class OpDataExport(Operator):
"""
Top-level operator for the export applet.
Mostly a simple wrapper for OpProcessedDataExport, but with extra formatting of the export path based on lane attributes.
"""
TransactionSlot = InputSlot() # To apply all settings in one 'transaction',
# disconnect this slot and reconnect it when all slots are ready
RawData = InputSlot(optional=True) # Display only
FormattedRawData = OutputSlot() # OUTPUT - for overlaying the transformed raw data with the export data.
# The dataset info for the original dataset (raw data)
RawDatasetInfo = InputSlot()
WorkingDirectory = (
InputSlot()
) # Non-absolute paths are relative to this directory. If not provided, paths must be absolute.
Inputs = InputSlot(level=1) # The exportable slots (should all be of the same shape, except for channel)
InputSelection = InputSlot(value=0)
SelectionNames = InputSlot() # A list of names corresponding to the exportable inputs
# Subregion params
RegionStart = InputSlot(optional=True)
RegionStop = InputSlot(optional=True)
# Normalization params
InputMin = InputSlot(optional=True)
InputMax = InputSlot(optional=True)
ExportMin = InputSlot(optional=True)
ExportMax = InputSlot(optional=True)
ExportDtype = InputSlot(optional=True)
OutputAxisOrder = InputSlot(optional=True)
# File settings
OutputFilenameFormat = InputSlot(
value="{dataset_dir}/{nickname}_{result_type}"
) # A format string allowing {dataset_dir} {nickname}, {roi}, {x_start}, {x_stop}, etc.
OutputInternalPath = InputSlot(value="exported_data")
OutputFormat = InputSlot(value="hdf5")
# Only export csv/HDF5 table (don't export volume)
TableOnlyName = InputSlot(value="Table-Only")
TableOnly = InputSlot(value=False)
ExportPath = OutputSlot() # Location of the saved file after export is complete.
ConvertedImage = OutputSlot() # Cropped image, not yet re-ordered (useful for guis)
ImageToExport = OutputSlot() # The image that will be exported
Dirty = OutputSlot() # Whether or not the result currently matches what's on disk
FormatSelectionErrorMsg = OutputSlot()
ALL_FORMATS = OpFormattedDataExport.ALL_FORMATS
####
# Simplified block diagram for actual export data and 'live preview' display:
#
# --> ExportPath
# /
# Input -> opFormattedExport --> ImageToExport (live preview)
# |\
# \ --> ConvertedImage
# \
# --> FormatSeletionIsValid
####
# Simplified block diagram for Raw data display:
#
# RegionStart --
# \
# RegionStop --> OpRawSubRegionHelper.RawStart -
# / .RawStop --\
# / \
# RawData ---->---------------------------------> opFormatRaw --> FormattedRawData
####
def __init__(self, *args, **kwargs):
super(OpDataExport, self).__init__(*args, **kwargs)
self._opFormattedExport = OpFormattedDataExport(parent=self)
opFormattedExport = self._opFormattedExport
# Forward almost all inputs to the 'real' exporter
opFormattedExport.TransactionSlot.connect(self.TransactionSlot)
opFormattedExport.RegionStart.connect(self.RegionStart)
opFormattedExport.RegionStop.connect(self.RegionStop)
opFormattedExport.InputMin.connect(self.InputMin)
opFormattedExport.InputMax.connect(self.InputMax)
opFormattedExport.ExportMin.connect(self.ExportMin)
opFormattedExport.ExportMax.connect(self.ExportMax)
opFormattedExport.ExportDtype.connect(self.ExportDtype)
opFormattedExport.OutputAxisOrder.connect(self.OutputAxisOrder)
opFormattedExport.OutputFormat.connect(self.OutputFormat)
self.ConvertedImage.connect(opFormattedExport.ConvertedImage)
self.ImageToExport.connect(opFormattedExport.ImageToExport)
self.ExportPath.connect(opFormattedExport.ExportPath)
self.FormatSelectionErrorMsg.connect(opFormattedExport.FormatSelectionErrorMsg)
self.progressSignal = opFormattedExport.progressSignal
self.Dirty.setValue(True) # Default to Dirty
# We don't export the raw data, but we connect it to it's own op
# so it can be displayed alongside the data to export in the same viewer.
# This keeps axis order, shape, etc. in sync with the displayed export data.
# Note that we must not modify the channels of the raw data, so it gets passed through a helper.
opHelper = OpRawSubRegionHelper(parent=self)
opHelper.RawImage.connect(self.RawData)
opHelper.ExportStart.connect(self.RegionStart)
opHelper.ExportStop.connect(self.RegionStop)
opFormatRaw = OpFormattedDataExport(parent=self)
opFormatRaw.TransactionSlot.connect(self.TransactionSlot)
opFormatRaw.Input.connect(self.RawData)
opFormatRaw.RegionStart.connect(opHelper.RawStart)
opFormatRaw.RegionStop.connect(opHelper.RawStop)
