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)