def testCleanup(self):
try:
CacheMemoryManager().disable()
op = OpBlockedArrayCache(graph=self.opProvider.graph)
op.Input.connect(self.opProvider.Output)
s = self.opProvider.Output.meta.shape
op.innerBlockShape.setValue(s)
op.outerBlockShape.setValue(s)
op.fixAtCurrent.setValue(False)
x = op.Output[...].wait()
op.Input.disconnect()
op.cleanUp()
r = weakref.ref(op)
del op
gc.collect()
ref = r()
if ref is not None:
for i, o in enumerate(gc.get_referrers(ref)):
print "Object", i, ":", type(o), ":", o
assert r(
) is None, "OpBlockedArrayCache was not cleaned up correctly"
finally:
CacheMemoryManager().enable()
def testCleanup(self):
try:
CacheMemoryManager().disable()
op = OpBlockedArrayCache(graph=self.opProvider.graph)
op.Input.connect(self.opProvider.Output)
s = self.opProvider.Output.meta.shape
op.innerBlockShape.setValue(s)
op.outerBlockShape.setValue(s)
op.fixAtCurrent.setValue(False)
x = op.Output[...].wait()
op.Input.disconnect()
op.cleanUp()
r = weakref.ref(op)
del op
gc.collect()
ref = r()
if ref is not None:
for i, o in enumerate(gc.get_referrers(ref)):
print "Object", i, ":", type(o), ":", o
assert r() is None, "OpBlockedArrayCache was not cleaned up correctly"
finally:
CacheMemoryManager().enable()
def import_labeling_layer(labelLayer, labelingSlots, parent_widget=None):
"""
Prompt the user for layer import settings, and perform the layer import.
:param labelLayer: The top label layer source
:param labelingSlots: An instance of LabelingGui.LabelingSlots
:param parent_widget: The Qt GUI parent object
"""
writeSeeds = labelingSlots.labelInput
assert isinstance(
writeSeeds,
lazyflow.graph.Slot), "slot is of type %r" % (type(writeSeeds))
opLabels = writeSeeds.getRealOperator()
assert isinstance(opLabels, lazyflow.graph.Operator
), "slot's operator is of type %r" % (type(opLabels))
recentlyImported = PreferencesManager().get('labeling',
'recently imported')
mostRecentProjectPath = PreferencesManager().get('shell',
'recently opened')
mostRecentImageFile = PreferencesManager().get('DataSelection',
'recent image')
if recentlyImported:
defaultDirectory = os.path.split(recentlyImported)[0]
elif mostRecentProjectPath:
defaultDirectory = os.path.split(mostRecentProjectPath)[0]
elif mostRecentImageFile:
defaultDirectory = os.path.split(mostRecentImageFile)[0]
else:
defaultDirectory = os.path.expanduser('~')
fileNames = DataSelectionGui.getImageFileNamesToOpen(
parent_widget, defaultDirectory)
fileNames = map(str, fileNames)
if not fileNames:
return
PreferencesManager().set('labeling', 'recently imported', fileNames[0])
try:
# Initialize operators
opImport = OpInputDataReader(parent=opLabels.parent)
opCache = OpBlockedArrayCache(parent=opLabels.parent)
opMetadataInjector = OpMetadataInjector(parent=opLabels.parent)
opReorderAxes = OpReorderAxes(parent=opLabels.parent)
# Set up the pipeline as follows:
#
# opImport --> opCache --> opMetadataInjector --------> opReorderAxes --(inject via setInSlot)--> labelInput
# / /
# User-specified axisorder labelInput.meta.axistags
opImport.WorkingDirectory.setValue(defaultDirectory)
opImport.FilePath.setValue(fileNames[0] if len(fileNames) ==
1 else os.path.pathsep.join(fileNames))
assert opImport.Output.ready()
opCache.Input.connect(opImport.Output)
opCache.CompressionEnabled.setValue(True)
assert opCache.Output.ready()
opMetadataInjector.Input.connect(opCache.Output)
metadata = opCache.Output.meta.copy()
opMetadataInjector.Metadata.setValue(metadata)
opReorderAxes.Input.connect(opMetadataInjector.Output)
# Transpose the axes for assignment to the labeling operator.
opReorderAxes.AxisOrder.setValue(writeSeeds.meta.getAxisKeys())
# We'll show a little window with a busy indicator while the data is loading
busy_dlg = QProgressDialog(parent=parent_widget)
busy_dlg.setLabelText("Importing Label Data...")
