diff --git a/aliby/pipeline.py b/aliby/pipeline.py index c77e56bafb587e6db9b14302e01eaecf088b8f3f..458ab147b672bfedba2eaa62da02992bb0440399 100644 --- a/aliby/pipeline.py +++ b/aliby/pipeline.py @@ -7,13 +7,13 @@ import re import traceback import typing as t from copy import copy -from itertools import groupby from pathlib import Path, PosixPath from time import perf_counter from typing import Union import h5py import numpy as np +import pandas as pd from agora.abc import ParametersABC, ProcessABC from agora.io.metadata import MetaData, parse_logfiles from agora.io.reader import StateReader @@ -24,12 +24,7 @@ from agora.io.writer import ( # BabyWriter, TilerWriter, ) from pathos.multiprocessing import Pool -# from postprocessor.core.processor import PostProcessor, PostProcessorParameters - -# import pandas as pd -from scipy import ndimage - -# import yaml +from postprocessor.core.processor import PostProcessor, PostProcessorParameters from tqdm import tqdm from aliby.baby_client import BabyParameters, BabyRunner @@ -144,10 +139,10 @@ class PipelineParameters(ParametersABC): defaults["postprocessing"] = {} defaults["reporting"] = {} - # defaults["postprocessing"] = PostProcessorParameters.default( - # **postprocessing - # ).to_dict() - # defaults["reporting"] = {} + defaults["postprocessing"] = PostProcessorParameters.default( + **postprocessing + ).to_dict() + defaults["reporting"] = {} return cls(**{k: v for k, v in defaults.items()}) @@ -488,7 +483,6 @@ class Pipeline(ProcessABC): frac_clogged_traps = self.check_earlystop( filename, earlystop, steps["tiler"].tile_size ) - print(f"Runs to frame {i}") logging.debug( f"Quality:Clogged_traps:{frac_clogged_traps}" ) @@ -506,13 +500,13 @@ class Pipeline(ProcessABC): break meta.add_fields({"last_processed": i}) - # Run post processing - # 1/0 + + # Run post-processing meta.add_fields({"end_status": "Success"}) - # post_proc_params = PostProcessorParameters.from_dict( - # config["postprocessing"] - # ) - # PostProcessor(filename, post_proc_params).run() + post_proc_params = PostProcessorParameters.from_dict( + config["postprocessing"] + ) + PostProcessor(filename, post_proc_params).run() return 1