def out_test_run(self, **kwargs):
dl_test_id = kwargs['dl_test_id']
test_type = kwargs['test_type']
tr_model_id = kwargs['tr_model_id']
file_path = kwargs['file_path']
local_path = file_path.replace('/public_open', '/medimg/public_open')
# /public_open/analysis/PCB64CAED/upload
open_save_path = file_path.replace('/upload', '/download/x')
ckpt_path = '/home/user01/Javis_dl_system/models/I66/'
# 불러와야될 tr_model의 설정값을 가져옴
cur = OraDB.prepareCursor()
cur.execute(
"select layer_cnt, loss_info, activation_info from training where tr_model_id=:tr_model_id",
{'tr_model_id': tr_model_id})
for row in cur:
layer_n, cost_name, act_func = list(row)
OraDB.releaseConn()
print('file path', file_path)
# 공공 구분. 공공이면 파일 패스에서 다이컴 컨버팅 실행
print('local path', local_path)
temp_path = local_path.replace(
'/medimg/public_open',
'/home/user01/Javis_dl_system/data_temp/public_open')
print('temp path', temp_path)
if not os.path.exists(temp_path):
os.makedirs(temp_path)
down_path = temp_path.replace('/upload', '/download') + '/x'
nas_down_path = down_path.replace(
'/home/user01/Javis_dl_system/data_temp/public_open',
'/medimg/public_open')
print('nas down path', nas_down_path)
if not os.path.exists(nas_down_path):
os.makedirs(nas_down_path)
data_mover.nas_to_dlserver(local_path, temp_path)
dcm_converting = Open_Dicom_converter.Converter(temp_path)
dcm_converting._convert()
data_loader = TestDataLoader.DataLoader(temp_path, test_type)
tester = out_Tester(file_path=temp_path,
ckpt_path=ckpt_path,
data_loader=data_loader,
act_func=act_func,
cost_name=cost_name,
layer_n=layer_n,
tr_model_id=tr_model_id,
dl_test_id=dl_test_id,
save_path=open_save_path)
tester.infer3(1, 1)
def in_test_run(self, **kwargs):
dl_test_id = kwargs['dl_test_id']
test_type = kwargs['test_type']
tr_model_id = kwargs['tr_model_id']
studylist_id = kwargs['studylist_id']
file_path = kwargs['file_path']
local_path = file_path
ckpt_path = '/home/user01/Javis_dl_system/models/I66/'
# 불러와야될 tr_model의 설정값을 가져옴
cur = OraDB.prepareCursor()
cur.execute(
"select layer_cnt, loss_info, activation_info from training where tr_model_id=:tr_model_id",
{'tr_model_id': tr_model_id})
for row in cur:
layer_n, cost_name, act_func = list(row)
OraDB.releaseConn()
# 공공 구분. 공공이면 파일 패스에서 다이컴 컨버팅 실행
temp_path = local_path.replace(
'/medimg/', '/home/user01/Javis_dl_system/data_temp/')
if not os.path.exists(temp_path):
os.makedirs(temp_path)
data_mover.nas_to_dlserver(local_path, temp_path)
data_loader = TestDataLoader.DataLoader(temp_path, test_type)
tester = in_Tester(file_path=temp_path,
ckpt_path=ckpt_path,
data_loader=data_loader,
act_func=act_func,
cost_name=cost_name,
layer_n=layer_n,
tr_model_id=tr_model_id,
dl_test_id=dl_test_id,
studylist_id=studylist_id)
a = data_loader._existence_label()
if a == 0:
tester.infer2(1, 1)
del_path = temp_path + '/img/DownLoad'
shutil.rmtree(del_path, ignore_errors=True)
else:
tester.infer1(1, 1)
del_path = temp_path + '/img/DownLoad'
shutil.rmtree(del_path, ignore_errors=True)
def __init__(self,
data_loader,
cost_name,
act_func,
layer_n,
ckpt_path,
file_path,
tr_model_id,
dl_test_id,
save_path,
opt_kwargs={}):
self.data_loader = data_loader
if tr_model_id == 1:
self.ckpt_path = '/home/user01/Javis_dl_system/models/I66/1/Unet.cpkt'
else:
# '/home/obsk/Javis_dl_system/models/I66/'
self.ckpt_path = ckpt_path + str(tr_model_id) + '/' + str(
tr_model_id) + '.ckpt'
self.file_path = file_path
self.dl_test_id = dl_test_id
self.save_path = save_path
# model loader. model id 1 : default model
if tr_model_id == 1:
self.net = default_Unet.Unet(
cost="mfc", cost_kwargs={"class_weights": [1e-6, 1 - 1e-6]})
else:
self.net = Unet.Unet(
cost=cost_name,
act_func=act_func,
layer_n=layer_n,
cost_kwargs={"class_weights": [1e-6, 1 - 1e-6]})
self.opt_kwargs = opt_kwargs
# default ai result
self.status = 'N'
# # mongo db information
# self.client = MongoClient('mongodb://172.16.52.79:27017')
# self.db = self.client.ohif_deployment
# self.ruserid = self.db.dl_test.find_one({"dl_test_id": int(self.dl_test_id)})['ruserid']
# self.test_labelinfo_collection = self.db.test_labelinfo
# self.dl_test_collection = self.db.dl_test
# self.table_indexing_collection = self.db.table_indexing
# # oracle db information
self.cursor = OraDB.prepareCursor()
self.ruserid = self.cursor.execute(
"select ruserid from dl_test where dl_test_id=:dl_test_id",
{'dl_test_id': self.dl_test_id})
print('tester initialized')
def __init__(self,
data_loader,
cost_name,
act_func,
layer_n,
ckpt_path,
file_path,
tr_model_id,
dl_test_id,
studylist_id,
opt_kwargs={}):
self.data_loader = data_loader
if tr_model_id == 1:
self.ckpt_path = '/home/user01/Javis_dl_system/models/I66/1/Unet.cpkt'
else:
self.ckpt_path = ckpt_path + str(tr_model_id) + '/' + str(
tr_model_id) + '.ckpt'
self.file_path = file_path
self.dl_test_id = dl_test_id
self.studylist_id = studylist_id
# model loader. model id 1 : default model
if tr_model_id == 1:
self.net = default_Unet.Unet(
cost="mfc", cost_kwargs={"class_weights": [1e-6, 1 - 1e-6]})
else:
self.net = Unet.Unet(
cost=cost_name,
act_func=act_func,
layer_n=layer_n,
cost_kwargs={"class_weights": [1e-6, 1 - 1e-6]})
self.opt_kwargs = opt_kwargs
# default ai result
self.status = 'N'
# oracle db information
self.cursor = OraDB.prepareCursor()
self.series_uid = self.cursor.execute(
"select series_uid from studylist where studylist_id=:studylist_id",
{'studylist_id': self.studylist_id})
self.ruserid = self.cursor.execute(
"select ruserid from dl_test where dl_test_id=:dl_test_id",
{'dl_test_id': self.dl_test_id})
print('tester initialized')
def __init__(self, path):
# /medimg/data/I66/DICOM/train/abnormal/I66_mri_AB_00000039
self.path = path
# print(self.path)
# I66_mri_AB_00000007
if '/abnormal' in self.path:
start_n = self.path.find('/abnormal')
leng = len('/abnormal')
else:
start_n = self.path.find('/normal')
leng = len('/normal')
# print(path[start_n + leng + 1:last_n])
self.patientName = self.path[start_n + leng + 1:]
print('DataSaver Initialized')
self.conn = OraDB.createConn(OraDB.INFO)
# -*- coding: utf-8 -*-
"""
Main Processor Module, Made by BJH, CGM, JYJ OBS Korea
"""
import subprocess
import time
from Oracle_connector import OraDB
OraDB.createConn(OraDB.INFO)
if __name__ == "__main__":
while True:
time.sleep(5)
cur = OraDB.prepareCursor()
cur.execute("select tr_model_id, tr_status, stop_yn from training")
# training
for row in cur:
tr_model_id, tr_status, stop_yn = list(row)
if tr_status == 'running':
train_proc = subprocess.Popen(['python', 'train_process.py'])
train_proc.wait()
OraDB.releaseConn()
def infer1(self, n_t_iters, b_size, keep_prob=1.0):
with tf.Session() as sess:
sess.run(tf.global_variables_initializer())
saver = tf.train.Saver()
saver.restore(sess, self.ckpt_path)
print('model restored')
t_accuracy = 0
positions = []
for _ in range(n_t_iters):
for up_down in range(2):
for crop_number in range(4):
x, y, files_list, files_list_down, he, wi = self.data_loader.test_load_batch_1(
b_size, up_down, crop_number) # testing=False
predictions, dice = sess.run(
(self.net.predict, self.net.dice),
feed_dict={
self.net.x: x,
self.net.y: y,
self.net.training: False,
self.net.keep_prob: keep_prob
})
if crop_number == 0:
x_offset, y_offset = 0, 0
elif crop_number == 1:
x_offset, y_offset = 44, 0
elif crop_number == 2:
x_offset, y_offset = 0, 44
else:
x_offset, y_offset = 44, 44
batch_size, nz, ny, nx, _ = np.shape(predictions)
