# -*- coding: utf-8 -*-
#  This software and supporting documentation are distributed by
#      Institut Federatif de Recherche 49
#      CEA/NeuroSpin, Batiment 145,
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#      France
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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 Classification'
userLevel = 0

# Argument declaration
signature = Signature(
    'side', Choice( 'left', 'right' ),
    't1mri_nobias', ReadDiskItem( 'T1 MRI Bias Corrected',
        'Aims readable volume formats' ),
    'histo_analysis', ReadDiskItem( 'Histo Analysis', 'Histo Analysis' ),
    'split_brain', ReadDiskItem( 'Split Brain Mask',
        'Aims readable volume formats' ),
    'edges', ReadDiskItem( 'T1 MRI Edges',
        'Aims readable volume formats' ),
    'commissure_coordinates', ReadDiskItem( 'Commissure coordinates',
        'Commissure coordinates'),
    'grey_white', WriteDiskItem( 'Morphologist Grey White Mask',
        'Aims writable volume formats' ),
    'fix_random_seed', Boolean(),
)

# Default values
def initialization( self ):
    def linkGW( self, dummy ):
        if self.t1mri_nobias is not None:
            return self.signature[ 'grey_white' ].findValue( self.t1mri_nobias, requiredAttributes={ 'side': self.side } )
    self.linkParameters( 'histo_analysis', 't1mri_nobias' )
    self.linkParameters( 'grey_white', ( 't1mri_nobias', 'side' ), linkGW )
    self.linkParameters( 'split_brain', 't1mri_nobias' )
    self.linkParameters( 'edges', 't1mri_nobias' )
    self.linkParameters( 'commissure_coordinates', 't1mri_nobias' )
    self.signature[ 'fix_random_seed' ].userLevel = 3
    self.fix_random_seed = False


def execution( self, context ):
    if os.path.exists(self.grey_white.fullName() + '.loc'):
        context.write(self.grey_white.fullName(), 'has been locked')
        context.write('Remove', self.grey_white.fullName(), '.loc if you want to trigger a new classification')
    else:
        context.write( 'Computing ' + self.side + ' hemisphere grey-white classification...' )
        if self.side == 'left':
            sideval = 2
        else:
            sideval = 1
        command = [ 'VipGreyWhiteClassif', '-i',
                    self.t1mri_nobias, '-h',
                    self.histo_analysis, '-m',
                    self.split_brain, '-edges',
                    self.edges, '-P',
                    self.commissure_coordinates, '-o',
                    self.grey_white, '-l', sideval,
                    '-w', 't', '-a', 'N' ]
        if self.fix_random_seed:
            command += ['-srand', '10']
        context.system( *command )
        
        tm = registration.getTransformationManager()
        tm.copyReferential(self.t1mri_nobias, self.grey_white)