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)