def train_autoencoder(cross_epoch=0,
data_index=None,
brain_map=None,
cut_shape=None,
data_type=['MCIc', 'MCInc'],
pre_dir='/home/anzeng/rhb/fmri_data',
num_batches=512 * 5 + 1,
test_size=6):
keras.backend.clear_session()
batch_size = 100
if cut_shape == None:
brain_map = [212, 213, 214, 215, 216, 217, 218]
cut_shape = [100, 0, 100, 0, 100, 0]
mask = nib.load(
'/home/anzeng/rhb/fmri/fMRI-deeping-learning/BN_Atlas_246_3mm.nii')
mask = mask.get_fdata()
#获取截取的sMRI大小
for x in brain_map:
tmp = np.where(mask == x)
for i in range(3):
cut_shape[2 * i] = min(cut_shape[2 * i], np.min(tmp[i]))
cut_shape[2 * i + 1] = max(cut_shape[2 * i + 1],
np.max(tmp[i]))
print(cut_shape)
# xyz = 32
logs_path = os.path.join(cfg.voxnet_checkpoint_dir,
'train_' + str(cross_epoch))
if os.path.isdir(logs_path):
shutil.rmtree(logs_path)
os.makedirs(logs_path)
model = Autoencoder()
dataset = fMRI_data(data_type,
data_index=data_index,
dir=pre_dir,
batch_mode='random',
varbass=cfg.varbass)
model.fit_generator(
dataset.get_smri_batch(cut_shape,
batch_size,
_batch_mode='oversampling',
_mode='train'),
steps_per_epoch=8,
epochs=num_batches,
callbacks=[keras.callbacks.TensorBoard(log_dir=logs_path)])
if not os.path.exists(cfg.voxnet_checkpoint_dir):
os.makedirs(cfg.voxnet_checkpoint_dir)
filepath = os.path.join(cfg.voxnet_checkpoint_dir,
'train_' + str(cross_epoch) + '.h5')
# for i in range(10):
# test_model = keras.Model(inputs=model.layers[0].input,outputs = model.layers[i].output)
# test_model.save(filepath=filepath)
# print(i)
model.save(filepath=filepath)
# del model
# model = keras.models.load_model(filepath)
return filepath
def emsemble(cross_epoch = 0,data_index=None,cut_shape=None,data_type=['MCIc','MCInc'],pre_dir='/home/anzeng/rhb/fmri_data',
num_batches = 256*5,voxnet_point=None,test_size = 6,brain_map=[217],f_handle = None):
# tf.reset_default_graph()
keras.backend.clear_session()
dataset = fMRI_data(data_type, data_index=data_index, varbass=False, dir=pre_dir)
# xyz = 32
# input_shape = [None, xyz, xyz, xyz, 1]
# voxnet = VoxNet(input_shape=input_shape, voxnet_type='cut')
true_shape = []
for x in range(0, len(cut_shape), 2):
true_shape.append(cut_shape[x + 1] - cut_shape[x] + 1)
# with tf.Session() as sess:
# sess.run(tf.global_variables_initializer())
# voxnet.npz_saver.restore(sess,voxnet_point)
#加载模型
model = keras.models.load_model(voxnet_point)
print('train_acc')
train_fmri_evaluation = evaluation()
train_smri_evaluation = evaluation()
train_iter = iter(dataset.get_fmri('train')).__next__
for i in range(100):
img,label,_ = train_iter()
predict,y_true = get_label(model,img,label,cut_shape,true_shape)
predict = np.argmax(predict,axis=1)
train_smri_evaluation += evaluation(y_predict=predict,y_true=y_true)
if i %10 == 0 and i > 0:
print(train_smri_evaluation)
y_predict = ensemble_label(predict,2)
train_fmri_evaluation += evaluation(y_predict = [y_predict],y_true=[label])
print(train_fmri_evaluation)
print('test_acc')
test_fmri_evaluation = evaluation()
test_smri_evaluation = evaluation()
test_iter = iter(dataset.get_fmri('test')).__next__
for i in range(test_size):
img, label,filename = test_iter()
predict, y_true = get_label(model, img, label, cut_shape, true_shape)
predict = np.argmax(predict,axis=1)
test_smri_evaluation_one = evaluation(y_predict=predict, y_true=y_true)
test_smri_evaluation += test_smri_evaluation_one
print(test_smri_evaluation_one)
print(test_smri_evaluation)
y_predict = ensemble_label(predict,2)
test_fmri_evaluation += evaluation(y_predict=[y_predict], y_true=[label])
print(y_predict,label,test_fmri_evaluation)
# if y_predict != label:
# print(filename)
# f_handle.write(filename+'\n')
if f_handle:
f_handle.write('ensemble train:\n')
f_handle.write(str(train_fmri_evaluation) + '\n')
f_handle.write('ensemble test:\n')
f_handle.write(str(test_fmri_evaluation) + '\n')
return test_fmri_evaluation
def svm_emsemble(cross_epoch = 0,data_index=None,cut_shape=None,data_type=['MCIc','MCInc'],pre_dir='/home/anzeng/rhb/fmri_data',
num_batches = 256*5,voxnet_point=None,test_size = 6,brain_map=[217],f_handle = None):
keras.backend.clear_session()
dataset = fMRI_data(data_type, data_index=data_index, varbass=False, dir=pre_dir)
true_shape = []
for x in range(0, len(cut_shape), 2):
true_shape.append(cut_shape[x + 1] - cut_shape[x] + 1)
# 加载模型
model = keras.models.load_model(voxnet_point)
layer_name = 'CNN_fc2'
model = keras.Model(inputs=model.layers[0].input, outputs=model.get_layer(layer_name).output)
#加载模型
train_len = 0
for i in data_type:
train_len += len(data_index[i]['train'])
# print('train_acc')
# train_fmri_evaluation = evaluation()
# train_smri_evaluation = evaluation()
train_iter = iter(dataset.get_fmri('train')).__next__
train_one_len = [0]
#训练数据
train_data = -1
train_label = -1
for i in range(train_len):
img, label, _ = train_iter()
predict, y_true = get_label(model, img, label, cut_shape, true_shape)
if isinstance(train_data,int):
train_data = predict
train_label = y_true
else:
train_data = np.vstack((train_data,predict))
train_label = np.hstack((train_label,y_true))
train_one_len.append(train_one_len[-1]+predict.shape[0])
# train_smri_evaluation += evaluation(y_predict=predict, y_true=y_true)
# y_predict = ensemble_label(predict, 2)
# train_fmri_evaluation += evaluation(y_predict=[y_predict], y_true=[label])
# print(train_fmri_evaluation)
clf = svm.SVC(C=1.0,kernel='rbf',gamma='auto')
clf.fit(train_data,train_label)
train_evaluation = evaluation()
for i in range(1,len(train_one_len),1):
predict = clf.predict(train_data[train_one_len[i-1]:train_one_len[i]])
# print(predict)
y_predict = ensemble_label(predict, 2)
y_true = train_label[train_one_len[i-1]]
train_evaluation += evaluation(y_predict=[y_predict], y_true=[y_true])
