def normal_evaluate(self, dataset='valid', train_step=None):
num_batch = self.num_test_batch if dataset == 'test' else self.num_val_batch
self.sess.run(tf.local_variables_initializer())
hist = np.zeros((self.conf.num_cls, self.conf.num_cls))
plot_inputs = np.zeros((0, self.conf.height, self.conf.width, self.conf.channel))
plot_mask = np.zeros((0, self.conf.height, self.conf.width))
plot_mask_pred = np.zeros((0, self.conf.height, self.conf.width))
for step in range(num_batch):
start = self.conf.val_batch_size * step
end = self.conf.val_batch_size * (step + 1)
data_x, data_y = self.data_reader.next_batch(start=start, end=end, mode=dataset)
feed_dict = {self.inputs_pl: data_x,
self.labels_pl: data_y,
self.is_training_pl: True,
self.with_dropout_pl: False,
self.keep_prob_pl: 1}
self.sess.run([self.mean_loss_op, self.mean_accuracy_op], feed_dict=feed_dict)
mask_pred = self.sess.run(self.y_pred, feed_dict=feed_dict)
hist += get_hist(mask_pred.flatten(), data_y.flatten(), num_cls=self.conf.num_cls)
if plot_inputs.shape[0] < 100: # randomly select a few slices to plot and save
# idx = np.random.randint(self.conf.batch_size)
plot_inputs = np.concatenate((plot_inputs, data_x.reshape(-1, self.conf.height, self.conf.width,
self.conf.channel)), axis=0)
plot_mask = np.concatenate((plot_mask, data_y.reshape(-1, self.conf.height, self.conf.width)),
axis=0)
plot_mask_pred = np.concatenate(
(plot_mask_pred, mask_pred.reshape(-1, self.conf.height, self.conf.width)), axis=0)
IOU, ACC = compute_iou(hist)
mean_IOU = np.mean(IOU)
loss, acc = self.sess.run([self.mean_loss, self.mean_accuracy])
if dataset == "valid": # save the summaries and improved model in validation mode
summary_valid = self.sess.run(self.merged_summary, feed_dict=feed_dict)
self.save_summary(summary_valid, train_step, is_train=False)
if loss < self.best_validation_loss:
self.best_validation_loss = loss
if mean_IOU > self.best_mean_IOU:
self.best_mean_IOU = mean_IOU
print('>>>>>>>> Both model validation loss and mean IOU improved; saving the model......')
else:
print('>>>>>>>> model validation loss improved; saving the model......')
self.save(train_step)
elif mean_IOU > self.best_mean_IOU:
self.best_mean_IOU = mean_IOU
print('>>>>>>>> model mean IOU improved; saving the model......')
self.save(train_step)
print('****** IoU & ACC ******')
print('Mean IoU = {0:.01%}, valid_loss = {1:.4f}'.format(mean_IOU, loss))
for ii in range(self.conf.num_cls):
print(' - {0:<15}: IoU={1:<5.01%}, ACC={2:<5.01%}'.format(self.conf.label_name[ii], IOU[ii], ACC[ii]))
print('-' * 20)
self.visualize(plot_inputs, plot_mask, plot_mask_pred, train_step=train_step, mode='valid')
def normal_evaluate(self, dataset='valid', train_step=None):
num_batch = self.num_test_batch if dataset == 'test' else self.num_val_batch
self.sess.run(tf.local_variables_initializer())
hist = np.zeros((self.conf.num_cls, self.conf.num_cls))
scan_num = 0
for image_index in range(num_batch):
data_x, data_y = self.data_reader.next_batch(num=scan_num, mode=dataset)
depth = data_x.shape[0] * data_x.shape[-2]
scan_input = np.zeros((self.conf.height, self.conf.width, depth, self.conf.channel))
scan_mask = np.zeros((self.conf.height, self.conf.width, depth))
scan_mask_pred = np.zeros((self.conf.height, self.conf.width, depth))
for slice_num in range(data_x.shape[0]): # for each slice of the 3D image
feed_dict = {self.inputs_pl: np.expand_dims(data_x[slice_num], 0),
self.labels_pl: np.expand_dims(data_y[slice_num], 0),
self.is_training_pl: True,
self.with_dropout_pl: False,
self.keep_prob_pl: 1}
self.sess.run([self.mean_loss_op, self.mean_accuracy_op], feed_dict=feed_dict)
inputs, mask, mask_pred = self.sess.run([self.inputs_pl,
self.labels_pl,
self.y_pred], feed_dict=feed_dict)
hist += get_hist(mask_pred.flatten(), mask.flatten(), num_cls=self.conf.num_cls)
idx_d, idx_u = slice_num * self.conf.Dcut_size, (slice_num + 1) * self.conf.Dcut_size
scan_input[:, :, idx_d:idx_u] = np.squeeze(inputs, axis=0)
scan_mask[:, :, idx_d:idx_u] = np.squeeze(mask, axis=0)
scan_mask_pred[:, :, idx_d:idx_u] = np.squeeze(mask_pred, axis=0)
self.visualize_me(np.squeeze(scan_input), scan_mask, scan_mask_pred, train_step=train_step,
img_idx=image_index, mode='valid')
scan_num += 1
IOU, ACC = compute_iou(hist)
mean_IOU = np.mean(IOU)
loss, acc = self.sess.run([self.mean_loss, self.mean_accuracy])
if dataset == "valid": # save the summaries and improved model in validation mode
summary_valid = self.sess.run(self.merged_summary, feed_dict=feed_dict)
self.save_summary(summary_valid, train_step, is_train=False)
if loss < self.best_validation_loss:
self.best_validation_loss = loss
print('>>>>>>>> model validation loss improved; saving the model......')
