##以下图为例,进行转换
转换后,针对每个文件生成对应得文件夹,文件夹下面有一个‘z’文件夹(沿着z轴划分的切片),该文件夹下面是所有切片后的png或者jpg图像。
转换后效果如下:
###只需要进行简单的路径修改即可实现批量转换!!!
代码如下(示例):
import matplotlib
matplotlib.use('TkAgg')
import nibabel as nib
import numpy as np
import os
import imageio
# ---------------------------------------------#
# nii_path : nii文件的路径
# img_save_path : 切片的保存路径
# axis : 说明是沿着哪个方向切片的
# ---------------------------------------------
def nii_to_png(nii_path, img_save_path, axis):
# 若保存路径不存在,则创建
if not os.path.exists(img_save_path):
os.makedirs(img_save_path)
nii = nib.load(nii_path)
nii_fdata = nii.get_fdata()
nii_fdata = np.rot90(nii_fdata)
# 以切片的轴向作为保存png的子文件夹名
foldername = axis
png_save_path = os.path.join(img_save_path, foldername)
if not os.path.exists(png_save_path):
os.mkdir(png_save_path)
flag = 100
if axis == 'x':
(axis, y, z) = nii.shape
flag = 0
elif axis == 'y':
(x, axis, z) = nii.shape
flag = 1
elif axis == 'z':
(x, y, axis) = nii.shape
flag = 2
else:
print("wrong axis")
for i in range(axis):
if flag == 0:
slice = nii_fdata[i, :, :]
elif flag == 1:
slice = nii_fdata[:, i, :]
elif flag == 2:
slice = nii_fdata[:, :, i]
# 以数字1,2,3...为png图片命名
imageio.imwrite(os.path.join(png_save_path, '{}.png'.format(i)), slice)
def all_nii_to_png(all_nii_path,all_image_save_path, axis):
all_nii_path_list = os.listdir(all_nii_path)
for i in range(len(all_nii_path_list)):
nii_to_png(os.path.join(all_nii_path,all_nii_path_list[i]),os.path.join(all_image_save_path, all_nii_path_list[i]), axis)
print("第{}个nii文件转换完成!".format(i))
if __name__ == "__main__":
all_nii_path = r'E:\all_dataset\covid-19-ct-seg\Lung_Mask'
all_image_save_path = r'E:\all_dataset\covid-19-ct-seg\Lung_Mask_processed'
all_nii_to_png(all_nii_path, all_image_save_path, 'z')