# -*- coding: utf-8 -*-
#  This software and supporting documentation are distributed by
#      Institut Federatif de Recherche 49
#      CEA/NeuroSpin, Batiment 145,
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# This software is governed by the CeCILL license version 2 under
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# terms of the CeCILL license version 2 as circulated by CEA, CNRS
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from brainvisa.processes import *
from soma import aims
import registration

name = 'Hemisphere Grey White Topological Correction'
userLevel = 0

# Argument declaration
signature = Signature(
    'grey_white', ReadDiskItem( 'Grey White Mask',
        'Aims readable volume formats' ),
    't1mri_nobias', ReadDiskItem( 'T1 MRI Bias Corrected',
        'Aims readable volume formats' ),
    'histo_analysis', ReadDiskItem( 'Histo Analysis', 'Histo Analysis' ),
    'hemi_cortex', WriteDiskItem( 'CSF+GREY Mask',
        'Aims writable volume formats' ),
    'fix_random_seed', Boolean(),
)

# Default values
def initialization( self ):
    self.linkParameters( 't1mri_nobias', 'grey_white' )
    self.linkParameters( 'histo_analysis', 't1mri_nobias' )
    self.linkParameters( 'hemi_cortex', 'grey_white' )
    self.signature[ 'fix_random_seed' ].userLevel = 3
    self.fix_random_seed = False


def execution( self, context ):
    tm = registration.getTransformationManager()
    
    side = self.grey_white.get( 'side' )
    if side is not None:
        context.write( "Detecting " + side + " hemisphere spherical inner cortical interface..." )
    else:
        context.write( "Detecting spherical inner cortical interface..." )
    
    command = [ "VipHomotopic", "-i",
                self.t1mri_nobias, "-cl",
                self.grey_white, "-h",
                self.histo_analysis, "-o",
                self.hemi_cortex,
                "-m", "C", "-w", "t" ]
    if self.fix_random_seed:
        command.extend(['-srand', '10'])
    context.system( *command )
    
    tm.copyReferential(self.grey_white, self.hemi_cortex)