def load_model(self, save_dir):
"""Load the model parameters from disk.
Parameters
----------
save_dir : str
Directory where the saved variables are placed.
"""
self.build()
path = os.path.abspath(save_dir)
saver = VariableSaver(self.get_param_variables(), path)
saver.restore(ignore_non_exist=False)
def _enter(self):
# open a temporary directory if the checkpoint dir is not specified
if self._checkpoint_dir is None:
self._temp_dir_ctx = TemporaryDirectory()
self._checkpoint_dir = self._temp_dir_ctx.__enter__()
else:
makedirs(self._checkpoint_dir, exist_ok=True)
# create the variable saver
self._saver = VariableSaver(self._param_vars, self._checkpoint_dir)
# return self as the context object
return self
def save_model(self, save_dir, overwrite=False):
"""Save the model parameters onto disk.
Parameters
----------
save_dir : str
Directory where to place the saved variables.
overwrite : bool
Whether or not to overwrite the existing directory?
"""
self.build()
path = os.path.abspath(save_dir)
if os.path.exists(path):
if overwrite:
if os.path.isdir(path):
shutil.rmtree(path)
else:
os.remove(path)
elif not os.path.isdir(path) or len(os.listdir(path)) > 0:
raise IOError('%r already exists.' % save_dir)
saver = VariableSaver(self.get_param_variables(), path)
saver.save()
def test_non_exist(self):
with TemporaryDirectory() as tempdir:
a = tf.get_variable('a', initializer=1, dtype=tf.int32)
saver = VariableSaver([a], tempdir)
with pytest.raises(
IOError,
match='Checkpoint file does not exist in directory'):
saver.restore()
saver.restore(ignore_non_exist=True)
kernel_regularizer=K.regularizers.l2(0.001),
activation=tf.nn.relu),
K.layers.Dense(100,
kernel_regularizer=K.regularizers.l2(0.001),
activation=tf.nn.relu),
]),
x_dims=120,
z_dims=5,
)
# To train the Donut model, and use a trained model for prediction
trainer = DonutTrainer(model=model, model_vs=model_vs)
predictor = DonutPredictor(model)
with tf.Session().as_default():
#trainer.fit(train_values, train_labels, train_missing, mean, std)
#var_dict = get_variables_as_dict(model_vs)
#saver = VariableSaver(var_dict, "donut_without_label_2.ckpt")
#saver.save()
# Restore variables from `save_dir`.
saver = VariableSaver(get_variables_as_dict(model_vs),
"donut_without_label_2.ckpt")
saver.restore()
test_score = predictor.get_score(test_values, test_missing)
result = np.array([test_labels[119:], test_score])
np.savetxt('result_arti_sin2.csv',
result.transpose(),
delimiter=',',
fmt='%.3f')
marker='^',
color='green',
label="Non Anomalies")
plt.legend(['Non Anomalies'])
plt.xlim(df3['timestamp'].min(), df3['timestamp'].max())
plt.ylim(-.0006, .0006)
plt.title('Non Anomalies from Fetal Brain Scan')
plt.ylabel('# Direct_1')
plt.xlabel('Date-Time')
plt.savefig('figs/out_brain_nanomaly.png')
from tfsnippet.utils import get_variables_as_dict, VariableSaver
session = K.backend.get_session()
init = tf.global_variables_initializer()
session.run(init)
with session.as_default():
var_dict = get_variables_as_dict(model_vs)
# save variables to `save_dir`
saver = VariableSaver(var_dict, save_dir)
saver.save()
print("Saved the model successfully")
with session.as_default():
# Restore the model.
saver = VariableSaver(get_variables_as_dict(model_vs), save_dir)
saver.restore()
print("Restored the model successfully")
class EarlyStopping(DisposableContext):
"""
Early-stopping context object.
This class provides a object for memorizing the parameters for best
metric, in an early-stopping context. An example of using this context:
.. code-block:: python
with EarlyStopping(param_vars) as es:
...
es.update(loss, global_step)
...
Where ``es.update(loss, global_step)`` should cause the parameters to
be saved on disk if `loss` is better than the current best metric.
One may also get the current best metric via ``es.best_metric``.
Notes:
If no loss is given via ``es.update``, then the variables
would keep their latest values when closing an early-stopping object.
"""
def __init__(self,
param_vars,
initial_metric=None,
checkpoint_dir=None,
smaller_is_better=True,
restore_on_error=False,
cleanup=True,
name=None):
"""
Construct the :class:`EarlyStopping`.
