首页 > 其他分享 >SimpleITK 图像配准

SimpleITK 图像配准

时间:2023-07-13 14:36:54浏览次数:33  
标签:配准 image sitk moving SimpleITK plt 图像 fixed method

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。

  1 # -*- coding : UTF-8 -*-
  2 # @file   : regist.py
  3 # @Time   : 2021-11-12 17:00
  4 # @Author : wmz
  5 
  6 import SimpleITK as sitk
  7 
  8 # Utility method that either downloads data from the MIDAS repository or
  9 # if already downloaded returns the file name for reading from disk (cached data).
 10 # %run update_path_to_download_script
 11 # from downloaddata import fetch_data as fdata
 12 
 13 # Always write output to a separate directory, we don't want to pollute the source directory.
 14 import os
 15 OUTPUT_DIR = 'Output'
 16 
 17 import matplotlib.pyplot as plt
 18 # % matplotlib
 19 # inline
 20 
 21 from ipywidgets import interact, fixed
 22 from IPython.display import clear_output
 23 
 24 
 25 # Callback invoked by the interact IPython method for scrolling through the image stacks of
 26 # the two images (moving and fixed).
 27 def display_images(fixed_image_z, moving_image_z, fixed_npa, moving_npa):
 28     # Create a figure with two subplots and the specified size.
 29     plt.subplots(1, 2, figsize=(10, 8))
 30 
 31     # Draw the fixed image in the first subplot.
 32     plt.subplot(1, 2, 1)
 33     plt.imshow(fixed_npa[fixed_image_z, :, :], cmap=plt.cm.Greys_r);
 34     plt.title('fixed image')
 35     plt.axis('off')
 36 
 37     # Draw the moving image in the second subplot.
 38     plt.subplot(1, 2, 2)
 39     plt.imshow(moving_npa[moving_image_z, :, :], cmap=plt.cm.Greys_r);
 40     plt.title('moving image')
 41     plt.axis('off')
 42 
 43     plt.show()
 44 
 45 
 46 # Callback invoked by the IPython interact method for scrolling and modifying the alpha blending
 47 # of an image stack of two images that occupy the same physical space.
 48 def display_images_with_alpha(image_z, alpha, fixed, moving):
 49     img = (1.0 - alpha) * fixed[:, :, image_z] + alpha * moving[:, :, image_z]
 50     plt.imshow(sitk.GetArrayViewFromImage(img), cmap=plt.cm.Greys_r);
 51     plt.axis('off')
 52     plt.show()
 53 
 54 
 55 # Callback invoked when the StartEvent happens, sets up our new data.
 56 def start_plot():
 57     global metric_values, multires_iterations
 58 
 59     metric_values = []
 60     multires_iterations = []
 61 
 62 
 63 # Callback invoked when the EndEvent happens, do cleanup of data and figure.
 64 def end_plot():
 65     global metric_values, multires_iterations
 66 
 67     del metric_values
 68     del multires_iterations
 69     # Close figure, we don't want to get a duplicate of the plot latter on.
 70     plt.close()
 71 
 72 
 73 # Callback invoked when the IterationEvent happens, update our data and display new figure.
 74 def plot_values(registration_method):
 75     global metric_values, multires_iterations
 76 
 77     metric_values.append(registration_method.GetMetricValue())
 78     # Clear the output area (wait=True, to reduce flickering), and plot current data
 79     clear_output(wait=True)
 80     # Plot the similarity metric values
 81     plt.plot(metric_values, 'r')
 82     plt.plot(multires_iterations, [metric_values[index] for index in multires_iterations], 'b*')
 83     plt.xlabel('Iteration Number', fontsize=12)
 84     plt.ylabel('Metric Value', fontsize=12)
 85     plt.show()
 86 
 87 
