def setupOutputs(self):
# sanity checks
shape = self.Prediction.meta.shape
assert len(shape) == 5,\
"Prediction maps must be a full 5d volume (txyzc)"
tags = self.Prediction.meta.getAxisKeys()
tags = "".join(tags)
assert tags == 'txyzc',\
"Prediction maps have wrong axes order"\
"(expected: txyzc, got: {})".format(tags)
if self._cache is not None:
self.CachedOutput.disconnect()
self._cache.cleanUp()
self._cache = None
cache = OpCompressedCache(parent=self)
cache.name = "{}._cache".format(self.name)
cache.Input.connect(self.Output)
self._cache = cache
self.CachedOutput.connect(self._cache.Output)
self.Output.meta.assignFrom(self.Prediction.meta)
# output is a label image
self.Output.meta.dtype = np.uint32
# cache should hold entire c-t-slices in memory
shape = list(self.Prediction.meta.shape)
shape[0] = 1
shape[4] = 1
self._cache.BlockShape.setValue(tuple(shape))
def setupOutputs(self):
# sanity checks
shape = self.Prediction.meta.shape
assert len(shape) == 5,\
"Prediction maps must be a full 5d volume (tzyxc)"
tags = self.Prediction.meta.getAxisKeys()
tags = "".join(tags)
assert tags == 'tzyxc',\
"Prediction maps have wrong axes order"\
"(expected: tzyxc, got: {})".format(tags)
if self._cache is not None:
self.CachedOutput.disconnect()
self._cache.cleanUp()
self._cache = None
cache = OpCompressedCache(parent=self)
cache.name = "{}._cache".format(self.name)
cache.Input.connect(self.Output)
self._cache = cache
self.CachedOutput.connect(self._cache.Output)
self.Output.meta.assignFrom(self.Prediction.meta)
# output is a label image
self.Output.meta.dtype = np.uint32
# cache should hold entire c-t-slices in memory
shape = list(self.Prediction.meta.shape)
shape[0] = 1
shape[4] = 1
self._cache.BlockShape.setValue(tuple(shape))
def __init__(self, *args, **kwargs):
super(OpGraphCut, self).__init__(*args, **kwargs)
cache = OpCompressedCache(parent=self)
cache.name = "{}._cache".format(self.name)
cache.Input.connect(self.Output)
self._cache = cache
self.CachedOutput.connect(self._cache.Output)
def __init__(self, parent=None, graph=None):
super(OpTrackingBase, self).__init__(parent=parent, graph=graph)
self.label2color = []
self.mergers = []
self.resolvedto = []
self.track_id = None
self.extra_track_ids = None
self.divisions = None
self._opCache = OpCompressedCache(parent=self)
self._opCache.InputHdf5.connect(self.InputHdf5)
self._opCache.Input.connect(self.Output)
self.CleanBlocks.connect(self._opCache.CleanBlocks)
self.OutputHdf5.connect(self._opCache.OutputHdf5)
self.CachedOutput.connect(self._opCache.Output)
self.zeroProvider = OpZeroDefault(parent=self)
self.zeroProvider.MetaInput.connect(self.LabelImage)
# As soon as input data is available, check its constraints
self.RawImage.notifyReady(self._checkConstraints)
self.LabelImage.notifyReady(self._checkConstraints)
self.export_progress_dialog = None
self.ExportSettings.setValue((None, None))
def __init__(self, parent=None, graph=None):
super(OpConservationTrackingPgmLink, self).__init__(parent=parent,
graph=graph)
self._mergerOpCache = OpCompressedCache(parent=self)
self._mergerOpCache.InputHdf5.connect(self.MergerInputHdf5)
self._mergerOpCache.Input.connect(self.MergerOutput)
self.MergerCleanBlocks.connect(self._mergerOpCache.CleanBlocks)
self.MergerOutputHdf5.connect(self._mergerOpCache.OutputHdf5)
self.MergerCachedOutput.connect(self._mergerOpCache.Output)
self._relabeledOpCache = OpCompressedCache(parent=self)
self._relabeledOpCache.InputHdf5.connect(self.RelabeledInputHdf5)
