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Models:
Tobias Harvey
tobiasharvey/
4Dsegment
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Diff of /code/meshfitting.py [000000] .. [32d261]

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a b/code/meshfitting.py 

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import os





  
  

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from multiprocessing import Pool





  
  

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from functools import partial





  
  

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def meshGeneration(subject_dir, template_dir, param_dir, tmps_dir, vtks_dir, dofs_dir): 





  
  

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    os.system('rm {0}/*.txt'.format(subject_dir))  





  
  

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    os.system('rm {0}/*'.format(vtks_dir))    





  
  

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    os.system('rm {0}/*'.format(tmps_dir))    





  
  

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    for fr in ['ED', 'ES']:





  
  

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        ###########################################################################    





  
  

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        # extract meshes of lvendo, lvepi, lvmyo, rv and rveip at ED and ES, respectively





  
  

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        os.system('binarize '





  
  

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                  '{0}/PHsegmentation_{2}.gipl '





  
  

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                  '{1}/vtk_RV_{2}.nii.gz '





  
  

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                  '4 4 255 0'





  
  

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                  .format(subject_dir, tmps_dir, fr))





  
  

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        os.system('mcubes '





  
  

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                  '{0}/vtk_RV_{2}.nii.gz '





  
  

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                  '{1}/RV_{2}.vtk '





  
  

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                  '120 -blur 2'





  
  

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                  .format(tmps_dir, vtks_dir, fr))





  
  

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        os.system('binarize '





  
  

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                  '{0}/PHsegmentation_{2}.gipl '





  
  

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                  '{1}/vtk_RVepi_{2}.nii.gz '





  
  

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                  '3 4 255 0'





  
  

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                  .format(subject_dir, tmps_dir, fr))





  
  

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        os.system('mcubes '





  
  

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                  '{0}/vtk_RVepi_{2}.nii.gz '





  
  

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                  '{1}/RVepi_{2}.vtk '





  
  

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                  '120 -blur 2'





  
  

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                  .format(tmps_dir, vtks_dir, fr))





  
  

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        os.system('padding '





  
  

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                  '{0}/PHsegmentation_{2}.gipl '





  
  

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                  '{0}/PHsegmentation_{2}.gipl '





  
  

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                  '{1}/vtk_LV_{2}.nii.gz '





  
  

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                  '4 0'





  
  

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                  .format(subject_dir, tmps_dir, fr))





  
  

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        os.system('padding '





  
  

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                  '{1}/vtk_LV_{2}.nii.gz '





  
  

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                  '{0}/PHsegmentation_{2}.gipl '





  
  

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                  '{1}/vtk_LV_{2}.nii.gz '





  
  

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                  '3 0'





  
  

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                  .format(subject_dir, tmps_dir, fr))





  
  

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        os.system('binarize '





  
  

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                  '{0}/PHsegmentation_{2}.gipl '





  
  

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                  '{1}/vtk_LVendo_{2}.nii.gz '





  
  

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                  '1 1 255 0'





  
  

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                  .format(subject_dir, tmps_dir, fr))





  
  

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        os.system('mcubes '





  
  

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                  '{0}/vtk_LVendo_{2}.nii.gz '





  
  

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                  '{1}/LVendo_{2}.vtk '





  
  

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                  '120 -blur 2'





  
  

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                  .format(tmps_dir, vtks_dir, fr))





  
  

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        os.system('binarize '





  
  

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                  '{0}/PHsegmentation_{2}.gipl '





  
  

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                  '{1}/vtk_LVepi_{2}.nii.gz '





  
  

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                  '1 2 255 0'





  
  

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                  .format(subject_dir, tmps_dir, fr))





  
  

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        os.system('mcubes '





  
  

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                  '{0}/vtk_LVepi_{2}.nii.gz '





  
  

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                  '{1}/LVepi_{2}.vtk '





  
  

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                  '120 -blur 2'





  
  

