def test2(self, position5d_start, position5d_stop):
print "test2"
roi = SubRegion(self.op.LabelInputs, position5d_start,
position5d_stop)
key = roi.toSlice()
#key = tuple(k for k in key if k != slice(0,0, None))
newKey = []
for k in key:
if k.stop < k.start:
k = slice(k.stop, k.start)
newKey.append(k)
newKey = tuple(newKey)
self.boxes[self.activeBox] = newKey
#self.op.BoxLabelImages[newKey] = self.activeBox + 2
#self.op.BoxLabelImages
labelShape = tuple([position5d_stop[i] + 1 - position5d_start[i] for i in range(5)])
labels = numpy.ones((labelShape), dtype = numpy.uint8) * (self.activeBox + 3)
self.boxlabelsrc.put(newKey, labels)
def test(self, position5d_start, position5d_stop):
print "test"
roi = SubRegion(self.op.Density, position5d_start,
position5d_stop)
key = roi.toSlice()
key = tuple(k for k in key if k != slice(0,0, None))
newKey = []
for k in key:
if k != slice(0,0,None):
if k.stop < k.start:
k = slice(k.stop, k.start)
newKey.append(k)
newKey = tuple(newKey)
try:
density = numpy.sum(self.op.Density[newKey].wait()) / 255
strdensity = "{0:.2f}".format(density)
self._labelControlUi.CountText.setText(strdensity)
except:
pass
def test(self, position5d_start, position5d_stop):
from lazyflow.rtype import SubRegion
import numpy
from sitecustomize import debug_trace
roi = SubRegion(self.op.Density, position5d_start,
position5d_stop)
key = roi.toSlice()
key = tuple(k for k in key if k != slice(0,0, None))
newKey = []
for k in key:
if k != slice(0,0,None):
if k.stop < k.start:
k = slice(k.stop, k.start)
newKey.append(k)
newKey = tuple(newKey)
try:
density = numpy.sum(self.op.Density[newKey].wait())
self._labelControlUi.CountText.setText(str(density))
except:
debug_trace()
def execute(self, slot, subindex, slot_roi, target):
assert slot == self.Features or slot == self.Output
if slot == self.Features:
feature_slice = roiToSlice(slot_roi.start, slot_roi.stop)
index = subindex[0]
feature_slice = list(feature_slice)
# Translate channel slice of this feature to the channel slice of the output slot.
output_channel_offset = self.featureOutputChannels[index][0]
feature_slice[1] = slice(
output_channel_offset + feature_slice[1].start,
output_channel_offset + feature_slice[1].stop)
slot_roi = SubRegion(self.Output, pslice=feature_slice)
# Get output slot region for this channel
return self.execute(self.Output, (), slot_roi, target)
elif slot == self.Output:
# Correlation of variable 'families' representing reference frames:
# ______________________________
# | input/output frame | input/output shape given by slots
# | _________________________ |
# | | smooth frame | | pre-smoothing op needs halo around filter roi
# | | ____________________ | |
# | | |filter frame | | | filter needs halo around target roi
# | | | _______________ | | |
# | | | | target frame | | | | target is given by output_roi
# note: The 'full_' variable prefix refers to the full 5D shape (tczyx), without 'full_' variables mostly
# refer to the 3D space subregion (zyx)
full_output_slice = slot_roi.toSlice()
logger.debug(
f"OpPixelFeaturesPresmoothed: request {slot_roi.pprint()}")
assert (slot_roi.stop <= self.Output.meta.shape).all()
full_output_shape = self.Output.meta.shape
full_output_start, full_output_stop = sliceToRoi(
full_output_slice, full_output_shape)
assert len(full_output_shape) == 5
if all(self.ComputeIn2d.value
): # todo: check for this particular slice
axes2enlarge = (0, 1, 1)
else:
axes2enlarge = (1, 1, 1)
output_shape = full_output_shape[2:]
output_start = full_output_start[2:]
output_stop = full_output_stop[2:]
axistags = self.Output.meta.axistags
target = target.view(vigra.VigraArray)
target.axistags = copy.copy(axistags)
# filter roi in input frame
# sigma = 0.7, because the features receive a pre-smoothed array and don't need much of a neighborhood
input_filter_start, input_filter_stop = roi.enlargeRoiForHalo(
output_start,
output_stop,
output_shape,
0.7,
self.WINDOW_SIZE,
enlarge_axes=axes2enlarge)
# smooth roi in input frame
input_smooth_start, input_smooth_stop = roi.enlargeRoiForHalo(
input_filter_start,
input_filter_stop,
output_shape,
self.max_sigma,
self.WINDOW_SIZE,
enlarge_axes=axes2enlarge,
)
# target roi in filter frame
filter_target_start = roi.TinyVector(output_start -