for index in range(batch_size):
files, offset = files_list[index]
for z_index in range(nz):
if offset == 0 or 128 <= offset + z_index:
if offset == 0:
file_path = files[z_index]
file_down_path = files_list_down[
z_index]
else:
file_path = files[offset + z_index]
file_down_path = files_list_down[
offset + z_index]
# merge_path = file_path.replace('.jpg', '_prediction.jpg')
image = cv2.imread(file_down_path)
# print(file_down_path)
if image is None:
image = np.zeros([300, 300, 3])
roi = image[y_offset:y_offset + 256,
x_offset:x_offset + 256]
b_prediction = predictions[index, z_index,
...,
0] > 0.5 # 255
b_image = cv2.bitwise_and(
roi,
roi,
mask=(~b_prediction * 255).astype(
np.uint8)) # np.expand_dims
f_image = np.stack(
[
np.zeros([ny, nx]),
np.zeros([ny, nx]),
b_prediction * 255
],
axis=-1) # np.tile np.append
merge = b_image + f_image
# merge = np.hstack([image, label, prediction])
image[y_offset:y_offset + 256,
x_offset:x_offset +
256] = merge # f_image
cv2.imwrite(file_down_path, image)
if crop_number == 3:
position_t = cv2.imread(file_down_path)
position = position_t[:, :, 2]
position = cv2.resize(
position, (wi, he),
interpolation=cv2.INTER_AREA)
_, position = cv2.threshold(
position, 127, 255,
cv2.THRESH_BINARY)
num_labels, markers, state, cent = cv2.connectedComponentsWithStats(
position)
if num_labels != 1:
self.status = 'Y'
for idx in range(1, num_labels):
x, y, w, h, size = state[idx]
infor_position = [
z_index, w, h, x, y
]
positions.append(
infor_position)
roi = cv2.imread(file_path)
b_image = cv2.bitwise_and(
roi,
roi,
mask=~position.astype(np.uint8))
f_image = np.stack([
np.zeros([he, wi]),
np.zeros([he, wi]), position
],
axis=-1)
merge = b_image + f_image
cv2.imwrite(file_down_path, merge)
t_accuracy += dice
print(positions)
# ai result save
self.cursor.execute(
"update dl_test set ai_result=:ai_result where dl_test_id = :dl_test_id",
{
'ai_result': self.status,
'dl_test_id': self.dl_test_id
})
OraDB.dbCommit()
print(self.status)
# test_labelinfo에 레이블 정보 저장
for imgs in positions:
print(imgs)
imgindex, width, height, x_left_up, y_left_up = imgs
x_right_down = x_left_up + width
y_right_down = y_left_up + height
handles = '{"start":{"x":' + str(x_left_up) + ',"y":' + str(y_left_up) + ',"highlight":true,"active":true},"end":{"x":' \
+ str(x_right_down) + ',"y":' + str(y_right_down) + ',"highlight":true,"active": false},"textBox":' \
'{"active":false,"hasMoved":false,"movesIndependently":false,' \
'"allowedOutsideImage": true,"hasBoundingBox": true,"x":' \
+ str(x_right_down) + ',"y":'+ str(y_right_down) + ',"boundingBox": {"width":' \
+ str(width) + ', "height": ' + str(height) + ',"left":0,"top":0}}}'
# self.test_labelinfo_collection.insert(data)
self.cursor.execute(
"insert into test_labelinfo(test_lb_id, dl_test_id, studylist_id, file_name, label_info, image_index_number, series_uid, tooltype, del_yn, createdate, ruserid) "
"values(test_labelinfo_test_lb_id_seq.nextval, :dl_test_id, :studylist_id, :file_name, :label_info, :image_index_number, :series_uid, :tooltype, :del_yn, :createdate, :ruserid)",
[
int(self.dl_test_id), self.studylist_id, None, handles,
imgindex, self.series_uid, 'rectangleRoi', 'N',
datetime.today().strftime("%Y%m%d%H%M%S"), self.ruserid
])
OraDB.dbCommit()
print('data restored to test_labelinfo_collection')
# dice score 저장
a_accuracy = t_accuracy / n_t_iters / 8
self.cursor.execute(
"update dl_test set dice_score=:a_accuracy where dl_test_id=:dl_test_id",
[a_accuracy, self.dl_test_id])
OraDB.dbCommit()
print("test accuracy {:}".format(a_accuracy))
OraDB.releaseConn()
del_path = self.file_path + 'DownLoad'
shutil.rmtree(del_path, ignore_errors=True)
def infer3(self, n_t_iters, b_size, keep_prob=1.0):
with tf.Session() as sess:
sess.run(tf.global_variables_initializer())
saver = tf.train.Saver()
saver.restore(sess, self.ckpt_path)
print('model restored')
target_img_number_set = ''
for _ in range(n_t_iters):
positions = []
for up_down in range(2):
for crop_number in range(4):
x, files_list, files_list_down, he, wi = self.data_loader.test_load_batch_2(
b_size, up_down, crop_number) # testing=False
predictions = sess.run(self.net.predict,
feed_dict={
self.net.x: x,
self.net.training: False,
self.net.keep_prob:
keep_prob
})
if crop_number == 0:
x_offset, y_offset = 0, 0
elif crop_number == 1:
x_offset, y_offset = 44, 0
elif crop_number == 2:
x_offset, y_offset = 0, 44
else:
x_offset, y_offset = 44, 44
batch_size, nz, ny, nx, _ = np.shape(predictions)
for index in range(batch_size):
files, offset = files_list[index]
for z_index in range(nz):
if offset == 0 or 128 <= offset + z_index:
if offset == 0:
file_path = files[z_index]
file_down_path = files_list_down[
z_index]
else:
file_path = files[offset + z_index]
file_down_path = files_list_down[
offset + z_index]
image = cv2.imread(file_down_path)
if image is None:
image = np.zeros([300, 300, 3])
roi = image[y_offset:y_offset + 256,
x_offset:x_offset + 256]
b_prediction = predictions[index, z_index,
...,
0] > 0.5 # 255
b_image = cv2.bitwise_and(
roi,
roi,
mask=(~b_prediction * 255).astype(
np.uint8)) # np.expand_dims
f_image = np.stack(
[
np.zeros([ny, nx]),
np.zeros([ny, nx]),
b_prediction * 255
],
axis=-1) # np.tile np.append
merge = b_image + f_image
# merge = np.hstack([image, label, prediction])
image[y_offset:y_offset + 256,
x_offset:x_offset +
256] = merge # f_image
cv2.imwrite(file_down_path, image)
if crop_number == 3:
position_t = cv2.imread(file_down_path)
position = position_t[:, :, 2]
position = cv2.resize(
position, (wi, he),
interpolation=cv2.INTER_AREA)
_, position = cv2.threshold(
position, 127, 255,
cv2.THRESH_BINARY)
num_labels, markers, state, cent = cv2.connectedComponentsWithStats(
position)
if num_labels != 1:
self.status = 'Y'
for idx in range(1, num_labels):
x, y, w, h, size = state[idx]
infor_position = [
z_index, w, h, x, y
]
positions.append(
infor_position)
roi = cv2.imread(file_path)
b_image = cv2.bitwise_and(
roi,
roi,
mask=~position.astype(np.uint8))
f_image = np.stack([
np.zeros([he, wi]),
np.zeros([he, wi]), position
],
axis=-1)
merge = b_image + f_image
# print('file_down_path', file_down_path)
cv2.imwrite(file_down_path, merge)
# positions = [ [imageindex, width, height, x_start, y_start] ]
print(positions)
for img_info in positions:
target_img_number_set += str(img_info[0] + 1) + '_'
# print(positions)
# ai result
self.cursor.execute(
"update dl_test set ai_result=:ai_result where dl_test_id = :dl_test_id",
{
'ai_result': self.status,
'dl_test_id': self.dl_test_id
})
OraDB.dbCommit()
self.cursor.execute(
"update op_test set file_path=:file_path where dl_test_id=:dl_test_id",
{
'file_path': self.save_path,
'dl_test_id': self.dl_test_id
})
OraDB.dbCommit()
self.cursor.execute(
"update op_test set valx1=:valx1 where dl_test_id=:dl_test_id",
{
'valx1': target_img_number_set[:-1],
'dl_test_id': self.dl_test_id
})
print(self.status)
OraDB.releaseConn()
print('data copying from local to nas')
down_path = self.file_path.replace('/upload',
'/download') + '/x'
# temp_path = nas_path.replace('/medimg/', '/home/Javis_dl_system/data_temp/')
nas_down_path = down_path.replace(
'/home/user01/Javis_dl_system/data_temp/', '/medimg/')
chmod_path = nas_down_path[:-2]
data_mover.on_copytree(down_path, nas_down_path, chmod_path)
print('data copy finished')
print('data deleting from local')
del_path = self.file_path[:self.file_path.find('analysis') + 8]