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                  .format(tmps_dir, vtks_dir, fr))





  
  

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        os.system('binarize '





  
  

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                  '{0}/PHsegmentation_{2}.gipl '





  
  

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                  '{1}/vtk_LVmyo_{2}.nii.gz '





  
  

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                  '2 2 255 0'





  
  

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                  .format(subject_dir, tmps_dir, fr))





  
  

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        os.system('mcubes '





  
  

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                  '{0}/vtk_LVmyo_{2}.nii.gz '





  
  

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                  '{1}/LVmyo_{2}.vtk '





  
  

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                  '120 -blur 2'





  
  

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                  .format(tmps_dir, vtks_dir, fr))





  
  

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#        os.system('binarize '





  
  

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#                  '{0}/seg_lvsa_SR_{2}.nii.gz '





  
  

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#                  '{1}/vtk_RV_{2}.nii.gz '





  
  

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#                  '4 4 255 0'





  
  

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#                  .format(subject_dir, tmps_dir, fr))





  
  

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#           





  
  

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#        os.system('mcubes '





  
  

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#                  '{0}/vtk_RV_{2}.nii.gz '





  
  

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#                  '{1}/RV_{2}.vtk '





  
  

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#                  '120 -blur 2'





  
  

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#                  .format(tmps_dir, vtks_dir, fr))





  
  

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#        





  
  

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#        os.system('binarize '





  
  

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#                  '{0}/seg_lvsa_SR_{2}.nii.gz '





  
  

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#                  '{1}/vtk_RVepi_{2}.nii.gz '





  
  

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#                  '3 4 255 0'





  
  

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#                  .format(subject_dir, tmps_dir, fr))





  
  

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#        





  
  

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#        os.system('mcubes '





  
  

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#                  '{0}/vtk_RVepi_{2}.nii.gz '





  
  

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#                  '{1}/RVepi_{2}.vtk '





  
  

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#                  '120 -blur 2'





  
  

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#                  .format(tmps_dir, vtks_dir, fr))





  
  

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#        





  
  

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#        os.system('padding '





  
  

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#                  '{0}/seg_lvsa_SR_{2}.nii.gz '





  
  

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#                  '{0}/seg_lvsa_SR_{2}.nii.gz '





  
  

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#                  '{1}/vtk_LV_{2}.nii.gz '





  
  

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#                  '4 0'





  
  

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#                  .format(subject_dir, tmps_dir, fr))





  
  

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#        





  
  

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#        os.system('padding '





  
  

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#                  '{1}/vtk_LV_{2}.nii.gz '





  
  

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#                  '{0}/seg_lvsa_SR_{2}.nii.gz '





  
  

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#                  '{1}/vtk_LV_{2}.nii.gz '





  
  

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#                  '3 0'





  
  

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#                  .format(subject_dir, tmps_dir, fr))





  
  

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#        





  
  

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#        os.system('binarize '





  
  

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#                  '{0}/seg_lvsa_SR_{2}.nii.gz '





  
  

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#                  '{1}/vtk_LVendo_{2}.nii.gz '





  
  

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#                  '1 1 255 0'





  
  

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#                  .format(subject_dir, tmps_dir, fr))





  
  

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#        





  
  

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#        os.system('mcubes '





  
  

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#                  '{0}/vtk_LVendo_{2}.nii.gz '





  
  

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#                  '{1}/LVendo_{2}.vtk '





  
  

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#                  '120 -blur 2'





  
  

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#                  .format(tmps_dir, vtks_dir, fr))





  
  

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#        





  
  

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#        os.system('binarize '





  
  

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#                  '{0}/seg_lvsa_SR_{2}.nii.gz '





  
  

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#                  '{1}/vtk_LVepi_{2}.nii.gz '





  
  

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#                  '1 2 255 0'





  
  

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#                  .format(subject_dir, tmps_dir, fr))





  
  

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#        





  
  

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#        os.system('mcubes '





