# -*- 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".
#
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from brainvisa.processes import *
import shfjGlobals, math
import registration
from brainvisa import anatomist
from brainvisa import quaternion

name = 'Normalization pipeline'
userLevel = 0

def validationDelayed():
  '''validation cannot be done at startup since some sub-processes may not be
loaded yet. But this validationDelayed method can be used later.
  '''
  try:
    fsl = getProcess( 'FSLnormalizationPipeline' )
  except:
    fsl = None
  try:
    spm = getProcess( 'SPMnormalizationPipeline' )
  except:
    spm = None
  try:
    bal = getProcess( 'BaladinNormalizationPipeline' )
  except:
    bal = None
  if not fsl and not spm and not bal:
    raise ValidationError( 'No normalization process could be found working' )
  return fsl, spm, bal

signature = Signature(
  't1mri', ReadDiskItem( "Raw T1 MRI", shfjGlobals.aimsVolumeFormats ),
  'transformation',
    WriteDiskItem( 'Transform Raw T1 MRI to Talairach-MNI template-SPM',
      'Transformation matrix' ),
  'allow_flip_initial_MRI', Boolean(),
  )

def initialization( self ):
  try:
    fsl = getProcess( 'FSLnormalizationPipeline' )
  except:
    fsl = None
  try:
    spm = getProcess( 'SPMnormalizationPipeline' )
  except:
    spm = None
  try:
    bal = getProcess( 'BaladinNormalizationPipeline' )
  except:
    bal = None

  self.linkParameters( 'transformation', 't1mri' )
  self.allow_flip_initial_MRI = False

  eNode = SelectionExecutionNode( self.name, parameterized=self )

  if fsl:
    eNode.addChild( 'NormalizeFSL',
      ProcessExecutionNode( fsl,
        selected=(spm is None) ) )

    eNode.NormalizeFSL.removeLink( 'transformation', 't1mri' )
    eNode.addLink( 'NormalizeFSL.t1mri', 't1mri' )
    eNode.addLink( 't1mri', 'NormalizeFSL.t1mri' )
    eNode.addLink( 'NormalizeFSL.transformation', 'transformation' )
    eNode.addLink( 'transformation', 'NormalizeFSL.transformation' )
    eNode.addLink( 'NormalizeFSL.allow_flip_initial_MRI',
      'allow_flip_initial_MRI' )
    eNode.addLink( 'allow_flip_initial_MRI',
      'NormalizeFSL.allow_flip_initial_MRI' )

  if spm:
    eNode.addChild( 'NormalizeSPM',
      ProcessExecutionNode( spm, selected=1 ) )

    eNode.NormalizeSPM.removeLink( 'transformation', 't1mri' )
    eNode.addDoubleLink( 'NormalizeSPM.t1mri', 't1mri' )
    eNode.addDoubleLink( 'NormalizeSPM.transformation', 'transformation' )
    eNode.addDoubleLink( 'NormalizeSPM.allow_flip_initial_MRI',
      'allow_flip_initial_MRI' )

  if bal:
    eNode.addChild( 'NormalizeBaladin',
      ProcessExecutionNode( bal,
        selected=(bal is None) ) )

    eNode.NormalizeBaladin.removeLink( 'transformation', 't1mri' )
    eNode.addLink( 'NormalizeBaladin.t1mri', 't1mri' )
    eNode.addLink( 't1mri', 'NormalizeBaladin.t1mri' )
    eNode.addLink( 'NormalizeBaladin.transformation', 'transformation' )
    eNode.addLink( 'transformation', 'NormalizeBaladin.transformation' )
    eNode.addLink( 'NormalizeBaladin.allow_flip_initial_MRI',
      'allow_flip_initial_MRI' )
    eNode.addLink( 'allow_flip_initial_MRI',
      'NormalizeBaladin.allow_flip_initial_MRI' )

  eNode.addChild( 'Normalization_AimsMIRegister',
    ProcessExecutionNode( 'normalization_aimsmiregister',
      selected=(fsl is None and spm is None and bal is None) ) )
  eNode.Normalization_AimsMIRegister.removeLink( 'transformation_to_MNI', 'anatomy_data' )
  eNode.addDoubleLink( 'Normalization_AimsMIRegister.anatomy_data', 't1mri' )
  eNode.addDoubleLink( 'Normalization_AimsMIRegister.transformation_to_MNI', 'transformation' )

  self.setExecutionNode( eNode )