/
generate_sublist.py
executable file
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/
generate_sublist.py
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import os
import numpy as np
import h5py
import random
import linecache
def mkdir(path):
if not os.path.exists(path):
os.makedirs(path)
def dir2list(path,sub_list_file):
if os.path.exists(sub_list_file):
fp = open(sub_list_file, 'r')
sublines = fp.readlines()
sub_names = []
for subline in sublines:
sub_info = subline.replace('\n', '').split(',')
sub_names.append(sub_info)
fp.close()
return sub_names
else:
fp = open(sub_list_file, 'w')
img_root_dir = os.path.join(path,'img')
subs = os.listdir(img_root_dir)
subs.sort()
sub_names = []
for sub in subs:
sub_dir = os.path.join(img_root_dir,sub)
views = os.listdir(sub_dir)
views.sort()
for view in views:
view_dir = os.path.join(sub_dir,view)
seg_dir = view_dir.replace('/img/','/seg/')
slices = os.listdir(view_dir)
slices.sort()
for slice in slices:
subinfo = (sub,view,slice,view_dir,seg_dir)
sub_names.append(subinfo)
line = "%s,%s,%s,%s,%s"%(sub,view,slice,view_dir,seg_dir)
fp.write(line + "\n")
fp.close()
def dir2list_folds(path,train_list_file,test_list_file,fold_list_file,fold):
train_subs,test_subs = get_subs(fold_list_file,fold)
if os.path.exists(train_list_file) and os.path.exists(test_list_file):
#train
fp = open(train_list_file, 'r')
sublines = fp.readlines()
train_sub_names = []
for subline in sublines:
sub_info = subline.replace('\n', '').split(',')
train_sub_names.append(sub_info)
fp.close()
#test
fp = open(test_list_file, 'r')
sublines = fp.readlines()
test_sub_names = []
for subline in sublines:
sub_info = subline.replace('\n', '').split(',')
test_sub_names.append(sub_info)
fp.close()
return train_sub_names,test_sub_names
else:
img_root_dir = os.path.join(path,'img')
#train subjects
train_sub_names = []
fp = open(train_list_file, 'w')
for sub in train_subs:
sub_dir = os.path.join(img_root_dir,sub)
views = os.listdir(sub_dir)
views.sort()
for view in views:
view_dir = os.path.join(sub_dir,view)
seg_dir = view_dir.replace('/img/','/seg/')
slices = os.listdir(view_dir)
slices.sort()
for slice in slices:
subinfo = (sub,view,slice,view_dir,seg_dir)
train_sub_names.append(subinfo)
line = "%s,%s,%s,%s,%s"%(sub,view,slice,view_dir,seg_dir)
fp.write(line + "\n")
fp.close()
#test subjects
test_sub_names = []
fp = open(test_list_file, 'w')
for sub in test_subs:
sub_dir = os.path.join(img_root_dir,sub)
views = os.listdir(sub_dir)
views.sort()
for view in views:
view_dir = os.path.join(sub_dir,view)
seg_dir = view_dir.replace('/img/','/seg/')
slices = os.listdir(view_dir)
slices.sort()
for slice in slices:
subinfo = (sub,view,slice,view_dir,seg_dir)
test_sub_names.append(subinfo)
line = "%s,%s,%s,%s,%s"%(sub,view,slice,view_dir,seg_dir)
fp.write(line + "\n")
fp.close()
return train_sub_names,test_sub_names
def get_subs(fold_list_file,fold):
train_subs = []
test_subs = []
fp = open(fold_list_file, 'r')
sublines = fp.readlines()
for subline in sublines:
sub_info = subline.replace('\n', '').split(',')
if sub_info[0] == 'Names':
continue
else:
grp_ind = sub_info[fold]
if grp_ind == '0':
train_subs.append(sub_info[0])
else:
test_subs.append(sub_info[0])
fp.close()
return train_subs,test_subs