self.save(train_step)
print('After {0} training step: val_loss= {1:.4f}, val_acc={2:.01%}'.format(train_step, loss, acc))
print('- IOU: bg={0:.01%}, liver={1:.01%}, spleen={2:.01%}, '
'kidney={3:.01%}, bone={4:.01%}, vessel={5:.01%}, mean_IoU={6:.01%}'
.format(IOU[0], IOU[1], IOU[2], IOU[3], IOU[4], IOU[5], mean_IOU))
print('- ACC: bg={0:.01%}, liver={1:.01%}, spleen={2:.01%}, '
'kidney={3:.01%}, bone={4:.01%}, vessel={5:.01%}'
.format(ACC[0], ACC[1], ACC[2], ACC[3], ACC[4], ACC[5]))
print('-' * 60)
def MC_evaluate(self, dataset='valid', train_step=None):
num_batch = self.num_test_batch if dataset == 'test' else self.num_val_batch
hist = np.zeros((self.conf.num_cls, self.conf.num_cls))
self.sess.run(tf.local_variables_initializer())
all_inputs = np.zeros(
(0, self.conf.height, self.conf.width, self.conf.channel))
all_mask = np.zeros((0, self.conf.height, self.conf.width))
all_pred = np.zeros((0, self.conf.height, self.conf.width))
all_var = np.zeros((0, self.conf.height, self.conf.width))
cls_uncertainty = np.zeros(
(0, self.conf.height, self.conf.width, self.conf.num_cls))
for step in tqdm(range(num_batch)):
start = self.conf.val_batch_size * step
end = self.conf.val_batch_size * (step + 1)
data_x, data_y = self.data_reader.next_batch(start=start,
end=end,
mode=dataset)
mask_pred_mc = [
np.zeros((self.conf.val_batch_size, self.conf.height,
self.conf.width))
for _ in range(self.conf.monte_carlo_simulations)
]
mask_prob_mc = [
np.zeros((self.conf.val_batch_size, self.conf.height,
self.conf.width, self.conf.num_cls))
for _ in range(self.conf.monte_carlo_simulations)
]
feed_dict = {
self.inputs_pl: data_x,
self.labels_pl: data_y,
self.is_training_pl: True,
self.with_dropout_pl: True,
self.keep_prob_pl: self.conf.keep_prob
}
for mc_iter in range(self.conf.monte_carlo_simulations):
inputs, mask, mask_prob, mask_pred = self.sess.run(
[self.inputs_pl, self.labels_pl, self.y_prob, self.y_pred],
feed_dict=feed_dict)
mask_prob_mc[mc_iter] = mask_prob
mask_pred_mc[mc_iter] = mask_pred
prob_mean = np.nanmean(mask_prob_mc, axis=0)
prob_variance = np.var(mask_prob_mc, axis=0)
pred = np.argmax(prob_mean, axis=-1)
var_one = np.nanmean(prob_variance, axis=-1)
# var_one = var_calculate_2d(pred, prob_variance)
hist += get_hist(pred.flatten(),
mask.flatten(),
num_cls=self.conf.num_cls)
# if all_inputs.shape[0] < 6:
# ii = np.random.randint(self.conf.val_batch_size)
# ii = 1
all_inputs = np.concatenate(
(all_inputs,
inputs.reshape(-1, self.conf.height, self.conf.width,
self.conf.channel)),
axis=0)
all_mask = np.concatenate(
(all_mask, mask.reshape(-1, self.conf.height,
self.conf.width)),
axis=0)
all_pred = np.concatenate(
(all_pred, pred.reshape(-1, self.conf.height,
self.conf.width)),
axis=0)
all_var = np.concatenate(
(all_var, var_one.reshape(-1, self.conf.height,
self.conf.width)),
axis=0)
cls_uncertainty = np.concatenate(
(cls_uncertainty,
prob_variance.reshape(-1, self.conf.height, self.conf.width,
self.conf.num_cls)),
axis=0)
# else:
self.visualize(all_inputs,
all_mask,
all_pred,
