From b30da837bc648d9083307809a84d164b21e94171 Mon Sep 17 00:00:00 2001
From: Laurent Guerard <laurent.guerard@unibas.ch>
Date: Tue, 14 Jan 2025 11:24:07 +0100
Subject: [PATCH] Refactor fiber typing to use loop
---
2c_fibertyping.py | 38 +++++++++++++++-----------------------
1 file changed, 15 insertions(+), 23 deletions(-)
diff --git a/2c_fibertyping.py b/2c_fibertyping.py
index e10c3a2..ffc1520 100755
--- a/2c_fibertyping.py
+++ b/2c_fibertyping.py
@@ -528,29 +528,21 @@ positive_c2_c3 = list( set(all_fiber_subsets[1]).intersection(all_fiber_subsets[
positive_c1_c2_c3 = list( set(positive_c1_c2).intersection(all_fiber_subsets[2]) )
# update ROI color & results table for double and triple positives
-if len(positive_c1_c2) > 0:
- preset_results_column( rt, "channel " + str(fiber_channel_1) + "," + str(fiber_channel_2) + " positive (magenta)", "NO" )
- change_subset_roi_color(rm, positive_c1_c2, "magenta")
- save_selected_rois( rm, positive_c1_c2, output_dir + "/" + raw_image_title + "_positive_fiber_rois_c" + str(fiber_channel_1) + "_c" + str(fiber_channel_2) + ".zip")
- add_results( rt, "channel " + str(fiber_channel_1) + "," + str(fiber_channel_2) + " positive (magenta)", positive_c1_c2, "YES")
-
-if len(positive_c1_c3) > 0:
- preset_results_column( rt, "channel " + str(fiber_channel_1) + "," + str(fiber_channel_3) + " positive (yellow)", "NO" )
- change_subset_roi_color(rm, positive_c1_c3, "yellow")
- save_selected_rois( rm, positive_c1_c3, output_dir + "/" + raw_image_title + "_positive_fiber_rois_c" + str(fiber_channel_1) + "_c" + str(fiber_channel_3) + ".zip")
- add_results( rt, "channel " + str(fiber_channel_1) + "," + str(fiber_channel_3) + " positive (yellow)", positive_c1_c3, "YES")
-
-if len(positive_c2_c3) > 0:
- preset_results_column( rt, "channel " + str(fiber_channel_2) + "," + str(fiber_channel_3) + " positive (cyan)", "NO" )
- change_subset_roi_color(rm, positive_c2_c3, "cyan")
- save_selected_rois( rm, positive_c2_c3, output_dir + "/" + raw_image_title + "_positive_fiber_rois_c" + str(fiber_channel_2) + "_c" + str(fiber_channel_3) + ".zip")
- add_results( rt, "channel " + str(fiber_channel_2) + "," + str(fiber_channel_3) + " positive (cyan)", positive_c2_c3, "YES")
-
-if len(positive_c1_c2_c3) > 0:
- preset_results_column( rt, "channel " + str(fiber_channel_1) + "," + str(fiber_channel_2) + "," + str(fiber_channel_3) + " positive(white)", "NO" )
- change_subset_roi_color(rm, positive_c1_c2_c3, "white")
- save_selected_rois( rm, positive_c1_c2_c3, output_dir + "/" + raw_image_title + "_positive_fiber_rois_c" + str(fiber_channel_1) + "_c" + str(fiber_channel_2) + "_c" + str(fiber_channel_3) + ".zip")
- add_results( rt, "channel " + str(fiber_channel_1) + "," + str(fiber_channel_2) + "," + str(fiber_channel_3) + " positive(white)", positive_c1_c2_c3, "YES")
+channels = [
+ (positive_c1_c2, [fiber_channel_1, fiber_channel_2], "magenta"),
+ (positive_c1_c3, [fiber_channel_1, fiber_channel_3], "yellow"),
+ (positive_c2_c3, [fiber_channel_2, fiber_channel_3], "cyan"),
+ (positive_c1_c2_c3, [fiber_channel_1, fiber_channel_2, fiber_channel_3], "white")
+]
+
+for positives, ch_nums, color in channels:
+ if positives:
+ ch_str = ",".join(map(str, ch_nums))
+ color_label = "channel %s positive (%s)" % (ch_str, color)
+ preset_results_column(rt, color_label.replace(',', '-'), "NO")
+ change_subset_roi_color(rm, positives, color)
+ save_selected_rois(rm, positives, "%s/%s_positive_fiber_rois_c%s.zip" % (output_dir, raw_image_title, '_c'.join(map(str, ch_nums))))
+ add_results(rt, color_label.replace(',', '-'), positives, "YES")
# save all results together
save_all_rois( rm, output_dir + "/" + raw_image_title + "_all_fiber_type_rois_color-coded.zip" )
--
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