From 52023e4ae7521824fb102cab2c77bb6db6528e24 Mon Sep 17 00:00:00 2001
From: Amir MOHAMMADI <amir.mohammadi@idiap.ch>
Date: Tue, 10 Oct 2017 12:14:36 +0200
Subject: [PATCH] Move code from bob.dap to here
---
.../tensorflow/script/db_to_tfrecords.py | 21 +--
bob/learn/tensorflow/script/eval_generic.py | 96 ++++++++++++
bob/learn/tensorflow/script/train_generic.py | 98 ++++++++++++
bob/learn/tensorflow/utils/eval.py | 110 ++++++++++++++
bob/learn/tensorflow/utils/hooks.py | 35 +++++
bob/learn/tensorflow/utils/reproducible.py | 37 +++++
bob/learn/tensorflow/utils/sequences.py | 143 ++++++++++++++++++
bob/learn/tensorflow/utils/tfrecords.py | 25 +++
8 files changed, 555 insertions(+), 10 deletions(-)
create mode 100644 bob/learn/tensorflow/script/eval_generic.py
create mode 100644 bob/learn/tensorflow/script/train_generic.py
create mode 100644 bob/learn/tensorflow/utils/eval.py
create mode 100644 bob/learn/tensorflow/utils/hooks.py
create mode 100644 bob/learn/tensorflow/utils/reproducible.py
create mode 100644 bob/learn/tensorflow/utils/sequences.py
create mode 100644 bob/learn/tensorflow/utils/tfrecords.py
diff --git a/bob/learn/tensorflow/script/db_to_tfrecords.py b/bob/learn/tensorflow/script/db_to_tfrecords.py
index 10cc5c19..9f9c2b46 100644
--- a/bob/learn/tensorflow/script/db_to_tfrecords.py
+++ b/bob/learn/tensorflow/script/db_to_tfrecords.py
@@ -91,20 +91,21 @@ from bob.core.log import setup, set_verbosity_level
logger = setup(__name__)
-def _bytes_feature(value):
- return tf.train.Feature(bytes_list=tf.train.BytesList(value=[value]))
+def bytes_feature(value):
+ return tf.train.Feature(bytes_list=tf.train.BytesList(value=[value]))
-def _int64_feature(value):
- return tf.train.Feature(int64_list=tf.train.Int64List(value=[value]))
+def int64_feature(value):
+ return tf.train.Feature(int64_list=tf.train.Int64List(value=[value]))
-def write_a_sample(writer, data, label):
- feature = {'train/data': _bytes_feature(data.tostring()),
- 'train/label': _int64_feature(label)}
+def write_a_sample(writer, data, label, feature=None):
+ if feature is None:
+ feature = {'train/data': bytes_feature(data.tostring()),
+ 'train/label': int64_feature(label)}
- example = tf.train.Example(features=tf.train.Features(feature=feature))
- writer.write(example.SerializeToString())
+ example = tf.train.Example(features=tf.train.Features(feature=feature))
+ writer.write(example.SerializeToString())
def main(argv=None):
@@ -167,4 +168,4 @@ def main(argv=None):
if __name__ == '__main__':
- main()
+ main()
diff --git a/bob/learn/tensorflow/script/eval_generic.py b/bob/learn/tensorflow/script/eval_generic.py
new file mode 100644
index 00000000..23127563
--- /dev/null
+++ b/bob/learn/tensorflow/script/eval_generic.py
@@ -0,0 +1,96 @@
+#!/usr/bin/env python
+
+"""Trains the VGG-audio network on the AVspoof database.
+
+Usage:
+ %(prog)s [options] <checkpoint_dir> <eval_tfrecords>...
+
+Options:
+ -h --help Show this screen.
+ --eval-dir PATH [default: /idiap/user/amohammadi/avspoof/specgram/avspoof-simple-cnn-eval]
+ --input-shape N [default: (50, 1024, 1)]
+ --batch-size N [default: 50]
+ --run-once Evaluate the model once only.
+ --eval-interval-secs N Interval to evaluations. [default: 300]
+ --num-examples N Number of examples to run. [default: None] Provide
+ ``None`` to consider all examples.
