def setupOutputs(self):
self.cleanupOnDiskView()
# FIXME: If RawData becomes unready() at the same time as RawDatasetInfo(), then
# we have no guarantees about which one will trigger setupOutputs() first.
# It is therefore possible for 'RawDatasetInfo' to appear ready() to us,
# even though it's upstream partner is UNready. We are about to get the
# unready() notification, but it will come too late to prevent our
# setupOutputs method from being called.
# Without proper graph setup transaction semantics, we have to use this
# hack as a workaround.
try:
rawInfo = self.RawDatasetInfo.value
except:
for oslot in self.outputs.values():
if oslot.partner is None:
oslot.meta.NOTREADY = True
return
dataset_dir = PathComponents(rawInfo.filePath).externalDirectory
abs_dataset_dir, _ = getPathVariants(dataset_dir,
self.WorkingDirectory.value)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
known_keys['nickname'] = rawInfo.nickname
# Disconnect to open the 'transaction'
if self._opImageOnDiskProvider is not None:
self._opImageOnDiskProvider.TransactionSlot.disconnect()
self._opFormattedExport.TransactionSlot.disconnect()
# Blank the internal path while we manipulate the external path
# to avoid invalid intermediate states of ExportPath
self._opFormattedExport.OutputInternalPath.setValue("")
# use partial formatting to fill in non-coordinate name fields
name_format = self.OutputFilenameFormat.value
partially_formatted_name = format_known_keys(name_format, known_keys)
# Convert to absolute path before configuring the internal op
abs_path, _ = getPathVariants(partially_formatted_name,
self.WorkingDirectory.value)
self._opFormattedExport.OutputFilenameFormat.setValue(abs_path)
# use partial formatting on the internal dataset name, too
internal_dataset_format = self.OutputInternalPath.value
partially_formatted_dataset_name = format_known_keys(
internal_dataset_format, known_keys)
self._opFormattedExport.OutputInternalPath.setValue(
partially_formatted_dataset_name)
# Re-connect to finish the 'transaction'
self._opFormattedExport.TransactionSlot.connect(self.TransactionSlot)
if self._opImageOnDiskProvider is not None:
self._opImageOnDiskProvider.TransactionSlot.connect(
self.TransactionSlot)
self.setupOnDiskView()
def setupOutputs(self):
# FIXME: If RawData becomes unready() at the same time as RawDatasetInfo(), then
# we have no guarantees about which one will trigger setupOutputs() first.
# It is therefore possible for 'RawDatasetInfo' to appear ready() to us,
# even though it's upstream partner is UNready. We are about to get the
# unready() notification, but it will come too late to prevent our
# setupOutputs method from being called.
# Without proper graph setup transaction semantics, we have to use this
# hack as a workaround.
try:
rawInfo = self.RawDatasetInfo.value
except:
for oslot in list(self.outputs.values()):
if oslot.upstream_slot is None:
oslot.meta.NOTREADY = True
return
selection_index = self.InputSelection.value
if not self.Inputs[selection_index].ready():
for oslot in list(self.outputs.values()):
if oslot.upstream_slot is None:
oslot.meta.NOTREADY = True
return
self._opFormattedExport.Input.connect(self.Inputs[selection_index])
dataset_dir = str(rawInfo.default_output_dir)
abs_dataset_dir, _ = getPathVariants(dataset_dir, self.WorkingDirectory.value)
known_keys = {}
known_keys["dataset_dir"] = abs_dataset_dir
nickname = rawInfo.nickname.replace("*", "")
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
known_keys["nickname"] = nickname
result_types = self.SelectionNames.value
known_keys["result_type"] = result_types[selection_index]
self._opFormattedExport.TransactionSlot.disconnect()
# Blank the internal path while we manipulate the external path
# to avoid invalid intermediate states of ExportPath
self._opFormattedExport.OutputInternalPath.setValue("")
# use partial formatting to fill in non-coordinate name fields
name_format = self.OutputFilenameFormat.value
partially_formatted_name = format_known_keys(name_format, known_keys)
# Convert to absolute path before configuring the internal op
abs_path, _ = getPathVariants(partially_formatted_name, self.WorkingDirectory.value)
self._opFormattedExport.OutputFilenameFormat.setValue(abs_path)
# use partial formatting on the internal dataset name, too
internal_dataset_format = self.OutputInternalPath.value
partially_formatted_dataset_name = format_known_keys(internal_dataset_format, known_keys)
self._opFormattedExport.OutputInternalPath.setValue(partially_formatted_dataset_name)
# Re-connect to finish the 'transaction'
self._opFormattedExport.TransactionSlot.connect(self.TransactionSlot)
def setupOutputs(self):
self.cleanupOnDiskView()
# FIXME: If RawData becomes unready() at the same time as RawDatasetInfo(), then
# we have no guarantees about which one will trigger setupOutputs() first.
# It is therefore possible for 'RawDatasetInfo' to appear ready() to us,
# even though it's upstream partner is UNready. We are about to get the
# unready() notification, but it will come too late to prevent our
# setupOutputs method from being called.
# Without proper graph setup transaction semantics, we have to use this
# hack as a workaround.
try:
rawInfo = self.RawDatasetInfo.value
except:
for oslot in self.outputs.values():
if oslot.partner is None:
oslot.meta.NOTREADY = True
return
dataset_dir = PathComponents(rawInfo.filePath).externalDirectory
abs_dataset_dir, _ = getPathVariants(dataset_dir, self.WorkingDirectory.value)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
known_keys['nickname'] = rawInfo.nickname
# Disconnect to open the 'transaction'
if self._opImageOnDiskProvider is not None:
self._opImageOnDiskProvider.TransactionSlot.disconnect()
self._opFormattedExport.TransactionSlot.disconnect()
# Blank the internal path while we manipulate the external path
# to avoid invalid intermediate states of ExportPath
self._opFormattedExport.OutputInternalPath.setValue( "" )
# use partial formatting to fill in non-coordinate name fields
name_format = self.OutputFilenameFormat.value
partially_formatted_name = format_known_keys( name_format, known_keys )
# Convert to absolute path before configuring the internal op
abs_path, _ = getPathVariants( partially_formatted_name, self.WorkingDirectory.value )
self._opFormattedExport.OutputFilenameFormat.setValue( abs_path )
# use partial formatting on the internal dataset name, too
internal_dataset_format = self.OutputInternalPath.value
partially_formatted_dataset_name = format_known_keys( internal_dataset_format, known_keys )
self._opFormattedExport.OutputInternalPath.setValue( partially_formatted_dataset_name )
# Re-connect to finish the 'transaction'
self._opFormattedExport.TransactionSlot.connect( self.TransactionSlot )
if self._opImageOnDiskProvider is not None:
self._opImageOnDiskProvider.TransactionSlot.connect( self.TransactionSlot )
self.setupOnDiskView()
def post_process_lane_export(self, lane_index):
# FIXME: This probably only works for the non-blockwise export slot.
# We should assert that the user isn't using the blockwise slot.
settings, selected_features = self.trackingApplet.topLevelOperator.getLane(lane_index).get_table_export_settings()
from lazyflow.utility import PathComponents, make_absolute, format_known_keys
if settings:
self.dataExportTrackingApplet.progressSignal.emit(-1)
raw_dataset_info = self.dataSelectionApplet.topLevelOperator.DatasetGroup[lane_index][0].value
project_path = self.shell.projectManager.currentProjectPath
project_dir = os.path.dirname(project_path)
dataset_dir = PathComponents(raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_dir)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
known_keys['nickname'] = nickname
# use partial formatting to fill in non-coordinate name fields
name_format = settings['file path']
partially_formatted_name = format_known_keys( name_format, known_keys )
settings['file path'] = partially_formatted_name
req = self.trackingApplet.topLevelOperator.getLane(lane_index).export_object_data(
lane_index,
# FIXME: Even in non-headless mode, we can't show the gui because we're running in a non-main thread.
# That's not a huge deal, because there's still a progress bar for the overall export.
show_gui=False)
req.wait()
self.dataExportTrackingApplet.progressSignal.emit(100)
def _executeExportPath(self, result):
path_format = self.OutputFilenameFormat.value
file_extension = self._export_impls[ self.OutputFormat.value ][0]
# Remove existing extension (if present) and add the correct extension (if any)
if file_extension:
path_format = os.path.splitext(path_format)[0]
path_format += '.' + file_extension
# Provide the TOTAL path (including dataset name)
if self.OutputFormat.value == 'hdf5':
path_format += '/' + self.OutputInternalPath.value
roi = numpy.array( roiFromShape(self.Input.meta.shape) )
# Intermediate state can cause coordinate offset and input shape to be mismatched.
# Just don't use the offset if it looks wrong.
# (The client will provide a valid offset later on.)
if self.CoordinateOffset.ready() and len(self.CoordinateOffset.value) == len(roi[0]):
offset = self.CoordinateOffset.value
assert len(roi[0] == len(offset))
roi += offset
optional_replacements = {}
optional_replacements['roi'] = map(tuple, roi)
for key, (start, stop) in zip( self.Input.meta.getAxisKeys(), roi.transpose() ):
optional_replacements[key + '_start'] = start
optional_replacements[key + '_stop'] = stop
formatted_path = format_known_keys( path_format, optional_replacements )
result[0] = formatted_path
return result
def _executeExportPath(self, result):
path_format = self.OutputFilenameFormat.value
file_extension = self._export_impls[self.OutputFormat.value][0]
# Remove existing extension (if present) and add the correct extension (if any)
if file_extension:
path_format = os.path.splitext(path_format)[0]
path_format += '.' + file_extension
# Provide the TOTAL path (including dataset name)
if self.OutputFormat.value == 'hdf5':
path_format += '/' + self.OutputInternalPath.value
roi = numpy.array(roiFromShape(self.Input.meta.shape))
