Update clean_duplicates.R

Author: jdknguyen

R/clean_duplicates.R

@@ -53,28 +53,30 @@ clean_duplicates <- function(setup, segs, xy_thresh = 1, z_thresh = 10, compare_
     # Search and identify cells that have the same x,y coordinate
     for (r in 1:n_rows){       # r for row
       for (c in 1:n_cols) {    # c for column
-        if (!is.na(segs$segmentations[[s]]$soma$x[r])) {
-          ind_x <- which.min(abs(segs$segmentations[[s+c]]$soma$x- segs$segmentations[[s]]$soma$x[r]))
-          ind_y <- which.min(abs(segs$segmentations[[s+c]]$soma$y- segs$segmentations[[s]]$soma$y[r]))
-          if((length(ind_x) != 0) & (length(ind_y) != 0)){
-            if (ind_x==ind_y){
-              comp_matrix[r,c+1] <- ind_x
-              # exact_overlap_cnt <- exact_overlap_cnt + 1
+        if(length(is.na(segs$segmentations[[s]]$soma$x[r])) != 0){
+          if (!is.na(segs$segmentations[[s]]$soma$x[r])) {
+            ind_x <- which.min(abs(segs$segmentations[[s+c]]$soma$x- segs$segmentations[[s]]$soma$x[r]))
+            ind_y <- which.min(abs(segs$segmentations[[s+c]]$soma$y- segs$segmentations[[s]]$soma$y[r]))
+            if((length(ind_x) != 0) & (length(ind_y) != 0)){
+              if (ind_x==ind_y){
+                comp_matrix[r,c+1] <- ind_x
+                # exact_overlap_cnt <- exact_overlap_cnt + 1
 
-            } else {
-              # in cells isolated by x, threshold by difference in y
-              diff_y <- abs(segs$segmentations[[s+c]]$soma$y[ind_x] - segs$segmentations[[s]]$soma$y[r])
+              } else {
+                # in cells isolated by x, threshold by difference in y
+                diff_y <- abs(segs$segmentations[[s+c]]$soma$y[ind_x] - segs$segmentations[[s]]$soma$y[r])
 
-              # in cells isolated by y, threshold by difference in x
-              diff_x <- abs(segs$segmentations[[s+c]]$soma$x[ind_y] - segs$segmentations[[s]]$soma$x[r])
+                # in cells isolated by y, threshold by difference in x
+                diff_x <- abs(segs$segmentations[[s+c]]$soma$x[ind_y] - segs$segmentations[[s]]$soma$x[r])
 
-              if (diff_y < diff_x & diff_y < xy_thresh) {
-                comp_matrix[r,c+1] <- ind_x
-                # thresh_overlap_cnt <- thresh_overlap_cnt + 1
+                if (diff_y < diff_x & diff_y < xy_thresh) {
+                  comp_matrix[r,c+1] <- ind_x
+                  # thresh_overlap_cnt <- thresh_overlap_cnt + 1
 
-              } else if (diff_x < diff_y & diff_x < xy_thresh) {
-                comp_matrix[r,c+1] <- ind_y
-                # thresh_overlap_cnt <- thresh_overlap_cnt + 1
+                } else if (diff_x < diff_y & diff_x < xy_thresh) {
+                  comp_matrix[r,c+1] <- ind_y
+                  # thresh_overlap_cnt <- thresh_overlap_cnt + 1
+                }
               }
             }
           }
@@ -90,7 +92,7 @@ clean_duplicates <- function(setup, segs, xy_thresh = 1, z_thresh = 10, compare_
 
 
       ### start if else statement for last 5 columns here
-      while (sep_cnt< sep_z &&  c != n_cols+1) {
+      while (sep_cnt< sep_z &&  c != n_cols+1 & length(comp_matrix > 0)) {
         prev <- is.na(comp_matrix[r,c])
         cur  <- is.na(comp_matrix[r,c+1])
         if (cur) {
@@ -114,8 +116,12 @@ clean_duplicates <- function(setup, segs, xy_thresh = 1, z_thresh = 10, compare_
         intensities <- vector(length=end_soma)
 
         for (c in 1:end_soma) {
-          if (!is.na(comp_matrix[r,c])) {
-            intensities[c] <- segs$segmentations[[s+c-1]]$soma$intensity[comp_matrix[r,c]]
+         if(length(comp_matrix) > 0){
+            if (!is.na(comp_matrix[r,c])) {
+              intensities[c] <- segs$segmentations[[s+c-1]]$soma$intensity[comp_matrix[r,c]]
+            } else {
+              intensities[c] <- NA
+            }
           } else {
             intensities[c] <- NA
           }