# predict = clf.predict(train_data)
# train_evaluation = evaluation(y_true = train_label,y_predict = predict)
print('svm ensemble train:')
print(train_evaluation)
test_evaluation = evaluation()
# test_smri_evaluation = evaluation()
print('svm ensemble test')
test_iter = iter(dataset.get_fmri('test')).__next__
for i in range(test_size):
img, label, filename = test_iter()
predict, y_true = get_label(model, img, label, cut_shape, true_shape)
# test_smri_evaluation_one = evaluation(y_predict=predict, y_true=y_true)
# test_smri_evaluation += test_smri_evaluation_one
# print(test_smri_evaluation_one)
# print(test_smri_evaluation)
predict = clf.predict(predict)
y_predict = ensemble_label(predict, 2)
test_evaluation += evaluation(y_predict=[y_predict], y_true=[label])
print(y_predict, label, test_evaluation)
# if y_predict != label:
# print(filename)
# f_handle.write(filename+'\n')
if f_handle:
f_handle.write('svm ensemble train:\n')
f_handle.write(str(train_evaluation)+'\n')
f_handle.write('svm ensemble test:\n')
f_handle.write(str(test_evaluation)+'\n')
return test_evaluation
def main(data_index=None,
cut_shape=None,
data_type=['MCIc', 'MCInc'],
pre_dir='/home/anzeng/rhb/fmri_data',
num_batches=256 * 5,
voxnet_point=None,
test_size=6,
brain_map=[217]):
# fr = open(cfg.output, 'w')
tf.reset_default_graph()
time_dim = 80 # 挑选时间片个数
batch_size = 8
dataset = fMRI_data(data_type,
data_index=data_index,
varbass=False,
dir=pre_dir)
#SVM index
#########################
svm_index = {}
train_len = 0
test_len = 0
for d_type in data_type:
t_dir = os.path.join(pre_dir, d_type)
t_len = os.listdir(t_dir)
t_len = len(t_len)
train_index = list(range(t_len))
test_index = data_index[d_type]['test']
for x in test_index:
train_index.remove(x)
_index = {'train': train_index, 'test': test_index}
train_len += len(train_index)
test_len += len(test_index)
svm_index[d_type] = _index
print(train_len)
print(test_len)
print(svm_index)
svm_dataset = fMRI_data(data_type,
data_index=svm_index,
varbass=False,
dir=pre_dir)
##########################
xyz = 32
input_shape = [None, xyz, xyz, xyz, 1]
# for i in range(3):
# input_shape.append(cut_shape[2 * i + 1] + 1 - cut_shape[2 * i])
# input_shape.append(1)
# print(input_shape)
voxnet = VoxNet(input_shape=input_shape, voxnet_type='cut')
FCNs = Classifier_FCN(tf.placeholder(tf.float32, [None, time_dim, 50]),
nb_classes=2)
data_value = [[1], [1]]
# 创建数据
p = dict() # placeholders
p['labels'] = tf.placeholder(tf.float32, [None, 2])
p['data_value'] = tf.placeholder(tf.float32, [2, 1])
p['Weight'] = tf.matmul(p['labels'], p['data_value'])
p['cross_loss'] = tf.nn.softmax_cross_entropy_with_logits(
logits=FCNs[-2], labels=p['labels'])
p['Weight'] = tf.reshape(p['Weight'], [-1])
p['x_loss'] = tf.multiply(p['Weight'], p['cross_loss'])
p['loss'] = tf.reduce_mean(p['x_loss'])
p['l2_loss'] = tf.add_n([tf.nn.l2_loss(w) for w in FCNs.kernels])
p['prediction'] = tf.argmax(FCNs[-1], 1)
p['y_true'] = tf.argmax(p['labels'], 1)
p['correct_prediction'] = tf.equal(p['prediction'], p['y_true'])
p['accuracy'] = tf.reduce_mean(tf.cast(p['correct_prediction'],
tf.float32))
p['learning_rate'] = tf.placeholder(tf.float32)
with tf.control_dependencies(tf.get_collection(tf.GraphKeys.UPDATE_OPS)):
p['train'] = tf.train.AdamOptimizer(p['learning_rate'],
epsilon=1e-3).minimize(p['loss'])
p['weights_decay'] = tf.train.GradientDescentOptimizer(
p['learning_rate']).minimize(p['l2_loss'])
# p['test_error'] = tf.placeholder(tf.float32)
# 超参数设置
initial_learning_rate = 0.01
min_learning_rate = 0.000001
learning_rate_decay_limit = 0.0001
num_batches_per_epoch = len(dataset.train) / float(batch_size)
learning_decay = 10 * num_batches_per_epoch
weights_decay_after = 5 * num_batches_per_epoch
checkpoint_num = 0
learning_step = 0
min_loss = 1e308
if voxnet_point:
cfg.voxnet_checkpoint = voxnet_point
accuracy_filename = os.path.join(cfg.fcn_checkpoint_dir, 'accuracies.txt')
if not os.path.isdir(cfg.fcn_checkpoint_dir):
os.mkdir(cfg.fcn_checkpoint_dir)
if not os.path.exists(accuracy_filename):
with open(accuracy_filename, 'a') as f:
f.write('')
with open(accuracy_filename, 'a') as f:
f.write(str(brain_map) + '\n')
#返回值
test_evaluation = evaluation()
with tf.Session() as session:
session.run(tf.global_variables_initializer())
voxnet.npz_saver.restore(session, cfg.voxnet_checkpoint)
#voxnet赋值
input_shape[0] = 1
voxnet_data = np.ones(input_shape, np.float32)
input_shape[0] = -1
for batch_index in range(num_batches):
start = time.time()
# learning_rate = max(min_learning_rate,
# initial_learning_rate * 0.5 ** (learning_step / learning_decay))
learning_rate = 0.0001
learning_step += 1
if batch_index > weights_decay_after and batch_index % 256 == 0:
session.run(p['weights_decay'], feed_dict=feed_dict)
voxs, labels = dataset.train.oversampling.get_time_batch(
session,
voxnet,
cut_shape,
time_dim=time_dim,
batch_size=batch_size)
feed_dict = {
FCNs[0]: voxs,
voxnet[0]: voxnet_data,
voxnet.keep_prob: 1.0,
FCNs.keep_prob: 0.7,
p['labels']: labels,
p['learning_rate']: learning_rate,
FCNs.training: True,
p['data_value']: data_value
}
session.run(p['train'], feed_dict=feed_dict)
if batch_index and batch_index % 32 == 0:
print("{} batch: {}".format(datetime.datetime.now(),
batch_index))
print('learning rate: {}'.format(learning_rate))
# fr.write("{} batch: {}".format(datetime.datetime.now(), batch_index))
# fr.write('learning rate: {}'.format(learning_rate))
feed_dict[FCNs.training] = False
loss = session.run(p['loss'], feed_dict=feed_dict)
print('loss: {}'.format(loss))
if (batch_index and loss > 1.5 * min_loss
and learning_rate > learning_rate_decay_limit):
min_loss = loss
learning_step *= 1.2
print("decreasing learning rate...")