shutil.rmtree(del_path, ignore_errors=True)
print('local data deleting finished')
def saveYdata_labeled(self):
cur = OraDB.prepareCursor()
study_uid = cur.execute(
'select study_uid from ADMIN.studylist where patient_uid=:patient_uid',
{'patient_uid': self.patientName})
labels = cur.execute(
'select * from ADMIN.ohif_labels where studyinstanceuid=:studyinstanceuid',
{'studyinstanceuid': study_uid})
global w, h
w = 0
h = 0
for row in labels:
id, measurementdata, userid, studyinstanceuid, tooltype, seriesinstanceuid, \
currentimageidindex, patientid, patientname, studyindexnumber, \
imagewidth, imageheight, seriesdescription = list(row)
if currentimageidindex == float:
continue
try:
# 파일 디렉토리만 포함되어있음 ex - /opt/home/data/I66/NonDICOM/train/abnormal/I66_mri_AB_00000007/x
# /home/bjh/obsk/v_nas2/I66/DICOM/train/abnormal/I66_mri_AB_00000039
labelPath = self.path + '/img/y/' + str(
currentimageidindex) + '.jpg'
imageLoc = self.path + '/img/y/'
if not os.path.exists(imageLoc):
os.makedirs(imageLoc)
w, h = imagewidth, imageheight
img = cv2.imread(labelPath)
# print(img)
if img is None:
img = np.zeros((h, w))
# print(img)
m_data = json.loads(measurementdata)
handles = m_data['handles']
# print(handles)
if tooltype == 'polygonRoi':
pts = []
for pt in handles.values():
pts.append((int(pt['x']), int(pt['y'])))
labeled = cv2.fillConvexPoly(img, np.array(pts),
(255, 255, 255))
# print(img)
cv2.imwrite(labelPath, labeled)
except:
continue
OraDB.releaseConn()
# self.path = /home/bjh/obsk/v_nas2/I66/DICOM/train/abnormal/I66_mri_AB_00000039
x_data_path = self.path + '/img/x/'
x_data_cnt = len(os.listdir(x_data_path))
x_data = self._sort_by_number(os.listdir(x_data_path))
for i in range(x_data_cnt):
if os.path.isfile(self.path + '/img/y/' + str(i + 1) +
'.jpg') is True:
os.rename(self.path + '/img/y/' + str(i + 1) + '.jpg',
x_data_path.replace('/x/', '/y/') + x_data[i])
else:
label = np.zeros((h, w))
file_name = x_data_path.replace('/x/', '/y/') + x_data[i]
cv2.imwrite(file_name, label)
def ts_main_process(self):
# DB 체크 후 process 정보 가져옴
time.sleep(3)
# if cur.execute("select seq where index_name = test_lb_id") is None:
# cur.execute("update table_indexing set seq = 0 where index_name = test_lb_id")
# cur.commit()
# if self.test_type == 'in':
# # 테스트 시작
# print('test start')
# db.dl_test.find_and_modify(query={'dl_test_id': int(self.dl_test_id)}, update={"$set": {'dl_status': "running"}}, upsert=False, full_response=True)
# self.in_test_run(dl_test_id = self.dl_test_id, test_type = self.test_type, tr_model_id = self.tr_model_id, studylist_id = int(self.studylist_id), file_path = self.file_path)
# # 테스트가 종료되면 dl_status를 end로 갱신
# db.dl_test.find_and_modify(query={'dl_test_id': int(self.dl_test_id)}, update={"$set": {'dl_status': "end"}}, upsert=False, full_response=True)
#
# elif self.test_type == 'out':
# # 테스트 시작
# print('test start')
# db.dl_test.find_and_modify(query={'dl_test_id': int(self.dl_test_id)}, update={"$set": {'dl_status': "running"}}, upsert=False, full_response=True)
# self.out_test_run(dl_test_id=int(self.dl_test_id), test_type=self.test_type, tr_model_id=self.tr_model_id, file_path=self.file_path)
#
# # 테스트가 종료되면 dl_status를 end로 갱신
# db.dl_test.find_and_modify(query={'dl_test_id': int(self.dl_test_id)}, update={"$set": {'dl_status': "end"}}, upsert=False, full_response=True)
try:
cur = OraDB.prepareCursor()
if self.test_type == 'in':
# 테스트 시작
print('test start')
cur.execute(
"update dl_test set dl_status = running where dl_test_id = :dl_test_id",
int(self.dl_test_id))
OraDB.dbCommit()
self.in_test_run(dl_test_id=self.dl_test_id,
test_type=self.test_type,
tr_model_id=self.tr_model_id,
studylist_id=self.studylist_id,
file_path=self.file_path)