all_var,
cls_uncertainty,
train_step=train_step)
import h5py
h5f = h5py.File(self.conf.run_name + '_bayes.h5', 'w')
h5f.create_dataset('x', data=all_inputs)
h5f.create_dataset('y', data=all_mask)
h5f.create_dataset('y_pred', data=all_pred)
h5f.create_dataset('y_var', data=all_var)
h5f.create_dataset('cls_uncertainty', data=cls_uncertainty)
h5f.close()
uncertainty_measure = get_uncertainty_measure(all_inputs, all_mask,
all_pred, all_var)
# break
IOU, ACC = compute_iou(hist)
mean_IOU = np.mean(IOU)
print('****** IoU & ACC ******')
print('Uncertainty Quality Measure = {}'.format(uncertainty_measure))
print('Mean IoU = {0:.01%}'.format(mean_IOU))
for ii in range(self.conf.num_cls):
print(' - {0} class: IoU={1:.01%}, ACC={2:.01%}'.format(
self.conf.label_name[ii], IOU[ii], ACC[ii]))
print('-' * 20)
def normal_evaluate(self, train_step=None):
hist = np.zeros((self.conf.num_cls, self.conf.num_cls))
plot_inputs = np.zeros(
(0, self.conf.height, self.conf.width, self.conf.channel))
plot_mask = np.zeros((0, self.conf.height, self.conf.width))
plot_mask_pred = np.zeros((0, self.conf.height, self.conf.width))
if self.conf.mode == 'train':
self.sess.run(self.valid_iterator.initializer)
self.handle_ = self.sess.run(self.valid_iterator.string_handle())
elif self.conf.mode == 'test':
self.sess.run(self.test_iterator.initializer)
self.handle_ = self.sess.run(self.test_iterator.string_handle())
while True:
try:
feed_dict = {
self.is_training_pl: True,
self.with_dropout_pl: False,
self.keep_prob_pl: 1,
self.handle: self.handle_
}
_, _, mask_pred, data_x, data_y, summary_valid = self.sess.run(
[
self.mean_loss_op, self.mean_accuracy_op, self.y_pred,
self.inputs_pl, self.labels_pl, self.merged_summary
],
feed_dict=feed_dict)
hist += get_hist(mask_pred.flatten(),
data_y.flatten(),
num_cls=self.conf.num_cls)
if plot_inputs.shape[
0] < 100: # randomly select a few slices to plot
# idx = np.random.randint(self.conf.batch_size)
plot_inputs = np.concatenate(
(plot_inputs,
data_x.reshape(-1, self.conf.height, self.conf.width,
self.conf.channel)),
axis=0)
plot_mask = np.concatenate(
(plot_mask,
data_y.reshape(-1, self.conf.height,
self.conf.width)),
axis=0)
plot_mask_pred = np.concatenate(
(plot_mask_pred,
mask_pred.reshape(-1, self.conf.height,
self.conf.width)),
axis=0)
except tf.errors.OutOfRangeError:
# assert len(validation_predictions) == VALIDATION_SIZE
IOU, ACC = compute_iou(hist)
mean_IOU = np.mean(IOU)
loss, acc = self.sess.run([self.mean_loss, self.mean_accuracy])
if self.conf.mode == "train": # save the summaries and improved model in validation mode
# summary_valid = self.sess.run(self.merged_summary, feed_dict=feed_dict)
self.save_summary(summary_valid,
train_step,
is_train=False)
if loss < self.best_validation_loss:
self.best_validation_loss = loss
print(
'>>>>>>>> model validation loss improved; saving the model......'
)
self.save(train_step)
elif mean_IOU > self.best_mean_IOU:
self.best_mean_IOU = mean_IOU
print(
'>>>>>>>> model mean IOU improved; saving the model......'
