""" 

Copyright (c) 2017, Jose Dolz .All rights reserved.

Redistribution and use in source and binary forms, with or without modification,

are permitted provided that the following conditions are met:

    1. Redistributions of source code must retain the above copyright notice,

       this list of conditions and the following disclaimer.

    2. Redistributions in binary form must reproduce the above copyright notice,

       this list of conditions and the following disclaimer in the documentation

       and/or other materials provided with the distribution.

    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,

    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES

    OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND

    NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT

    HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,

    WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING

    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR

    OTHER DEALINGS IN THE SOFTWARE.

Jose Dolz. Dec, 2017.

email: jose.dolz.upv@gmail.com

LIVIA Department, ETS, Montreal.

"""

import sys

import pdb

from os.path import isfile, join

import os

import numpy as np

import nibabel as nib

import scipy.io as sio

from LiviaNet.Modules.IO.loadData import load_nii

from LiviaNet.Modules.IO.loadData import load_matlab

from LiviaNet.Modules.IO.saveData import saveImageAsNifti

from LiviaNet.Modules.IO.saveData import saveImageAsMatlab

# NOTE: Only has been tried on nifti images. However, it should not give any error for Matlab images. 

""" To print function usage """

def printUsage(error_type):

    if error_type == 1:

        print(" ** ERROR!!: Few parameters used.")

    else:

        print(" ** ERROR!!: ...") # TODO

    print(" ******** USAGE ******** ")

    print(" --- argv 1: Folder containing mr images")

    print(" --- argv 2: Folder to save corrected label images")

    print(" --- argv 3: Image type")

    print(" ------------- 0: nifti format")

    print(" ------------- 1: matlab format")

def getImageImageList(imagesFolder):

    if os.path.exists(imagesFolder):

       imageNames = [f for f in os.listdir(imagesFolder) if isfile(join(imagesFolder, f))]

    imageNames.sort()

    return imageNames

def checkAnotatedLabels(argv):

    # Number of input arguments

    #    1: Folder containing label images

    #    2: Folder to save corrected label images

    #    3: Image type

    #             0: nifti format

    #             1: matlab format  

    # Do some sanity checks

    if len(argv) < 3:

        printUsage(1)

        sys.exit()

    imagesFolder = argv[0]

    imagesFolderdst  = argv[1]

    imageType = int(argv[2])

    imageNames = getImageImageList(imagesFolder)

    printFileNames = False

    for i_d in xrange(len(imageNames)) :

        if imageType == 0:

            imageFileName = imagesFolder + '/' + imageNames[i_d]

            [imageData,img_proxy] = load_nii(imageFileName, printFileNames)

        else:

            imageFileName = imagesFolder + '/' + imageNames[i_d]

            imageData = load_matlab(imageFileName, printFileNames)

        # Find voxels different to 0

        # NOTE: I assume voxels equal to 0 are outside my ROI (like in the skull stripped datasets)

        idx = np.where(imageData > 0 )

        # Create ROI and assign those indexes to 1

        roiImage = np.zeros(imageData.shape,dtype=np.int8)

        roiImage[idx] = 1

        print(" ... Saving roi...")

        nameToSave =  imagesFolderdst + '/ROI_' + imageNames[i_d]

        if imageType == 0: # nifti

            imageTypeToSave = np.dtype(np.int8)

            saveImageAsNifti(roiImage,

                             nameToSave,

                             imageFileName,

                             imageTypeToSave)

        else: # Matlab

            # Cast to int8 for saving purposes

            saveImageAsMatlab(labelCorrectedImage.astype('int8'),nameToSave)

    print " ******************************************  PROCESSING LABELS DONE  ******************************************"

if __name__ == '__main__':

   checkAnotatedLabels(sys.argv[1:])