I have a 32x32x3 (height, width, depth) image that I am trying to rotate around the z axis by 45 degrees in sitk. It appears however that the z/depth axis I am getting sitk to rotate around is at an angle. How would I be able to rotate the image such that if I look at one slice of my image, I will see the slice rotated from the center by 45 degrees?

Below is my code, and below the code are the images (first one is original image, second is failed attempt at rotation). Additionally, these are public images, not confidential data.

```
def resample(image, transform):
"""
This function resamples (updates) an image using a specified transform
:param image: The sitk image we are trying to transform
:param transform: An sitk transform (ex. resizing, rotation, etc.
:return: The transformed sitk image
"""
reference_image = image
interpolator = sitk.sitkBSpline
default_value = 0
return sitk.Resample(image, reference_image, transform,
interpolator, default_value)
def get_center(img):
"""
This function returns the physical center point of a 3d sitk image
:param img: The sitk image we are trying to find the center of
:return: The physical center point of the image
"""
width, height, depth = img.GetSize()
return img.TransformIndexToPhysicalPoint((int(np.ceil(width/2)),
int(np.ceil(height/2)),
int(np.ceil(depth/2))))
def rotation3d(image, theta_x, theta_y, theta_z, show=False):
"""
This function rotates an image across each of the x, y, z axes by theta_x, theta_y, and theta_z degrees
respectively
:param image: An sitk MRI image
:param theta_x: The amount of degrees the user wants the image rotated around the x axis
:param theta_y: The amount of degrees the user wants the image rotated around the y axis
:param theta_z: The amount of degrees the user wants the image rotated around the z axis
:param show: Boolean, whether or not the user wants to see the result of the rotation
:return: The rotated image
"""
theta_x = np.deg2rad(theta_x)
theta_y = np.deg2rad(theta_y)
theta_z = np.deg2rad(theta_z)
euler_transform = sitk.Euler3DTransform(get_center(image), theta_x, theta_y, theta_z, (0, 0, 0))
image_center = get_center(image)
euler_transform.SetCenter(image_center)
euler_transform.SetRotation(theta_x, theta_y, theta_z)
resampled_image = resample(image, euler_transform)
if show:
plt.imshow(sitk.GetArrayFromImage(resampled_image)[0])
plt.show()
return resampled_image
if __name__ == "__main__":
img = sitk.ReadImage("...")
img_arr = sitk.GetArrayFromImage(img)[0] # Represents the 0th slice, since numpy swaps the first and third axes default to sitk
plt.imshow(img_arr); plt.show()
input("Press enter to continue...")
rotation3d(img, 0, 0, 45, show=True)
```