# -*- 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
#
# This software is governed by the CeCILL license version 2 under
# French law and abiding by the rules of distribution of free software.
# You can  use, modify and/or redistribute the software under the 
# terms of the CeCILL license version 2 as circulated by CEA, CNRS
# and INRIA at the following URL "http://www.cecill.info". 
#
# As a counterpart to the access to the source code and  rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty  and the software's author,  the holder of the
# economic rights,  and the successive licensors  have only  limited
# liability.
#
# In this respect, the user's attention is drawn to the risks associated
# with loading,  using,  modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean  that it is complicated to manipulate,  and  that  also
# therefore means  that it is reserved for developers  and  experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
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# same conditions as regards security.
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# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license version 2 and that you accept its terms.

from brainvisa.processes import *
from brainvisa import shelltools


name = 'RicGyrificationIndex'
roles = ('misc',)
userLevel = 0

signature = Signature(
  'Graymatteroutermeshfile', ReadDiskItem( 'Mesh', ['MESH mesh', 'GIFTI file'] ),
  'ConvexHullMesh', ReadDiskItem( 'Mesh', ['MESH mesh', 'GIFTI file']  ),
  'SubjectName', String(),
  'Outputfile', WriteDiskItem( 'Mesh', ['MESH mesh']  ),
  'ventriclevolumename', ReadDiskItem( '4D Volume', ['gz compressed NIFTI-1 image', 'GIS image','NIFTI-1 image']),
    'BrainVisaStandardOutput', Boolean(),
    'Maximumtrianglearea', Float(),
    'transformationmatrix', ReadDiskItem( 'Text file', []),
    'verbose' , Boolean(),
 
)


def initialization( self ):
  self.setOptional( 'SubjectName', 
                    'Outputfile',
                    'ventriclevolumename',
                    'BrainVisaStandardOutput',
                    'Maximumtrianglearea',
                    'verbose',
                     'transformationmatrix' )
  self.SubjectName = None
  self.Outputfile = None
  self.ventriclevolumename = None
  self.BrainVisaStandardOutput = False
  self.Maximumtrianglearea = None 
  self.verbose = False     
  self.transformationmatrix = None
    
  self.signature[ 'SubjectName' ].userLevel = 2
  self.signature[ 'Outputfile' ].userLevel = 2
  self.signature[ 'ventriclevolumename' ].userLevel = 2
  self.signature[ 'BrainVisaStandardOutput' ].userLevel = 2
  self.signature[ 'Maximumtrianglearea' ].userLevel = 2
  self.signature[ 'verbose' ].userLevel = 2   
  self.signature[ 'transformationmatrix' ].userLevel = 2        
                    
                    
  
 



 


def execution( self, context ):
  convert = 0
  command = ['RicGyrificationIndex' , '--cm', self.ConvexHullMesh, '--gm',  self.Graymatteroutermeshfile]
  
  
  
  if self.SubjectName != None:
	  command += ['-s',self.SubjectName]
  
  if self.Outputfile != None:
	  command += ['-o', self.Outputfile]
  
  if self.ventriclevolumename != None:
	  command += ['-vv', self.ventriclevolumename]
	  
  if self.BrainVisaStandardOutput:
	  command += ['--bv']
	  
  if self.Maximumtrianglearea != None:
	  command += ['--ta' , self.Maximumtrianglearea]
	  
  if self.verbose :
	  command += ['-v']	  
	  
  if self.transformationmatrix :
	  command += ['--tm', self.transformationmatrix]	  
      
  if apply( context.system, command ):
    raise Exception( _t_('Error while reading <em>%s</em> to <em>%s</em>') % \
                         ( command[ 2 ], command[ 4 ] ) )

	
