using FileIO
using TiffImages
using MAT
include("findyourcell.jl")

DATA_DIR = "../0417-22-processed-stack-noRball/2021041720-preprocess"
RET_DIR = "../0417-22-processed-stack-noRball/result"

stack_list= filter(x->occursin(r"G-stack.tiff$", x), readdir(DATA_DIR))
unfinished = true
while unfinished
    for idx in 1:length(stack_list)
        raw_name = stack_list[idx]
        if time() - stat("$DATA_DIR/$raw_name").mtime > 300 # 300s, be careful 
            img = try
                TiffImages.load("$DATA_DIR/$raw_name", mmap=true)
            catch e
                @warn "Failed to load $raw_name, skip to next stack"
                continue #TODO: or wait util tiff is free to read
            end
            mask_name = "$RET_DIR/$(raw_name[1:end-4])_mask.tiff"
            info_name = "$RET_DIR/$(raw_name[1:end-4])_info.mat"
            raw_frame_num = size(img, 3)
	    	if isfile(info_name)
	            prev_info = matread(info_name)           
	            prev_frame_num = length(prev_info["info"])
            	append_num = raw_frame_num - prev_frame_num
	            # only process the new coming frames
	            if append_num > 0
	                println("Appending $raw_name:$(prev_frame_num+1):$raw_frame_num")
	                prev_mask = try
	                    reinterpret(UInt16, TiffImages.load(mask_name))
	                catch
	                    @warn "Failed to load mask $mask_name, skip to next stack"
	                    continue 	                
					end
	                mask_patch = Array{UInt16}(undef, size(img)[1:2], append_num)
	                new_mask = cat(prev_mask, mask_patch, dims=3)
	                info_patch = Array{Any}(undef, append_num)
	                new_info = cat(prev_info, info_patch, dims=1)
	                Threads.@threads for t in prev_frame_num+1:raw_frame_num
	                    print("*")
	                    new_mask[:, :, t], new_info[t] = find_your_cell(img[:, :, t])
	                end
				end
			else  # start from 0
	            println("Processing $raw_name: 1:$raw_frame_num")
    			new_mask = Array{UInt16}(undef, size(img))
    			new_info = Array{Any}(undef, raw_frame_num)
    			@time @inbounds Threads.@threads for t in 1:raw_frame_num
        			print("*")
        			new_mask[:, :, t], new_info[t] = find_your_cell(img[:, :, t])
    			end
			end
			save(mask_name, new_mask) 
	        matwrite(info_name, Dict("info"=>new_info ))
			println("")
	        println("Done!")
        end
    end
    sleep(1)   
end