# Don't normalize the raw data.
# opFormatRaw.InputMin.connect( self.InputMin )
# opFormatRaw.InputMax.connect( self.InputMax )
# opFormatRaw.ExportMin.connect( self.ExportMin )
# opFormatRaw.ExportMax.connect( self.ExportMax )
# opFormatRaw.ExportDtype.connect( self.ExportDtype )
opFormatRaw.OutputAxisOrder.connect(self.OutputAxisOrder)
opFormatRaw.OutputFormat.connect(self.OutputFormat)
self._opFormatRaw = opFormatRaw
self.FormattedRawData.connect(opFormatRaw.ImageToExport)
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 execute(self, slot, subindex, roi, result):
assert False, "Shouldn't get here"
def propagateDirty(self, slot, subindex, roi):
# Out input data changed, so we have work to do when we get executed.
self.Dirty.setValue(True)
def run_export(self):
# If Table-Only is disabled or we're not dirty, we don't have to do anything.
if not self.TableOnly.value and self.Dirty.value:
self._opFormattedExport.run_export()
self.Dirty.setValue(False)
def run_export_to_array(self):
# This function can be used to export the results to an in-memory array, instead of to disk
# (Typically used from pure-python clients in batch mode.)
return self._opFormattedExport.run_export_to_array()
class OpDataExport(Operator):
"""
Top-level operator for the export applet.
Mostly a simple wrapper for OpProcessedDataExport, but with extra formatting of the export path based on lane attributes.
"""
TransactionSlot = InputSlot() # To apply all settings in one 'transaction',
# disconnect this slot and reconnect it when all slots are ready
RawData = InputSlot(optional=True) # Display only
FormattedRawData = OutputSlot() # OUTPUT - for overlaying the transformed raw data with the export data.
# The dataset info for the original dataset (raw data)
RawDatasetInfo = InputSlot()
WorkingDirectory = InputSlot() # Non-absolute paths are relative to this directory. If not provided, paths must be absolute.
Inputs = InputSlot(level=1) # The exportable slots (should all be of the same shape, except for channel)
InputSelection = InputSlot(value=0)
SelectionNames = InputSlot() # A list of names corresponding to the exportable inputs
# Subregion params
RegionStart = InputSlot(optional=True)
RegionStop = InputSlot(optional=True)
# Normalization params
InputMin = InputSlot(optional=True)
InputMax = InputSlot(optional=True)
ExportMin = InputSlot(optional=True)
ExportMax = InputSlot(optional=True)
ExportDtype = InputSlot(optional=True)
OutputAxisOrder = InputSlot(optional=True)
# File settings
OutputFilenameFormat = InputSlot(value='{dataset_dir}/{nickname}_{result_type}') # A format string allowing {dataset_dir} {nickname}, {roi}, {x_start}, {x_stop}, etc.
OutputInternalPath = InputSlot(value='exported_data')
OutputFormat = InputSlot(value='hdf5')
# Only export csv/HDF5 table (don't export volume)
TableOnlyName = InputSlot(value='Table-Only')
TableOnly = InputSlot(value=False)
ExportPath = OutputSlot() # Location of the saved file after export is complete.
ConvertedImage = OutputSlot() # Cropped image, not yet re-ordered (useful for guis)
ImageToExport = OutputSlot() # The image that will be exported
ImageOnDisk = OutputSlot() # This slot reads the exported image from disk (after the export is complete)
Dirty = OutputSlot() # Whether or not the result currently matches what's on disk
FormatSelectionErrorMsg = OutputSlot()
ALL_FORMATS = OpFormattedDataExport.ALL_FORMATS
####
# Simplified block diagram for actual export data and 'live preview' display:
#
# --> ExportPath
# /
# Input -> opFormattedExport --> ImageToExport (live preview)
# |\
# \ --> ConvertedImage
# \
# --> FormatSeletionIsValid
####
# Simplified block diagram for Raw data display:
#
# RegionStart --
# \
# RegionStop --> OpRawSubRegionHelper.RawStart -
# / .RawStop --\
# / \
# RawData ---->---------------------------------> opFormatRaw --> FormattedRawData
####
# Simplified block diagram for "on-disk view" of the exported results file:
#
# opFormattedExport.ImageToExport (for metadata only) -->
# \
# opFormattedExport.ExportPath -------------------------> opImageOnDiskProvider --> ImageOnDisk
def __init__(self, *args, **kwargs):
super( OpDataExport, self ).__init__(*args, **kwargs)
self._opFormattedExport = OpFormattedDataExport( parent=self )
opFormattedExport = self._opFormattedExport
# Forward almost all inputs to the 'real' exporter
opFormattedExport.TransactionSlot.connect( self.TransactionSlot )
opFormattedExport.RegionStart.connect( self.RegionStart )
opFormattedExport.RegionStop.connect( self.RegionStop )
opFormattedExport.InputMin.connect( self.InputMin )
opFormattedExport.InputMax.connect( self.InputMax )
opFormattedExport.ExportMin.connect( self.ExportMin )
opFormattedExport.ExportMax.connect( self.ExportMax )
opFormattedExport.ExportDtype.connect( self.ExportDtype )
opFormattedExport.OutputAxisOrder.connect( self.OutputAxisOrder )
opFormattedExport.OutputFormat.connect( self.OutputFormat )
self.ConvertedImage.connect( opFormattedExport.ConvertedImage )
self.ImageToExport.connect( opFormattedExport.ImageToExport )
self.ExportPath.connect( opFormattedExport.ExportPath )
self.FormatSelectionErrorMsg.connect( opFormattedExport.FormatSelectionErrorMsg )
