82 lines
No EOL
2.8 KiB
Python
82 lines
No EOL
2.8 KiB
Python
from pprint import pprint
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import os
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import tempfile
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from skimage.metrics import normalized_mutual_information
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import ants
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class ants_reg:
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def register_aux(self, fi, mv):
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mytx = ants.registration(fixed=fi, moving=mv, type_of_transform = 'Rigid',
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# verbose=True,
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)
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# print(mytx['fwdtransforms'][0])
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fwdtransforms = ants.read_transform(mytx['fwdtransforms'][0])
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m1 = normalized_mutual_information(fi.numpy(), mytx['warpedmovout'].numpy())
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m2 = normalized_mutual_information(mv.numpy(), mytx['warpedfixout'].numpy())
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print(m1, m2)
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return {
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'fwdtransforms': fwdtransforms,
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'invtransforms': fwdtransforms.invert(),
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'warpedfixout': mytx['warpedfixout'],
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'warpedmovout': mytx['warpedmovout'],
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'metrics': max(m1, m2)
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}
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def __init__(self, fi, mv, debug=False):
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fixed_image = ants.image_read(fi, dimension=3)
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moving_image = ants.image_read(mv, dimension=3)
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r1 = self.register_aux(fixed_image, moving_image)
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r2 = self.register_aux(moving_image, fixed_image)
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if r1['metrics'] > r2['metrics']:
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self.res = r1
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else:
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self.res = dict(r2)
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self.res.update({
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'fwdtransforms': r2['invtransforms'],
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'invtransforms': r2['fwdtransforms'],
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'warpedfixout': r2['warpedmovout'],
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'warpedmovout': r2['warpedfixout'],
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})
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self.res.update({
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'fix': fixed_image,
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'mov': moving_image,
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})
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if debug:
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pprint(self.res)
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ants.image_write(fixed_image, '0fixed.nii.gz')
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ants.image_write(moving_image, '0moving.nii.gz')
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ants.image_write(r1['warpedfixout'], '0mf1.nii.gz')
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ants.image_write(r1['warpedmovout'], '0fm1.nii.gz')
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ants.image_write(r2['warpedmovout'], '0mf2.nii.gz')
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ants.image_write(r2['warpedfixout'], '0fm2.nii.gz')
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def get_metrics(self):
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return self.res['metrics']
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def transform(self, moving, output_filename, is_label=False):
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transform1 = next(tempfile._get_candidate_names())+'.mat'
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# print(transform1)
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ants.write_transform(self.res['fwdtransforms'], transform1)
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mi = ants.image_read(moving, dimension=3)
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if is_label:
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transformed = ants.apply_transforms(self.res['fix'], mi,
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transformlist=[transform1], interpolator='genericLabel').astype('uint8')
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else:
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transformed = ants.apply_transforms(self.res['fix'], mi,
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transformlist=[transform1])
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# print(transformed)
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ants.image_write(transformed, output_filename)
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os.remove(transform1) |