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from brainvisa.processes import *
import shfjGlobals

name = 'White matter mask'
userLevel=1

signature=Signature(
  'fractional_anisotropy', ReadDiskItem( 'Fractional Anisotropy',
                                          'GIS Image' ),
  'brain_mask', ReadDiskItem( 'T2 Brain mask', ('Graph and Data',)+ shfjGlobals.anatomistVolumeFormats ),
  'FA_threshold', Float(),
  'white_mask', WriteDiskItem( 'T2 White matter Mask', 'Aims writable volume formats' ),
)

def initialization( self ):
  self.FA_threshold = 0
  self.linkParameters( 'brain_mask', 'fractional_anisotropy')
  self.linkParameters( 'white_mask', 'brain_mask')
  
def execution( self, context ):
  if self.FA_threshold > 0:
    thresholded = context.temporary( 'GIS image' )
    context.system( 'AimsThreshold', '-i', self.fractional_anisotropy, '-o', thresholded, '-m', 'gt',
                    '-t', self.FA_threshold, '-b' )
    if self.brain_mask.format is getFormat( 'Graph and data' ):
      convertedMask = context.temporary( 'Graph and data' )
      context.system( 'AimsFileConvert', '-i', self.brain_mask, '-o', convertedMask,
                      '--volume' )
      context.system( 'AimsMask', '-i', 
        os.path.join( convertedMask.fullPath(1), 'roi_Volume.ima' ), 
        '-m', thresholded, '-o', self.white_mask )
    else:
      context.system( 'AimsMask', '-i', self.brain_mask, '-m', thresholded, 
                      '-o', self.white_mask )
  else:
    context.warning("Threshold is null, white matter mask not created.")