mralign.py

#!/usr/bin/env python


def usage(cmdline):
  cmdline.set_author('Max Pietsch')
  cmdline.set_synopsis('Landmark-based manual alignment')
  cmdline.add_description('Calculates the rigid transformation between two images based on three or more matching landmarks.')
  cmdline.add_argument('fixed', help='The reference input image')
  cmdline.add_argument('moving', help='The moving input image')
  cmdline.add_argument('rigid', help='The output transformation')
  cmdline.add_argument('-show', action='store_true', help='Show the transformed moving with the fixed image overlaid')
  cmdline.add_example_usage('To calculate the rigid transformation between two images based on landmarks',
                            'mralign fixed.mif moving.mif rigid')

def parse_coords(fixed, moving):
  from mrtrix3 import app, run, MRtrixError
  annotation = run.command('mrview ' + fixed + ' ' + moving).stdout.rstrip().split('\n')
  n_anno = len(annotation)

  app.console("annotation:")
  for line in annotation:
    app.console(line)

  if n_anno % 2 != 0 or n_anno < 6:
    raise MRtrixError('requires at least 3 coordinates for each image')

  with open('F', 'w') as f:
    f.write('\n'.join(annotation[:n_anno//2]))
  with open('M', 'w') as f:
    f.write('\n'.join(annotation[n_anno//2:]))


def execute():
  import shutil
  from mrtrix3 import MRtrixError, app, image, path, run
  # check input and output
  if len(image.Header(path.from_user(app.ARGS.moving, False)).size()) < 3:
    raise MRtrixError('Input image must be at least 3D')
  if len(image.Header(path.from_user(app.ARGS.fixed, False)).size()) < 3:
    raise MRtrixError('Input image must be at least 3D')
  app.check_output_path(app.ARGS.rigid)

  app.make_scratch_dir()
  app.goto_scratch_dir()

  app.console('open view options tool, mark 3+ landmarks with the cross hair and "copy" their positions in sequence, repeat for other image')
  parse_coords(path.from_user(app.ARGS.fixed), path.from_user(app.ARGS.moving))

  run.command('transformcalc M F align_vertices_rigid rigid')

  if app.ARGS.show:
    run.command('mrtransform ' + path.from_user(app.ARGS.moving) + ' -linear rigid -reorient no - | ' +
                ' mrview - -overlay.load ' + path.from_user(app.ARGS.fixed) + ' -overlay.opa 0.2')

  run.function(shutil.copy, 'rigid', path.from_user(app.ARGS.rigid, False))


# Execute the script
import mrtrix3
mrtrix3.execute()