# -*- coding: utf-8 -*-
# This software and supporting documentation are distributed by
#     bioPICSEL
#     CEA/DSV/I²BM/MIRCen/LMN, Batiment 61,
#     18, route du Panorama
#     92265 Fontenay-aux-Roses
#     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
# with a limited warranty  and the software's author,  the holder of the
# economic rights,  and the successive licensors  have only  limited
# liability.
#
# In this respect, the user's attention is drawn to the risks associated
# with loading,  using,  modifying and/or developing or reproducing the
# 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
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or 
# data to be ensured and,  more generally, to use and operate it in the 
# same conditions as regards security.
#
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license version 2 and that you accept its terms.

# Ligne obligatoire
from brainvisa.processes import *
import os, math, copy, os.path

# Pour les formats de fichier Aims
import shfjGlobals

# Import brainrat libraries
import brainrat.uicheck as uicheck

name = 'IntensityVolumeNormalization'
userLevel = 0

signature = Signature(
    'Input_3dImage',  ReadDiskItem( '3D Volume', 'Biology 3D volume formats' ),
    'Multiplicative_Coefficient',  Float(),
    'Additive_Coefficient',  Float(),
    'Output_3dImage', WriteDiskItem( '3D Volume', 'Biology 3D volume formats' ),
  )

def initialization( self ):

  # Sets default parameters value
  self.Multiplicative_Coefficient = 1
  self.Additive_Coefficient = 0

  # Sets optional parameters
  self.setOptional( 'Output_3dImage' )

def execution( self, context ):
  try :
    outputImage = self.Output_3dImage
    
    # Check parameters
    if outputImage is None :
      if context.ask( _t_( uicheck.messages[ 'overwritemessage' ]  ) %
                          { 'inputfield' : 'Input_3dImage',
                            'outputfield' : 'Output_3dImage',
                            'file' : self.Input_3dImage }, 'OK', 'Cancel' ) == 0 :
        outputImage = self.Input_3dImage
      else :
        return
  
    # Write start message
    context.write( _t_( 'Normalizing volume intensity' ), ' ...' )

    command = [ 'AimsLinearComb',
                '-i', self.Input_3dImage.fullPath(),
                '-a', self.Multiplicative_Coefficient,
                '-e', self.Additive_Coefficient,
                '-o', outputImage.fullPath() ]

    context.system( *command )
    
    command = [ 'AimsThreshold',
                '-i', outputImage.fullPath(),
                '-m', 'ge',
                '-t', 0,
                '-o', outputImage.fullPath() ]

    context.system( *command )

  except Exception, error :
    context.error( _t_( uicheck.messages[ 'processingerrormessage' ] ) )