class TrackingBaseDataExportApplet( DataExportApplet ):
"""
This a specialization of the generic data export applet that
provides a special viewer for trackign output.
"""
def __init__(self, *args, **kwargs):
if 'default_export_filename' in kwargs:
default_export_filename = kwargs['default_export_filename']
del kwargs['default_export_filename']
else:
default_export_filename = ""
super(TrackingBaseDataExportApplet, self).__init__(*args, **kwargs)
self.export_op = None
self._default_export_filename = default_export_filename
def set_exporting_operator(self, op):
self.export_op = op
def getMultiLaneGui(self):
if self._gui is None:
# Gui is a special subclass of the generic gui
from trackingBaseDataExportGui import TrackingBaseDataExportGui
self._gui = TrackingBaseDataExportGui( self, self.topLevelOperator )
assert self.export_op is not None, "Exporting Operator must be set!"
self._gui.set_exporting_operator(self.export_op)
self._gui.set_default_export_filename(self._default_export_filename)
return self._gui
class TrackingBaseDataExportApplet( DataExportApplet ):
"""
This a specialization of the generic data export applet that
provides a special viewer for trackign output.
"""
def __init__(self, *args, **kwargs):
if 'default_export_filename' in kwargs:
default_export_filename = kwargs['default_export_filename']
del kwargs['default_export_filename']
super(TrackingBaseDataExportApplet, self).__init__(*args, **kwargs)
self.export_op = None
self._default_export_filename = default_export_filename
def set_exporting_operator(self, op):
self.export_op = op
def getMultiLaneGui(self):
if self._gui is None:
# Gui is a special subclass of the generic gui
from trackingBaseDataExportGui import TrackingBaseDataExportGui
self._gui = TrackingBaseDataExportGui( self, self.topLevelOperator )
assert self.export_op is not None, "Exporting Operator must be set!"
self._gui.set_exporting_operator(self.export_op)
self._gui.set_default_export_filename(self._default_export_filename)
return self._gui
def getMultiLaneGui(self):
if self._gui is None:
# Gui is a special subclass of the generic gui
from trackingBaseDataExportGui import TrackingBaseDataExportGui
self._gui = TrackingBaseDataExportGui( self, self.topLevelOperator )
assert self.export_op is not None, "Exporting Operator must be set!"
self._gui.set_exporting_operator(self.export_op)
return self._gui
def getMultiLaneGui(self):
if self._gui is None:
# Gui is a special subclass of the generic gui
from trackingBaseDataExportGui import TrackingBaseDataExportGui
self._gui = TrackingBaseDataExportGui(self, self.topLevelOperator)
assert self.export_op is not None, "Exporting Operator must be set!"
self._gui.set_exporting_operator(self.export_op)
self._gui.set_default_export_filename(
self._default_export_filename
) # remove once the PGMLINK version is gone
return self._gui
def getMultiLaneGui(self):
if self._gui is None:
# Gui is a special subclass of the generic gui
from trackingBaseDataExportGui import TrackingBaseDataExportGui
self._gui = TrackingBaseDataExportGui(self, self.topLevelOperator)
return self._gui
class TrackingBaseDataExportApplet(DataExportApplet):
"""
This a specialization of the generic data export applet that
provides a special viewer for trackign output.
"""
def __init__(self, workflow, *args, **kwargs):
if 'default_export_filename' in kwargs:
default_export_filename = kwargs['default_export_filename']
del kwargs['default_export_filename']
else:
default_export_filename = ""
self.export_op = None
self._default_export_filename = default_export_filename
self.__topLevelOperator = OpMultiLaneWrapper(
OpTrackingBaseDataExport,
parent=workflow,
promotedSlotNames=set(['RawData', 'Inputs', 'RawDatasetInfo']))
super(TrackingBaseDataExportApplet,
self).__init__(workflow, *args, **kwargs)
def set_exporting_operator(self, op):
self.export_op = op
def getMultiLaneGui(self):
if self._gui is None:
# Gui is a special subclass of the generic gui
from trackingBaseDataExportGui import TrackingBaseDataExportGui
self._gui = TrackingBaseDataExportGui(self, self.topLevelOperator)
assert self.export_op is not None, "Exporting Operator must be set!"
self._gui.set_exporting_operator(self.export_op)
self._gui.set_default_export_filename(
self._default_export_filename
) # remove once the PGMLINK version is gone
return self._gui
@staticmethod
def postprocessCanCheckForExistingFiles():
'''
While exporting, we can check whether files would be overwritten.
This is handled by an additional parameter to post_process_lane_export called "checkOverwriteFiles",
and that method should return True if the export files do NOT exist yet.
In Tracking export we want to check for existing files, so return True.
'''
return True
@property
def topLevelOperator(self):
return self.__topLevelOperator
@classmethod
def make_cmdline_parser(cls, starting_parser=None):
"""
Returns a command line parser that includes all parameters from the parent applet and adds export_plugin.
"""
arg_parser = DataExportApplet.make_cmdline_parser(starting_parser)
arg_parser.add_argument(
'--export_plugin',
help='Plugin name for exporting tracking results',
required=False,
default=None)
return arg_parser
@classmethod
def parse_known_cmdline_args(cls, cmdline_args, parsed_args=None):
"""
Helper function for headless workflows.
Parses commandline args that can be used to configure the ``TrackingBaseDataExportApplet`` top-level operator
as well as its parent, the ``DataExportApplet``,
and returns ``(parsed_args, unused_args)``, similar to ``argparse.ArgumentParser.parse_known_args()``
See also: :py:meth:`configure_operator_with_parsed_args()`.
parsed_args: Already-parsed args as returned from an ArgumentParser from make_cmdline_parser(), above.
If not provided, make_cmdline_parser().parse_known_args() will be used.
"""
unused_args = []
if parsed_args is None:
arg_parser = cls.make_cmdline_parser()
parsed_args, unused_args = arg_parser.parse_known_args(
cmdline_args)
msg = "Error parsing command-line arguments for tracking data export applet.\n"
if parsed_args.export_plugin is not None:
if parsed_args.export_source is None or parsed_args.export_source.lower(
) != "plugin":
msg += "export_plugin should only be specified if export_source is set to Plugin."
raise Exception(msg)
if parsed_args.export_source is not None and parsed_args.export_source.lower(
) == "plugin" and parsed_args.export_plugin is None:
msg += "export_plugin MUST be specified if export_source is set to Plugin!"
raise Exception(msg)
# configure parent applet
DataExportApplet.parse_known_cmdline_args(cmdline_args, parsed_args)
return parsed_args, unused_args
def configure_operator_with_parsed_args(self, parsed_args):
"""
Helper function for headless workflows.
Configures this applet's top-level operator according to the settings provided in ``parsed_args``.
:param parsed_args: Must be an ``argparse.Namespace`` as returned by :py:meth:`parse_known_cmdline_args()`.
"""
opTrackingDataExport = self.topLevelOperator
self._configure_operator_with_parsed_args(parsed_args,
opTrackingDataExport)
@classmethod
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)
