def extract_dataset(dataset, config, cv, out_dir):
"""Save dataset npys into a directory"""
dataset_module = py_utils.import_module(pre_path=config.dataset_classes,
module=dataset)
dataset_module = dataset_module.data_processing()
(train_data, _, _) = py_utils.get_data_pointers(
dataset=dataset_module.output_name,
base_dir=
"/media/data_cifs/cluttered_nist_experiments/tf_records", # config.tf_records,
local_dir=
"/media/data_cifs/cluttered_nist_experiments/tf_records", # config.local_tf_records,
cv=cv)
train_images, train_labels, train_aux = data_loader.inputs(
dataset=train_data,
batch_size=1000, # config.train_batch_size,
model_input_image_size=dataset_module.model_input_image_size,
tf_dict=dataset_module.tf_dict,
data_augmentations=[], # config.train_augmentations,
num_epochs=1, # config.epochs,
aux=None, # train_aux_loss,
tf_reader_settings=dataset_module.tf_reader,
shuffle=False) # config.shuffle_train)
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
sess.run(
tf.group(tf.global_variables_initializer(),
tf.local_variables_initializer()))
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
count = 0
try:
while not coord.should_stop():
images, labels = sess.run([train_images, train_labels])
np.savez(os.path.join(out_dir, "{}".format(count)),
images=images,
labels=labels)
count += 1
except tf.errors.OutOfRangeError:
print("Finished loop")
finally:
coord.request_stop()
coord.join(threads)
sess.close()
def plot_fits(
experiment='760_cells_2017_11_04_16_29_09',
query_db=False,
num_models=3,
template_exp='ALLEN_selected_cells_1',
process_pnodes=False):
"""Plot fits across the RF.
experiment: Name of Allen experiment you're plotting.
query_db: Use data from DB versus data in Numpys.
num_models: The number of architectures you're testing.
template_exp: The name of the contextual_circuit model template used."""
if process_pnodes:
from pnodes_declare_datasets_loop import query_hp_hist, sel_exp_query
else:
from declare_datasets_loop import query_hp_hist, sel_exp_query
main_config = Allen_Brain_Observatory_Config()
sys.path.append(main_config.cc_path)
from db import credentials
from ops import data_loader
db_config = credentials.postgresql_connection()
files = glob(
os.path.join(
main_config.multi_exps,
experiment, '*.npz'))
out_data, xs, ys = [], [], []
perfs, model_types, exps, arg_perf = [], [], [], []
count = 0
for f in files:
data = np.load(f)
d = {
'x': data['rf_data'].item()['on_center_x'],
'y': data['rf_data'].item()['on_center_y'],
# x: files['dataset_method'].item()['x_min'],
# y: files['dataset_method'].item()['y_min'],
}
exp_name = {
'experiment_name': data['dataset_method'].item()[
'experiment_name']}
if query_db:
perf = query_hp_hist(
exp_name['experiment_name'],
db_config=db_config)
if perf is None:
print 'No fits for: %s' % exp_name['experiment_name']
else:
raise NotImplementedError
d['perf'] = perf
d['max_val'] = np.max(perf)
out_data += [d]
xs += [np.round(d['x'])]
ys += [np.round(d['y'])]
perfs += [np.max(d['perf'])]
count += 1
else:
data_files = glob(
os.path.join(
main_config.ccbp_exp_evals,
exp_name['experiment_name'],
'*val_losses.npy')) # Scores has preds, labels has GT
for gd in data_files:
mt = gd.split(
os.path.sep)[-1].split(
template_exp + '_')[-1].split('_' + 'val')[0]
it_data = np.load(gd).item()
sinds = np.asarray(it_data.keys())[np.argsort(it_data.keys())]
sit_data = [it_data[idx] for idx in sinds]
d['perf'] = sit_data
d['max_val'] = np.max(sit_data)
d['max_idx'] = np.argmax(sit_data)
d['mt'] = mt
out_data += [d]
xs += [np.round(d['x'])]
ys += [np.round(d['y'])]
perfs += [np.max(sit_data)]
arg_perf += [np.argmax(sit_data)]
exps += [gd.split(os.path.sep)[-2]]
model_types += [mt]
count += 1
# Package as a df
xs = np.round(np.asarray(xs)).astype(int)
ys = np.round(np.asarray(ys)).astype(int)
perfs = np.asarray(perfs)
arg_perf = np.asarray(arg_perf)
exps = np.asarray(exps)
model_types = np.asarray(model_types)
# Filter to only keep top-scoring values at each x/y (dirty trick)
fxs, fys, fperfs, fmodel_types, fexps, fargs = [], [], [], [], [], []
xys = np.vstack((xs, ys)).transpose()
cxy = np.ascontiguousarray( # Unique rows
xys).view(
np.dtype((np.void, xys.dtype.itemsize * xys.shape[1])))
_, idx = np.unique(cxy, return_index=True)
uxys = xys[idx]
for xy in uxys:
sel_idx = (xys == xy).sum(axis=-1) == 2
sperfs = perfs[sel_idx]
sexps = exps[sel_idx]
sargs = arg_perf[sel_idx]
sel_mts = model_types[sel_idx]
bp = np.argmax(sperfs)
fxs += [xy[0]]
fys += [xy[1]]
fperfs += [sperfs[bp]]
fargs += [sargs[bp]]
fmodel_types += [sel_mts[bp]]
fexps += [sexps[bp]]
xs = np.asarray(fxs)
ys = np.asarray(fys)
perfs = np.asarray(fperfs)
arg_perf = np.asarray(fargs)
exps = np.asarray(fexps)
model_types = np.asarray(fmodel_types)
umt, model_types_inds = np.unique(model_types, return_inverse=True)
# Get weights for the top-n fitting models of each type
top_n = 1
target_layer = 'conv2d'
it_perfs = perfs[model_types == target_layer]
it_exps = exps[model_types == target_layer]
# it_args = arg_perf[model_types == target_layer]
sorted_perfs = np.argsort(it_perfs)[::-1][:top_n]
for idx in sorted_perfs:
perf = sel_exp_query(
experiment_name=it_exps[idx],
model=target_layer,
db_config=db_config)
# perf_steps = np.argsort([v['training_step'] for v in perf])[::-1]
perf_steps = [v['validation_loss'] for v in perf]
max_score = np.max(perf_steps)
arg_perf_steps = np.argmax(perf_steps)
sel_model = perf[arg_perf_steps] # perf_steps[it_args[idx]]]
print 'Using %s' % sel_model
model_file = sel_model['ckpt_file'].split('.')[0]
model_ckpt = '%s.ckpt-%s' % (
model_file,
model_file.split(os.path.sep)[-1].split('_')[-1])
model_meta = '%s.meta' % model_ckpt
import ipdb;ipdb.set_trace()
# Pull stimuli
stim_dir = os.path.join(
main_config.tf_record_output,
sel_model['experiment_name'])
stim_files = glob(os.path.join(stim_dir, '*'))
stim_meta_file = [x for x in stim_files if 'meta' in x]
stim_val_data = [x for x in stim_files if 'val.tfrecords' in x]
stim_val_mean = [x for x in stim_files if 'val_means' in x]
stim_meta_data = np.load(stim_meta_file).item()
# Store sparse noise for reference
sparse_rf_on = {
'center_x': stim_meta_data['on_center_x'],
'center_y': stim_meta_data['on_center_y'],
'width_x': stim_meta_data['on_width_x'],
'width_y': stim_meta_data['on_width_y'],
'distance': stim_meta_data['on_distance'],
'area': stim_meta_data['on_area'],
'rotation': stim_meta_data['on_rotation'],
}
sparse_rf_off = {
'center_x': stim_meta_data['off_center_x'],
'center_y': stim_meta_data['off_center_y'],
'width_x': stim_meta_data['off_width_x'],
'width_y': stim_meta_data['off_width_y'],
'distance': stim_meta_data['off_distance'],
'area': stim_meta_data['off_area'],
'rotation': stim_meta_data['off_rotation'],
}
sparse_rf = {'on': sparse_rf_on, 'off': sparse_rf_off}
# Pull responses
val_images, val_labels = data_loader.inputs(
dataset=stim_val_data,
batch_size=config.batch_size,
model_input_image_size=dataset_module.model_input_image_size,
tf_dict=dataset_module.tf_dict,
data_augmentations=config.data_augmentations,
num_epochs=config.epochs,
tf_reader_settings=dataset_module.tf_reader,
shuffle=config.shuffle
)
# Mean normalize
if target_layer == 'DoG':
pass
else:
with tf.Session() as sess:
saver = tf.train.import_meta_graph(
model_meta,
clear_devices=True)
saver.restore(sess, model_ckpt)
if target_layer == 'conv2d':
fname = [
x for x in tf.global_variables()
if 'conv1_1_filters:0' in x.name]
elif target_layer == 'sep_conv2d':
fname = [
x for x in tf.global_variables()
if 'sep_conv1_1_filters:0' in x.name]
filts = sess.run(fname)
import ipdb;ipdb.set_trace()
save_mosaic(
maps=filts[0].squeeze().transpose(2, 0, 1),
output='%s_filters' % target_layer,
rc=8,
cc=4,
title='%s filters for cell where rho=%s' % (
target_layer,
np.around(max_score, 2)))
def train_classifier_on_model(train_pointer, model_type, model_weights,
selected_layer, config):
# Make output directories if they do not exist
dt_stamp = '%s_%s_%s_%s' % (model_type, selected_layer, str(
config.lr)[2:], re.split('\.', str(datetime.now()))[0].replace(
' ', '_').replace(':', '_').replace('-', '_'))
config.checkpoint_directory = os.path.join(config.checkpoint_directory,
dt_stamp) # timestamp this run
dir_list = [config.checkpoint_directory]
[utilities.make_dir(d) for d in dir_list]
print '-' * 60
print 'Training %s over a %s. Saving to %s' % (config.classifier,
model_type, dt_stamp)
print '-' * 60
dcn_flavor = import_cnn(model_type)
# Prepare data on CPU
with tf.device('/cpu:0'):
train_images, train_labels, train_files = inputs(
train_pointer,
config.train_batch,
config.train_image_size,
config.model_image_size[:2],
num_epochs=config.epochs,
shuffle_batch=True)
# Prepare pretrained model on GPU
with tf.device('/gpu:0'):
with tf.variable_scope('cnn'):
if 'ckpt' in model_weights:
cnn = dcn_flavor.model()
else:
cnn = dcn_flavor.model(weight_path=model_weights)
cnn.build(train_images)
sample_layer = cnn[selected_layer]
class_accuracy = tf_loss.class_accuracy(cnn.prob, train_labels)
saver = tf.train.Saver(tf.all_variables(), max_to_keep=10)
# Initialize the graph
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# Need to initialize both of these if supplying num_epochs to inputs
sess.run(
tf.group(tf.initialize_all_variables(),
tf.initialize_local_variables()))
# Set up exemplar threading
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
# Start training loop
np.save(os.path.join(config.checkpoint_directory, 'training_config_file'),
config)
step, scores, labs = 0, [], []
if 'ckpt' in model_weights:
saver.restore(sess, model_weights)
try:
print 'Getting scores'
while not coord.should_stop():
import ipdb
ipdb.set_trace()
start_time = time.time()
score, lab, acc = sess.run(
[sample_layer, train_labels, class_accuracy])
scores += [score]
labs += [lab]
duration = time.time() - start_time
# End iteration
print_status(step, 1, config, duration, acc, '')
step += 1
except tf.errors.OutOfRangeError:
print 'Finished extracting scores.'
finally:
coord.request_stop()
X = np.concatenate(scores)
y = np.concatenate(labs)
mu = np.mean(X, axis=0)
sd = np.std(X, axis=0)
X = (X - mu) / sd
svc = svm.LinearSVC(dual=False, C=config.c, verbose=True).fit(X, y)
ckpt_path = os.path.join(config.checkpoint_directory,
'model_%s.pkl' % step)
with open(ckpt_path, 'wb') as fid:
cPickle.dump(svc, fid)
norm_path = os.path.join(config.checkpoint_directory,
'model_%s_normalization' % step)
np.savez(norm_path, mu=mu, sd=sd, scores=scores, labs=labs)
print 'Saved to: %s' % config.checkpoint_directory
print 'Saved checkpoint to: %s' % ckpt_path
coord.join(threads)
sess.close()
# Return the final checkpoint for testing
return ckpt_path, config.checkpoint_directory
def main(experiment_name, list_experiments=False, gpu_device='/gpu:0'):
"""Create a tensorflow worker to run experiments in your DB."""
if list_experiments:
exps = db.list_experiments()
print '_' * 30
print 'Initialized experiments:'
print '_' * 30
for l in exps:
print l.values()[0]
print '_' * 30
print 'You can add to the DB with: '\
'python prepare_experiments.py --experiment=%s' % \
exps[0].values()[0]
return
if experiment_name is None:
print 'No experiment specified. Pulling one out of the DB.'
experiment_name = db.get_experiment_name()
# Prepare to run the model
config = Config()
condition_label = '%s_%s' % (experiment_name, py_utils.get_dt_stamp())
experiment_label = '%s' % (experiment_name)
log = logger.get(os.path.join(config.log_dir, condition_label))
experiment_dict = experiments.experiments()[experiment_name]()
config = add_to_config(d=experiment_dict, config=config) # Globals
config, exp_params = process_DB_exps(
experiment_name=experiment_name, log=log,
config=config) # Update config w/ DB params
dataset_module = py_utils.import_module(model_dir=config.dataset_info,
dataset=config.dataset)
dataset_module = dataset_module.data_processing() # hardcoded class name
train_data, train_means = get_data_pointers(
dataset=config.dataset,
base_dir=config.tf_records,
cv=dataset_module.folds.keys()[1], # TODO: SEARCH FOR INDEX.
log=log)
val_data, val_means = get_data_pointers(dataset=config.dataset,
base_dir=config.tf_records,
cv=dataset_module.folds.keys()[0],
log=log)
# Initialize output folders
dir_list = {
'checkpoints':
os.path.join(config.checkpoints, condition_label),
'summaries':
os.path.join(config.summaries, condition_label),
'condition_evaluations':
os.path.join(config.condition_evaluations, condition_label),
'experiment_evaluations':
os.path.join( # DEPRECIATED
config.experiment_evaluations, experiment_label),
'visualization':
os.path.join(config.visualizations, condition_label),
'weights':
os.path.join(config.condition_evaluations, condition_label, 'weights')
}
[py_utils.make_dir(v) for v in dir_list.values()]
# Prepare data loaders on the cpu
config.data_augmentations = py_utils.flatten_list(
config.data_augmentations, log)
with tf.device('/cpu:0'):
train_images, train_labels = data_loader.inputs(
dataset=train_data,
batch_size=config.batch_size,
model_input_image_size=dataset_module.model_input_image_size,
tf_dict=dataset_module.tf_dict,
data_augmentations=config.data_augmentations,
num_epochs=config.epochs,
tf_reader_settings=dataset_module.tf_reader,
shuffle=config.shuffle)
val_images, val_labels = data_loader.inputs(
dataset=val_data,
batch_size=config.batch_size,
model_input_image_size=dataset_module.model_input_image_size,
tf_dict=dataset_module.tf_dict,
data_augmentations=config.data_augmentations,
num_epochs=config.epochs,
tf_reader_settings=dataset_module.tf_reader,
shuffle=config.shuffle)
log.info('Created tfrecord dataloader tensors.')