)
self.save(train_step)
print('****** IoU & ACC ******')
print('Mean IoU = {0:.01%}'.format(mean_IOU))
for ii in range(self.conf.num_cls):
print(' - {0:<15}: IoU={1:<5.01%}, ACC={2:<5.01%}'.
format(self.conf.label_name[ii], IOU[ii], ACC[ii]))
print('-' * 20)
self.visualize(plot_inputs,
plot_mask,
plot_mask_pred,
train_step=train_step)
break
def normal_evaluate(self, dataset='valid', train_step=None):
valiter = CityscapesDataset(which_set='val',
batch_size=self.conf.val_batch_size,
seq_per_subset=0,
seq_length=0,
return_one_hot=False,
return_01c=True,
use_threads=True,
return_list=True,
nthreads=8,
infinite_iterator=False)
num_batch = self.num_test_batch if dataset == 'test' else 500
self.sess.run(tf.local_variables_initializer())
hist = np.zeros((self.conf.num_cls, self.conf.num_cls))
plot_inputs = np.zeros(
(0, self.conf.height, self.conf.width, self.conf.channel))
plot_mask = np.zeros((0, self.conf.height, self.conf.width))
plot_mask_pred = np.zeros((0, self.conf.height, self.conf.width))
for step in range(num_batch):
valid_data = valiter.__next__()
feed_dict = {
self.inputs_pl: valid_data[0],
self.labels_pl: valid_data[1],
self.is_training_pl: True,
self.with_dropout_pl: False,
self.keep_prob_pl: 1
}
self.sess.run([self.mean_loss_op, self.mean_accuracy_op],
feed_dict=feed_dict)
mask_pred = self.sess.run(self.y_pred, feed_dict=feed_dict)
hist += get_hist(mask_pred.flatten(),
valid_data[1].flatten(),
num_cls=self.conf.num_cls)
if plot_inputs.shape[
0] < 20: # randomly select a few slices to plot and save
# idx = np.random.randint(self.conf.batch_size)
plot_inputs = np.concatenate(
(plot_inputs, valid_data[0].reshape(
-1, self.conf.height, self.conf.width,
self.conf.channel)),
axis=0)
plot_mask = np.concatenate((plot_mask, valid_data[1].reshape(
-1, self.conf.height, self.conf.width)),
axis=0)
plot_mask_pred = np.concatenate(
(plot_mask_pred,
mask_pred.reshape(-1, self.conf.height, self.conf.width)),
axis=0)
# self.visualize(plot_inputs, plot_mask, plot_mask_pred, train_step=train_step, mode='valid')
IOU, ACC = compute_iou(hist)
mean_IOU = np.mean(IOU)
loss, acc = self.sess.run([self.mean_loss, self.mean_accuracy])
if dataset == "valid": # save the summaries and improved model in validation mode
summary_valid = self.sess.run(self.merged_summary,
feed_dict=feed_dict)
self.save_summary(summary_valid, train_step, is_train=False)
if loss < self.best_validation_loss:
self.best_validation_loss = loss
if mean_IOU > self.best_mean_IOU:
self.best_mean_IOU = mean_IOU
print(
'>>>>>>>> Both model validation loss and mean IOU improved; saving the model......'
)
else:
print(
'>>>>>>>> model validation loss improved; saving the model......'
)
self.save(train_step)
elif mean_IOU > self.best_mean_IOU:
self.best_mean_IOU = mean_IOU
print(
'>>>>>>>> model mean IOU improved; saving the model......')