busy_dlg.setCancelButton(None)
busy_dlg.setMinimum(100)
busy_dlg.setMaximum(100)
def close_busy_dlg(*args):
QApplication.postEvent(busy_dlg, QCloseEvent())
# Load the data from file into our cache
# When it's done loading, close the progress dialog.
req = opCache.Output[:]
req.notify_finished(close_busy_dlg)
req.notify_failed(close_busy_dlg)
req.submit()
busy_dlg.exec_()
readData = req.result
maxLabels = len(labelingSlots.labelNames.value)
# Can't use return_counts feature because that requires numpy >= 1.9
#unique_read_labels, readLabelCounts = numpy.unique(readData, return_counts=True)
# This does the same as the above, albeit slower, and probably with more ram.
unique_read_labels = numpy.sort(vigra.analysis.unique(readData))
readLabelCounts = vigra_bincount(readData)[unique_read_labels]
labelInfo = (maxLabels, (unique_read_labels, readLabelCounts))
del readData
# Ask the user how to interpret the data.
settingsDlg = LabelImportOptionsDlg(parent_widget, fileNames,
opMetadataInjector.Output,
labelingSlots.labelInput,
labelInfo)
def handle_updated_axes():
# The user is specifying a new interpretation of the file's axes
updated_axisorder = str(settingsDlg.axesEdit.text())
metadata = opMetadataInjector.Metadata.value.copy()
metadata.axistags = vigra.defaultAxistags(updated_axisorder)
opMetadataInjector.Metadata.setValue(metadata)
if opReorderAxes._invalid_axes:
settingsDlg.buttonBox.button(
QDialogButtonBox.Ok).setEnabled(False)
# Red background
settingsDlg.axesEdit.setStyleSheet(
"QLineEdit { background: rgb(255, 128, 128);"
"selection-background-color: rgb(128, 128, 255); }")
settingsDlg.axesEdit.editingFinished.connect(handle_updated_axes)
# Initialize
handle_updated_axes()
dlg_result = settingsDlg.exec_()
if dlg_result != LabelImportOptionsDlg.Accepted:
return
# Get user's chosen label mapping from dlg
labelMapping = settingsDlg.labelMapping
# Get user's chosen offsets, ordered by the 'write seeds' slot
axes_5d = opReorderAxes.Output.meta.getAxisKeys()
tagged_offsets = collections.OrderedDict(
zip(axes_5d, [0] * len(axes_5d)))
tagged_offsets.update(
dict(
zip(opReorderAxes.Output.meta.getAxisKeys(),
settingsDlg.imageOffsets)))
imageOffsets = tagged_offsets.values()
# Optimization if mapping is identity
if labelMapping.keys() == labelMapping.values():
labelMapping = None
# This will be fast (it's already cached)
label_data = opReorderAxes.Output[:].wait()
# Map input labels to output labels
if labelMapping:
# There are other ways to do a relabeling (e.g skimage.segmentation.relabel_sequential)
# But this supports potentially huge values of unique_read_labels (in the billions),
# without needing GB of RAM.
mapping_indexes = numpy.searchsorted(unique_read_labels,
label_data)
new_labels = numpy.array(
[labelMapping[x] for x in unique_read_labels])
label_data[:] = new_labels[mapping_indexes]
label_roi = numpy.array(roiFromShape(opReorderAxes.Output.meta.shape))
label_roi += imageOffsets
label_slice = roiToSlice(*label_roi)
writeSeeds[label_slice] = label_data
finally:
opReorderAxes.cleanUp()
opMetadataInjector.cleanUp()
opCache.cleanUp()
opImport.cleanUp()
def import_labeling_layer(labelLayer, labelingSlots, parent_widget=None):
"""
Prompt the user for layer import settings, and perform the layer import.
