def testSetInSlot(self):
logger.info("Generating sample data...")
sampleData = numpy.indices((100, 200, 150), dtype=numpy.float32).sum(0)
sampleData = sampleData.view( vigra.VigraArray )
sampleData.axistags = vigra.defaultAxistags('xyz')
graph = Graph()
opData = OpArrayPiper( graph=graph )
opData.Input.setValue( sampleData )
op = OpCompressedCache( parent=None, graph=graph )
#logger.debug("Setting block shape...")
op.BlockShape.setValue( [100, 75, 50] )
op.Input.connect( opData.Output )
assert op.Output.ready()
slicing = numpy.s_[ 0:100, 0:75, 0:50 ]
expectedData = numpy.ones( slicing2shape(slicing), dtype=int )
# This is what we're testing.
#logger.debug("Forcing external data...")
op.Input[slicing] = expectedData
#logger.debug("Requesting data...")
readData = op.Output[slicing].wait()
#logger.debug("Checking data...")
assert (readData == expectedData).all(), "Incorrect output!"
def testDirtyPropagation(self):
g = Graph()
vol = np.asarray(
[[0, 0, 0, 0],
[0, 0, 1, 1],
[0, 1, 0, 1],
[0, 1, 0, 1]], dtype=np.uint8)
vol = vigra.taggedView(vol, axistags='xy').withAxes(*'xyz')
chunkShape = (2, 2, 1)
opCache = OpCompressedCache(graph=g)
opCache.Input.setValue(vol)
opCache.BlockShape.setValue(chunkShape)
op = OpLazyCC(graph=g)
op.Input.connect(opCache.Output)
op.ChunkShape.setValue(chunkShape)
out1 = op.Output[:2, :2].wait()
assert np.all(out1 == 0)
opCache.Input[0:1, 0:1, 0:1] = np.asarray([[[1]]], dtype=np.uint8)
out2 = op.Output[:1, :1].wait()
assert np.all(out2 > 0)
def setupOutputs(self):
self._disconnectInternals()
# we need a new cache
cache = OpCompressedCache(parent=self)
cache.name = self.name + "WrappedCache"
# connect cache outputs
self.CleanBlocks.connect(cache.CleanBlocks)
self.OutputHdf5.connect(cache.OutputHdf5)
self._op2.Input.connect(cache.Output)
# connect cache inputs
cache.InputHdf5.connect(self.InputHdf5)
cache.Input.connect(self._op1.Output)
# set the cache block shape
tagged_shape = self._op1.Output.meta.getTaggedShape()
tagged_shape['t'] = 1
tagged_shape['c'] = 1
cacheshape = map(lambda k: tagged_shape[k], 'xyzct')
if _labeling_impl == "lazy":
#HACK hardcoded block shape
blockshape = numpy.minimum(cacheshape, 256)
else:
# use full spatial volume if not lazy
blockshape = cacheshape
cache.BlockShape.setValue(tuple(blockshape))
self._cache = cache
def testHDF5(self):
logger.info("Generating sample data...")
sampleData = numpy.indices((150, 250, 150), dtype=numpy.float32).sum(0)
sampleData = sampleData.view( vigra.VigraArray )
sampleData.axistags = vigra.defaultAxistags('xyz')
graph = Graph()
opData = OpArrayPiper( graph=graph )
opData.Input.setValue( sampleData )
op = OpCompressedCache( parent=None, graph=graph )
#logger.debug("Setting block shape...")
op.BlockShape.setValue( [75, 125, 150] )
op.Input.connect( opData.Output )
assert op.OutputHdf5.ready()
slicing = numpy.s_[ 0:75, 125:250, 0:150 ]
slicing_str = str([list(_) for _ in zip(*[[_.start, _.stop] for _ in slicing])])
expectedData = sampleData[slicing].view(numpy.ndarray)
slicing_2 = numpy.s_[ 0:75, 0:125, 0:150 ]
expectedData_2 = expectedData[slicing_2].view(numpy.ndarray)
#logger.debug("Requesting data...")
tempdir = tempfile.mkdtemp()
try:
with h5py.File(os.path.join(tempdir, "data.h5"), "w") as h5_file:
op.OutputHdf5[slicing].writeInto(h5_file).wait()
assert slicing_str in h5_file, "Missing dataset!"
assert (h5_file[slicing_str][()] == expectedData).all(), "Incorrect output!"
with h5py.File(os.path.join(tempdir, "data.h5"), "r") as h5_file:
graph = Graph()
opData = OpArrayPiper( graph=graph )
opData.Input.meta.axistags = vigra.AxisTags('xyz')
opData.Input.setValue( numpy.empty_like(expectedData_2) )
op = OpCompressedCache( parent=None, graph=graph )
op.InputHdf5.meta.axistags = vigra.AxisTags('xyz')
op.InputHdf5.meta.shape = (75, 125, 150)
#logger.debug("Setting block shape...")
op.BlockShape.setValue( [75, 125, 150] )
op.Input.connect( opData.Output )
op.InputHdf5[slicing_2] = h5_file[slicing_str]
result = op.Output[slicing_2].wait()
assert (result == expectedData_2).all(), "Incorrect output!"
finally:
shutil.rmtree(tempdir)
def __init__(self, *args, **kwargs):
super( OpSplitBodySupervoxelExport, self ).__init__(*args, **kwargs)
# HACK: Be sure that the output slots are resized if the raveler body list changes
self.AnnotationBodyIds.notifyDirty( bind(self._setupOutputs) )
# Prepare a set of OpSelectLabels for easy access to raveler object masks
self._opSelectLabel = OperatorWrapper( OpSelectLabel, parent=self, broadcastingSlotNames=['Input'] )
self._opSelectLabel.Input.connect( self.RavelerLabels )
self.EditedRavelerBodies.connect( self._opSelectLabel.Output )
# Mask in the body of interest
self._opMaskedSelect = OperatorWrapper( OpMaskedSelectUint32, parent=self, broadcastingSlotNames=['Input'] )
self._opMaskedSelect.Input.connect( self.Supervoxels )
self._opMaskedSelect.Mask.connect( self._opSelectLabel.Output )
self.MaskedSupervoxels.connect( self._opMaskedSelect.Output )