min_loss = min(loss, min_loss)
if batch_index and batch_index % 16 == 0:
num_accuracy_batches = 20
train_evaluation = evaluation()
for x in range(num_accuracy_batches):
voxs, labels = dataset.train.random_sampling.get_time_batch(
session,
voxnet,
cut_shape,
time_dim=time_dim,
batch_size=batch_size)
feed_dict = {
FCNs[0]: voxs,
voxnet[0]: voxnet_data,
voxnet.keep_prob: 1.0,
FCNs.keep_prob: 1.0,
p['labels']: labels,
FCNs.training: False
}
predictions, y_true = session.run(
[p['prediction'], p['y_true']], feed_dict=feed_dict)
train_evaluation += evaluation(y_true=y_true,
y_predict=predictions)
print('training accuracy \n' + str(train_evaluation))
num_accuracy_batches = test_size
test_evaluation = evaluation()
for x in range(num_accuracy_batches):
voxs, labels = dataset.test.random_sampling.get_time_batch(
session,
voxnet,
cut_shape,
time_dim=time_dim,
batch_size=batch_size)
feed_dict = {
FCNs[0]: voxs,
voxnet[0]: voxnet_data,
voxnet.keep_prob: 1.0,
FCNs.keep_prob: 1.0,
p['labels']: labels,
FCNs.training: False
}
predictions, y_true = session.run(
[p['prediction'], p['y_true']], feed_dict=feed_dict)
test_evaluation += evaluation(y_true=y_true,
y_predict=predictions)
print(test_evaluation)
print('test accuracy \n' + str(test_evaluation))
with open(accuracy_filename, 'a') as f:
f.write('checkpoint_num:' + str(checkpoint_num) + ':\n')
f.write('train:\n' + str(train_evaluation) + '\n')
f.write('test:\n' + str(test_evaluation) + '\n')
if batch_index % 64 or train_evaluation.ACC >= 0.8 == 0:
######SVM分类器####################
svm_feature = np.zeros((train_len + test_len, 128))
svm_label = np.zeros(train_len + test_len)
for x in range(train_len):
voxs, labels = svm_dataset.train.random_sampling.get_time_batch(
session,
voxnet,
cut_shape,
time_dim=time_dim,
batch_size=1)
feed_dict = {
FCNs[0]: voxs,
voxnet[0]: voxnet_data,
voxnet.keep_prob: 1.0,
FCNs.keep_prob: 1.0,
p['labels']: labels,
FCNs.training: False
}
feature, y_true = session.run(
[FCNs['gap'], p['y_true']], feed_dict=feed_dict)
feature = np.reshape(feature, [1, 128])
svm_feature[x] = feature
# print(svm_feature[x])
svm_label[x] = y_true
for x in range(test_len):
voxs, labels = svm_dataset.test.random_sampling.get_time_batch(
session,
voxnet,
cut_shape,
time_dim=time_dim,
batch_size=1)
feed_dict = {
FCNs[0]: voxs,
voxnet[0]: voxnet_data,
voxnet.keep_prob: 1.0,
FCNs.keep_prob: 1.0,
p['labels']: labels,
FCNs.training: False
}
feature, y_true = session.run(
[FCNs['gap'], p['y_true']], feed_dict=feed_dict)
feature = np.reshape(feature, [1, 128])
svm_feature[train_len + x] = feature
svm_label[train_len + x] = y_true
# print(svm_feature[0:train_len])
# print(svm_label[0:train_len])
clf = svm.SVC(C=1.0, kernel='rbf', gamma='auto')
clf.fit(svm_feature[0:train_len], svm_label[0:train_len])
predictions = clf.predict(svm_feature)
svm_train_evaluation = evaluation(
y_true=svm_label[:train_len],
y_predict=predictions[:train_len])
svm_test_evaluation = evaluation(
y_true=svm_label[train_len:],
y_predict=predictions[train_len:])
print('svm_train:\n' + str(svm_train_evaluation))
print('svm_test:\n' + str(svm_test_evaluation))
with open(accuracy_filename, 'a') as f:
f.write('svm_train:\n' + str(svm_train_evaluation) +
'\n')
f.write('svm_test:\n' + str(svm_test_evaluation) +
'\n')
#################################################
# fr.write('test accuracy: {}'.format(test_accuracy))
if batch_index % 128 == 0 or train_evaluation.ACC >= 0.85:
print('saving checkpoint {}...'.format(checkpoint_num))
filename = 'cx-{}.npz'.format(checkpoint_num)
filename = os.path.join(cfg.fcn_checkpoint_dir, filename)
FCNs.npz_saver.save(session, filename)
print('checkpoint saved!')
checkpoint_num += 1
if train_evaluation.ACC >= 0.85:
break
end = time.time()
print('time:', (end - start) / 60)
return test_evaluation
def syn_train(*argv):
input_weight = [2, 1, 1, 1]
data_value = [[1.0], [1.0]]
time_dim = 80 # 挑选时间片个数
batch_size = 8
brain_map = [217, 218, 219]
cut_shape = [100, 0, 100, 0, 100, 0]
mask = nib.load(
'/home/anzeng/rhb/fmri/fMRI-deeping-learning/BN_Atlas_246_3mm.nii')
mask = mask.get_fdata()
# 获取截取的sMRI大小
for x in brain_map:
tmp = np.where(mask == x)
for i in range(3):
cut_shape[2 * i] = min(cut_shape[2 * i], np.min(tmp[i]))
cut_shape[2 * i + 1] = max(cut_shape[2 * i + 1], np.max(tmp[i]))
print(brain_map, cut_shape)
dataset = fMRI_data(['AD', 'NC'],
dir='/home/anzeng/rhb/fmri_data',
batch_mode='random',
varbass=cfg.varbass)
input_shape = [None, 32, 32, 32, 1]
# for i in range(3):
# input_shape.append(cut_shape[2 * i + 1] + 1 - cut_shape[2 * i])
# input_shape.append(1)
print(input_shape)
# input_shape=[40,2,2,2,1]
voxnet = VoxNet(input_shape=input_shape, voxnet_type='all_conv')
FCN_input = tf.reshape(voxnet['gap'], (-1, time_dim, 128))
print(FCN_input)
FCNs = Classifier_FCN(FCN_input, nb_classes=2)
# 创建数据
p = dict() # placeholders
p['labels'] = tf.placeholder(tf.float32, [None, 2])
p['data_value'] = tf.placeholder(tf.float32, [2, 1])
p['input_pw'] = tf.placeholder(tf.float32, [None]) #预测权值
p['Weight'] = tf.matmul(p['labels'], p['data_value'])
p['cross_loss'] = tf.nn.softmax_cross_entropy_with_logits(
logits=FCNs[-2], labels=p['labels'])
p['Weight'] = tf.reshape(p['Weight'], [-1])
p['x_loss'] = tf.multiply(p['Weight'], p['cross_loss'])
p['loss'] = tf.reduce_mean(p['x_loss'])
p['l2_loss'] = tf.add_n([tf.nn.l2_loss(w) for w in FCNs.kernels])
# 预测时进行集成
p['p_w'] = tf.reshape(p['input_pw'], [-1, 1])
p['sum_w'] = tf.reduce_sum(p['p_w'])
p['test_prediction'] = tf.cast(tf.argmax(FCNs[-1], 1), tf.float32)
p['test_prediction'] = tf.reshape(p['test_prediction'], [-1, 4])
p['test_prediction'] = tf.matmul(p['test_prediction'], p['p_w'])
p['test_prediction'] = tf.round(tf.divide(p['test_prediction'],
p['sum_w']))
p['prediction'] = tf.argmax(FCNs[-1], 1)
p['y_true'] = tf.argmax(p['labels'], 1)
p['correct_prediction'] = tf.equal(p['prediction'], p['y_true'])
p['accuracy'] = tf.reduce_mean(tf.cast(p['correct_prediction'],
tf.float32))
p['learning_rate'] = tf.placeholder(tf.float32)
with tf.control_dependencies(tf.get_collection(tf.GraphKeys.UPDATE_OPS)):
p['train'] = tf.train.AdamOptimizer(p['learning_rate'],
epsilon=1e-3).minimize(p['loss'])
p['weights_decay'] = tf.train.GradientDescentOptimizer(
p['learning_rate']).minimize(p['l2_loss'])
# p['test_error'] = tf.placeholder(tf.float32)
# 超参数设置
num_batches = 2147483647
initial_learning_rate = 0.01
min_learning_rate = 0.0001
learning_rate_decay_limit = 0.0001
num_batches_per_epoch = len(dataset.train) / float(batch_size)
learning_decay = 10 * num_batches_per_epoch
weights_decay_after = 5 * num_batches_per_epoch
checkpoint_num = cfg.checkpoint_start_num
learning_step = 0
min_loss = 1e308
accuracy_filename = os.path.join(cfg.fcn_checkpoint_dir, 'accuracies.txt')
if not os.path.isdir(cfg.fcn_checkpoint_dir):
os.mkdir(cfg.fcn_checkpoint_dir)
if not os.path.exists(accuracy_filename):
with open(accuracy_filename, 'a') as f:
f.write('')
with open(accuracy_filename, 'a') as f:
f.write(str(brain_map) + '\n')
with tf.Session() as session:
session.run(tf.global_variables_initializer())
if cfg.istraining:
voxnet.npz_saver.restore(session, cfg.voxnet_checkpoint)
FCNs.npz_saver.restore(session, cfg.fcn_checkpoint)
#voxnet赋值
for batch_index in range(num_batches):
start = time.time()
learning_rate = max(
min_learning_rate,
initial_learning_rate * 0.8**(learning_step / learning_decay))
learning_step += 1
if batch_index > weights_decay_after and batch_index % 256 == 0:
session.run(p['weights_decay'], feed_dict=feed_dict)
voxs, labels = dataset.train.oversampling.get_fmri_brain(
cut_shape, batch_size, time_dim)
# voxs = np.zeros(input_shape)
# labels = np.zeros((8,2))
feed_dict = {
voxnet[0]: voxs,
p['labels']: labels,
p['learning_rate']: learning_rate,
FCNs.training: True,
voxnet.training: True,
p['data_value']: data_value
}
# print(voxs.shape,labels.shape)
session.run(p['train'], feed_dict=feed_dict)
if batch_index and batch_index % 32 == 0:
print("{} batch: {}".format(datetime.datetime.now(),
batch_index))
print('learning rate: {}'.format(learning_rate))
# fr.write("{} batch: {}".format(datetime.datetime.now(), batch_index))
# fr.write('learning rate: {}'.format(learning_rate))
feed_dict[FCNs.training] = False
loss = session.run(p['loss'], feed_dict=feed_dict)
print('loss: {}'.format(loss))
if (batch_index and loss > 1.5 * min_loss
and learning_rate > learning_rate_decay_limit):
min_loss = loss
learning_step *= 1.2
print("decreasing learning rate...")
min_loss = min(loss, min_loss)
if batch_index and batch_index % 16 == 0:
num_accuracy_batches = 20
train_evaluation = evaluation()
for x in range(num_accuracy_batches):
voxs, labels = dataset.train.random_sampling.get_fmri_brain(
cut_shape, 5, time_dim)
feed_dict = {
voxnet[0]: voxs,
p['labels']: labels,
FCNs.training: False,
voxnet.training: False,
p['input_pw']: input_weight
}
predictions, y_true = session.run(
[p['test_prediction'], p['y_true']],
feed_dict=feed_dict)
train_evaluation += evaluation(y_true=y_true,
y_predict=predictions)
print(train_evaluation)
print('train accuracy \n' + str(train_evaluation))
num_accuracy_batches = 27
test_evaluation = evaluation()
for x in range(num_accuracy_batches):
voxs, labels = dataset.test.random_sampling.get_fmri_brain(
cut_shape, 1, time_dim)
feed_dict = {
voxnet[0]: voxs,
p['labels']: labels,
FCNs.training: False,
voxnet.training: False,
p['input_pw']: input_weight
}
predictions, y_true = session.run(
[p['test_prediction'], p['y_true']],
feed_dict=feed_dict)
test_evaluation += evaluation(y_true=y_true,
y_predict=predictions)
print(test_evaluation)
print('test accuracy \n' + str(test_evaluation))
# fr.write('test accuracy: {}'.format(test_accuracy))
with open(accuracy_filename, 'a') as f:
f.write(str(checkpoint_num) + ':\n')
f.write(str(train_evaluation) + '\n')
f.write(str(test_evaluation) + '\n')
if batch_index % 256 == 0:
print('saving checkpoint {}...'.format(checkpoint_num))
filename = 'voxnet-{}.npz'.format(checkpoint_num)
filename = os.path.join(cfg.fcn_checkpoint_dir, filename)
voxnet.npz_saver.save(session, filename)
filename = 'fcn-{}.npz'.format(checkpoint_num)
filename = os.path.join(cfg.fcn_checkpoint_dir, filename)
FCNs.npz_saver.save(session, filename)
print('checkpoint saved!')
checkpoint_num += 1
end = time.time()
print('time:', (end - start) / 60)
def main(data_index=None,
brain_map=[218],
data_type=['MCIc', 'MCInc'],
pre_dir='/home/anzeng/rhb/fmri_data',
num_batches=512 * 5 + 1,
test_size=6):
tf.reset_default_graph()
dataset = fMRI_data(data_index=data_index,
data_type=data_type,
varbass=False,
dir=pre_dir)
# 超参数设置
num_batches = num_batches
batch_size = 16
initial_learning_rate = 0.0001
min_learning_rate = 0.000001
learning_rate_decay_limit = 0.0001
num_batches_per_epoch = len(dataset.train) / float(batch_size)
learning_decay = 10 * num_batches_per_epoch
weights_decay_after = 5 * num_batches_per_epoch
feature_index = brain_map
data_value = [[1.0], [1.0]]
checkpoint_num = 0
learning_step = 0
min_loss = 1e308
time_dim = 80
varbass = True
#模型框架
mask = nib.load(
'/home/anzeng/rhb/fmri/fMRI-deeping-learning/BN_Atlas_246_3mm.nii')
mask = mask.get_fdata()
f_len = 0
for i in feature_index:
f_len += len(np.where(mask == i)[0])
FCNs = Classifier_FCN(tf.placeholder(tf.float32, [None, time_dim, 25]),
nb_classes=2)
# 创建数据
p = dict() # placeholders
p['labels'] = tf.placeholder(tf.float32, [None, 2])
p['data_value'] = tf.placeholder(tf.float32, [2, 1])
p['Weight'] = tf.matmul(p['labels'], p['data_value'])
p['cross_loss'] = tf.nn.softmax_cross_entropy_with_logits(
logits=FCNs[-2], labels=p['labels'])
p['Weight'] = tf.reshape(p['Weight'], [-1])
p['x_loss'] = tf.multiply(p['Weight'], p['cross_loss'])
p['loss'] = tf.reduce_mean(p['x_loss'])
p['l2_loss'] = tf.add_n([tf.nn.l2_loss(w) for w in FCNs.kernels])
p['prediction'] = tf.argmax(FCNs[-1], 1)
p['y_true'] = tf.argmax(p['labels'], 1)
p['correct_prediction'] = tf.equal(tf.argmax(FCNs[-1], 1),
tf.argmax(p['labels'], 1))
p['accuracy'] = tf.reduce_mean(tf.cast(p['correct_prediction'],
tf.float32))
p['learning_rate'] = tf.placeholder(tf.float32)
with tf.control_dependencies(tf.get_collection(tf.GraphKeys.UPDATE_OPS)):
p['train'] = tf.train.AdamOptimizer(0.00001,
epsilon=1e-3).minimize(p['loss'])
p['weights_decay'] = tf.train.GradientDescentOptimizer(0.0001).minimize(
p['l2_loss'])
accuracy_filename = os.path.join(cfg.fcn_checkpoint_dir, 'accuracies.txt')
if not os.path.isdir(cfg.fcn_checkpoint_dir):
os.mkdir(cfg.fcn_checkpoint_dir)
with open(accuracy_filename, 'a') as f:
f.write(str(feature_index))
with tf.Session() as session:
session.run(tf.global_variables_initializer())
# voxnet_data = np.ones([1,61,73,61,1],np.float32)
for batch_index in range(num_batches):
# learning_rate = max(min_learning_rate,
# initial_learning_rate * 0.5 ** (learning_step / learning_decay))
learning_step += 1
if batch_index > weights_decay_after and batch_index % 256 == 0:
session.run(p['weights_decay'], feed_dict=feed_dict)
voxs, labels = dataset.train.oversampling.get_brain_batch(
mask,
batch_size=batch_size,
time_dim=time_dim,
feature_index=feature_index)
feed_dict = {
FCNs[0]: voxs,
p['labels']: labels,
FCNs.training: True,
p['data_value']: data_value
}
Weight, cross_loss, x_loss, _ = session.run(
[p['Weight'], p['cross_loss'], p['x_loss'], p['train']],
feed_dict=feed_dict)
# print("Weight\n",Weight)
# print("cross_loss\n",cross_loss)
# print("x_loss\n",x_loss)
if batch_index and batch_index % 64 == 0:
print("{} batch: {}".format(datetime.datetime.now(),
batch_index))
# print('learning rate: {}'.format(learning_rate))
feed_dict[FCNs.training] = False
loss = session.run(p['loss'], feed_dict=feed_dict)
print('loss: {}'.format(loss))
