for num in range(len(inphase_paths)):
dst_inphasepath = os.path.join(dst_TrainData, "T1\_Patient%s\_No%d.dcm" % (sub_dir, num))
shutil.copy(inphase_paths[num], dst_inphasepath)
i += 1
else:
patient_dir = os.path.join(root, sub_dir)
ground_paths, inphase_paths = collect_T1_name(patient_dir)
for num in range(len(ground_paths)):
dst_groundpath = os.path.join(dst_TestGround, "T1\_Patient%s\_No%d.png" % (sub_dir, num))
shutil.copy(ground_paths[num], dst_groundpath)
for num in range(len(inphase_paths)):
dst_inphasepath = os.path.join(dst_TestData, "T1\_Patient%s\_No%d.dcm" % (sub_dir, num))
shutil.copy(inphase_paths[num], dst_inphasepath)
i += 1
该段程序的作用就是将训练集中T1/InPhase 的20个病例划分成16个训练集,4个测试集,并重新存储到自定义的文件夹下. 对于图像文件也进行了命名规范,对第i个病人的第j张slice,命名规则为**T1\_Patienti\_Noj.dcm**
## 分离出肝脏
GroundTruth的图像是多器官的,根据灰度范围进行判断。
![在这里插入图片描述](https://img-blog.csdnimg.cn/20200806143226468.png?x-oss-process=image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM0MDAzODc2,size_16,color_FFFFFF,t_70)
从自带的config文件中可以查看灰度范围:
![在这里插入图片描述](https://img-blog.csdnimg.cn/20200806143343610.png?x-oss-process=image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM0MDAzODc2,size_16,color_FFFFFF,t_70)
因为GroundTruth是png格式,我们使用OpenCV做一下简单的阈值处理就可以提取肝脏部分了.
“”"
@ Date: 2020/6/29
@ Author: Xiao Zhuo
@ Brief: Extract liver part from GroundTruth and set white color
@ Filename: extract_only_liver_2.py
“”"
-*- coding: utf-8 -*-
import os
import cv2
def makedir(dir):
if not os.path.exists(dir):
os.mkdir(dir)
def extract_liver(dataset_dir):
src_names = os.listdir(dataset_dir)
if src_names[0] == ‘Liver’:
src_names.remove(‘Liver’)
src_count = len(src_names)
dst_dir = os.path.join(dataset_dir, “Liver”)
makedir(dst_dir)
for num in range(src_count):
src_path = os.path.join(dataset_dir, src_names[num])
src = cv2.imread(src_path) # OpenCV读进来要指定是灰度图像,不然默认三通道。这里之前忘记指定了
# flag = 0
flag = 1
for i in range(src.shape[0]):
for j in range(src.shape[1]):
for k in range(src.shape[2]):
if 55 <= src.item(i, j, k) <= 70:
flag = 1 # 表示有肝脏
src.itemset((i, j, k), 255)
else:
src.itemset((i, j, k), 0)
if flag == 1:
dst_path = os.path.join(dst_dir, src_names[num])
cv2.imwrite(dst_path, src)
if name == ‘__main__’:
train_dir = os.path.join(“data”, “train”, “Ground”)
test_dir = os.path.join(“data”, “val”, “Ground”)
extract_liver(train_dir)
extract_liver(test_dir)
提取后的肝脏二值化掩膜如图所示: