From 2c6afe8e3b650fa6903587504ae828841bc3b99b Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Wed, 16 Apr 2025 13:32:55 +0200
Subject: [PATCH] Remove RoiManager import, get from script parameter instead.
---
2d_spots_in_fibers.py | 16 ++++------------
1 file changed, 4 insertions(+), 12 deletions(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 22b3a45..acf308f 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -18,7 +18,6 @@ from fiji.plugin.trackmate.action import LabelImgExporter
# ij imports
from ij import IJ
from ij.plugin import ImageCalculator
-from ij.plugin.frame import RoiManager
from ij.measure import ResultsTable
from ij.measure import Measurements as M
from ij.plugin.filter import Analyzer
@@ -386,7 +385,7 @@ def save_results_table(results_table, filename, suffix, target):
results_table.save(savepath)
-def save_labelimage_as_ijroiset(label_imp, filename, suffix, target):
+def save_labelimage_as_ijroiset(label_imp, rm, filename, suffix, target):
"""Save all labels i a label Images as IJ-ROIset to target location.
Only 2D, requires PTBIOP update site.
@@ -401,10 +400,6 @@ def save_labelimage_as_ijroiset(label_imp, filename, suffix, target):
target : str
the target directory in which to save the table
"""
- rm = RoiManager.getInstance()
- if not rm:
- rm = RoiManager()
- rm.reset()
command.run( Labels2Rois , False , 'imp' , label_imp , 'rm', rm).get()
savename = filename + "_" + str(suffix) + ".zip"
savepath = os.path.join(target, savename)
@@ -412,19 +407,16 @@ def save_labelimage_as_ijroiset(label_imp, filename, suffix, target):
rm.reset()
-def load_rois_from_zip(path):
+def load_rois_from_zip(path, rm):
"""Load ROIs from the given zip file and add them to the RoiManager.
Parameters
----------
path : string
Path to the ROI zip file.
+ rm : RoiManager
+ The ROI Manager.
"""
- rm = RoiManager.getInstance()
- if not rm:
- rm = RoiManager()
- rm.reset()
-
rm.runCommand("Open", path)
--
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