def parseClusterConfigFile(configFilePath):
"""
Convenience function for parsing cluster configs.
Returns a Namespace object.
(Similar to the behavior of argparse.ArgumentParser.parse_args() )
"""
schema = JsonConfigParser(ClusterConfigFields)
return schema.parseConfigFile(configFilePath)
def parseClusterConfigFile( configFilePath ):
"""
Convenience function for parsing cluster configs.
Returns a Namespace object.
(Similar to the behavior of argparse.ArgumentParser.parse_args() )
"""
schema = JsonConfigParser( ClusterConfigFields )
return schema.parseConfigFile( configFilePath )
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)
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)
