Commit d2351bce authored by Lucy McNeill's avatar Lucy McNeill
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get_pachytene outputs red and green channel images into a folder called pachytene-RGB

parent 2cc7dfec
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...@@ -45,6 +45,7 @@ get_pachytene <- function(img_path, species_num = 20, offset = 0.2,ecc_thresh = ...@@ -45,6 +45,7 @@ get_pachytene <- function(img_path, species_num = 20, offset = 0.2,ecc_thresh =
colnames(df_cells) <- df_cols colnames(df_cells) <- df_cols
img_path_new <- paste0(img_path,"/crops") img_path_new <- paste0(img_path,"/crops")
dir.create(paste0(img_path_new,"/pachytene")) dir.create(paste0(img_path_new,"/pachytene"))
dir.create(paste0(img_path_new,"/pachytene-RGB"))
file_list <- list.files(img_path_new) file_list <- list.files(img_path_new)
for (img_file in file_list){ for (img_file in file_list){
file_base <- img_file file_base <- img_file
...@@ -124,6 +125,12 @@ get_pachytene <- function(img_path, species_num = 20, offset = 0.2,ecc_thresh = ...@@ -124,6 +125,12 @@ get_pachytene <- function(img_path, species_num = 20, offset = 0.2,ecc_thresh =
file_foci <- tools::file_path_sans_ext(file_base_foci) file_foci <- tools::file_path_sans_ext(file_base_foci)
filename_crop_foci <- paste0(img_path_new,"/pachytene/", file_foci,".jpeg") filename_crop_foci <- paste0(img_path_new,"/pachytene/", file_foci,".jpeg")
writeImage(img_orig_foci, filename_crop_foci) writeImage(img_orig_foci, filename_crop_foci)
### add RGB channel
ch1 <-channel(img_orig,"grey")
ch2 <- channel(img_orig_foci,"grey")
RGB_img <- rgbImage(ch1,ch2,0*ch1)
filename_crop_RGB <- paste0(img_path_new,"/pachytene-RGB/", file_dna,".jpeg")
writeImage(RGB_img, filename_crop_RGB)
} }
} }
} }
......
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