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[WIP] Add reorient functionality to main() function. #13

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[WIP] Add reorient functionality to main() function. #13

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19 changes: 17 additions & 2 deletions src/unigradicon/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -217,6 +217,14 @@ def preprocess(image, modality="ct", segmentation=None):
image = apply_mask(image, segmentation)
return image

def reorient(moving, fixed):
from itk.ITKCommonBasePython import itkSpatialOrientationAdapter

return itk.orient_image_filter(
moving,
desired_coordinate_orientation=itkSpatialOrientationAdapter().FromDirectionCosines(fixed.GetDirection()),
use_image_direction=True)

def main():
import itk
import argparse
Expand All @@ -241,6 +249,7 @@ def main():
default=None, type=str, help="The path to save the warped image.")
parser.add_argument("--io_iterations", required=False,
default="50", help="The number of IO iterations. Default is 50. Set to 'None' to disable IO.")
parser.add_argument("--reorient", action="store_true", help="Reorient the source image to the orientation of the target image.")

args = parser.parse_args()

Expand All @@ -264,10 +273,16 @@ def main():
else:
io_iterations = int(args.io_iterations)

moving_processed = preprocess(moving, args.moving_modality, moving_segmentation)
fixed_processed = preprocess(fixed, args.fixed_modality, fixed_segmentation)

if args.reorient:
moving_processed = reorient(moving_processed, fixed_processed)

phi_AB, phi_BA = icon_registration.itk_wrapper.register_pair(
net,
preprocess(moving, args.moving_modality, moving_segmentation),
preprocess(fixed, args.fixed_modality, fixed_segmentation),
moving_processed,
fixed_processed,
finetune_steps=io_iterations)

itk.transformwrite([phi_AB], args.transform_out)
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