From a4f2f48abc16dfcda69f6209405ea0c151bd00d2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Wed, 2 Feb 2022 15:11:12 +0000
Subject: [PATCH] add apparent interruption continuation
---
aliby/pipeline.py | 21 +++++++++++++--------
1 file changed, 13 insertions(+), 8 deletions(-)
diff --git a/aliby/pipeline.py b/aliby/pipeline.py
index c0bd873e..d6057dea 100644
--- a/aliby/pipeline.py
+++ b/aliby/pipeline.py
@@ -213,6 +213,7 @@ class Pipeline(ProcessABC):
filename = f"{directory}/{image.name}.h5"
meta = MetaData(directory, filename)
from_start = True
+ trackers_state = None
if (
not general_config.get("overwrite", False)
and Path(filename).exists()
@@ -230,7 +231,9 @@ class Pipeline(ProcessABC):
or 0
)
# get state array
- state_array = StateReader(filename).get_formatted_states()
+ trackers_state = StateReader(
+ filename
+ ).get_formatted_states()
tiler.n_processed = process_from
process_from += 1
from_start = False
@@ -261,9 +264,10 @@ class Pipeline(ProcessABC):
runner = BabyRunner.from_tiler(
BabyParameters.from_dict(config["baby"]), tiler
)
- bwriter = BabyWriter(filename)
+ if trackers_state:
+ runner.crawler.trackers_state = trackers_state
- # State Writer to recover interrupted experiments
+ bwriter = BabyWriter(filename)
swriter = StateWriter(filename)
# Limit extraction parameters during run using the available channels in tiler
@@ -318,11 +322,7 @@ class Pipeline(ProcessABC):
# f"Segmentation failed:Segmentation:{perf_counter() - t}s"
# )
t = perf_counter()
- bwriter.write(seg, overwrite=["mother_assign"])
- swriter.write(
- data=runner.crawler.tracker_states,
- overwrite=swriter.datatypes.keys(),
- )
+ bwriter.write(seg, overwrite=["mother_assign"], tp=i)
logging.debug(f"Timing:Writing-baby:{perf_counter() - t}s")
# TODO add time-skipping for cases when the
@@ -353,6 +353,11 @@ class Pipeline(ProcessABC):
logging.debug(f"Quality:Clogged_traps:{frac_clogged_traps}")
print("Frac clogged traps: ", frac_clogged_traps)
+ # State Writer to recover interrupted experiments
+ swriter.write(
+ data=runner.crawler.tracker_states,
+ overwrite=swriter.datatypes.keys(),
+ )
meta.add_fields({"last_processed": i})
# Run post processing
--
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