From 5d439842b07557f7290e7536d62c982f4e97f04f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Wed, 7 Sep 2022 11:22:09 +0100
Subject: [PATCH] fix(pipeline): revert postprocessing inactivation
---
aliby/pipeline.py | 30 ++++++++++++------------------
1 file changed, 12 insertions(+), 18 deletions(-)
diff --git a/aliby/pipeline.py b/aliby/pipeline.py
index c77e56ba..458ab147 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
--
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