Commit 825fb10e authored by Lucy McNeill's avatar Lucy McNeill
Browse files

remove superfluous if statement in auto_crop_fast.R

parent 91dba4e4
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......@@ -191,88 +191,86 @@ crop_single_object_fast <- function(retained, OOI_final,counter_final,img_orig,i
### use the features of tmp_img
### here we have the single object. Need to identify its centre value and radius..
crop_r <- floor(r_max[counter_final])
cx <- cx[counter_final]
cy <- cy[counter_final]
# might want to do this as a matrix
top_left_x <- floor(cx-crop_r)
top_left_y <- floor(cy-crop_r)
if (1>0){
crop_r <- floor(r_max[counter_final])
cx <- cx[counter_final]
cy <- cy[counter_final]
# might want to do this as a matrix
top_left_x <- floor(cx-crop_r)
top_left_y <- floor(cy-crop_r)
bottom_left_x <- floor(cx-crop_r)
bottom_left_y <- floor(cy+crop_r)
bottom_left_x <- floor(cx-crop_r)
bottom_left_y <- floor(cy+crop_r)
bottom_right_x <- floor(cx+crop_r)
bottom_right_y <- floor(cy+crop_r)
bottom_right_x <- floor(cx+crop_r)
bottom_right_y <- floor(cy+crop_r)
top_right_x <- floor(cx-crop_r)
top_right_y <- floor(cy+crop_r)
top_right_x <- floor(cx-crop_r)
top_right_y <- floor(cy+crop_r)
## crop image
ix <- bottom_left_x:bottom_right_x
iy <- top_left_y:bottom_left_y
## crop image
ix <- bottom_left_x:bottom_right_x
iy <- top_left_y:bottom_left_y
### cropping finished
## we just need ix and iy
##
# determine the dimensions, 2 in this case
## cropping part
tryCatch({
new_img <- noise_gone[ix, iy]
## want all images to have the same mean to 0.1
orig_mean <- mean(new_img)
mean_factor <- mean_pix/orig_mean
new_img <- new_img*mean_factor
#file_dna <- tools::file_path_sans_ext(file_dna)
file_stub <- paste0('-',channel2_string,'.',file_ext)
file_dna <- gsub(file_stub,'', file_base)
filename_crop = paste0(img_path,"/crops/", file_dna,"-crop-",cell_count,file_stub)
writeImage(new_img, filename_crop)
new_img_foci <- noise_gone_foci[ix, iy]
file_stub <- paste0('-',channel1_string,'.',file_ext)
file_foci <- gsub(file_stub,'', file_foci)
filename_crop_foci = paste0(img_path,"/crops/", file_dna,"-crop-",cell_count,file_stub)
writeImage(new_img_foci, filename_crop_foci)
if(third_channel == "on"){
new_img_DAPI <- noise_gone_DAPI[ix, iy]
#file_DAPI <- gsub('-DAPI.jpeg','', file_DAPI)
file_stub <- paste0('-',channel3_string,'.',file_ext)
file_DAPI <- gsub(file_stub,'', file_DAPI)
filename_crop_DAPI = paste0(img_path,"/crops/", file_dna,"-crop-",cell_count,file_stub)
writeImage(new_img_DAPI, filename_crop_DAPI)
}
## we just need ix and iy
##
# determine the dimensions, 2 in this case
## cropping part
tryCatch({
new_img <- noise_gone[ix, iy]
## want all images to have the same mean to 0.1
orig_mean <- mean(new_img)
mean_factor <- mean_pix/orig_mean
new_img <- new_img*mean_factor
#file_dna <- tools::file_path_sans_ext(file_dna)
file_stub <- paste0('-',channel2_string,'.',file_ext)
file_dna <- gsub(file_stub,'', file_base)
filename_crop = paste0(img_path,"/crops/", file_dna,"-crop-",cell_count,file_stub)
writeImage(new_img, filename_crop)
new_img_foci <- noise_gone_foci[ix, iy]
file_stub <- paste0('-',channel1_string,'.',file_ext)
file_foci <- gsub(file_stub,'', file_foci)
filename_crop_foci = paste0(img_path,"/crops/", file_dna,"-crop-",cell_count,file_stub)
writeImage(new_img_foci, filename_crop_foci)
if(third_channel == "on"){
new_img_DAPI <- noise_gone_DAPI[ix, iy]
#file_DAPI <- gsub('-DAPI.jpeg','', file_DAPI)
file_stub <- paste0('-',channel3_string,'.',file_ext)
file_DAPI <- gsub(file_stub,'', file_DAPI)
filename_crop_DAPI = paste0(img_path,"/crops/", file_dna,"-crop-",cell_count,file_stub)
writeImage(new_img_DAPI, filename_crop_DAPI)
}
if(annotation=="on"){
print("from the file:")
print(file_dna)
display(img_orig)
print("I cropped this cell:")
display(new_img)
print("using this mask")
display(tmp_img)
print("whose cell number is")
print(cell_count)
}
#### strand related stuff here
},
error = function(e) {
#what should be done in case of exception?
if(annotation=="on"){
#str(e) # #prints structure of exception
print("couldn't crop it since cell is on the edge. Neglected the following mask of a cell candidate:")
display(tmp_img)
}
if(annotation=="on"){
print("from the file:")
print(file_dna)
display(img_orig)
print("I cropped this cell:")
display(new_img)
print("using this mask")
display(tmp_img)
print("whose cell number is")
print(cell_count)
}
#### strand related stuff here
},
error = function(e) {
#what should be done in case of exception?
if(annotation=="on"){
#str(e) # #prints structure of exception
print("couldn't crop it since cell is on the edge. Neglected the following mask of a cell candidate:")
display(tmp_img)
}
}
)
}
)
}
......
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