from register_virtual_stack import Register_Virtual_Stack_MT

from register_virtual_stack import Transform_Virtual_Stack_MT

import os

from ij import IJ, ImagePlus, WindowManager

temp_dir =IJ.getDirectory("temp")

IJ.log(temp_dir)

imp = WindowManager.getCurrentImage()

cslice = imp.getFrame()

channel = imp.getChannel()

print(type(cslice))

IJ.log(str(cslice))

# source directory

source_dir = temp_dir + '/Source/'

# output directory

target_dir = temp_dir + '/Target/'

# transforms directory

transf_dir = temp_dir + '/Transforms/'

# reference image

reference_name = "Tiffs"+str(cslice).zfill(4)+".tif"

# shrinkage option (false)

use_shrinking_constraint = 0

if not os.path.exists(source_dir):

os.makedirs(source_dir)

if not os.path.exists(target_dir):

os.makedirs(target_dir)

if not os.path.exists(transf_dir):

os.makedirs(transf_dir)

lst = os.listdir(source_dir)

for f in lst:

os.remove(source_dir+'/'+f)

lst = os.listdir(transf_dir)

for f in lst:

os.remove(transf_dir+'/'+f)

lst = os.listdir(target_dir)

for f in lst:

os.remove(target_dir+'/'+f)

IJ.run("Duplicate...", "duplicate channels="+str(channel));

IJ.run("Image Sequence... ", "dir="+source_dir+" format=TIFF, name=Tiffs");

lst = os.listdir(source_dir)

for f in lst:

os.rename(source_dir+'/'+f, source_dir+'/'+f[0:-6])

p = Register_Virtual_Stack_MT.Param()

#p.registrationModelIndex=5

Register_Virtual_Stack_MT.exec(source_dir, target_dir, transf_dir,

reference_name, p, use_shrinking_constraint)

WindowManager.getCurrentImage().setTitle("Orig")

lst = os.listdir(source_dir)

for f in lst:

os.remove(source_dir+'/'+f)

IJ.log(imp.getTitle())

IJ.selectWindow(imp.getTitle())

nchannels = imp.getNChannels()

merge_string = ""

for i in range(1,nchannels+1):

IJ.selectWindow(imp.getTitle())

IJ.run("Duplicate...", "duplicate channels="+str(i));

IJ.run("Image Sequence... ", "dir="+source_dir+" format=TIFF, name=Tiffs");

lst = os.listdir(source_dir)

for f in lst:

os.rename(source_dir+'/'+f, source_dir+'/'+f[0:-6])

Transform_Virtual_Stack_MT.exec(source_dir, target_dir, transf_dir, True)

WindowManager.getCurrentImage().setTitle("Ch"+str(i))

IJ.run("Duplicate...", "title=CH"+str(i)+" duplicate");

lst = os.listdir(source_dir)

for f in lst:

os.remove(source_dir+'/'+f)

merge_string = merge_string+"c"+str(i)+"=CH"+str(i)+" "

IJ.log(merge_string)

IJ.run("Merge Channels...", merge_string+"create")