def __init__(self,
graph=None,
hintOverlayFile=None,
pmapOverlayFile=None,
parent=None):
super(OpCarving, self).__init__(graph=graph, parent=parent)
self.opLabelArray = OpDenseLabelArray(parent=self)
# self.opLabelArray.EraserLabelValue.setValue( 100 )
self.opLabelArray.MetaInput.connect(self.InputData)
self._hintOverlayFile = hintOverlayFile
self._mst = None
self.has_seeds = (
False
) # keeps track of whether or not there are seeds currently loaded, either drawn by the user or loaded from a saved object
self.LabelNames.setValue(["Background", "Object"])
# supervoxels of finished and saved objects
self._done_seg_lut = None
self._hints = None
self._pmap = None
if hintOverlayFile is not None:
try:
f = h5py.File(hintOverlayFile, "r")
except Exception as e:
logger.info("Could not open hint overlay '%s'" %
hintOverlayFile)
raise e
self._hints = f["/hints"].value[numpy.newaxis, :, :, :,
numpy.newaxis]
if pmapOverlayFile is not None:
try:
f = h5py.File(pmapOverlayFile, "r")
except Exception as e:
raise RuntimeError("Could not open pmap overlay '%s'" %
pmapOverlayFile)
self._pmap = f["/data"].value[numpy.newaxis, :, :, :,
numpy.newaxis]
self._setCurrObjectName("<not saved yet>")
self.HasSegmentation.setValue(False)
# keep track of a set of object names that have changed since
# the last serialization of this object to disk
self._dirtyObjects = set()
self.preprocessingApplet = None
self._opMstCache = OpValueCache(parent=self)
self.MstOut.connect(self._opMstCache.Output)
self.InputData.notifyReady(self._checkConstraints)
self.ObjectPrefix.setValue(DEFAULT_LABEL_PREFIX)
def __init__(self, *args, **kwargs):
super(OpLabelPipeline, self).__init__(*args, **kwargs)
self.opLabelArray = OpDenseLabelArray(parent=self)
self.opLabelArray.MetaInput.connect(self.RawImage)
self.opLabelArray.LabelSinkInput.connect(self.LabelInput)
self.opLabelArray.EraserLabelValue.setValue(100)
self.opBoxArray = OpDenseLabelArray(parent=self)
self.opBoxArray.MetaInput.connect(self.RawImage)
self.opBoxArray.LabelSinkInput.connect(self.BoxLabelInput)
self.opBoxArray.EraserLabelValue.setValue(100)
# Initialize the delete input to -1, which means "no label".
# Now changing this input to a positive value will cause label deletions.
# (The deleteLabel input is monitored for changes.)
self.opLabelArray.DeleteLabel.setValue(-1)
# Connect external outputs to their internal sources
self.Output.connect(self.opLabelArray.Output)
self.nonzeroBlocks.connect(self.opLabelArray.NonzeroBlocks)
self.MaxLabel.connect(self.opLabelArray.MaxLabelValue)
self.BoxOutput.connect(self.opBoxArray.Output)
def setup(self):
graph = Graph()
op = OpDenseLabelArray(graph=graph)
arrayshape = (1,100,100,10,1)
op.EraserLabelValue.setValue(100)
dummyData = vigra.VigraArray(arrayshape, axistags=vigra.defaultAxistags('txyzc'))
op.MetaInput.setValue( dummyData )
slicing = sl[0:1, 1:15, 2:36, 3:7, 0:1]
inDataShape = slicing2shape(slicing)
inputData = ( 3*numpy.random.random(inDataShape) ).astype(numpy.uint8)
op.LabelSinkInput[slicing] = inputData
data = numpy.zeros(arrayshape, dtype=numpy.uint8)
data[slicing] = inputData
self.op = op
self.slicing = slicing
self.inData = inputData
self.data = data
def setup(self):
graph = Graph()
op = OpDenseLabelArray(graph=graph)
arrayshape = (1, 100, 100, 10, 1)
op.EraserLabelValue.setValue(100)
dummyData = vigra.VigraArray(arrayshape,
axistags=vigra.defaultAxistags("txyzc"))
op.MetaInput.setValue(dummyData)
slicing = numpy.s_[0:1, 1:15, 2:36, 3:7, 0:1]
inDataShape = slicing2shape(slicing)
inputData = (3 * numpy.random.random(inDataShape)).astype(numpy.uint8)
op.LabelSinkInput[slicing] = inputData
data = numpy.zeros(arrayshape, dtype=numpy.uint8)
data[slicing] = inputData
self.op = op
self.slicing = slicing
self.inData = inputData
self.data = data