# Intermediate state can cause coordinate offset and input shape to be mismatched.
# Just don't use the offset if it looks wrong.
# (The client will provide a valid offset later on.)
if self.CoordinateOffset.ready() and len(
self.CoordinateOffset.value) == len(roi[0]):
offset = self.CoordinateOffset.value
assert len(roi[0] == len(offset))
roi += offset
optional_replacements = {}
optional_replacements['roi'] = map(tuple, roi)
for key, (start, stop) in zip(self.Input.meta.getAxisKeys(),
roi.transpose()):
optional_replacements[key + '_start'] = start
optional_replacements[key + '_stop'] = stop
formatted_path = format_known_keys(path_format, optional_replacements)
result[0] = formatted_path
return result
def _handleFormatChange(self, index):
file_format = str(self.formatCombo.currentText())
option_widget = self._format_option_editors[file_format]
self._opDataExport.OutputFormat.setValue(file_format)
# Auto-remove any instance of 'slice_index' from the
# dataset path if the user switches to a non-sequence type
# TODO: This is a little hacky. Could be fixed by defining an ABC for
# file option widgets with a 'repair path' method or something
# similar, but that seems like overkill for now.
export_path = str(self._opDataExport.OutputFilenameFormat.value)
if not isinstance(option_widget, StackExportFileOptionsWidget) \
and re.search('{slice_index.*}', export_path):
try:
from lazyflow.utility import format_known_keys
export_path = format_known_keys(export_path,
{'slice_index': 1234567890})
export_path = export_path.replace('1234567890', '')
except:
pass
else:
self._opDataExport.OutputFilenameFormat.setValue(export_path)
# Show the new option widget
self.stackedWidget.setCurrentWidget(option_widget)
self._handlePathValidityChange()
def _handleFormatChange(self, index):
file_format = str(self.formatCombo.currentText())
option_widget = self._format_option_editors[file_format]
self._opDataExport.OutputFormat.setValue(file_format)
# Auto-remove any instance of 'slice_index' from the
# dataset path if the user switches to a non-sequence type
# TODO: This is a little hacky. Could be fixed by defining an ABC for
# file option widgets with a 'repair path' method or something
# similar, but that seems like overkill for now.
export_path = str(self._opDataExport.OutputFilenameFormat.value)
if not isinstance(option_widget, StackExportFileOptionsWidget) and re.search("{slice_index.*}", export_path):
try:
from lazyflow.utility import format_known_keys
export_path = format_known_keys(export_path, {"slice_index": 1234567890})
export_path = export_path.replace("1234567890", "")
except:
pass
else:
self._opDataExport.OutputFilenameFormat.setValue(export_path)
# Show the new option widget
self.stackedWidget.setCurrentWidget(option_widget)
self._handlePathValidityChange()
def _executeExportPath(self, result):
path_format = self.OutputFilenameFormat.value
file_extension = self._export_impls[ self.OutputFormat.value ][0]
# Remove existing extension (if present) and add the correct extension
path_format = os.path.splitext(path_format)[0]
path_format += '.' + file_extension
# Provide the TOTAL path (including dataset name)
if self.OutputFormat.value == 'hdf5':
path_format += '/' + self.OutputInternalPath.value
roi = numpy.array( roiFromShape(self.Input.meta.shape) )
if self.CoordinateOffset.ready():
offset = self.CoordinateOffset.value
assert len(roi[0] == len(offset))
roi += offset
optional_replacements = {}
optional_replacements['roi'] = map(tuple, roi)
for key, (start, stop) in zip( self.Input.meta.getAxisKeys(), roi.transpose() ):
optional_replacements[key + '_start'] = start
optional_replacements[key + '_stop'] = stop
formatted_path = format_known_keys( path_format, optional_replacements )
result[0] = formatted_path
return result
def post_process_lane_export(self, lane_index):
# FIXME: This probably only works for the non-blockwise export slot.
# We should assert that the user isn't using the blockwise slot.
settings, selected_features = self.trackingApplet.topLevelOperator.getLane(lane_index).get_table_export_settings()
from lazyflow.utility import PathComponents, make_absolute, format_known_keys
if settings:
self.dataExportTrackingApplet.progressSignal.emit(-1)
raw_dataset_info = self.dataSelectionApplet.topLevelOperator.DatasetGroup[lane_index][0].value
project_path = self.shell.projectManager.currentProjectPath
project_dir = os.path.dirname(project_path)
dataset_dir = PathComponents(raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_dir)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
known_keys['nickname'] = nickname
# use partial formatting to fill in non-coordinate name fields
name_format = settings['file path']
partially_formatted_name = format_known_keys( name_format, known_keys )
settings['file path'] = partially_formatted_name
req = self.trackingApplet.topLevelOperator.getLane(lane_index).export_object_data(
