timeout error fixed. Colorlabels not used when the appropriate size and shaped...

timeout error fixed. Colorlabels not used when the appropriate size and shaped cell objects are left in the mask

R/auto_crop_fast.R

@@ -98,6 +98,10 @@ auto_crop_fast <- function(img_path,  max_cell_area = 20000, min_cell_area = 700
       img_orig_highres <- img_orig
       img_orig <- resize(img_orig, w = resize_l, h = resize_l)
       antibody1_store <- 1
+      if(annotation == "on"){
+        cat("\n displaying enhanced image of cell channel")
+        plot(rgbImage(blob_factor*img_orig, 0*img_orig, 0*img_orig))
+      }
     }
     if(grepl(paste0('*',channel1_string,'.',file_ext,'$'), img_file)){
       file_foci <- img_file
@@ -385,7 +389,14 @@ get_blobs <- function(img_orig, blob_factor, bg_blob_factor, offset,final_blob_a
   if(annotation == "on"){
     cat("\n here is the mask")
     if(crowded_cells == "TRUE"){
-      plot(colorLabels(blob_th))
+      tryCatch({
+        if(nrow(data.frame(blob_th)) > 0){
+          plot(colorLabels(blob_th))
+        }
+      },
+      error = function(e) {
+      }
+      )
     }
     else{
       plot(blob_th)
@@ -438,8 +449,8 @@ keep_cells <- function(candidate, max_cell_area, min_cell_area, cell_aspect_rati
     cat("\n displaying the retained cells in mask (correct size/ shape)")
     if(crowded_cells == "TRUE"){
       tryCatch({
-        if(nrow(retained > 0)){
-          plot(colorLabels(retained))
+        if(nrow(data.frame(retained)) > 0){
+          plot(retained)
         }
       },
       error = function(e) {