input_filter_start)
filter_target_stop = roi.TinyVector(output_stop -
input_filter_start)
# filter roi in smooth frame
smooth_filter_start = roi.TinyVector(input_filter_start -
input_smooth_start)
smooth_filter_stop = roi.TinyVector(input_filter_stop -
input_smooth_start)
filter_target_slice = roi.roiToSlice(filter_target_start,
filter_target_stop)
input_smooth_slice = roi.roiToSlice(input_smooth_start,
input_smooth_stop)
# pre-smooth for all requested time slices and all channels
full_input_smooth_slice = (full_output_slice[0], slice(None),
*input_smooth_slice)
req = self.Input[full_input_smooth_slice]
source = req.wait()
req.clean()
req.destination = None
if source.dtype != numpy.float32:
sourceF = source.astype(numpy.float32)
try:
source.resize((1, ), refcheck=False)
except Exception:
pass
del source
source = sourceF
sourceV = source.view(vigra.VigraArray)
sourceV.axistags = copy.copy(self.Input.meta.axistags)
dimCol = len(self.scales)
dimRow = self.matrix.shape[0]
presmoothed_source = [None] * dimCol
source_smooth_shape = tuple(smooth_filter_stop -
smooth_filter_start)
full_source_smooth_shape = (
full_output_stop[0] - full_output_start[0],
self.Input.meta.shape[1],
) + source_smooth_shape
try:
for j in range(dimCol):
for i in range(dimRow):
if self.matrix[i, j]:
# There is at least one filter op with this scale
break
else:
# There is no filter op at this scale
continue
if self.scales[j] > 1.0:
tempSigma = math.sqrt(self.scales[j]**2 - 1.0)
else:
tempSigma = self.scales[j]
presmoothed_source[j] = numpy.ndarray(
full_source_smooth_shape, numpy.float32)
droi = (
(0, *tuple(smooth_filter_start._asint())),
(sourceV.shape[1],
*tuple(smooth_filter_stop._asint())),
)
for i, vsa in enumerate(sourceV.timeIter()):
presmoothed_source[j][
i, ...] = self._computeGaussianSmoothing(
vsa,
tempSigma,
droi,
in2d=self.ComputeIn2d.value[j])
except RuntimeError as e:
if "kernel longer than line" in str(e):
raise RuntimeError(
"Feature computation error:\nYour image is too small to apply a filter with "
f"sigma={self.scales[j]:.1f}. Please select features with smaller sigmas."
)
else:
raise e
del sourceV
try:
source.resize((1, ), refcheck=False)
except ValueError:
# Sometimes this fails, but that's okay.
logger.debug("Failed to free array memory.")
del source
cnt = 0
written = 0
closures = []
# connect individual operators
for i in range(dimRow):
for j in range(dimCol):
if self.matrix[i, j]:
oslot = self.featureOps[i][j].Output
req = None
slices = oslot.meta.shape[1]
if (cnt + slices >= slot_roi.start[1]
and slot_roi.start[1] - cnt < slices
and slot_roi.start[1] + written <
slot_roi.stop[1]):
begin = 0
if cnt < slot_roi.start[1]:
begin = slot_roi.start[1] - cnt
end = slices
if cnt + end > slot_roi.stop[1]:
end = slot_roi.stop[1] - cnt
# feature slice in output frame
feature_slice = (slice(None),
slice(
written, written + end -
begin)) + (slice(None), ) * 3
subtarget = target[feature_slice]
# readjust the roi for the new source array
full_filter_target_slice = [
full_output_slice[0],
slice(begin, end), *filter_target_slice
]
filter_target_roi = SubRegion(
oslot, pslice=full_filter_target_slice)
closure = partial(
oslot.operator.execute,
oslot,
(),
filter_target_roi,
subtarget,
sourceArray=presmoothed_source[j],
)
closures.append(closure)
written += end - begin
cnt += slices
pool = RequestPool()
for c in closures:
pool.request(c)
pool.wait()
pool.clean()
for i in range(len(presmoothed_source)):
if presmoothed_source[i] is not None:
try:
presmoothed_source[i].resize((1, ))
except Exception:
presmoothed_source[i] = None
def execute(self, slot, subindex, roi, result):
if slot == self.Dirty:
assert False # Shouldn't get to this line because the dirty output is given a value directly
if slot == self.OutputDataPath:
assert False # This slot is already set via setupOutputs
if slot == self.ExportResult:
# We can stop now if the output isn't dirty
if not self.Dirty.value:
result[0] = True
return
exportFormat = self.Format.value
# Export H5
if exportFormat == ExportFormat.H5:
pathComp = PathComponents(self.OutputDataPath.value)
# Ensure the directory exists
if not os.path.exists(pathComp.externalDirectory):
with self._createDirLock:
# Check again now that we have the lock.
if not os.path.exists(pathComp.externalDirectory):
os.makedirs(pathComp.externalDirectory)
# Open the file
try:
hdf5File = h5py.File(pathComp.externalPath)
except:
logger.error("Unable to open hdf5File: " + pathComp.externalPath)
logger.error( traceback.format_exc() )
result[0] = False
return
# Set up the write operator
opH5Writer = OpH5WriterBigDataset(parent=self)
opH5Writer.hdf5File.setValue( hdf5File )
opH5Writer.hdf5Path.setValue( pathComp.internalPath )
#opH5Writer.Image.connect( self.ImageToExport )
opH5Writer.Image.connect(self.ImageCache.Output)
print "computing predictions for the selected slices:"
self.ImageCache.fixAtCurrent.setValue(False)
#check readiness
for inp in self.ImageCache.inputs:
print inp, self.ImageCache.inputs[inp].ready()
print "input shape:", self.ImageCache.Input.meta.shape
print "output shape:", self.ImageCache.Output.meta.shape
selectedSlices = self.SelectedSlices.value
zaxis = self.ImageToExport.meta.axistags.index('z')
for isl, sl in enumerate(selectedSlices):
print "computing for slice ...", isl
start = [0]*len(self.ImageToExport.meta.shape)
start[zaxis]=sl
stop = list(self.ImageToExport.meta.shape)
stop[zaxis]=sl+1
roi = SubRegion(self.ImageCache, start=start, stop=stop)
print roi
temp = self.ImageCache.Output[roi.toSlice()].wait()
#print temp
self.ImageCache.fixAtCurrent.setValue(True)
#tstart = [0]*len(self.ImageToExport.meta.shape)
#tstop = list(self.ImageToExport.meta.shape)
#troi = SubRegion(self.ImageCache, start=tstart, stop=tstop)
#tttemp = self.ImageCache.Output[troi.toSlice()].wait()
#print tttemp
# The H5 Writer provides it's own progress signal, so just connect ours to it.
opH5Writer.progressSignal.subscribe( self.progressSignal )
# Trigger the write
self.Dirty.setValue( not opH5Writer.WriteImage.value )
hdf5File.close()
opH5Writer.cleanUp()
# elif exportFormat == ExportFormat.Npy:
# assert False # TODO
# elif exportFormat == ExportFormat.Npy:
# assert False # TODO
else:
assert False, "Unknown export format"
result[0] = not self.Dirty.value
def execute(self, slot, subindex, slot_roi, target):
assert slot == self.Features or slot == self.Output
if slot == self.Features:
feature_slice = roiToSlice(slot_roi.start, slot_roi.stop)
index = subindex[0]
feature_slice = list(feature_slice)
# Translate channel slice of this feature to the channel slice of the output slot.
output_channel_offset = self.featureOutputChannels[index][0]
feature_slice[1] = slice(
output_channel_offset + feature_slice[1].start, output_channel_offset + feature_slice[1].stop
)
slot_roi = SubRegion(self.Output, pslice=feature_slice)
# Get output slot region for this channel
return self.execute(self.Output, (), slot_roi, target)
elif slot == self.Output:
# Correlation of variable 'families' representing reference frames:
# ______________________________
# | input/output frame | input/output shape given by slots
# | _________________________ |
# | | smooth frame | | pre-smoothing op needs halo around filter roi
# | | ____________________ | |
# | | |filter frame | | | filter needs halo around target roi
# | | | _______________ | | |
# | | | | target frame | | | | target is given by output_roi
# note: The 'full_' variable prefix refers to the full 5D shape (tczyx), without 'full_' variables mostly
# refer to the 3D space subregion (zyx)
full_output_slice = slot_roi.toSlice()
logger.debug(f"OpPixelFeaturesPresmoothed: request {slot_roi.pprint()}")
assert (slot_roi.stop <= self.Output.meta.shape).all()
full_output_shape = self.Output.meta.shape
full_output_start, full_output_stop = sliceToRoi(full_output_slice, full_output_shape)
assert len(full_output_shape) == 5
if all(self.ComputeIn2d.value): # todo: check for this particular slice
axes2enlarge = (0, 1, 1)
else:
axes2enlarge = (1, 1, 1)
output_shape = full_output_shape[2:]
output_start = full_output_start[2:]
output_stop = full_output_stop[2:]
axistags = self.Output.meta.axistags
target = target.view(vigra.VigraArray)
target.axistags = copy.copy(axistags)
# filter roi in input frame
# sigma = 0.7, because the features receive a pre-smoothed array and don't need much of a neighborhood
input_filter_start, input_filter_stop = roi.enlargeRoiForHalo(
output_start, output_stop, output_shape, 0.7, self.WINDOW_SIZE, enlarge_axes=axes2enlarge
)
# smooth roi in input frame
input_smooth_start, input_smooth_stop = roi.enlargeRoiForHalo(
