From c63f03eb3da0ce71ca3e207f397439358684ac74 Mon Sep 17 00:00:00 2001
From: "kai.schleicher@unibas.ch" <kai.schleicher@unibas.ch>
Date: Mon, 12 Oct 2020 14:56:14 +0200
Subject: [PATCH] fix: fixes bugs
---
myosoft-imcf_identify_fibers.py | 27 ++++++++++++++++++++++++---
1 file changed, 24 insertions(+), 3 deletions(-)
diff --git a/myosoft-imcf_identify_fibers.py b/myosoft-imcf_identify_fibers.py
index cca6074..1951368 100644
--- a/myosoft-imcf_identify_fibers.py
+++ b/myosoft-imcf_identify_fibers.py
@@ -351,6 +351,24 @@ def save_all_rois(rm, target):
rm.runCommand("Save", target)
+def save_selected_rois( rm, selected_rois, target ):
+ """save selected ROIs in the RoiManager as zip to target path
+
+ Parameters
+ ----------
+ rm : RoiManager
+ a reference of the IJ-RoiManager
+ selected_rois : array
+ ROIs in the RoiManager to save
+ target : string
+ the path in to store the ROIs. e.g. /my-images/resulting_rois_subset.zip
+ """
+ rm.runCommand("Deselect")
+ rm.setSelectedIndexes(selected_rois)
+ rm.runCommand("save selected", target)
+ rm.runCommand("Deselect")
+
+
def enlarge_all_rois( amount_in_um, rm, pixel_size_in_um ):
"""enlarges all ROIs in the RoiManager by x scaled units
@@ -548,17 +566,20 @@ if fiber_channel > 0:
min_fiber_intensity = get_threshold_from_method(raw, fiber_channel, "Mean")[0]
IJ.log( "fiber intensity threshold: " + str(min_fiber_intensity) )
+ change_all_roi_color(rm, "blue")
positive_fibers = select_positive_fibers( raw, fiber_channel, rm, min_fiber_intensity )
change_subset_roi_color(rm, positive_fibers, "magenta")
save_selected_rois( rm, positive_fibers, output_dir + "mhc_positive_fiber_rois.zip")
- change_all_roi_color(rm, "blue")
# measure size & shape, save
IJ.run("Set Measurements...", "area perimeter shape feret's redirect=None decimal=4")
IJ.run("Clear Results", "")
measure_in_all_rois( raw, membrane_channel, rm )
-preset_results_column( rt, "MHC Positive Fibers (magenta)", "NO" )
-add_results( rt, "MHC Positive Fibers (magenta)", positive_fibers, "YES")
+
+if fiber_channel > 0:
+ preset_results_column( rt, "MHC Positive Fibers (magenta)", "NO" )
+ add_results( rt, "MHC Positive Fibers (magenta)", positive_fibers, "YES")
+
rt.save(output_dir + "all_fibers_results.csv")
# dress up the original image, save a overlay-png, present original to the user
--
GitLab