Commit 66ebcaa0 authored by Lucy McNeill's avatar Lucy McNeill
Browse files

replace instaces of file with img_file

parent 28f0e5e8
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......@@ -43,31 +43,31 @@ auto_crop_fast <- function(img_path, max_cell_area = 20000, min_cell_area = 700
antibody3_store <- 0
## for each image that is *-dna.jpeg,
for (file in file_list){
file_base = file
filename_path_test = paste0(img_path,"/", file)
file = filename_path_test
for (img_file in file_list){
file_base = img_file
filename_path_test = paste0(img_path,"/",img_file)
img_file = filename_path_test
#if(grepl("*DAPI.jpeg$", file)){
if(third_channel == "on"){
if(grepl(paste0('*',channel3_string,'.',file_ext,'$'), file)){
file_DAPI = file
if(grepl(paste0('*',channel3_string,'.',file_ext,'$'),img_file)){
file_DAPI = img_file
image <- readImage(file_DAPI)
img_orig_DAPI <- channel(image, "grey")
antibody3_store <- 1
}
}
#if(grepl("*SYCP3.jpeg$", file)){
if(grepl(paste0('*',channel2_string,'.',file_ext,'$'), file)){
if(grepl(paste0('*',channel2_string,'.',file_ext,'$'), img_file)){
file_dna = file
file_dna = img_file
print(file)
image <- readImage(file_dna)
img_orig <- channel(2*image, "grey")
antibody1_store <- 1
}
#if(grepl("*MLH3.jpeg$", file)){
if(grepl(paste0('*',channel1_string,'.',file_ext,'$'), file)){
file_foci = file
if(grepl(paste0('*',channel1_string,'.',file_ext,'$'), img_file)){
file_foci = img_file
image <- readImage(file_foci)
img_orig_foci <- channel(image, "gray")
# call functions: get
......
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