# Must run CC before filter, to ensure that discontiguous labels can't avoid the filter.
self._opRelabelMaskedSupervoxels = OperatorWrapper( OpVigraLabelVolume, parent=self )
self._opRelabelMaskedSupervoxels.Input.connect( self._opMaskedSelect.Output )
self._opRelabeledMaskedSupervoxelCaches = OperatorWrapper( OpCompressedCache, parent=self )
self._opRelabeledMaskedSupervoxelCaches.Input.connect( self._opRelabelMaskedSupervoxels.Output )
# Filter out the small CC to eliminate tiny pieces of supervoxels that overlap the mask boundaries
self._opSmallLabelFilter = OperatorWrapper( OpFilterLabels, parent=self, broadcastingSlotNames=['MinLabelSize'] )
self._opSmallLabelFilter.MinLabelSize.setValue( 10 )
self._opSmallLabelFilter.Input.connect( self._opRelabeledMaskedSupervoxelCaches.Output )
self._opSmallLabelFilterCaches = OperatorWrapper( OpCompressedCache, parent=self )
self._opSmallLabelFilterCaches.Input.connect( self._opSmallLabelFilter.Output )
self.FilteredMaskedSupervoxels.connect( self._opSmallLabelFilterCaches.Output )
# Re-fill the holes left by the filter using region growing (with a mask)
self._opMaskedWatersheds = OperatorWrapper( OpMaskedWatershed, parent=self )
self._opMaskedWatersheds.Input.connect( self.InputData )
self._opMaskedWatersheds.Mask.connect( self._opSelectLabel.Output )
self._opMaskedWatersheds.Seeds.connect( self._opSmallLabelFilterCaches.Output )
# Cache is necessary because it ensures that the entire volume is used for watershed.
self._opMaskedWatershedCaches = OperatorWrapper( OpCompressedCache, parent=self )
self._opMaskedWatershedCaches.Input.connect( self._opMaskedWatersheds.Output )
self.HoleFilledSupervoxels.connect( self._opMaskedWatershedCaches.Output )
# Relabel the supervoxels in the mask to ensure contiguous supervoxels (after mask) and consecutive labels
self._opRelabelMergedSupervoxels = OperatorWrapper( OpVigraLabelVolume, parent=self )
self._opRelabelMergedSupervoxels.Input.connect( self._opMaskedWatershedCaches.Output )
self._opRelabeledMergedSupervoxelCaches = OperatorWrapper( OpCompressedCache, parent=self )
self._opRelabeledMergedSupervoxelCaches.Input.connect( self._opRelabelMergedSupervoxels.Output )
self.RelabeledSupervoxels.connect( self._opRelabeledMergedSupervoxelCaches.Output )
self._opAccumulateFinalImage = OpAccumulateFragmentSegmentations( parent=self )
self._opAccumulateFinalImage.RavelerLabels.connect( self.RavelerLabels )
self._opAccumulateFinalImage.FragmentSegmentations.connect( self._opRelabeledMergedSupervoxelCaches.Output )
self._opFinalCache = OpCompressedCache( parent=self )
self._opFinalCache.Input.connect( self._opAccumulateFinalImage.Output )
self.FinalSupervoxels.connect( self._opFinalCache.Output )
self.SupervoxelMapping.connect( self._opAccumulateFinalImage.Mapping )
def testBasic4d_txyc_masked(self):
logger.info("Generating sample data...")
sampleData = numpy.indices((3, 200, 150, 2),
dtype=numpy.float32).sum(0)
sampleData = sampleData.view(numpy.ma.masked_array)
sampleData.set_fill_value(numpy.float32(numpy.nan))
sampleData[0] = numpy.ma.masked
graph = Graph()
opData = OpArrayPiper(graph=graph)
opData.Input.meta.has_mask = True
opData.Input.meta.axistags = vigra.defaultAxistags("txyc")
opData.Input.setValue(sampleData)
op = OpCompressedCache(parent=None, graph=graph)
# logger.debug("Setting block shape...")
op.BlockShape.setValue([1, 75, 50, 2])
op.Input.connect(opData.Output)
assert op.Output.ready()
slicing = numpy.s_[1:3, 50:150, 75:150, 0:1]
expectedData = sampleData[slicing]
# logger.debug("Requesting data...")
readData = op.Output[slicing].wait()
# logger.debug("Checking data...")
assert ((readData == expectedData).all()
and (readData.mask == expectedData.mask).all()
and ((readData.fill_value == expectedData.fill_value)
| (numpy.isnan(readData.fill_value) & numpy.isnan(
expectedData.fill_value))).all()), "Incorrect output!"
def testBasic4d_txyc(self):
logger.info("Generating sample data...")
sampleData = numpy.indices((3, 200, 150, 2),
dtype=numpy.float32).sum(0)
sampleData = sampleData.view(vigra.VigraArray)
sampleData.axistags = vigra.defaultAxistags("txyc")
graph = Graph()
opData = OpArrayPiper(graph=graph)
opData.Input.setValue(sampleData)
op = OpCompressedCache(parent=None, graph=graph)
# logger.debug("Setting block shape...")
op.BlockShape.setValue([1, 75, 50, 2])
op.Input.connect(opData.Output)
assert op.Output.ready()
slicing = numpy.s_[1:3, 50:150, 75:150, 0:1]
expectedData = sampleData[slicing].view(numpy.ndarray)
# logger.debug("Requesting data...")
readData = op.Output[slicing].wait()
# logger.debug("Checking data...")
assert (readData == expectedData).all(), "Incorrect output!"
def testLazyness(self):
g = Graph()
vol = np.asarray(
[[0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 1, 0, 0, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0]],
dtype=np.uint8)
vol = vigra.taggedView(vol, axistags='xy').withAxes(*'xyz')
chunkShape = (3, 3, 1)
opCount = OpExecuteCounter(graph=g)
opCount.Input.setValue(vol)
opCache = OpCompressedCache(graph=g)
opCache.Input.connect(opCount.Output)
opCache.BlockShape.setValue(chunkShape)
op = OpLazyCC(graph=g)
op.Input.connect(opCache.Output)
op.ChunkShape.setValue(chunkShape)
out = op.Output[:3, :3].wait()
n = 3
assert opCount.numCalls <= n,\
"Executed {} times (allowed: {})".format(opCount.numCalls,
n)
def __init__(self, *args, **kwargs):
super(_OpCachedLabelImage, self).__init__(*args, **kwargs)
# Hook up the labeler
self._opLabelImage = OpLabelImage(parent=self)
self._opLabelImage.Input.connect(self.Input)
self._opLabelImage.BackgroundLabels.connect(self.BackgroundLabels)
# Hook up the cache
self._opCache = OpCompressedCache(parent=self)
self._opCache.Input.connect(self._opLabelImage.Output)
self._opCache.InputHdf5.connect(self.InputHdf5)
# Hook up our output slots
self.Output.connect(self._opCache.Output)
self.CleanBlocks.connect(self._opCache.CleanBlocks)
self.OutputHdf5.connect(self._opCache.OutputHdf5)
def __init__(self, *args, **kwargs):
super(OpLabelingABC, self).__init__(*args, **kwargs)
self._cache = OpCompressedCache(parent=self)
self._cache.name = "OpLabelVolume.OutputCache"
self._cache.Input.connect(self.Output)
