# -*- coding: utf-8 -*-
# This software and supporting documentation are distributed by
#      Institut Federatif de Recherche 49
#      CEA/NeuroSpin, Batiment 145,
#      91191 Gif-sur-Yvette cedex
#      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 *
import registration

name = 'Hemisphere Sulci Skeleton'
userLevel = 0

# Argument declaration
signature = Signature(
    'hemi_cortex', ReadDiskItem( 'CSF+GREY Mask',
        'Aims readable volume formats' ),
    'grey_white', ReadDiskItem( 'Grey White Mask',
        'Aims readable volume formats' ),
    't1mri_nobias', ReadDiskItem( 'T1 MRI Bias Corrected',
        'Aims readable volume formats' ),
    'skeleton', WriteDiskItem( 'Cortex Skeleton',
        'Aims writable volume formats' ),
    'roots', WriteDiskItem( 'Cortex Catchment Bassins',
        'Aims writable volume formats' ),
    'fix_random_seed', Boolean(),
)

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


def execution( self, context ):
    trManager = registration.getTransformationManager()
    
    side = self.hemi_cortex.get( 'side' )
    if side is not None:
        context.write("Computing " + side + " sulci skeleton and buried gyrus watershed...")
    else:
        context.write("Computing sulci skeleton and buried gyrus watershed...")
    
    braing = context.temporary( 'NIFTI-1 Image' )
    context.system( "VipMask", "-i", self.t1mri_nobias,
                    "-m", self.grey_white, "-o", braing,
                    "-w", "t" )
    command = [ "VipSkeleton", "-i", self.hemi_cortex,
                "-so", self.skeleton, "-vo", self.roots,
                "-g", braing, "-w", "t" ]
    if self.fix_random_seed:
        command.extend(['-srand', 10])
    context.system( *command )
    
    trManager.copyReferential( self.hemi_cortex, self.skeleton )
    trManager.copyReferential( self.hemi_cortex, self.roots )
    
    del braing