From af7df230c58b8ba6cd0503602b410426a6219808 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 14:35:29 +0000
Subject: [PATCH] add statereader
---
aliby/pipeline.py | 5 +++--
pyproject.toml | 2 +-
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/aliby/pipeline.py b/aliby/pipeline.py
index 70f52a4d..f41eadf6 100644
--- a/aliby/pipeline.py
+++ b/aliby/pipeline.py
@@ -27,6 +27,7 @@ from aliby.tile.tiler import Tiler, TilerParameters
from aliby.io.omero import Dataset, Image
from agora.abc import ParametersABC, ProcessABC
from agora.io.writer import TilerWriter, BabyWriter, StateWriter
+from agora.io.reader import StateReader
from agora.io.signal import Signal
from extraction.core.extractor import Extractor, ExtractorParameters
from extraction.core.functions.defaults import exparams_from_meta
@@ -88,7 +89,7 @@ class PipelineParameters(ParametersABC):
directory=str(directory),
filter="",
earlystop=dict(
- min_tp=50,
+ min_tp=100,
thresh_pos_clogged=0.3,
thresh_trap_clogged=7,
ntps_to_eval=5,
@@ -229,7 +230,7 @@ class Pipeline(ProcessABC):
or 0
)
# get state array
- state_array = f.get("state_array", 0)
+ state_array = StateReader(filename).get_formatted_states()
tiler.n_processed = process_from
process_from += 1
from_start = False
diff --git a/pyproject.toml b/pyproject.toml
index 7a0c821e..d714c5ca 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[tool.poetry]
name = "aliby"
-version = "0.1.15"
+version = "0.1.16"
description = ""
authors = ["Alan Munoz <alan.munoz@ed.ac.uk>"]
packages = [
--
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