# -*- 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
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# economic rights,  and the successive licensors  have only  limited
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# 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
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from brainvisa.processes import *
from registration import getTransformationManager
import operator
from copy import copy

name='Generic Diffusion Importation'
userLevel=0


signature = Signature(
  'files', ListOf( ReadDiskItem( 'Raw DW Diffusion MR', 'Aims readable volume formats' ) ),
  'bValuesAndOrientations', ReadDiskItem( 'Text file', 'Text file' ),
  't2_diffusion', WriteDiskItem( 'Raw T2 Diffusion MR', 'Aims writable volume formats' ),
  'dw_diffusion', WriteDiskItem( 'Raw DW Diffusion MR', 'Aims writable volume formats' ),
  'dw_already_corrected', Boolean(),
)

def switchCorrection( self, dw_already_corrected ):
  if dw_already_corrected:
    dwType = 'Non oriented DW Diffusion MR'
  else:
    dwType = 'Raw DW Diffusion MR'
  if dwType == self.signature[ 'dw_diffusion' ].type.name:
    return
  signature = copy( self.signature )
  signature[ 'dw_diffusion' ] = WriteDiskItem( dwType, 'GIS image' )
  self.changeSignature( signature )
    
  
def initialization( self ):
  self.linkParameters( 'dw_diffusion', 't2_diffusion' )
  self.dw_already_corrected = False
  self.addLink( None, 'dw_already_corrected', self.switchCorrection )
  self.signature[ 'files' ].databaseUserLevel = 2
  self.signature[ 't2_diffusion' ].browseUserLevel = 3
  self.signature[ 'dw_diffusion' ].browseUserLevel = 3


def execution( self, context ):
  #for v in self.files:
    #context.write( '<b>', v, '</b>' )
    #context.write( v.attributes() )
  #return
  volumesCount = reduce( operator.add, [ int( v.get( 'volume_dimension', search_header=True )[ 3 ] ) for v in self.files] )
  bValues = []
  orientations = []
  lineNumber = 0
  for line in open( self.bValuesAndOrientations.fullPath() ):
    lineNumber += 1
    line = line.strip()
    if not line or line[ 0 ] == '#': continue
    if line == '-':
      # Volumes with negative b-value are ignored
      b, x, y, z = -1, 0, 0, 0
    else:
      try:
        b, x, y, z = line.split()
      except:
        raise RuntimeError( _t_( 'Error in orientation file "%(file)s" on line %(line)d' ) % { 'file': self.bValuesAndOrientations.fullPath(), 'line': lineNumber } )
    bValues.append( float( b ) )
    orientations.append( [ float(x), float(y), float(z) ] )
  if len( orientations ) != volumesCount:
    raise RuntimeError( _t_( 'The b-values and orientation file must have as many lines as the number of input volumes. Input was %(volumes)d volumes and %(lines)d lines.' % { 'volumes': volumesCount, 'lines': len( orientations ) } ) )

  # Create temporary headers
  headers = []
  volumeIndex = 0
  for image in self.files:
    lastVolume = volumeIndex + image.get( 'volume_dimension' )[ 3 ]
    header = context.temporary( 'Text file' )
    headers.append( header )
    context.write( _t_('Building meta-info for data %s') % image.fullName() )
    header.setMinf( 'bvalues', bValues[ volumeIndex : lastVolume ] )
    header.setMinf( 'diffusion_gradient_orientations', orientations[ volumeIndex : lastVolume] )
    volumeIndex = lastVolume
    
  context.write( _t_('Concatenating data') )
  command = [ 'comistConcatenation',
              '-verbose',
              '-t2', self.t2_diffusion,
              '-dw', self.dw_diffusion,
              '-i' ] + self.files + [
              '-m' ] + [ x.minfFileName() for x in headers ]
  apply( context.system, command )
  
  transformManager = getTransformationManager()
  transformManager.createNewReferentialFor( self.t2_diffusion )
  transformManager.copyReferential( self.t2_diffusion,
                                    self.dw_diffusion )