From e63491ecab497816ee68dbb342e9cbab24afcc3c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Tue, 16 Nov 2021 11:41:58 +0000
Subject: [PATCH] bugfix
---
pcore/pipeline.py | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/pcore/pipeline.py b/pcore/pipeline.py
index dd6c3fdc..a2323320 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"])
--
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