# if (batch_index and loss > 1.5 * min_loss and
# learning_rate > learning_rate_decay_limit):
# min_loss = loss
# learning_step *= 1.2
# print("decreasing learning rate...")
# min_loss = min(loss, min_loss)
if batch_index and batch_index % 64 == 0:
num_accuracy_batches = 50
train_evaluation = evaluation()
for x in range(num_accuracy_batches):
voxs, labels = dataset.train.random_sampling.get_brain_batch(
mask,
batch_size=batch_size,
time_dim=time_dim,
feature_index=feature_index)
feed_dict = {
FCNs[0]: voxs,
p['labels']: labels,
FCNs.training: False
}
start_time = time.time()
predictions, y_true = session.run(
[p['prediction'], p['y_true']], feed_dict=feed_dict)
train_evaluation += evaluation(y_true=y_true,
y_predict=predictions)
end_time = time.time()
print('total time: %f' % ((end_time - start_time) / 60))
print(train_evaluation)
print('training accuracy \n' + str(train_evaluation))
# num_accuracy_batches = 10
print('loss: {}'.format(loss))
num_accuracy_batches = test_size
test_evaluation = evaluation()
for x in range(num_accuracy_batches):
voxs, labels = dataset.test.random_sampling.get_brain_batch(
mask,
batch_size=1,
time_dim=time_dim,
feature_index=feature_index)
feed_dict = {
FCNs[0]: voxs,
p['labels']: labels,
FCNs.training: False
}
y_true, prediction = session.run(
[p['y_true'], p['prediction']], feed_dict=feed_dict)
test_evaluation += evaluation(y_true=y_true,
y_predict=prediction)
# print(y_true, prediction)
print(test_evaluation)
print('test accuracy \n' + str(test_evaluation))
with open(accuracy_filename, 'a') as f:
f.write(str(checkpoint_num) + ':\n')
f.write(str(train_evaluation) + '\n')
f.write(str(test_evaluation) + '\n')
# fr.write('test accuracy: {}'.format(test_accuracy))
if batch_index % 1024 == 0:
print('saving checkpoint {}...'.format(checkpoint_num))
filename = 'cx-{}.npz'.format(checkpoint_num)
filename = os.path.join(cfg.fcn_checkpoint_dir, filename)
FCNs.npz_saver.save(session, filename)
print('checkpoint saved!')
checkpoint_num += 1
if train_evaluation.ACC > 0.95 and batch_index % 1024 == 0:
break
return test_evaluation
def main(*argv):
dataset = fMRI_data(['MCIc', 'MCInc'],
dir='/home/anzeng/rhb/fmri_data/MRI_data/217',
batch_mode='random',
varbass=True)
voxnet = VoxNet()
#数据权值
data_value = [[1], [1]]
#创建数据
p = dict() # placeholders
p['labels'] = tf.placeholder(tf.float32, [None, 2])
p['data_value'] = tf.placeholder(tf.float32, [2, 1])
p['Weight'] = tf.matmul(p['labels'], p['data_value'])
p['cross_loss'] = tf.nn.softmax_cross_entropy_with_logits(
logits=voxnet[-2], labels=p['labels'])
p['Weight'] = tf.reshape(p['Weight'], [-1])
p['x_loss'] = tf.multiply(p['Weight'], p['cross_loss'])
p['loss'] = tf.reduce_mean(p['x_loss'])
p['l2_loss'] = tf.add_n([tf.nn.l2_loss(w) for w in voxnet.kernels])
p['prediction'] = tf.argmax(voxnet[-1], 1)
p['y_true'] = tf.argmax(p['labels'], 1)
p['correct_prediction'] = tf.equal(tf.argmax(voxnet[-1], 1),
tf.argmax(p['labels'], 1))
p['accuracy'] = tf.reduce_mean(tf.cast(p['correct_prediction'],
tf.float32))
p['learning_rate'] = tf.placeholder(tf.float32)
with tf.control_dependencies(tf.get_collection(tf.GraphKeys.UPDATE_OPS)):
p['train'] = tf.train.AdamOptimizer(p['learning_rate'],
epsilon=1e-3).minimize(p['loss'])
p['weights_decay'] = tf.train.GradientDescentOptimizer(
p['learning_rate']).minimize(p['l2_loss'])
# Hyperparameters
num_batches = 2147483647
batch_size = 16
initial_learning_rate = 0.01
min_learning_rate = 0.00001
learning_rate_decay_limit = 0.0001
num_batches_per_epoch = len(dataset.train) / float(batch_size)
learning_decay = 10 * num_batches_per_epoch
weights_decay_after = 5 * num_batches_per_epoch
checkpoint_num = 0
learning_step = 0
min_loss = 1e308
accuracy_filename = os.path.join(cfg.checkpoint_dir, 'accuracies.txt')
if not os.path.isdir(cfg.checkpoint_dir):
os.mkdir(cfg.checkpoint_dir)
with open(accuracy_filename, 'w') as f:
f.write('')
with tf.Session() as session:
session.run(tf.global_variables_initializer())
if cfg.istraining:
voxnet.npz_saver.restore(session, cfg.voxnet_checkpoint_dir)
for batch_index in range(num_batches):
learning_rate = max(
min_learning_rate,
initial_learning_rate * 0.5**(learning_step / learning_decay))
learning_step += 1
if batch_index > weights_decay_after and batch_index % 256 == 0:
session.run(p['weights_decay'], feed_dict=feed_dict)
voxs, labels = dataset.train.get_batch(batch_size)
feed_dict = {
voxnet[0]: voxs,
p['labels']: labels,
p['learning_rate']: learning_rate,
voxnet.training: True,
p['data_value']: data_value
}
session.run(p['train'], feed_dict=feed_dict)
if batch_index and batch_index % 512 == 0:
print("{} batch: {}".format(datetime.datetime.now(),
batch_index))
print('learning rate: {}'.format(learning_rate))
feed_dict[voxnet.training] = False
loss = session.run(p['loss'], feed_dict=feed_dict)
print('loss: {}'.format(loss))
if (batch_index and loss > 1.5 * min_loss
and learning_rate > learning_rate_decay_limit):
min_loss = loss
learning_step *= 1.2
print("decreasing learning rate...")