:param labelLayer: The top label layer source
:param labelingSlots: An instance of LabelingGui.LabelingSlots
:param parent_widget: The Qt GUI parent object
"""
writeSeeds = labelingSlots.labelInput
assert isinstance(writeSeeds, lazyflow.graph.Slot), "slot is of type %r" % (type(writeSeeds))
opLabels = writeSeeds.getRealOperator()
assert isinstance(opLabels, lazyflow.graph.Operator), "slot's operator is of type %r" % (type(opLabels))
recentlyImported = PreferencesManager().get('labeling', 'recently imported')
mostRecentProjectPath = PreferencesManager().get('shell', 'recently opened')
mostRecentImageFile = PreferencesManager().get( 'DataSelection', 'recent image' )
if recentlyImported:
defaultDirectory = os.path.split(recentlyImported)[0]
elif mostRecentProjectPath:
defaultDirectory = os.path.split(mostRecentProjectPath)[0]
elif mostRecentImageFile:
defaultDirectory = os.path.split(mostRecentImageFile)[0]
else:
defaultDirectory = os.path.expanduser('~')
fileNames = DataSelectionGui.getImageFileNamesToOpen(parent_widget, defaultDirectory)
fileNames = list(map(str, fileNames))
if not fileNames:
return
PreferencesManager().set('labeling', 'recently imported', fileNames[0])
try:
# Initialize operators
opImport = OpInputDataReader( parent=opLabels.parent )
opCache = OpBlockedArrayCache( parent=opLabels.parent )
opMetadataInjector = OpMetadataInjector( parent=opLabels.parent )
opReorderAxes = OpReorderAxes( parent=opLabels.parent )
# Set up the pipeline as follows:
#
# opImport --> (opCache) --> opMetadataInjector --------> opReorderAxes --(inject via setInSlot)--> labelInput
# / /
# User-specified axisorder labelInput.meta.axistags
opImport.WorkingDirectory.setValue(defaultDirectory)
opImport.FilePath.setValue(fileNames[0] if len(fileNames) == 1 else
os.path.pathsep.join(fileNames))
assert opImport.Output.ready()
maxLabels = len(labelingSlots.labelNames.value)
# We don't bother with counting the label pixels
# (and caching the data) if it's big (1 GB)
if numpy.prod(opImport.Output.meta.shape) > 1e9:
reading_slot = opImport.Output
# For huge data, we don't go through and search for the pixel values,
# because that takes an annoyingly long amount of time.
# Instead, we make the reasonable assumption that the input labels are already 1,2,3..N
# and we don't tell the user what the label pixel counts are.
unique_read_labels = numpy.array(list(range(maxLabels+1)))
readLabelCounts = numpy.array([-1]*(maxLabels+1))
labelInfo = (maxLabels, (unique_read_labels, readLabelCounts))
else:
opCache.Input.connect( opImport.Output )
opCache.CompressionEnabled.setValue(True)
assert opCache.Output.ready()
reading_slot = opCache.Output
# We'll show a little window with a busy indicator while the data is loading
busy_dlg = QProgressDialog(parent=parent_widget)
busy_dlg.setLabelText("Scanning Label Data...")
busy_dlg.setCancelButton(None)
busy_dlg.setMinimum(100)
busy_dlg.setMaximum(100)
def close_busy_dlg(*args):
QApplication.postEvent(busy_dlg, QCloseEvent())
# Load the data from file into our cache
# When it's done loading, close the progress dialog.
req = reading_slot[:]
req.notify_finished( close_busy_dlg )
req.notify_failed( close_busy_dlg )
req.submit()
busy_dlg.exec_()
readData = req.result
# Can't use return_counts feature because that requires numpy >= 1.9
#unique_read_labels, readLabelCounts = numpy.unique(readData, return_counts=True)
# This does the same as the above, albeit slower, and probably with more ram.
bincounts = chunked_bincount(readData)
unique_read_labels = bincounts.nonzero()[0].astype(readData.dtype, copy=False)
readLabelCounts = bincounts[unique_read_labels]
labelInfo = (maxLabels, (unique_read_labels, readLabelCounts))
del readData
opMetadataInjector.Input.connect( reading_slot )
metadata = reading_slot.meta.copy()
opMetadataInjector.Metadata.setValue( metadata )
opReorderAxes.Input.connect( opMetadataInjector.Output )
# Transpose the axes for assignment to the labeling operator.
opReorderAxes.AxisOrder.setValue( writeSeeds.meta.getAxisKeys() )
