def convert_predictions_to_uncertainties( input_path, parsed_export_args ):
"""
Read exported pixel predictions and calculate/export the uncertainties.
input_path: The path to the prediction output file. If hdf5, must include the internal dataset name.
parsed_export_args: The already-parsed cmd-line arguments generated from a DataExportApplet-compatible ArgumentParser.
"""
graph = Graph()
opReader = OpInputDataReader(graph=graph)
opReader.WorkingDirectory.setValue( os.getcwd() )
opReader.FilePath.setValue(input_path)
opUncertainty = OpEnsembleMargin( graph=graph )
opUncertainty.Input.connect( opReader.Output )
opExport = OpFormattedDataExport( graph=graph )
opExport.Input.connect( opUncertainty.Output )
# Apply command-line arguments.
DataExportApplet._configure_operator_with_parsed_args(parsed_export_args, opExport)
last_progress = [-1]
def print_progress(progress_percent):
if progress_percent != last_progress[0]:
last_progress[0] = progress_percent
sys.stdout.write( " {}".format(progress_percent) )
print "Exporting results to : {}".format( opExport.ExportPath.value )
sys.stdout.write("Progress:")
opExport.progressSignal.subscribe(print_progress)
# Begin export
opExport.run_export()
sys.stdout.write("\n")
print "DONE."
def _configure_operator_with_parsed_args(cls, parsed_args, opTrackingDataExport):
"""
Helper function for headless workflows.
Configures the given export operator according to the settings provided in ``parsed_args``,
and depending on the chosen export source it also configures the parent operator opDataExport
:param parsed_args: Must be an ``argparse.Namespace`` as returned by :py:meth:`parse_known_cmdline_args()`.
"""
if parsed_args.export_source is not None:
opTrackingDataExport.SelectedExportSource.setValue(parsed_args.export_source)
if parsed_args.export_source == OpTrackingBaseDataExport.PluginOnlyName:
opTrackingDataExport.SelectedPlugin.setValue(parsed_args.export_plugin)
# if a plugin was selected, the only thing we need is the export name
if parsed_args.output_filename_format:
if hasattr(opTrackingDataExport, 'WorkingDirectory'):
# By default, most workflows consider the project directory to be the 'working directory'
# for transforming relative paths (e.g. export locations) into absolute locations.
# A user would probably expect paths to be relative to his cwd when he launches
# ilastik from the command line.
opTrackingDataExport.WorkingDirectory.disconnect()
opTrackingDataExport.WorkingDirectory.setValue(os.getcwd())
opTrackingDataExport.OutputFilenameFormat.setValue(parsed_args.output_filename_format)
return # We don't want to configure the super operator so we quit now!
else:
# set some value to the SelectedPlugin slot so that it is ready
opTrackingDataExport.SelectedPlugin.setValue("None")
# configure super operator
DataExportApplet._configure_operator_with_parsed_args(parsed_args, opTrackingDataExport)
def convert_predictions_to_segmentation(input_paths, parsed_export_args):
"""
Read exported pixel predictions and calculate/export the segmentation.
input_path: The path to the prediction output file. If hdf5, must include the internal dataset name.
parsed_export_args: The already-parsed cmd-line arguments generated from a DataExportApplet-compatible ArgumentParser.
"""
graph = Graph()
opReader = OpInputDataReader(graph=graph)
opReader.WorkingDirectory.setValue(os.getcwd())
opArgmaxChannel = OpArgmaxChannel(graph=graph)
opArgmaxChannel.Input.connect(opReader.Output)
opExport = OpFormattedDataExport(graph=graph)
opExport.Input.connect(opArgmaxChannel.Output)
# Apply command-line arguments.
DataExportApplet._configure_operator_with_parsed_args(
parsed_export_args, opExport)
last_progress = [-1]
def print_progress(progress_percent):
if progress_percent != last_progress[0]:
last_progress[0] = progress_percent
sys.stdout.write(" {}".format(progress_percent))
opExport.progressSignal.subscribe(print_progress)
for input_path in input_paths:
opReader.FilePath.setValue(input_path)
input_pathcomp = PathComponents(input_path)
opExport.OutputFilenameFormat.setValue(str(
input_pathcomp.externalPath))
output_path = opExport.ExportPath.value
output_pathcomp = PathComponents(output_path)
output_pathcomp.filenameBase += "_Segmentation"
opExport.OutputFilenameFormat.setValue(
str(output_pathcomp.externalPath))
print("Exporting results to : {}".format(opExport.ExportPath.value))
sys.stdout.write("Progress:")
# Begin export
opExport.run_export()
sys.stdout.write("\n")
print("DONE.")
def _configure_operator_with_parsed_args(cls, parsed_args,
opTrackingDataExport):
"""
Helper function for headless workflows.