lane_index,
# FIXME: Even in non-headless mode, we can't show the gui because we're running in a non-main thread.
# That's not a huge deal, because there's still a progress bar for the overall export.
show_gui=False)
req.wait()
self.dataExportTrackingApplet.progressSignal.emit(100)
def format_path(self, path_template: str) -> str:
dataset_dir = str(self._dataset_info.default_output_dir)
abs_dataset_dir, _ = getPathVariants(dataset_dir, self._working_dir)
nickname = self._dataset_info.nickname.replace("*", "")
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(
os.path.pathsep)[0]).fileNameBase
known_keys = {"dataset_dir": abs_dataset_dir, "nickname": nickname}
if self._result_type:
known_keys["result_type"] = self._result_type
return format_known_keys(path_template, known_keys)
def getPartiallyFormattedName(self, lane_index, path_format_string):
''' Takes the format string for the output file, fills in the most important placeholders, and returns it '''
raw_dataset_info = self.dataSelectionApplet.topLevelOperator.DatasetGroup[lane_index][0].value
project_path = self.shell.projectManager.currentProjectPath
project_dir = os.path.dirname(project_path)
dataset_dir = PathComponents(raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_dir)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
known_keys['nickname'] = nickname
known_keys['result_type'] = self.dataExportTrackingApplet.topLevelOperator.SelectedPlugin._value
# use partial formatting to fill in non-coordinate name fields
partially_formatted_name = format_known_keys(path_format_string, known_keys)
return partially_formatted_name
def getPartiallyFormattedName(self, lane_index, path_format_string):
''' Takes the format string for the output file, fills in the most important placeholders, and returns it '''
raw_dataset_info = self.dataSelectionApplet.topLevelOperator.DatasetGroup[lane_index][0].value
project_path = self.shell.projectManager.currentProjectPath
project_dir = os.path.dirname(project_path)
dataset_dir = PathComponents(raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_dir)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
known_keys['nickname'] = nickname
known_keys['result_type'] = self.dataExportTrackingApplet.topLevelOperator.SelectedPlugin._value
# use partial formatting to fill in non-coordinate name fields
partially_formatted_name = format_known_keys(path_format_string, known_keys)
return partially_formatted_name
def post_process_lane_export(self, lane_index):
settings, selected_features = self.trackingApplet.topLevelOperator.getLane(
lane_index).get_table_export_settings()
if settings:
self.dataExportApplet.progressSignal.emit(0)
raw_dataset_info = self.dataSelectionApplet.topLevelOperator.DatasetGroup[
lane_index][0].value
project_path = self.shell.projectManager.currentProjectPath
project_dir = os.path.dirname(project_path)
dataset_dir = PathComponents(
raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_dir)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(
os.path.pathsep)[0]).fileNameBase
known_keys['nickname'] = nickname
# use partial formatting to fill in non-coordinate name fields
name_format = settings['file path']
partially_formatted_name = format_known_keys(
name_format, known_keys)
settings['file path'] = partially_formatted_name
req = self.trackingApplet.topLevelOperator.getLane(
lane_index
).export_object_data(
lane_index,
# FIXME: Even in non-headless mode, we can't show the gui because we're running in a non-main thread.
# That's not a huge deal, because there's still a progress bar for the overall export.
show_gui=False)
req.wait()
self.dataExportApplet.progressSignal.emit(100)
# Restore state of axis ranges
parameters = self.trackingApplet.topLevelOperator.Parameters.value
parameters['time_range'] = self.prev_time_range
parameters['x_range'] = self.prev_x_range
parameters['y_range'] = self.prev_y_range
parameters['z_range'] = self.prev_z_range
def getPartiallyFormattedName(self, lane_index: int, path_format_string: str) -> str:
''' Takes the format string for the output file, fills in the most important placeholders, and returns it '''
raw_dataset_info = self.topLevelOperator.RawDatasetInfo[lane_index].value
project_path = self.topLevelOperator.WorkingDirectory.value
dataset_dir = PathComponents(raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_path)
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
known_keys = {
'dataset_dir': abs_dataset_dir,
'nickname': nickname,
'result_type': self.topLevelOperator.SelectedPlugin._value,
}
return format_known_keys(path_format_string, known_keys)
def post_process_lane_export(self, lane_index):
settings, selected_features = self.trackingApplet.topLevelOperator.getLane(lane_index).get_table_export_settings()
if settings:
self.dataExportApplet.progressSignal.emit(0)
raw_dataset_info = self.dataSelectionApplet.topLevelOperator.DatasetGroup[lane_index][0].value
project_path = self.shell.projectManager.currentProjectPath
project_dir = os.path.dirname(project_path)
dataset_dir = PathComponents(raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_dir)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
known_keys['nickname'] = nickname
# use partial formatting to fill in non-coordinate name fields
name_format = settings['file path']
partially_formatted_name = format_known_keys( name_format, known_keys )
settings['file path'] = partially_formatted_name
req = self.trackingApplet.topLevelOperator.getLane(lane_index).export_object_data(