  
  

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#                  '{0}/vtk_LVepi_{2}.nii.gz '





  
  

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#                  '{1}/LVepi_{2}.vtk '





  
  

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#                  '120 -blur 2'





  
  

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#                  .format(tmps_dir, vtks_dir, fr))





  
  

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#        





  
  

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#        os.system('binarize '





  
  

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#                  '{0}/seg_lvsa_SR_{2}.nii.gz '





  
  

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#                  '{1}/vtk_LVmyo_{2}.nii.gz '





  
  

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#                  '2 2 255 0'





  
  

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#                  .format(subject_dir, tmps_dir, fr))





  
  

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#        





  
  

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#        os.system('mcubes '





  
  

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#                  '{0}/vtk_LVmyo_{2}.nii.gz '





  
  

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#                  '{1}/LVmyo_{2}.vtk '





  
  

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#                  '120 -blur 2'





  
  

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#                  .format(tmps_dir, vtks_dir, fr))





  
  

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    ###############################################################################





  
  

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    #use landmark to initialise the registration





  
  

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#    os.system('prreg '





  
  

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#              '{0}/landmarks.vtk '





  
  

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#              '{1}/landmarks.vtk '





  
  

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#              '-dofout {2}/landmarks.dof.gz'





  
  

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#              .format(subject_dir, template_dir, dofs_dir))





  
  

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    ###############################################################################





  
  

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    for fr in ['ED', 'ES']:





  
  

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#        os.system('msrreg 3 '





  
  

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#                  '{0}/RV_{4}.vtk '





  
  

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#                  '{0}/LVendo_{4}.vtk '





  
  

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#                  '{0}/LVepi_{4}.vtk '





  
  

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#                  '{1}/RV_{4}.vtk '





  
  

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#                  '{1}/LVendo_{4}.vtk '





  
  

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#                  '{1}/LVepi_{4}.vtk '





  
  

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#                  '-dofin {2}/landmarks.dof.gz '





  
  

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#                  '-dofout {3}/{4}.dof.gz '





  
  

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#                  '-symmetric'





  
  

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#                  .format(vtks_dir, template_dir, dofs_dir, tmps_dir, fr))





  
  

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        os.system('msrreg 3 '





  
  

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                  '{0}/RV_{3}.vtk '





  
  

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                  '{0}/LVendo_{3}.vtk '





  
  

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                  '{0}/LVepi_{3}.vtk '





  
  

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                  '{1}/RV_{3}.vtk '





  
  

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                  '{1}/LVendo_{3}.vtk '





  
  

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                  '{1}/LVepi_{3}.vtk '





  
  

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                  '-dofout {2}/{3}.dof.gz '





  
  

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                  '-symmetric'





  
  

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                  .format(vtks_dir, template_dir, tmps_dir, fr))





  
  

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        os.system('msrreg 2 '





  
  

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                  '{0}/LVendo_{3}.vtk '





  
  

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                  '{0}/LVepi_{3}.vtk '





  
  

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                  '{1}/LVendo_{3}.vtk '





  
  

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                  '{1}/LVepi_{3}.vtk '





  
  

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                  '-dofin {2}/{3}.dof.gz '





  
  

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                  '-dofout {2}/lv_{3}_rreg.dof.gz '





  
  

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                  '-symmetric'





  
  

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                  .format(vtks_dir, template_dir, tmps_dir, fr))





  
  

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        os.system('srreg '





  
  

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                  '{0}/RV_{3}.vtk '





  
  

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                  '{1}/RV_{3}.vtk '





  
  

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                  '-dofin {2}/{3}.dof.gz '





  
  

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                  '-dofout {2}/rv_{3}_rreg.dof.gz '





  
  

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                  '-symmetric'





  
  

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                  .format(vtks_dir, template_dir, tmps_dir, fr))





  
  

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        ###########################################################################     





  
  

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        os.system('ptransformation '





  
  