Configures the given export operator according to the settings provided in ``parsed_args``,
and depending on the chosen export source it also configures the parent operator opDataExport
:param parsed_args: Must be an ``argparse.Namespace`` as returned by :py:meth:`parse_known_cmdline_args()`.
"""
if parsed_args.export_source is not None:
opTrackingDataExport.SelectedExportSource.setValue(
parsed_args.export_source)
if parsed_args.export_source == OpTrackingBaseDataExport.PluginOnlyName:
opTrackingDataExport.SelectedPlugin.setValue(
parsed_args.export_plugin)
if parsed_args.export_plugin == "Fiji-MaMuT":
if opTrackingDataExport.AdditionalPluginArguments.ready():
additional_plugin_args = opTrackingDataExport.AdditionalPluginArguments.value
else:
additional_plugin_args = {}
additional_plugin_args[
"bdvFilepath"] = parsed_args.big_data_viewer_xml_file
opTrackingDataExport.AdditionalPluginArguments.setValue(
additional_plugin_args)
# if a plugin was selected, the only thing we need is the export name
if parsed_args.output_filename_format:
if hasattr(opTrackingDataExport, "WorkingDirectory"):
# By default, most workflows consider the project directory to be the 'working directory'
# for transforming relative paths (e.g. export locations) into absolute locations.
# A user would probably expect paths to be relative to his cwd when he launches
# ilastik from the command line.
opTrackingDataExport.WorkingDirectory.disconnect()
opTrackingDataExport.WorkingDirectory.setValue(
os.getcwd())
opTrackingDataExport.OutputFilenameFormat.setValue(
parsed_args.output_filename_format)
return # We don't want to configure the super operator so we quit now!
else:
# set some value to the SelectedPlugin slot so that it is ready
opTrackingDataExport.SelectedPlugin.setValue("None")
# configure super operator
DataExportApplet._configure_operator_with_parsed_args(
parsed_args, opTrackingDataExport)
def convert_predictions_to_segmentation( input_paths, parsed_export_args ):
"""
Read exported pixel predictions and calculate/export the segmentation.
input_path: The path to the prediction output file. If hdf5, must include the internal dataset name.
parsed_export_args: The already-parsed cmd-line arguments generated from a DataExportApplet-compatible ArgumentParser.
"""
graph = Graph()
opReader = OpInputDataReader(graph=graph)
opReader.WorkingDirectory.setValue( os.getcwd() )
opArgmaxChannel = OpArgmaxChannel( graph=graph )
opArgmaxChannel.Input.connect( opReader.Output )
opExport = OpFormattedDataExport( graph=graph )
opExport.Input.connect( opArgmaxChannel.Output )
# Apply command-line arguments.
DataExportApplet._configure_operator_with_parsed_args(parsed_export_args, opExport)
last_progress = [-1]
def print_progress(progress_percent):
if progress_percent != last_progress[0]:
last_progress[0] = progress_percent
sys.stdout.write( " {}".format(progress_percent) )
opExport.progressSignal.subscribe(print_progress)
for input_path in input_paths:
opReader.FilePath.setValue(input_path)
input_pathcomp = PathComponents(input_path)
opExport.OutputFilenameFormat.setValue(str(input_pathcomp.externalPath))
output_path = opExport.ExportPath.value
output_pathcomp = PathComponents( output_path )
output_pathcomp.filenameBase += "_Segmentation"
opExport.OutputFilenameFormat.setValue(str(output_pathcomp.externalPath))
print "Exporting results to : {}".format( opExport.ExportPath.value )
sys.stdout.write("Progress:")
# Begin export
opExport.run_export()
sys.stdout.write("\n")
print "DONE."