self.progressSignal = opFormattedExport.progressSignal
self.Dirty.setValue(True) # Default to Dirty
self._opImageOnDiskProvider = None
# We don't export the raw data, but we connect it to it's own op
# so it can be displayed alongside the data to export in the same viewer.
# This keeps axis order, shape, etc. in sync with the displayed export data.
# Note that we must not modify the channels of the raw data, so it gets passed through a helper.
opHelper = OpRawSubRegionHelper( parent=self )
opHelper.RawImage.connect( self.RawData )
opHelper.ExportStart.connect( self.RegionStart )
opHelper.ExportStop.connect( self.RegionStop )
opFormatRaw = OpFormattedDataExport( parent=self )
opFormatRaw.TransactionSlot.connect( self.TransactionSlot )
opFormatRaw.Input.connect( self.RawData )
opFormatRaw.RegionStart.connect( opHelper.RawStart )
opFormatRaw.RegionStop.connect( opHelper.RawStop )
# Don't normalize the raw data.
#opFormatRaw.InputMin.connect( self.InputMin )
#opFormatRaw.InputMax.connect( self.InputMax )
#opFormatRaw.ExportMin.connect( self.ExportMin )
#opFormatRaw.ExportMax.connect( self.ExportMax )
#opFormatRaw.ExportDtype.connect( self.ExportDtype )
opFormatRaw.OutputAxisOrder.connect( self.OutputAxisOrder )
opFormatRaw.OutputFormat.connect( self.OutputFormat )
self._opFormatRaw = opFormatRaw
self.FormattedRawData.connect( opFormatRaw.ImageToExport )
def cleanupOnDiskView(self):
if self._opImageOnDiskProvider is not None:
self.ImageOnDisk.disconnect()
self._opImageOnDiskProvider.cleanUp()
self._opImageOnDiskProvider = None
def setupOnDiskView(self):
# Set up the output that let's us view the exported file
self._opImageOnDiskProvider = OpImageOnDiskProvider( parent=self )
self._opImageOnDiskProvider.TransactionSlot.connect( self.TransactionSlot )
self._opImageOnDiskProvider.Input.connect( self._opFormattedExport.ImageToExport )
self._opImageOnDiskProvider.WorkingDirectory.connect( self.WorkingDirectory )
self._opImageOnDiskProvider.DatasetPath.connect( self._opFormattedExport.ExportPath )
# Not permitted to make this connection because we can't connect our own output to a child operator.
# Instead, dirty state is copied manually into the child op whenever we change it.
#self._opImageOnDiskProvider.Dirty.connect( self.Dirty )
self._opImageOnDiskProvider.Dirty.setValue( False )
self.ImageOnDisk.connect( self._opImageOnDiskProvider.Output )
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 list(self.outputs.values()):
if oslot.partner 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.partner is None:
oslot.meta.NOTREADY = True
return
self._opFormattedExport.Input.connect( self.Inputs[selection_index] )
if os.path.pathsep in rawInfo.filePath:
first_dataset = rawInfo.filePath.split(os.path.pathsep)[0]
dataset_dir = PathComponents(first_dataset).externalDirectory
else:
dataset_dir = PathComponents(rawInfo.filePath).externalDirectory
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]
# 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 execute(self, slot, subindex, roi, result):
assert False, "Shouldn't get here"
def propagateDirty(self, slot, subindex, roi):
# Out input data changed, so we have work to do when we get executed.
self.Dirty.setValue(True)
if self._opImageOnDiskProvider:
self._opImageOnDiskProvider.Dirty.setValue( False )
def run_export(self):
# If Table-Only is disabled or we're not dirty, we don't have to do anything.
if not self.TableOnly.value and self.Dirty.value:
self.cleanupOnDiskView()
self._opFormattedExport.run_export()
self.Dirty.setValue( False )
self.setupOnDiskView()
self._opImageOnDiskProvider.Dirty.setValue( False )
def run_export_to_array(self):
# This function can be used to export the results to an in-memory array, instead of to disk
# (Typically used from pure-python clients in batch mode.)
return self._opFormattedExport.run_export_to_array()
