BraTs2020数据集处理及python读取.nii文件 批量转图片

BraTs2020数据集下载地址https://aistudio.baidu.com/datasetdetail/225057
这是文件目录，代码在proccess_code下面

批量转图片

import nibabel as nib
import matplotlib.pyplot as plt
import numpy as np

path = '../BraTS2020_TrainingData/MICCAI_BraTS2020_TrainingData/'
file_list = os.listdir(path)
file_list = file_list[146:]
print(file_list)
for file_item in file_list:
    sub_path = os.path.join(path,file_item)
    nii_list = os.listdir(sub_path)
    for nii_item in nii_list:
        if 't1.nii' in nii_item:
            print(nii_item)
            nii_path = os.path.join(sub_path,nii_item)
            img = nib.load(nii_path)
            # print(img.shape)  # shape(240, 240, 155)
            # print(img.header['db_name'])
            width, height, queue = img.dataobj.shape  # 由文件本身维度确定，可能是3维，也可能是4维
            # print("width",width)  # 240
            # print("height",height) # 240
            # print("queue",queue)   # 155
            # nib.viewers.OrthoSlicer3D(img.dataobj).show()
            choice=[20, 30, 60 ,70, 100, 110, 140, 150 ]
            num = 1
            for i in range(0, queue, 10):
                if i<50:
                    continue
                if i>120:
                    break
                # print(i)
                # if i not in choice:
                #     num += 1
                #     continue
                # print(i)
                img_arr = img.dataobj[:, :, i]

                # plt.subplot(5, 4, num)
                plt.tight_layout()
                plt.imshow(img_arr,)
                plt.savefig("../t1/"+nii_item[:-4]+'_'+str(i)+'_.png')

                num += 1
            # plt.show()
        elif 't2.nii' in nii_item:
            nii_path = os.path.join(sub_path,nii_item)
            img = nib.load(nii_path)
            width, height, queue = img.dataobj.shape  # 由文件本身维度确定，可能是3维，也可能是4维
            choice=[20, 30, 60 ,70, 100, 110, 140, 150 ]
            num = 1
            for i in range(0, queue, 10):
                if i<50:
                    continue
                if i>120:
                    break
                # print(i)
                # if i not in choice:
                #     num += 1
                #     continue
                # print(i)
                plt.tight_layout()
                img_arr = img.dataobj[:, :, i]
                # plt.subplot(5, 4, num)
                plt.imshow(img_arr, )

                plt.savefig("../t2/"+nii_item[:-4]+'_'+str(i)+'_.png')

                num += 1
            # plt.show()

对图片批量切割然后resize到256*256

import os

import cv2

def crop_border(image, y_up,y_down,x_left,x_right):
    height, width = image.shape[:2]
    # border_height, border_width = border_size

    cropped_image = image[y_up:height-y_down, x_left:width-x_right]

    return cropped_image

# 读取图像
# image = cv2.imread('../t1/BraTS20_Training_001_t1_50_.png')

# 指定要切掉的边框大小
# border_size = (55, 120)  # 假设要切掉上下左右各 10 个像素
y_up=59
y_down=53
x_left=144
x_right=127

# # 切割图像
# cropped_image = crop_border(image, y_up,y_down,x_left,x_right)
#
# # 显示切割后的图像
# cv2.imshow('Cropped Image', cropped_image)
# cv2.waitKey(0)
# cv2.destroyAllWindows()
#
# # 保存切割后的图像
# cv2.imwrite('cropped_image.jpg', cropped_image)

path  = '../t1'
file_list = os.listdir(path)
for file in file_list:
    subpath = os.path.join(path,file)
    image = cv2.imread(subpath)
    cropped_image = crop_border(image, y_up, y_down, x_left, x_right)
    cropped_image = cv2.resize(cropped_image, (256, 256))
    cv2.imwrite('../A/'+file, cropped_image)


path  = '../t2'
file_list = os.listdir(path)
for file in file_list:
    subpath = os.path.join(path,file)
    image = cv2.imread(subpath)
    cropped_image = crop_border(image, y_up, y_down, x_left, x_right)
    cropped_image = cv2.resize(cropped_image, (256, 256))
    cv2.imwrite('../B/'+file, cropped_image)