input_filter_start,
input_filter_stop,
output_shape,
self.max_sigma,
self.WINDOW_SIZE,
enlarge_axes=axes2enlarge,
)
# target roi in filter frame
filter_target_start = roi.TinyVector(output_start - input_filter_start)
filter_target_stop = roi.TinyVector(output_stop - input_filter_start)
# filter roi in smooth frame
smooth_filter_start = roi.TinyVector(input_filter_start - input_smooth_start)
smooth_filter_stop = roi.TinyVector(input_filter_stop - input_smooth_start)
filter_target_slice = roi.roiToSlice(filter_target_start, filter_target_stop)
input_smooth_slice = roi.roiToSlice(input_smooth_start, input_smooth_stop)
# pre-smooth for all requested time slices and all channels
full_input_smooth_slice = (full_output_slice[0], slice(None), *input_smooth_slice)
req = self.Input[full_input_smooth_slice]
source = req.wait()
req.clean()
req.destination = None
if source.dtype != numpy.float32:
sourceF = source.astype(numpy.float32)
try:
source.resize((1,), refcheck=False)
except Exception:
pass
del source
source = sourceF
sourceV = source.view(vigra.VigraArray)
sourceV.axistags = copy.copy(self.Input.meta.axistags)
dimCol = len(self.scales)
dimRow = self.matrix.shape[0]
presmoothed_source = [None] * dimCol
source_smooth_shape = tuple(smooth_filter_stop - smooth_filter_start)
full_source_smooth_shape = (
full_output_stop[0] - full_output_start[0],
self.Input.meta.shape[1],
) + source_smooth_shape
try:
for j in range(dimCol):
for i in range(dimRow):
if self.matrix[i, j]:
# There is at least one filter op with this scale
break
else:
# There is no filter op at this scale
continue
if self.scales[j] > 1.0:
tempSigma = math.sqrt(self.scales[j] ** 2 - 1.0)
else:
tempSigma = self.scales[j]
presmoothed_source[j] = numpy.ndarray(full_source_smooth_shape, numpy.float32)
droi = (
(0, *tuple(smooth_filter_start._asint())),
(sourceV.shape[1], *tuple(smooth_filter_stop._asint())),
)
for i, vsa in enumerate(sourceV.timeIter()):
presmoothed_source[j][i, ...] = self._computeGaussianSmoothing(
vsa, tempSigma, droi, in2d=self.ComputeIn2d.value[j]
)
except RuntimeError as e:
if "kernel longer than line" in str(e):
raise RuntimeError(
"Feature computation error:\nYour image is too small to apply a filter with "
f"sigma={self.scales[j]:.1f}. Please select features with smaller sigmas."
)
else:
raise e
del sourceV
try:
source.resize((1,), refcheck=False)
except ValueError:
# Sometimes this fails, but that's okay.
logger.debug("Failed to free array memory.")
del source
cnt = 0
written = 0
closures = []
# connect individual operators
for i in range(dimRow):
for j in range(dimCol):
if self.matrix[i, j]:
oslot = self.featureOps[i][j].Output
req = None
slices = oslot.meta.shape[1]
if (
cnt + slices >= slot_roi.start[1]
and slot_roi.start[1] - cnt < slices
and slot_roi.start[1] + written < slot_roi.stop[1]
):
begin = 0
if cnt < slot_roi.start[1]:
begin = slot_roi.start[1] - cnt
end = slices
if cnt + end > slot_roi.stop[1]:
end = slot_roi.stop[1] - cnt
# feature slice in output frame
feature_slice = (slice(None), slice(written, written + end - begin)) + (slice(None),) * 3
subtarget = target[feature_slice]
# readjust the roi for the new source array
full_filter_target_slice = [full_output_slice[0], slice(begin, end), *filter_target_slice]
filter_target_roi = SubRegion(oslot, pslice=full_filter_target_slice)
closure = partial(
oslot.operator.execute,
oslot,
(),
filter_target_roi,
subtarget,
sourceArray=presmoothed_source[j],
)
closures.append(closure)
written += end - begin
cnt += slices
pool = RequestPool()
for c in closures:
pool.request(c)
pool.wait()
pool.clean()
for i in range(len(presmoothed_source)):
if presmoothed_source[i] is not None:
try:
presmoothed_source[i].resize((1,))
except Exception:
presmoothed_source[i] = None
def execute(self, slot, subindex, roi, result):
if slot == self.Dirty:
assert False # Shouldn't get to this line because the dirty output is given a value directly
if slot == self.OutputDataPath:
assert False # This slot is already set via setupOutputs
if slot == self.ExportResult:
# We can stop now if the output isn't dirty
if not self.Dirty.value:
result[0] = True
return
exportFormat = self.Format.value
# Export H5
if exportFormat == ExportFormat.H5:
pathComp = PathComponents(self.OutputDataPath.value)
# Ensure the directory exists
if not os.path.exists(pathComp.externalDirectory):
with self._createDirLock:
# Check again now that we have the lock.
if not os.path.exists(pathComp.externalDirectory):
os.makedirs(pathComp.externalDirectory)
# Open the file
try:
hdf5File = h5py.File(pathComp.externalPath)
except:
logger.error("Unable to open hdf5File: " +
pathComp.externalPath)
logger.error(traceback.format_exc())
result[0] = False
return
# Set up the write operator
opH5Writer = OpH5WriterBigDataset(parent=self)
opH5Writer.hdf5File.setValue(hdf5File)
opH5Writer.hdf5Path.setValue(pathComp.internalPath)
#opH5Writer.Image.connect( self.ImageToExport )
opH5Writer.Image.connect(self.ImageCache.Output)
print "computing predictions for the selected slices:"
self.ImageCache.fixAtCurrent.setValue(False)
#check readiness
for inp in self.ImageCache.inputs:
print inp, self.ImageCache.inputs[inp].ready()
print "input shape:", self.ImageCache.Input.meta.shape
print "output shape:", self.ImageCache.Output.meta.shape
selectedSlices = self.SelectedSlices.value
zaxis = self.ImageToExport.meta.axistags.index('z')
for isl, sl in enumerate(selectedSlices):
print "computing for slice ...", isl
start = [0] * len(self.ImageToExport.meta.shape)
start[zaxis] = sl
stop = list(self.ImageToExport.meta.shape)
stop[zaxis] = sl + 1
roi = SubRegion(self.ImageCache, start=start, stop=stop)
print roi
temp = self.ImageCache.Output[roi.toSlice()].wait()
#print temp
self.ImageCache.fixAtCurrent.setValue(True)
#tstart = [0]*len(self.ImageToExport.meta.shape)
#tstop = list(self.ImageToExport.meta.shape)
#troi = SubRegion(self.ImageCache, start=tstart, stop=tstop)
#tttemp = self.ImageCache.Output[troi.toSlice()].wait()
#print tttemp
# The H5 Writer provides it's own progress signal, so just connect ours to it.
opH5Writer.progressSignal.subscribe(self.progressSignal)
# Trigger the write
self.Dirty.setValue(not opH5Writer.WriteImage.value)
hdf5File.close()
opH5Writer.cleanUp()
# elif exportFormat == ExportFormat.Npy:
# assert False # TODO
# elif exportFormat == ExportFormat.Npy:
# assert False # TODO
else:
assert False, "Unknown export format"
result[0] = not self.Dirty.value
def execute(self, slot, subindex, rroi, result):
assert slot == self.Features or slot == self.Output
if slot == self.Features:
key = roiToSlice(rroi.start, rroi.stop)
index = subindex[0]
subslot = self.Features[index]
key = list(key)
channelIndex = self.Input.meta.axistags.index('c')
# Translate channel slice to the correct location for the output slot.
key[channelIndex] = slice(self.featureOutputChannels[index][0] + key[channelIndex].start,
self.featureOutputChannels[index][0] + key[channelIndex].stop)
rroi = SubRegion(subslot, pslice=key)
# Get output slot region for this channel
return self.execute(self.Output, (), rroi, result)
elif slot == self.outputs["Output"]:
key = rroi.toSlice()
cnt = 0
written = 0
assert (rroi.stop<=self.outputs["Output"].meta.shape).all()
flag = 'c'
channelAxis=self.inputs["Input"].meta.axistags.index('c')
axisindex = channelAxis
oldkey = list(key)
oldkey.pop(axisindex)
inShape = self.inputs["Input"].meta.shape
shape = self.outputs["Output"].meta.shape
axistags = self.inputs["Input"].meta.axistags
result = result.view(vigra.VigraArray)
result.axistags = copy.copy(axistags)
hasTimeAxis = self.inputs["Input"].meta.axistags.axisTypeCount(vigra.AxisType.Time)
timeAxis=self.inputs["Input"].meta.axistags.index('t')
subkey = popFlagsFromTheKey(key,axistags,'c')
subshape=popFlagsFromTheKey(shape,axistags,'c')
at2 = copy.copy(axistags)
at2.dropChannelAxis()
subshape=popFlagsFromTheKey(subshape,at2,'t')
subkey = popFlagsFromTheKey(subkey,at2,'t')
oldstart, oldstop = roi.sliceToRoi(key, shape)
start, stop = roi.sliceToRoi(subkey,subkey)
maxSigma = max(0.7,self.maxSigma)
# The region of the smoothed image we need to give to the feature filter (in terms of INPUT coordinates)
vigOpSourceStart, vigOpSourceStop = roi.extendSlice(start, stop, subshape, 0.7, window = 2)
# The region of the input that we need to give to the smoothing operator (in terms of INPUT coordinates)
newStart, newStop = roi.extendSlice(vigOpSourceStart, vigOpSourceStop, subshape, maxSigma, window = 3.5)
# Translate coordinates (now in terms of smoothed image coordinates)
vigOpSourceStart = roi.TinyVector(vigOpSourceStart - newStart)
vigOpSourceStop = roi.TinyVector(vigOpSourceStop - newStart)
readKey = roi.roiToSlice(newStart, newStop)
writeNewStart = start - newStart
writeNewStop = writeNewStart + stop - start
treadKey=list(readKey)
if hasTimeAxis:
