diff --git a/pcore/pipeline.py b/pcore/pipeline.py index dd6c3fdc2ebd6ceff31917aae2b5abcd8520d850..a232332026b68068b473c4e64baadb5cf9defa55 100644 --- a/pcore/pipeline.py +++ b/pcore/pipeline.py @@ -1,6 +1,7 @@ """ Pipeline and chaining elements. """ +import logging import os from abc import ABC, abstractmethod from typing import List @@ -9,6 +10,8 @@ import traceback import itertools import yaml +from tqdm import tqdm +from time import perf_counter import pandas as pd @@ -23,7 +26,7 @@ from pcore.io.signal import Signal from extraction.core.functions.defaults import exparams_from_meta from extraction.core.extractor import Extractor from extraction.core.parameters import Parameters -from postprocessor.core.processor import PostProcessor +from postprocessor.core.processor import PostProcessor, PostProcessorParameters # from pcore.experiment import ExperimentOMERO, ExperimentLocal # from pcore.utils import timed @@ -60,7 +63,7 @@ class PipelineParameters(ParametersABC): tiler=dict(), baby=dict(tf_version=2), extraction=dict(), - postprocessing=dict(), + postprocessing=PostProcessorParameters.default().to_dict(), ) @@ -167,8 +170,8 @@ class Pipeline(ProcessABC): # tiler.n_processed = process_from writer = TilerWriter(filename) - runner = BabyRunner(tiler) # , baby_config=config["baby"]) session = initialise_tf(2) + runner = BabyRunner(tiler) # , baby_config=config["baby"]) bwriter = BabyWriter(filename) params = ( Parameters.from_dict(config["extraction"])