def random_walk_epoch(hdf_file, beta, threshold, random_walk=True):
if not 'postprocessed' in hdf_file:
logging.warning('Attempted to random walk for data file which '
'does not have postprocessed predictions from '
'previous epoch')
else:
#reopen data file in read mode
data_fpath = hdf_file.filename
hdf_file.close()
hdf_file = h5py.File(data_fpath, 'r+')
#get images from base data file
base_data_file = h5py.File(
os.path.join(os.path.dirname(hdf_file.filename), 'base_data.hdf5'),
'r')
images = np.array(base_data_file['images_train'])
base_data_file.close()
#get scribble data as output of previous epoch
seeds = hdf_file['postprocessed']
random_walked = hdf_file['random_walked']
#get checkpoint metadata
processed = random_walked.attrs.get('processed')
processed_to = random_walked.attrs.get('processed_to')
recursion = utils.get_recursion_from_hdf5(hdf_file)
if not processed:
#process in batches of 20
#doesn't really make a time difference
logging.info("Random walking for recursion {}".format(recursion))
batch_size = 20
for scr_idx in range(processed_to, len(seeds), batch_size):
if random_walk:
logging.info(
'Random walking range {} to {} of recursion {}'.format(
scr_idx, scr_idx + batch_size - 1, recursion))
random_walked[scr_idx:scr_idx + batch_size, ...] = segment(
images[scr_idx:scr_idx + batch_size, ...],
seeds[scr_idx:scr_idx + batch_size, ...],
beta=beta,
threshold=threshold)
else:
random_walked[scr_idx:scr_idx + batch_size,
...] = seeds[scr_idx:scr_idx + batch_size,
...]
random_walked.attrs.modify('processed_to',
scr_idx + batch_size)
random_walked.attrs.modify('processed', True)
#reopen in read mode
hdf_file.close()
hdf_file = h5py.File(data_fpath, 'r')
return hdf_file
def postprocess_gt(data, images_train, scribbles_train=None):
'''
Postprocesses predictions of CNN to create ground truths for recursion
:param data: Data of this recursion - e.g. if given data file for recursion n,
It will set up ground truths to be random walked for recursion n
:param images_train: Numpy array of training images
:param scribbles_train: Numpy array of weakly annotated images
:return: data file with postprocessed ground truths
'''
#reopen in write mode
data_fpath = data.filename
data.close()
data = h5py.File(data_fpath)
#get recursions and previous progress
recursion = utils.get_recursion_from_hdf5(data)
predictions = np.array(data['predicted'])
postprocessed = data['postprocessed']
done = postprocessed.attrs.get('processed')
if not done:
processed_to = data['postprocessed'].attrs.get('processed_to')
scr_max = len(images_train)
#LOGGING: Print the postprocessing options
if exp_config.postprocessing:
logging.info("Postprocessing options chosen:")
if exp_config.reinit:
logging.info(
"\treinit = True\n\t\t\t\t\t"
"Reinitialising network weights on each recursion")
if exp_config.keep_largest_cluster:
logging.info(
"\tkeep_largest_blob = True\n\t\t\t\t\t"
"Keeping only largest cluster from ground truth prediction"
)
if exp_config.cnn_threshold:
logging.info("\tcnn_threshold = {0}\n\t\t\t\t\t"
"Segmentation predictions of CNN with probability"
" of less than {0} are left unlabelled".format(
exp_config.cnn_threshold))
if exp_config.rw_intersection:
logging.info("\trw_intersection = True\n\t\t\t\t\t"
"Random walker segmentation used as "
"upper bound")
if exp_config.rw_reversion:
logging.info(
"\trw_reversion = True\n\t\t\t\t\tIf after post processing the"
" network has predicted less than the original ground truth, "
"it will revert to the original ground truth to prevent "
"propagation of bad predictions")
if exp_config.smooth_edges:
logging.info(
"\t smooth_edges with sigma = {} and threshold = {}\n\t\t\t\t\t"
"Will use a gaussian filter to smooth edges of the segmentation"
)
else:
logging.info("No postprocessing options enabled")
for scr_idx in range(processed_to, scr_max, exp_config.batch_size):
# get indices to process
if scr_idx + exp_config.batch_size > scr_max:
ind = list(range(scr_max - exp_config.batch_size, scr_max))
else:
ind = list(range(scr_idx, scr_idx + exp_config.batch_size))
logging.info(
'Postprocessing groundtruth of recursion {0} for images {1} to {2} '
.format(recursion, ind[0], ind[-1]))
mask_out = postprocess(np.array(predictions[ind, ...]),
images_train[ind, ...],
scribbles_train[ind, ...])
