forked from flamehaze1115/WholeHeartSegmentation
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathprepare_data.py
172 lines (130 loc) · 7.38 KB
/
prepare_data.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
# -*- coding: utf-8 -*-
"""
Created on Fri Jul 28 13:59:36 2017
@author: Think
"""
import os
import numpy as np
import nibabel as nib
from fFindImageBoundaryCoordinate3D import fFindImageBoundaryCoordinate3D
data_dir = './Data/data_1mm'
#data_split_dir = './Data/data_1mm/Split_whole'
data_split_dir = './Data/data_1mm/WholeHeart_Test_20'
label_split_dir = os.path.join(data_split_dir,"Labels")
image_split_dir = os.path.join(data_split_dir, "Images") #分割成patch之后存储的地址
label_dir = os.path.join(data_dir, "Labels")
image_dir = os.path.join(data_dir, "Images") #原始的nii文件存储地址
BoundingBox_Images_dir = os.path.join(data_dir, "Images_boundingBox_Whole")
BoundingBox_Labels_dir = os.path.join(data_dir, "Labels_boundingBox_Whole")
#BoundingBox_Labels_205_dir = os.path.join(data_dir, "BoundingBox_Labels_205_smooth")
def changeFilename():
#修改label的名字
for filename in os.listdir(label_dir):
print(filename)
if filename.endswith("_label.nii.gz"):
filename_new = filename.strip("_label.nii.gz") + ".nii.gz"
print(filename_new)
filename = os.path.join(label_dir,filename)
filename_new = os.path.join(label_dir,filename_new)
os.rename(filename,filename_new)
#修改Image的名字
for filename in os.listdir(image_dir):
print(filename)
if filename.endswith("_image.nii.gz"):
filename_new = filename.strip("_image.nii.gz") + ".nii.gz"
print(filename_new)
filename = os.path.join(image_dir,filename)
filename_new = os.path.join(image_dir,filename_new)
os.rename(filename,filename_new)
def CreatNii_save(data,dir,filename,original_image):
img = nib.Nifti1Image(data,original_image.affine) #新建的图片与原始的affine不能变
img.header.get_xyzt_units()
nib.save(img,os.path.join(dir,filename))
def CutBoundingBox(img,cube_size,xdim,ydim,zdim,dir,filename):
#==============================================================================
# img: the image which should be splited
# cube_size: the size of patch_cube
# dir : the directory which the splited images store
# xdim,ydim,zdim: the coordinates of bounding box
#==============================================================================
xdim = xdim.astype(int)
ydim = ydim.astype(int)
zdim = zdim.astype(int) #convert float to int
image_data = img.get_data()
image_bouding_box = image_data[xdim[0]:xdim[1],ydim[0]:ydim[1],zdim[0]:zdim[1]]
bounding_box_filename = filename.strip(".nii.gz")+"_boundingBox.nii.gz"
CreatNii_save(image_bouding_box,dir,bounding_box_filename,img)
def FindBoundingBox():
for label_root, dir , files in os.walk(label_dir): #label_root=“./Data/Train\Labels”
for file in files: #其中一个file为“mr_train_1020_label.nii.gz”，files是file们的list
try:
folder = os.path.relpath(label_root, label_dir) #Return a relative filepath to path either from the current directory or from an optional start directory
# image_root = os.path.join(image_dir, folder)
label = nib.load(os.path.join(label_dir, file))
image = nib.load(os.path.join(image_dir, file))
print(label.shape)
print(type(label.get_data()))
xdim, ydim, zdim = fFindImageBoundaryCoordinate3D(label.get_data(),15)
print(file)
print("xdim: ")
print(xdim)
print("ydim: ")
print(ydim)
print("zdim: ")
print(zdim)
print("==================================")
CutBoundingBox(label,30,xdim,ydim,zdim,BoundingBox_Labels_dir,file)
CutBoundingBox(image,30,xdim,ydim,zdim,BoundingBox_Images_dir,file)
# print ("file:"+file)
#
# print ("label_root: "+label_root)
except Exception as e:
print(e)
def SplitImageToCubes(img,label,cube_size,stride,image_split_dir,label_split_dir,filename):
image_data = img.get_data()
label_data = label.get_data()
number = 0
x,y,z = label_data.shape
for i in range(0,x,stride):
for j in range(0, y, stride):
for k in range(0, z, stride):
if i+cube_size <= x and j+cube_size <= y and k+cube_size <= z:
image_cube_data = image_data[i:i+cube_size,j:j+cube_size,k:k+cube_size]
label_cube_data = label_data[i:i+cube_size,j:j+cube_size,k:k+cube_size]
file_fn = filename.strip(".nii.gz") + "_" + str(number).zfill(3) + ".nii.gz"
number = number+1
CreatNii_save(image_cube_data,image_split_dir,file_fn,img)
CreatNii_save(label_cube_data,label_split_dir,file_fn,label)
# #方向割出几个
# for i in reversed(range(x-2*cube_size,x,stride)):
# for j in reversed(range(y-2*cube_size,y,stride)):
# for k in reversed(range(z-2*cube_size,z,stride)):
# if i-cube_size >= 0 and j-cube_size >= 0 and k-cube_size >= 0:
# image_cube_data = image_data[i-cube_size:i,j-cube_size:j,k-cube_size:k]
# label_cube_data = label_data[i-cube_size:i,j-cube_size:j,k-cube_size:k]
#
# file_fn = filename.strip(".nii.gz") + "_" + str(number) + ".nii.gz"
# number = number+1
#
# CreatNii_save(image_cube_data,image_split_dir,file_fn,img)
# CreatNii_save(label_cube_data,label_split_dir,file_fn,label)
#
def main():
# FindBoundingBox()
#os.walk(top),通过遍历目录树，自顶向下或自底向上生成目录树下的文件名。
#对于以top 为根的目录树下的每个子目录（包括top自己），
#它生成一个三元组(dirpath, dirnames, filenames)。
#dirpath 为目录路径的字符串。dirnames 为dirpath 下子目录的名称列表（不包括'.' 和'..'）。
#filenames 为dirpath 下非目录文件的名称列表。注意，列表中的名词不包含路径部分。
#要获取dirpath 下目录或文件的完整路径（以top 开始），需要用os.path.join(dirpath, name)。
for label_root, dir , files in os.walk(BoundingBox_Labels_dir): #label_root=“./Data/Train\Labels”
for file in files: #其中一个file为“mr_train_1020_label.nii.gz”，files是file们的list
if file.endswith('mr_train_1020_boundingBox.nii.gz'):
try:
label = nib.load(os.path.join(BoundingBox_Labels_dir, file))
image = nib.load(os.path.join(BoundingBox_Images_dir, file))
SplitImageToCubes(image,label,64,8,image_split_dir,label_split_dir,file)
except Exception as e:
print(e)
if __name__ == '__main__':
main()