self.CachedOutput.connect(self._cache.Output)
self._cache.InputHdf5.connect(self.InputHdf5)
self.OutputHdf5.connect(self._cache.OutputHdf5)
self.CleanBlocks.connect(self._cache.CleanBlocks)
def __init__(self, *args, **kwargs):
warn_deprecated(
"OpCachedLabelImage is deprecated, use OpLabelVolume instead")
super(OpCachedLabelImage, self).__init__(*args, **kwargs)
# Hook up the labeler
self._opLabelImage = OpLabelImage(parent=self)
self._opLabelImage.Input.connect(self.Input)
self._opLabelImage.BackgroundLabels.connect(self.BackgroundLabels)
# Hook up the cache
self._opCache = OpCompressedCache(parent=self)
self._opCache.Input.connect(self._opLabelImage.Output)
self._opCache.InputHdf5.connect(self.InputHdf5)
# Hook up our output slots
self.Output.connect(self._opCache.Output)
self.CleanBlocks.connect(self._opCache.CleanBlocks)
self.OutputHdf5.connect(self._opCache.OutputHdf5)
def testReasonableCompression(self):
# compression should be *way* better than this
expected_factor = 4.0
graph = Graph()
sampleData = numpy.zeros((10000, 1000), dtype=numpy.uint8)
sampleData = vigra.taggedView(sampleData, axistags="xy")
opData = OpArrayPiper(graph=graph)
opData.Input.setValue(sampleData)
op = OpCompressedCache(parent=None, graph=graph)
op.Input.connect(opData.Output)
assert op.Output.ready()
assert op.usedMemory() == 0.0, "cache must not be filled at this point"
op.Output[...].wait()
assert op.usedMemory() <= (
sampleData.nbytes / expected_factor
), "Compression of all-zeroes should be better than factor " "{}".format(expected_factor)
def testIdealBlockShapeChoice(self):
sampleData = numpy.indices((150, 250, 350), dtype=numpy.float32).sum(0)
sampleData = vigra.taggedView(sampleData, axistags='xyz')
graph = Graph()
opData = OpArrayPiper(graph=graph)
# 1) input has valid ideal_blockshape, no block shape given
print("1)")
ideal = (33, 33, 33)
opData.Input.meta.ideal_blockshape = ideal
opData.Input.setValue(sampleData)
op = OpCompressedCache(graph=graph)
op.Input.connect(opData.Output)
assert op.Output.ready()
assert_array_equal(op.Output.meta.ideal_blockshape, op._blockshape)
# 2) input has invalid ideal_blockshape
print("2)")
ideal = (33, 33)
opData.Input.meta.ideal_blockshape = ideal
opData.Input.setValue(None)
opData.Input.setValue(sampleData)
op = OpCompressedCache(graph=graph)
op.Input.connect(opData.Output)
assert op.Output.ready()
assert len(op.Output.meta.ideal_blockshape) == 3
# 3) input has valid ideal_blockshape, but BlockShape is incompatible
print("3)")
ideal = (33, 33, 33)
blockShape = (50, 50, 50)
opData.Input.meta.ideal_blockshape = ideal
opData.Input.setValue(None)
opData.Input.setValue(sampleData)
op = OpCompressedCache(graph=graph)
op.Input.connect(opData.Output)
op.BlockShape.setValue(blockShape)
assert op.Output.ready()
assert_array_equal(op.Output.meta.ideal_blockshape, blockShape)
def testReasonableCompression(self):
# compression should be *way* better than this
expected_factor = 4.0
graph = Graph()
sampleData = numpy.zeros((10000, 1000), dtype=numpy.uint8)
sampleData = vigra.taggedView(sampleData, axistags='xy')
opData = OpArrayPiper(graph=graph)
opData.Input.setValue(sampleData)
op = OpCompressedCache(parent=None, graph=graph)
op.Input.connect(opData.Output)
assert op.Output.ready()
assert op.usedMemory() == 0.0,\
"cache must not be filled at this point"
op.Output[...].wait()
assert op.usedMemory() <= (sampleData.nbytes /expected_factor),\
"Compression of all-zeroes should be better than factor "\
"{}".format(expected_factor)
def mkH5source(fname, gname):
h5file = h5py.File(fname)
source = OpStreamingHdf5Reader(graph=graph)
source.Hdf5File.setValue(h5file)
source.InternalPath.setValue(gname)
op = OpCompressedCache(parent=None, graph=graph)
op.BlockShape.setValue([100, 100, 100])
op.Input.connect(source.OutputImage)
return op.Output
def testSetInSlot_masked(self):
logger.info("Generating sample data...")
sampleData = numpy.indices((100, 200, 150), dtype=numpy.float32).sum(0)
sampleData = sampleData.view(numpy.ma.masked_array)
sampleData.set_fill_value(numpy.float32(numpy.nan))
sampleData[0] = numpy.ma.masked
graph = Graph()
opData = OpArrayPiper(graph=graph)
opData.Input.meta.has_mask = True
opData.Input.meta.axistags = vigra.defaultAxistags("xyz")
opData.Input.setValue(sampleData)
op = OpCompressedCache(parent=None, graph=graph)
# logger.debug("Setting block shape...")
op.BlockShape.setValue([100, 75, 50])
op.Input.connect(opData.Output)
assert op.Output.ready()
slicing = numpy.s_[0:100, 0:75, 0:50]
expectedData = numpy.ma.ones(slicing2shape(slicing), dtype=int)
sampleData.set_fill_value(numpy.float32(numpy.nan))
expectedData[0] = numpy.ma.masked
# This is what we're testing.
# logger.debug("Forcing external data...")
op.Input[slicing] = expectedData
# logger.debug("Requesting data...")
readData = op.Output[slicing].wait()
# logger.debug("Checking data...")
assert (
(readData == expectedData).all()
and (readData.mask == expectedData.mask).all()
and (
(readData.fill_value == expectedData.fill_value)
| (numpy.isnan(readData.fill_value) & numpy.isnan(expectedData.fill_value))
).all()
), "Incorrect output!"
def testChangeBlockshape_masked(self):
logger.info("Generating sample data...")
sampleData = numpy.indices((100, 200, 150), dtype=numpy.float32).sum(0)
sampleData = sampleData.view(numpy.ma.masked_array)
sampleData.set_fill_value(numpy.float32(numpy.nan))
sampleData[0] = numpy.ma.masked
graph = Graph()
opData = OpArrayPiper(graph=graph)
opData.Input.meta.has_mask = True
opData.Input.meta.axistags = vigra.defaultAxistags('xyz')
opData.Input.setValue(sampleData)
op = OpCompressedCache(parent=None, graph=graph)
#logger.debug("Setting block shape...")
op.BlockShape.setValue([100, 75, 50])
op.Input.connect(opData.Output)
assert op.Output.ready()
slicing = numpy.s_[0:100, 50:150, 75:150]
expectedData = sampleData[slicing]
#logger.debug("Requesting data...")
readData = op.Output[slicing].wait()
#logger.debug("Checking data...")
assert (readData == expectedData).all() and \
(readData.mask == expectedData.mask).all() and \
((readData.fill_value == expectedData.fill_value) |
(numpy.isnan(readData.fill_value) & numpy.isnan(expectedData.fill_value))).all(),\
"Incorrect output!"