#save to dataset
postprocessed[ind, ...] = np.squeeze(mask_out)
data['postprocessed'].attrs.modify('processed_to',
scr_idx + exp_config.batch_size)
data['postprocessed'].attrs.modify('processed', True)
logging.info(
'Finished postprocessing ground truths for recursion {}'.format(
recursion))
#reopen in read only mode
data.close()
data = h5py.File(data_fpath, 'r')
return data
def load_different_recursion(data, step):
recursion = utils.get_recursion_from_hdf5(data) + step
return h5py.File(recursion_filepath(recursion, data_file=data))
def predict_next_gt(data, images_train, images_placeholder,
training_time_placeholder, keep_prob, logits, sess):
'''
Uses current network weights to segment images for next recursion
After postprocessing, these are used as the ground truth for further training
:param data: Data of the current recursion - if this is of recursion n, this function
predicts ground truths for recursion n + 1
:param images_train: Numpy array of training images
:param images_placeholder: Tensorflow placeholder for image feed
:param training_time_placeholder: Boolean tensorflow placeholder
:param logits: Logits operator for calculating segmentation mask probabilites
:param sess: Tensorflow session
:return: The data file for recursion n + 1
'''
#get recursion from filename
recursion = utils.get_recursion_from_hdf5(data)
new_recursion_fname = acdc_data.recursion_filepath(recursion + 1,
data_file=data)
if not os.path.exists(new_recursion_fname):
fpath = os.path.dirname(data.filename)
data.close()
data = acdc_data.create_recursion_dataset(fpath, recursion + 1)
else:
data.close()
data = h5py.File(new_recursion_fname, 'r+')
#attributes to track processing
prediction = data['predicted']
prediction_pre_cor = data['predicted_pre_cor']
p_vals = data['p_vals']
processed = data['predicted'].attrs.get('processed')
if not processed:
processed_to = data['predicted'].attrs.get('processed_to')
scr_max = len(images_train)
print("SCR max = " + str(scr_max))
for scr_idx in range(processed_to, scr_max, exp_config.batch_size):
if scr_idx + exp_config.batch_size > scr_max:
print("Entered last")
# At the end of the dataset
# Must ensure feed_dict is 20 images long however
ind = list(range(scr_max - exp_config.batch_size, scr_max))
else:
ind = list(range(scr_idx, scr_idx + exp_config.batch_size))
x = np.expand_dims(np.array(images_train[ind, ...]), -1)
feed_dict = {
images_placeholder: x,
training_time_placeholder: False,
keep_prob: 0.5
}
temp = np.zeros((50, exp_config.batch_size, 212, 212, 5))
ps = np.zeros((exp_config.batch_size, 212, 212))
for k in range(50):
temp[k, :, :, :, :] = sess.run(logits, feed_dict=feed_dict)
temp_mean = np.squeeze(np.mean(temp, axis=0))
conf = 0.05
mask = tf.arg_max(temp_mean, dimension=-1)
mask_out = sess.run(mask, feed_dict=feed_dict)
pre_cor_mask = np.copy(mask_out)
for t in range(exp_config.batch_size):
for m in range(212):
for n in range(212):
estim = mask_out[t, m, n]
temp_mean[t, m, n, estim] = -1000000
best_ind = np.argmax(
np.squeeze(np.copy(temp_mean[t, m, n, :])))
# [st,p] = ttest_ind(np.squeeze(temp[:,t,m,n,estim]),np.squeeze(temp[:,t,m,n,best_ind]),equal_var=False)
# ps[t,m,n] = p
# if p > conf:
# mask_out[t,m,n] = 0
# for k in range(5):
# locs = np.where(mask_out==k)
# if (locs[0].size!=0):
#
# temp_max_vals = np.copy(max_vals)
# temp_max_vals[locs] = -100
# temp_arg_max = temp_max_vals
# min_vals[locs]
#
# cur_vals = temp_mean[locs]
# cur_stds = temp_std[locs]
# min_vals = cur_vals - conf*cur_stds
#save to dataset
for indice in range(len(ind)):
prediction_pre_cor[ind[indice],
...] = np.squeeze(pre_cor_mask[indice, ...])
prediction[ind[indice], ...] = np.squeeze(mask_out[indice,
...])
p_vals[ind[indice], ...] = np.squeeze(ps[indice, ...])
data['predicted'].attrs.modify('processed_to',
scr_idx + exp_config.batch_size)
if exp_config.reinit:
logging.info("Initialising variables")
sess.run(tf.global_variables_initializer())
data['predicted'].attrs.modify('processed', True)
logging.info(
'Created unprocessed ground truths for recursion {}'.format(
recursion + 1))
#Reopen in read only mode
data.close()
data = h5py.File(new_recursion_fname, 'r')
return data
def predict_next_gt(data2,
images_train,
images_placeholder,
training_time_placeholder,
keep_prob,
logits,
sess,
random_walked):
'''
Uses current network weights to segment images for next recursion
After postprocessing, these are used as the ground truth for further training
:param data: Data of the current recursion - if this is of recursion n, this function
predicts ground truths for recursion n + 1
:param images_train: Numpy array of training images
:param images_placeholder: Tensorflow placeholder for image feed
:param training_time_placeholder: Boolean tensorflow placeholder
:param logits: Logits operator for calculating segmentation mask probabilites
:param sess: Tensorflow session
:return: The data file for recursion n + 1
'''
#get recursion from filename
recursion = utils.get_recursion_from_hdf5(data2)
new_recursion_fname = acdc_data.recursion_filepath(recursion + 1, data_file=data2)
fpath = os.path.dirname(data2.filename)
data = acdc_data.create_recursion_dataset(fpath, recursion + 1)
#attributes to track processing
prediction = data['predicted']
logits_h5 = data['logits']
pre_logits_h5 = data['pre_logits']
predicted_pre_crf = data['predicted_pre_crf']
processed = data['predicted'].attrs.get('processed')
ran = data['random_walked']
ran2 = data2['random_walked']
means_h_2 = data2['means']
p_vals = data2['p_vals']
if not processed:
processed_to = data['predicted'].attrs.get('processed_to')
scr_max = len(images_train)
print("SCR max = " + str(scr_max))
for scr_idx in range(processed_to, scr_max, exp_config.batch_size):
if scr_idx+exp_config.batch_size > scr_max:
print("Entered last")
# At the end of the dataset
# Must ensure feed_dict is 20 images long however
ind = list(range(scr_max - exp_config.batch_size, scr_max))
else:
ind = list(range(scr_idx, scr_idx + exp_config.batch_size))
print(str(ind))
# logging.info('Saving prediction after recursion {0} for images {1} to {2} '
# .format(ind[0], ind[-1]))
x = np.expand_dims(np.array(images_train[ind, ...]), -1)
temp_mean = np.array(means_h_2[ind, ...])
logs = tf.nn.softmax(temp_mean)
cur_rand = np.array(ran2[ind, ...])
for t in range(exp_config.batch_size):
for m in range(212):
for n in range(212):
if cur_rand[t,m,n] != 0:
logs[t,m,n,:] =0
logs[t,m,n,cur_rand[t,m,n]] = 1
temp_maps = np.argmax(temp_mean, axis=-1)
mask_out = apply_crf(logs,x)
conf = 0.05
temp_p = np.array(p_vals[ind, ...])
for t in range(exp_config.batch_size):
for m in range(212):
for n in range(212):
if temp_p[t,m,n] > conf:
mask_out[t,m,n] = 0
for t in range(exp_config.batch_size):
for m in range(212):
for n in range(212):
if cur_rand[t,m,n] != 0:
mask_out[t,m,n] = cur_rand[t,m,n]
#save to dataset
for indice in range(len(ind)):
prediction[ind[indice], ...] = np.squeeze(mask_out[indice, ...])
predicted_pre_crf[ind[indice], ...] = np.squeeze(temp_maps[indice, ...])
logits_h5[ind[indice], ...] = np.squeeze(temp_mean[indice, ...])
ran[ind[indice], ...] = np.squeeze(cur_rand[indice, ...])