min_loss = min(loss, min_loss)
if batch_index and batch_index % 128 == 0:
num_accuracy_batches = 30
total_accuracy = 0
for x in range(num_accuracy_batches):
voxs, labels = dataset.train.get_batch(batch_size)
feed_dict = {
voxnet[0]: voxs,
p['labels']: labels,
voxnet.training: False
}
total_accuracy += session.run(p['accuracy'],
feed_dict=feed_dict)
training_accuracy = total_accuracy / num_accuracy_batches
print('training accuracy: {}'.format(training_accuracy))
num_accuracy_batches = 90
total_evaluation = evaluation()
for x in range(num_accuracy_batches):
voxs, labels = dataset.test.get_batch(batch_size)
feed_dict = {
voxnet[0]: voxs,
p['labels']: labels,
voxnet.training: False
}
predictions, y_true = session.run(
[p['prediction'], p['y_true']], feed_dict=feed_dict)
total_evaluation += evaluation(y_true=y_true,
y_predict=predictions)
# print(y_true, predictions)
print(total_evaluation)
test_evaluation = total_evaluation / num_accuracy_batches
print('test accuracy \n' + str(test_evaluation))
with open(accuracy_filename, 'a') as f:
f.write(' '.join(
map(str, (checkpoint_num, training_accuracy,
test_evaluation))) + '\n')
if batch_index % 2048 == 0:
print('saving checkpoint {}...'.format(checkpoint_num))
filename = 'cx-{}.npz'.format(checkpoint_num)
filename = os.path.join(cfg.checkpoint_dir, filename)
voxnet.npz_saver.save(session, filename)
print('checkpoint saved!')
checkpoint_num += 1
def main(cross_epoch=0,
data_index=None,
brain_map=None,
cut_shape=None,
data_type=['MCIc', 'MCInc'],
pre_dir='/home/anzeng/rhb/fmri_data',
num_batches=512 * 5 + 1,
test_size=6):
tf.reset_default_graph()
if cut_shape == None:
brain_map = [212, 213, 214, 215, 216, 217, 218]
cut_shape = [100, 0, 100, 0, 100, 0]
mask = nib.load(
'/home/anzeng/rhb/fmri/fMRI-deeping-learning/BN_Atlas_246_3mm.nii')
mask = mask.get_fdata()
#获取截取的sMRI大小
for x in brain_map:
tmp = np.where(mask == x)
for i in range(3):
cut_shape[2 * i] = min(cut_shape[2 * i], np.min(tmp[i]))
cut_shape[2 * i + 1] = max(cut_shape[2 * i + 1],
np.max(tmp[i]))
print(cut_shape)
xyz = 32
dataset = fMRI_data(data_type,
data_index=data_index,
dir=pre_dir,
batch_mode='random',
varbass=cfg.varbass)
voxnet = VoxNet(input_shape=[None, xyz, xyz, xyz, 1], voxnet_type='cut')
#数据权值
data_value = [[1], [1]]
#创建数据
p = dict() # placeholders
p['labels'] = tf.placeholder(tf.float32, [None, 2])
p['data_value'] = tf.placeholder(tf.float32, [2, 1])
p['Weight'] = tf.matmul(p['labels'], p['data_value'])
p['cross_loss'] = tf.nn.softmax_cross_entropy_with_logits(
logits=voxnet[-2], labels=p['labels'])
p['Weight'] = tf.reshape(p['Weight'], [-1])
p['x_loss'] = tf.multiply(p['Weight'], p['cross_loss'])
p['loss'] = tf.reduce_mean(p['x_loss'])
p['l2_loss'] = tf.add_n([tf.nn.l2_loss(w) for w in voxnet.kernels])
p['loss'] = p['loss'] + 0.0001 * p['l2_loss']
p['prediction'] = tf.argmax(voxnet[-1], 1)
p['y_true'] = tf.argmax(p['labels'], 1)
p['correct_prediction'] = tf.equal(tf.argmax(voxnet[-1], 1),
tf.argmax(p['labels'], 1))
p['accuracy'] = tf.reduce_mean(tf.cast(p['correct_prediction'],
tf.float32))
p['learning_rate'] = tf.placeholder(tf.float32)
with tf.control_dependencies(tf.get_collection(tf.GraphKeys.UPDATE_OPS)):
p['train'] = tf.train.AdamOptimizer(p['learning_rate'],
epsilon=1e-3).minimize(p['loss'])
p['weights_decay'] = tf.train.GradientDescentOptimizer(
p['learning_rate']).minimize(p['l2_loss'])
# Hyperparameters
batch_size = 50
initial_learning_rate = 0.0001
min_learning_rate = 0.00001
learning_rate_decay_limit = 0.0001
num_batches_per_epoch = len(dataset.train) / batch_size
learning_decay = 10 * num_batches_per_epoch
weights_decay_after = 5 * num_batches_per_epoch
checkpoint_num = 0
learning_step = 0
min_loss = 1e308
wait = 0
paitence = 10
accuracy_filename = os.path.join(cfg.voxnet_checkpoint_dir,
'accuracies.txt')
if not os.path.isdir(cfg.voxnet_checkpoint_dir):
os.mkdir(cfg.voxnet_checkpoint_dir)
with open(accuracy_filename, 'a') as f:
f.write(str(brain_map) + '\n')
filename = ""
with tf.Session() as session:
session.run(tf.global_variables_initializer())
if cfg.istraining:
voxnet.npz_saver.restore(session, cfg.voxnet_checkpoint)
for batch_index in range(num_batches):
# learning_rate = max(min_learning_rate,
# initial_learning_rate * 0.8 ** (learning_step / learning_decay))
learning_rate = 0.0001
learning_step += 1
# if batch_index > weights_decay_after and batch_index % 256 == 0:
# session.run(p['weights_decay'], feed_dict=feed_dict)
voxs, labels = dataset.train.oversampling.get_smri_batch(
cut_shape, batch_size)
feed_dict = {
voxnet[0]: voxs,
p['labels']: labels,
voxnet.keep_prob: 0.3,
p['learning_rate']: learning_rate,
voxnet.training: True,
p['data_value']: data_value,
}
session.run(p['train'], feed_dict=feed_dict)
if batch_index and batch_index % 512 == 0:
print("{} batch: {}".format(datetime.datetime.now(),
batch_index))
print('learning rate: {}'.format(learning_rate))
feed_dict[voxnet.training] = False
loss = session.run(p['loss'], feed_dict=feed_dict)
print('loss: {}'.format(loss))
if (batch_index and loss > 1.5 * min_loss
and learning_rate > learning_rate_decay_limit):
min_loss = loss
learning_step *= 1.2
print("decreasing learning rate...")