# Now change the blockshape and the input and try again...
sampleDataWithChannel = sampleData[..., None]
opData.Input.meta.axistags = vigra.defaultAxistags('xyzc')
opData.Input.setValue(sampleDataWithChannel)
op.BlockShape.setValue([45, 33, 40, 1])
assert op.Output.ready()
slicing = numpy.s_[60:70, 50:110, 60:120, 0:1]
expectedData = sampleDataWithChannel[slicing]
#logger.debug("Requesting data...")
readData = op.Output[slicing].wait()
#logger.debug("Checking data...")
assert (readData == expectedData).all() and \
(readData.mask == expectedData.mask).all() and \
((readData.fill_value == expectedData.fill_value) |
(numpy.isnan(readData.fill_value) & numpy.isnan(expectedData.fill_value))).all(),\
"Incorrect output!"
def __init__(self, *args, **kwargs):
super(OpIpht, self).__init__(*args, **kwargs)
self._opIpht = OpIphtNoCache(parent=self)
self._opIpht.InputImage.connect(self.InputImage)
self._opIpht.MinSize.connect(self.MinSize)
self._opIpht.MaxSize.connect(self.MaxSize)
self._opIpht.HighThreshold.connect(self.HighThreshold)
self._opIpht.LowThreshold.connect(self.LowThreshold)
self.Output.connect(self._opIpht.Output)
self._opCache = OpCompressedCache(parent=self)
self._opCache.Input.connect(self._opIpht.Output)
self.CachedOutput.connect(self._opCache.Output)
def testDirtyPropagation(self):
g = Graph()
vol = np.asarray([[0, 0, 0, 0], [0, 0, 1, 1], [0, 1, 0, 1], [0, 1, 0, 1]], dtype=np.uint8)
vol = vigra.taggedView(vol, axistags="yx").withAxes(*"zyx")
chunkShape = (1, 2, 2)
opCache = OpCompressedCache(graph=g)
opCache.Input.setValue(vol)
opCache.BlockShape.setValue(chunkShape)
op = OpLazyCC(graph=g)
op.Input.connect(opCache.Output)
op.ChunkShape.setValue(chunkShape)
out1 = op.Output[:, :2, :2].wait()
assert np.all(out1 == 0)
opCache.Input[0:1, 0:1, 0:1] = np.asarray([[[1]]], dtype=np.uint8)
out2 = op.Output[:, :1, :1].wait()
assert np.all(out2 > 0)
def testSetInSlot_masked(self):
logger.info("Generating sample data...")
sampleData = numpy.indices((100, 200, 150), dtype=numpy.float32).sum(0)
sampleData = sampleData.view(numpy.ma.masked_array)
sampleData.set_fill_value(numpy.float32(numpy.nan))
sampleData[0] = numpy.ma.masked
graph = Graph()
opData = OpArrayPiper(graph=graph)
opData.Input.meta.has_mask = True
opData.Input.meta.axistags = vigra.defaultAxistags('xyz')
opData.Input.setValue(sampleData)
op = OpCompressedCache(parent=None, graph=graph)
#logger.debug("Setting block shape...")
op.BlockShape.setValue([100, 75, 50])
op.Input.connect(opData.Output)
assert op.Output.ready()
slicing = numpy.s_[0:100, 0:75, 0:50]
expectedData = numpy.ma.ones(slicing2shape(slicing), dtype=int)
sampleData.set_fill_value(numpy.float32(numpy.nan))
expectedData[0] = numpy.ma.masked
# This is what we're testing.
#logger.debug("Forcing external data...")
op.Input[slicing] = expectedData
#logger.debug("Requesting data...")
readData = op.Output[slicing].wait()
#logger.debug("Checking data...")
assert (readData == expectedData).all() and \
(readData.mask == expectedData.mask).all() and \
((readData.fill_value == expectedData.fill_value) |
(numpy.isnan(readData.fill_value) & numpy.isnan(expectedData.fill_value))).all(),\
"Incorrect output!"
def testMultiThread_masked(self):
logger.info("Generating sample data...")
sampleData = numpy.indices((3, 100, 200, 150, 2),
dtype=numpy.float32).sum(0)
sampleData = sampleData.view(numpy.ma.masked_array)
sampleData.set_fill_value(numpy.float32(numpy.nan))
sampleData[0] = numpy.ma.masked
graph = Graph()
opData = OpArrayPiper(graph=graph)
opData.Input.meta.has_mask = True
opData.Input.meta.axistags = vigra.defaultAxistags("txyzc")
opData.Input.setValue(sampleData)
op = OpCompressedCache(parent=None, graph=graph)
# logger.debug("Setting block shape...")
op.BlockShape.setValue([1, 100, 75, 50, 2])
op.Input.connect(opData.Output)
assert op.Output.ready()
slicing = numpy.s_[0:2, 0:100, 50:150, 75:150, 0:1]
expectedData = sampleData[slicing]
results = {}
def readData(resultIndex):
results[resultIndex] = op.Output[slicing].wait()
threads = []
for i in range(10):
threads.append(
threading.Thread(target=functools.partial(readData, i)))
for th in threads:
th.start()
for th in threads:
th.join()
assert len(results) == len(threads), "Didn't get all results."
# logger.debug("Checking data...")
for i, data in list(results.items()):
assert ((data == expectedData).all()
and (data.mask == expectedData.mask).all()
and ((data.fill_value == expectedData.fill_value)
| (numpy.isnan(data.fill_value)
& numpy.isnan(expectedData.fill_value))).all()
), "Incorrect output for index {}".format(i)
def setupOutputs(self):
self._disconnectInternals()
# we need a new cache
cache = OpCompressedCache(parent=self)
cache.name = self.name + "WrappedCache"
# connect cache outputs
self.CleanBlocks.connect(cache.CleanBlocks)
self.OutputHdf5.connect(cache.OutputHdf5)
self._op2.Input.connect(cache.Output)
# connect cache inputs
cache.InputHdf5.connect(self.InputHdf5)
cache.Input.connect(self._op1.Output)
# set the cache block shape
tagged_shape = self._op1.Output.meta.getTaggedShape()
tagged_shape['t'] = 1
tagged_shape['c'] = 1
blockshape = map(lambda k: tagged_shape[k], 'xyzct')
cache.BlockShape.setValue(tuple(blockshape))
self._cache = cache
def __init__(self, *args, **kwargs):
super(OpObjectExtraction, self).__init__(*args, **kwargs)
# internal operators
#TODO BinaryImage is not binary in some workflows, could be made more
# efficient
self._opLabelVolume = OpLabelVolume(parent=self)
self._opLabelVolume.name = "OpObjectExtraction._opLabelVolume"
self._opRegFeats = OpCachedRegionFeatures(parent=self)
self._opRegFeatsAdaptOutput = OpAdaptTimeListRoi(parent=self)
self._opObjectCenterImage = OpObjectCenterImage(parent=self)
# connect internal operators
self._opLabelVolume.Input.connect(self.BinaryImage)
self._opLabelVolume.InputHdf5.connect(self.LabelInputHdf5)
self._opLabelVolume.Background.connect(self.BackgroundLabels)
self._opRegFeats.RawImage.connect(self.RawImage)
self._opRegFeats.LabelImage.connect(self._opLabelVolume.CachedOutput)
self._opRegFeats.Features.connect(self.Features)
self.RegionFeaturesCleanBlocks.connect(self._opRegFeats.CleanBlocks)
self._opRegFeats.CacheInput.connect(self.RegionFeaturesCacheInput)
self._opRegFeatsAdaptOutput.Input.connect(self._opRegFeats.Output)
self._opObjectCenterImage.BinaryImage.connect(self.BinaryImage)
self._opObjectCenterImage.RegionCenters.connect(
self._opRegFeatsAdaptOutput.Output)
self._opCenterCache = OpCompressedCache(parent=self)
self._opCenterCache.name = "OpObjectExtraction._opCenterCache"
self._opCenterCache.Input.connect(self._opObjectCenterImage.Output)
# connect outputs
self.LabelImage.connect(self._opLabelVolume.CachedOutput)
self.ObjectCenterImage.connect(self._opCenterCache.Output)
self.RegionFeatures.connect(self._opRegFeatsAdaptOutput.Output)
self.BlockwiseRegionFeatures.connect(self._opRegFeats.Output)
self.LabelOutputHdf5.connect(self._opLabelVolume.OutputHdf5)
self.CleanLabelBlocks.connect(self._opLabelVolume.CleanBlocks)
self.ComputedFeatureNames.connect(self.Features)
# As soon as input data is available, check its constraints
self.RawImage.notifyReady(self._checkConstraints)
self.BinaryImage.notifyReady(self._checkConstraints)
def __init__(self, *args, **kwargs):
super(_OpCachedLabelImage, self).__init__(*args, **kwargs)
# Hook up the labeler
self._opLabelImage = OpLabelImage( parent=self )
self._opLabelImage.Input.connect( self.Input )
self._opLabelImage.BackgroundLabels.connect( self.BackgroundLabels )
# Hook up the cache
self._opCache = OpCompressedCache( parent=self )
self._opCache.Input.connect( self._opLabelImage.Output )
self._opCache.InputHdf5.connect( self.InputHdf5 )
# Hook up our output slots
self.Output.connect( self._opCache.Output )
self.CleanBlocks.connect( self._opCache.CleanBlocks )
self.OutputHdf5.connect( self._opCache.OutputHdf5 )
def testCleanup(self):
sampleData = numpy.indices((100, 200, 150), dtype=numpy.float32).sum(0)
sampleData = vigra.taggedView(sampleData, axistags='xyz')
graph = Graph()
opData = OpArrayPiper(graph=graph)
opData.Input.setValue(sampleData)
op = OpCompressedCache(graph=graph)
#logger.debug("Setting block shape...")
op.BlockShape.setValue([100, 75, 50])
op.Input.connect(opData.Output)
x = op.Output[...].wait()
op.Input.disconnect()
r = weakref.ref(op)
del op
gc.collect()
assert r() is None, "OpBlockedArrayCache was not cleaned up correctly"
def __init__(self, *args, **kwargs):
warn_deprecated("OpCachedLabelImage is deprecated, use OpLabelVolume instead")
super(OpCachedLabelImage, self).__init__(*args, **kwargs)
# Hook up the labeler
self._opLabelImage = OpLabelImage( parent=self )
self._opLabelImage.Input.connect( self.Input )
self._opLabelImage.BackgroundLabels.connect( self.BackgroundLabels )
# Hook up the cache
self._opCache = OpCompressedCache( parent=self )
self._opCache.Input.connect( self._opLabelImage.Output )
self._opCache.InputHdf5.connect( self.InputHdf5 )
# Hook up our output slots
self.Output.connect( self._opCache.Output )
self.CleanBlocks.connect( self._opCache.CleanBlocks )
self.OutputHdf5.connect( self._opCache.OutputHdf5 )
def testReconnectWithoutRequest(self):
vol = numpy.zeros((200, 100, 50), dtype=numpy.float32)
vol1 = vigra.taggedView(vol, axistags='xyz')
vol2 = vigra.taggedView(vol, axistags='zyx').withAxes(*'xyz')
graph = Graph()
opData1 = OpArrayPiper(graph=graph)
opData1.Input.setValue(vol1)
op = OpCompressedCache(graph=graph)
op.Input.connect(opData1.Output)
op.BlockShape.setValue((200, 100, 10))
out = op.Output[...].wait()
op.BlockShape.setValue((50, 100, 10))
# Older versions of OpCompressedCache threw an exception here because
# we tried to access the cache after changing the blockshape.
# But in the current version, we claim that's okay.
out = op.Output[...].wait()
def testChangeBlockshape(self):
logger.info("Generating sample data...")
sampleData = numpy.indices((100, 200, 150), dtype=numpy.float32).sum(0)
sampleData = sampleData.view(vigra.VigraArray)
sampleData.axistags = vigra.defaultAxistags('xyz')
graph = Graph()
opData = OpArrayPiper(graph=graph)
opData.Input.setValue(sampleData)
op = OpCompressedCache(parent=None, graph=graph)
#logger.debug("Setting block shape...")
op.BlockShape.setValue([100, 75, 50])
op.Input.connect(opData.Output)
assert op.Output.ready()
slicing = numpy.s_[0:100, 50:150, 75:150]
expectedData = sampleData[slicing].view(numpy.ndarray)
#logger.debug("Requesting data...")
readData = op.Output[slicing].wait()
#logger.debug("Checking data...")
assert (readData == expectedData).all(), "Incorrect output!"
# Now change the blockshape and the input and try again...
sampleDataWithChannel = sampleData.withAxes(*'xyzc')
opData.Input.setValue(sampleDataWithChannel)
op.BlockShape.setValue([45, 33, 40, 1])
assert op.Output.ready()
slicing = numpy.s_[60:70, 50:110, 60:120, 0:1]
expectedData = sampleDataWithChannel[slicing].view(numpy.ndarray)
#logger.debug("Requesting data...")
readData = op.Output[slicing].wait()
#logger.debug("Checking data...")
assert (readData == expectedData).all(), "Incorrect output!"
def testFree(self):
sampleData = numpy.indices((100, 200, 150), dtype=numpy.float32).sum(0)
sampleData = vigra.taggedView(sampleData, axistags='xyz')
graph = Graph()
opData = OpArrayPiperWithAccessCount(graph=graph)
opData.Input.setValue(sampleData)
op = OpCompressedCache(graph=graph)
#logger.debug("Setting block shape...")