data['predicted'].attrs.modify('processed_to', scr_idx + exp_config.batch_size)
if exp_config.reinit:
logging.info("Initialising variables")
sess.run(tf.global_variables_initializer())
data['predicted'].attrs.modify('processed', True)
logging.info('Created unprocessed ground truths for recursion {}'.format(recursion + 1))
#Reopen in read only mode
data.close()
data = h5py.File(new_recursion_fname, 'r')
return data
def predict_next_gt(data, images_train, images_placeholder,
training_time_placeholder, logits, sess):
'''
Uses current network weights to segment images for next recursion
After postprocessing, these are used as the ground truth for further training
:param data: Data of the current recursion - if this is of recursion n, this function
predicts ground truths for recursion n + 1
:param images_train: Numpy array of training images
:param images_placeholder: Tensorflow placeholder for image feed
:param training_time_placeholder: Boolean tensorflow placeholder
:param logits: Logits operator for calculating segmentation mask probabilites
:param sess: Tensorflow session
:return: The data file for recursion n + 1
'''
#get recursion from filename
recursion = utils.get_recursion_from_hdf5(data)
new_recursion_fname = acdc_data.recursion_filepath(recursion + 1,
data_file=data)
if not os.path.exists(new_recursion_fname):
fpath = os.path.dirname(data.filename)
data.close()
data = acdc_data.create_recursion_dataset(fpath, recursion + 1)
else:
data.close()
data = h5py.File(new_recursion_fname, 'r+')
#attributes to track processing
prediction = data['predicted']
processed = data['predicted'].attrs.get('processed')
if not processed:
processed_to = data['predicted'].attrs.get('processed_to')
scr_max = len(images_train)
print("SCR max = " + str(scr_max))
for scr_idx in range(processed_to, scr_max, exp_config.batch_size):
if scr_idx + exp_config.batch_size > scr_max:
print("Entered last")
# At the end of the dataset
# Must ensure feed_dict is 20 images long however
ind = list(range(scr_max - exp_config.batch_size, scr_max))
else:
ind = list(range(scr_idx, scr_idx + exp_config.batch_size))
print(str(ind))
# logging.info('Saving prediction after recursion {0} for images {1} to {2} '
# .format(ind[0], ind[-1]))
x = np.expand_dims(np.array(images_train[ind, ...]), -1)
feed_dict = {
images_placeholder: x,
training_time_placeholder: False
}
softmax = tf.nn.softmax(logits)
print("softmax")
#threshold output of cnn
if exp_config.cnn_threshold:
threshold = tf.constant(exp_config.cnn_threshold,
dtype=tf.float32)
s = tf.multiply(
tf.ones(shape=[exp_config.batch_size, 212, 212, 1]),
threshold)
softmax = tf.concat([s, softmax[..., 1:]], axis=-1)
print("threshold")
# if exp_config.use_crf:
# #get unary from softmax
# unary = tf.multiply(-1, tf.log(softmax))
#
#calculate mask
mask = tf.arg_max(softmax, dimension=-1)
print("before sess")
mask_out = sess.run(mask, feed_dict=feed_dict)
print("after sess : " + str(mask_out))
#save to dataset
for indice in range(len(ind)):
prediction[ind[indice], ...] = np.squeeze(mask_out[indice,
...])
print("added " + str(ind[indice]))
data['predicted'].attrs.modify('processed_to',
scr_idx + exp_config.batch_size)
if exp_config.reinit:
logging.info("Initialising variables")
sess.run(tf.global_variables_initializer())
data['predicted'].attrs.modify('processed', True)
logging.info(
'Created unprocessed ground truths for recursion {}'.format(
recursion + 1))
#Reopen in read only mode
data.close()
data = h5py.File(new_recursion_fname, 'r')
return data
def predict_next_gt(data, images_train, images_placeholder,
training_time_placeholder, keep_prob, logits,
network_output, rnn_in_placeholder, sess):
'''
Uses current network weights to segment images for next recursion
After postprocessing, these are used as the ground truth for further training
:param data: Data of the current recursion - if this is of recursion n, this function
predicts ground truths for recursion n + 1
:param images_train: Numpy array of training images
:param images_placeholder: Tensorflow placeholder for image feed
:param training_time_placeholder: Boolean tensorflow placeholder
:param logits: Logits operator for calculating segmentation mask probabilites
:param sess: Tensorflow session
:return: The data file for recursion n + 1
'''
#get recursion from filename
recursion = utils.get_recursion_from_hdf5(data)
new_recursion_fname = acdc_data.recursion_filepath(recursion + 1,