if timeAxis < channelAxis:
treadKey.insert(timeAxis, key[timeAxis])
else:
treadKey.insert(timeAxis-1, key[timeAxis])
if self.inputs["Input"].meta.axistags.axisTypeCount(vigra.AxisType.Channels) == 0:
treadKey = popFlagsFromTheKey(treadKey,axistags,'c')
else:
treadKey.insert(channelAxis, slice(None,None,None))
treadKey=tuple(treadKey)
req = self.inputs["Input"][treadKey].allocate()
sourceArray = req.wait()
req.result = None
req.destination = None
if sourceArray.dtype != numpy.float32:
sourceArrayF = sourceArray.astype(numpy.float32)
sourceArray.resize((1,), refcheck = False)
del sourceArray
sourceArray = sourceArrayF
sourceArrayV = sourceArray.view(vigra.VigraArray)
sourceArrayV.axistags = copy.copy(axistags)
dimCol = len(self.scales)
dimRow = self.matrix.shape[0]
sourceArraysForSigmas = [None]*dimCol
#connect individual operators
for j in range(dimCol):
hasScale = False
for i in range(dimRow):
if self.matrix[i,j]:
hasScale = True
if not hasScale:
continue
destSigma = 1.0
if self.scales[j] > destSigma:
tempSigma = math.sqrt(self.scales[j]**2 - destSigma**2)
else:
destSigma = 0.0
tempSigma = self.scales[j]
vigOpSourceShape = list(vigOpSourceStop - vigOpSourceStart)
if hasTimeAxis:
if timeAxis < channelAxis:
vigOpSourceShape.insert(timeAxis, ( oldstop - oldstart)[timeAxis])
else:
vigOpSourceShape.insert(timeAxis-1, ( oldstop - oldstart)[timeAxis])
vigOpSourceShape.insert(channelAxis, inShape[channelAxis])
sourceArraysForSigmas[j] = numpy.ndarray(tuple(vigOpSourceShape),numpy.float32)
for i,vsa in enumerate(sourceArrayV.timeIter()):
droi = (tuple(vigOpSourceStart._asint()), tuple(vigOpSourceStop._asint()))
tmp_key = getAllExceptAxis(len(sourceArraysForSigmas[j].shape),timeAxis, i)
sourceArraysForSigmas[j][tmp_key] = vigra.filters.gaussianSmoothing(vsa,tempSigma, roi = droi, window_size = 3.5 )
else:
droi = (tuple(vigOpSourceStart._asint()), tuple(vigOpSourceStop._asint()))
#print droi, sourceArray.shape, tempSigma,self.scales[j]
sourceArraysForSigmas[j] = vigra.filters.gaussianSmoothing(sourceArrayV, sigma = tempSigma, roi = droi, window_size = 3.5)
#sourceArrayForSigma = sourceArrayForSigma.view(numpy.ndarray)
del sourceArrayV
try:
sourceArray.resize((1,), refcheck = False)
except ValueError:
# Sometimes this fails, but that's okay.
logger.debug("Failed to free array memory.")
del sourceArray
closures = []
#connect individual operators
for i in range(dimRow):
for j in range(dimCol):
val=self.matrix[i,j]
if val:
vop= self.featureOps[i][j]
oslot = vop.outputs["Output"]
req = None
inTagKeys = [ax.key for ax in oslot.meta.axistags]
if flag in inTagKeys:
slices = oslot.meta.shape[axisindex]
if cnt + slices >= rroi.start[axisindex] and rroi.start[axisindex]-cnt<slices and rroi.start[axisindex]+written<rroi.stop[axisindex]:
begin = 0
if cnt < rroi.start[axisindex]:
begin = rroi.start[axisindex] - cnt
end = slices
if cnt + end > rroi.stop[axisindex]:
end -= cnt + end - rroi.stop[axisindex]
key_ = copy.copy(oldkey)
key_.insert(axisindex, slice(begin, end, None))
reskey = [slice(None, None, None) for x in range(len(result.shape))]
reskey[axisindex] = slice(written, written+end-begin, None)
destArea = result[tuple(reskey)]
roi_ = SubRegion(self.Input, pslice=key_)
closure = partial(oslot.operator.execute, oslot, (), roi_, destArea, sourceArray = sourceArraysForSigmas[j])
closures.append(closure)
written += end - begin
cnt += slices
else:
if cnt>=rroi.start[axisindex] and rroi.start[axisindex] + written < rroi.stop[axisindex]:
reskey = copy.copy(oldkey)
reskey.insert(axisindex, written)
#print "key: ", key, "reskey: ", reskey, "oldkey: ", oldkey
#print "result: ", result.shape, "inslot:", inSlot.shape
destArea = result[tuple(reskey)]
logger.debug(oldkey, destArea.shape, sourceArraysForSigmas[j].shape)
oldroi = SubRegion(self.Input, pslice=oldkey)
closure = partial(oslot.operator.execute, oslot, (), oldroi, destArea, sourceArray = sourceArraysForSigmas[j])
closures.append(closure)
written += 1
cnt += 1
pool = Pool()
for c in closures:
r = pool.request(c)
pool.wait()
pool.clean()
for i in range(len(sourceArraysForSigmas)):
if sourceArraysForSigmas[i] is not None:
try:
sourceArraysForSigmas[i].resize((1,))
except:
sourceArraysForSigmas[i] = None
def execute(self, slot, subindex, rroi, result):
assert slot == self.Features or slot == self.Output
if slot == self.Features:
key = roiToSlice(rroi.start, rroi.stop)
index = subindex[0]
key = list(key)
channelIndex = self.Input.meta.axistags.index('c')