lane_index,
# FIXME: Even in non-headless mode, we can't show the gui because we're running in a non-main thread.
# That's not a huge deal, because there's still a progress bar for the overall export.
show_gui=False)
req.wait()
self.dataExportApplet.progressSignal.emit(100)
# Restore state of axis ranges
parameters = self.trackingApplet.topLevelOperator.Parameters.value
parameters['time_range'] = self.prev_time_range
parameters['x_range'] = self.prev_x_range
parameters['y_range'] = self.prev_y_range
parameters['z_range'] = self.prev_z_range
def setupOutputs(self):
# Prepare subregion operator
total_roi = roiFromShape( self.Input.meta.shape )
total_roi = map( tuple, total_roi )
# Default to full roi
new_start, new_stop = total_roi
if self.RegionStart.ready():
# RegionStart is permitted to contain 'None' values, which we replace with zeros
new_start = map(lambda x: x or 0, self.RegionStart.value)
if self.RegionStop.ready():
# RegionStop is permitted to contain 'None' values,
# which we replace with the full extent of the corresponding axis
new_stop = map( lambda (x, extent): x or extent, zip(self.RegionStop.value, total_roi[1]) )
else:
self._opSubRegion.Stop.setValue( tuple(total_roi[1]) )
if not self._opSubRegion.Start.ready() or \
not self._opSubRegion.Stop.ready() or \
self._opSubRegion.Start.value != new_start or \
self._opSubRegion.Stop.value != new_stop:
# Disconnect first to ensure that the start/stop slots are applied together (atomically)
self._opSubRegion.Stop.disconnect()
# Provide the coordinate offset, but only for the axes that are present in the output image
tagged_input_offset = collections.defaultdict( lambda: -1, zip(self.Input.meta.getAxisKeys(), new_start ) )
output_axes = self._opReorderAxes.AxisOrder.value
output_offset = [ tagged_input_offset[axis] for axis in output_axes ]
output_offset = tuple( filter( lambda x: x != -1, output_offset ) )
self._opExportSlot.CoordinateOffset.setValue( output_offset )
self._opSubRegion.Start.setValue( tuple(new_start) )
self._opSubRegion.Stop.setValue( tuple(new_stop) )
# Set up normalization and dtype conversion
export_dtype = self.Input.meta.dtype
if self.ExportDtype.ready():
export_dtype = self.ExportDtype.value
need_normalize = ( self.InputMin.ready() and
self.InputMax.ready() and
self.ExportMin.ready() and
self.ExportMax.ready() )
if need_normalize:
minVal, maxVal = self.InputMin.value, self.InputMax.value
outputMinVal, outputMaxVal = self.ExportMin.value, self.ExportMax.value
# Force a drange onto the input slot metadata.
# opNormalizeAndConvert is an OpPixelOperator,
# which transforms the drange correctly in this case.
self._opDrangeInjection.Metadata.setValue( { 'drange' : (minVal, maxVal) } )
def normalize(a):
numerator = numpy.float64(outputMaxVal) - numpy.float64(outputMinVal)
denominator = numpy.float64(maxVal) - numpy.float64(minVal)
if denominator != 0.0:
frac = numpy.float32(numerator / denominator)
else:
# Denominator was zero. The user is probably just temporarily changing the values.
frac = numpy.float32(0.0)
result = numpy.asarray(outputMinVal + (a - minVal) * frac, export_dtype)
return result
self._opNormalizeAndConvert.Function.setValue( normalize )
# The OpPixelOperator sets the drange correctly using the function we give it.
output_drange = self._opNormalizeAndConvert.Output.meta.drange
assert type(output_drange[0]) == export_dtype
assert type(output_drange[1]) == export_dtype
else:
# We have no drange to set.
# If the original slot metadata had a drange,
# it will be propagated downstream anyway.
self._opDrangeInjection.Metadata.setValue( {} )
# No normalization: just identity function with dtype conversion
self._opNormalizeAndConvert.Function.setValue( lambda a: numpy.asarray(a, export_dtype) )
# Use user-provided axis order if specified
if self.OutputAxisOrder.ready():
self._opReorderAxes.AxisOrder.setValue( self.OutputAxisOrder.value )
else:
axistags = self.Input.meta.axistags
self._opReorderAxes.AxisOrder.setValue( "".join( tag.key for tag in axistags ) )
# Obtain values for possible name fields
roi = [ tuple(self._opSubRegion.Start.value), tuple(self._opSubRegion.Stop.value) ]
known_keys = { 'roi' : roi }
# Blank the internal path while we update the external path
# to avoid invalid intermediate states of ExportPath
self._opExportSlot.OutputInternalPath.setValue( "" )
# use partial formatting to fill in non-coordinate name fields
name_format = self.OutputFilenameFormat.value
partially_formatted_path = format_known_keys( name_format, known_keys )
self._opExportSlot.OutputFilenameFormat.setValue( partially_formatted_path )
internal_dataset_format = self.OutputInternalPath.value
partially_formatted_dataset_name = format_known_keys( internal_dataset_format, known_keys )
self._opExportSlot.OutputInternalPath.setValue( partially_formatted_dataset_name )
def setupOutputs(self):
new_start, new_stop = self.get_new_roi()
# If we're in the process of switching input data,
# then the roi dimensionality might not match up.
# Just leave the roi disconnected for now.
if len(self.Input.meta.shape) != len(new_start) or len(self.Input.meta.shape) != len(new_stop):
self._opSubRegion.Roi.disconnect()
elif not self._opSubRegion.Roi.ready() or self._opSubRegion.Roi.value != (new_start, new_stop):
self._opSubRegion.Roi.setValue((new_start, new_stop))
# Set up normalization and dtype conversion
export_dtype = self.Input.meta.dtype
if self.ExportDtype.ready():
export_dtype = self.ExportDtype.value
need_normalize = (
self.InputMin.ready() and self.InputMax.ready() and self.ExportMin.ready() and self.ExportMax.ready()
)
if need_normalize:
minVal, maxVal = self.InputMin.value, self.InputMax.value
outputMinVal, outputMaxVal = self.ExportMin.value, self.ExportMax.value
# Force a drange onto the input slot metadata.
# opNormalizeAndConvert is an OpPixelOperator,
# which transforms the drange correctly in this case.
self._opDrangeInjection.Metadata.setValue({"drange": (minVal, maxVal)})
def normalize(a):
numerator = numpy.float64(outputMaxVal) - numpy.float64(outputMinVal)
denominator = numpy.float64(maxVal) - numpy.float64(minVal)
if denominator != 0.0:
frac = numpy.float32(numerator / denominator)
else:
# Denominator was zero. The user is probably just temporarily changing the values.
frac = numpy.float32(0.0)
result = numpy.asarray(outputMinVal + (a - minVal) * frac, export_dtype)
return result
self._opNormalizeAndConvert.Function.setValue(normalize)
# The OpPixelOperator sets the drange correctly using the function we give it.
output_drange = self._opNormalizeAndConvert.Output.meta.drange
assert type(output_drange[0]) == export_dtype
assert type(output_drange[1]) == export_dtype
else:
# We have no drange to set.
# If the original slot metadata had a drange,
# it will be propagated downstream anyway.
self._opDrangeInjection.Metadata.setValue({})
# No normalization: just identity function with dtype conversion
self._opNormalizeAndConvert.Function.setValue(lambda a: numpy.asarray(a, export_dtype))
# Use user-provided axis order if specified
user_provided = False
if self.OutputAxisOrder.ready():
try:
self._opReorderAxes.AxisOrder.setValue(self.OutputAxisOrder.value)
user_provided = True
except KeyError:
# FIXME: Why does the above line fail sometimes?
warnings.warn("Ignoring invalid axis order setting")
if not user_provided:
if self.Input.meta.original_axistags is None:
axiskeys = self.Input.meta.getAxisKeys()
else:
axiskeys = self.Input.meta.getOriginalAxisKeys()
self._opReorderAxes.AxisOrder.setValue("".join(axiskeys))
# Provide the coordinate offset, but only for the axes that are present in the output image
tagged_input_offset = collections.defaultdict(lambda: -1, list(zip(self.Input.meta.getAxisKeys(), new_start)))
output_axes = self._opReorderAxes.AxisOrder.value
output_offset = [tagged_input_offset[axis] for axis in output_axes]
output_offset = tuple([x for x in output_offset if x != -1])
self._opExportSlot.CoordinateOffset.setValue(output_offset)
# Obtain values for possible name fields
known_keys = {"roi": list(self._opSubRegion.Roi.value)}
roi = numpy.array(self._opSubRegion.Roi.value)
for key, (start, stop) in zip(self.Input.meta.getAxisKeys(), roi.transpose()):
known_keys[key + "_start"] = start
known_keys[key + "_stop"] = stop
# Blank the internal path while we update the external path
# to avoid invalid intermediate states of ExportPath
self._opExportSlot.OutputInternalPath.setValue("")
# use partial formatting to fill in non-coordinate name fields
name_format = self.OutputFilenameFormat.value
partially_formatted_path = format_known_keys(name_format, known_keys, strict=False)
self._opExportSlot.OutputFilenameFormat.setValue(partially_formatted_path)
internal_dataset_format = self.OutputInternalPath.value
partially_formatted_dataset_name = format_known_keys(internal_dataset_format, known_keys)
self._opExportSlot.OutputInternalPath.setValue(partially_formatted_dataset_name)
def setupOutputs(self):
# Prepare subregion operator
total_roi = roiFromShape(self.Input.meta.shape)
total_roi = list(map(tuple, total_roi))
# Default to full roi
new_start, new_stop = total_roi
if self.RegionStart.ready():
# RegionStart is permitted to contain 'None' values, which we replace with zeros
new_start = [x or 0 for x in self.RegionStart.value]
if self.RegionStop.ready():
# RegionStop is permitted to contain 'None' values,
# which we replace with the full extent of the corresponding axis
new_stop = [x_extent[0] or x_extent[1] for x_extent in zip(self.RegionStop.value, total_roi[1])]
clipped_start = numpy.maximum(0, new_start)
clipped_stop = numpy.minimum(total_roi[1], new_stop)
if (clipped_start != new_start).any() or (clipped_stop != new_stop).any():
warnings.warn(
"The ROI you are attempting to export exceeds the extents of your dataset. Clipping to dataset bounds."
)
new_start, new_stop = tuple(clipped_start), tuple(clipped_stop)
# If we're in the process of switching input data,
# then the roi dimensionality might not match up.
# Just leave the roi disconnected for now.
if len(self.Input.meta.shape) != len(new_start) or len(self.Input.meta.shape) != len(new_stop):
self._opSubRegion.Roi.disconnect()
elif not self._opSubRegion.Roi.ready() or self._opSubRegion.Roi.value != (new_start, new_stop):
self._opSubRegion.Roi.setValue((new_start, new_stop))
# Set up normalization and dtype conversion
export_dtype = self.Input.meta.dtype
if self.ExportDtype.ready():
export_dtype = self.ExportDtype.value
need_normalize = (
self.InputMin.ready() and self.InputMax.ready() and self.ExportMin.ready() and self.ExportMax.ready()
)
if need_normalize:
minVal, maxVal = self.InputMin.value, self.InputMax.value
outputMinVal, outputMaxVal = self.ExportMin.value, self.ExportMax.value
# Force a drange onto the input slot metadata.
# opNormalizeAndConvert is an OpPixelOperator,
# which transforms the drange correctly in this case.
self._opDrangeInjection.Metadata.setValue({"drange": (minVal, maxVal)})
def normalize(a):
numerator = numpy.float64(outputMaxVal) - numpy.float64(outputMinVal)
denominator = numpy.float64(maxVal) - numpy.float64(minVal)
if denominator != 0.0:
frac = numpy.float32(numerator / denominator)
else:
# Denominator was zero. The user is probably just temporarily changing the values.
frac = numpy.float32(0.0)
result = numpy.asarray(outputMinVal + (a - minVal) * frac, export_dtype)
return result
self._opNormalizeAndConvert.Function.setValue(normalize)
# The OpPixelOperator sets the drange correctly using the function we give it.
output_drange = self._opNormalizeAndConvert.Output.meta.drange
assert type(output_drange[0]) == export_dtype
assert type(output_drange[1]) == export_dtype
else:
# We have no drange to set.
# If the original slot metadata had a drange,
# it will be propagated downstream anyway.
self._opDrangeInjection.Metadata.setValue({})
# No normalization: just identity function with dtype conversion
self._opNormalizeAndConvert.Function.setValue(lambda a: numpy.asarray(a, export_dtype))
# Use user-provided axis order if specified
user_provided = False
if self.OutputAxisOrder.ready():
try:
self._opReorderAxes.AxisOrder.setValue(self.OutputAxisOrder.value)
user_provided = True
except KeyError:
# FIXME: Why does the above line fail sometimes?
warnings.warn("Ignoring invalid axis order setting")
if not user_provided:
if self.Input.meta.original_axistags is None:
axiskeys = self.Input.meta.getAxisKeys()
else:
axiskeys = self.Input.meta.getOriginalAxisKeys()
self._opReorderAxes.AxisOrder.setValue("".join(axiskeys))
# Provide the coordinate offset, but only for the axes that are present in the output image
tagged_input_offset = collections.defaultdict(lambda: -1, list(zip(self.Input.meta.getAxisKeys(), new_start)))
output_axes = self._opReorderAxes.AxisOrder.value
output_offset = [tagged_input_offset[axis] for axis in output_axes]
output_offset = tuple([x for x in output_offset if x != -1])
self._opExportSlot.CoordinateOffset.setValue(output_offset)
# Obtain values for possible name fields
known_keys = {"roi": list(self._opSubRegion.Roi.value)}
roi = numpy.array(self._opSubRegion.Roi.value)
for key, (start, stop) in zip(self.Input.meta.getAxisKeys(), roi.transpose()):
known_keys[key + "_start"] = start
known_keys[key + "_stop"] = stop
# Blank the internal path while we update the external path
# to avoid invalid intermediate states of ExportPath
self._opExportSlot.OutputInternalPath.setValue("")
# use partial formatting to fill in non-coordinate name fields
name_format = self.OutputFilenameFormat.value
partially_formatted_path = format_known_keys(name_format, known_keys, strict=False)
self._opExportSlot.OutputFilenameFormat.setValue(partially_formatted_path)
internal_dataset_format = self.OutputInternalPath.value
partially_formatted_dataset_name = format_known_keys(internal_dataset_format, known_keys)
self._opExportSlot.OutputInternalPath.setValue(partially_formatted_dataset_name)
def setupOutputs(self):
# Prepare subregion operator
total_roi = roiFromShape(self.Input.meta.shape)
total_roi = map(tuple, total_roi)
# Default to full roi
new_start, new_stop = total_roi
if self.RegionStart.ready():
# RegionStart is permitted to contain 'None' values, which we replace with zeros
new_start = map(lambda x: x or 0, self.RegionStart.value)
if self.RegionStop.ready():
# RegionStop is permitted to contain 'None' values,
# which we replace with the full extent of the corresponding axis
new_stop = map(lambda (x, extent): x or extent,
zip(self.RegionStop.value, total_roi[1]))
else:
self._opSubRegion.Stop.setValue(tuple(total_roi[1]))
if not self._opSubRegion.Start.ready() or \
not self._opSubRegion.Stop.ready() or \
self._opSubRegion.Start.value != new_start or \
self._opSubRegion.Stop.value != new_stop:
# Disconnect first to ensure that the start/stop slots are applied together (atomically)
self._opSubRegion.Stop.disconnect()
# Provide the coordinate offset, but only for the axes that are present in the output image
tagged_input_offset = collections.defaultdict(
lambda: -1, zip(self.Input.meta.getAxisKeys(), new_start))
output_axes = self._opReorderAxes.AxisOrder.value
output_offset = [tagged_input_offset[axis] for axis in output_axes]
output_offset = tuple(filter(lambda x: x != -1, output_offset))
self._opExportSlot.CoordinateOffset.setValue(output_offset)
self._opSubRegion.Start.setValue(tuple(new_start))
self._opSubRegion.Stop.setValue(tuple(new_stop))
# Set up normalization and dtype conversion
export_dtype = self.Input.meta.dtype
if self.ExportDtype.ready():
export_dtype = self.ExportDtype.value
need_normalize = (self.InputMin.ready() and self.InputMax.ready()
and self.ExportMin.ready()
and self.ExportMax.ready())
if need_normalize:
minVal, maxVal = self.InputMin.value, self.InputMax.value
outputMinVal, outputMaxVal = self.ExportMin.value, self.ExportMax.value
# Force a drange onto the input slot metadata.
# opNormalizeAndConvert is an OpPixelOperator,
# which transforms the drange correctly in this case.
self._opDrangeInjection.Metadata.setValue(
{'drange': (minVal, maxVal)})
def normalize(a):
numerator = numpy.float64(outputMaxVal) - numpy.float64(
outputMinVal)
denominator = numpy.float64(maxVal) - numpy.float64(minVal)
if denominator != 0.0:
frac = numpy.float32(numerator / denominator)
else:
# Denominator was zero. The user is probably just temporarily changing the values.
frac = numpy.float32(0.0)
result = numpy.asarray(outputMinVal + (a - minVal) * frac,
export_dtype)
return result
self._opNormalizeAndConvert.Function.setValue(normalize)
# The OpPixelOperator sets the drange correctly using the function we give it.
output_drange = self._opNormalizeAndConvert.Output.meta.drange
assert type(output_drange[0]) == export_dtype
assert type(output_drange[1]) == export_dtype
else:
# We have no drange to set.
# If the original slot metadata had a drange,
# it will be propagated downstream anyway.
self._opDrangeInjection.Metadata.setValue({})
# No normalization: just identity function with dtype conversion
self._opNormalizeAndConvert.Function.setValue(
lambda a: numpy.asarray(a, export_dtype))
# Use user-provided axis order if specified
if self.OutputAxisOrder.ready():
self._opReorderAxes.AxisOrder.setValue(self.OutputAxisOrder.value)
else:
axistags = self.Input.meta.axistags
self._opReorderAxes.AxisOrder.setValue("".join(
tag.key for tag in axistags))
# Obtain values for possible name fields
roi = [
tuple(self._opSubRegion.Start.value),
tuple(self._opSubRegion.Stop.value)
]
known_keys = {'roi': roi}
# Blank the internal path while we update the external path
# to avoid invalid intermediate states of ExportPath
self._opExportSlot.OutputInternalPath.setValue("")
# use partial formatting to fill in non-coordinate name fields
name_format = self.OutputFilenameFormat.value
partially_formatted_path = format_known_keys(name_format, known_keys)
self._opExportSlot.OutputFilenameFormat.setValue(
partially_formatted_path)
internal_dataset_format = self.OutputInternalPath.value
partially_formatted_dataset_name = format_known_keys(
internal_dataset_format, known_keys)
self._opExportSlot.OutputInternalPath.setValue(
partially_formatted_dataset_name)
def post_process_lane_export(self, lane_index, checkOverwriteFiles=False):
# FIXME: This probably only works for the non-blockwise export slot.
# We should assert that the user isn't using the blockwise slot.
# Plugin export if selected
logger.info("Export source is: " + self.dataExportTrackingApplet.
topLevelOperator.SelectedExportSource.value)
print "in post_process_lane_export"
if self.dataExportTrackingApplet.topLevelOperator.SelectedExportSource.value == OpTrackingBaseDataExport.PluginOnlyName:
logger.info("Export source plugin selected!")
selectedPlugin = self.dataExportTrackingApplet.topLevelOperator.SelectedPlugin.value
exportPluginInfo = pluginManager.getPluginByName(
selectedPlugin, category="TrackingExportFormats")
if exportPluginInfo is None:
logger.error("Could not find selected plugin %s" %
exportPluginInfo)
else:
exportPlugin = exportPluginInfo.plugin_object
logger.info("Exporting tracking result using %s" %
selectedPlugin)
name_format = self.dataExportTrackingApplet.topLevelOperator.getLane(
lane_index).OutputFilenameFormat.value
partially_formatted_name = self.getPartiallyFormattedName(
lane_index, name_format)
if exportPlugin.exportsToFile:
filename = partially_formatted_name
if os.path.basename(filename) == '':
filename = os.path.join(filename, 'pluginExport.txt')
else:
filename = os.path.dirname(partially_formatted_name)
if filename is None or len(str(filename)) == 0:
logger.error(
"Cannot export from plugin with empty output filename")
return
exportStatus = self.trackingApplet.topLevelOperator.getLane(
lane_index).exportPlugin(filename, exportPlugin,
checkOverwriteFiles)
if not exportStatus:
return False
logger.info("Export done")
return
# CSV Table export (only if plugin was not selected)
settings, selected_features = self.trackingApplet.topLevelOperator.getLane(
lane_index).get_table_export_settings()
from lazyflow.utility import PathComponents, make_absolute, format_known_keys
if settings:
self.dataExportTrackingApplet.progressSignal.emit(-1)
raw_dataset_info = self.dataSelectionApplet.topLevelOperator.DatasetGroup[
lane_index][0].value
project_path = self.shell.projectManager.currentProjectPath
project_dir = os.path.dirname(project_path)
dataset_dir = PathComponents(
raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_dir)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(
os.path.pathsep)[0]).fileNameBase
known_keys['nickname'] = nickname
# use partial formatting to fill in non-coordinate name fields
name_format = settings['file path']
partially_formatted_name = format_known_keys(
name_format, known_keys)
settings['file path'] = partially_formatted_name
req = self.trackingApplet.topLevelOperator.getLane(
lane_index
).export_object_data(
lane_index,
# FIXME: Even in non-headless mode, we can't show the gui because we're running in a non-main thread.
# That's not a huge deal, because there's still a progress bar for the overall export.
show_gui=False)
req.wait()
self.dataExportTrackingApplet.progressSignal.emit(100)
