Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

2318 image registration #2319

Merged
merged 3 commits into from
Aug 28, 2024
Merged

2318 image registration #2319

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
6dda5b6
Fix #2315 by causing the ITK libraries to load at a time when other t…
akenmorris Aug 27, 2024
cd01326
Address issues from #2318
akenmorris Aug 27, 2024
abc1171
Merge branch 'master' into 2318-image-registration
akenmorris Aug 27, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion Python/DeepSSMUtilsPackage/DeepSSMUtils/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ def analyzeResults(out_dir, DT_dir, prediction_dir, mean_prefix):

def get_image_registration_transform(fixed_image_file, moving_image_file, transform_type='rigid'):
itk_transform = image_utils.get_image_registration_transform(fixed_image_file, moving_image_file,
transform_type='rigid')
transform_type=transform_type)
return itk_transform


Expand Down
19 changes: 13 additions & 6 deletions Python/DeepSSMUtilsPackage/DeepSSMUtils/image_utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
import numpy as np

def get_image_registration_transform(fixed_image_file, moving_image_file, transform_type='rigid'):
# Import Default Parameter Map
# Prepare parameter map
parameter_object = itk.ParameterObject.New()
parameter_map = parameter_object.GetDefaultParameterMap('rigid')
if transform_type == 'similarity':
Expand All @@ -12,11 +12,15 @@ def get_image_registration_transform(fixed_image_file, moving_image_file, transf
parameter_map['Transform'] = ['TranslationTransform']
parameter_map['MaximumNumberOfIterations'] = ['1024']
parameter_object.AddParameterMap(parameter_map)
# Call registration function

# Load images
fixed_image = itk.imread(fixed_image_file, itk.F)
moving_image = itk.imread(moving_image_file, itk.F)

# Call registration method
result_image, result_transform_parameters = itk.elastix_registration_method(
fixed_image, moving_image, parameter_object=parameter_object)

# Get transform matrix
parameter_map = result_transform_parameters.GetParameterMap(0)
transform_params = np.array(parameter_map['TransformParameters'], dtype=float)
Expand All @@ -25,11 +29,14 @@ def get_image_registration_transform(fixed_image_file, moving_image_file, transf
elif transform_type == 'similarity':
itk_transform = SimpleITK.Similarity3DTransform()
elif transform_type == 'translation':
itk_transform = SimpleITK.TranslationTransform()
itk_transform = SimpleITK.TranslationTransform(3)
else:
print("Error: " + transform_type + " transform unimplemented.")
raise NotImplementedError("Error: " + transform_type + " transform unimplemented.")
itk_transform.SetParameters(transform_params)
itk_transform_matrix = np.eye(4)
itk_transform_matrix[:3,:3] = np.array(itk_transform.GetMatrix()).reshape(3,3)
itk_transform_matrix[-1,:3] = np.array(itk_transform.GetTranslation())
if transform_type == 'translation':
itk_transform_matrix[-1, :3] = np.array(itk_transform.GetOffset())
else:
itk_transform_matrix[:3,:3] = np.array(itk_transform.GetMatrix()).reshape(3,3)
itk_transform_matrix[-1,:3] = np.array(itk_transform.GetTranslation())
return itk_transform_matrix
Loading