op.BlockShape.setValue([100, 75, 50])
op.Input.connect(opData.Output)
op.Output[...].wait()
mem = op.usedMemory()
keys = [x[0] for x in op.getBlockAccessTimes()]
key = keys[0]
op.freeBlock(key)
assert op.usedMemory() < mem
def testReportGeneration(self):
graph = Graph()
sampleData = numpy.random.randint(0, 256, size=(50, 50, 50))
sampleData = sampleData.astype(numpy.uint8)
sampleData = vigra.taggedView(sampleData, axistags='xyz')
opData = OpArrayPiper(graph=graph)
opData.Input.setValue(sampleData)
op = OpCompressedCache(parent=None, graph=graph)
op.BlockShape.setValue((25, 25, 25))
op.Input.connect(opData.Output)
before = time.time()
assert op.Output.ready()
assert op.usedMemory() == 0.0,\
"cache must not be filled at this point"
op.Output[...].wait()
assert op.usedMemory() > 0.0,\
"cache must contain data at this point"
after = time.time()
r = MemInfoNode()
op.generateReport(r)
# not sure how good this can be compressed, but the cache
# should hold memory by now
assert r.usedMemory > 0
# check sanity of last access time
assert r.lastAccessTime >= before, str(r.lastAccessTime)
assert r.lastAccessTime <= after, str(r.lastAccessTime)
assert r.fractionOfUsedMemoryDirty == 0.0
opData.Input.setDirty((slice(0, 25), slice(0, 25), slice(0, 25)))
assert op.fractionOfUsedMemoryDirty() < 1.0
assert op.fractionOfUsedMemoryDirty() > 0
opData.Input.setDirty(slice(None))
assert op.fractionOfUsedMemoryDirty() == 1.0
def testReportGeneration(self):
graph = Graph()
sampleData = numpy.random.randint(0, 256, size=(50, 50, 50))
sampleData = sampleData.astype(numpy.uint8)
sampleData = vigra.taggedView(sampleData, axistags='xyz')
opData = OpArrayPiper(graph=graph)
opData.Input.setValue(sampleData)
op = OpCompressedCache(parent=None, graph=graph)
op.BlockShape.setValue((25, 25, 25))
op.Input.connect(opData.Output)
before = time.time()
assert op.Output.ready()
assert op.usedMemory() == 0.0,\
"cache must not be filled at this point"
op.Output[...].wait()
assert op.usedMemory() > 0.0,\
"cache must contain data at this point"
after = time.time()
r = MemInfoNode()
op.generateReport(r)
# not sure how good this can be compressed, but the cache
# should hold memory by now
assert r.usedMemory > 0
# check sanity of last access time
assert r.lastAccessTime >= before, str(r.lastAccessTime)
assert r.lastAccessTime <= after, str(r.lastAccessTime)
assert r.fractionOfUsedMemoryDirty == 0.0
opData.Input.setDirty(
(slice(0, 25), slice(0, 25), slice(0, 25)))
assert op.fractionOfUsedMemoryDirty() < 1.0
assert op.fractionOfUsedMemoryDirty() > 0
opData.Input.setDirty(slice(None))
assert op.fractionOfUsedMemoryDirty() == 1.0
def testReconnectWithoutRequest_masked(self):
vol = numpy.ma.zeros((200, 100, 50), dtype=numpy.float32)
vol.set_fill_value(numpy.float32(numpy.nan))
vol[0] = numpy.ma.masked
vol1 = vol
vol2 = vol1.T
graph = Graph()
opData1 = OpArrayPiper(graph=graph)
opData1.Input.meta.has_mask = True
opData1.Input.meta.axistags = vigra.defaultAxistags('xyz')
opData1.Input.setValue(vol1)
op = OpCompressedCache(graph=graph)
op.Input.connect(opData1.Output)
op.BlockShape.setValue((200, 100, 10))
out = op.Output[...].wait()
assert (out == vol).all() and \
(out.mask == vol.mask).all() and \
((out.fill_value == vol.fill_value) |
(numpy.isnan(out.fill_value) & numpy.isnan(vol.fill_value))).all(),\
"Incorrect output!"
op.BlockShape.setValue((50, 100, 10))
# Older versions of OpCompressedCache threw an exception here because
# we tried to access the cache after changing the blockshape.
# But in the current version, we claim that's okay.
out = op.Output[...].wait()
assert (out == vol).all() and \
(out.mask == vol.mask).all() and \
((out.fill_value == vol.fill_value) |
(numpy.isnan(out.fill_value) & numpy.isnan(vol.fill_value))).all(),\
"Incorrect output!"
def testFree(self):
sampleData = numpy.indices((100, 200, 150), dtype=numpy.float32).sum(0)
sampleData = vigra.taggedView(sampleData, axistags='xyz')
graph = Graph()
opData = OpArrayPiperWithAccessCount(graph=graph)
opData.Input.setValue(sampleData)
op = OpCompressedCache(graph=graph)
#logger.debug("Setting block shape...")
op.BlockShape.setValue([100, 75, 50])
op.Input.connect(opData.Output)
op.Output[...].wait()
mem = op.usedMemory()
keys = map(lambda x: x[0], op.getBlockAccessTimes())
key = keys[0]
op.freeBlock(key)
assert op.usedMemory() < mem
def __init__(self, *args, **kwargs):
super(_OpThresholdTwoLevels, self).__init__(*args, **kwargs)
self._opLowThresholder = OpPixelOperator(parent=self)
self._opLowThresholder.Input.connect(self.InputImage)
self._opHighThresholder = OpPixelOperator(parent=self)
self._opHighThresholder.Input.connect(self.InputImage)
self._opLowLabeler = OpLabelVolume(parent=self)
self._opLowLabeler.Method.setValue(_labeling_impl)
self._opLowLabeler.Input.connect(self._opLowThresholder.Output)
self._opHighLabeler = OpLabelVolume(parent=self)
self._opHighLabeler.Method.setValue(_labeling_impl)
self._opHighLabeler.Input.connect(self._opHighThresholder.Output)
self._opHighLabelSizeFilter = OpFilterLabels(parent=self)
self._opHighLabelSizeFilter.Input.connect(self._opHighLabeler.Output)
self._opHighLabelSizeFilter.MinLabelSize.connect(self.MinSize)
self._opHighLabelSizeFilter.MaxLabelSize.connect(self.MaxSize)
self._opHighLabelSizeFilter.BinaryOut.setValue(
False) # we do the binarization in opSelectLabels
# this way, we get to display pretty colors
self._opSelectLabels = OpSelectLabels(parent=self)
self._opSelectLabels.BigLabels.connect(self._opLowLabeler.Output)
self._opSelectLabels.SmallLabels.connect(
self._opHighLabelSizeFilter.Output)
# remove the remaining very large objects -
# they might still be present in case a big object
# was split into many small ones for the higher threshold
# and they got reconnected again at lower threshold
self._opFinalLabelSizeFilter = OpFilterLabels(parent=self)
self._opFinalLabelSizeFilter.Input.connect(self._opSelectLabels.Output)
self._opFinalLabelSizeFilter.MinLabelSize.connect(self.MinSize)
self._opFinalLabelSizeFilter.MaxLabelSize.connect(self.MaxSize)
self._opFinalLabelSizeFilter.BinaryOut.setValue(False)
self._opCache = OpCompressedCache(parent=self)
self._opCache.name = "_OpThresholdTwoLevels._opCache"
self._opCache.InputHdf5.connect(self.InputHdf5)
self._opCache.Input.connect(self._opFinalLabelSizeFilter.Output)
# Connect our own outputs
self.Output.connect(self._opFinalLabelSizeFilter.Output)