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                  '{0}/RV_{2}.vtk '





  
  

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                  '{0}/N_RV_{2}.vtk '





  
  

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                  '-dofin {1}/rv_{2}_rreg.dof.gz'





  
  

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                  .format(vtks_dir, tmps_dir, fr))





  
  

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        os.system('ptransformation '





  
  

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                  '{0}/RVepi_{2}.vtk '





  
  

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                  '{0}/N_RVepi_{2}.vtk '





  
  

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                  '-dofin {1}/rv_{2}_rreg.dof.gz'





  
  

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                  .format(vtks_dir, tmps_dir, fr))





  
  

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        os.system('ptransformation '





  
  

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                  '{0}/LVendo_{2}.vtk '





  
  

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                  '{0}/N_LVendo_{2}.vtk '





  
  

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                  '-dofin {1}/lv_{2}_rreg.dof.gz'





  
  

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                  .format(vtks_dir, tmps_dir, fr))





  
  

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        os.system('ptransformation '





  
  

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                  '{0}/LVepi_{2}.vtk '





  
  

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                  '{0}/N_LVepi_{2}.vtk '





  
  

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                  '-dofin {1}/lv_{2}_rreg.dof.gz'





  
  

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                  .format(vtks_dir, tmps_dir, fr))





  
  

  242
  
        





  
  

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        os.system('ptransformation '





  
  

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                  '{0}/LVmyo_{2}.vtk '





  
  

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                  '{0}/N_LVmyo_{2}.vtk '





  
  

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                  '-dofin {1}/lv_{2}_rreg.dof.gz'





  
  

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                  .format(vtks_dir, tmps_dir, fr))





  
  

  248
  
        





  
  

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        os.system('transformation '





  
  

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                  '{0}/vtk_RV_{1}.nii.gz '





  
  

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                  '{0}/N_vtk_RV_{1}.nii.gz '





  
  

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                  '-dofin {0}/lv_{1}_rreg.dof.gz '





  
  

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                  '-invert'





  
  

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                  .format(tmps_dir, fr))





  
  

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        os.system('transformation '





  
  

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                  '{0}/vtk_LV_{1}.nii.gz '





  
  

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                  '{0}/N_vtk_LV_{1}.nii.gz '





  
  

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                  '-dofin {0}/lv_{1}_rreg.dof.gz '





  
  

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                  '-invert'





  
  

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                  .format(tmps_dir, fr))





  
  

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        ###########################################################################





  
  

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        #affine





  
  

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        os.system('areg '





  
  

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                  '{0}/vtk_RV_{3}.nii.gz '





  
  

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                  '{1}/N_vtk_RV_{3}.nii.gz '





  
  

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                  '-dofout {1}/rv_{3}_areg.dof.gz '





  
  

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                  '-parin {2}/segareg.txt'





  
  

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                  .format(template_dir, tmps_dir, param_dir, fr))





  
  

  271
  
        





  
  

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        os.system('areg '





  
  

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                  '{0}/vtk_LV_{3}.nii.gz '





  
  

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                  '{1}/N_vtk_LV_{3}.nii.gz '





  
  

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                  '-dofout {1}/lv_{3}_areg.dof.gz '





  
  

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                  '-parin {2}/segareg.txt'





  
  

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                  .format(template_dir, tmps_dir, param_dir, fr))





  
  

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        #non-rigid





  
  

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        os.system('nreg '





  
  

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                  '{0}/vtk_RV_{3}.nii.gz '





  
  

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                  '{1}/N_vtk_RV_{3}.nii.gz '





  
  

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                  '-dofin {1}/rv_{3}_areg.dof.gz '





  
  

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                  '-dofout {1}/rv_{3}_nreg.dof.gz '





  
  

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                  '-parin {2}/segreg.txt'





  
  

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                  .format(template_dir, tmps_dir, param_dir, fr))





  
  

  287
  
        





  
  

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        os.system('snreg '