data_file=data)
if not os.path.exists(new_recursion_fname):
fpath = os.path.dirname(data.filename)
data.close()
data = acdc_data.create_recursion_dataset(fpath, recursion + 1)
else:
data.close()
data = h5py.File(new_recursion_fname, 'r+')
#attributes to track processing
prediction = data['predicted']
prediction_pre_cor = data['predicted_pre_cor']
p_vals = data['p_vals']
processed = data['predicted'].attrs.get('processed')
if not processed:
processed_to = data['predicted'].attrs.get('processed_to')
scr_max = len(images_train)
print("SCR max = " + str(scr_max))
for scr_idx in range(processed_to, scr_max):
ind = np.copy(scr_idx)
x = np.expand_dims(
np.expand_dims(np.array(images_train[ind, ...]), -1), 0)
feed_dict = {
images_placeholder: x,
training_time_placeholder: False,
keep_prob: 0.5
}
ps = np.zeros((212, 212))
temp, temp_mean = average_outputs(sess, network_output,
images_placeholder, x, keep_prob)
logits_out = np.squeeze(
sess.run(logits,
feed_dict={
images_placeholder: x,
rnn_in_placeholder: temp_mean
}))
mask = tf.arg_max(logits_out, dimension=-1)
mask_out = np.squeeze(sess.run(mask, feed_dict=feed_dict))
pre_cor_mask = np.copy(mask_out)
# for m in range(212):
# for n in range(212):
#
#
# estim = mask_out[m,n]
#
#
# temp_mean[0,m,n,estim] = -1000000
#
# best_ind = np.argmax(np.squeeze(np.copy(temp_mean[0,m,n,:])))
# [st,p] = ttest_ind(np.squeeze(temp[:,0,m,n,estim]),np.squeeze(temp[:,0,m,n,best_ind]),equal_var=False)
# ps[m,n] = p
# if p > conf:
# mask_out[m,n] = 0
prediction_pre_cor[ind, ...] = np.squeeze(pre_cor_mask)
prediction[ind, ...] = np.squeeze(mask_out)
p_vals[ind, ...] = np.squeeze(ps)
data['predicted'].attrs.modify('processed_to',
scr_idx + exp_config.batch_size)
data['predicted'].attrs.modify('processed', True)
logging.info(
'Created unprocessed ground truths for recursion {}'.format(
recursion + 1))
#Reopen in read only mode
data.close()
data = h5py.File(new_recursion_fname, 'r')
return data
def predict_next_gt(data, images_train, images_placeholder,
training_time_placeholder, keep_prob, logits,
network_output, rnn_in_placeholder, sess):
'''
Uses current network weights to segment images for next recursion
After postprocessing, these are used as the ground truth for further training
:param data: Data of the current recursion - if this is of recursion n, this function
predicts ground truths for recursion n + 1
:param images_train: Numpy array of training images
:param images_placeholder: Tensorflow placeholder for image feed
:param training_time_placeholder: Boolean tensorflow placeholder
:param logits: Logits operator for calculating segmentation mask probabilites
:param sess: Tensorflow session
:return: The data file for recursion n + 1
'''
#get recursion from filename
recursion = utils.get_recursion_from_hdf5(data)
new_recursion_fname = acdc_data.recursion_filepath(recursion + 1,
data_file=data)
if not os.path.exists(new_recursion_fname):
fpath = os.path.dirname(data.filename)
data.close()
data = acdc_data.create_recursion_dataset(fpath, recursion + 1)
else:
data.close()
data = h5py.File(new_recursion_fname, 'r+')
#attributes to track processing
prediction = data['predicted']
soft_o = data['predicted_pre_crf']
prediction_pre_cor = data['network_output']
processed = data['predicted'].attrs.get('processed')
if not processed:
processed_to = data['predicted'].attrs.get('processed_to')
scr_max = len(images_train)
print("SCR max = " + str(scr_max))
for scr_idx in range(processed_to, scr_max):
ind = np.copy(scr_idx)
x = np.expand_dims(
np.expand_dims(np.array(images_train[ind, ...]), -1), 0)
feed_dict = {
images_placeholder: x,
training_time_placeholder: False
}
temp_mean = sess.run(network_output, feed_dict={images_pl: x})
temp_soft = sess.run(tf.nn.softmax(temp_mean))
logits_out = np.squeeze(
sess.run(logits,
feed_dict={
images_placeholder: x,
rnn_in_placeholder: temp_mean
}))
mask = tf.arg_max(logits_out, dimension=-1)
mask_out = np.squeeze(sess.run(mask, feed_dict=feed_dict))
prediction_pre_cor[ind, ...] = np.squeeze(temp_mean)
prediction[ind, ...] = np.squeeze(mask_out)
soft_o[ind, ...] = np.squeeze(temp_soft)
data['predicted'].attrs.modify('processed_to',
scr_idx + exp_config.batch_size)
data['predicted'].attrs.modify('processed', True)
logging.info(
'Created unprocessed ground truths for recursion {}'.format(
recursion + 1))
#Reopen in read only mode
data.close()
data = h5py.File(new_recursion_fname, 'r')
return data