self.CachedOutput.connect(self._opCache.Output)
# Serialization outputs
self.CleanBlocks.connect(self._opCache.CleanBlocks)
self.OutputHdf5.connect(self._opCache.OutputHdf5)
#self.InputChannel.connect( self._opChannelSelector.Output )
# More debug outputs. These all go through their own caches
self._opBigRegionCache = OpCompressedCache(parent=self)
self._opBigRegionCache.name = "_OpThresholdTwoLevels._opBigRegionCache"
self._opBigRegionCache.Input.connect(self._opLowThresholder.Output)
self.BigRegions.connect(self._opBigRegionCache.Output)
self._opSmallRegionCache = OpCompressedCache(parent=self)
self._opSmallRegionCache.name = "_OpThresholdTwoLevels._opSmallRegionCache"
self._opSmallRegionCache.Input.connect(self._opHighThresholder.Output)
self.SmallRegions.connect(self._opSmallRegionCache.Output)
self._opFilteredSmallLabelsCache = OpCompressedCache(parent=self)
self._opFilteredSmallLabelsCache.name = "_OpThresholdTwoLevels._opFilteredSmallLabelsCache"
self._opFilteredSmallLabelsCache.Input.connect(
self._opHighLabelSizeFilter.Output)
self._opColorizeSmallLabels = OpColorizeLabels(parent=self)
self._opColorizeSmallLabels.Input.connect(
self._opFilteredSmallLabelsCache.Output)
self.FilteredSmallLabels.connect(self._opColorizeSmallLabels.Output)
def __init__(self, *args, **kwargs):
super( OpSplitBodyPostprocessing, self ).__init__(*args, **kwargs)
# HACK: Be sure that the output slots are resized if the raveler body list changes
self.EditedRavelerBodyList.notifyDirty( bind(self._setupOutputs) )
# Prepare a set of OpSelectLabels for easy access to raveler object masks
self._opSelectLabel = OperatorWrapper( OpSelectLabel, parent=self, broadcastingSlotNames=['Input'] )
self._opSelectLabel.Input.connect( self.RavelerLabels )
self.EditedRavelerBodies.connect( self._opSelectLabel.Output )
# Prepare a set of OpFragmentSetLuts to compute the lut of each body's fragments
self._opFragmentSetLuts = OperatorWrapper( OpFragmentSetLut, parent=self,
broadcastingSlotNames=['MST', 'CurrentEditingFragment', 'Trigger'] )
self._opFragmentSetLuts.MST.connect( self.MST )
self._opFragmentSetLuts.CurrentEditingFragment.setValue("")
# Prepare a set of Fragment image generators
self._opFragments = OperatorWrapper( OpFragment, parent=self, broadcastingSlotNames=['MST'] )
self._opFragments.BodyMask.connect( self._opSelectLabel.Output )
self._opFragments.FragmentLut.connect( self._opFragmentSetLuts.Lut )
self._opFragments.MST.connect( self.MST )
# Cache the fragment segmentations for each body
self._opFragmentCaches = OperatorWrapper( OpCompressedCache, parent=self )
self._opFragmentCaches.Input.connect( self._opFragments.Output )
self.FragmentedBodies.connect( self._opFragmentCaches.Output )
# CC is performed on the cached output, in part to ensure that the entire block is used.
self._opRelabelFragments = OperatorWrapper( OpVigraLabelVolume, parent=self )
self._opRelabelFragments.Input.connect( self._opFragmentCaches.Output )
self._opRelabeledFragmentCaches = OperatorWrapper( OpCompressedCache, parent=self )
self._opRelabeledFragmentCaches.Input.connect( self._opRelabelFragments.Output )
self.RelabeledFragments.connect( self._opRelabeledFragmentCaches.Output )
# Filter the small CC objects from the (relabeled) fragment segmentations
self._opSmallFragmentFilter = OperatorWrapper( OpFilterLabels, parent=self, broadcastingSlotNames=['MinLabelSize'] )
self._opSmallFragmentFilter.MinLabelSize.setValue( 50 )
self._opSmallFragmentFilter.Input.connect( self._opRelabeledFragmentCaches.Output )
self._opFilteredFragmentCaches = OperatorWrapper( OpCompressedCache, parent=self )
self._opFilteredFragmentCaches.Input.connect( self._opSmallFragmentFilter.Output )
self.FilteredFragmentedBodies.connect( self._opFilteredFragmentCaches.Output )
# Watershed to fill the holes created by filtering.
# Use a masked watershed to ensure that the watersheds stay within the bounds of the body
self._opMaskedWatersheds = OperatorWrapper( OpMaskedWatershed, parent=self )
self._opMaskedWatersheds.Input.connect( self.InputData )
self._opMaskedWatersheds.Mask.connect( self._opSelectLabel.Output )
self._opMaskedWatersheds.Seeds.connect( self._opSmallFragmentFilter.Output )
# Cache is necessary because it ensures that the entire volume is used for watershed.
self._opMaskedWatershedCaches = OperatorWrapper( OpCompressedCache, parent=self )
self._opMaskedWatershedCaches.Input.connect( self._opMaskedWatersheds.Output )
self.WatershedFilledBodies.connect( self._opMaskedWatershedCaches.Output )
self._opAccumulateFinalImage = OpAccumulateFragmentSegmentations( parent=self )
self._opAccumulateFinalImage.RavelerLabels.connect( self.RavelerLabels )
self._opAccumulateFinalImage.FragmentSegmentations.connect( self.WatershedFilledBodies )
self._opFinalCache = OpCompressedCache( parent=self )
self._opFinalCache.Input.connect( self._opAccumulateFinalImage.Output )
self.FinalSegmentation.connect( self._opFinalCache.Output )
# Cache serialization slots
self._opFinalCache.InputHdf5.connect( self.FinalSegmentationHdf5CacheInput )
self.FinalSegmentationCleanBlocks.connect( self._opFinalCache.CleanBlocks )
self.FinalSegmentationHdf5CacheOutput.connect( self._opFinalCache.OutputHdf5 )
def testHDF5_masked(self):
logger.info("Generating sample data...")
sampleData = numpy.indices((150, 250, 150), dtype=numpy.float32).sum(0)
sampleData = sampleData.view(numpy.ma.masked_array)
sampleData.set_fill_value(numpy.float32(numpy.nan))
sampleData[0] = numpy.ma.masked
graph = Graph()
opData = OpArrayPiper(graph=graph)
opData.Input.meta.axistags = vigra.defaultAxistags('xyz')
opData.Input.meta.has_mask = True
opData.Input.setValue(sampleData)
op = OpCompressedCache(parent=None, graph=graph)
#logger.debug("Setting block shape...")
op.BlockShape.setValue([75, 125, 150])
op.Input.connect(opData.Output)
assert op.OutputHdf5.ready()
slicing = numpy.s_[0:75, 125:250, 0:150]
slicing_str = str(
[list(_) for _ in zip(*[[_.start, _.stop] for _ in slicing])])
expectedData = sampleData[slicing]
slicing_2 = numpy.s_[0:75, 0:125, 0:150]
expectedData_2 = expectedData[slicing_2]
#logger.debug("Requesting data...")
tempdir = tempfile.mkdtemp()
try:
with h5py.File(os.path.join(tempdir, "data.h5"), "w") as h5_file:
op.OutputHdf5[slicing].writeInto(h5_file).wait()
assert slicing_str in h5_file, "Missing dataset!"
