From 0bf837592e26e9c58ceacc0d4c50565a07f81966 Mon Sep 17 00:00:00 2001
From: Laurent Guerard <laurent.guerard@unibas.ch>
Date: Tue, 29 Apr 2025 14:52:58 +0200
Subject: [PATCH] Add method for measuring mean intensity in all fibers
---
2c_fibertyping.py | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/2c_fibertyping.py b/2c_fibertyping.py
index d57919d..8b68e71 100644
--- a/2c_fibertyping.py
+++ b/2c_fibertyping.py
@@ -114,20 +114,21 @@ def measure_mean_of_rois(imp, channel, rm):
The channel on which to measure. starts at 1.
rm : ij.plugin.frame.RoiManager
A reference of the IJ-RoiManager.
- min_intensity : int
- The selection criterion (here: intensity threshold).
Returns
-------
- list
- A selection of ROIs which passed the selection criterion (are above the threshold).
+ list of float
+ A list of mean intensity values for each ROI in the specified channel.
"""
imp.setC(channel)
all_rois = rm.getRoisAsArray()
+ mean_intensities = []
for i, roi in enumerate(all_rois):
imp.setRoi(roi)
stats = imp.getStatistics()
+ mean_intensities.append(stats.mean)
+ return mean_intensities
--
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