def setup(self):
graph = Graph()
op = OpSparseLabelArray(graph=graph)
arrayshape = numpy.array([1,10,10,10,1])
op.inputs["shape"].setValue( tuple(arrayshape) )
op.eraser.setValue(100)
slicing = sl[0:1, 1:5, 2:6, 3:7, 0:1]
inDataShape = slicing2shape(slicing)
inputData = ( 3*numpy.random.random(inDataShape) ).astype(numpy.uint8)
op.Input[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 = OpSparseLabelArray(graph=graph)
arrayshape = numpy.array([1, 10, 10, 10, 1])
op.inputs["shape"].setValue(tuple(arrayshape))
op.eraser.setValue(100)
slicing = sl[0:1, 1:5, 2:6, 3:7, 0:1]
inDataShape = slicing2shape(slicing)
inputData = (3 * numpy.random.random(inDataShape)).astype(numpy.uint8)
op.Input[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):
try:
import blist
except ImportError:
raise unittest.SkipTest
from lazyflow.operators.opSparseLabelArray import OpSparseLabelArray
graph = Graph()
op = OpSparseLabelArray(graph=graph)
arrayshape = numpy.array([1, 10, 10, 10, 1])
op.inputs["shape"].setValue(tuple(arrayshape))
op.eraser.setValue(100)
slicing = sl[0:1, 1:5, 2:6, 3:7, 0:1]
inDataShape = slicing2shape(slicing)
inputData = (3 * numpy.random.random(inDataShape)).astype(numpy.uint8)
op.Input[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):
try:
import blist
except ImportError:
raise unittest.SkipTest
from lazyflow.operators.opSparseLabelArray import OpSparseLabelArray
graph = Graph()
op = OpSparseLabelArray(graph=graph)
arrayshape = numpy.array([1,10,10,10,1])
op.inputs["shape"].setValue( tuple(arrayshape) )
op.eraser.setValue(100)
slicing = sl[0:1, 1:5, 2:6, 3:7, 0:1]
inDataShape = slicing2shape(slicing)
inputData = ( 3*numpy.random.random(inDataShape) ).astype(numpy.uint8)
op.Input[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 setInSlot(self, slot, subindex, roi, value):
key = roi.toSlice()
time1 = time.time()
start, stop = sliceToRoi(key, self._cacheShape)
blockStart = (1.0 * start / self._blockShape).floor()
blockStop = (1.0 * stop / self._blockShape).ceil()
blockStop = numpy.where(stop == self._cacheShape, self._dirtyShape,
blockStop)
blockKey = roiToSlice(blockStart, blockStop)
innerBlocks = self._blockNumbers[blockKey]
for b_ind in innerBlocks.ravel():
offset = self._blockShape * self._flatBlockIndices[b_ind]
bigstart = numpy.maximum(offset, start)
bigstop = numpy.minimum(offset + self._blockShape, stop)
smallstart = bigstart - offset
smallstop = bigstop - offset
bigkey = roiToSlice(bigstart - start, bigstop - start)
smallkey = roiToSlice(smallstart, smallstop)
smallvalues = value[tuple(bigkey)]
if (smallvalues != 0).any():
if not b_ind in self._labelers:
self._labelers[b_ind] = OpSparseLabelArray(self)
# Don't connect deletelabel; it is set manually (here and also above)
self._labelers[b_ind].inputs["deleteLabel"].setValue(
self.inputs["deleteLabel"].value)
self._labelers[b_ind].inputs["shape"].setValue(
tuple(self._blockShape))
self._labelers[b_ind].inputs["eraser"].setValue(
self.inputs["eraser"].value)
# remember old max labele, i.e. 0 since we just created
self._oldMaxLabels[b_ind] = 0
# add the 0 to the histogram
self._maxLabelHistogram[0] += 1
def max_label_changed(b_ind, slot, *args):
self.lock.acquire()
newmax = slot.value
# make sure histogram is large enough
if newmax > self._maxLabelHistogram.shape[0] - 1:
self._maxLabelHistogram.resize((newmax + 1, ))
# update histogram
oldmax = self._oldMaxLabels[b_ind]
self._maxLabelHistogram[oldmax] -= 1
self._maxLabelHistogram[newmax] += 1
self._oldMaxLabels[b_ind] = newmax
# check wether self._maxlabel needs to be updated (up and down)
maxdirty = False
if newmax > self._maxLabel:
assert self._maxLabelHistogram[newmax] == 1
self._maxLabel = newmax
elif self._maxLabelHistogram[oldmax] == 0:
self._maxLabel = numpy.max(
numpy.nonzero(self._maxLabelHistogram)[0])
self.lock.release()
self.maxLabel.setValue(self._maxLabel)
self._labelers[b_ind].inputs["maxLabel"].notifyDirty(
partial(max_label_changed, b_ind))
self._labelers[b_ind].inputs["Input"][smallkey] = smallvalues
time2 = time.time()
logger.debug("OpBlockedSparseLabelArray: setInSlot writing took %fs" %
(time2 - time1, ))
# Trade-off here:
# Instead of sending a separate dirty notification for each block we touched,
# we just send a single dirty notification for the entire encompassing roi.
# This results in fewer notifications, but more "dirty" pixels.
# Downstream operators will probably ask for updated values for all of the
# blocks we said were "dirty" even though some of them were not really touched.
self.Output.setDirty(key)
time3 = time.time()
logger.debug("OpBlockedSparseLabelArray: setInSlot setDirty took %fs" %
(time3 - time2, ))
logger.debug("OpBlockedSparseLabelArray: setInSlot total took %fs" %
(time3 - time1, ))