# -*- 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

# Pour les formats de fichier Aims
import shfjGlobals
import os.path, string

# Import brainrat libraries
import brainrat.iosupport as iosupport
import brainrat.uicheck as uicheck

name = 'StackingIndividualSlices'
userLevel = 0

signature = Signature(
  'Input_ListOf_2dImage', ListOf( ReadDiskItem( '2D Image', 'Biology 2D image formats' ) ),
  'Dimension_X', Integer(),
  'Dimension_Y', Integer(),
  'Scanner_Resolution', Integer(),
  'Inter_Slice_Thickness', Float(),
  'Output_3dImage', WriteDiskItem( '3D Volume', 'Biology 3D volume formats' ),
)

def initialization( self ):
  
  # Sets default parameters value
  self.Scanner_Resolution = 600

  # Sets optional parameters
  self.setOptional( 'Dimension_X', 'Dimension_Y' )

def execution( self, context ):
  try :
    # Check parameters
    if not uicheck.objectattr( context, self, 'Scanner_Resolution', 0, operator.gt ) :
      return

    if not uicheck.objectattr( context, self, 'Inter_Slice_Thickness', 0, operator.gt ) :
      return
    
    if not self.Dimension_X is None :
      if not uicheck.objectattr( context, self, 'Dimension_X', 0, operator.gt ) :
        return

    if not self.Dimension_Y is None :
      if not uicheck.objectattr( context, self, 'Dimension_Y', 0, operator.gt ) :
        return

    # Write start message
    context.write( _t_( 'Converting input images to S16 images' ), ' ...' )
    
    temporaryimages = list()
    for i in xrange( len( self.Input_ListOf_2dImage ) ):
      temporaryimages.append( context.temporary('GIS image') )
      iosupport.normalizeFile( context, self.Input_ListOf_2dImage[i].fullPath(), temporaryimages[i].fullPath() )

    context.write( _t_( 'Stacking and centering individual slices using gravity centers [ count : %s ]' ) % len(temporaryimages), ' ...' )
    
    command = ['AimsCenterSlices',
            '-resol', self.Scanner_Resolution,
            '-z', self.Inter_Slice_Thickness,
            '-o', self.Output_3dImage,
            '-i'] + temporaryimages

    if not self.Dimension_X is None :
      command += [ '-dx', self.Dimension_X ]

    if not self.Dimension_Y is None :
      command += [ '-dy', self.Dimension_Y ]
      
    context.system(*command)

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