min_loss = min(loss, min_loss)
if batch_index and batch_index % 128 == 0:
num_accuracy_batches = 30
# train_accuracy = 0
training_evaluation = evaluation()
for x in range(num_accuracy_batches):
voxs, labels = dataset.train.random_sampling.get_smri_batch(
cut_shape, batch_size)
feed_dict = {
voxnet[0]: voxs,
p['labels']: labels,
voxnet.training: False,
voxnet.keep_prob: 1.0
}
start_time = time.time()
predictions, y_true = session.run(
[p['prediction'], p['y_true']], feed_dict=feed_dict)
training_evaluation += evaluation(y_true=y_true,
y_predict=predictions)
end_time = time.time()
print('total time: %f' % ((end_time - start_time) / 60))
print(training_evaluation)
# training_accuracy = total_accuracy / num_accuracy_batgetches
print('training accuracy \n' + str(training_evaluation))
num_accuracy_batches = test_size
test_evaluation = evaluation()
for x in range(num_accuracy_batches):
voxs, labels = dataset.test.random_sampling.get_smri_batch(
cut_shape, batch_size)
feed_dict = {
voxnet[0]: voxs,
p['labels']: labels,
voxnet.training: False,
voxnet.keep_prob: 1.0
}
predictions, y_true = session.run(
[p['prediction'], p['y_true']], feed_dict=feed_dict)
test_evaluation += evaluation(y_true=y_true,
y_predict=predictions)
# print(y_true, predictions)
print(test_evaluation)
print('test accuracy \n' + str(test_evaluation))
with open(accuracy_filename, 'a') as f:
f.write(str(checkpoint_num) + ':\n')
f.write(str(training_evaluation) + '\n')
f.write(str(test_evaluation) + '\n')
if training_evaluation.ACC >= 0.95:
wait += 1
if wait >= paitence:
filename = 'cx-{}.npz'.format(cross_epoch)
filename = os.path.join(cfg.voxnet_checkpoint_dir,
filename)
voxnet.npz_saver.save(session, filename)
print('checkpoint saved!')
return filename
else:
wait = 0
# if batch_index % 1024 == 0 or training_evaluation.ACC >= 0.9:
# print('saving checkpoint {}...'.format(checkpoint_num))
# filename = 'cx-{}.npz'.format(checkpoint_num)
# filename = os.path.join(cfg.voxnet_checkpoint_dir,filename)
# voxnet.npz_saver.save(session, filename)
# print('checkpoint saved!')
# checkpoint_num += 1
# if training_evaluation.ACC >= 0.9:
# break
filename = 'cx-{}.npz'.format(cross_epoch)
filename = os.path.join(cfg.voxnet_checkpoint_dir, filename)
voxnet.npz_saver.save(session, filename)
print('checkpoint saved!')
return filename
def main(*argv):
data_value = [[1.0], [1.0]]
time_dim = 80 # 挑选时间片个数
batch_size = 8
brain_map = [219]
cut_shape = [100, 0, 100, 0, 100, 0]
mask = nib.load(
'/home/anzeng/rhb/fmri/fMRI-deeping-learning/BN_Atlas_246_3mm.nii')
mask = mask.get_fdata()
# 获取截取的sMRI大小
for x in brain_map:
tmp = np.where(mask == x)
for i in range(3):
cut_shape[2 * i] = min(cut_shape[2 * i], np.min(tmp[i]))
cut_shape[2 * i + 1] = max(cut_shape[2 * i + 1], np.max(tmp[i]))
print(cut_shape)
dataset = fMRI_data(['AD', 'NC'],
dir='/home/anzeng/rhb/fmri_data',
batch_mode='random',
varbass=cfg.varbass)
input_shape = [time_dim * batch_size]
for i in range(3):
input_shape.append(cut_shape[2 * i + 1] + 1 - cut_shape[2 * i])
input_shape.append(1)
print(input_shape)
# input_shape=[40,2,2,2,1]
voxnet = VoxNet(input_shape=input_shape, voxnet_type='cut')
FCN_input = tf.reshape(voxnet['gap'], (-1, time_dim, 128))
print(FCN_input)
FCNs = Classifier_FCN(FCN_input, nb_classes=2)
# 创建数据
p = dict() # placeholders
p['labels'] = tf.placeholder(tf.float32, [None, 2])
p['prediction'] = tf.argmax(FCNs[-1], 1)
p['y_true'] = tf.argmax(p['labels'], 1)
# p['test_error'] = tf.placeholder(tf.float32)
# 超参数设置
num_batches = 2147483647
initial_learning_rate = 0.01
min_learning_rate = 0.0001
learning_rate_decay_limit = 0.0001
num_batches_per_epoch = len(dataset.train) / float(batch_size)
learning_decay = 10 * num_batches_per_epoch
weights_decay_after = 5 * num_batches_per_epoch
checkpoint_num = 0
learning_step = 0
min_loss = 1e308
accuracy_filename = os.path.join(cfg.checkpoint_dir, 'accuracies.txt')
with tf.Session() as session:
session.run(tf.global_variables_initializer())
voxnet.npz_saver.restore(session, cfg.voxnet_checkpoint_dir)
FCNs.npz_saver.restore(session, cfg.fcn_checkpoint_dir)
# voxnet.npz_saver.restore(session, cfg.voxnet_checkpoint_dir)
#voxnet赋值
num_accuracy_batches = 90
total_evaluation = evaluation()
for x in range(num_accuracy_batches):
voxs, labels = dataset.train.random_sampling.get_fmri_brain(
cut_shape, batch_size, time_dim)
feed_dict = {
voxnet[0]: voxs,
p['labels']: labels,
FCNs.training: False,
voxnet.training: False
}
predictions, y_true = session.run([p['prediction'], p['y_true']],
feed_dict=feed_dict)
total_evaluation += evaluation(y_true=y_true,
y_predict=predictions)
print(total_evaluation)
print('train accuracy \n' + str(total_evaluation))
num_accuracy_batches = 15
total_evaluation = evaluation()
for x in range(num_accuracy_batches):
voxs, labels = dataset.test.random_sampling.get_fmri_brain(
cut_shape, batch_size, time_dim)
feed_dict = {
voxnet[0]: voxs,
p['labels']: labels,
FCNs.training: False,
voxnet.training: False
}
predictions, y_true = session.run([p['prediction'], p['y_true']],
feed_dict=feed_dict)
total_evaluation += evaluation(y_true=y_true,
y_predict=predictions)
print(total_evaluation)
print('test accuracy \n' + str(total_evaluation))
def train_GRUs(cross_epoch=0,
data_index=None,
cut_shape=None,
data_type=['MCIc', 'MCInc'],
pre_dir='/home/anzeng/rhb/fmri_data',
num_batches=256 * 5,
voxnet_point=None,
test_size=6,
brain_map=[217],
f_handle=None):
#清除keras后台数据
keras.backend.clear_session()
# #####超参##########
time_dim = 80
batch_size = 50
g1 = tf.Graph()
g2 = tf.Graph()
# keras.optimizers.Adam()
# #####################
# #加载模型#
xyz = 32
# input_shape = [xyz, xyz, xyz, 1]
# inputs = keras.layers.Input(input_shape)
# _3D_CNN = keras.models.load_model(voxnet_point)
auto = keras.models.load_model(voxnet_point)
# _3D_CNN.predict(np.zeros([1,32,32,32,1]),1)
# for i in _3D_CNN.layers:
# print(i.name)
layer_name = 'feature'
feature_generator = keras.Model(inputs=auto.layers[0].input,
outputs=auto.get_layer(layer_name).output)