# Load model specification
struct_name = config.model_struct.split(os.path.sep)[-1]
try:
model_dict = py_utils.import_module(
dataset=struct_name,
model_dir=os.path.join('models', 'structs',
experiment_name).replace(os.path.sep, '.'))
except IOError:
print 'Could not find the model structure: %s' % experiment_name
# Inject model_dict with hyperparameters if requested
model_dict.layer_structure = hp_opt_utils.inject_model_with_hps(
layer_structure=model_dict.layer_structure, exp_params=exp_params)
# Prepare model on GPU
with tf.device(gpu_device):
with tf.variable_scope('cnn') as scope:
# Training model
if len(dataset_module.output_size) > 1:
log.warning('Found > 1 dimension for your output size.'
'Converting to a scalar.')
dataset_module.output_size = np.prod(
dataset_module.output_size)
if hasattr(model_dict, 'output_structure'):
# Use specified output layer
output_structure = model_dict.output_structure
else:
output_structure = None
model = model_utils.model_class(
mean=train_means,
training=True,
output_size=dataset_module.output_size)
train_scores, model_summary = model.build(
data=train_images,
layer_structure=model_dict.layer_structure,
output_structure=output_structure,
log=log,
tower_name='cnn')
log.info('Built training model.')
log.debug(json.dumps(model_summary, indent=4), verbose=0)
print_model_architecture(model_summary)
# Prepare the loss function
train_loss, _ = loss_utils.loss_interpreter(
logits=train_scores,
labels=train_labels,
loss_type=config.loss_function,
dataset_module=dataset_module)
# Add weight decay if requested
if len(model.regularizations) > 0:
train_loss = loss_utils.wd_loss(
regularizations=model.regularizations,
loss=train_loss,
wd_penalty=config.regularization_strength)
train_op = loss_utils.optimizer_interpreter(
loss=train_loss,
lr=config.lr,
optimizer=config.optimizer,
constraints=config.optimizer_constraints,
model=model)
log.info('Built training loss function.')
train_accuracy = eval_metrics.metric_interpreter(
metric=dataset_module.score_metric,
pred=train_scores,
labels=train_labels) # training accuracy
if int(train_images.get_shape()[-1]) <= 3:
tf.summary.image('train images', train_images)
tf.summary.scalar('training loss', train_loss)
tf.summary.scalar('training accuracy', train_accuracy)
log.info('Added training summaries.')
# Validation model
scope.reuse_variables()
val_model = model_utils.model_class(
mean=val_means,
training=True,
output_size=dataset_module.output_size)
val_scores, _ = val_model.build( # Ignore summary
data=val_images,
layer_structure=model_dict.layer_structure,
output_structure=output_structure,
log=log,
tower_name='cnn')
log.info('Built validation model.')
val_loss, _ = loss_utils.loss_interpreter(
logits=val_scores,
labels=val_labels,
loss_type=config.loss_function,
dataset_module=dataset_module)
val_accuracy = eval_metrics.metric_interpreter(
metric=dataset_module.score_metric,
pred=val_scores,
labels=val_labels) # training accuracy
if int(train_images.get_shape()[-1]) <= 3:
tf.summary.image('val images', val_images)
tf.summary.scalar('validation loss', val_loss)
tf.summary.scalar('validation accuracy', val_accuracy)
log.info('Added validation summaries.')
# Set up summaries and saver
saver = tf.train.Saver(tf.global_variables())
summary_op = tf.summary.merge_all()
# Initialize the graph
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# Need to initialize both of these if supplying num_epochs to inputs
sess.run(
tf.group(tf.global_variables_initializer(),
tf.local_variables_initializer()))
summary_writer = tf.summary.FileWriter(dir_list['summaries'], sess.graph)
# Set up exemplar threading
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
# Create dictionaries of important training and validation information
train_dict = {
'train_loss': train_loss,
'train_accuracy': train_accuracy,
'train_images': train_images,
'train_labels': train_labels,
'train_op': train_op,
'train_scores': train_scores
}
val_dict = {
'val_loss': val_loss,
'val_accuracy': val_accuracy,
'val_images': val_images,
'val_labels': val_labels,
'val_scores': val_scores,
}
# Start training loop
np.save(
os.path.join(dir_list['condition_evaluations'],
'training_config_file'), config)
log.info('Starting training')
output_dict = training.training_loop(
config=config,
db=db,
coord=coord,
sess=sess,
summary_op=summary_op,
summary_writer=summary_writer,
saver=saver,
threads=threads,
summary_dir=dir_list['summaries'],
checkpoint_dir=dir_list['checkpoints'],
weight_dir=dir_list['weights'],
train_dict=train_dict,
val_dict=val_dict,
train_model=model,
val_model=val_model,
exp_params=exp_params)
log.info('Finished training.')
model_name = config.model_struct.replace('/', '_')
py_utils.save_npys(data=output_dict,
model_name=model_name,
output_string=dir_list['experiment_evaluations'])
def main(experiment_name,
list_experiments=False,
load_and_evaluate_ckpt=None,
config_file=None,
ckpt_file=None,
gpu_device='/gpu:0'):
"""Create a tensorflow worker to run experiments in your DB."""
if list_experiments:
exps = db.list_experiments()
print '_' * 30
print 'Initialized experiments:'
print '_' * 30
for l in exps:
print l.values()[0]
print '_' * 30
if len(exps) == 0:
print 'No experiments found.'
else:
print 'You can add to the DB with: '\
'python prepare_experiments.py --experiment=%s' % \
exps[0].values()[0]
return
if experiment_name is None:
print 'No experiment specified. Pulling one out of the DB.'
experiment_name = db.get_experiment_name()
# Prepare to run the model
config = Config()
condition_label = '%s_%s' % (experiment_name, py_utils.get_dt_stamp())
experiment_label = '%s' % (experiment_name)
log = logger.get(os.path.join(config.log_dir, condition_label))
experiment_dict = experiments.experiments()[experiment_name]()
config = add_to_config(d=experiment_dict, config=config) # Globals
config.load_and_evaluate_ckpt = load_and_evaluate_ckpt
config, exp_params = process_DB_exps(
experiment_name=experiment_name, log=log,
config=config) # Update config w/ DB params
config = np.load(config_file).item()
dataset_module = py_utils.import_module(model_dir=config.dataset_info,
dataset=config.dataset)
dataset_module = dataset_module.data_processing() # hardcoded class name
train_data, train_means_image, train_means_label = get_data_pointers(
dataset=config.dataset,
base_dir=config.tf_records,
cv=dataset_module.folds.keys()[1], # TODO: SEARCH FOR INDEX.
log=log)
val_data, val_means_image, val_means_label = get_data_pointers(
dataset=config.dataset,
base_dir=config.tf_records,
cv=dataset_module.folds.keys()[0],
log=log)
# Initialize output folders
dir_list = {
'checkpoints':
os.path.join(config.checkpoints, condition_label),
'summaries':
os.path.join(config.summaries, condition_label),
'condition_evaluations':
os.path.join(config.condition_evaluations, condition_label),
'experiment_evaluations':
os.path.join( # DEPRECIATED
config.experiment_evaluations, experiment_label),
'visualization':
os.path.join(config.visualizations, condition_label),
'weights':
os.path.join(config.condition_evaluations, condition_label, 'weights')
}
[py_utils.make_dir(v) for v in dir_list.values()]
# Prepare data loaders on the cpu
if all(isinstance(i, list) for i in config.data_augmentations):
if config.data_augmentations:
config.data_augmentations = py_utils.flatten_list(
config.data_augmentations, log)
config.epochs = 1
config.shuffle = False
with tf.device('/cpu:0'):
train_images, train_labels = data_loader.inputs(
dataset=train_data,
batch_size=config.batch_size,
model_input_image_size=dataset_module.model_input_image_size,
tf_dict=dataset_module.tf_dict,
data_augmentations=config.data_augmentations,
num_epochs=config.epochs,
tf_reader_settings=dataset_module.tf_reader,
shuffle=config.shuffle_train,
resize_output=config.resize_output)
if hasattr(config, 'val_augmentations'):
val_augmentations = config.val_augmentations
else:
val_augmentations = config.data_augmentations
val_images, val_labels = data_loader.inputs(
dataset=val_data,
batch_size=config.batch_size,
model_input_image_size=dataset_module.model_input_image_size,
tf_dict=dataset_module.tf_dict,
data_augmentations=['resize_and_crop'],
num_epochs=config.epochs,
tf_reader_settings=dataset_module.tf_reader,
shuffle=config.shuffle_val,
resize_output=config.resize_output)
log.info('Created tfrecord dataloader tensors.')
# Load model specification
struct_name = config.model_struct.split(os.path.sep)[-1]
try:
model_dict = py_utils.import_module(
dataset=struct_name,
model_dir=os.path.join('models', 'structs',
experiment_name).replace(os.path.sep, '.'))
except IOError:
print 'Could not find the model structure: %s in folder %s' % (
struct_name, experiment_name)
# Inject model_dict with hyperparameters if requested
model_dict.layer_structure = hp_opt_utils.inject_model_with_hps(
layer_structure=model_dict.layer_structure, exp_params=exp_params)
# Prepare model on GPU
with tf.device(gpu_device):
with tf.variable_scope('cnn') as scope:
# Normalize labels if needed
if 'normalize_labels' in exp_params.keys():
if exp_params['normalize_labels'] == 'zscore':
train_labels -= train_means_label['mean']
train_labels /= train_means_label['std']
log.info('Z-scoring labels.')
elif exp_params['normalize_labels'] == 'mean':
train_labels -= train_means_label['mean']
log.info('Mean-centering labels.')
# Training model
if len(dataset_module.output_size) == 2:
log.warning('Found > 1 dimension for your output size.'
'Converting to a scalar.')
dataset_module.output_size = np.prod(
dataset_module.output_size)
if hasattr(model_dict, 'output_structure'):
# Use specified output layer
output_structure = model_dict.output_structure
else:
output_structure = None
model = model_utils.model_class(
mean=train_means_image,
training=True,
output_size=dataset_module.output_size)
train_scores, model_summary = model.build(
data=train_images,
layer_structure=model_dict.layer_structure,
output_structure=output_structure,
log=log,
tower_name='cnn')
eval_graph = tf.Graph()
with eval_graph.as_default():
with eval_graph.gradient_override_map({'selu': 'GradLRP'}):
train_grad_images = tf.gradients(
train_scores[0] * tf.cast(train_labels, tf.float32),
train_images)[0]
log.info('Built training model.')
log.debug(json.dumps(model_summary, indent=4), verbose=0)
print_model_architecture(model_summary)
# Check the shapes of labels and scores
if not isinstance(train_scores, list):
if len(train_scores.get_shape()) != len(
train_labels.get_shape()):
train_shape = train_scores.get_shape().as_list()
label_shape = train_labels.get_shape().as_list()
if len(train_shape) == 2 and len(
label_shape) == 1 and train_shape[-1] == 1:
train_labels = tf.expand_dims(train_labels, axis=-1)
elif len(train_shape) == 2 and len(
label_shape) == 1 and train_shape[-1] == 1:
train_scores = tf.expand_dims(train_scores, axis=-1)
# Prepare the loss function
train_loss, _ = loss_utils.loss_interpreter(
logits=train_scores, # TODO
labels=train_labels,
loss_type=config.loss_function,
weights=config.loss_weights,
dataset_module=dataset_module)
# Add loss tensorboard tracking
if isinstance(train_loss, list):
for lidx, tl in enumerate(train_loss):
tf.summary.scalar('training_loss_%s' % lidx, tl)
train_loss = tf.add_n(train_loss)
else:
tf.summary.scalar('training_loss', train_loss)
# Add weight decay if requested
if len(model.regularizations) > 0:
train_loss = loss_utils.wd_loss(
regularizations=model.regularizations,
loss=train_loss,
wd_penalty=config.regularization_strength)
train_op = loss_utils.optimizer_interpreter(
loss=train_loss,
lr=config.lr,
optimizer=config.optimizer,
constraints=config.optimizer_constraints,
model=model)
log.info('Built training loss function.')
# Add a score for the training set
train_accuracy = eval_metrics.metric_interpreter(
metric=dataset_module.score_metric, # TODO: Attach to exp cnfg
pred=train_scores, # TODO
labels=train_labels)
# Add aux scores if requested
train_aux = {}
if hasattr(dataset_module, 'aux_scores'):
for m in dataset_module.aux_scores:
train_aux[m] = eval_metrics.metric_interpreter(
metric=m, pred=train_scores,
labels=train_labels)[0] # TODO: Fix for multiloss
# Prepare remaining tensorboard summaries
if len(train_images.get_shape()) == 4:
tf_fun.image_summaries(train_images, tag='Training images')
if len(train_labels.get_shape()) > 2:
tf_fun.image_summaries(train_labels, tag='Training_targets')
tf_fun.image_summaries(train_scores,
tag='Training_predictions')
if isinstance(train_accuracy, list):
for tidx, ta in enumerate(train_accuracy):
tf.summary.scalar('training_accuracy_%s' % tidx, ta)
else:
tf.summary.scalar('training_accuracy', train_accuracy)
if config.pr_curve:
if isinstance(train_scores, list):
for pidx, train_score in enumerate(train_scores):
train_label = train_labels[:, pidx]
pr_summary.op(
tag='training_pr_%s' % pidx,
predictions=tf.cast(
tf.argmax(train_score, axis=-1), tf.float32),
labels=tf.cast(train_label, tf.bool),
display_name='training_precision_recall_%s' % pidx)
else:
pr_summary.op(tag='training_pr',
predictions=tf.cast(
tf.argmax(train_scores, axis=-1),
tf.float32),
labels=tf.cast(train_labels, tf.bool),
display_name='training_precision_recall')
log.info('Added training summaries.')
# Validation model
scope.reuse_variables()
val_model = model_utils.model_class(
mean=train_means_image, # Normalize with train data
training=False, # False,
output_size=dataset_module.output_size)
val_scores, _ = val_model.build( # Ignore summary
data=val_images,
layer_structure=model_dict.layer_structure,
output_structure=output_structure,
log=log,
tower_name='cnn')
eval_graph = tf.Graph()
with eval_graph.as_default():
with eval_graph.gradient_override_map({'selu': 'GradLRP'}):
val_grad_images = tf.gradients(
val_scores[0] * tf.cast(val_labels, tf.float32),
val_images)[0]
log.info('Built validation model.')
# Check the shapes of labels and scores
if not isinstance(train_scores, list):
if len(val_scores.get_shape()) != len(val_labels.get_shape()):
val_shape = val_scores.get_shape().as_list()
val_label_shape = val_labels.get_shape().as_list()
if len(val_shape) == 2 and len(
val_label_shape) == 1 and val_shape[-1] == 1:
val_labels = tf.expand_dims(val_labels, axis=-1)
if len(val_shape) == 2 and len(
val_label_shape) == 1 and val_shape[-1] == 1:
val_scores = tf.expand_dims(val_scores, axis=-1)
val_loss, _ = loss_utils.loss_interpreter(
logits=val_scores,
labels=val_labels,
loss_type=config.loss_function,
weights=config.loss_weights,
dataset_module=dataset_module)
# Add loss tensorboard tracking
if isinstance(val_loss, list):
for lidx, tl in enumerate(val_loss):
tf.summary.scalar('validation_loss_%s' % lidx, tl)
val_loss = tf.add_n(val_loss)
else:
tf.summary.scalar('validation_loss', val_loss)
# Add a score for the validation set
val_accuracy = eval_metrics.metric_interpreter(
metric=dataset_module.score_metric, # TODO
pred=val_scores,
labels=val_labels)
# Add aux scores if requested
val_aux = {}
if hasattr(dataset_module, 'aux_scores'):
for m in dataset_module.aux_scores:
val_aux[m] = eval_metrics.metric_interpreter(
metric=m, pred=val_scores,
labels=val_labels)[0] # TODO: Fix for multiloss
# Prepare tensorboard summaries
if len(val_images.get_shape()) == 4:
tf_fun.image_summaries(val_images, tag='Validation')
if len(val_labels.get_shape()) > 2:
tf_fun.image_summaries(val_labels, tag='Validation_targets')
tf_fun.image_summaries(val_scores,
tag='Validation_predictions')
if isinstance(val_accuracy, list):
for vidx, va in enumerate(val_accuracy):
tf.summary.scalar('validation_accuracy_%s' % vidx, va)
else:
tf.summary.scalar('validation_accuracy', val_accuracy)
if config.pr_curve:
if isinstance(val_scores, list):
for pidx, val_score in enumerate(val_scores):
val_label = val_labels[:, pidx]
pr_summary.op(
tag='validation_pr_%s' % pidx,
predictions=tf.cast(tf.argmax(val_score, axis=-1),
tf.float32),
labels=tf.cast(val_label, tf.bool),
display_name='validation_precision_recall_%s' %
pidx)
else:
pr_summary.op(tag='validation_pr',
predictions=tf.cast(
tf.argmax(val_scores, axis=-1),
tf.float32),
labels=tf.cast(val_labels, tf.bool),
display_name='validation_precision_recall')
log.info('Added validation summaries.')
# Set up summaries and saver
saver = tf.train.Saver(tf.global_variables())
# Initialize the graph
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# Need to initialize both of these if supplying num_epochs to inputs
sess.run(
tf.group(tf.global_variables_initializer(),
tf.local_variables_initializer()))
# Set up exemplar threading
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
# Create dictionaries of important training and validation information
train_dict = {
'train_loss': train_loss,
'train_images': train_images,
'train_labels': train_labels,
'train_op': train_op,
'train_scores': train_scores,
'train_grad_images': train_grad_images
}
val_dict = {
'val_loss': val_loss,
'val_images': val_images,
'val_labels': val_labels,
'val_scores': val_scores,
'val_grad_images': val_grad_images
}
if isinstance(train_accuracy, list):
for tidx, (ta, va) in enumerate(zip(train_accuracy, val_accuracy)):
train_dict['train_accuracy_%s' % tidx] = ta
val_dict['val_accuracy_%s' % tidx] = va
else:
train_dict['train_accuracy_0'] = train_accuracy
val_dict['val_accuracy_0'] = val_accuracy
if load_and_evaluate_ckpt is not None:
# Remove the train operation and add a ckpt pointer
del train_dict['train_op']
if hasattr(dataset_module, 'aux_score'):
# Attach auxillary scores to tensor dicts
for m in dataset_module.aux_scores:
train_dict['train_aux_%s' % m] = train_aux[m]
val_dict['val_aux_%s' % m] = val_aux[m]
# Start training loop
checkpoint_dir = dir_list['checkpoints']
step = 0
train_losses, train_accs, train_aux, timesteps = {}, {}, {}, {}
val_scores, val_aux, val_labels, val_grads = {}, {}, {}, {}
train_images, val_images = {}, {}
train_scores, train_labels = {}, {}
train_aux_check = np.any(['aux_score' in k for k in train_dict.keys()])
val_aux_check = np.any(['aux_score' in k for k in val_dict.keys()])
# Restore model
saver.restore(sess, ckpt_file)
# Start evaluation
try:
while not coord.should_stop():
start_time = time.time()
train_vars = sess.run(train_dict.values())
it_train_dict = {
k: v
for k, v in zip(train_dict.keys(), train_vars)
}
duration = time.time() - start_time
train_losses[step] = it_train_dict['train_loss']
train_accs[step] = it_train_dict['train_accuracy_0']
train_images[step] = it_train_dict['train_images']
train_labels[step] = it_train_dict['train_labels']
train_scores[step] = it_train_dict['train_scores']
timesteps[step] = duration
if train_aux_check:
# Loop through to find aux scores
it_train_aux = {
itk: itv
for itk, itv in it_train_dict.iteritems()
if 'aux_score' in itk
}
train_aux[step] = it_train_aux
assert not np.isnan(it_train_dict['train_loss']).any(
), 'Model diverged with loss = NaN'
if step % config.validation_iters == 0:
it_val_scores, it_val_labels, it_val_aux, it_val_grads, it_val_ims = [], [], [], [], []
for num_vals in range(config.num_validation_evals):
# Validation accuracy as the average of n batches
val_vars = sess.run(val_dict.values())
it_val_dict = {
k: v
for k, v in zip(val_dict.keys(), val_vars)
}
it_val_labels += [it_val_dict['val_labels']]
it_val_scores += [it_val_dict['val_scores']]
it_val_grads += [it_val_dict['val_grad_images']]
it_val_ims += [it_val_dict['val_images']]
if val_aux_check:
iva = {
itk: itv
for itk, itv in it_val_dict.iteritems()
if 'aux_score' in itk
}
it_val_aux += [iva]
val_scores[step] = it_val_scores
val_labels[step] = it_val_labels
val_aux[step] = it_val_aux
val_images[step] = it_val_grads
val_grads[step] = it_val_ims
# End iteration
step += 1
except tf.errors.OutOfRangeError:
print 'Done with evaluation for %d epochs, %d steps.' % (config.epochs,
step)
print 'Saved to: %s' % checkpoint_dir
finally:
coord.request_stop()
coord.join(threads)
sess.close()
import ipdb
ipdb.set_trace()
np.savez(
'val_imgs_grads',
val_images=val_images, # it_val_dict['val_images'],
val_grads=val_grads, # it_val_dict['val_grad_images'],
val_labels=val_labels, # it_val_dict['val_labels'],
val_scores=val_scores) # it_val_dict['val_scores'][0])
def main(
experiment_name,
list_experiments=False,
load_and_evaluate_ckpt=None,
placeholder_data=None,
grad_images=False,
gpu_device='/gpu:0'):
"""Create a tensorflow worker to run experiments in your DB."""
if list_experiments:
exps = db.list_experiments()
print '_' * 30
print 'Initialized experiments:'
print '_' * 30
for l in exps:
print l.values()[0]
print '_' * 30
if len(exps) == 0:
print 'No experiments found.'
else:
print 'You can add to the DB with: '\
'python prepare_experiments.py --experiment=%s' % \
exps[0].values()[0]
return
if experiment_name is None:
print 'No experiment specified. Pulling one out of the DB.'
experiment_name = db.get_experiment_name()
# Prepare to run the model
config = Config()
condition_label = '%s_%s' % (experiment_name, py_utils.get_dt_stamp())
experiment_label = '%s' % (experiment_name)
log = logger.get(os.path.join(config.log_dir, condition_label))
assert experiment_name is not None, 'Empty experiment name.'
experiment_dict = experiments.experiments()[experiment_name]()
config = add_to_config(d=experiment_dict, config=config) # Globals
config.load_and_evaluate_ckpt = load_and_evaluate_ckpt
if load_and_evaluate_ckpt is not None:
# Remove the train operation and add a ckpt pointer
from ops import evaluation
config, exp_params = process_DB_exps(
experiment_name=experiment_name,
log=log,
config=config) # Update config w/ DB params
dataset_module = py_utils.import_module(
model_dir=config.dataset_info,
dataset=config.dataset)
dataset_module = dataset_module.data_processing() # hardcoded class name
train_key = [k for k in dataset_module.folds.keys() if 'train' in k]
if not len(train_key):
train_key = 'train'
else:
train_key = train_key[0]
train_data, train_means_image, train_means_label = get_data_pointers(
dataset=config.dataset,
base_dir=config.tf_records,
cv=train_key,
log=log)
val_key = [k for k in dataset_module.folds.keys() if 'val' in k]
if not len(val_key):
val_key = 'train'
else:
val_key = val_key[0]
val_data, val_means_image, val_means_label = get_data_pointers(
dataset=config.dataset,
base_dir=config.tf_records,
cv=val_key,
log=log)
# Initialize output folders
dir_list = {
'checkpoints': os.path.join(
config.checkpoints, condition_label),
'summaries': os.path.join(
config.summaries, condition_label),
'condition_evaluations': os.path.join(
config.condition_evaluations, condition_label),
'experiment_evaluations': os.path.join( # DEPRECIATED
config.experiment_evaluations, experiment_label),
'visualization': os.path.join(
config.visualizations, condition_label),
'weights': os.path.join(
config.condition_evaluations, condition_label, 'weights')
}
[py_utils.make_dir(v) for v in dir_list.values()]
# Prepare data loaders on the cpu
if all(isinstance(i, list) for i in config.data_augmentations):
if config.data_augmentations:
config.data_augmentations = py_utils.flatten_list(
config.data_augmentations,
log)
if load_and_evaluate_ckpt is not None:
config.epochs = 1
config.train_shuffle = False
config.val_shuffle = False
with tf.device('/cpu:0'):
if placeholder_data:
placeholder_shape = placeholder_data['train_image_shape']
placeholder_dtype = placeholder_data['train_image_dtype']
original_train_images = tf.placeholder(
dtype=placeholder_dtype,
shape=placeholder_shape,
name='train_images')
placeholder_shape = placeholder_data['train_label_shape']
placeholder_dtype = placeholder_data['train_label_dtype']
original_train_labels = tf.placeholder(
dtype=placeholder_dtype,
shape=placeholder_shape,
name='train_labels')
placeholder_shape = placeholder_data['val_image_shape']
placeholder_dtype = placeholder_data['val_image_dtype']
original_val_images = tf.placeholder(
dtype=placeholder_dtype,
shape=placeholder_shape,
name='val_images')
placeholder_shape = placeholder_data['val_label_shape']
placeholder_dtype = placeholder_data['val_label_dtype']
original_val_labels = tf.placeholder(
dtype=placeholder_dtype,
shape=placeholder_shape,
name='val_labels')
# Apply augmentations
(
train_images,
train_labels
) = data_loader.placeholder_image_augmentations(
images=original_train_images,
model_input_image_size=dataset_module.model_input_image_size,
labels=original_train_labels,
data_augmentations=config.data_augmentations,
batch_size=config.batch_size)
(
val_images,
val_labels
) = data_loader.placeholder_image_augmentations(
images=original_val_images,
model_input_image_size=dataset_module.model_input_image_size,
labels=original_val_labels,
data_augmentations=config.data_augmentations,
batch_size=config.batch_size)
# Store in the placeholder dict
placeholder_data['train_images'] = original_train_images
placeholder_data['train_labels'] = original_train_labels
placeholder_data['val_images'] = original_val_images
placeholder_data['val_labels'] = original_val_labels
else:
train_images, train_labels = data_loader.inputs(
dataset=train_data,
batch_size=config.batch_size,
model_input_image_size=dataset_module.model_input_image_size,
tf_dict=dataset_module.tf_dict,
data_augmentations=config.data_augmentations,
num_epochs=config.epochs,
tf_reader_settings=dataset_module.tf_reader,
shuffle=config.shuffle_train,
resize_output=config.resize_output)
if hasattr(config, 'val_augmentations'):
val_augmentations = config.val_augmentations
else:
val_augmentations = config.data_augmentations
val_images, val_labels = data_loader.inputs(
dataset=val_data,
batch_size=config.batch_size,
model_input_image_size=dataset_module.model_input_image_size,
tf_dict=dataset_module.tf_dict,
data_augmentations=val_augmentations,
num_epochs=config.epochs,
tf_reader_settings=dataset_module.tf_reader,
shuffle=config.shuffle_val,
resize_output=config.resize_output)
log.info('Created tfrecord dataloader tensors.')
# Load model specification
struct_name = config.model_struct.split(os.path.sep)[-1]
try:
model_dict = py_utils.import_module(
dataset=struct_name,
model_dir=os.path.join(
'models',
'structs',
experiment_name).replace(os.path.sep, '.')
)
except IOError:
print 'Could not find the model structure: %s in folder %s' % (
struct_name,
experiment_name)
# Inject model_dict with hyperparameters if requested
model_dict.layer_structure = hp_opt_utils.inject_model_with_hps(
layer_structure=model_dict.layer_structure,
exp_params=exp_params)
# Prepare variables for the models
if len(dataset_module.output_size) == 2:
log.warning(
'Found > 1 dimension for your output size.'
