Index exceeds the number of array elements on valid image

[dlee489]

Got an error message when running ct_FIRE.m with the images below:
fiber_image_2.tif
fiber_image_3.tif

Error message being:

fiberproc
  linking fibers (5) - 1, ctFIRE on reconstruction image is skipped, error message:Index exceeds the number of array elements. Index must not exceed 0.

These have been generated using the synthetic fiber generator. The diagnosis (by AI, so with a grain of salt), states that these caused an error due to brightness generating an increased number of nucleation points in the background, triggering the n > 2 if statement more than once.

Debugged through:

diff --git a/src/FIRE/fiberproc/fiberproc.m b/src/FIRE/fiberproc/fiberproc.m
index b71cab0..f56d785 100644
--- a/src/FIRE/fiberproc/fiberproc.m
+++ b/src/FIRE/fiberproc/fiberproc.m
@@ -75,6 +75,10 @@
     %GETVECT - gets the fiber orientation vector that starts at the end
     %vertex i and points along the fiber
     len = length(fiber);
+    if isempty(fiber)   % ADD THIS GUARD
+        vect = zeros(1,3);
+        return;
+    end
     if fiber(1)==vi %if the fiber starts at vertex i
         ii = min(sp,len);
         vj = fiber(ii);
@@ -278,8 +282,12 @@
                 fk = fe(2);               
                 fiber1 = F(fj).v;
                 fiber2 = F(fk).v;
-                vect1  = getvect(X,vi,fiber1,sp);
-                vect2  = getvect(X,vi,fiber2,sp);
+                if isempty(fiber1) || isempty(fiber2)
+                    % skip -- stale fe entry points to already-merged fiber
+                else
+                    vect1  = getvect(X,vi,fiber1,sp);
+                    vect2  = getvect(X,vi,fiber2,sp);
+                end
                 a      = dot(vect1,vect2);
                 if a < thresha
                     if plotflag==1
@@ -294,13 +302,16 @@
                 end
             elseif n > 2 %if the vi end of fiber i touches another fiber
                 fe = V(vi).fe;
+                A = zeros(n, n);
                 for j=1:n-1                    
                     fj     = fe(j);
                     fiber1 = F(fj).v;
+                    if isempty(fiber1), continue; end % GUARD
                     vect1   = getvect(X,vi,fiber1,sp);
                     for k=j+1:n
                         fk = fe(k);
                         fiber2 = F(fk).v;
+                        if isempty(fiber2), continue; end % GUARD
                         vect2 = getvect(X,vi,fiber2,sp);
                         A(j,k)= dot(vect1,vect2);
                     end

This has been diagnosed by comparing with fiber_image_1.tif, which has successfully been run but was also generated using the synthetic fiber generator.