Args:
param_vars (list[tf.Variable] or dict[str, tf.Variable]): List or
dict of variables to be memorized. If a dict is specified, the
keys of the dict would be used as the serializations keys via
:class:`VariableSaver`.
initial_metric (float or tf.Tensor or tf.Variable): The initial best
metric (for recovering from previous session).
checkpoint_dir (str): The directory where to save the checkpoint
files. If not specified, will use a temporary directory.
smaller_is_better (bool): Whether or not it is better to have
smaller metric values? (default :obj:`True`)
restore_on_error (bool): Whether or not to restore the memorized
parameters even on error? (default :obj:`False`)
cleanup (bool): Whether or not to cleanup the checkpoint directory
on exit? This argument will be ignored if `checkpoint_dir` is
:obj:`None`, where the temporary directory will always be
deleted on exit.
name (str): Name scope of all TensorFlow operations. (default
"early_stopping").
"""
# regularize the parameters
if not param_vars:
raise ValueError('`param_vars` must not be empty')
if isinstance(initial_metric, (tf.Tensor, tf.Variable)):
initial_metric = initial_metric.eval()
if checkpoint_dir is not None:
checkpoint_dir = os.path.abspath(checkpoint_dir)
# memorize the parameters
self._param_vars = copy.copy(param_vars)
self._checkpoint_dir = checkpoint_dir
self._smaller_is_better = smaller_is_better
self._restore_on_error = restore_on_error
self._cleanup = cleanup
self._name = name
# internal states of the object
self._best_metric = initial_metric
self._ever_updated = False
self._temp_dir_ctx = None
self._saver = None # type: VariableSaver
def _enter(self):
# open a temporary directory if the checkpoint dir is not specified
if self._checkpoint_dir is None:
self._temp_dir_ctx = TemporaryDirectory()
self._checkpoint_dir = self._temp_dir_ctx.__enter__()
else:
makedirs(self._checkpoint_dir, exist_ok=True)
# create the variable saver
self._saver = VariableSaver(self._param_vars, self._checkpoint_dir)
# return self as the context object
return self
def _exit(self, exc_type, exc_val, exc_tb):
try:
# restore the variables
# exc_info = (exc_type, exc_val, exc_tb)
if exc_type is None or exc_type is KeyboardInterrupt or \
self._restore_on_error:
self._saver.restore(ignore_non_exist=True)
finally:
# cleanup the checkpoint directory
try:
if self._temp_dir_ctx is not None:
self._temp_dir_ctx.__exit__(exc_type, exc_val, exc_tb)
elif self._cleanup:
if os.path.exists(self._checkpoint_dir):
shutil.rmtree(self._checkpoint_dir)
except Exception: # pragma: no cover
getLogger(__name__).error(
'Failed to cleanup validation save dir %r.',
self._checkpoint_dir,
exc_info=True)
# warning if metric never updated
if not self._ever_updated:
warnings.warn('Early-stopping metric has never been updated. '
'The variables will keep their latest values. '
'Did you forget to add corresponding metric?')
def update(self, metric, global_step=None):
"""
Update the best metric.
Args:
metric (float): New metric value.
global_step (int): Optional global step counter.
Returns:
bool: Whether or not the best loss has been updated?
"""
self._require_entered()
self._ever_updated = True
if self._best_metric is None or \
(self._smaller_is_better and metric < self._best_metric) or \
(not self._smaller_is_better and metric > self._best_metric):
self._saver.save(global_step)
self._best_metric = metric
return True
return False
@property
def best_metric(self):
"""Get the current best loss."""
return self._best_metric
@property
def ever_updated(self):
"""Check whether or not `update` method has ever been called."""
return self._ever_updated
def early_stopping(param_vars, initial_metric=None, save_dir=None,
smaller_is_better=True, restore_on_error=False,
cleanup=True, name=None):
"""Open a context to memorize the values of parameters at best metric.
This method will open a context with an object to memorize the best
metric for early-stopping. An example of using this early-stopping
context is:
with early_stopping(param_vars) as es:
...
es.update(loss, global_step)
...
Where ``es.update(loss, global_step)`` should cause the parameters to
be saved on disk if `loss` is better than the current best metric.
One may also get the best metric via ``es.best_metric``.
Note that if no loss is given via ``es.update``, then the variables
would keep their latest values when exiting the early-stopping context.
Parameters
----------
param_vars : list[tf.Variable] | dict[str, tf.Variable]
List or dict of variables to be memorized.