# Translate channel slice to the correct location for the output slot.
key[channelIndex] = slice(self.featureOutputChannels[index][0] + key[channelIndex].start,
self.featureOutputChannels[index][0] + key[channelIndex].stop)
rroi = SubRegion(self.Output, pslice=key)
# Get output slot region for this channel
return self.execute(self.Output, (), rroi, result)
elif slot == self.outputs["Output"]:
key = rroi.toSlice()
logger.debug("OpPixelFeaturesPresmoothed: request %s" % (rroi.pprint(),))
cnt = 0
written = 0
assert (rroi.stop<=self.outputs["Output"].meta.shape).all()
flag = 'c'
channelAxis=self.inputs["Input"].meta.axistags.index('c')
axisindex = channelAxis
oldkey = list(key)
oldkey.pop(axisindex)
inShape = self.inputs["Input"].meta.shape
hasChannelAxis = (self.Input.meta.axistags.axisTypeCount(vigra.AxisType.Channels) > 0)
#if (self.Input.meta.axistags.axisTypeCount(vigra.AxisType.Channels) == 0):
# noChannels = True
inAxistags = self.inputs["Input"].meta.axistags
shape = self.outputs["Output"].meta.shape
axistags = self.outputs["Output"].meta.axistags
result = result.view(vigra.VigraArray)
result.axistags = copy.copy(axistags)
hasTimeAxis = self.inputs["Input"].meta.axistags.axisTypeCount(vigra.AxisType.Time)
timeAxis=self.inputs["Input"].meta.axistags.index('t')
subkey = popFlagsFromTheKey(key,axistags,'c')
subshape=popFlagsFromTheKey(shape,axistags,'c')
at2 = copy.copy(axistags)
at2.dropChannelAxis()
subshape=popFlagsFromTheKey(subshape,at2,'t')
subkey = popFlagsFromTheKey(subkey,at2,'t')
oldstart, oldstop = roi.sliceToRoi(key, shape)
start, stop = roi.sliceToRoi(subkey,subkey)
maxSigma = max(0.7,self.maxSigma) #we use 0.7 as an approximation of not doing any smoothing
#smoothing was already applied previously
# The region of the smoothed image we need to give to the feature filter (in terms of INPUT coordinates)
# 0.7, because the features receive a pre-smoothed array and don't need much of a neighborhood
vigOpSourceStart, vigOpSourceStop = roi.enlargeRoiForHalo(start, stop, subshape, 0.7, self.WINDOW_SIZE)
# The region of the input that we need to give to the smoothing operator (in terms of INPUT coordinates)
newStart, newStop = roi.enlargeRoiForHalo(vigOpSourceStart, vigOpSourceStop, subshape, maxSigma, self.WINDOW_SIZE)
newStartSmoother = roi.TinyVector(start - vigOpSourceStart)
newStopSmoother = roi.TinyVector(stop - vigOpSourceStart)
roiSmoother = roi.roiToSlice(newStartSmoother, newStopSmoother)
# Translate coordinates (now in terms of smoothed image coordinates)
vigOpSourceStart = roi.TinyVector(vigOpSourceStart - newStart)
vigOpSourceStop = roi.TinyVector(vigOpSourceStop - newStart)
readKey = roi.roiToSlice(newStart, newStop)
writeNewStart = start - newStart
writeNewStop = writeNewStart + stop - start
treadKey=list(readKey)
if hasTimeAxis:
if timeAxis < channelAxis:
treadKey.insert(timeAxis, key[timeAxis])
else:
treadKey.insert(timeAxis-1, key[timeAxis])
if self.inputs["Input"].meta.axistags.axisTypeCount(vigra.AxisType.Channels) == 0:
treadKey = popFlagsFromTheKey(treadKey,axistags,'c')
else:
treadKey.insert(channelAxis, slice(None,None,None))
treadKey=tuple(treadKey)
req = self.inputs["Input"][treadKey]
sourceArray = req.wait()
req.clean()
#req.result = None
req.destination = None
if sourceArray.dtype != numpy.float32:
sourceArrayF = sourceArray.astype(numpy.float32)
try:
sourceArray.resize((1,), refcheck = False)
except:
pass
del sourceArray
sourceArray = sourceArrayF
#if (self.Input.meta.axistags.axisTypeCount(vigra.AxisType.Channels) == 0):
#add a channel dimension to make the code afterwards more uniform
# sourceArray = sourceArray.view(numpy.ndarray)
# sourceArray = sourceArray.reshape(sourceArray.shape+(1,))
sourceArrayV = sourceArray.view(vigra.VigraArray)
sourceArrayV.axistags = copy.copy(inAxistags)
dimCol = len(self.scales)
dimRow = self.matrix.shape[0]
sourceArraysForSigmas = [None]*dimCol
#connect individual operators
try:
for j in range(dimCol):
hasScale = False