+"""
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+# for bob imports to work properly:
+import pkg_resources
+import os
+import time
+from functools import partial
+import tensorflow as tf
+from docopt import docopt
+from bob.io.base import create_directories_safe
+from bob.dap.voice.architectures.simple_cnn import architecture
+from bob.dap.base.database.tfrecords import example_parser
+from bob.dap.base.util.eval import get_global_step, eval_once
+
+
+def main(argv=None):
+ arguments = docopt(__doc__, argv=argv)
+ print(arguments)
+ input_shape = eval(arguments['--input-shape'])
+ tfrecord_filenames = arguments['<eval_tfrecords>']
+ eval_dir = arguments['--eval-dir']
+ batch_size = eval(arguments['--batch-size'])
+ run_once = arguments['--run-once']
+ eval_interval_secs = eval(arguments['--eval-interval-secs'])
+ checkpoint_dir = arguments['<checkpoint_dir>']
+ num_examples = eval(arguments['--num-examples'])
+
+ create_directories_safe(eval_dir)
+ with tf.Graph().as_default() as g:
+
+ # Get images and labels
+ with tf.name_scope('input'):
+ dataset = tf.contrib.data.TFRecordDataset(tfrecord_filenames)
+ feature = {'train/data': tf.FixedLenFeature([], tf.string),
+ 'train/label': tf.FixedLenFeature([], tf.int64)}
+ my_example_parser = partial(
+ example_parser, feature=feature, data_shape=input_shape)
+ dataset = dataset.map(
+ my_example_parser, num_threads=1, output_buffer_size=batch_size)
+ dataset = dataset.batch(batch_size)
+ images, labels = dataset.make_one_shot_iterator().get_next()
+
+ # Build a Graph that computes the logits predictions from the
+ # inference model.
+ logits = architecture(images, mode=tf.estimator.ModeKeys.EVAL)
+
+ # Calculate predictions.
+ top_k_op = tf.nn.in_top_k(logits, labels, 1)
+
+ saver = tf.train.Saver()
+ # Build the summary operation based on the TF collection of Summaries.
+ summary_op = tf.summary.merge_all()
+ summary_writer = tf.summary.FileWriter(eval_dir, g)
+ evaluated_file = os.path.join(eval_dir, 'evaluated')
+
+ while True:
+ evaluated_steps = []
+ if os.path.exists(evaluated_file):
+ with open(evaluated_file) as f:
+ evaluated_steps = f.read().split()
+ ckpt = tf.train.get_checkpoint_state(checkpoint_dir)
+ if ckpt and ckpt.model_checkpoint_path:
+ for path in ckpt.all_model_checkpoint_paths:
+ global_step = get_global_step(path)
+ if global_step not in evaluated_steps:
+ ret_val = eval_once(saver, summary_writer, top_k_op, summary_op,
+ path, global_step, num_examples,
+ batch_size)
+ if ret_val == 0:
+ with open(evaluated_file, 'a') as f:
+ f.write(global_step + '\n')
+ if run_once:
+ break
+ time.sleep(eval_interval_secs)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/bob/learn/tensorflow/script/train_generic.py b/bob/learn/tensorflow/script/train_generic.py
new file mode 100644
index 00000000..246b1c12
--- /dev/null
+++ b/bob/learn/tensorflow/script/train_generic.py
@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+
+"""Trains the VGG-audio network on the AVspoof database.
+
+Usage:
+ %(prog)s [options] <train_tfrecords>...
+
+Options:
+ -h --help Show this screen.
+ --save-dir PATH [default: /idiap/user/amohammadi/avspoof/specgram/avspoof-simple-cnn-train]
+ --input-shape N [default: (50, 1024, 1)]
+ --epochs N [default: None]
+ --batch-size N [default: 32]
+ --capacity-samples N The capacity of the queue [default: 10**4/2].
+ --learning-rate N The learning rate [default: 0.00001].
+ --log-frequency N How often to log results to the console.
