From 7003049f6dc21462ae461664c51b0bcef503601f Mon Sep 17 00:00:00 2001
From: "kai.schleicher@unibas.ch" <kai.schleicher@unibas.ch>
Date: Fri, 3 Feb 2023 14:38:29 +0100
Subject: [PATCH] fix bug that expected a certain channel sequence
changed result table column and file naming accordingly
---
2c_fibertyping.py | 28 ++++++++++++++--------------
1 file changed, 14 insertions(+), 14 deletions(-)
diff --git a/2c_fibertyping.py b/2c_fibertyping.py
index 91b8c6a..bb58eab 100755
--- a/2c_fibertyping.py
+++ b/2c_fibertyping.py
@@ -409,7 +409,7 @@ all_fiber_subsets =[ [], [], [] ]
for index, fiber_channel in enumerate(all_fiber_channels):
if fiber_channel > 0:
- preset_results_column( rt, "channel " + str(fiber_channel) + " positive (" + roi_colors[fiber_channel-1] + ")", "NO" )
+ preset_results_column( rt, "channel " + str(fiber_channel) + " positive (" + roi_colors[index] + ")", "NO" )
if all_min_fiber_intensities[index] == 0:
all_min_fiber_intensities[index] = get_threshold_from_method(raw, fiber_channel, "Mean")[0]
IJ.log( "fiber channel " + str(fiber_channel) + " intensity threshold: " + str(all_min_fiber_intensities[index]) )
@@ -418,7 +418,7 @@ for index, fiber_channel in enumerate(all_fiber_channels):
if len(positive_fibers) > 0:
change_subset_roi_color(rm, positive_fibers, roi_colors[index])
save_selected_rois( rm, positive_fibers, output_dir + "/" + raw_image_title + "_positive_fiber_rois_c" + str( fiber_channel ) + ".zip")
- add_results( rt, "channel " + str(fiber_channel) + " positive (" + roi_colors[fiber_channel-1] + ")", positive_fibers, "YES")
+ add_results( rt, "channel " + str(fiber_channel) + " positive (" + roi_colors[index] + ")", positive_fibers, "YES")
# single positive
positive_c1 = all_fiber_subsets[0]
@@ -433,28 +433,28 @@ 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 1,2 positive (magenta)", "NO" )
+ 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_c1_c2.zip")
- add_results( rt, "channel 1,2 positive (magenta)", positive_c1_c2, "YES")
+ 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 1,3 positive (yellow)", "NO" )
+ 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_c1_c3.zip")
- add_results( rt, "channel 1,3 positive (yellow)", positive_c1_c3, "YES")
+ 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 2,3 positive (cyan)", "NO" )
+ 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_c2_c3.zip")
- add_results( rt, "channel 2,3 positive (cyan)", positive_c2_c3, "YES")
+ 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 1,2,3 positive (white)", "NO" )
+ 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_c1_c2_c3.zip")
- add_results( rt, "channel 1,2,3 positive (white)", positive_c1_c2_c3, "YES")
+ 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")
# save all results together
save_all_rois( rm, output_dir + "/" + raw_image_title + "_all_fiber_type_rois_color-coded.zip" )
--
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