""" 
Copyright (c) 2016, 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.

    THIS SOFTWARE IS PROVIDED BY THE FREEBSD PROJECT "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE FREEBSD PROJECT OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
    The views and conclusions contained in the software and documentation are those of the authors and should not be interpreted as representing official policies, either expressed or implied, of the FreeBSD Project.

Jose Dolz. Dec, 2016.
email: jose.dolz.upv@gmail.com
LIVA Department, ETS, Montreal.
"""

import os
import numpy
import numpy as np
import nibabel as nib
import pdb
import scipy.io

from loadData import load_nii


## ========  For Nifti files  ========= ##
def saveImageAsNifti(imageToSave,
                     imageName,
                     imageOriginalName,
                     imageType):

    printFileNames = False
    
    if printFileNames == True:
        print(" ... Saving image in {}".format(imageName))

    [imageData,img_proxy] = load_nii(imageOriginalName, printFileNames)
    
    # Generate the nii file
    niiToSave = nib.Nifti1Image(imageToSave, img_proxy.affine)
    niiToSave.set_data_dtype(imageType)
    
    dim = len(imageToSave.shape)
    zooms = list(img_proxy.header.get_zooms()[:dim])
    if len(zooms) < dim :
        zooms = zooms + [1.0]*(dim-len(zooms))
    
    niiToSave.header.set_zooms(zooms)
    nib.save(niiToSave, imageName)
    
    print "... Image succesfully saved..."


## ========= For Matlab files ========== ##
def saveImageAsMatlab(imageToSave,
                      imageName):

    printFileNames = False
    
    if printFileNames == True:
        print(" ... Saving image in {}".format(imageName))

    scipy.io.savemat(imageName, mdict={'vol': imageToSave})
    
    print "... Image succesfully saved..."

""" 
Copyright (c) 2016, 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.

    THIS SOFTWARE IS PROVIDED BY THE FREEBSD PROJECT "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE FREEBSD PROJECT OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
    The views and conclusions contained in the software and documentation are those of the authors and should not be interpreted as representing official policies, either expressed or implied, of the FreeBSD Project.

Jose Dolz. Dec, 2016.
email: jose.dolz.upv@gmail.com
LIVIA Department, ETS, Montreal.
"""

import os
import numpy
import numpy as np
import nibabel as nib
import pdb
import scipy.io

from loadData import load_nii


## ========  For Nifti files  ========= ##
def saveImageAsNifti(imageToSave,
                     imageName,
                     imageOriginalName,
                     imageType):

    printFileNames = False
    
    if printFileNames == True:
        print(" ... Saving image in {}".format(imageName))

    [imageData,img_proxy] = load_nii(imageOriginalName, printFileNames)
    
    # Generate the nii file
    niiToSave = nib.Nifti1Image(imageToSave, img_proxy.affine)
    niiToSave.set_data_dtype(imageType)
    
    dim = len(imageToSave.shape)
    zooms = list(img_proxy.header.get_zooms()[:dim])
    if len(zooms) < dim :
        zooms = zooms + [1.0]*(dim-len(zooms))
    
    niiToSave.header.set_zooms(zooms)
    nib.save(niiToSave, imageName)
    
    print "... Image succesfully saved..."


## ========= For Matlab files ========== ##
def saveImageAsMatlab(imageToSave,
                      imageName):

    printFileNames = False
    
    if printFileNames == True:
        print(" ... Saving image in {}".format(imageName))

    scipy.io.savemat(imageName, mdict={'vol': imageToSave})
    
    print "... Image succesfully saved..."

Update saveData.py