  
  

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                  '{0}/RV_{3}.vtk '





  
  

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                  '{1}/N_RV_{3}.vtk '





  
  

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                  '-dofin {2}/rv_{3}_nreg.dof.gz '





  
  

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                  '-dofout {2}/rv{3}ds8.dof.gz '





  
  

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                  '-ds 8 -symmetric'





  
  

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                  .format(template_dir, vtks_dir, tmps_dir, fr))





  
  

  295
  
        





  
  

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        os.system('nreg '





  
  

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                  '{0}/vtk_LV_{3}.nii.gz '





  
  

  298
  
                  '{1}/N_vtk_LV_{3}.nii.gz '





  
  

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                  '-dofin {1}/lv_{3}_areg.dof.gz '





  
  

  300
  
                  '-dofout {1}/lv_{3}_nreg.dof.gz '





  
  

  301
  
                  '-parin {2}/segreg.txt'





  
  

  302
  
                  .format(template_dir, tmps_dir, param_dir, fr))





  
  

  303
  
        





  
  

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        os.system('msnreg 2 '





  
  

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                  '{0}/LVendo_{3}.vtk '





  
  

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                  '{0}/LVepi_{3}.vtk '





  
  

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                  '{1}/N_LVendo_{3}.vtk '





  
  

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                  '{1}/N_LVepi_{3}.vtk '





  
  

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                  '-dofin {2}/lv_{3}_nreg.dof.gz '





  
  

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                  '-dofout {2}/lv{3}final.dof.gz '





  
  

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                  '-ds 4 -symmetric'





  
  

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                  .format(template_dir, vtks_dir, tmps_dir, fr))





  
  

  313
  
    





  
  

  314
  
        # same number of points    





  
  

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        os.system('cardiacsurfacemap '





  
  

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                  '{0}/LVendo_{3}.vtk '





  
  

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                  '{1}/N_LVendo_{3}.vtk '





  
  

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                  '{2}/lv{3}final.dof.gz '





  
  

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                  '{1}/F_LVendo_{3}.vtk'





  
  

  320
  
                  .format(template_dir, vtks_dir, tmps_dir, fr))





  
  

  321
  
    





  
  

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        os.system('cardiacsurfacemap '





  
  

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                  '{0}/LVepi_{3}.vtk '





  
  

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                  '{1}/N_LVepi_{3}.vtk '





  
  

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                  '{2}/lv{3}final.dof.gz '





  
  

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                  '{1}/F_LVepi_{3}.vtk'





  
  

  327
  
                  .format(template_dir, vtks_dir, tmps_dir, fr))





  
  

  328
  
    





  
  

  329
  
        os.system('ptransformation '





  
  

  330
  
                  '{0}/LVmyo_{3}.vtk '





  
  

  331
  
                  '{1}/F_LVmyo_{3}.vtk '





  
  

  332
  
                  '-dofin {2}/lv{3}final.dof.gz'





  
  

  333
  
                  .format(template_dir, vtks_dir, tmps_dir, fr))





  
  

  334
  
        





  
  

  335
  
        os.system('cardiacsurfacemap '





  
  

  336
  
                  '{0}/RV_{3}.vtk '





  
  

  337
  
                  '{1}/N_RV_{3}.vtk '





  
  

  338
  
                  '{2}/rv{3}ds8.dof.gz '





  
  

  339
  
                  '{1}/C_RV_{3}.vtk'





  
  

  340
  
                  .format(template_dir, vtks_dir, tmps_dir, fr))





  
  

  341
  
     





  
  

  342
  
        ###########################################################################





  
  

  343
  
        os.system('cp {0}/F_LVendo_{1}.vtk {0}/S_LVendo_{1}.vtk'.format(vtks_dir, fr))





  
  

  344
  
        os.system('cp {0}/F_LVepi_{1}.vtk {0}/S_LVepi_{1}.vtk'.format(vtks_dir, fr))





