4D医学影像处理

Crystallize_Malfoy

已于 2023-02-15 10:35:49 修改

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分类专栏：医学影像处理 Python学习深度学习文章标签：图像处理深度学习人工智能 python 1024程序员节

于 2022-07-23 11:09:18 首次发布

本文链接：https://blog.csdn.net/weixin_52137590/article/details/125943529

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背景

心脏CT在二叶主动脉瓣狭窄评估中的诊断价值

1.数据处理

SimpleITK学习笔记

TorchIO库函数

MONAI库函数

0）Pyradiomics

官方介绍

【影像组学】理论学习——特征类型

使用pyradiomics提取影像组学特征【详细】

【影像组学pyradiomics教程】(一)简介与安装

【影像组学pyradiomics教程】(二) 简单的使用-调用类方法

【影像组学pyradiomics教程】(三) 使用配置文件进行特征提取

影像组学pyradiomics教程

1）重采样

CT医学影像中的重采样

重采样数据到固定尺寸

def resampleSize(sitkImage, newsize):
    # 重采样函数
    euler3d = sitk.Euler3DTransform()

    xsize, ysize, zsize = sitkImage.GetSize()

    xspacing, yspacing, zspacing = sitkImage.GetSpacing()
    new_spacing_x = xspacing / (newsize[0] / float(xsize))
    new_spacing_y = yspacing / (newsize[0] / float(ysize))
    new_spacing_z = zspacing / (newsize[0] / float(zsize))

    origin = sitkImage.GetOrigin()
    direction = sitkImage.GetDirection()
    # 根据新的spacing 计算新的size
    newspace = (new_spacing_x, new_spacing_y, new_spacing_z)
    sitkImage = sitk.Resample(sitkImage, newsize, euler3d, sitk.sitkNearestNeighbor, origin, newspace, direction)
    shapeImage = sitkImage.GetSize()
    print(f'shape of resampledImage: {shapeImage}')
    return sitkImage

基于数组做线性插值的scipy.ndimage.interpolation.zoom

numpy取整方法

from scipy.ndimage import zoom
from numpy import *
import SimpleITK as sitk
import numpy as np
import torch

img_pth = 'heart_004.nii.gz'
img = sitk.ReadImage(img_pth)
array3D = sitk.GetArrayFromImage(img)
array3D = array3D.transpose(2, 1, 0)
x, y, z = array3D.shape

# one-hot
# 设置类别的数量
num_classes = 4
one_hot = torch.ones((num_classes, 112, 112, 112))
for i in range(num_classes):
    tmp = torch.ones(array3D.shape)
    tmp[array3D != i] = 0
    # zoom + round
    zoom_tmp = zoom(tmp, 0.5, order=1)
    # # 四舍五入
    # newArray3D = np.around(newArray3D)
    # # 向下取整
    # newArray3D = np.floor(newArray3D)
    # 向上取整
    round_tmp = np.ceil(zoom_tmp)
    round_tmp = torch.from_numpy(round_tmp)

    one_hot[i] = round_tmp

print(one_hot.shape)

# label
label = torch.zeros((112, 112, 112))
for i in range(num_classes):
    label[one_hot[i] == 1] = i

# label = torch.topk(one_hot, 1)[1].squeeze()
print(label.shape)
newArray3D = label.numpy()
print(newArray3D.shape)

newArray3D = newArray3D.transpose(2, 1, 0)
new_img = sitk.GetImageFromArray(newArray3D)
sitk.WriteImage(new_img, '04_112.nii.gz')

2)Padding

如何读取3D图像数据并进行padding

# padding
    # 先判断是否是偶数长度，不是则先单向填充
    if imgCrop.shape[0] % 2 == 1:
        imgCrop = np.pad(imgCrop, [(1, 0), (0, 0), (0, 0)],
                         mode='constant', constant_values=0)
    if imgCrop.shape[1] % 2 == 1:
        imgCrop = np.pad(imgCrop, [(0, 0), (1, 0), (0, 0)],
                         mode='constant', constant_values=0)
    if imgCrop.shape[2] % 2 == 1:
        imgCrop = np.pad(imgCrop, [(0, 0), (0, 0), (1, 0)],
                         mode='constant', constant_values=0)
    # 再分别从z,x,y轴正负方向+1填充0
    while imgCrop.shape[0] < paddingSize[2]:
        imgCrop = np.pad(imgCrop, [(1, 1), (0, 0), (0, 0)],
                         mode='constant', constant_values=0)
    while imgCrop.shape[1] < paddingSize[1]:
        imgCrop = np.pad(imgCrop, [(0, 0), (1, 1), (0, 0)],
                         mode='constant', constant_values=0)
    while imgCrop.shape[2] < paddingSize[0]:
        imgCrop = np.pad(imgCrop, [(0, 0), (0, 0), (1, 1)],
                         mode='constant', constant_values=0)