SimpleITK 图像配准

SimpleITK 图像配准

在网上找的资源，效果不佳，等清楚了函数和原理再细改，调试效果。

# -*- coding : UTF-8 -*-
# @file   : regist.py
# @Time   : 2021-11-12 17:00
# @Author : wmz

import SimpleITK as sitk

# Utility method that either downloads data from the MIDAS repository or
# if already downloaded returns the file name for reading from disk (cached data).
# %run update_path_to_download_script
# from downloaddata import fetch_data as fdata

# Always write output to a separate directory, we don't want to pollute the source directory.
import os
OUTPUT_DIR = 'Output'

import matplotlib.pyplot as plt
# % matplotlib
# inline

from ipywidgets import interact, fixed
from IPython.display import clear_output


# Callback invoked by the interact IPython method for scrolling through the image stacks of
# the two images (moving and fixed).
def display_images(fixed_image_z, moving_image_z, fixed_npa, moving_npa):
    # Create a figure with two subplots and the specified size.
    plt.subplots(1, 2, figsize=(10, 8))

    # Draw the fixed image in the first subplot.
    plt.subplot(1, 2, 1)
    plt.imshow(fixed_npa[fixed_image_z, :, :], cmap=plt.cm.Greys_r);
    plt.title('fixed image')
    plt.axis('off')

    # Draw the moving image in the second subplot.
    plt.subplot(1, 2, 2)
    plt.imshow(moving_npa[moving_image_z, :, :], cmap=plt.cm.Greys_r);
    plt.title('moving image')
    plt.axis('off')

    plt.show()


# Callback invoked by the IPython interact method for scrolling and modifying the alpha blending
# of an image stack of two images that occupy the same physical space.
def display_images_with_alpha(image_z, alpha, fixed, moving):
    img = (1.0 - alpha) * fixed[:, :, image_z] + alpha * moving[:, :, image_z]
    plt.imshow(sitk.GetArrayViewFromImage(img), cmap=plt.cm.Greys_r);
    plt.axis('off')
    plt.show()


# Callback invoked when the StartEvent happens, sets up our new data.
def start_plot():
    global metric_values, multires_iterations

    metric_values = []
    multires_iterations = []


# Callback invoked when the EndEvent happens, do cleanup of data and figure.
def end_plot():
    global metric_values, multires_iterations

    del metric_values
    del multires_iterations
    # Close figure, we don't want to get a duplicate of the plot latter on.
    plt.close()


# Callback invoked when the IterationEvent happens, update our data and display new figure.
def plot_values(registration_method):
    global metric_values, multires_iterations

    metric_values.append(registration_method.GetMetricValue())
    # Clear the output area (wait=True, to reduce flickering), and plot current data
    clear_output(wait=True)
    # Plot the similarity metric values
    plt.plot(metric_values, 'r')
    plt.plot(multires_iterations, [metric_values[index] for index in multires_iterations], 'b*')
    plt.xlabel('Iteration Number', fontsize=12)
    plt.ylabel('Metric Value', fontsize=12)
    plt.show()


# Callback invoked when the sitkMultiResolutionIterationEvent happens, update the index into the
# metric_values list.
def update_multires_iterations():
    global metric_values, multires_iterations
    multires_iterations.append(len(metric_values))


fixed_image =  sitk.ReadImage(r"E:\Data\right_knee\01-YCQ-cl-L.nrrd", sitk.sitkFloat32)
moving_image = sitk.ReadImage(r"E:\Data\right_knee\02-LAXI-r-cl lv.nrrd", sitk.sitkFloat32)

interact(display_images, fixed_image_z=(0,fixed_image.GetSize()[2]-1), moving_image_z=(0,moving_image.GetSize()[2]-1), fixed_npa = fixed(sitk.GetArrayViewFromImage(fixed_image)), moving_npa=fixed(sitk.GetArrayViewFromImage(moving_image)));


initial_transform = sitk.CenteredTransformInitializer(fixed_image,
                                                      moving_image,
                                                      sitk.Euler3DTransform(),
                                                      sitk.CenteredTransformInitializerFilter.GEOMETRY)

moving_resampled = sitk.Resample(moving_image, fixed_image, initial_transform, sitk.sitkLinear, 0.0, moving_image.GetPixelID())

interact(display_images_with_alpha, image_z=(0,fixed_image.GetSize()[2]), alpha=(0.0,1.0,0.05), fixed = fixed(fixed_image), moving=fixed(moving_resampled));

registration_method = sitk.ImageRegistrationMethod()

# Similarity metric settings.
registration_method.SetMetricAsMattesMutualInformation(numberOfHistogramBins=50)
registration_method.SetMetricSamplingStrategy(registration_method.RANDOM)
registration_method.SetMetricSamplingPercentage(0.01)

registration_method.SetInterpolator(sitk.sitkLinear)

# Optimizer settings.
registration_method.SetOptimizerAsGradientDescent(learningRate=1.0, numberOfIterations=100, convergenceMinimumValue=1e-6, convergenceWindowSize=10)
registration_method.SetOptimizerScalesFromPhysicalShift()

# Setup for the multi-resolution framework.
registration_method.SetShrinkFactorsPerLevel(shrinkFactors = [4,2,1])
registration_method.SetSmoothingSigmasPerLevel(smoothingSigmas=[2,1,0])
registration_method.SmoothingSigmasAreSpecifiedInPhysicalUnitsOn()

# Don't optimize in-place, we would possibly like to run this cell multiple times.
registration_method.SetInitialTransform(initial_transform, inPlace=False)

# Connect all of the observers so that we can perform plotting during registration.
registration_method.AddCommand(sitk.sitkStartEvent, start_plot)
registration_method.AddCommand(sitk.sitkEndEvent, end_plot)
registration_method.AddCommand(sitk.sitkMultiResolutionIterationEvent, update_multires_iterations)
registration_method.AddCommand(sitk.sitkIterationEvent, lambda: plot_values(registration_method))

final_transform = registration_method.Execute(sitk.Cast(fixed_image, sitk.sitkFloat32),
                                              sitk.Cast(moving_image, sitk.sitkFloat32))

print('Final metric value: {0}'.format(registration_method.GetMetricValue()))
print('Optimizer\'s stopping condition, {0}'.format(registration_method.GetOptimizerStopConditionDescription()))

moving_resampled = sitk.Resample(moving_image, fixed_image, final_transform, sitk.sitkLinear, 0.0, moving_image.GetPixelID())

interact(display_images_with_alpha, image_z=(0,fixed_image.GetSize()[2]), alpha=(0.0,1.0,0.05), fixed = fixed(fixed_image), moving=fixed(moving_resampled));

sitk.WriteImage(moving_resampled, os.path.join(OUTPUT_DIR, 'RIRE_training_001_mr_T1_resampled.mha'))
sitk.WriteTransform(final_transform, os.path.join(OUTPUT_DIR, 'RIRE_training_001_CT_2_mr_T1.tfm'))