From 461ada6cce5a717b62ee57dfafec9f302621a602 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Mon, 18 Jul 2022 12:25:37 +0100
Subject: [PATCH] fix(pipeline): Differentiate Meta dict and class
---
aliby/pipeline.py | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/aliby/pipeline.py b/aliby/pipeline.py
index 910114cc..4e4e3d35 100644
--- a/aliby/pipeline.py
+++ b/aliby/pipeline.py
@@ -99,16 +99,16 @@ class PipelineParameters(ParametersABC):
# Download logs to use for metadata
conn.cache_logs(directory)
try:
- meta = MetaData(directory, None).load_logs()
+ meta_d = MetaData(directory, None).load_logs()
except Exception as e:
print("WARNING: Metadata could not be loaded: {}".format(e))
# Set minimal metadata
- meta = {
+ meta_d = {
"channels/channel": "Brightfield",
"time_settings/ntimepoints": [200],
}
- tps = meta["time_settings/ntimepoints"][0]
+ tps = meta_d["time_settings/ntimepoints"][0]
defaults = {
"general": dict(
id=expt_id,
@@ -138,7 +138,7 @@ class PipelineParameters(ParametersABC):
defaults["tiler"] = TilerParameters.default(**tiler).to_dict()
defaults["baby"] = BabyParameters.default(**baby).to_dict()
defaults["extraction"] = (
- exparams_from_meta(meta)
+ exparams_from_meta(meta_d)
or BabyParameters.default(**extraction).to_dict()
)
defaults["postprocessing"] = PostProcessorParameters.default(
@@ -603,14 +603,14 @@ class Pipeline(ProcessABC):
# Set up
directory = general_config["directory"]
+ trackers_state: t.List[np.ndarray] = []
with get_image_class(image_id)(
image_id, **self.general.get("server_info", {})
) as image:
filename = Path(f"{directory}/{image.name}.h5")
meta = MetaData(directory, filename)
- from_start = False if np.any(ow.values()) else True
- trackers_state = []
+ from_start = True if np.any(ow.values()) else False
# If no previous segmentation and keep tiler
if filename.exists():
if not ow["tiler"]:
--
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