# Ask the user how to interpret the data.
settingsDlg = LabelImportOptionsDlg( parent_widget,
fileNames, opMetadataInjector.Output,
labelingSlots.labelInput, labelInfo )
def handle_updated_axes():
# The user is specifying a new interpretation of the file's axes
updated_axisorder = str(settingsDlg.axesEdit.text())
metadata = opMetadataInjector.Metadata.value.copy()
metadata.axistags = vigra.defaultAxistags(updated_axisorder)
opMetadataInjector.Metadata.setValue( metadata )
if opReorderAxes._invalid_axes:
settingsDlg.buttonBox.button(QDialogButtonBox.Ok).setEnabled(False)
# Red background
settingsDlg.axesEdit.setStyleSheet("QLineEdit { background: rgb(255, 128, 128);"
"selection-background-color: rgb(128, 128, 255); }")
settingsDlg.axesEdit.editingFinished.connect( handle_updated_axes )
# Initialize
handle_updated_axes()
dlg_result = settingsDlg.exec_()
if dlg_result != LabelImportOptionsDlg.Accepted:
return
# Get user's chosen label mapping from dlg
labelMapping = settingsDlg.labelMapping
# Get user's chosen offsets, ordered by the 'write seeds' slot
axes_5d = opReorderAxes.Output.meta.getAxisKeys()
tagged_offsets = collections.OrderedDict( list(zip( axes_5d, [0]*len(axes_5d) )) )
tagged_offsets.update( dict( list(zip( opReorderAxes.Output.meta.getAxisKeys(), settingsDlg.imageOffsets )) ) )
imageOffsets = list(tagged_offsets.values())
# Optimization if mapping is identity
if list(labelMapping.keys()) == list(labelMapping.values()):
labelMapping = None
# If the data was already cached, this will be fast.
label_data = opReorderAxes.Output[:].wait()
# Map input labels to output labels
if labelMapping:
# There are other ways to do a relabeling (e.g skimage.segmentation.relabel_sequential)
# But this supports potentially huge values of unique_read_labels (in the billions),
# without needing GB of RAM.
mapping_indexes = numpy.searchsorted(unique_read_labels, label_data)
new_labels = numpy.array([labelMapping[x] for x in unique_read_labels])
label_data[:] = new_labels[mapping_indexes]
label_roi = numpy.array( roiFromShape(opReorderAxes.Output.meta.shape) )
label_roi += imageOffsets
label_slice = roiToSlice(*label_roi)
writeSeeds[label_slice] = label_data
finally:
opReorderAxes.cleanUp()
opMetadataInjector.cleanUp()
opCache.cleanUp()
opImport.cleanUp()
def import_labeling_layer(labelLayer, labelingSlots, parent_widget=None):
"""
Prompt the user for layer import settings, and perform the layer import.
:param labelLayer: The top label layer source
:param labelingSlots: An instance of LabelingGui.LabelingSlots
:param parent_widget: The Qt GUI parent object
"""
writeSeeds = labelingSlots.labelInput
assert isinstance(
writeSeeds,
lazyflow.graph.Slot), "slot is of type %r" % (type(writeSeeds))
opLabels = writeSeeds.getRealOperator()
assert isinstance(opLabels, lazyflow.graph.Operator
), "slot's operator is of type %r" % (type(opLabels))
fileNames = ImageFileDialog(
parent_widget,
preferences_group="labeling",
preferences_setting="recently imported").getSelectedPaths()
fileNames = list(map(str, fileNames))
if not fileNames:
return
try:
# Initialize operators
opImport = OpInputDataReader(parent=opLabels.parent)
opCache = OpBlockedArrayCache(parent=opLabels.parent)
opMetadataInjector = OpMetadataInjector(parent=opLabels.parent)
opReorderAxes = OpReorderAxes(parent=opLabels.parent)
# Set up the pipeline as follows:
#
# opImport --> (opCache) --> opMetadataInjector --------> opReorderAxes --(inject via setInSlot)--> labelInput
# / /
# User-specified axisorder labelInput.meta.axistags
opImport.FilePath.setValue(fileNames[0] if len(fileNames) ==
1 else os.path.pathsep.join(fileNames))
assert opImport.Output.ready()
maxLabels = len(labelingSlots.labelNames.value)
# We don't bother with counting the label pixels
# (and caching the data) if it's big (1 GB)
if numpy.prod(opImport.Output.meta.shape) > 1e9:
reading_slot = opImport.Output
# For huge data, we don't go through and search for the pixel values,
# because that takes an annoyingly long amount of time.
# Instead, we make the reasonable assumption that the input labels are already 1,2,3..N
# and we don't tell the user what the label pixel counts are.
unique_read_labels = numpy.array(list(range(maxLabels + 1)))
readLabelCounts = numpy.array([-1] * (maxLabels + 1))
labelInfo = (maxLabels, (unique_read_labels, readLabelCounts))
else:
opCache.Input.connect(opImport.Output)
opCache.CompressionEnabled.setValue(True)
assert opCache.Output.ready()
reading_slot = opCache.Output
# We'll show a little window with a busy indicator while the data is loading
busy_dlg = QProgressDialog(parent=parent_widget)
busy_dlg.setLabelText("Scanning Label Data...")