# 테스트가 종료되면 dl_status를 end로 갱신
cur.execute(
"update dl_test set dl_status = end where dl_test_id = :dl_test_id",
int(self.dl_test_id))
OraDB.dbCommit()
OraDB.releaseConn()
elif self.test_type == 'out':
# 테스트 시작
print('test start')
cur.execute(
"update dl_test set dl_status = running where dl_test_id = :dl_test_id",
int(self.dl_test_id))
OraDB.dbCommit()
self.out_test_run(dl_test_id=int(self.dl_test_id),
test_type=self.test_type,
tr_model_id=self.tr_model_id,
file_path=self.file_path)
# 테스트가 종료되면 dl_status를 end로 갱신
cur.execute(
"update dl_test set dl_status = end where dl_test_id = :dl_test_id",
int(self.dl_test_id))
OraDB.dbCommit()
OraDB.releaseConn()
except:
cur = OraDB.prepareCursor()
# 에러 발생시 dl_status를 fail로 갱신
cur.execute(
"update dl_test set dl_status = fail where dl_test_id = :dl_test_id",
int(self.dl_test_id))
OraDB.dbCommit()
OraDB.releaseConn()
print('Test Process Error Occurred')
except:
cur = OraDB.prepareCursor()
# 에러 발생시 dl_status를 fail로 갱신
cur.execute(
"update dl_test set dl_status = fail where dl_test_id = :dl_test_id",
int(self.dl_test_id))
OraDB.dbCommit()
OraDB.releaseConn()
print('Test Process Error Occurred')
# process runner
if __name__ == "__main__":
time.sleep(3)
try:
cur = OraDB.prepareCursor()
cur.execute(
"select dl_test_id, test_type, tr_model_id, studylist_id, file_path, dl_status from dl_test"
)
for row in cur:
dl_test_id, test_type, tr_model_id, studylist_id, file_path, dl_status = list(
row)
if dl_status == 'run':
test = test_proc(dl_test_id=dl_test_id,
test_type=test_type,
tr_model_id=tr_model_id,
studylist_id=studylist_id,
file_path=file_path)
test.ts_main_process()
break
def train(self, n_epochs, n_t_iters, n_v_iters, b_size=1, keep_prob=1.0):
# tf.reset_default_graph()
global_step = tf.Variable(0, trainable=False)
with tf.control_dependencies(tf.get_collection(tf.GraphKeys.UPDATE_OPS)):
self._get_optimizer(global_step, n_t_iters)
with tf.Session() as sess:
# sess = tf_debug.LocalCLIDebugWrapperSession(sess)
# sess.add_tensor_filter("has_inf_or_nan", tf_debug.has_inf_or_nan)
sess.run(tf.global_variables_initializer())
saver = tf.train.Saver()
ckpt_st = tf.train.get_checkpoint_state(self.net_path)
if ckpt_st is not None:
saver.restore(sess, ckpt_st.model_checkpoint_path)
for epoch in range(n_epochs):
# epoch 진행 상황 저장
total_acc = 0
total_loss = 0
for up_down in range(2):
for crop_number in range(4):
offset = (crop_number + (up_down + epoch * 2) * 4) * (n_t_iters // 8 * 3 + n_v_iters // 8)
for t_index in range(n_t_iters // 8):
for augment_number in range(3):
step = offset + t_index * 3 + augment_number + 1
total_step = offset + t_index * 3 + 3 + 1
x, y = self.data_loader.load_batch(b_size=1, up_down=up_down, crop_number=crop_number, augment_number=augment_number, training=True, testing=False)
loss, _ = sess.run((self.net.cost, self.optimizer), feed_dict={self.net.x: x, self.net.y: y, self.net.training: True, self.net.keep_prob: keep_prob})
total_loss += loss / total_step
print("step {:} : loss {:.4f}".format(step, loss), 'Training')
for v_index in range(n_v_iters // 8):
step = offset + n_t_iters // 8 * 3 + v_index + 1 # 3 + crop_number
total_step = offset + n_t_iters // 8 * 3 + v_index + 1
x, y, files_list = self.data_loader.load_batch(b_size=1, up_down=up_down, crop_number=crop_number, augment_number=0, training=False, testing=True) # testing=False
predictions, accuracy, dice = sess.run(
(self.net.predict, self.net.accuracy, self.net.dice),
feed_dict={
self.net.x: x,
self.net.y: y,
self.net.training: False,
self.net.keep_prob: keep_prob
}
)
total_acc += accuracy / total_step
print('validation')
print("step {:} : accuracy {:.4f} dice {:.4f}".format(step, accuracy, dice), 'Validation')
