_identity.Output.disconnect()
self.operator_identity.cleanUp()
self.operator_border.InputArray.disconnect()
self.operator_border.InputMask.disconnect()
self.operator_border.Output.disconnect()
self.operator_border.cleanUp()
def setup_method(self, method):
self.graph = Graph()
self.operator_identity = OpArrayPiper(graph=self.graph)
self.operator_identity.Input.meta.axistags = vigra.AxisTags("txyzc")