  
  

  345
  
        os.system('cp {0}/F_LVmyo_{1}.vtk {0}/S_LVmyo_{1}.vtk'.format(vtks_dir, fr))





  
  

  346
  
        os.system('cp {0}/F_LVmyo_{1}.vtk {0}/C_LVmyo_{1}.vtk'.format(vtks_dir, fr))





  
  

  347
  
        os.system('cp {0}/F_LVmyo_{1}.vtk {0}/W_LVmyo_{1}.vtk'.format(vtks_dir, fr))





  
  

  348
  
        os.system('cp {0}/C_RV_{1}.vtk {0}/S_RV_{1}.vtk'.format(vtks_dir, fr))





  
  

  349
  
        os.system('cp {0}/C_RV_{1}.vtk {0}/W_RV_{1}.vtk'.format(vtks_dir, fr))





  
  

  350
  
        





  
  

  351
  
        ###########################################################################





  
  

  352
  
        # compute the quantities of the heart with respect to template





  
  

  353
  
        os.system('cardiacwallthickness '





  
  

  354
  
                  '{0}/F_LVendo_{1}.vtk '





  
  

  355
  
                  '{0}/F_LVepi_{1}.vtk '





  
  

  356
  
                  '-myocardium '





  
  

  357
  
                  '{0}/W_LVmyo_{1}.vtk'





  
  

  358
  
                  .format(vtks_dir, fr))





  
  

  359
  
    





  
  

  360
  
        os.system('cardiacenlargedistance '





  
  

  361
  
                  '{0}/S_LVendo_{2}.vtk '





  
  

  362
  
                  '{0}/S_LVepi_{2}.vtk '





  
  

  363
  
                  '{1}/LVendo_{2}.vtk '





  
  

  364
  
                  '{1}/LVepi_{2}.vtk '





  
  

  365
  
                  '-myocardium '





  
  

  366
  
                  '{0}/S_LVmyo_{2}.vtk'





  
  

  367
  
                  .format(vtks_dir, template_dir, fr))





  
  

  368
  
        





  
  

  369
  
        os.system('DiscreteCurvatureEstimator '





  
  

  370
  
                  '{0}/C_LVmyo_{1}.vtk '





  
  

  371
  
                  '{0}/FC_LVmyo_{1}.vtk'





  
  

  372
  
                  .format(vtks_dir, fr))





  
  

  373
  
        





  
  

  374
  
        os.system('cardiaccurvature '





  
  

  375
  
                  '{0}/FC_LVmyo_{1}.vtk '





  
  

  376
  
                  '{0}/C_LVmyo_{1}.vtk '





  
  

  377
  
                  '-smooth 64'





  
  

  378
  
                  .format(vtks_dir, fr))





  
  

  379
  
        





  
  

  380
  
        os.system('DiscreteCurvatureEstimator '





  
  

  381
  
                  '{0}/C_RV_{1}.vtk '





  
  

  382
  
                  '{0}/FC_RV_{1}.vtk'





  
  

  383
  
                  .format(vtks_dir, fr))





  
  

  384
  
        





  
  

  385
  
        os.system('cardiaccurvature '





  
  

  386
  
                  '{0}/FC_RV_{1}.vtk '





  
  

  387
  
                  '{0}/C_RV_{1}.vtk '





  
  

  388
  
                  '-smooth 64'





  
  

  389
  
                  .format(vtks_dir, fr))





  
  

  390
  
        





  
  

  391
  
        os.system('sevaluation '





  
  

  392
  
                  '{0}/S_RV_{2}.vtk '





  
  

  393
  
                  '{1}/RV_{2}.vtk '





  
  

  394
  
                  '-scalar '





  
  

  395
  
                  '-signed'





  
  

  396
  
                  .format(vtks_dir, template_dir, fr))





  
  

  397
  
        





  
  

  398
  
        os.system('cardiacwallthickness '





  
  

