fix bug that expected a certain channel sequence

changed result table column and file naming accordingly

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" )