'Converting to a scalar.')
dataset_module.output_size = np.prod(
dataset_module.output_size)
if hasattr(model_dict, 'output_structure'):
# Use specified output layer
output_structure = model_dict.output_structure
else:
output_structure = None
# Correct number of output neurons if needed
if config.dataloader_override and\
'weights' in output_structure[-1].keys():
output_neurons = output_structure[-1]['weights'][0]
size_check = output_neurons != dataset_module.output_size
fc_check = output_structure[-1]['layers'][0] == 'fc'
if size_check and fc_check:
output_structure[-1]['weights'][0] = dataset_module.output_size
log.warning('Adjusted output neurons from %s to %s.' % (
output_neurons,
dataset_module.output_size))
# Prepare model on GPU
if not hasattr(dataset_module, 'input_normalization'):
dataset_module.input_normalization = None
with tf.device(gpu_device):
with tf.variable_scope('cnn') as scope:
# Training model
model = model_utils.model_class(
mean=train_means_image,
training=True,
output_size=dataset_module.output_size,
input_normalization=dataset_module.input_normalization)
train_scores, model_summary, _ = model.build(
data=train_images,
layer_structure=model_dict.layer_structure,
output_structure=output_structure,
log=log,
tower_name='cnn')
if grad_images:
oh_dims = int(train_scores.get_shape()[-1])
target_scores = tf.one_hot(train_labels, oh_dims) * train_scores
train_gradients = tf.gradients(target_scores, train_images)[0]
log.info('Built training model.')
log.debug(
json.dumps(model_summary, indent=4),
verbose=0)
print_model_architecture(model_summary)
# Normalize labels on GPU if needed
if 'normalize_labels' in exp_params.keys():
if exp_params['normalize_labels'] == 'zscore':
train_labels -= train_means_label['mean']
train_labels /= train_means_label['std']
val_labels -= train_means_label['mean']
val_labels /= train_means_label['std']
log.info('Z-scoring labels.')
elif exp_params['normalize_labels'] == 'mean':
train_labels -= train_means_label['mean']
val_labels -= val_means_label['mean']
log.info('Mean-centering labels.')
# Check the shapes of labels and scores
if not isinstance(train_scores, list):
if len(
train_scores.get_shape()) != len(
train_labels.get_shape()):
train_shape = train_scores.get_shape().as_list()
label_shape = train_labels.get_shape().as_list()
val_shape = val_scores.get_shape().as_list()
val_label_shape = val_labels.get_shape().as_list()
if len(
train_shape) == 2 and len(
label_shape) == 1 and train_shape[-1] == 1:
train_labels = tf.expand_dims(train_labels, axis=-1)
val_labels = tf.expand_dims(val_labels, axis=-1)
elif len(
train_shape) == 2 and len(
label_shape) == 1 and train_shape[-1] == 1:
train_scores = tf.expand_dims(train_scores, axis=-1)
val_scores = tf.expand_dims(val_scores, axis=-1)
# Prepare the loss function
train_loss, _ = loss_utils.loss_interpreter(
logits=train_scores, # TODO
labels=train_labels,
loss_type=config.loss_function,
weights=config.loss_weights,
dataset_module=dataset_module)
# Add loss tensorboard tracking
if isinstance(train_loss, list):
for lidx, tl in enumerate(train_loss):
tf.summary.scalar('training_loss_%s' % lidx, tl)
train_loss = tf.add_n(train_loss)
else:
tf.summary.scalar('training_loss', train_loss)
# Add weight decay if requested
if len(model.regularizations) > 0:
train_loss = loss_utils.wd_loss(
regularizations=model.regularizations,
loss=train_loss,
wd_penalty=config.regularization_strength)
assert config.lr is not None, 'No learning rate.' # TODO: Make a QC function
if config.lr > 1:
old_lr = config.lr
config.lr = loss_utils.create_lr_schedule(
train_batch=config.batch_size,
num_training=config.lr)
config.optimizer = 'momentum'
log.info('Forcing momentum classifier.')
else:
old_lr = None
train_op = loss_utils.optimizer_interpreter(
loss=train_loss,
lr=config.lr,
optimizer=config.optimizer,
constraints=config.optimizer_constraints,
model=model)
log.info('Built training loss function.')
# Add a score for the training set
train_accuracy = eval_metrics.metric_interpreter(
metric=dataset_module.score_metric, # TODO: Attach to exp cnfg
pred=train_scores, # TODO
labels=train_labels)
# Add aux scores if requested
train_aux = {}
if hasattr(dataset_module, 'aux_scores'):
for m in dataset_module.aux_scores:
train_aux[m] = eval_metrics.metric_interpreter(
metric=m,
pred=train_scores,
labels=train_labels) # [0] # TODO: Fix for multiloss
# Prepare remaining tensorboard summaries
if config.tensorboard_images:
if len(train_images.get_shape()) == 4:
tf_fun.image_summaries(train_images, tag='Training images')
if (np.asarray(
train_labels.get_shape().as_list()) > 1).sum() > 2:
tf_fun.image_summaries(
train_labels,
tag='Training_targets')
tf_fun.image_summaries(
train_scores,
tag='Training_predictions')
if isinstance(train_accuracy, list):
for tidx, ta in enumerate(train_accuracy):
tf.summary.scalar('training_accuracy_%s' % tidx, ta)
else:
tf.summary.scalar('training_accuracy', train_accuracy)
if config.pr_curve:
if isinstance(train_scores, list):
for pidx, train_score in enumerate(train_scores):
train_label = train_labels[:, pidx]
pr_summary.op(
tag='training_pr_%s' % pidx,
predictions=tf.cast(
tf.argmax(
train_score,
axis=-1),
tf.float32),
labels=tf.cast(train_label, tf.bool),
display_name='training_precision_recall_%s' % pidx)
else:
pr_summary.op(
tag='training_pr',
predictions=tf.cast(
tf.argmax(
train_scores,
axis=-1),
tf.float32),
labels=tf.cast(train_labels, tf.bool),
display_name='training_precision_recall')
log.info('Added training summaries.')
with tf.variable_scope('cnn', tf.AUTO_REUSE) as scope:
# Validation model
scope.reuse_variables()
val_model = model_utils.model_class(
mean=train_means_image, # Normalize with train data
training=False,
output_size=dataset_module.output_size,
input_normalization=dataset_module.input_normalization)
val_scores, _, _ = val_model.build( # Ignore summary
data=val_images,
layer_structure=model_dict.layer_structure,
output_structure=output_structure,
log=log,
tower_name='cnn')
if grad_images:
oh_dims = int(val_scores.get_shape()[-1])
target_scores = tf.one_hot(val_labels, oh_dims) * val_scores
val_gradients = tf.gradients(target_scores, val_images)[0]
log.info('Built validation model.')
# Check the shapes of labels and scores
val_loss, _ = loss_utils.loss_interpreter(
logits=val_scores,
labels=val_labels,
loss_type=config.loss_function,
weights=config.loss_weights,
dataset_module=dataset_module)
# Add loss tensorboard tracking
if isinstance(val_loss, list):
for lidx, tl in enumerate(val_loss):
tf.summary.scalar('validation_loss_%s' % lidx, tl)
val_loss = tf.add_n(val_loss)
else:
tf.summary.scalar('validation_loss', val_loss)
# Add a score for the validation set
val_accuracy = eval_metrics.metric_interpreter(
metric=dataset_module.score_metric, # TODO
pred=val_scores,
labels=val_labels)
# Add aux scores if requested
val_aux = {}
if hasattr(dataset_module, 'aux_scores'):
for m in dataset_module.aux_scores:
val_aux[m] = eval_metrics.metric_interpreter(
metric=m,
pred=val_scores,
labels=val_labels) # [0] # TODO: Fix for multiloss
# Prepare tensorboard summaries
if config.tensorboard_images:
if len(val_images.get_shape()) == 4:
tf_fun.image_summaries(
val_images,
tag='Validation')
if (np.asarray(
val_labels.get_shape().as_list()) > 1).sum() > 2:
tf_fun.image_summaries(
val_labels,
tag='Validation_targets')
tf_fun.image_summaries(
val_scores,
tag='Validation_predictions')
if isinstance(val_accuracy, list):
for vidx, va in enumerate(val_accuracy):
tf.summary.scalar('validation_accuracy_%s' % vidx, va)
else:
tf.summary.scalar('validation_accuracy', val_accuracy)
if config.pr_curve:
if isinstance(val_scores, list):
for pidx, val_score in enumerate(val_scores):
val_label = val_labels[:, pidx]
pr_summary.op(
tag='validation_pr_%s' % pidx,
predictions=tf.cast(
tf.argmax(
val_score,
axis=-1),
tf.float32),
labels=tf.cast(val_label, tf.bool),
display_name='validation_precision_recall_%s' %
pidx)
else:
pr_summary.op(
tag='validation_pr',
predictions=tf.cast(
tf.argmax(
val_scores,
axis=-1),
tf.float32),
labels=tf.cast(val_labels, tf.bool),
display_name='validation_precision_recall')
log.info('Added validation summaries.')
# Set up summaries and saver
if not hasattr(config, 'max_to_keep'):
config.max_to_keep = None
saver = tf.train.Saver(
var_list=tf.global_variables(),
max_to_keep=config.max_to_keep)
summary_op = tf.summary.merge_all()
# Initialize the graph
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# Need to initialize both of these if supplying num_epochs to inputs
sess.run(
tf.group(
tf.global_variables_initializer(),
tf.local_variables_initializer())
)
summary_writer = tf.summary.FileWriter(dir_list['summaries'], sess.graph)
# Set up exemplar threading
if placeholder_data:
coord, threads = None, None
else:
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
# Create dictionaries of important training and validation information
train_dict = {
'train_loss': train_loss,
'train_images': train_images,
'train_labels': train_labels,
'train_op': train_op,
'train_scores': train_scores
}
val_dict = {
'val_loss': val_loss,
'val_images': val_images,
'val_labels': val_labels,
'val_scores': val_scores,
}
if grad_images:
train_dict['train_gradients'] = train_gradients
val_dict['val_gradients'] = val_gradients
if isinstance(train_accuracy, list):
for tidx, (ta, va) in enumerate(zip(train_accuracy, val_accuracy)):
train_dict['train_accuracy_%s' % tidx] = ta
val_dict['val_accuracy_%s' % tidx] = va
else:
train_dict['train_accuracy_0'] = train_accuracy
val_dict['val_accuracy_0'] = val_accuracy
if load_and_evaluate_ckpt is not None:
# Remove the train operation and add a ckpt pointer
del train_dict['train_op']
if hasattr(dataset_module, 'aux_score'):
# Attach auxillary scores to tensor dicts
for m in dataset_module.aux_scores:
train_dict['train_aux_%s' % m] = train_aux[m]
val_dict['val_aux_%s' % m] = val_aux[m]
# Start training loop
if old_lr is not None:
config.lr = old_lr
np.save(
os.path.join(
dir_list['condition_evaluations'], 'training_config_file'),
config)
log.info('Starting training')
if load_and_evaluate_ckpt is not None:
return evaluation.evaluation_loop(
config=config,
db=db,
coord=coord,
sess=sess,
summary_op=summary_op,
summary_writer=summary_writer,
saver=saver,
threads=threads,
summary_dir=dir_list['summaries'],
checkpoint_dir=dir_list['checkpoints'],
weight_dir=dir_list['weights'],
train_dict=train_dict,
val_dict=val_dict,
train_model=model,
val_model=val_model,
exp_params=exp_params,
placeholder_data=placeholder_data)
else:
output_dict = training.training_loop(
config=config,
db=db,
coord=coord,
sess=sess,
summary_op=summary_op,
summary_writer=summary_writer,
saver=saver,
threads=threads,
summary_dir=dir_list['summaries'],
checkpoint_dir=dir_list['checkpoints'],
weight_dir=dir_list['weights'],
train_dict=train_dict,
val_dict=val_dict,
train_model=model,
val_model=val_model,
exp_params=exp_params)
log.info('Finished training.')
model_name = config.model_struct.replace('/', '_')
if output_dict is not None:
py_utils.save_npys(
data=output_dict,
model_name=model_name,
output_string=dir_list['experiment_evaluations'])
def train_vgg16(device):
os.environ['CUDA_VISIBLE_DEVICES'] = str(device)
config = vggConfig()
train_data = config.training_images
train_meta = np.load(config.training_meta)
print 'Using train tfrecords: %s | %s image/heatmap combos' % (
[train_data], len(train_meta['labels']))
validation_data = config.validation_images
val_meta = np.load(config.validation_meta)
print 'Using validation tfrecords: %s | %s images' % (
validation_data, len(val_meta['labels']))
# Make output directories if they do not exist
dt_stamp = 'grayscale_' +\
str(config.initial_learning_rate)[2:] + '_' + str(
len(train_meta['labels'])) + '_' + re.split(
'\.', str(datetime.now()))[0].\
replace(' ', '_').replace(':', '_').replace('-', '_')
config.train_checkpoint = os.path.join(config.train_checkpoint,
dt_stamp) # timestamp this run
out_dir = os.path.join(config.results, dt_stamp)
dir_list = [
config.train_checkpoint, config.train_summaries, config.results,
out_dir
]
[make_dir(d) for d in dir_list]
print '-' * 60
print('Training model:' + dt_stamp)
print '-' * 60
# Prepare data on CPU
train_images, train_labels = inputs(train_data,
config.train_batch,
config.image_size,
config.model_image_size[:2],
train=config.data_augmentations,
num_epochs=config.epochs,
return_heatmaps=False,
is_grayscale=True)
val_images, val_labels = inputs(validation_data,
config.validation_batch,
config.image_size,
config.model_image_size[:2],
num_epochs=None,
return_heatmaps=False,
is_grayscale=True)
step = get_or_create_global_step()
step_op = tf.assign(step, step + 1)
# Prepare model on GPU
with tf.variable_scope('cnn') as scope:
vgg = vgg16.model_struct()
train_mode = tf.get_variable(name='training', initializer=True)
vgg.build(train_images,
is_training=True,
is_grayscale=True,
batchnorm=True)
# Prepare the loss function
loss = softmax_loss(logits=vgg.fc8, labels=train_labels)
# Add weight decay of fc6/7/8
if config.wd_penalty is not None:
loss = wd_loss(loss=loss,
trainables=tf.trainable_variables(),
config=config)
lr = tf.train.exponential_decay(
learning_rate=config.initial_learning_rate,
global_step=step_op,
decay_steps=config.decay_steps,
decay_rate=config.learning_rate_decay_factor,
staircase=True)
if config.optimizer == "adam":
update_ops = tf.get_collection(tf.GraphKeys.UPDATE_OPS)
with tf.control_dependencies(update_ops):
train_op = tf.train.AdamOptimizer(lr).minimize(loss)
elif config.optimizer == "sgd":
update_ops = tf.get_collection(tf.GraphKeys.UPDATE_OPS)
with tf.control_dependencies(update_ops):
train_op = tf.train.GradientDescentOptimizer(lr).minimize(loss)
elif config.optimizer == "nestrov":
update_ops = tf.get_collection(tf.GraphKeys.UPDATE_OPS)
with tf.control_dependencies(update_ops):
train_op = tf.train.MomentumOptimizer(
lr, config.momentum, use_nesterov=True).minimize(loss)
else:
raise Exception(
"Not known optimizer! options are adam, sgd or nestrov")
train_accuracy = class_accuracy(vgg.prob,
train_labels) # training accuracy
# Add summaries for debugging
tf.summary.image('train images', train_images)
tf.summary.image('validation images', val_images)
tf.summary.scalar("loss", loss)
tf.summary.scalar("training accuracy", train_accuracy)
# Setup validation op
scope.reuse_variables()
# Validation graph is the same as training except no batchnorm
val_vgg = vgg16.model_struct()
val_vgg.build(val_images,
is_training=False,
is_grayscale=True,
batchnorm=True)
# Calculate validation accuracy
val_accuracy = class_accuracy(val_vgg.prob, val_labels)
tf.summary.scalar("validation accuracy", val_accuracy)
# Set up summaries and saver
saver = tf.train.Saver(tf.global_variables(),
max_to_keep=config.keep_checkpoints)
restorer = tf.train.Saver()
summary_op = tf.summary.merge_all()
# Initialize the graph
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# Need to initialize both of these if supplying num_epochs to inputs
sess.run(
tf.group(tf.global_variables_initializer(),
tf.local_variables_initializer()))
restorer.restore(
sess,
'/media/data_cifs/andreas/vgg_train/checkpoints/grayscale_-05_1283163_2017_09_09_19_20_09/model_228000.ckpt-228000'
)
summary_dir = os.path.join(config.train_summaries, dt_stamp)
summary_writer = tf.summary.FileWriter(summary_dir, sess.graph)
# Set up exemplar threading
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
# Start training loop
np.save(os.path.join(out_dir, 'training_config_file'), config)
training_loop(config, coord, sess, train_op, step_op, summary_op,
summary_writer, loss, saver, threads, out_dir, summary_dir,
validation_data, val_accuracy, train_accuracy, lr)
def test_vgg16():
dbc = config.config()
validation_pointer = os.path.join(
dbc.packaged_data_path,
'%s_%s.%s' % ('validation', dbc.packaged_data_file, dbc.output_format))
# Prepare data on CPU
with tf.device('/cpu:0'):
val_images, val_labels, val_files = inputs(
tfrecord_file=validation_pointer,
batch_size=dbc.validation_batch,
im_size=dbc.validation_image_size,
model_input_shape=dbc.model_image_size[:2],
num_epochs=1,
data_augmentations=dbc.validation_augmentations,
shuffle_batch=True)
# Prepare pretrained model on GPU
with tf.device('/gpu:0'):
with tf.variable_scope('cnn'):
cnn = vgg16.Vgg16()
validation_mode = tf.Variable(False, name='training')
cnn.build(val_images,
output_shape=1000,
train_mode=validation_mode)
sample_layer = cnn['fc7']
accs = class_accuracy(cnn.prob, val_labels)
saver = tf.train.Saver(tf.all_variables(), max_to_keep=10)
# Initialize the graph
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
sess.run(
tf.group(tf.initialize_all_variables(),
tf.initialize_local_variables()))
# Set up exemplar threading
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
saver.restore(sess, dbc.model_types['vgg16'][0])
# Start training loop
results = {'accs': [], 'preds': [], 'labs': [], 'files': []}
np_path = os.path.join(dbc.checkpoint_directory, 'validation_results')
step = 0
scores, labels = [], []
try:
print 'Testing model'
while not coord.should_stop():
start_time = time.time()
score, lab, f, probs = sess.run(
[sample_layer, val_labels, val_files, cnn['prob']])
import ipdb
ipdb.set_trace()
print acc
except tf.errors.OutOfRangeError:
print 'Done testing.'
finally:
np.savez(np_path, **results)
print 'Saved to: %s' % np_path
coord.request_stop()
coord.join(threads)
sess.close()
print '%.4f%% correct' % np.mean(results['accs'])
if simulate_subjects:
sim_subs = []
print 'Simulating subjects'
scores = np.concatenate(scores)
labels = np.concatenate(results['labs'])
for sub in tqdm(range(simulate_subjects)):
it_results = {'accs': [], 'preds': [], 'labs': [], 'files': []}
neuron_drop = np.random.rand(scores.shape[1]) > .95
it_scores = np.copy(scores)
it_scores[:, neuron_drop] = 0
pred = svc.predict(it_scores)
acc = np.mean(pred == labels)
it_results['accs'] += [acc]
it_results['preds'] += [pred]
it_results['labs'] += [labels]
it_results['files'] += [np.concatenate(results['files'])]
sim_subs += [it_results]
np.save(np_path + '_sim_subs', sim_subs)
def model_builder(
params,
config,
model_spec,
gpu_device,
cpu_device,
placeholders=False,
tensorboard_images=False):
"""Standard model building routines."""
config = py_utils.add_to_config(
d=params,
config=config)
exp_label = '%s_%s' % (params['exp_name'], py_utils.get_dt_stamp())
directories = py_utils.prepare_directories(config, exp_label)
dataset_module = py_utils.import_module(
model_dir=config.dataset_info,
dataset=config.dataset)
dataset_module = dataset_module.data_processing() # hardcoded class name
train_key = [k for k in dataset_module.folds.keys() if 'train' in k]
if not len(train_key):
train_key = 'train'
else:
train_key = train_key[0]
(
train_data,
train_means_image,
train_means_label) = py_utils.get_data_pointers(
dataset=config.dataset,
base_dir=config.tf_records,
cv=train_key)
val_key = [k for k in dataset_module.folds.keys() if 'val' in k]
if not len(val_key):
val_key = 'train'
else:
val_key = val_key[0]
if hasattr(config, 'val_dataset'):
val_dataset = config.val_dataset
else:
val_dataset = config.dataset
val_data, val_means_image, val_means_label = py_utils.get_data_pointers(
dataset=val_dataset,
base_dir=config.tf_records,
cv=val_key)
# Create data tensors
with tf.device(cpu_device):
if placeholders:
(
train_images,
train_labels,
val_images,
val_labels) = get_placeholders(dataset_module, config)
placeholders = dataset_module.get_data()
else:
train_images, train_labels = data_loader.inputs(
dataset=train_data,
batch_size=config.batch_size,
model_input_image_size=dataset_module.model_input_image_size,
tf_dict=dataset_module.tf_dict,
data_augmentations=config.data_augmentations,
num_epochs=config.epochs,
tf_reader_settings=dataset_module.tf_reader,
shuffle=config.shuffle_train)
val_images, val_labels = data_loader.inputs(
dataset=val_data,
batch_size=config.batch_size,
model_input_image_size=dataset_module.model_input_image_size,
tf_dict=dataset_module.tf_dict,
data_augmentations=config.val_augmentations,
num_epochs=config.epochs,
tf_reader_settings=dataset_module.tf_reader,
shuffle=config.shuffle_val)
# Build training and val models
with tf.device(gpu_device):
train_logits, train_hgru_act = model_spec(
data_tensor=train_images,
reuse=None,
training=True)
val_logits, val_hgru_act = model_spec(
data_tensor=val_images,
reuse=tf.AUTO_REUSE,
training=False)
# Derive loss
loss_type = None
if hasattr(config, 'loss_type'):
loss_type = config.loss_type
train_loss = losses.derive_loss(
labels=train_labels,
logits=train_logits,
loss_type=loss_type)
val_loss = losses.derive_loss(
labels=val_labels,
logits=val_logits,
loss_type=loss_type)
if hasattr(config, 'metric_type'):
metric_type = config.metric_type
else:
metric_type = 'accuracy'
if metric_type == 'pearson':
train_accuracy = metrics.pearson_score(
labels=train_labels,
pred=train_logits,
REDUCTION=tf.reduce_mean)
val_accuracy = metrics.pearson_score(
labels=val_labels,
pred=val_logits,
REDUCTION=tf.reduce_mean)
else:
train_accuracy = metrics.class_accuracy(
labels=train_labels,
logits=train_logits)
val_accuracy = metrics.class_accuracy(
labels=val_labels,
logits=val_logits)
tf.summary.scalar('train_accuracy', train_accuracy)
tf.summary.scalar('val_accuracy', val_accuracy)
if tensorboard_images:
tf.summary.image('train_images', train_images)
tf.summary.image('val_images', val_images)
# Build optimizer
train_op = optimizers.get_optimizer(
train_loss,
config['lr'],
config['optimizer'])
# Initialize tf variables
saver = tf.train.Saver(
var_list=tf.global_variables())
summary_op = tf.summary.merge_all()
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
sess.run(
tf.group(
tf.global_variables_initializer(),
tf.local_variables_initializer()))
summary_writer = tf.summary.FileWriter(
directories['summaries'],
sess.graph)
if not placeholders:
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
else:
coord, threads = None, None
# Create dictionaries of important training and validation information
train_dict = {
'train_loss': train_loss,
'train_images': train_images,
'train_labels': train_labels,
'train_op': train_op,
'train_accuracy': train_accuracy
}
if isinstance(train_hgru_act, dict):
for k, v in train_hgru_act.iteritems():
train_dict[k] = v
else:
train_dict['activity'] = train_hgru_act
val_dict = {
'val_loss': val_loss,
'val_images': val_images,
'val_labels': val_labels,
'val_accuracy': val_accuracy,
}
if isinstance(val_hgru_act, dict):
for k, v in val_hgru_act.iteritems():
val_dict[k] = v
else:
val_dict['activity'] = val_hgru_act
# Count parameters
num_params = np.sum(
[np.prod(x.get_shape().as_list()) for x in tf.trainable_variables()])
print 'Model has approximately %s trainable params.' % num_params
# Create datastructure for saving data
ds = data_structure.data(
batch_size=config.batch_size,
validation_iters=config.validation_iters,
num_validation_evals=config.num_validation_evals,
shuffle_val=config.shuffle_val,
lr=config.lr,
loss_function=config.loss_function,
optimizer=config.optimizer,
model_name=config.model_name,
dataset=config.dataset,
num_params=num_params,
output_directory=config.results)
# Start training loop
training.training_loop(
config=config,
coord=coord,
sess=sess,
summary_op=summary_op,
summary_writer=summary_writer,
saver=saver,
threads=threads,
directories=directories,
train_dict=train_dict,
val_dict=val_dict,
exp_label=exp_label,
data_structure=ds,
placeholders=placeholders)
def build_model(exp_params,
config,
log,
dt_string,
gpu_device,
cpu_device,
use_db=True,
add_config=None,
placeholders=False,
checkpoint=None,
test=False,
map_out=None,
num_batches=None,
tensorboard_images=False):
"""Standard model building routines."""
config = py_utils.add_to_config(d=exp_params, config=config)
if not hasattr(config, 'force_path'):
config.force_path = False
exp_label = '%s_%s_%s' % (exp_params['model'], exp_params['experiment'],
py_utils.get_dt_stamp())
directories = py_utils.prepare_directories(config, exp_label)
dataset_module = py_utils.import_module(pre_path=config.dataset_classes,
module=config.train_dataset)
train_dataset_module = dataset_module.data_processing()
if not config.force_path:
(train_data, _, _) = py_utils.get_data_pointers(
dataset=train_dataset_module.output_name,
base_dir=config.tf_records,
local_dir=config.local_tf_records,
cv='train')
else:
train_data = train_dataset_module.train_path
dataset_module = py_utils.import_module(pre_path=config.dataset_classes,
module=config.val_dataset)
val_dataset_module = dataset_module.data_processing()
if not config.force_path:
val_data, _, _ = py_utils.get_data_pointers(
dataset=val_dataset_module.output_name,
base_dir=config.tf_records,
local_dir=config.local_tf_records,
cv='val')
else:
val_data = train_dataset_module.val_path
# val_means_image, val_means_label = None, None
# Create data tensors
if hasattr(train_dataset_module, 'aux_loss'):
train_aux_loss = train_dataset_module.aux_loss
else:
train_aux_loss = None
with tf.device(cpu_device):
if placeholders and not test:
# Train with placeholders
(pl_train_images, pl_train_labels, pl_val_images, pl_val_labels,
train_images, train_labels, val_images,
val_labels) = get_placeholders(train_dataset=train_dataset_module,
val_dataset=val_dataset_module,
config=config)
train_module_data = train_dataset_module.get_data()
val_module_data = val_dataset_module.get_data()
placeholders = {
'train': {
'images': train_module_data[0]['train'],
'labels': train_module_data[1]['train']
},
'val': {
'images': val_module_data[0]['val'],
'labels': val_module_data[1]['val']
},
}
train_aux, val_aux = None, None
elif placeholders and test:
test_dataset_module = train_dataset_module
# Test with placeholders
(pl_test_images, pl_test_labels, test_images,
test_labels) = get_placeholders_test(
test_dataset=test_dataset_module, config=config)
test_module_data = test_dataset_module.get_data()
placeholders = {
'test': {
'images': test_module_data[0]['test'],
'labels': test_module_data[1]['test']
},
}
train_aux, val_aux = None, None
else:
train_images, train_labels, train_aux = data_loader.inputs(
dataset=train_data,
batch_size=config.train_batch_size,
model_input_image_size=train_dataset_module.
model_input_image_size,
tf_dict=train_dataset_module.tf_dict,
data_augmentations=config.train_augmentations,
num_epochs=config.epochs,
aux=train_aux_loss,
tf_reader_settings=train_dataset_module.tf_reader,
shuffle=config.shuffle_train)
if hasattr(val_dataset_module, 'val_model_input_image_size'):
val_dataset_module.model_input_image_size = val_dataset_module.val_model_input_image_size
val_images, val_labels, val_aux = data_loader.inputs(
dataset=val_data,
batch_size=config.val_batch_size,
model_input_image_size=val_dataset_module.
model_input_image_size,
tf_dict=val_dataset_module.tf_dict,
data_augmentations=config.val_augmentations,
num_epochs=None,
tf_reader_settings=val_dataset_module.tf_reader,
shuffle=config.shuffle_val)
# Build training and val models
model_spec = py_utils.import_module(module=config.model,
pre_path=config.model_classes)
if hasattr(train_dataset_module, 'force_output_size'):
train_dataset_module.output_size = train_dataset_module.force_output_size
if hasattr(val_dataset_module, 'force_output_size'):
val_dataset_module.output_size = val_dataset_module.force_output_size
if hasattr(config, 'loss_function'):
train_loss_function = config.loss_function
val_loss_function = config.loss_function
else:
train_loss_function = config.train_loss_function
val_loss_function = config.val_loss_function
# Route test vs train/val
h_check = [
x for x in tf.trainable_variables()
if 'homunculus' in x.name or 'humonculus' in x.name
]
if not hasattr(config, 'default_restore'):
config.default_restore = False
if test:
assert len(gpu_device) == 1, 'Testing only works with 1 gpu.'
gpu_device = gpu_device[0]
with tf.device(gpu_device):
if not placeholders:
test_images = val_images
test_labels = val_labels
test_dataset_module = val_dataset_module
test_logits, test_vars = model_spec.build_model(
data_tensor=test_images,
reuse=None,
training=False,
output_shape=test_dataset_module.output_size)
if test_logits.dtype is not tf.float32:
test_logits = tf.cast(test_logits, tf.float32)
# Derive loss
if not hasattr(config, 'test_loss_function'):
test_loss_function = val_loss_function
else:
test_loss_function = config.test_loss_function
test_loss = losses.derive_loss(labels=test_labels,
logits=test_logits,
loss_type=test_loss_function)
# Derive score
test_score = losses.derive_score(labels=test_labels,
logits=test_logits,
loss_type=test_loss_function,
score_type=config.score_function)
# Initialize model
(sess, saver, summary_op, summary_writer, coord, threads,
restore_saver) = initialize_tf(config=config,
placeholders=placeholders,
ckpt=checkpoint,
default_restore=config.default_restore,
directories=directories)
if placeholders:
proc_images = test_images
proc_labels = test_labels
test_images = pl_test_images
test_labels = pl_test_labels
_, H, W, _ = test_vars['model_output_y'].shape
jacobian = tf.gradients(test_logits, test_vars['model_output_x'])[
0] # g.batch_jacobian(test_vars['model_output_x'], test_images)
test_dict = {
'test_loss': test_loss,
'test_score': test_score,
'test_images': test_images,
'test_labels': test_labels,
'test_logits': test_logits,
'test_jacobian': jacobian
}
if placeholders:
test_dict['test_proc_images'] = proc_images
test_dict['test_proc_labels'] = proc_labels
if len(h_check):
test_dict['homunculus'] = h_check[0]
if isinstance(test_vars, dict):
for k, v in test_vars.iteritems():
test_dict[k] = v
else:
test_dict['activity'] = test_vars
else:
train_losses, val_losses, tower_grads, norm_updates = [], [], [], []
train_scores, val_scores = [], []
train_image_list, train_label_list = [], []
val_image_list, val_label_list = [], []
train_reuse = None
if not hasattr(config, 'lr_schedule'):
config.lr_schedule = None
if hasattr(config, 'loss_function'):
train_loss_function = config.loss_function
val_loss_function = config.loss_function
else:
train_loss_function = config.train_loss_function
val_loss_function = config.val_loss_function
# Prepare loop
if not placeholders:
train_batch_queue = tf_fun.get_batch_queues(images=train_images,
labels=train_labels,
gpu_device=gpu_device)
val_batch_queue = tf_fun.get_batch_queues(images=val_images,
labels=val_labels,
gpu_device=gpu_device)
config.lr = optimizers.get_lr_schedule(lr=config.lr,
lr_schedule=config.lr_schedule)
opt = optimizers.get_optimizers(optimizer=config.optimizer,
lr=config.lr,
dtype=train_images.dtype)
with tf.device(cpu_device):
global_step = tf.train.get_or_create_global_step()
for i, gpu in enumerate(gpu_device):
# rs = tf.AUTO_REUSE if i > 0 else None
with tf.device(gpu):
with tf.name_scope('tower_%d' % i) as scope:
# Prepare tower data
if placeholders:
# Multi-gpu: will have to split
# train_images per gpu by hand
train_image_batch = train_images
val_image_batch = val_images
train_label_batch = train_labels
val_label_batch = val_labels
else:
(train_image_batch,
train_label_batch) = train_batch_queue.dequeue()
(val_image_batch,
val_label_batch) = val_batch_queue.dequeue()
train_image_list += [train_image_batch]
train_label_list += [train_label_batch]
val_image_list += [val_image_batch]
val_label_list += [val_label_batch]
# Build models
train_logits, train_vars = model_spec.build_model(
data_tensor=train_image_batch,
reuse=train_reuse,
training=True,
output_shape=train_dataset_module.output_size)
num_training_vars = len(tf.trainable_variables())
val_logits, val_vars = model_spec.build_model(
data_tensor=val_image_batch,
reuse=True,
training=False,
output_shape=val_dataset_module.output_size)
num_validation_vars = len(tf.trainable_variables())
assert num_training_vars == num_validation_vars, \
'Found a different # of train and val variables.'
train_reuse = True
# Derive losses
if train_logits.dtype is not tf.float32:
train_logits = tf.cast(train_logits, tf.float32)
if val_logits.dtype is not tf.float32:
val_logits = tf.cast(val_logits, tf.float32)
train_loss = losses.derive_loss(
labels=train_label_batch,
logits=train_logits,
images=train_image_batch,
loss_type=train_loss_function)
val_loss = losses.derive_loss(
labels=val_label_batch,
logits=val_logits,
images=val_image_batch,
loss_type=val_loss_function)
# Derive score
train_score = losses.derive_score(
labels=train_labels,
logits=train_logits,
loss_type=train_loss_function,
score_type=config.score_function)
val_score = losses.derive_score(
labels=val_labels,
logits=val_logits,
loss_type=val_loss_function,
score_type=config.score_function)
# Add aux losses if requested
if hasattr(model_spec, 'weight_decay'):
wd = (model_spec.weight_decay() * tf.add_n([
tf.nn.l2_loss(v)
for v in tf.trainable_variables()
if 'batch_normalization' not in v.name
and 'horizontal' not in v.name
and 'mu' not in v.name and 'beta' not in v.name
and 'intercept' not in v.name
]))
tf.summary.scalar('weight_decay', wd)
train_loss += wd
if hasattr(model_spec, 'bsds_weight_decay'):
wd = (model_spec.bsds_weight_decay()['l2'] *
tf.add_n([
tf.nn.l2_loss(v)
for v in tf.trainable_variables()
if 'horizontal' not in v.name
and 'norm' not in v.name
]))
tf.summary.scalar('weight_decay_readout', wd)
train_loss += wd
wd = (model_spec.bsds_weight_decay()['l1'] *
tf.add_n([
tf.reduce_sum(tf.abs(v))
for v in tf.trainable_variables()
if 'horizontal' in v.name
]))
tf.summary.scalar('weight_decay_horizontal', wd)
train_loss += wd
if hasattr(model_spec, 'orthogonal'):
weights = [
v for v in tf.trainable_variables()
if 'horizontal' in v.name
]
assert len(weights) is not None, \
'No horizontal weights for laplace.'
wd = model_spec.orthogonal() * tf.add_n(
[tf_fun.orthogonal(w) for w in weights])
tf.summary.scalar('weight_decay', wd)
train_loss += wd
if hasattr(model_spec, 'laplace'):
weights = [
v for v in tf.trainable_variables()
if 'horizontal' in v.name
]
assert len(weights) is not None, \
'No horizontal weights for laplace.'
wd = model_spec.laplace() * tf.add_n(
[tf_fun.laplace(w) for w in weights])
tf.summary.scalar('weight_decay', wd)
train_loss += wd
# Derive auxilary losses
if hasattr(config, 'aux_loss'):
aux_loss_type, scale = config.aux_loss.items()[0]
for k, v in train_vars.iteritems():
# if k in train_dataset_module.aux_loss.keys():
# (
# aux_loss_type,
# scale
# ) = train_dataset_module.aux_loss[k]
train_loss += (losses.derive_loss(
labels=train_labels,
logits=v,
loss_type=aux_loss_type) * scale)
# Gather everything
train_losses += [train_loss]
val_losses += [val_loss]
train_scores += [train_score]
val_scores += [val_score]
# Compute and store gradients
with tf.variable_scope(tf.get_variable_scope(),
reuse=tf.AUTO_REUSE):
grads = opt.compute_gradients(train_loss)
optimizers.check_grads(grads)
tower_grads += [grads]
# Gather normalization variables
norm_updates += [
tf.get_collection(tf.GraphKeys.UPDATE_OPS,
scope=scope)
]
# Recompute and optimize gradients
grads = optimizers.average_gradients(tower_grads)
if hasattr(config, 'clip_gradients') and config.clip_gradients:
grads = optimizers.apply_grad_clip(grads, config.clip_gradients)
op_vars = []
if hasattr(config, 'exclusion_lr') and hasattr(config,
'exclusion_scope'):
grads_0 = [
x for x in grads if config.exclusion_scope not in x[1].name
]
grads_1 = [x for x in grads if config.exclusion_scope in x[1].name]
op_vars_0 = optimizers.apply_gradients(opt=opt,
grads=grads_0,
global_step=global_step)
opt_1 = optimizers.get_optimizers(optimizer=config.optimizer,
lr=config.exclusion_lr,
dtype=train_images.dtype)
op_vars_1 = optimizers.apply_gradients(opt=opt_1,
grads=grads_1,
global_step=global_step)
op_vars += [op_vars_0]
op_vars += [op_vars_1]
else:
op_vars += [
optimizers.apply_gradients(opt=opt,
grads=grads,
global_step=global_step)
]
if not hasattr(config, 'variable_moving_average'):
config.variable_moving_average = False
if config.variable_moving_average:
variable_averages = tf.train.ExponentialMovingAverage(
config.variable_moving_average, global_step)
op_vars += [variable_averages.apply(tf.trainable_variables())]
if len(norm_updates):
op_vars += [tf.group(*norm_updates)]
train_op = tf.group(*op_vars)
# Summarize losses and scores
train_loss = tf.reduce_mean(train_losses)
val_loss = tf.reduce_mean(val_losses)
train_score = tf.reduce_mean(train_scores)
val_score = tf.reduce_mean(val_scores)
if len(train_image_list) > 1:
train_image_list = tf.stack(train_image_list, axis=0)
train_label_list = tf.stack(train_label_list, axis=0)
else:
train_image_list = train_image_list[0]
train_label_list = train_label_list[0]
if len(val_image_list) > 1:
val_image_list = tf.stack(val_image_list, axis=0)
val_label_list = tf.stack(val_label_list, axis=0)
else:
val_image_list = val_image_list[0]
val_label_list = val_label_list[0]
tf.summary.scalar('train_loss', train_loss)
tf.summary.scalar('val_loss', val_loss)
if tensorboard_images:
tf.summary.image('train_images', train_images)
tf.summary.image('val_images', val_images)
# Initialize model
(sess, saver, summary_op, summary_writer, coord, threads,
restore_saver) = initialize_tf(config=config,
placeholders=placeholders,
ckpt=checkpoint,
default_restore=config.default_restore,
directories=directories)
# Create dictionaries of important training and validation information
if placeholders:
proc_train_images = train_images
proc_train_labels = train_labels
proc_val_images = val_images
proc_val_labels = val_labels
train_images = pl_train_images
train_labels = pl_train_labels
val_images = pl_val_images
val_labels = pl_val_labels
train_dict = {
'train_loss': train_loss,
'train_score': train_score,
'train_images': train_image_list,
'train_labels': train_label_list,
'train_logits': train_logits,
'train_op': train_op
}
if placeholders:
train_dict['proc_train_images'] = proc_train_images
train_dict['proc_train_labels'] = proc_train_labels
if train_aux is not None:
train_dict['train_aux'] = train_aux
if tf.contrib.framework.is_tensor(config.lr):
train_dict['lr'] = config.lr
else:
train_dict['lr'] = tf.constant(config.lr)
if isinstance(train_vars, dict):
for k, v in train_vars.iteritems():
train_dict[k] = v
else:
train_dict['activity'] = train_vars
if hasattr(config, 'save_gradients') and config.save_gradients:
grad = tf.gradients(train_logits, train_images)[0]
if grad is not None:
train_dict['gradients'] = grad
else:
log.warning('Could not calculate val gradients.')
val_dict = {
'val_loss': val_loss,
'val_score': val_score,
'val_images': val_image_list,
'val_logits': val_logits,
'val_labels': val_label_list,
}
if placeholders:
val_dict['proc_val_images'] = proc_val_images
val_dict['proc_val_labels'] = proc_val_labels
if val_aux is not None:
val_dict['aux'] = val_aux
if isinstance(val_vars, dict):
for k, v in val_vars.iteritems():
val_dict[k] = v
else:
val_dict['activity'] = val_vars
if hasattr(config, 'save_gradients') and config.save_gradients:
grad = tf.gradients(val_logits, val_images)[0]
if grad is not None:
val_dict['gradients'] = grad
else:
log.warning('Could not calculate val gradients.')
if len(h_check):
val_dict['homunculus'] = h_check[0]
# Add optional info to the config
if add_config is not None:
extra_list = add_config.split(',')
for eidx, extra in enumerate(extra_list):
setattr(config, 'extra_%s' % eidx, extra)
# Count parameters
num_params = tf_fun.count_parameters(var_list=tf.trainable_variables())
print 'Model has approximately %s trainable params.' % num_params
if test:
return training.test_loop(log=log,
config=config,
sess=sess,
summary_op=summary_op,
summary_writer=summary_writer,
saver=saver,
restore_saver=restore_saver,
directories=directories,
test_dict=test_dict,
exp_label=exp_label,
num_params=num_params,
checkpoint=checkpoint,
num_batches=num_batches,
save_weights=config.save_weights,
save_checkpoints=config.save_checkpoints,
save_activities=config.save_activities,
save_gradients=config.save_gradients,
map_out=map_out,
placeholders=placeholders)
else:
# Start training loop
training.training_loop(log=log,
config=config,
coord=coord,
sess=sess,
summary_op=summary_op,
summary_writer=summary_writer,
saver=saver,
restore_saver=restore_saver,
threads=threads,
directories=directories,
train_dict=train_dict,
val_dict=val_dict,
exp_label=exp_label,
num_params=num_params,
checkpoint=checkpoint,
use_db=use_db,
save_weights=config.save_weights,
save_checkpoints=config.save_checkpoints,
save_activities=config.save_activities,
save_gradients=config.save_gradients,
placeholders=placeholders)
def train_classifier_on_model(train_pointer, model_type, model_weights,
selected_layer, config):
# Make output directories if they do not exist
dt_stamp = '%s_%s_%s_%s' % (model_type, selected_layer, str(
config.lr)[2:], re.split('\.', str(datetime.now()))[0].replace(
' ', '_').replace(':', '_').replace('-', '_'))
config.checkpoint_directory = os.path.join(config.checkpoint_directory,
dt_stamp) # timestamp this run
dir_list = [config.checkpoint_directory]
[utilities.make_dir(d) for d in dir_list]
print '-' * 60
print 'Training %s over a %s. Saving to %s' % (config.classifier,
model_type, dt_stamp)
print '-' * 60
dcn_flavor = import_cnn(model_type)
# Prepare data on CPU
with tf.device('/cpu:0'):
train_images, train_labels, train_files = inputs(
train_pointer,
config.train_batch,
config.train_image_size,
config.model_image_size[:2],
num_epochs=config.epochs,
shuffle_batch=True)
# Prepare pretrained model on GPU
with tf.device('/gpu:0'):
with tf.variable_scope('cnn'):
if 'ckpt' in model_weights:
cnn = dcn_flavor.model()
else:
cnn = dcn_flavor.model(weight_path=model_weights)
cnn.build(train_images)
sample_layer = cnn[selected_layer]
weights, yhat, classifier, class_loss = tf_loss.choose_classifier(
sample_layer=sample_layer, y=train_labels, config=config)
saver = tf.train.Saver(tf.all_variables(), max_to_keep=10)
# Initialize the graph
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# Need to initialize both of these if supplying num_epochs to inputs
sess.run(
tf.group(tf.initialize_all_variables(),
tf.initialize_local_variables()))
# Set up exemplar threading
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
# Start training loop
np.save(os.path.join(config.checkpoint_directory, 'training_config_file'),
config)
step, losses = 0, []
if 'ckpt' in model_weights:
saver.restore(sess, model_weights)
try:
print 'Training model'
while not coord.should_stop():
start_time = time.time()
_, loss_value, labels = sess.run(
[classifier, class_loss, train_labels])
losses.append(loss_value)
duration = time.time() - start_time
assert not np.isnan(loss_value), 'Model diverged with loss = NaN'
# End iteration
print_status(step, loss_value, config, duration, 0, '')
step += 1
except tf.errors.OutOfRangeError:
print 'Done training for %d epochs, %d steps.' % (config.epochs, step)
print 'Saved to: %s' % config.checkpoint_directory
finally:
ckpt_path = os.path.join(config.checkpoint_directory,
'model_' + str(step) + '.ckpt')
saver.save(sess, ckpt_path, global_step=step)
print 'Saved checkpoint to: %s' % ckpt_path
coord.request_stop()
coord.join(threads)
sess.close()
# Return the final checkpoint for testing
return ckpt_path, config.checkpoint_directory
def plot_fits(
experiment='760_cells_2017_11_04_16_29_09',
query_db=False,
num_models=3,
template_exp='ALLEN_selected_cells_1',
process_pnodes=False,
allen_dir='/home/drew/Documents/Allen_Brain_Observatory',
output_dir='tests/ALLEN_files',
stimulus_type='tfrecord',
top_n=1,
grad='lrp',
target_layer='conv1_1', # conv1_1, sep_conv1_1, dog1_1
target_model='conv2d'): # conv2d, sep_conv2d, dog
"""Plot fits across the RF.
experiment: Name of Allen experiment you're plotting.
query_db: Use data from DB versus data in Numpys.
num_models: The number of architectures you're testing.
template_exp: The name of the contextual_circuit model template used."""
sys.path.append(allen_dir)
from allen_config import Allen_Brain_Observatory_Config
if process_pnodes:
from pnodes_declare_datasets_loop import query_hp_hist, sel_exp_query
else:
from declare_datasets_loop import query_hp_hist, sel_exp_query
config = Config()
main_config = Allen_Brain_Observatory_Config()
db_config = credentials.postgresql_connection()
files = glob(
os.path.join(
allen_dir,
main_config.multi_exps,
experiment, '*.npz'))
assert len(files), 'Couldn\'t find files.'
out_data, xs, ys = [], [], []
perfs, model_types, exps, arg_perf = [], [], [], []
count = 0
for f in files:
data = np.load(f)
d = {
'x': data['rf_data'].item()['on_center_x'],
'y': data['rf_data'].item()['on_center_y'],
# x: files['dataset_method'].item()['x_min'],
# y: files['dataset_method'].item()['y_min'],
}
exp_name = {
'experiment_name': data['dataset_method'].item()[
'experiment_name']}
if query_db:
perf = query_hp_hist(
exp_name['experiment_name'],
db_config=db_config)
if perf is None:
print 'No fits for: %s' % exp_name['experiment_name']
else:
raise NotImplementedError
d['perf'] = perf
d['max_val'] = np.max(perf)
out_data += [d]
xs += [np.round(d['x'])]
ys += [np.round(d['y'])]
perfs += [np.max(d['perf'])]
count += 1
else:
data_files = glob(
os.path.join(
main_config.ccbp_exp_evals,
exp_name['experiment_name'],
'*val_losses.npy')) # Scores has preds, labels has GT
for gd in data_files:
mt = gd.split(
os.path.sep)[-1].split(
template_exp + '_')[-1].split('_' + 'val')[0]
it_data = np.load(gd).item()
sinds = np.asarray(it_data.keys())[np.argsort(it_data.keys())]
sit_data = [it_data[idx] for idx in sinds]
d['perf'] = sit_data
d['max_val'] = np.max(sit_data)
d['max_idx'] = np.argmax(sit_data)
d['mt'] = mt
out_data += [d]
xs += [np.round(d['x'])]
ys += [np.round(d['y'])]
perfs += [np.max(sit_data)]
arg_perf += [np.argmax(sit_data)]
exps += [gd.split(os.path.sep)[-2]]
model_types += [mt]
count += 1
# Package as a df
xs = np.round(np.asarray(xs)).astype(int)
ys = np.round(np.asarray(ys)).astype(int)
perfs = np.asarray(perfs)
arg_perf = np.asarray(arg_perf)
exps = np.asarray(exps)
model_types = np.asarray(model_types)
# Filter to only keep top-scoring values at each x/y (dirty trick)
fxs, fys, fperfs, fmodel_types, fexps, fargs = [], [], [], [], [], []
xys = np.vstack((xs, ys)).transpose()
cxy = np.ascontiguousarray( # Unique rows
xys).view(
np.dtype((np.void, xys.dtype.itemsize * xys.shape[1])))
_, idx = np.unique(cxy, return_index=True)
uxys = xys[idx]
scores = []
for xy in uxys:
sel_idx = (xys == xy).sum(axis=-1) == 2
sperfs = perfs[sel_idx]
sexps = exps[sel_idx]
sargs = arg_perf[sel_idx]
sel_mts = model_types[sel_idx]
# Only get top conv/sep spots
sperfs = sperfs[sel_mts != 'dog']
sperfs = sperfs[sel_mts != 'DoG']
scores += [sperfs.mean() / sperfs.std()]
best_fits = np.argmax(np.asarray(scores))
xs = np.asarray([uxys[best_fits][0]])
ys = np.asarray([uxys[best_fits][1]])
sel_idx = (xys == uxys[best_fits]).sum(axis=-1) == 2
perfs = np.asarray(perfs[sel_idx])
exps = np.asarray(exps[sel_idx])
model_types = np.asarray(model_types[sel_idx])
umt, model_types_inds = np.unique(model_types, return_inverse=True)
# Get weights for the top-n fitting models of each type
it_perfs = perfs[model_types == target_model]
it_exps = exps[model_types == target_model]
# it_args = arg_perf[model_types == target_model]
sorted_perfs = np.argsort(it_perfs)[::-1][:top_n]
for idx in sorted_perfs:
perf = sel_exp_query(
experiment_name=it_exps[idx],
model=target_model,
db_config=db_config)
# perf_steps = np.argsort([v['training_step'] for v in perf])[::-1]
perf_steps = [v['validation_loss'] for v in perf]
max_score = np.max(perf_steps)
arg_perf_steps = np.argmax(perf_steps)
sel_model = perf[arg_perf_steps] # perf_steps[it_args[idx]]]
print 'Using %s' % sel_model
model_file = sel_model['ckpt_file'].split('.')[0]
model_ckpt = '%s.ckpt-%s' % (
model_file,
model_file.split(os.path.sep)[-1].split('_')[-1])
model_meta = '%s.meta' % model_ckpt
# Pull stimuli
stim_dir = os.path.join(
main_config.tf_record_output,
sel_model['experiment_name'])
stim_files = glob(stim_dir + '*')
stim_meta_file = [x for x in stim_files if 'meta' in x][0]
# stim_val_data = [x for x in stim_files if 'val.tfrecords' in x][0]
stim_val_data = [x for x in stim_files if 'train.tfrecords' in x][0]
stim_val_mean = [x for x in stim_files if 'train_means' in x][0]
assert stim_meta_file is not None
assert stim_val_data is not None
assert stim_val_mean is not None
stim_meta_data = np.load(stim_meta_file).item()
rf_stim_meta_data = stim_meta_data['rf_data']
stim_mean_data = np.load(
stim_val_mean).items()[0][1].item()['image']['mean']
# Store sparse noise for reference
sparse_rf_on = {
'center_x': rf_stim_meta_data.get('on_center_x', None),
'center_y': rf_stim_meta_data.get('on_center_y', None),
'width_x': rf_stim_meta_data.get('on_width_x', None),
'width_y': rf_stim_meta_data.get('on_width_y', None),
'distance': rf_stim_meta_data.get('on_distance', None),
'area': rf_stim_meta_data.get('on_area', None),
'rotation': rf_stim_meta_data.get('on_rotation', None),
}
sparse_rf_off = {
'center_x': rf_stim_meta_data.get('off_center_x', None),
'center_y': rf_stim_meta_data.get('off_center_y', None),
'width_x': rf_stim_meta_data.get('off_width_x', None),
'width_y': rf_stim_meta_data.get('off_width_y', None),
'distance': rf_stim_meta_data.get('off_distance', None),
'area': rf_stim_meta_data.get('off_area', None),
'rotation': rf_stim_meta_data.get('off_rotation', None),
}
sparse_rf = {'on': sparse_rf_on, 'off': sparse_rf_off}
# Pull responses
dataset_module = py_utils.import_module(
model_dir=config.dataset_info,
dataset=sel_model['experiment_name'])
dataset_module = dataset_module.data_processing()
with tf.device('/cpu:0'):
if stimulus_type == 'sparse_noise':
pass
elif stimulus_type == 'drifting_grating':
pass
elif stimulus_type == 'tfrecord':
val_images, val_labels = data_loader.inputs(
dataset=stim_val_data,
batch_size=1,
model_input_image_size=dataset_module.model_input_image_size,
tf_dict=dataset_module.tf_dict,
data_augmentations=[None], # dataset_module.preprocess,
num_epochs=1,
tf_reader_settings=dataset_module.tf_reader,
shuffle=False
)
# Mean normalize
log = logger.get(os.path.join(output_dir, 'sta_logs', target_model))
data_dir = os.path.join(output_dir, 'data', target_model)
py_utils.make_dir(data_dir)
sys.path.append(os.path.join('models', 'structs', sel_model['experiment_name']))
model_dict = __import__(target_model)
if hasattr(model_dict, 'output_structure'):
# Use specified output layer
output_structure = model_dict.output_structure
else:
output_structure = None
model = model_utils.model_class(
mean=stim_mean_data,
training=True, # FIXME
output_size=dataset_module.output_size)
with tf.device('/gpu:0'):
with tf.variable_scope('cnn') as scope:
val_scores, model_summary = model.build(
data=val_images,
layer_structure=model_dict.layer_structure,
output_structure=output_structure,
log=log,
tower_name='cnn')
if grad == 'vanilla':
grad_image = tf.gradients(model.output, val_images)[0]
elif grad == 'lrp':
eval_graph = tf.Graph()
with eval_graph.as_default():
with eval_graph.gradient_override_map(
{'Relu': 'GradLRP'}):
grad_image = tf.gradients(model.output, val_images)[0]
elif grad == 'cam':
eval_graph = tf.Graph()
with eval_graph.as_default():
with eval_graph.gradient_override_map(
{'Relu': 'GuidedRelu'}):
grad_image = tf.gradients(model.output, val_images)[0]
else:
raise NotImplementedError
print(json.dumps(model_summary, indent=4))
# Set up summaries and saver
saver = tf.train.Saver(tf.global_variables())
summary_op = tf.summary.merge_all()
# Initialize the graph
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# Need to initialize both of these if supplying num_epochs to inputs
sess.run(
tf.group(
tf.global_variables_initializer(),
tf.local_variables_initializer())
)
saver.restore(sess, model_ckpt)
# Set up exemplar threading
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
if target_model == 'conv2d':
fname = [
x for x in tf.global_variables()
if 'conv1_1_filters:0' in x.name]
elif target_model == 'sep_conv2d':
fname = [
x for x in tf.global_variables()
if 'sep_conv1_1_filters:0' in x.name]
elif target_model == 'dog' or target_model == 'DoG':
fname = [
x for x in tf.global_variables()
if 'dog1_1_filters:0' in x.name]
else:
raise NotImplementedError
val_tensors = {
'images': val_images,
'labels': val_labels,
'filts': fname,
'responses': model.output, # model[target_layer],
'grads': grad_image
}
all_images, all_preds, all_grads, all_responses = [], [], [], []
step = 0
try:
while not coord.should_stop():
val_vals = sess.run(val_tensors.values())
val_dict = {k: v for k, v in zip(val_tensors.keys(), val_vals)}
all_images += [val_dict['images']]
all_responses += [val_dict['responses']]
all_preds += [val_dict['labels'].squeeze()]
all_grads += [val_dict['grads'].squeeze()]
print 'Finished step %s' % step
step += 1
except:
print 'Finished tfrecords'
finally:
coord.request_stop()
coord.join(threads)
sess.close()
# Process and save data
# if target_model != 'dog':
# filters = val_dict['filts'][0].squeeze().transpose(2, 0, 1)
all_images = np.concatenate(all_images).squeeze()
all_grads = np.asarray(all_grads)
all_preds = np.asarray(all_preds).reshape(-1, 1)
all_responses = np.asarray(all_responses).squeeze()
np.savez(
os.path.join(data_dir, 'data'),
images=all_images,
pred=all_preds,
# filters=filters,
grads=all_grads)
# if target_model != 'dog':
# save_mosaic(
# maps=filters, # [0].squeeze().transpose(2, 0, 1),
# output=os.path.join(data_dir, '%s_filters' % target_layer),
# rc=8,
# cc=4,
# title='%s filters' % (
# target_layer))
print 'Complete.'
def test_classifier(validation_pointer,
model_ckpt,
model_dir,
model_type,
model_weights,
selected_layer,
config,
simulate_subjects=120):
# Make output directories if they do not exist
config.checkpoint_directory = model_dir
print '-' * 60
print 'Testing the model over a %s. Saving to %s' % (model_type, model_dir)
print '-' * 60
dcn_flavor = import_cnn(model_type)
# Prepare data on CPU
with tf.device('/cpu:0'):
val_images, val_labels, val_files = inputs(
tfrecord_file=validation_pointer,
batch_size=config.validation_batch,
im_size=config.validation_image_size,
model_input_shape=config.model_image_size[:2],
num_epochs=1,
data_augmentations=config.validation_augmentations,
shuffle_batch=True)
# Prepare pretrained model on GPU
with tf.device('/gpu:0'):
with tf.variable_scope('cnn'):
if 'ckpt' in model_weights:
cnn = dcn_flavor.model()
else:
cnn = dcn_flavor.model(weight_path=model_weights)
cnn.build(val_images)
sample_layer = cnn[selected_layer]
saver = tf.train.Saver(tf.all_variables(), max_to_keep=10)
# Initialize the graph
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# Need to initialize both of these if supplying num_epochs to inputs
sess.run(
tf.group(tf.initialize_all_variables(),
tf.initialize_local_variables()))
# Set up exemplar threading
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
# Start training loop
results = {'accs': [], 'preds': [], 'labs': [], 'files': []}
with open(model_ckpt, 'rb') as fid:
svc = cPickle.load(fid)
zscorer = np.load(model_ckpt.split('.')[0] + '_normalization.npz')
np_path = os.path.join(config.checkpoint_directory, 'validation_results')
step = 0
scores, labels = [], []
if '.ckpt' in model_weights:
saver.restore(sess, model_weights)
print 'Restored model from %s' % model_weights
try:
print 'Testing model'
while not coord.should_stop():
start_time = time.time()
score, lab, f = sess.run([sample_layer, val_labels, val_files])
norm_score = (score - zscorer['mu']) / zscorer['sd']
scores += [norm_score]
pred = svc.predict(norm_score)
acc = np.mean(pred == lab)
results['accs'] += [acc]
results['preds'] += [pred]
results['labs'] += [lab]
results['files'] += [f]
duration = time.time() - start_time
print_status(step, 0, config, duration, acc, np_path)
step += 1
except tf.errors.OutOfRangeError:
print 'Done testing.'
finally:
np.savez(np_path, **results)
print 'Saved to: %s' % np_path
coord.request_stop()
coord.join(threads)
sess.close()
print '%.4f%% correct' % np.mean(results['accs'])
if simulate_subjects:
sim_subs = []
print 'Simulating subjects'
scores = np.concatenate(scores)
labels = np.concatenate(results['labs'])
for sub in tqdm(range(simulate_subjects)):
it_results = {'accs': [], 'preds': [], 'labs': [], 'files': []}
neuron_drop = np.random.rand(scores.shape[1]) > .95
it_scores = np.copy(scores)
it_scores[:, neuron_drop] = 0
pred = svc.predict(it_scores)
acc = np.mean(pred == labels)
it_results['accs'] += [acc]
it_results['preds'] += [pred]
it_results['labs'] += [labels]
it_results['files'] += [np.concatenate(results['files'])]
sim_subs += [it_results]
np.save(np_path + '_sim_subs', sim_subs)
def train_and_eval(config):
"""Train and evaluate the model."""
# Prepare model training
dt_stamp = re.split(
'\.', str(datetime.now()))[0].\
replace(' ', '_').replace(':', '_').replace('-', '_')
dt_dataset = config.model_type + '_' + dt_stamp + '/'
config.train_checkpoint = os.path.join(config.model_output,
dt_dataset) # timestamp this run
config.summary_dir = os.path.join(config.train_summaries,
config.model_output, dt_dataset)
dir_list = [config.train_checkpoint, config.summary_dir]
[make_dir(d) for d in dir_list]
# Prepare model inputs
train_data = config.train_data
validation_data = config.val_data
# Prepare data on CPU
with tf.device('/cpu:0'):
train_images, train_labels = inputs(
tfrecord_file=train_data,
batch_size=config.train_batch,
im_size=config.resize,
model_input_shape=config.resize,
train=None,
img_mean_value='train_mean_big.npz',
num_epochs=config.num_epochs)
val_images, val_labels = inputs(tfrecord_file=validation_data,
batch_size=config.train_batch,
im_size=config.resize,
model_input_shape=config.resize,
train=None,
img_mean_value='train_mean_big.npz',
num_epochs=config.num_epochs)
tf.summary.image('train images', tf.cast(train_images, tf.uint8))
tf.summary.image('validation images', tf.cast(val_images, tf.uint8))
tf.summary.image(
'train labels',
tf.cast(
tf.reshape(train_labels, [config.train_batch, 112, 112, 1]),
tf.float32))
tf.summary.image(
'validation labels',
tf.cast(tf.reshape(val_labels, [config.train_batch, 112, 112, 1]),
tf.float32))
num_train_imgs = 0
for record in tf.python_io.tf_record_iterator(train_data):
num_train_imgs += 1
num_val_imgs = 0
for record in tf.python_io.tf_record_iterator(validation_data):
num_val_imgs += 1
print 'Number of training images', num_train_imgs
print 'Number of validation images', num_val_imgs
# Prepare model on GPU
with tf.device('/gpu:0'):
with tf.variable_scope('cnn') as scope:
model = model_struct(config.vgg16_npy_path)
train_mode = tf.get_variable(name='training', initializer=True)
model.build(train_images,
train_mode=train_mode,
batchnorm=config.batch_norm,
trainable_layers=config.trainable_layers,
config=config,
shuffled=False)
# Prepare the cost function
cost, train_error_matrix = euclidean_loss(model.prediction,
train_labels,
config.train_batch)
tf.summary.scalar("train cost", cost)
train_op = tf.train.AdamOptimizer(config.lr).minimize(cost)
tf.summary.image("prediction", model.prediction)
# Setup validation op
if validation_data is not False:
scope.reuse_variables()
# Validation graph is the same as training except no batchnorm
val_model = model_struct(
vgg16_npy_path=
'/media/data_cifs/ajones/deepgaze/salicon_prep_g11/vgg19.npy'
)
val_model.build(val_images,
train_mode=train_mode,
batchnorm=config.batch_norm,
trainable_layers=config.trainable_layers,
config=config,
shuffled=True)
# Calculate validation accuracy
val_cost, val_error_matrix = euclidean_loss(
val_model.prediction, val_labels, config.train_batch)
tf.summary.scalar("validation cost", val_cost)
tf.summary.image("val prediction", val_model.prediction)
# Set up summaries and saver
saver = tf.train.Saver(tf.global_variables(), max_to_keep=5)
summary_op = tf.summary.merge_all()
# Initialize the graph
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# Need to initialize both of these if supplying num_epochs to inputs
sess.run([
tf.group(tf.global_variables_initializer()),
tf.local_variables_initializer()
])
sess.run([tf.local_variables_initializer()])
summary_writer = tf.summary.FileWriter(config.summary_dir, sess.graph)
# Set up exemplar threading
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
# Start training loop
np.save(config.train_checkpoint, config)
step, epoch_no, val_max, losses = 0, 0, 0, []
epoch_loss_values = []
best_val_loss = float('inf')
try:
while not coord.should_stop():
start_time = time.time()
halt = False
if step % 20 == 0:
if config.show_output:
_, loss_value, val_loss, summary_str, imgs, labs, predictions, cb_logits, logits, te_mat, preds_presoft = sess.run(
[
train_op, cost, val_cost, summary_op,
tf.reshape(train_images[0:3], [3, 224, 224, 3]),
tf.reshape(train_labels[0:3], [3, 112, 112]),
tf.reshape(model.prediction[0:3], [3, 112, 112]),
tf.reshape(model.center_bias_logits[0:3],
[3, 112, 112]),
tf.reshape(model.logits[0:3], [3, 112, 112]),
tf.reshape(train_error_matrix[0:3], [3, 112, 112]),
tf.reshape(model.prediction_presoft[0:3],
[3, 112, 112])
])
# plt.imshow(np.mean(sess.run(model.feature_encoder)[0], 2))
# plt.show()
# import ipdb; ipdb.set_trace()
else:
_, loss_value, val_loss, summary_str, imgs, labs, predictions, logits = sess.run(
[
train_op, cost, val_cost, summary_op,
tf.reshape(train_images[0:3], [3, 224, 224, 3]),
tf.reshape(train_labels[0:3], [3, 112, 112]),
tf.reshape(model.prediction[0:3], [3, 112, 112]),
tf.reshape(model.logits[0:3], [3, 112, 112])
])
if step % 60 == 0:
np.save('running_imgs', imgs)
np.save('running_labs', labs)
np.save('running_preds', predictions)
np.save('running_logits', logits)
summary_writer.add_summary(summary_str, step)
duration = time.time() - start_time
# Training status
format_str = (
'%s: step %d, loss = %.2f, val loss = %.2f (%.1f examples/sec; '
'%.3f sec/batch) | logdir = %s\n')
print(format_str % (datetime.now(), step, loss_value, val_loss,
config.train_batch / duration,
float(duration), config.summary_dir))
if val_loss < best_val_loss:
saver.save(sess,
os.path.join(config.train_checkpoint,
'model_' + str(step) + '.ckpt'),
global_step=step)
if config.show_output: # and step > 300 and step % 20 == 0:
num_columns = 6
num_imgs_plot = 3
for i in range(num_imgs_plot):
plt.subplot(num_imgs_plot, num_columns,
i * num_columns + 1)
im = plt.imshow(imgs[i])
plt.colorbar(im)
plt.subplot(num_imgs_plot, num_columns,
i * num_columns + 2)
lab = plt.imshow(labs[i])
plt.colorbar(lab)
plt.subplot(num_imgs_plot, num_columns,
i * num_columns + 3)
logits_out = plt.imshow(logits[i])
plt.colorbar(logits_out)
plt.subplot(num_imgs_plot, num_columns,
i * num_columns + 4)
cbl = plt.imshow(cb_logits[i])
plt.colorbar(cbl)
plt.subplot(num_imgs_plot, num_columns,
i * num_columns + 5)
preds = plt.imshow(preds_presoft[i])
plt.colorbar(preds)
plt.subplot(num_imgs_plot, num_columns,
i * num_columns + 6)
preds = plt.imshow(predictions[i])
plt.colorbar(preds)
plt.show()
else:
_, loss_value = sess.run([train_op, cost])
# assert not np.isnan(loss_value), 'Model diverged with loss = NaN'
if np.isnan(loss_value):
print 'yikes. nan loss -- check your cost function.'
import pdb
pdb.set_trace()
# End iteration
step += 1
except tf.errors.OutOfRangeError:
print('Done training for %d epochs, %d steps.' % (epoch_no, step))
finally:
coord.request_stop()
np.save(os.path.join(config.tfrecord_dir, 'training_loss'), losses)
coord.join(threads)
sess.close()
def test_classifier(validation_pointer,
model_ckpt,
model_dir,
model_type,
model_weights,
selected_layer,
config,
simulate_subjects=121):
# Make output directories if they do not exist
config.checkpoint_directory = model_dir
print '-' * 60
print 'Testing the model over a %s. Saving to %s' % (model_type, model_dir)
print '-' * 60
dcn_flavor = import_cnn(model_type)
# Prepare data on CPU
with tf.device('/cpu:0'):
val_images, val_labels, val_files = inputs(
validation_pointer,
config.validation_batch,
config.validation_image_size,
config.model_image_size[:2],
1,
shuffle_batch=False)
# Prepare pretrained model on GPU
with tf.device('/gpu:0'):
with tf.variable_scope('cnn'):
if 'ckpt' in model_weights:
cnn = dcn_flavor.model()
else:
cnn = dcn_flavor.model(weight_path=model_weights)
cnn.build(val_images)
sample_layer = cnn[selected_layer]
weights, yhat, classifier, class_loss = tf_loss.choose_classifier(
sample_layer=sample_layer, y=val_labels, config=config)
saver = tf.train.Saver(tf.all_variables(), max_to_keep=10)
# Initialize the graph
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# Need to initialize both of these if supplying num_epochs to inputs
sess.run(
tf.group(tf.initialize_all_variables(),
tf.initialize_local_variables()))
# Set up exemplar threading
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
# Start training loop
results = {'accs': [], 'preds': [], 'labs': [], 'files': []}
# if int(tf.__version__.split('.')[1]) > 10:
model_ckpt += '-%s' % re.search('\d+.ckpt',
model_ckpt).group().split('.ckpt')[0]
saver.restore(sess, model_ckpt)
np_path = os.path.join(config.checkpoint_directory, 'validation_results')
step = 0
scores, labels = [], []
try:
print 'Testing model'
while not coord.should_stop():
start_time = time.time()
pred, lab, f = sess.run([yhat, val_labels, val_files])
pred = (pred > 0).astype(int).reshape(1, -1)
acc = np.mean(pred == lab)
scores += [pred]
results['accs'] += [acc]
results['preds'] += [pred]
results['labs'] += [lab]
results['files'] += [f]
duration = time.time() - start_time
print_status(step, 0, config, duration, acc, np_path)
step += 1
except tf.errors.OutOfRangeError:
print 'Done testing.'
finally:
np.savez(np_path, **results)
print 'Saved to: %s' % np_path
coord.request_stop()
coord.join(threads)
sess.close()
print '%.4f%% correct' % np.mean(results['accs'])
if simulate_subjects:
sim_subs = []
print 'Simulating subjects'
scores = np.concatenate(scores)
labels = np.concatenate(results['labs'])
for sub in tqdm(range(simulate_subjects)):
it_results = {'accs': [], 'preds': [], 'labs': [], 'files': []}
neuron_drop = np.random.rand(scores.shape[1]) > .95
it_scores = np.copy(scores)
it_scores[:, neuron_drop] = 0
acc = np.mean(pred == labels)
it_results['accs'] += [acc]
it_results['preds'] += [pred]
it_results['labs'] += [labels]
it_results['files'] += [np.concatenate(results['files'])]
sim_subs += [it_results]
np.save(np_path + '_sim_subs', sim_subs)