# feature_generator = keras.Model(inputs=_3D_CNN.layers[0].input, outputs=_3D_CNN.get_layer(layer_name).output)
# sample = np.zeros([1, xyz, xyz, xyz, 1])
# y = feature_generator.predict_on_batch(sample)
# print(y)
dataset = fMRI_data(data_type,
data_index=data_index,
varbass=False,
dir=pre_dir,
model=feature_generator,
cut_shape=cut_shape)
grus = GRUs(input_shape=[time_dim, 100], nb_class=2)
# feature_generator = keras.Sequential()
# feature_generator.get_layer()
# voxnet = VoxNet(input_shape=input_shape, voxnet_type='cut')
# with tf.Session() as session:
# session.run(tf.global_variables_initializer())
# voxnet.npz_saver.restore(session, voxnet_point)
logs_path = os.path.join(cfg.fcn_checkpoint_dir,
'train_' + str(cross_epoch))
if os.path.isdir(logs_path):
shutil.rmtree(logs_path)
grus.fit_generator(
dataset.get_time_batch(cut_shape=cut_shape,
time_dim=time_dim,
batch_size=batch_size,
_batch_mode='oversampling',
_mode='train'),
steps_per_epoch=8,
epochs=num_batches,
validation_data=dataset.get_time_batch(cut_shape=cut_shape,
time_dim=time_dim,
batch_size=1,
_batch_mode='random',
_mode='test',
flag=1),
validation_steps=test_size,
callbacks=[
toolbox.EarlyStoppingByACC('acc', 0.90, patience=10),
keras.callbacks.TensorBoard(log_dir=logs_path)
])
# 预测
#构造循环迭代器，顺序不打乱的
train_iter = iter(
dataset.get_time_batch(cut_shape=cut_shape,
time_dim=time_dim,
batch_size=1,
_batch_mode='random',
_mode='train',
flag=1))
test_iter = iter(
dataset.get_time_batch(cut_shape=cut_shape,
time_dim=time_dim,
batch_size=1,
_batch_mode='random',
_mode='test',
flag=1))
# for i in range(num_batches / 16):
# fcn.fit_generator(dataset.train.oversampling.get_time_batch(session, voxnet, cut_shape, time_dim=time_dim,
# batch_size=batch_size), steps_per_epoch=8,
# epochs=num_batches)
test_evaluation = evaluation.evaluation()
print('test evaluation:')
for i in range(test_size):
vosx, onehot = test_iter.__next__()
prediction = grus.predict_on_batch(vosx)
test_evaluation += evaluation.evaluation(y_true=np.argmax(onehot,
axis=1),
y_predict=np.argmax(
prediction, axis=1))
print(test_evaluation)
train_len = 0
for i in data_type:
train_len += len(data_index[i]['train'])
# train_evaluation = evaluation.evaluation()
# for i in range(train_len):
# vosx, onehot = train_iter.__next__()
# prediction = grus.predict_on_batch(vosx)
# train_evaluation += evaluation.evaluation(y_true=np.argmax(onehot, axis=1),
# y_predict=np.argmax(prediction, axis=1))
# print(train_evaluation)
# 利用svm作为最后的分类器
# print('svm evaluation:')
# # 构造数据集
# #BGRU特征提取模型
# BGRU_feature = keras.Model(inputs=grus.get_layer('BGRU_input').input,outputs=grus.get_layer('fc_1').output)
# train_data = -1
# train_label = -1
# for i in range(train_len):
# vosx,onehot = train_iter.__next__()
# feature = BGRU_feature.predict_on_batch(vosx)
# y_true = np.argmax(onehot,axis=1)
# if isinstance(train_data,int):
# train_data = feature
# train_label = y_true
# else:
# train_data = np.vstack((train_data,feature))
# train_label = np.hstack((train_label,y_true))
# clf = svm.SVC(C=1.0,kernel='rbf',gamma='auto')
# clf.fit(train_data,train_label)
# predict = clf.predict(train_data)
# svm_train = evaluation.evaluation(y_true=train_label,y_predict=predict)
# print('svm_train:')
# print(svm_train)
#
# test_data = -1
# test_label = -1
# for i in range(test_size):
# vosx,onehot = test_iter.__next__()
# feature = BGRU_feature.predict_on_batch(vosx)
# y_true = np.argmax(onehot,axis=1)
# if isinstance(test_data,int):
# test_data = feature
# test_label = y_true
# else:
# test_data = np.vstack((test_data,feature))
# test_label = np.hstack((test_label,y_true))
# predict = clf.predict(test_data)
# svm_test = evaluation.evaluation(y_true=test_label, y_predict=predict)
# print('svm_test:')
# print(svm_test)
if f_handle:
# f_handle.write('svm_train:\n')
# f_handle.write(str(svm_train)+'\n')
# f_handle.write('svm_test:\n')
# f_handle.write(str(svm_test)+'\n')
# f_handle.write('train_evaluation\n')
# f_handle.write(str(train_evaluation) + '\n')
f_handle.write('test_evaluation\n')
f_handle.write(str(test_evaluation) + '\n')
if not os.path.exists(cfg.fcn_checkpoint_dir):
os.makedirs(cfg.fcn_checkpoint_dir)
filepath = os.path.join(cfg.fcn_checkpoint_dir,
'train_' + str(cross_epoch) + '.h5')
grus.save(filepath=filepath)
return test_evaluation, evaluation.evaluation()
def train_fcn(cross_epoch=0,
data_index=None,
cut_shape=None,
data_type=['MCIc', 'MCInc'],
pre_dir='/home/anzeng/rhb/fmri_data',
num_batches=256 * 5,
voxnet_point=None,
test_size=6,
brain_map=[217]):
tf.reset_default_graph()
#####超参##########
time_dim = 20
batch_size = 8
#####################
dataset = fMRI_data(data_type,
data_index=data_index,
varbass=False,
dir=pre_dir)
fcn = FCNs()
input_shape = [None, 32, 32, 32, 1]
voxnet = VoxNet(input_shape=input_shape, voxnet_type='cut')
with tf.Session() as session:
session.run(tf.global_variables_initializer())
voxnet.npz_saver.restore(session, voxnet_point)
fcn.fit_generator(
dataset.get_time_batch(session,
voxnet,
cut_shape,
time_dim=time_dim,
batch_size=batch_size,
_batch_mode='oversampling',
_mode='train'),
steps_per_epoch=8,
epochs=num_batches,
validation_data=dataset.test.random_sampling.get_time_batch(
session,
voxnet,
cut_shape,
time_dim=time_dim,
batch_size=1,
_batch_mode='random',
_mode='test'),
validation_steps=test_size,
callbacks=[toolbox.EarlyStoppingByACC('loss', 0.3, patience=10)])
#预测
data_iter = iter(
dataset.test.random_sampling.get_time_batch(session,
voxnet,
cut_shape,
time_dim=time_dim,
batch_size=1))
# for i in range(num_batches / 16):
# fcn.fit_generator(dataset.train.oversampling.get_time_batch(session, voxnet, cut_shape, time_dim=time_dim,
# batch_size=batch_size), steps_per_epoch=8,
# epochs=num_batches)
test_evaluation = evaluation.evaluation()
for i in range(test_size):
vosx, onehot = data_iter.__next__()
prediction = fcn.predict_on_batch(vosx)
test_evaluation += evaluation.evaluation(y_true=np.argmax(onehot,
axis=1),
y_predict=np.argmax(
prediction, axis=1))
print(test_evaluation)
filepath = os.path.join(cfg.fcn_checkpoint_dir,
'train_' + str(cross_epoch) + '.h5')
fcn.save(filepath)
return test_evaluation