# -*- coding: utf-8 -*-
#  This software and supporting documentation are distributed by
#      Institut Federatif de Recherche 49
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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 brainvisa import registration
from brainvisa.tools import aimsGlobals
from soma import aims


name = 'AddScannerBasedReferential'
userLevel = 2

signature = Signature( 
  'volume_input', ReadDiskItem( "T1 MRI", 'Aims readable volume formats',
    enableConversion=False ),
  'referential_volume_input', WriteDiskItem( 'Referential of Raw T1 MRI', 'Referential' ),
  'T1_TO_Scanner_Based', WriteDiskItem( 'Transformation to Scanner Based Referential', 'Transformation matrix' ),
  'new_referential', WriteDiskItem( 'Scanner Based Referential', 'Referential' ),
 )
  

def initialization( self ):
  self.linkParameters( 'referential_volume_input', 'volume_input' )
  self.linkParameters( 'new_referential', 'volume_input' )
  self.linkParameters( 'T1_TO_Scanner_Based', 'volume_input' )


def execution( self, context ):
  #Read header information
  atts = aimsGlobals.aimsVolumeAttributes( self.volume_input )
  ref = atts[ 'referentials' ]
  trf = atts[ 'transformations' ]
  if ("Scanner-based anatomical coordinates" in ref ):
    trm_to_scannerBased = trf[ref.index("Scanner-based anatomical coordinates")]
  
  
  #Create a referential for Scanner-based
  tm = registration.getTransformationManager()
  dest = tm.referential( self.new_referential )
  context.write( 'dest:', dest )
  if dest is None :
    dest = tm.createNewReferentialFor(self.new_referential, referentialType='Scanner Based Referential' )
    
  #Create a new referential if needed for the volume
  
  #src = tm.referential( self.volume_input )
  #print "Attributes"
  #print self.volume_input.hierarchyAttributes()
  #if src is None:
    #print "create src"
    #src = tm.createNewReferentialFor(self.volume_input)
    #print "apres"
    #print src
    
  src = tm.referential( self.referential_volume_input )
  context.write( 'src:', src )
  #print "Attributes"
  #print self.volume_input.hierarchyAttributes()
  if src is None:
    src = tm.createNewReferentialFor(self.volume_input ,
      referentialType='Referential of Raw T1 MRI',
      output_diskitem=self.referential_volume_input )
  dest.setMinf( 'direct_referential', 1, saveMinf=True )

  #Store information into the trm file
  mot = aims.Motion( trm_to_scannerBased )
  aims.write( mot, self.T1_TO_Scanner_Based.fullPath() )
  
  #set and update database
  tm.setNewTransformationInfo( self.T1_TO_Scanner_Based, source_referential=src, destination_referential=dest )