import os

import numpy as np

from multiprocessing import Pool

from functools import partial

from image_utils import *  

def output3DRefinement(atlases, DLSeg, param_dir, tmps_dir, dofs_dir, subject_dir, savedInd, fr, mirtk):

    segstring = ''

    ind = 0

    atlasUsedNo = len(atlases)

    for i in range(atlasUsedNo):

        if mirtk:

            os.system('mirtk register '

                      '{0} '

                      '{1} '

                      '-parin {2}/ffd_label_1.cfg ' 

                      '-dofin {3}/shapelandmarks_{4}.dof.gz '

                      '-dofout {3}/shapeffd_{5}_{6}.dof.gz' 

                      .format(DLSeg, atlases[i], param_dir, dofs_dir, savedInd[i], i, fr))

            os.system('mirtk transform-image '

                      '{0} '

                      '{1}/seg_lvsa_SR_{4}_{5}.nii.gz ' 

                      '-dofin {2}/shapeffd_{4}_{5}.dof.gz '

                      '-target {3}/lvsa_SR_{5}.nii.gz -interp NN'  

                      .format(atlases[i], tmps_dir, dofs_dir, subject_dir, i, fr)) 

        else:

            os.system('nreg '

                      '{0} '

                      '{1} '

                      '-parin {2}/segreg.txt ' 

                      '-dofin {3}/shapelandmarks_{4}.dof.gz '

                      '-dofout {3}/shapeffd_{5}_{6}.dof.gz' 

                      .format(DLSeg, atlases[i], param_dir, dofs_dir, savedInd[i], i, fr))

            os.system('transformation '

                      '{0} '

                      '{1}/seg_lvsa_SR_{4}_{5}.nii.gz ' 

                      '-dofin {2}/shapeffd_{4}_{5}.dof.gz '

                      '-target {3}/lvsa_SR_{5}.nii.gz -nn' 

                      .format(atlases[i], tmps_dir, dofs_dir, subject_dir, i, fr))    

        segstring += '{0}/seg_lvsa_SR_{1}_{2}.nii.gz '.format(tmps_dir, i, fr)

        ind += 1

    # apply label fusion    

    os.system('combineLabels {0}/seg_lvsa_SR_{1}.nii.gz {2} {3}'.format(subject_dir, fr, ind, segstring))

def apply_PC(subject, data_dir, param_dir, atlases_list, landmarks_list, mirtk):

    print('  registering {0}'.format(subject))    

    subject_dir = os.path.join(data_dir, subject)

    if os.path.isdir(subject_dir):

        tmps_dir = '{0}/tmps'.format(subject_dir)

        dofs_dir = '{0}/dofs'.format(subject_dir)

        segs_dir = '{0}/segs'.format(subject_dir)

        sizes_dir = '{0}/sizes'.format(subject_dir)

        subject_landmarks = '{0}/landmarks.vtk'.format(subject_dir)

        for fr in ['ED', 'ES']:

            DLSeg = '{0}/seg_lvsa_{1}.nii.gz'.format(segs_dir, fr)

            if not os.path.exists(DLSeg):

                print(' segmentation {0} does not exist. Skip.'.format(DLSeg))

                continue

            topSimilarAtlases_list, savedInd = topSimilarAtlasShapeSelection(atlases_list[fr], landmarks_list[fr], 

                                               subject_landmarks, tmps_dir, dofs_dir, DLSeg, param_dir, 3) 

            formHighResolutionImg(subject_dir, fr)

            output3DRefinement(topSimilarAtlases_list, DLSeg, param_dir, tmps_dir, dofs_dir, subject_dir, savedInd, fr, mirtk)

            if mirtk:

                refineFusionResults(subject_dir, 'seg_lvsa_SR_{0}.nii.gz'.format(fr), 2)

#                clearBaseManbrance(subject_dir, 'seg_lvsa_SR_{0}.nii.gz'.format(fr)) 

#            

#                refineFusionResults(subject_dir, 'seg_lvsa_SR_{0}.nii.gz'.format(fr), 2) 

            else:

                refineFusionResults(subject_dir, 'seg_lvsa_SR_{0}.nii.gz'.format(fr), 2) 

            convertImageSegment(subject_dir, fr)

            outputVolumes(subject_dir, data_dir, subject, fr)

            moveVolumes(subject_dir, sizes_dir, fr)

        print('  finish 3D nonrigid-registering one subject {}'.format(subject))

    else:  

        print('  {0} is not a valid directory, do nothing'.format(subject_dir))

def multiatlasreg3D(dir_0, dir_1, dir_2, coreNo, parallel, mirtk):

    print('Select all the shape atlases for 3D multi-atlas registration')

    atlases_list, landmarks_list = allAtlasShapeSelection(dir_1)

    if parallel:

        print('Start 3D multi-atlas registration and program running on {0} cores'.format(coreNo))

        pool = Pool(processes = coreNo) 

        # partial only in Python 2.7+

        pool.map(partial(apply_PC, 

                         data_dir=dir_0,  

                         param_dir=dir_2, 

                         atlases_list=atlases_list, 

                         landmarks_list=landmarks_list,

                         mirtk=mirtk), 

                         sorted(os.listdir(dir_0)))       

    else:

        print('Start 3D multi-atlas registration and program running subsequently')

        data_dir, param_dir = dir_0, dir_2

        for subject in sorted(os.listdir(data_dir)):

            print('  registering {0}'.format(subject))   

            subject_dir = os.path.join(data_dir, subject)

            if not os.path.isdir(subject_dir):

                print('  {0} is not a valid folder, Skip'.format(subject_dir))

                continue 

            tmps_dir = '{0}/tmps'.format(subject_dir)

            dofs_dir = '{0}/dofs'.format(subject_dir)

            segs_dir = '{0}/segs'.format(subject_dir)

            sizes_dir = '{0}/sizes'.format(subject_dir)

            subject_landmarks = '{0}/landmarks.vtk'.format(subject_dir)

            for fr in ['ED', 'ES']:

                DLSeg = '{0}/seg_lvsa_{1}.nii.gz'.format(segs_dir, fr)

                if not os.path.exists(DLSeg):

                    print(' segmentation {0} does not exist. Skip.'.format(DLSeg))

                    continue

                topSimilarAtlases_list, savedInd = topSimilarAtlasShapeSelection(atlases_list[fr], landmarks_list[fr], 

                                                   subject_landmarks, tmps_dir, dofs_dir, DLSeg, param_dir, 3) 

                formHighResolutionImg(subject_dir, fr)

                output3DRefinement(topSimilarAtlases_list, DLSeg, param_dir, tmps_dir, dofs_dir, subject_dir, savedInd, fr, mirtk)

                if mirtk:

                    refineFusionResults(subject_dir, 'seg_lvsa_SR_{0}.nii.gz'.format(fr), 2) 

#                    clearBaseManbrance(subject_dir, 'seg_lvsa_SR_{0}.nii.gz'.format(fr)) 

#            

#                    refineFusionResults(subject_dir, 'seg_lvsa_SR_{0}.nii.gz'.format(fr), 2) 

                else:

                    refineFusionResults(subject_dir, 'seg_lvsa_SR_{0}.nii.gz'.format(fr), 2) 

                convertImageSegment(subject_dir, fr)

                outputVolumes(subject_dir, data_dir, subject, fr)

                moveVolumes(subject_dir, sizes_dir, fr)

            print('  finish 3D nonrigid-registering one subject {}'.format(subject))