self._relabeledOpCache.Input.connect(self.RelabeledImage)
self.RelabeledCleanBlocks.connect(self._relabeledOpCache.CleanBlocks)
self.RelabeledOutputHdf5.connect(self._relabeledOpCache.OutputHdf5)
self.RelabeledCachedOutput.connect(self._relabeledOpCache.Output)
self.tracker = None
self._ndim = 3
def __init__(self, parent=None, graph=None):
super(OpConservationTracking, self).__init__(parent=parent,
graph=graph)
self._mergerOpCache = OpCompressedCache(parent=self)
self._mergerOpCache.InputHdf5.connect(self.MergerInputHdf5)
self._mergerOpCache.Input.connect(self.MergerOutput)
self.MergerCleanBlocks.connect(self._mergerOpCache.CleanBlocks)
self.MergerOutputHdf5.connect(self._mergerOpCache.OutputHdf5)
self.MergerCachedOutput.connect(self._mergerOpCache.Output)
def __init__(self, parent=None, graph=None):
super(OpStructuredTracking, self).__init__(parent=parent, graph=graph)
self.labels = {}
self.divisions = {}
self.Annotations.setValue({})
self._mergerOpCache = OpCompressedCache(parent=self)
self._mergerOpCache.InputHdf5.connect(self.MergerInputHdf5)
self._mergerOpCache.Input.connect(self.MergerOutput)
self.MergerCleanBlocks.connect(self._mergerOpCache.CleanBlocks)
self.MergerOutputHdf5.connect(self._mergerOpCache.OutputHdf5)
self.MergerCachedOutput.connect(self._mergerOpCache.Output)
self._relabeledOpCache = OpCompressedCache(parent=self)
self._relabeledOpCache.InputHdf5.connect(self.RelabeledInputHdf5)
self._relabeledOpCache.Input.connect(self.RelabeledImage)
self.RelabeledCleanBlocks.connect(self._relabeledOpCache.CleanBlocks)
self.RelabeledOutputHdf5.connect(self._relabeledOpCache.OutputHdf5)
self.RelabeledCachedOutput.connect(self._relabeledOpCache.Output)
self._ndim = 3
self.consTracker = None
self._parent = parent
self.DivisionWeight.setValue(1)
self.DetectionWeight.setValue(1)
self.TransitionWeight.setValue(1)
self.AppearanceWeight.setValue(1)
self.DisappearanceWeight.setValue(1)
self.MaxNumObjOut.setValue(1)
self.transition_parameter = 5
self.detectionWeight = 1
self.divisionWeight = 1
self.transitionWeight = 1
self.appearanceWeight = 1
self.disappearanceWeight = 1
def setupOutputs(self):
self.Output.meta.assignFrom(self.LabelImage.meta)
#cache our own output, don't propagate from internal operator
chunks = list(self.LabelImage.meta.shape)
# FIXME: assumes t,x,y,z,c
chunks[0] = 1 # 't'
self._opCache = OpCompressedCache(parent=self)
self._opCache.InputHdf5.connect(self.InputHdf5)
self._opCache.Input.connect(self.Output)
self._opCache.BlockShape.setValue(tuple(chunks))
self.CleanBlocks.connect(self._opCache.CleanBlocks)
self.OutputHdf5.connect(self._opCache.OutputHdf5)
self.CachedOutput.connect(self._opCache.Output)
self.zeroProvider = OpZeroDefault(parent=self)
self.zeroProvider.MetaInput.connect(self.LabelImage)
def __init__(self, parent=None, graph=None):
super(OpTrackingBase, self).__init__(parent=parent, graph=graph)
self.label2color = []
self.mergers = []
self._opCache = OpCompressedCache(parent=self)
self._opCache.InputHdf5.connect(self.InputHdf5)
self._opCache.Input.connect(self.Output)
self.CleanBlocks.connect(self._opCache.CleanBlocks)
self.OutputHdf5.connect(self._opCache.OutputHdf5)
self.CachedOutput.connect(self._opCache.Output)
self.zeroProvider = OpZeroDefault(parent=self)
self.zeroProvider.MetaInput.connect(self.LabelImage)
# As soon as input data is available, check its constraints
self.RawImage.notifyReady(self._checkConstraints)
self.LabelImage.notifyReady(self._checkConstraints)