assert (h5_file[slicing_str]["data"][()] == expectedData).all() and \
(h5_file[slicing_str]["mask"][()] == expectedData.mask).all() and \
((h5_file[slicing_str]["fill_value"][()] == expectedData.fill_value) |
(numpy.isnan(h5_file[slicing_str]["fill_value"][()]) & numpy.isnan(expectedData.fill_value))).all(),\
"Incorrect output!"
with h5py.File(os.path.join(tempdir, "data.h5"), "r") as h5_file:
graph = Graph()
opData = OpArrayPiper(graph=graph)
opData.Input.meta.axistags = vigra.AxisTags('xyz')
opData.Input.meta.has_mask = True
opData.Input.setValue(numpy.empty_like(expectedData_2))
op = OpCompressedCache(parent=None, graph=graph)
op.InputHdf5.meta.axistags = vigra.AxisTags('xyz')
op.InputHdf5.meta.has_mask = True
op.InputHdf5.meta.shape = (75, 125, 150)
#logger.debug("Setting block shape...")
op.BlockShape.setValue([75, 125, 150])
op.Input.connect(opData.Output)
op.InputHdf5[slicing_2] = h5_file[slicing_str]
result = op.Output[slicing_2].wait()
assert (result == expectedData).all() and \
(result.mask == expectedData.mask).all() and \
((result.fill_value == expectedData.fill_value) |
(numpy.isnan(result.fill_value) & numpy.isnan(expectedData.fill_value))).all(),\
"Incorrect output!"
finally:
shutil.rmtree(tempdir)
class OpCachedLabelImage(OpCache):
"""
Combines OpLabelImage with OpCompressedCache, and provides a default block shape.
"""
Input = InputSlot()
BackgroundLabels = InputSlot(optional=True) # Optional. See OpLabelImage for details.
BlockShape = InputSlot(optional=True) # If not provided, blockshape is 1 time slice, 1 channel slice,
# and the entire volume in xyz.
Output = OutputSlot()
# Serialization support
InputHdf5 = InputSlot(optional=True)
CleanBlocks = OutputSlot()
OutputHdf5 = OutputSlot() # See OpCachedLabelImage for details
# Schematic:
#
# BackgroundLabels -- BlockShape --
# \ \
# Input ------------> OpLabelImage ---> OpCompressedCache --> Output
# \
# --> CleanBlocks
def __init__(self, *args, **kwargs):
warn_deprecated("OpCachedLabelImage is deprecated, use OpLabelVolume instead")
super(OpCachedLabelImage, self).__init__(*args, **kwargs)
# Hook up the labeler
self._opLabelImage = OpLabelImage( parent=self )
self._opLabelImage.Input.connect( self.Input )
self._opLabelImage.BackgroundLabels.connect( self.BackgroundLabels )
# Hook up the cache
self._opCache = OpCompressedCache( parent=self )
self._opCache.Input.connect( self._opLabelImage.Output )
self._opCache.InputHdf5.connect( self.InputHdf5 )
# Hook up our output slots
self.Output.connect( self._opCache.Output )
self.CleanBlocks.connect( self._opCache.CleanBlocks )
self.OutputHdf5.connect( self._opCache.OutputHdf5 )
def generateReport(self, report):
return self._opCache.generateReport(report)
def usedMemory(self):
return self._opCache.usedMemory()
def fractionOfUsedMemoryDirty(self):
return self._opCache.fractionOfUsedMemoryDirty()
def lastAccessTime(self):
return self._opCache.lastAccessTime()
def setupOutputs(self):
if self.BlockShape.ready():
self._opCache.BlockShape.setValue( self.BlockShape.value )
else:
# By default, block shape is the same as the entire image shape,
# but only 1 time slice and 1 channel slice
taggedBlockShape = self.Input.meta.getTaggedShape()
taggedBlockShape['t'] = 1
taggedBlockShape['c'] = 1
self._opCache.BlockShape.setValue( tuple( taggedBlockShape.values() ) )
def execute(self, slot, subindex, roi, destination):
assert False, "Shouldn't get here."
def propagateDirty(self, slot, subindex, roi):
pass # Nothing to do...
def setInSlot(self, slot, subindex, roi, value):
assert slot == self.Input or slot == self.InputHdf5, "Invalid slot for setInSlot(): {}".format( slot.name )
class OpCachedLabelImage(OpCache):
"""
Combines OpLabelImage with OpCompressedCache, and provides a default block shape.
"""
Input = InputSlot()
BackgroundLabels = InputSlot(
optional=True) # Optional. See OpLabelImage for details.
BlockShape = InputSlot(
optional=True
) # If not provided, blockshape is 1 time slice, 1 channel slice,
# and the entire volume in xyz.
Output = OutputSlot()
# Serialization support
InputHdf5 = InputSlot(optional=True)
CleanBlocks = OutputSlot()
OutputHdf5 = OutputSlot() # See OpCachedLabelImage for details
# Schematic:
#
# BackgroundLabels -- BlockShape --
# \ \
# Input ------------> OpLabelImage ---> OpCompressedCache --> Output
# \
# --> CleanBlocks
def __init__(self, *args, **kwargs):
warn_deprecated(
"OpCachedLabelImage is deprecated, use OpLabelVolume instead")
super(OpCachedLabelImage, self).__init__(*args, **kwargs)
# Hook up the labeler
self._opLabelImage = OpLabelImage(parent=self)
self._opLabelImage.Input.connect(self.Input)
self._opLabelImage.BackgroundLabels.connect(self.BackgroundLabels)
# Hook up the cache
self._opCache = OpCompressedCache(parent=self)
self._opCache.Input.connect(self._opLabelImage.Output)
self._opCache.InputHdf5.connect(self.InputHdf5)
# Hook up our output slots
self.Output.connect(self._opCache.Output)
self.CleanBlocks.connect(self._opCache.CleanBlocks)
self.OutputHdf5.connect(self._opCache.OutputHdf5)
def generateReport(self, report):
return self._opCache.generateReport(report)
def usedMemory(self):
return self._opCache.usedMemory()
def fractionOfUsedMemoryDirty(self):
return self._opCache.fractionOfUsedMemoryDirty()
def lastAccessTime(self):
return self._opCache.lastAccessTime()
def setupOutputs(self):
if self.BlockShape.ready():
self._opCache.BlockShape.setValue(self.BlockShape.value)
else:
# By default, block shape is the same as the entire image shape,
# but only 1 time slice and 1 channel slice
taggedBlockShape = self.Input.meta.getTaggedShape()
taggedBlockShape['t'] = 1
taggedBlockShape['c'] = 1
self._opCache.BlockShape.setValue(tuple(taggedBlockShape.values()))
def execute(self, slot, subindex, roi, destination):
assert False, "Shouldn't get here."
def propagateDirty(self, slot, subindex, roi):
pass # Nothing to do...
def setInSlot(self, slot, subindex, roi, value):
assert slot == self.Input or slot == self.InputHdf5, "Invalid slot for setInSlot(): {}".format(
slot.name)
