#!/usr/bin/env python
import sys,os,os.path
inputfile = ''
outputfile = ''
refmask=''
reforiginal=''
threshold=''
if len(sys.argv)==1:
	print "Usage: python skullstripper.py -in <inputvolume> -ref <referencevolume> -refmask <referencemaskvolume> -out <outputfilename> \nOptional:\n\t-thr <valuetothreshold>"
	sys.exit()
for x in range(1,len(sys.argv)):
	if x%2 != 0:
		if sys.argv[x]=='-in':
			inputfile=sys.argv[x+1]
		elif sys.argv[x]=='-ref':
			reforiginal=sys.argv[x+1]
		elif sys.argv[x]=='-refmask':
			refmask=sys.argv[x+1]
		elif sys.argv[x]=='-out':
			outputfile=sys.argv[x+1]
		elif sys.argv[x]=='-thr':
			threshold=sys.argv[x+1]
		elif sys.argv[x]=='-h':
			print "Usage: python skullstripper.py -in <inputvolume> -ref <referencevolume> -refmask <referencemaskvolume> -out <outputfilename> \nOptional:\n\t-thr <valuetothreshold>"
			sys.exit()
		else:
			print "\nError invalid input.\n"
			print "Usage: python skullstripper.py -in <inputvolume> -ref <referencevolume> -refmask <referencemaskvolume> -out <outputfilename> \nOptional:\n\t-thr <valuetothreshold>"
			sys.exit()
if os.path.exists(inputfile)!=True:
	print 'Inputfile does not exist in this directory'
	sys.exit()
if os.path.exists(refmask)!=True:
	print 'Reference mask does not exist in this directory'
	sys.exit()
if os.path.exists(reforiginal)!=True:
	print 'Reference file does not exist in this directory'
	sys.exit()
#create output folders 
masks_folder = "masks"
stripped_folder = "stripped_images"
if not os.path.exists(masks_folder):
	os.makedirs(masks_folder)
if not os.path.exists(stripped_folder):
	os.makedirs(stripped_folder) 	
#path to niftyreg programs: reg_aladin, reg_f3d, reg_tools
registeraffinepath="reg_aladin"
registerf3dpath="reg_f3d"
regtoolspath="reg_tools"
#finds all files and folders
workingdir=os.getcwd()
os.system(registeraffinepath+" -target "+inputfile+" -source "+ reforiginal+" -aff affinetransformcurrent.txt")
os.system(registerf3dpath+" -target "+inputfile+" -source "+ reforiginal+" -aff affinetransformcurrent.txt -cpp ccptemp.nii")
#cleanup files
os.remove("outputResult.nii")
os.remove("affinetransformcurrent.txt")
os.system(registerf3dpath+" -target "+inputfile+" -source "+refmask+" -ln 0 -maxit 0 -incpp ccptemp.nii -res "+masks_folder+'/'+outputfile)
#binarizes images and converts it to a char so it can be edited in brainsuite
os.remove("outputCPP.nii")
os.remove("ccptemp.nii")
#add -thr 800 if needed
if threshold !='':
	print 'Starting Thresholding'
	# this command places the mask in the masks/ folder. 
	os.system(regtoolspath+" -in "+masks_folder+'/'+outputfile+" -out "+masks_folder+'/'+outputfile+" -thr "+threshold)
	print 'Done Thresholding'
	print 'Starting Masking'
	# this command places the stripped images in the stripped_images/ folder. 
	os.system(regtoolspath+" -in "+inputfile+" -nan "+masks_folder+'/'+outputfile+ " -out " + stripped_folder+'/'+outputfile + "_stripped")
	print 'Done Masking'