Elastix¶
This notebooks show very basic image registration examples with on-the-fly generated binary images.
In [1]:
from itk import itkElastixRegistrationMethodPython
from itk import itkTransformixFilterPython
import itk
import numpy as np
import matplotlib.pyplot as plt
Image generators¶
In [2]:
def image_generator(x1, x2, y1, y2):
image = np.zeros([100, 100], np.float32)
image[y1:y2, x1:x2] = 1
image = itk.image_view_from_array(image)
return image
Groupwise Registration Test¶
In [3]:
# Create a vector of images for a 2D+time example in numpy
vector_of_images = np.zeros([6, 100, 100], np.float32)
i = 0
for x in range(0, 30, 5):
image = image_generator(x, x+50, x, x+50)
vector_of_images[i] = image
i += 1
vector_itk = itk.image_view_from_array(vector_of_images)
# Create Groupwise Parameter Object
parameter_object = itk.ParameterObject.New()
groupwise_parameter_map = parameter_object.GetDefaultParameterMap('groupwise')
parameter_object.AddParameterMap(groupwise_parameter_map)
result_image, result_transform_parameters = itk.elastix_registration_method(
vector_itk, vector_itk,
parameter_object=parameter_object,
log_to_console=True)
Groupwise Registration Test Visualization (to be continued...)¶
In [4]:
%matplotlib inline
# Plot images
fig, axs = plt.subplots(2,3, sharey=True, figsize=[30,30])
plt.figsize=[100,100]
axs[0,0].imshow(vector_of_images[0])
axs[0,0].set_title('Image0', fontsize=30)
axs[0,1].imshow(vector_of_images[1])
axs[0,1].set_title('Image1', fontsize=30)
axs[0,2].imshow(vector_of_images[2])
axs[0,2].set_title('Image2', fontsize=30)
axs[1,0].imshow(vector_of_images[3])
axs[1,0].set_title('Image3', fontsize=30)
axs[1,1].imshow(vector_of_images[4])
axs[1,1].set_title('Image4', fontsize=30)
# axs[1,2].imshow(result_image)
# axs[1,2].set_title('Result', fontsize=30)
plt.show()
