replace instaces of file with img_file in get_pachytene

R/get_pachytene.R

@@ -36,13 +36,13 @@ get_pachytene <- function(img_path, species_num = 20, offset = 0.2,ecc_thresh =
   dir.create(paste0(img_path_new,"/pachytene"))
   file_list <- list.files(img_path_new)
   ## for each image that is *-dna.jpeg,
-  for (file in file_list){
-    file_base = file
-    filename_path_test = paste0(img_path,"/crops/", file)
-    file = filename_path_test
+  for (img_file in file_list){
+    file_base = img_file
+    filename_path_test = paste0(img_path,"/crops/", img_file)
+    img_file = filename_path_test
     #if(grepl("*SYCP3.jpeg", file)){
-    if(grepl(paste0('*',channel2_string,'.',file_ext,'$'), file)){
-      file_dna = file
+    if(grepl(paste0('*',channel2_string,'.',file_ext,'$'), img_file)){
+      file_dna = img_file
       file_base_dna = file_base
       image_count <- image_count +1
       image <- readImage(file_dna)
@@ -50,9 +50,9 @@ get_pachytene <- function(img_path, species_num = 20, offset = 0.2,ecc_thresh =
       antibody1_store <- 1
     }
     #if(grepl("*MLH3.jpeg", file)){
-    if(grepl(paste0('*',channel1_string,'.',file_ext,'$'), file)){
+    if(grepl(paste0('*',channel1_string,'.',file_ext,'$'), img_file)){
       file_base_foci = file_base
-      file_foci = file
+      file_foci = img_file
       #print(file_foci)
       image <- readImage(file_foci)
       img_orig_foci <- channel(image, "gray")
@@ -77,10 +77,10 @@ get_pachytene <- function(img_path, species_num = 20, offset = 0.2,ecc_thresh =
         cell_count <- cell_count + 1
         ### identified a good image. count foci
         ### data frame stuff
-        if(grepl( WT_str, file, fixed = TRUE) == TRUE){
+        if(grepl( WT_str, img_file, fixed = TRUE) == TRUE){
           genotype <- WT_out
         }
-        if(grepl( KO_str, file, fixed = TRUE) == TRUE){
+        if(grepl( KO_str, img_file, fixed = TRUE) == TRUE){
           genotype <- KO_out
         }
         image_mat <- as.matrix(new_img)
@@ -108,7 +108,7 @@ get_pachytene <- function(img_path, species_num = 20, offset = 0.2,ecc_thresh =
         if(mean_ecc > ecc_thresh){
           if(px_fraction > area_thresh){
             stage_classification <- "pachytene"
-            df_cells <- rbind(df_cells,t(c(file,cell_count,genotype,px_mask, px_total,px_fraction, mean_ecc,mean_ratio,skew,sd_bright_px,stage_classification)))
+            df_cells <- rbind(df_cells,t(c(img_file,cell_count,genotype,px_mask, px_total,px_fraction, mean_ecc,mean_ratio,skew,sd_bright_px,stage_classification)))
             pachytene_count <- pachytene_count + 1
             file_dna <- tools::file_path_sans_ext(file_base_dna)
             filename_crop = paste0(img_path_new,"/pachytene/", file_dna,".jpeg")