def testWithCustomBackground(self):
graph = Graph()
# OpDummyData needs an input array to decide what shape/dtype/axes to make the output
a = numpy.ndarray(shape=(2, 100, 100, 100, 3), dtype=numpy.uint32)
v = a.view(vigra.VigraArray)
v.axistags = vigra.defaultAxistags('txyzc')
# OpDummyData provides a simple binary image with a bunch of thick diagonal planes.
opData = OpDummyData(graph=graph)
opData.Input.setValue(v)
assert opData.Output.ready()
assert opData.Output.meta.axistags is not None
# Each diagonal plane should get it's own label...
op = OpCachedLabelImage(graph=graph)
op.Input.connect(opData.Output)
op.BackgroundLabels.setValue(
[0, 1, 0]) # Use inverted background for the second channel
assert op.Output.ready()
data = opData.Output[:].wait()
labels = op.Output[:].wait()
channel = 0
#logger.debug( "data-c0:\n{}".format( str(data[0,:80:5,:80:5,0,channel])) )
#logger.debug( "labels-c0:\n{}".format( str(labels[0,:80:5,:80:5,0,channel])) )
channel = 1
#logger.debug( "data-c1:\n{}".format( str(data[0,:80:5,:80:5,0,channel])) )
#logger.debug( "labels-c1:\n{}".format( str(labels[0,:80:5,:80:5,0,channel])) )
assert labels[0, 0, 0, 0, 0] == 1
assert labels[
0, 0, 0, 0,
1] == 0, "Expected inverted background for the second channel"
class OpBlockwiseFilesetReader(Operator):
"""
Adapter that provides an operator interface to the BlockwiseFileset class for reading ONLY.
"""
name = "OpBlockwiseFilesetReader"
DescriptionFilePath = InputSlot(stype="filestring")
Output = OutputSlot()
class MissingDatasetError(Exception):
pass
def __init__(self, *args, **kwargs):
super(OpBlockwiseFilesetReader, self).__init__(*args, **kwargs)
self._blockwiseFileset = None
self._opDummyData = OpDummyData(parent=self)
def setupOutputs(self):
if not os.path.exists(self.DescriptionFilePath.value):
raise OpBlockwiseFilesetReader.MissingDatasetError(
"Dataset description not found: {}".format(
self.DescriptionFilePath.value))
# Load up the class that does the real work
self._blockwiseFileset = BlockwiseFileset(
self.DescriptionFilePath.value)
# Check for errors in the description file
descriptionFields = self._blockwiseFileset.description
axes = descriptionFields.axes
assert False not in [
a in "txyzc" for a in axes
], "Unknown axis type. Known axes: txyzc Your axes:".format(axes)
self.Output.meta.shape = tuple(descriptionFields.view_shape)
self.Output.meta.dtype = descriptionFields.dtype
self.Output.meta.axistags = vigra.defaultAxistags(
str(descriptionFields.axes))
drange = descriptionFields.drange
if drange is not None:
self.Output.meta.drange = drange
def execute(self, slot, subindex, roi, result):
assert slot == self.Output, "Unknown output slot"
try:
self._blockwiseFileset.readData((roi.start, roi.stop), result)
except BlockwiseFileset.BlockNotReadyError:
result[:] = self._opDummyData.execute(slot, subindex, roi, result)
return result
def propagateDirty(self, slot, subindex, roi):
assert slot == self.DescriptionFilePath, "Unknown input slot."
self.Output.setDirty(slice(None))
def cleanUp(self):
if self._blockwiseFileset is not None:
self._blockwiseFileset.close()
super(OpBlockwiseFilesetReader, self).cleanUp()
class OpBlockwiseFilesetReader(Operator):
"""
Adapter that provides an operator interface to the BlockwiseFileset class for reading ONLY.
"""
name = "OpBlockwiseFilesetReader"
DescriptionFilePath = InputSlot(stype="filestring")
Output = OutputSlot()
class MissingDatasetError(Exception):
pass
def __init__(self, *args, **kwargs):
super(OpBlockwiseFilesetReader, self).__init__(*args, **kwargs)
self._blockwiseFileset = None
self._opDummyData = OpDummyData(parent=self)
def setupOutputs(self):
if not os.path.exists(self.DescriptionFilePath.value):
raise OpBlockwiseFilesetReader.MissingDatasetError(
"Dataset description not found: {}".format(self.DescriptionFilePath.value)
)
# Load up the class that does the real work
self._blockwiseFileset = BlockwiseFileset(self.DescriptionFilePath.value)
# Check for errors in the description file
descriptionFields = self._blockwiseFileset.description
axes = descriptionFields.axes
assert False not in map(
lambda a: a in "txyzc", axes
), "Unknown axis type. Known axes: txyzc Your axes:".format(axes)
self.Output.meta.shape = tuple(descriptionFields.view_shape)
self.Output.meta.dtype = descriptionFields.dtype
self.Output.meta.axistags = vigra.defaultAxistags(descriptionFields.axes)
drange = descriptionFields.drange
if drange is not None:
self.Output.meta.drange = drange
def execute(self, slot, subindex, roi, result):
assert slot == self.Output, "Unknown output slot"
try:
self._blockwiseFileset.readData((roi.start, roi.stop), result)
except BlockwiseFileset.BlockNotReadyError:
result[:] = self._opDummyData.execute(slot, subindex, roi, result)
return result
def propagateDirty(self, slot, subindex, roi):
assert slot == self.DescriptionFilePath, "Unknown input slot."
self.Output.setDirty(slice(None))
def cleanUp(self):
if self._blockwiseFileset is not None:
self._blockwiseFileset.close()
super(OpBlockwiseFilesetReader, self).cleanUp()
def testBasic(self):
graph = Graph()
# OpDummyData needs an input array to decide what shape/dtype/axes to make the output
a = numpy.ndarray(shape=(2, 100, 100, 100, 3), dtype=numpy.uint32)
v = a.view(vigra.VigraArray)
v.axistags = vigra.defaultAxistags('txyzc')
# OpDummyData provides a simple binary image with a bunch of thick diagonal planes.
opData = OpDummyData(graph=graph)
opData.Input.setValue(v)
assert opData.Output.ready()
assert opData.Output.meta.axistags is not None
data = opData.Output[:].wait()
#logger.debug( "data:\n{}".format( str(data[0,:80:5,:80:5,0,0])) )
# Each diagonal plane should get it's own label...
op = OpCachedLabelImage(graph=graph)
op.Input.connect(opData.Output)
assert op.Output.ready()
labels = op.Output[:].wait()
def __init__(self, *args, **kwargs):
super(OpBlockwiseFilesetReader, self).__init__(*args, **kwargs)
self._blockwiseFileset = None
self._opDummyData = OpDummyData(parent=self)
def __init__(self, *args, **kwargs):
super(OpBlockwiseFilesetReader, self).__init__(*args, **kwargs)
self._blockwiseFileset = None
self._opDummyData = OpDummyData( parent=self )
def __init__(self, *args, **kwargs):
super(OpExportedImageProvider, self).__init__(*args, **kwargs)
self._opReader = None
self._opDummyData = OpDummyData(parent=self)