# 에폭별로 학습이 종료되면 에폭의 평균 loss, 평균 accuracy를 db에 업데이트
progress = epoch+1 // n_epochs * 100
cur = OraDB.prepareCursor()
cur.execute("update training set epoch_cost=:epoch_cost, epoch_accuracy=:epoch_accuracy, epoch_num=:epoch_num, tr_progress=:tr_progress, ed_runtime=:ed_runtime where tr_model_id=:tr_model_id limit 1",
[round(total_loss, 4), round(total_acc, 4), epoch + 1, progress, datetime.today().strftime("%Y%m%d%H%M%S")])
print('epoch_cost', round(total_loss, 4), 'epoch_accuracy', round(total_acc, 4),
'epoch_num', epoch + 1, 'tr_progress', progress, 'ed_runtime', datetime.today().strftime("%Y%m%d%H%M%S"))
OraDB.dbCommit()
OraDB.releaseConn()
print('db writing finished')
saver.save(sess, self.net_path)
print('model saved')
tf.reset_default_graph()
sess.close()
def tr_main_process():
# DB 체크 후 process 정보 가져옴
time.sleep(5)
# client = MongoClient('mongodb://172.16.52.79:27017')
# db = client.ohif_deployment
# cursor = db.training.find()
cur = OraDB.prepareCursor()
cur.execute(
"select tr_status, tr_model_info, layer_cnt, tr_validation, loss_info, optimizer_info, learning_rate, drop_out_rate, activation_info, tr_model_id, normal_data, abnormal_data from training"
)
for row in cur:
tr_status, tr_model_info, layer_cnt, tr_validation, loss_info, optimizer_info, learning_rate, drop_out_rate, activation_info, tr_model_id, normal_data, abnormal_data = list(
row)
if tr_status == 'running':
try:
# 학습 시작
cur.execute(
"update training set tr_status='running_now' where tr_model_id=:tr_model_id",
{'tr_model_id': tr_model_id})
OraDB.dbCommit()
print('Train Started')
train_start_time = time.time()
# print(row)
train_run(tr_model_info=tr_model_info,
layer_cnt=layer_cnt,
tr_validation=tr_validation,
loss_info=loss_info,
optimizer_info=optimizer_info,
learning_rate=learning_rate,
drop_out_rate=drop_out_rate,
act_func=activation_info,
tr_model_id=tr_model_id,
normal_data=normal_data,
abnormal_data=abnormal_data)
# 학습 종료되면 tr_status를 end로 갱신
print('Training Finished')
train_end_time = time.time()
duration = (train_end_time - train_start_time) // 60
cur.execute(
"update training set tr_status='end', duration=:duration where tr_model_id=:tr_model_id",
{
'duration': str(duration),
'tr_model_id': tr_model_id
})
OraDB.dbCommit()
OraDB.releaseConn()
except:
# 에러 발생시 tr_status를 fail로 갱신
cur.execute(
"update training set tr_status='fail' where tr_model_id=:tr_model_id",
{'tr_model_id': tr_model_id})
OraDB.dbCommit()
OraDB.releaseConn()
print('Error Occurred')
def train_run(**kwargs):
cost = kwargs['loss_info']
optimizer = kwargs['optimizer_info']
learning_rate = kwargs['learning_rate']
drop_out_rate = kwargs['drop_out_rate']
act_func = kwargs['act_func']
layer_cnt = int(kwargs['layer_cnt'])
model_id = int(kwargs['tr_model_id'])
normal_data = kwargs['normal_data']
abnormal_data = kwargs['abnormal_data']
validation = kwargs['tr_validation']
k_fold_list = []
# validation 수치 변경
if int(validation) == 2:
print(validation, type(validation))
k_fold_list.append(50)
elif int(validation) == 5:
print(validation, type(validation))
k_fold_list.append(20)
elif int(validation) == 10:
print(validation, type(validation))
k_fold_list.append(10)
elif int(validation) == 15:
print(validation, type(validation))
k_fold_list.append(18)
elif int(validation) == 20:
print(validation, type(validation))
k_fold_list.append(5)
# print('dl_option : ', cost, optimizer, learning_rate, drop_out_rate, act_func, layer_cnt, model_id, validation)
k_fold = k_fold_list[0]
def _return_loop_number(string):
if string != '_':
under_Bar = string.find('_')
first_data_n = int(string[:under_Bar])
last_data_n = int(string[under_Bar + 1:])
return first_data_n, last_data_n
