#  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 registration
try:
  from connectomist.qball import availableOrientationSets, getOrientationSet
except:
  pass

def validation():
  try:
    from connectomist.qball import availableOrientationSets, getOrientationSet
  except:
    raise ValidationError( 'connectomist.qball module is not present or does not work.' )

name ='Diffusion QBall'
userLevel = 2


signature = Signature(
  't2_diffusion', ReadDiskItem( 'T2 Diffusion MR',
                               'Aims readable volume formats' ),
  'dw_diffusion', ReadDiskItem( 'DW Diffusion MR', 
                                           'Aims readable volume formats' ),
  
  'orientations', Choice(),
  'diffusion_model', WriteDiskItem('QBall Model', 'Bucket'),
  'mask', ReadDiskItem( 'Diffusion mask',
                          'Aims readable volume formats' ),
  'circle_point_count', Integer(),
  'maximum_alpha', Float(),
  'alpha_deviation', Float(),
  'ascii', Boolean(),
)

def initialization( self ):
  
  self.signature[ 'orientations' ].setChoices( *availableOrientationSets() )
  self.linkParameters( 'dw_diffusion', 't2_diffusion' )
  self.linkParameters( 'mask', 't2_diffusion' )
  self.linkParameters( 'diffusion_model', 't2_diffusion' )
  
  self.setOptional( 'mask' )
  
  self.orientations = 'connectomist_0400'
  self.circle_point_count = 36
  self.maximum_alpha = 20.0
  self.alpha_deviation = 10.0
  self.ascii = 0  
  
def execution( self, context ):
  orientations = getOrientationSet( self.orientations )
  orientation_file = context.temporary( 'Text file' )
  f = open( orientation_file.fullPath(), 'w' )
  print >> f, len( orientations )
  for x, y, z in orientations:
    print >> f, x, y, z
  f.close()
  
  command = [
    'comistQBallField',
    '--verbose',
    '-t2', self.t2_diffusion,
    '-dw', self.dw_diffusion,
    '-ori', orientation_file,
    '-o', self.diffusion_model,
    '-c', self.circle_point_count,
    '-a', self.maximum_alpha,
    '-s', self.alpha_deviation,
  ]
  if self.mask is not None:
    command += [ '-m', self.mask ]
  if self.ascii:
    command += ['-ascii' ]    
  context.system( *command )
  
  self.diffusion_model.setMinf( 'qball_orientations', orientations )
  
  # Set referentials of new objects
  trManager = registration.getTransformationManager()
  trManager.copyReferential( self.t2_diffusion, self.diffusion_model )