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"
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(OpExportedImageProvider, self).__init__(*args, **kwargs) self._opReader = None self._opDummyData = OpDummyData(parent=self)