from net.imglib2.img.display.imagej import ImageJFunctions
from java.awt.event import TextListener
from ij import Menus
from ij.gui import GenericDialog
from ij.io import OpenDialog
from ij.measure import ResultsTable
from ij.gui import WaitForUserDialog
from ij.plugin import ZProjector
from ij.plugin import ChannelSplitter
from ij.plugin import RGBStackMerge
from ij.plugin import HyperStackConverter
import java.util.ArrayList as ArrayList
from ij import ImagePlus
import csv
import os
import sys
from ij import IJ

def reduceZ():
    imp = IJ.getImage()  #get the standardtack
    title_1 = imp.getTitle()
    title = title_1.split(' - ')[1]
    print(title)
    dimentions = imp.getDimensions()
    numZ, numChannels, numframes  = dimentions[3], dimentions[2], dimentions[4]
    print(numChannels)
    
 
    IJ.run(imp, "Set Measurements...", "kurtosis redirect=None decimal=3")
    
    kurtTotal = []
    for time in range(numframes):
        print(time)
        time = time+1
        imp.setPosition(1, 1, time)
        kurt = []
        for z in range(numZ):
            z = z+1
            imp.setPosition(1, z, time)
            imp.setRoi(70,40,437,459)
            IJ.setAutoThreshold(imp, "MaxEntropy dark")
            IJ.run(imp, "Measure", "")
            IJ.resetThreshold(imp)
            rt = ResultsTable()
            t = rt.getResultsTable() 
            kurt.append(t.getValueAsDouble(23, z-1)) # 23 = kurtosis
        kurtTotal.append(kurt.index(max(kurt))+1)
        IJ.run(imp, "Clear Results", "")
    print(kurtTotal)
    
    IJ.run(imp, "Select All", "")

    imp2 = IJ.createImage("GFP", "16-bit black", dimentions[0], dimentions[1], numframes)
    imp2 = HyperStackConverter.toHyperStack(imp2, 1, 1, numframes, "Color")
    print(' ------------')
    print(numframes)
    channel = 1
    i = 0
    for time in range(numframes):
        time = time+1
        imp.setPosition(channel, kurtTotal[i], time)
        imp.copy()
        imp2.setPosition(channel, 1, time)
        imp2.paste()
        print(time)
        i=i+1
    IJ.run(imp2, "Delete Slice", "delete=slice")
    imp2.show()
    
    imp4 = IJ.createImage("RFP", "16-bit black", dimentions[0], dimentions[1], numframes)
    imp4 = HyperStackConverter.toHyperStack(imp4, 1, 1, numframes, "Color")
    print(' ------------')
    channel = 2  
    i = 0
    for time in range(numframes):
        time = time+1
        imp.setPosition(channel, kurtTotal[i], time)
        imp.copy()
        print(imp.title)
        imp4.setPosition(channel, 1, time)
        imp4.paste()
        i=i+1
    IJ.run(imp4, "Delete Slice", "delete=slice")
    imp4.show()

    IJ.selectWindow(title_1)
    IJ.run("Close")
    
    imp5 = ImagePlus()
    IJ.run(imp5, "Merge Channels...", "c1=RFP c2=GFP create")
    imp5 = IJ.getImage()
    IJ.run(imp5, "Bio-Formats Exporter", "save=/home/rickettsia/Desktop/data/Clamydial_Image_Analysis/EMS_BMEC_20X_01192020/Zreduced/" + title + ".ome.tif export compression=LZW")
    IJ.selectWindow('Merged')
    IJ.run("Close")


od = OpenDialog("Time Laps Images", "")
firstDir = od.getDirectory()
fileList = os.listdir(firstDir)

if "DisplaySettings.json" in fileList:
    fileList.remove("DisplaySettings.json")
if ".DS_Store" in fileList:  
    fileList.remove(".DS_Store")  
fileList.sort()
totalCount = []
i = 1
for fileName in fileList:
    IJ.run("Collect Garbage")
    currentFile = firstDir + fileName
    print(firstDir)
    IJ.run("Bio-Formats Importer", "open=[" + currentFile + "] autoscale color_mode=Composite view=Hyperstack stack_order=XYCZT series_list="+str(i))
    reduceZ()
    i=i+1