 88 # Callback invoked when the sitkMultiResolutionIterationEvent happens, update the index into the
 89 # metric_values list.
 90 def update_multires_iterations():
 91     global metric_values, multires_iterations
 92     multires_iterations.append(len(metric_values))
 93 
 94 
 95 fixed_image =  sitk.ReadImage(r"E:\Data\right_knee\01-YCQ-cl-L.nrrd", sitk.sitkFloat32)
 96 moving_image = sitk.ReadImage(r"E:\Data\right_knee\02-LAXI-r-cl lv.nrrd", sitk.sitkFloat32)
 97 
 98 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)));
 99 
100 
101 initial_transform = sitk.CenteredTransformInitializer(fixed_image,
102                                                       moving_image,
103                                                       sitk.Euler3DTransform(),
104                                                       sitk.CenteredTransformInitializerFilter.GEOMETRY)
105 
106 moving_resampled = sitk.Resample(moving_image, fixed_image, initial_transform, sitk.sitkLinear, 0.0, moving_image.GetPixelID())
107 
108 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));
109 
110 registration_method = sitk.ImageRegistrationMethod()
111 
112 # Similarity metric settings.
113 registration_method.SetMetricAsMattesMutualInformation(numberOfHistogramBins=50)
114 registration_method.SetMetricSamplingStrategy(registration_method.RANDOM)
115 registration_method.SetMetricSamplingPercentage(0.01)
116 
117 registration_method.SetInterpolator(sitk.sitkLinear)
118 
119 # Optimizer settings.
120 registration_method.SetOptimizerAsGradientDescent(learningRate=1.0, numberOfIterations=100, convergenceMinimumValue=1e-6, convergenceWindowSize=10)
121 registration_method.SetOptimizerScalesFromPhysicalShift()
122 
123 # Setup for the multi-resolution framework.
124 registration_method.SetShrinkFactorsPerLevel(shrinkFactors = [4,2,1])
125 registration_method.SetSmoothingSigmasPerLevel(smoothingSigmas=[2,1,0])
126 registration_method.SmoothingSigmasAreSpecifiedInPhysicalUnitsOn()
127 
128 # Don't optimize in-place, we would possibly like to run this cell multiple times.
129 registration_method.SetInitialTransform(initial_transform, inPlace=False)
130 
131 # Connect all of the observers so that we can perform plotting during registration.
132 registration_method.AddCommand(sitk.sitkStartEvent, start_plot)
133 registration_method.AddCommand(sitk.sitkEndEvent, end_plot)
134 registration_method.AddCommand(sitk.sitkMultiResolutionIterationEvent, update_multires_iterations)
135 registration_method.AddCommand(sitk.sitkIterationEvent, lambda: plot_values(registration_method))
136 
137 final_transform = registration_method.Execute(sitk.Cast(fixed_image, sitk.sitkFloat32),
138                                               sitk.Cast(moving_image, sitk.sitkFloat32))
139 
140 print('Final metric value: {0}'.format(registration_method.GetMetricValue()))
141 print('Optimizer\'s stopping condition, {0}'.format(registration_method.GetOptimizerStopConditionDescription()))
142 
143 moving_resampled = sitk.Resample(moving_image, fixed_image, final_transform, sitk.sitkLinear, 0.0, moving_image.GetPixelID())
144 
145 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));
146 
147 sitk.WriteImage(moving_resampled, os.path.join(OUTPUT_DIR, 'RIRE_training_001_mr_T1_resampled.mha'))
148 sitk.WriteTransform(final_transform, os.path.join(OUTPUT_DIR, 'RIRE_training_001_CT_2_mr_T1.tfm'))