  399
  
                  '{0}/W_RV_{1}.vtk '





  
  

  400
  
                  '{0}/N_RVepi_{1}.vtk'





  
  

  401
  
                  .format(vtks_dir, fr))





  
  

  402
  
        





  
  

  403
  
        ###########################################################################





  
  

  404
  
#        os.system('vtk2txt {0}/C_RV_{1}.vtk {2}/rv_{1}_curvature.txt'.format(vtks_dir, fr, subject_dir))





  
  

  405
  
#        os.system('vtk2txt {0}/W_RV_{1}.vtk {2}/rv_{1}_wallthickness.txt'.format(vtks_dir, fr, subject_dir))





  
  

  406
  
#        os.system('vtk2txt {0}/S_RV_{1}.vtk {2}/rv_{1}_signeddistances.txt'.format(vtks_dir, fr, subject_dir))





  
  

  407
  
#        os.system('vtk2txt {0}/W_LVmyo_{1}.vtk {2}/lv_myo{1}_wallthickness.txt'.format(vtks_dir, fr, subject_dir))





  
  

  408
  
#        os.system('vtk2txt {0}/C_LVmyo_{1}.vtk {2}/lv_myo{1}_curvature.txt'.format(vtks_dir, fr, subject_dir))





  
  

  409
  
#        os.system('vtk2txt {0}/S_LVmyo_{1}.vtk {2}/lv_myo{1}_signeddistances.txt'.format(vtks_dir, fr, subject_dir))





  
  

  410
  
        if fr == 'ED':





  
  

  411
  
            fr_ = 'ed'





  
  

  412
  
            os.system('vtk2txt {0}/C_RV_{1}.vtk {2}/rv_{3}_curvature.txt'.format(vtks_dir, fr, subject_dir, fr_))





  
  

  413
  
            os.system('vtk2txt {0}/W_RV_{1}.vtk {2}/rv_{3}_wallthickness.txt'.format(vtks_dir, fr, subject_dir, fr_))





  
  

  414
  
            os.system('vtk2txt {0}/S_RV_{1}.vtk {2}/rv_{3}_signeddistances.txt'.format(vtks_dir, fr, subject_dir, fr_))





  
  

  415
  
            os.system('vtk2txt {0}/W_LVmyo_{1}.vtk {2}/lv_myo{3}_wallthickness.txt'.format(vtks_dir, fr, subject_dir, fr_))





  
  

  416
  
            os.system('vtk2txt {0}/C_LVmyo_{1}.vtk {2}/lv_myo{3}_curvature.txt'.format(vtks_dir, fr, subject_dir, fr_))





  
  

  417
  
            os.system('vtk2txt {0}/S_LVmyo_{1}.vtk {2}/lv_myo{3}_signeddistances.txt'.format(vtks_dir, fr, subject_dir, fr_))





  
  

  418
  
        if fr == 'ES':





  
  

  419
  
            fr_ = 'es'





  
  

  420
  
            os.system('vtk2txt {0}/C_RV_{1}.vtk {2}/rv_{3}_curvature.txt'.format(vtks_dir, fr, subject_dir, fr_))





  
  

  421
  
            os.system('vtk2txt {0}/W_RV_{1}.vtk {2}/rv_{3}_wallthickness.txt'.format(vtks_dir, fr, subject_dir, fr_))





  
  

  422
  
            os.system('vtk2txt {0}/S_RV_{1}.vtk {2}/rv_{3}_signeddistances.txt'.format(vtks_dir, fr, subject_dir, fr_))





  
  

  423
  
            os.system('vtk2txt {0}/W_LVmyo_{1}.vtk {2}/lv_myo{3}_wallthickness.txt'.format(vtks_dir, fr, subject_dir, fr_))





  
  

  424
  
            os.system('vtk2txt {0}/C_LVmyo_{1}.vtk {2}/lv_myo{3}_curvature.txt'.format(vtks_dir, fr, subject_dir, fr_))