self.save(train_step)
print('****** IoU & ACC ******')
print('Mean IoU = {0:.01%}, valid_loss = {1:.4f}'.format(
mean_IOU, loss))
for ii in range(self.conf.num_cls):
print(' - {0:<15}: IoU={1:<5.01%}, ACC={2:<5.01%}'.format(
self.conf.label_name[ii], IOU[ii], ACC[ii]))
print('-' * 20)
self.visualize(plot_inputs,
plot_mask,
plot_mask_pred,
train_step=train_step,
mode='valid')
def MC_evaluate(self, dataset='valid', train_step=None):
num_batch = self.num_test_batch if dataset == 'test' else self.num_val_batch
hist = np.zeros((self.conf.num_cls, self.conf.num_cls))
self.sess.run(tf.local_variables_initializer())
all_inputs = np.zeros(
(0, self.conf.height, self.conf.width, self.conf.channel))
all_mask = np.zeros((0, self.conf.height, self.conf.width))
all_pred = np.zeros((0, self.conf.height, self.conf.width))
all_var = np.zeros((0, self.conf.height, self.conf.width))
cls_uncertainty = np.zeros(
(0, self.conf.height, self.conf.width, self.conf.num_cls))
mask_prob_mc_list = []
mask_prob_mean_list = []
for step in tqdm(range(num_batch)):
start = self.conf.val_batch_size * step
end = self.conf.val_batch_size * (step + 1)
data_x, data_y = self.data_reader.next_batch(start=start,
end=end,
mode=dataset)
# mask_pred_mc = [np.zeros((self.conf.val_batch_size, self.conf.height, self.conf.width))
# for _ in range(self.conf.monte_carlo_simulations)]
mask_prob_mc = [
np.zeros((self.conf.val_batch_size, self.conf.height,
self.conf.width, self.conf.num_cls))
for _ in range(self.conf.monte_carlo_simulations)
]
feed_dict = {
self.inputs_pl: data_x,
self.labels_pl: data_y,
self.is_training_pl: True,
self.with_dropout_pl: True,
self.keep_prob_pl: self.conf.keep_prob
}
for mc_iter in range(self.conf.monte_carlo_simulations):
inputs, mask, mask_prob = self.sess.run(
[self.inputs_pl, self.labels_pl, self.y_prob],
feed_dict=feed_dict)
mask_prob_mc[mc_iter] = mask_prob
# mask_pred_mc[mc_iter] = mask_pred
mask_prob_mc_list.append(mask_prob_mc)
prob_mean = np.nanmean(mask_prob_mc, axis=0)
prob_variance = np.var(mask_prob_mc, axis=0)
pred = np.argmax(prob_mean, axis=-1)
# var_one = np.nanmean(prob_variance, axis=-1)
# var_one = var_calculate_2d(pred, prob_variance)
# var_one = predictive_entropy(prob_mean)
var_one = mutual_info(prob_mean, mask_prob_mc)
mask_prob_mean_list.append([pred, var_one])
hist += get_hist(pred.flatten(),
mask.flatten(),
num_cls=self.conf.num_cls)
if all_inputs.shape[0] < 1000:
all_inputs = np.concatenate(
(all_inputs,
inputs.reshape(-1, self.conf.height, self.conf.width,
self.conf.channel)),
axis=0)
all_mask = np.concatenate(
(all_mask,
mask.reshape(-1, self.conf.height, self.conf.width)),
axis=0)
all_pred = np.concatenate(
(all_pred,
pred.reshape(-1, self.conf.height, self.conf.width)),
axis=0)
all_var = np.concatenate(
(all_var,
var_one.reshape(-1, self.conf.height, self.conf.width)),
axis=0)
cls_uncertainty = np.concatenate(
(cls_uncertainty,
prob_variance.reshape(-1, self.conf.height,
self.conf.width,
self.conf.num_cls)),
axis=0)
# savePickle("dropconnect_pred_1.pkl", mask_prob_mc_list[:25])
# savePickle("dropconnect_pred_mean_1.pkl", mask_prob_mean_list[:25])
# savePickle("dropconnect_pred_2.pkl", mask_prob_mc_list[25:])
# savePickle("dropconnect_pred_mean_2.pkl", mask_prob_mean_list[25:])
self.visualize(all_inputs,
all_mask,
all_pred,
all_var,
cls_uncertainty,
train_step=train_step,
mode='test')
IOU, ACC = compute_iou(hist)
mean_IOU = np.mean(IOU)
print('****** IoU & ACC ******')
print('Mean IoU = {0:.01%}'.format(mean_IOU))
for ii in range(self.conf.num_cls):
print(' - {0} class: IoU={1:.01%}, ACC={2:.01%}'.format(
self.conf.label_name[ii], IOU[ii], ACC[ii]))
print('-' * 20)
import h5py
import numpy as np
from utils.eval_utils import get_hist
run_name = 'dropconnect_MI_uncertainty'
num_cls = 6
def compute_metrics(hist):
intersection = np.diag(hist)
ground_truth_set = hist.sum(axis=1)
predicted_set = hist.sum(axis=0)
union = ground_truth_set + predicted_set - intersection
mIoU = np.mean(intersection / union.astype(np.float32))
p_acc = np.sum(np.diag(hist)) / np.sum(hist)
m_acc = (1 / hist.shape[0]) * np.sum(np.diag(hist) / np.sum(hist, axis=1))
return mIoU, p_acc, m_acc
h5f = h5py.File(run_name + '.h5', 'r')
y = h5f['y'][:]
y_pred = h5f['y_pred'][:]
h5f.close()
hist = get_hist(y_pred.astype(int), y.astype(int), num_cls)
mean_iou, pixel_acc, mean_acc = compute_metrics(hist)
print()