#  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
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# 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
from brainvisa import shelltools
from registration import getTransformationManager

name='Import Diffusion NmrSmsVB13ADwSpinEchoEpi (sequence NeuroSpin)'
userLevel=1


def validation():
  if distutils.spawn.find_executable( 'NmrSplitDwData' ) is None:
    raise ValidationError( _t_( 'Nmr command(s) not found' ) )

signature = Signature(
  'file', ReadDiskItem( 'Raw DW Diffusion MR', shfjGlobals.aimsVolumeFormats ),
  't2_diffusion', WriteDiskItem( 'Raw T2 Diffusion MR', 'GIS image' ),
  'raw_dw_diffusion', WriteDiskItem( 'Raw DW Diffusion MR', 'GIS image' ),
  'ignoreFileIndices', ListOf( Integer() ),
)

def initialization( self ):

  self.linkParameters( 'raw_dw_diffusion', 't2_diffusion' )
  self.setOptional( 'ignoreFileIndices' )
  self.signature[ 'ignoreFileIndices' ].userLevel = 2

def execution( self, context ):

  if self.ignoreFileIndices:
    temporary = context.temporary( 'GIS image' )
    command = [ 'NmrSplitDwData',
                '-i', self.file,
                '-t2', self.t2_diffusion,
                '-dw', temporary,
                '-verbose' ]
    apply( context.system, command )
    command = [ 'NmrSubDwData',
                '-i', temporary,
                '-o', self.raw_dw_diffusion,
                '-ignoredIndices', self.ignoreFileIndices,
                '-verbose' ]
    apply( context.system, command )


  else:
    command = [ 'NmrSplitDwData',
                '-i', self.file,
                '-t2', self.t2_diffusion,
                '-dw', self.raw_dw_diffusion,
                '-verbose' ]
    apply( context.system, command )
  
  shelltools.mv( self.t2_diffusion.fullName() + '.header',
                 self.t2_diffusion.fullName() + '.ima.minf' )
  shelltools.mv( self.raw_dw_diffusion.fullName() + '.header',
                 self.raw_dw_diffusion.fullName() + '.ima.minf' )

  # flipping T2 data along z axis
  command = [ 'NmrFlipper',
              '-i', self.t2_diffusion,
              '-o', self.t2_diffusion,
              '-t', 'z',
              '-verbose' ]
  apply( context.system, command )
  
  # flipping DW data along z axis
  command = [ 'NmrFlipper',
              '-i', self.raw_dw_diffusion,
              '-o', self.raw_dw_diffusion,
              '-t', 'z',
              '-verbose' ]
  apply( context.system, command )

  transformManager = getTransformationManager()
  transformManager.createNewReferentialFor( self.t2_diffusion )
  transformManager.copyReferential( self.t2_diffusion,
                                    self.raw_dw_diffusion )