# path = '/home/obsk/Javis_dl_system/data/I66'
# /opt/home/data/I66/DICOM/train/abnormal/I66_mri_AB_00000029
# /home/obsk/v_nas2/I66/DICOM/train/abnormal/I66_mri_AB_00000029
# path = 'D:/data/I66'
# normal data get
normal_file_path_list = []
normal_data_chklist = []
if normal_data != '_':
normal_start, normal_fin = _return_loop_number(normal_data)
# normal_length = normal_fin - normal_start + 1
# client = MongoClient('mongodb://172.16.52.79:27017')
# db = client.ohif_deployment
# cursor = db.study_normtraining.find().sort('normtrain_id', pymongo.ASCENDING)
cur = OraDB.prepareCursor()
cur.execute(
"select del_yn, dataid, file_path, normtrain_id from study_normtraining order by normtrain_id asc"
)
for row in cur:
del_yn, dataid, file_path, normtrain_id = list(row)
if 'del_yn' != 'y' and 'I66' in dataid:
normal_data_chklist.append(file_path)
print(normal_data_chklist)
for idx in range(normal_start - 1, normal_fin):
normal_file_path_list.append(normal_data_chklist[idx])
print(normal_file_path_list)
OraDB.releaseConn()
# abnormal data get
abnormal_file_path_list = []
abnormal_data_chklist = []
if abnormal_data != '_':
abnormal_start, abnormal_fin = _return_loop_number(abnormal_data)
# abnormal_length = abnormal_fin - abnormal_start + 1
# client = MongoClient('mongodb://172.16.52.79:27017')
# db = client.ohif_deployment
# cursor = db.study_abnormtraining.find().sort('abnormtrain_id', pymongo.ASCENDING)
cur = OraDB.prepareCursor()
cur.execute(
"select del_yn, dataid, file_path, normtrain_id from study_abnormtraining order by abnormtrain_id asc"
)
for row in cur:
del_yn, dataid, file_path, normtrain_id = list(row)
if del_yn != 'y' and 'I66' in dataid:
abnormal_data_chklist.append(file_path)
print(abnormal_data_chklist)
for idx in range(abnormal_start - 1, abnormal_fin):
abnormal_file_path_list.append(abnormal_data_chklist[idx])
print(abnormal_file_path_list)
OraDB.releaseConn()
# copy nas normal data to local temp directory
local_n_datapath_list = []
for nas_path in normal_file_path_list:
temp_path = nas_path.replace(
'/medimg/', '/home/user01/Javis_dl_system/data_temp/')
if not os.path.exists(temp_path):
os.makedirs(temp_path)
data_mover.nas_to_dlserver(nas_path, temp_path)
local_n_datapath_list.append(temp_path)
# copy nas abnormal data to local temp directory
local_ab_datapath_list = []
for nas_path in abnormal_file_path_list:
temp_path = nas_path.replace(
'/medimg/', '/home/user01/Javis_dl_system/data_temp/')
if not os.path.exists(temp_path):
os.makedirs(temp_path)
data_mover.nas_to_dlserver(nas_path, temp_path)
local_ab_datapath_list.append(temp_path)
tot_datapath_list = local_n_datapath_list + local_ab_datapath_list
# print('tot_data_id_list : ', tot_datapath_list)
if len(tot_datapath_list) <= 1:
print('CANNOT RUN WITH 0, 1 DATA SET')
raise FileNotFoundError
shuffle(tot_datapath_list)
fin_datapath_list = []
# path : /home/bjh/obsk/v_nas2/I66/DICOM/train/abnormal/I66_mri_AB_00000039
for path in tot_datapath_list:
datasaver = LabelDataSaver.DataSaver(path)
datasaver.saveYdata_labeled()
x_path = path + '/img/x'
y_path = path + '/img/y'
if os.path.isdir(y_path) is True:
if len(os.listdir(y_path)) == len(os.listdir(x_path)):
fin_datapath_list.append(path)
dataset_cnt = len(fin_datapath_list) # n
# b_size = 1
# k = k_fold
data_loader = TrainDataLoader.DataLoader(data_path_list=fin_datapath_list,
k_fold=k_fold,
c_size=256,
i_channel=1,
n_class=2)
trainer = Trainer(data_loader=data_loader,
model_id=model_id,
optimizer=optimizer,
learning_rate=learning_rate,
cost_name=cost,
act_func=act_func,
layer_n=layer_cnt)
trainer.train(n_epochs=1,
n_t_iters=(math.ceil(dataset_cnt / k_fold *
(k_fold - 1)) - 1) * 8,
n_v_iters=math.ceil(dataset_cnt / k_fold) * 8,
b_size=1,
keep_prob=drop_out_rate)
