From 8ccc2135f656836a33bf965b339bf4b31c871c72 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Fri, 22 Oct 2021 16:24:33 +0100
Subject: [PATCH] clean yaml output
Former-commit-id: 29b205655997c2eaf32c1f56da054e14496e658a
---
core/processes/picker.py | 11 ++++-------
core/processor.py | 16 ++++++++--------
2 files changed, 12 insertions(+), 15 deletions(-)
diff --git a/core/processes/picker.py b/core/processes/picker.py
index a7221e6f..ef986cfa 100644
--- a/core/processes/picker.py
+++ b/core/processes/picker.py
@@ -1,6 +1,3 @@
-import seaborn as sns
-from matplotlib import pyplot as plt # TODO DELETE THIS
-
from typing import Tuple, Union, List
from abc import ABC, abstractmethod
@@ -29,10 +26,10 @@ class pickerParameters(ParametersABC):
{
"sequence": [
# ("lineage", "intersection", "families"),
- ("condition", "intersection", "any_present", 0.8),
- ("condition", "intersection", "growing", 40),
- ("condition", "intersection", "present", 8),
- ("condition", "intersection", "mother_buds", 5, 0.8),
+ ["condition", "intersection", "any_present", 0.8],
+ ["condition", "intersection", "growing", 40],
+ ["condition", "intersection", "present", 8],
+ ["condition", "intersection", "mother_buds", 5, 0.8],
# ("lineage", "full_families", "intersection"),
],
}
diff --git a/core/processor.py b/core/processor.py
index 81c54b6f..46bbd6cb 100644
--- a/core/processor.py
+++ b/core/processor.py
@@ -49,16 +49,16 @@ class PostProcessorParameters(ParametersABC):
"merger": "/extraction/general/None/area",
"picker": ["/extraction/general/None/area"],
},
- "processes": (
- (
+ "processes": [
+ [
"bud_metric",
[
"/extraction/general/None/volume",
"/extraction/em_ratio/np_max/mean",
"/extraction/em_ratio/np_max/median",
],
- ),
- (
+ ],
+ [
"dsignal",
[
"/extraction/general/None/volume",
@@ -70,7 +70,7 @@ class PostProcessorParameters(ParametersABC):
"/postprocessing/bud_metric/extraction_em_ratio_np_max_mean",
"/postprocessing/bud_metric/extraction_em_ratio_np_max_median",
],
- ),
+ ],
(
"aggregate",
[
@@ -93,12 +93,12 @@ class PostProcessorParameters(ParametersABC):
],
),
# "savgol": ["/extraction/general/None/area"],
- ),
+ ],
},
parameters={
"prepost": {
- "merger": mergerParameters.default(),
- "picker": pickerParameters.default(),
+ "merger": mergerParameters.default().to_dict(),
+ "picker": pickerParameters.default().to_dict(),
}
},
outpaths={"aggregate": "/postprocessing/experiment_wide/aggregated/"},
--
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