for i in range(dimRow):
if self.matrix[i,j]:
hasScale = True
if not hasScale:
continue
destSigma = 1.0
if self.scales[j] > destSigma:
tempSigma = math.sqrt(self.scales[j]**2 - destSigma**2)
else:
destSigma = 0.0
tempSigma = self.scales[j]
vigOpSourceShape = list(vigOpSourceStop - vigOpSourceStart)
if hasTimeAxis:
if timeAxis < channelAxis:
vigOpSourceShape.insert(timeAxis, ( oldstop - oldstart)[timeAxis])
else:
vigOpSourceShape.insert(timeAxis-1, ( oldstop - oldstart)[timeAxis])
vigOpSourceShape.insert(channelAxis, inShape[channelAxis])
sourceArraysForSigmas[j] = numpy.ndarray(tuple(vigOpSourceShape),numpy.float32)
for i,vsa in enumerate(sourceArrayV.timeIter()):
droi = (tuple(vigOpSourceStart._asint()), tuple(vigOpSourceStop._asint()))
tmp_key = getAllExceptAxis(len(sourceArraysForSigmas[j].shape),timeAxis, i)
sourceArraysForSigmas[j][tmp_key] = self._computeGaussianSmoothing(vsa, tempSigma, droi)
else:
droi = (tuple(vigOpSourceStart._asint()), tuple(vigOpSourceStop._asint()))
sourceArraysForSigmas[j] = self._computeGaussianSmoothing(sourceArrayV, tempSigma, droi)
except RuntimeError as e:
if e.message.find('kernel longer than line') > -1:
message = "Feature computation error:\nYour image is too small to apply a filter with sigma=%.1f. Please select features with smaller sigmas." % self.scales[j]
raise RuntimeError(message)
else:
raise e
del sourceArrayV
try:
sourceArray.resize((1,), refcheck = False)
except ValueError:
# Sometimes this fails, but that's okay.
logger.debug("Failed to free array memory.")
del sourceArray
closures = []
#connect individual operators
for i in range(dimRow):
for j in range(dimCol):
val=self.matrix[i,j]
if val:
vop= self.featureOps[i][j]
oslot = vop.outputs["Output"]
req = None
#inTagKeys = [ax.key for ax in oslot.meta.axistags]
#print inTagKeys, flag
if hasChannelAxis:
slices = oslot.meta.shape[axisindex]
if cnt + slices >= rroi.start[axisindex] and rroi.start[axisindex]-cnt<slices and rroi.start[axisindex]+written<rroi.stop[axisindex]:
begin = 0
if cnt < rroi.start[axisindex]:
begin = rroi.start[axisindex] - cnt
end = slices
if cnt + end > rroi.stop[axisindex]:
end -= cnt + end - rroi.stop[axisindex]
key_ = copy.copy(oldkey)
key_.insert(axisindex, slice(begin, end, None))
reskey = [slice(None, None, None) for x in range(len(result.shape))]
reskey[axisindex] = slice(written, written+end-begin, None)
destArea = result[tuple(reskey)]
#readjust the roi for the new source array
roiSmootherList = list(roiSmoother)
roiSmootherList.insert(axisindex, slice(begin, end, None))
if hasTimeAxis:
# The time slice in the ROI doesn't matter:
# The sourceArrayParameter below overrides the input data to be used.
roiSmootherList.insert(timeAxis, 0)
roiSmootherRegion = SubRegion(oslot, pslice=roiSmootherList)
closure = partial(oslot.operator.execute, oslot, (), roiSmootherRegion, destArea, sourceArray = sourceArraysForSigmas[j])
closures.append(closure)
written += end - begin
cnt += slices
else:
if cnt>=rroi.start[axisindex] and rroi.start[axisindex] + written < rroi.stop[axisindex]:
reskey = [slice(None, None, None) for x in range(len(result.shape))]
slices = oslot.meta.shape[axisindex]
reskey[axisindex]=slice(written, written+slices, None)
#print "key: ", key, "reskey: ", reskey, "oldkey: ", oldkey, "resshape:", result.shape
#print "roiSmoother:", roiSmoother
destArea = result[tuple(reskey)]
#print "destination area:", destArea.shape
logger.debug(oldkey, destArea.shape, sourceArraysForSigmas[j].shape)
oldroi = SubRegion(oslot, pslice=oldkey)
#print "passing roi:", oldroi
closure = partial(oslot.operator.execute, oslot, (), oldroi, destArea, sourceArray = sourceArraysForSigmas[j])
closures.append(closure)
written += 1
cnt += 1
pool = RequestPool()
for c in closures:
r = pool.request(c)
pool.wait()
pool.clean()
for i in range(len(sourceArraysForSigmas)):
if sourceArraysForSigmas[i] is not None:
try:
sourceArraysForSigmas[i].resize((1,))
except:
sourceArraysForSigmas[i] = None