def __init__(self, shell, headless, workflow_cmdline_args, project_creation_args, hintoverlayFile=None, pmapoverlayFile=None, *args, **kwargs):
if hintoverlayFile is not None:
assert isinstance(hintoverlayFile, str), "hintoverlayFile should be a string, not '%s'" % type(hintoverlayFile)
if pmapoverlayFile is not None:
assert isinstance(pmapoverlayFile, str), "pmapoverlayFile should be a string, not '%s'" % type(pmapoverlayFile)
graph = Graph()
super(CarvingWorkflow, self).__init__(shell, headless, workflow_cmdline_args, project_creation_args, graph=graph, *args, **kwargs)
data_instructions = "Select your input data using the 'Raw Data' tab shown on the right"
## Create applets
self.projectMetadataApplet = ProjectMetadataApplet()
self.dataSelectionApplet = DataSelectionApplet( self,
"Input Data",
"Input Data",
supportIlastik05Import=True,
batchDataGui=False,
instructionText=data_instructions,
max_lanes=1 )
opDataSelection = self.dataSelectionApplet.topLevelOperator
opDataSelection.DatasetRoles.setValue( ['Raw Data'] )
self.preprocessingApplet = PreprocessingApplet(workflow=self,
title = "Preprocessing",
projectFileGroupName="preprocessing")
self.carvingApplet = CarvingApplet(workflow=self,
projectFileGroupName="carving",
hintOverlayFile=hintoverlayFile,
pmapOverlayFile=pmapoverlayFile)
#self.carvingApplet.topLevelOperator.MST.connect(self.preprocessingApplet.topLevelOperator.PreprocessedData)
# Expose to shell
self._applets = []
self._applets.append(self.projectMetadataApplet)
self._applets.append(self.dataSelectionApplet)
self._applets.append(self.preprocessingApplet)
self._applets.append(self.carvingApplet)
def __init__(self, headless, workflow_cmdline_args, hintoverlayFile=None, pmapoverlayFile=None, *args, **kwargs):
if workflow_cmdline_args:
assert False, "Not using workflow cmdline args yet."
if hintoverlayFile is not None:
assert isinstance(hintoverlayFile, str), "hintoverlayFile should be a string, not '%s'" % type(hintoverlayFile)
if pmapoverlayFile is not None:
assert isinstance(pmapoverlayFile, str), "pmapoverlayFile should be a string, not '%s'" % type(pmapoverlayFile)
graph = Graph()
super(CarvingFromPixelPredictionsWorkflow, self).__init__(headless, *args, graph=graph, **kwargs)
## Create applets
self.projectMetadataApplet = ProjectMetadataApplet()
self.dataSelectionApplet = DataSelectionApplet(self, "Input Data", "Input Data", supportIlastik05Import=True, batchDataGui=False)
opDataSelection = self.dataSelectionApplet.topLevelOperator
opDataSelection.DatasetRoles.setValue( ['Raw Data'] )
self.featureSelectionApplet = FeatureSelectionApplet(self, "Feature Selection", "FeatureSelections")
self.pixelClassificationApplet = PixelClassificationApplet(self, "PixelClassification")
self.carvingApplet = CarvingApplet(workflow=self,
projectFileGroupName="carving",
hintOverlayFile=hintoverlayFile,
pmapOverlayFile=pmapoverlayFile)
self.preprocessingApplet = PreprocessingApplet(workflow=self,
title = "Preprocessing",
projectFileGroupName="carving")
#self.carvingApplet.topLevelOperator.MST.connect(self.preprocessingApplet.topLevelOperator.PreprocessedData)
# Expose to shell
self._applets = []
self._applets.append(self.projectMetadataApplet)
self._applets.append(self.dataSelectionApplet)
self._applets.append(self.featureSelectionApplet)
self._applets.append(self.pixelClassificationApplet)
self._applets.append(self.preprocessingApplet)
self._applets.append(self.carvingApplet)
def __init__(self,
shell,
headless,
workflow_cmdline_args,
project_creation_args,
hintoverlayFile=None,
pmapoverlayFile=None,
*args,
**kwargs):
graph = Graph()
super(SplitBodyCarvingWorkflow, self).__init__(shell,
headless,
workflow_cmdline_args,
project_creation_args,
*args,
graph=graph,
**kwargs)
## Create applets
self.projectMetadataApplet = ProjectMetadataApplet()
self.dataSelectionApplet = DataSelectionApplet(
self,
"Input Data",
"Input Data",
supportIlastik05Import=True,
batchDataGui=False)
opDataSelection = self.dataSelectionApplet.topLevelOperator
opDataSelection.DatasetRoles.setValue(
['Raw Data', 'Pixel Probabilities', 'Raveler Labels'])
self.preprocessingApplet = PreprocessingApplet(
workflow=self,
title="Preprocessing",
projectFileGroupName="preprocessing")
self.splitBodyCarvingApplet = SplitBodyCarvingApplet(
workflow=self, projectFileGroupName="carving")
self.splitBodyPostprocessingApplet = SplitBodyPostprocessingApplet(
workflow=self)
self.splitBodySupervoxelExportApplet = SplitBodySupervoxelExportApplet(
workflow=self)
# Expose to shell
self._applets = []
self._applets.append(self.projectMetadataApplet)
self._applets.append(self.dataSelectionApplet)
self._applets.append(self.preprocessingApplet)
self._applets.append(self.splitBodyCarvingApplet)
self._applets.append(self.splitBodyPostprocessingApplet)
self._applets.append(self.splitBodySupervoxelExportApplet)
self._split_tool_params = None
if workflow_cmdline_args:
arg_parser = argparse.ArgumentParser(
description=
"Specify parameters for the split-body carving workflow")
arg_parser.add_argument('--split_tool_param_file', required=False)
parsed_args, unused_args = arg_parser.parse_known_args(
workflow_cmdline_args)
if unused_args:
logger.warn("Unused command-line args: {}".format(unused_args))
if parsed_args.split_tool_param_file is None:
logger.warn("Missing cmd-line arg: --split_tool_param_file")
else:
logger.debug("Parsing split tool parameters: {}".format(
parsed_args.split_tool_param_file))
json_parser = JsonConfigParser(SplitToolParamsSchema)
self._split_tool_params = json_parser.parseConfigFile(
parsed_args.split_tool_param_file)