  
  

  425
  
            os.system('vtk2txt {0}/S_LVmyo_{1}.vtk {2}/lv_myo{3}_signeddistances.txt'.format(vtks_dir, fr, subject_dir, fr_))





  
  

  426
  
  





  
  

  427
  
      





  
  

  428
  
def apply_PC(subject, data_dir, param_dir, template_dir, mirtk):





  
  

  429
  
    





  
  

  430
  
    print('  co-registering {0}'.format(subject))    





  
  

  431
  
    





  
  

  432
  
    subject_dir = os.path.join(data_dir, subject)





  
  

  433
  
        





  
  

  434
  
    if os.path.isdir(subject_dir):





  
  

  435
  
        





  
  

  436
  
        tmps_dir = '{0}/tmps'.format(subject_dir)





  
  

  437
  





  
  

  438
  
        vtks_dir = '{0}/vtks'.format(subject_dir)





  
  

  439
  





  
  

  440
  
        dofs_dir = '{0}/dofs'.format(subject_dir)





  
  

  441
  





  
  

  442
  
        meshGeneration(subject_dir, template_dir, param_dir, tmps_dir, vtks_dir, dofs_dir)





  
  

  443
  
        





  
  

  444
  
        print('  finish generating meshes from segmentations in {0}'.format(subject))





  
  

  445
  
        





  
  

  446
  
    else:  





  
  

  447
  
        print('  {0} is not a valid directory, do nothing'.format(subject_dir))





  
  

  448
  





  
  

  449
  





  
  

  450
  
def meshCoregstration(dir_0, dir_2, dir_3, coreNo, parallel, mirtk):





  
  

  451
  
               





  
  

  452
  
    if parallel:





  
  

  453
  
    





  
  

  454
  
        print('Generate meshes from segmentations running on {0} cores'.format(coreNo))





  
  

  455
  
        





  
  

  456
  
        pool = Pool(processes = coreNo) 





  
  

  457
  
        





  
  

  458
  
        # partial only in Python 2.7+





  
  

  459
  
        pool.map(partial(apply_PC, 





  
  

  460
  
                         data_dir=dir_0,  





  
  

  461
  
                         param_dir=dir_2, 





  
  

  462
  
                         template_dir=dir_3,





  
  

  463
  
                         mirtk=mirtk), 





  
  

  464
  
                         sorted(os.listdir(dir_0)))       





  
  

  465
  
                





  
  

  466
  
    else:





  
  

  467
  
        





  
  

  468
  
        print('Generate meshes from segmentations running subsequently')





  
  

  469
  
                





  
  

  470
  
        data_dir, param_dir, template_dir = dir_0, dir_2, dir_3





  
  

  471
  
                                     





  
  

  472
  
        for subject in sorted(os.listdir(data_dir)):





  
  

  473
  
            





  
  

  474
  
            print('  co-registering {0}'.format(subject))    





  
  

  475
  
            





  
  

  476
  
            subject_dir = os.path.join(data_dir, subject)





  
  

  477
  





  
  

  478
  
            if not os.path.isdir(subject_dir):





  
  

  479
  
                





  
  

  480
  
                print('  {0} is not a valid folder, Skip'.format(subject_dir))





  
  

  481
  
                





  
  

  482
  
                continue 





  
  

  483
  
                   





  
  

  484
  
            tmps_dir = '{0}/tmps'.format(subject_dir)





  
  

  485
  





  
  

  486
  
            vtks_dir = '{0}/vtks'.format(subject_dir)





  
  

  487
  





  
  

  488
  
            dofs_dir = '{0}/dofs'.format(subject_dir)





  
  

  489
  





  
  

  490
  
            meshGeneration(subject_dir, template_dir, param_dir, tmps_dir, vtks_dir, dofs_dir)





  
  

  491
  
            





  
  

  492
  
            print('  finish generating meshes from segmentations in {0}'.format(subject))