run.py

 
 
import argparse
import pickle
 
from tracking.run.event_generation import StandardEventGenerationRun
from tracking.run.mixins import BrowseTFileOnTerminateRunMixin, PostProcessingRunMixin
 
 
class HarvestingRunMixin(BrowseTFileOnTerminateRunMixin, PostProcessingRunMixin):
    """Harvester to select crops, postprocess, and inspect"""
 
    
    output_file_name = None
 
    def harvesting_module(self, path=None):
        """This virtual method must be overridden by the inheriting class"""
        raise RuntimeError("Override the harvesting_module method")
 
    def create_argument_parser(self, **kwds):
        """Parse the arguments and append them to the harvester's list"""
        argument_parser = super().create_argument_parser(**kwds)
        harvesting_argument_group = argument_parser.add_argument_group("Harvest arguments")
 
        harvesting_argument_group.add_argument(
            "-o",
            "--output",
            dest="output_file_name",
            default=argparse.SUPPRESS,
            help="File name for the harvest products"
        )
 
        return argument_parser
 
    def pickle_crops(self, harvesting_module, crops, **kwds):
        """Save the raw crops as a pickle file"""
        with open(self.output_file_nameoutput_file_nameoutput_file_name + ".pickle", "wb") as pickle_file:
            pickle.dump(crops, pickle_file)
 
    def unpickle_crops(self):
        """Load the raw crops from a pickle file"""
        with open(self.output_file_nameoutput_file_nameoutput_file_name + ".pickle", "rb") as pickle_file:
            return pickle.load(pickle_file)
 
    def postprocess(self):
        """Post-process the crops"""
        if self.postprocess_onlypostprocess_only:
            harvesting_module = self.harvesting_moduleharvesting_module()
            if self.output_file_nameoutput_file_nameoutput_file_name:
                harvesting_module.output_file_name = self.output_file_nameoutput_file_nameoutput_file_name
            try:
                crops = self.unpickle_cropsunpickle_crops()
            except FileNotFoundError:
                print("Crops pickle file not found. Create it now.")
            else:
                harvesting_module.refine(crops)
 
        super().postprocess()
 
    def adjust_path(self, path):
        """Add the harvester to the basf2 path"""
        super().adjust_path(path)
        harvesting_module = self.harvesting_moduleharvesting_module()
        if self.output_file_nameoutput_file_nameoutput_file_name:
            harvesting_module.output_file_name = self.output_file_nameoutput_file_nameoutput_file_name
        harvesting_module.refiners.append(self.pickle_cropspickle_crops)
        path.add_module(harvesting_module)
        return path
 
 
class HarvestingRun(HarvestingRunMixin, StandardEventGenerationRun):
    """Harvester to generate MC events followed by crop selection, postprocessing, inspection"""