# -*- 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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# 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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# that may mean  that it is complicated to manipulate,  and  that  also
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from brainvisa.processes import *
import shfjGlobals
import registration


name = 'Diffusion Bundles Transformation'
userLevel = 1

signature=Signature(
  'bundles', ReadDiskItem( 'Fascicles bundles', 'Aims bundles' ),
  'bundles_transformation', ReadDiskItem( 'Transformation matrix',
                                          'Transformation matrix' ),
  'selection_regions', ReadDiskItem( 'ROI',
                       ('Graph and Data',)+ shfjGlobals.anatomistVolumeFormats),
  'selection_regions_transformation', ReadDiskItem( 'Transformation matrix',
                                                 'Transformation matrix' ),
  'selection_rules', ReadDiskItem( 'Bundle Selection Rules',
                                   'Bundle Selection Rules' ),
  'selection_overlap', Number(),
  'split_regions', ReadDiskItem( 'ROI',
                       ('Graph and Data',)+ shfjGlobals.anatomistVolumeFormats),
  'split_regions_transformation', ReadDiskItem( 'Transformation matrix','Transformation matrix' ),
  'split_keep_original_bundle', Boolean(),
  'minimum_length', Float(),
  'transformed_bundles', WriteDiskItem( 'Fascicles bundles', 'Aims bundles', requiredAttributes={'transformed' : 'yes'} ),
  'ascii_bundles_file', Boolean(),
)

def initialization( self ):
  self.linkParameters( 'transformed_bundles', 'bundles')
  self.selection_overlap = 0
  self.ascii_bundles_file = 0
  self.split_keep_original_bundle = False
  self.setOptional( 'bundles_transformation',
                    'selection_regions', 'selection_regions_transformation',
                    'selection_rules', 'split_regions',
                    'split_regions_transformation', 'minimum_length' )

  
  
def execution( self, context ):
  command = [ 'comistBundleAnalysis_old',
              '--verbose',
              '-i', self.bundles,
            ]
  if self.ascii_bundles_file:
    command += [ '-b', self.transformed_bundles.fullPath() + '{"ascii":1}' ]
  else:
    command += [ '-b', self.transformed_bundles ]
  if self.bundles_transformation is not None:
    command += [ '-t', self.bundles_transformation ]
  if self.selection_regions is not None:
    command += [ '--selectionROI', self.selection_regions,
                 '--selectionOverlap', self.selection_overlap ]
    if self.selection_rules is None:
      raise RuntimeError( _t_( '<em>selection_rules</em> is mandatory if <em>selection_regions</em> is used' ) )
    command += [ '--selectionRules', self.selection_rules ]
    if self.selection_regions_transformation is not None:
      command += [ '--selectionROITransformation', self.selection_regions_transformation ]
  if self.split_regions is not None:
    command += [ '--split', self.split_regions ]
    if self.split_regions_transformation is not None:
      command += [ '--splitTransformation', self.split_regions_transformation ]
    if self.split_keep_original_bundle:
      command += [ '--splitKeepBundle' ]
  if self.minimum_length > 0:
    command += [ '--minimumLength', self.minimum_length ]    
  context.system( *command )

  # Set referentials of new objects
  trManager = registration.getTransformationManager()
  if self.bundles_transformation is None:
    referential = self.bundles
  else:
    referential = self.bundles_transformation.get( 'destination_referential' )
    if referential is None:
      context.warning( _t_( '<em>bundles_transformation</em> does not have <em>destination_referential</em> attribute. Cannot set <em>transformed_bundles</em> referential.' ) )
      referential = trManager.referential( referential )
  trManager.copyReferential( referential, self.transformed_bundles )