 

标签:配准,image,sitk,moving,SimpleITK,plt,图像,fixed,method
From: https://www.cnblogs.com/ybqjymy/p/17550348.html

相关文章

  • SimpleITK 图像对齐
    1、使用SimpleITK对齐图像在看voxelmorph的代码,看到图像对齐部分,记录一下。下面是从voxelmorph项目中截取的一段保存图像的函数。函数输入分别是:配准后的图像、固定图像、要将配准图像保存的名字。将图像对齐的操作需要将对齐的图像的原点、方向、间距设置成与被对齐的图像一致。......
  • SimpleITK 读写nii.gz文件
    1、读写nii.gz文件1##usingsimpleITKtoloadandsavedata.2importSimpleITKassitk3itk_img=sitk.ReadImage('./nifti.nii.gz')4img=sitk.GetArrayFromImage(itk_img)5print("imgshape:",img.shape)67##save8out=si......
  • SimpleITK 三维图像分析
    1、去除3D小连通域在一些计算机视觉任务中,需要对模型的输出做一些后处理以优化视觉效果,连通域就是一种常见的后处理方式。尤其对于分割任务,有时的输出mask会存在一些假阳(小的无用轮廓),通过3D连通域找出面积较小的独立轮廓并去除可以有效地提升视觉效果。二维图像连通域一......
  • SimpleITK 简单使用
    SimpleITKITK是一个开源、跨平台的框架,提供给开发者增强功能的图像分析和处理套件(推荐使用)。Note:注意SimpleITK不支持中文,即路径中不能有中文X射线图像对应的读取1#@file:itk_p1.py2#@Time:2021/8/2816:273#@Author:wmz4importSimpleITKassitk......
  • VTK 生成MIP图像-vtkImageSlabReslice类
    MIPMIP(Maximum/MinimumIntensityProjection),最大/最小密度投影重建。MIP可以较真实地反应组织密度差异,使得血管的异常改变、形态、走形强化;但是只适用于外观形态的显示。在容积扫描数据中对每条径线上每个像素的最大强度值进行编码并投射成像。MIP的灰阶度反映CT值的......
  • iOS MachineLearning 系列(3)—— 静态图像分析之区域识别
    iOSMachineLearning系列(3)——静态图像分析之区域识别本系列的前一篇文章介绍了如何使用iOS中自带的API对图片中的矩形区域进行分析。在图像静态分析方面,矩形区域分析是非常基础的部分。API还提供了更多面向应用的分析能力,如文本区域分析,条形码二维码的分析,人脸区域分析,人体分析......
  • PyQt,PySide2中嵌入Matplotlib图像
    PyQt,PySide2中嵌入Matplotlib图像方式1使用QtDesigner新建一个MainWindow,在此之上创建一个VerticalLayout。importsysimportnumpyasnpfromPySide2.QtUiToolsimportQUiLoaderfromPySide2.QtWidgetsimportQApplicationimportmatplotlibmatplotlib.use("Qt5......
  • 高速图像采集卡:基于TI DSP TMS320C6678、Xilinx K7 FPGA XC7K325T的高速数据处理核心
    基于TIDSPTMS320C6678、XilinxK7FPGAXC7K325T的高速数据处理核心板一、板卡概述该DSP+FPGA高速信号采集处理板由北京太速科技自主研发,包含一片TIDSPTMS320C6678和一片XilinxFPGAK7XC72K325T-1ffg900。包含1个千兆网口,1个FMCHPC接口。可搭配使用ADFM......
  • Topaz DeNoise AI mac版(AI智能图像降噪工具)
    TopazDeNoiseAI是一款基于人工智能技术的图像降噪工具,能够帮助用户快速高效地去除图像中的噪点和杂色,提升图像的清晰度和细节。该软件采用了最新的深度学习算法,能够自动识别并去除各种类型的噪点,包括色斑、颗粒、条纹等,同时还能够保持图像的细节和色彩饱和度,避免出现过度平滑的......
  • NV21、NV12、YV12、RGB、YUV、RGBA、RGBX8888等图像色彩编码格式区别
    常用图像颜色编码格式NV21、NV12、YV12、RGB、YUV、RGBA、RGBX8888都是常见的图像颜色编码格式,它们之间的主要区别在于色彩空间和数据排列方式。NV21:NV21是Android系统使用的一种图像颜色编码格式,它采用的是YUV4:2:0的采样方式,意味着垂直方向上每两个像素采样一次,水平方向上每个像......