If a dict is specified, the keys of the dict would be used as the
serializations keys via `VariableSaver`.
initial_metric : float | tf.Tensor | tf.Variable
The initial best loss (usually for recovering from previous session).
save_dir : str
The directory where to save the variable values.
If not specified, will use a temporary directory.
smaller_is_better : bool
Whether or not the less, the better loss? (default True)
restore_on_error : bool
Whether or not to restore the memorized parameters even on error?
(default False)
cleanup : bool
Whether or not to cleanup the saving directory on exit?
This argument will be ignored if `save_dir` is None, while
the temporary directory will always be deleted on exit.
name : str
Optional name of this scope.
Yields
------
_EarlyStopping
The object to receive loss during early-stopping context.
"""
if not param_vars:
raise ValueError('`param_vars` must not be empty.')
if save_dir is None:
with TemporaryDirectory() as tempdir:
with early_stopping(param_vars, initial_metric=initial_metric,
save_dir=tempdir, cleanup=False,
smaller_is_better=smaller_is_better,
restore_on_error=restore_on_error,
name=name) as es:
yield es
else:
if isinstance(initial_metric, (tf.Tensor, tf.Variable)):
initial_metric = initial_metric.eval()
with tf.name_scope(name):
saver = VariableSaver(param_vars, save_dir)
save_dir = os.path.abspath(save_dir)
makedirs(save_dir, exist_ok=True)
es = _EarlyStopping(saver,
best_metric=initial_metric,
smaller_is_better=smaller_is_better)
try:
yield es
except Exception as ex:
if isinstance(ex, KeyboardInterrupt) or restore_on_error:
saver.restore()
raise
else:
saver.restore()
finally:
if cleanup:
try:
if os.path.exists(save_dir):
shutil.rmtree(save_dir)
except Exception:
getLogger(__name__).error(
'Failed to cleanup validation save dir %r.',
save_dir, exc_info=True
)
if not es.ever_updated:
warnings.warn(
'Early-stopping metric has never been updated. '
'The variables will keep their latest values. '
'Did you forget to add corresponding metric?'
)
def test_save_restore(self):
a = tf.get_variable('a', initializer=1, dtype=tf.int32)
b = tf.get_variable('b', initializer=2, dtype=tf.int32)
c = tf.get_variable('c', initializer=3, dtype=tf.int32)
a_ph = tf.placeholder(dtype=tf.int32, shape=(), name='a_ph')
b_ph = tf.placeholder(dtype=tf.int32, shape=(), name='b_ph')
c_ph = tf.placeholder(dtype=tf.int32, shape=(), name='c_ph')
assign_op = tf.group(tf.assign(a, a_ph), tf.assign(b, b_ph),
tf.assign(c, c_ph))
def get_values(sess):
return sess.run([a, b, c])
def set_values(sess, a, b, c):
sess.run(assign_op, feed_dict={a_ph: a, b_ph: b, c_ph: c})
with TemporaryDirectory() as tempdir1, \
TemporaryDirectory() as tempdir2:
saver1 = VariableSaver([a, b, c], tempdir1)
saver2 = VariableSaver({'aa': a, 'bb': b}, tempdir2)
with self.test_session() as sess:
sess.run(tf.global_variables_initializer())
self.assertEqual(get_values(sess), [1, 2, 3])
set_values(sess, 10, 20, 30)
self.assertEqual(get_values(sess), [10, 20, 30])
saver1.save()
set_values(sess, 100, 200, 300)
self.assertEqual(get_values(sess), [100, 200, 300])
saver1.restore()
self.assertEqual(get_values(sess), [10, 20, 30])
saver2.save()
set_values(sess, 100, 200, 300)
self.assertEqual(get_values(sess), [100, 200, 300])
saver2.restore()
self.assertEqual(get_values(sess), [10, 20, 300])
saver1.restore()
self.assertEqual(get_values(sess), [10, 20, 30])
set_values(sess, 101, 201, 301)
saver2.save()
set_values(sess, 100, 200, 300)
self.assertEqual(get_values(sess), [100, 200, 300])
saver2.restore()
self.assertEqual(get_values(sess), [101, 201, 300])
def test_errors(self):
with TemporaryDirectory() as tempdir:
a = tf.get_variable('a', initializer=1, dtype=tf.int32)
with pytest.raises(ValueError,
match='At least 2 versions should be kept'):
_ = VariableSaver([a], tempdir, max_versions=1)