busy_dlg.setCancelButton(None)
busy_dlg.setMinimum(100)
busy_dlg.setMaximum(100)
def close_busy_dlg(*args):
QApplication.postEvent(busy_dlg, QCloseEvent())
# Load the data from file into our cache
# When it's done loading, close the progress dialog.
req = reading_slot[:]
req.notify_finished(close_busy_dlg)
req.notify_failed(close_busy_dlg)
req.submit()
busy_dlg.exec_()
readData = req.result
# Can't use return_counts feature because that requires numpy >= 1.9
# unique_read_labels, readLabelCounts = numpy.unique(readData, return_counts=True)
# This does the same as the above, albeit slower, and probably with more ram.
bincounts = chunked_bincount(readData)
unique_read_labels = bincounts.nonzero()[0].astype(readData.dtype,
copy=False)
readLabelCounts = bincounts[unique_read_labels]
labelInfo = (maxLabels, (unique_read_labels, readLabelCounts))
del readData
opMetadataInjector.Input.connect(reading_slot)
metadata = reading_slot.meta.copy()
opMetadataInjector.Metadata.setValue(metadata)
opReorderAxes.Input.connect(opMetadataInjector.Output)
# Transpose the axes for assignment to the labeling operator.
opReorderAxes.AxisOrder.setValue(writeSeeds.meta.getAxisKeys())
# Ask the user how to interpret the data.
settingsDlg = LabelImportOptionsDlg(parent_widget, fileNames,
opMetadataInjector.Output,
labelingSlots.labelInput,
labelInfo)
def handle_updated_axes():
# The user is specifying a new interpretation of the file's axes
updated_axisorder = str(settingsDlg.axesEdit.text())
metadata = opMetadataInjector.Metadata.value.copy()
metadata.axistags = vigra.defaultAxistags(updated_axisorder)
opMetadataInjector.Metadata.setValue(metadata)
if opReorderAxes._invalid_axes:
settingsDlg.buttonBox.button(
QDialogButtonBox.Ok).setEnabled(False)
# Red background
settingsDlg.axesEdit.setStyleSheet(
"QLineEdit { background: rgb(255, 128, 128); selection-background-color: rgb(128, 128, 255); }"
)
settingsDlg.axesEdit.editingFinished.connect(handle_updated_axes)
# Initialize
handle_updated_axes()
dlg_result = settingsDlg.exec_()
if dlg_result != LabelImportOptionsDlg.Accepted:
return
# Get user's chosen label mapping from dlg
labelMapping = settingsDlg.labelMapping
# Get user's chosen offsets, ordered by the 'write seeds' slot
axes_5d = opReorderAxes.Output.meta.getAxisKeys()
tagged_offsets = collections.OrderedDict(
list(zip(axes_5d, [0] * len(axes_5d))))
tagged_offsets.update(
dict(
list(
zip(opReorderAxes.Output.meta.getAxisKeys(),
settingsDlg.imageOffsets))))
imageOffsets = list(tagged_offsets.values())
# Optimization if mapping is identity
if list(labelMapping.keys()) == list(labelMapping.values()):
labelMapping = None
# If the data was already cached, this will be fast.
label_data = opReorderAxes.Output[:].wait()
# Map input labels to output labels
if labelMapping:
# There are other ways to do a relabeling (e.g skimage.segmentation.relabel_sequential)
# But this supports potentially huge values of unique_read_labels (in the billions),
# without needing GB of RAM.
mapping_indexes = numpy.searchsorted(unique_read_labels,
label_data)
new_labels = numpy.array(
[labelMapping[x] for x in unique_read_labels])
label_data[:] = new_labels[mapping_indexes]
label_roi = numpy.array(roiFromShape(opReorderAxes.Output.meta.shape))
label_roi += imageOffsets
label_slice = roiToSlice(*label_roi)
writeSeeds[label_slice] = label_data
finally:
opReorderAxes.cleanUp()
opMetadataInjector.cleanUp()
opCache.cleanUp()
opImport.cleanUp()