+ [default: 100]
+"""
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+# for bob imports to work properly:
+import pkg_resources
+# for creating reproducible nets
+from bob.dap.base.sandbox.reproducible import session_conf
+
+import tensorflow as tf
+from docopt import docopt
+from bob.io.base import create_directories_safe
+from bob.dap.voice.architectures.simple_cnn import architecture
+from bob.dap.base.database.tfrecords import read_and_decode
+from bob.dap.base.util.hooks import LoggerHook
+
+
+def main(argv=None):
+ arguments = docopt(__doc__, argv=argv)
+ print(arguments)
+ input_shape = eval(arguments['--input-shape'])
+ tfrecord_filenames = arguments['<train_tfrecords>']
+ save_dir = arguments['--save-dir']
+ epochs = eval(arguments['--epochs'])
+ batch_size = eval(arguments['--batch-size'])
+ capacity_samples = eval(arguments['--capacity-samples'])
+ learning_rate = eval(arguments['--learning-rate'])
+ log_frequency = eval(arguments['--log-frequency'])
+
+ create_directories_safe(save_dir)
+ with tf.Graph().as_default():
+ global_step = tf.contrib.framework.get_or_create_global_step()
+
+ # Get images and labels
+ with tf.name_scope('input'):
+ filename_queue = tf.train.string_input_producer(
+ tfrecord_filenames, num_epochs=epochs, name="tfrecord_filenames")
+
+ image, label = read_and_decode(filename_queue, input_shape)
+ images, labels = tf.train.shuffle_batch(
+ [image, label], batch_size=batch_size,
+ capacity=capacity_samples // batch_size,
+ min_after_dequeue=int(capacity_samples // batch_size // 2),
+ num_threads=1, name="shuffle_batch")
+
+ # Build a Graph that computes the logits predictions from the
+ # inference model.
+ logits = architecture(images)
+ tf.add_to_collection('logits', logits)
+
+ # Calculate loss.
+ predictor = tf.nn.sparse_softmax_cross_entropy_with_logits(
+ logits=logits, labels=labels)
+ loss = tf.reduce_mean(predictor)
+ tf.summary.scalar('loss', loss)
+
+ # Build a Graph that trains the model with one batch of examples and
+ # updates the model parameters.
+ optimizer = tf.train.GradientDescentOptimizer(learning_rate)
+ train_op = optimizer.minimize(loss, global_step=global_step)
+
+ saver = tf.train.Saver(max_to_keep=10**5)
+ scaffold = tf.train.Scaffold(saver=saver)
+ with tf.train.MonitoredTrainingSession(
+ checkpoint_dir=save_dir,
+ scaffold=scaffold,
+ hooks=[
+ tf.train.CheckpointSaverHook(
+ save_dir, save_secs=60 * 29, scaffold=scaffold),
+ tf.train.NanTensorHook(loss),
+ LoggerHook(loss, batch_size, log_frequency)],
+ config=session_conf,
+ save_checkpoint_secs=None,
+ save_summaries_steps=100,
+ ) as mon_sess:
+ while not mon_sess.should_stop():
+ mon_sess.run(train_op)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/bob/learn/tensorflow/utils/eval.py b/bob/learn/tensorflow/utils/eval.py
new file mode 100644
index 00000000..a431f8d2
--- /dev/null
+++ b/bob/learn/tensorflow/utils/eval.py
@@ -0,0 +1,110 @@
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+
+import math
+import numpy as np
+import tensorflow as tf
+from datetime import datetime
+
+
+def get_global_step(path):
+ """Returns the global number associated with the model checkpoint path. The
+ checkpoint must have been saved with the
+ :any:`tf.train.MonitoredTrainingSession`.
+
+ Parameters
+ ----------
+ path : str
+ The path to model checkpoint, usually ckpt.model_checkpoint_path
+
+ Returns
+ -------
+ global_step : str
+ The global step number as a string.
+ """
+ # Assuming model_checkpoint_path looks something like:
+ # /my-favorite-path/train/model.ckpt-0,
+ # extract global_step from it.
+ global_step = path.split('/')[-1].split('-')[-1]
+ return global_step
+
+
+def eval_once(saver, summary_writer, prediction_op, summary_op,
+ model_checkpoint_path, global_step, num_examples, batch_size):
+ """Run Eval once.
+
+ Parameters
+ ----------
+ saver
+ Saver.
+ summary_writer
+ Summary writer.
+ prediction_op
+ Prediction operator.
+ summary_op
+ Summary operator.
+ model_checkpoint_path : str
+ Path to the model checkpoint.
+ global_step : str
+ The global step.
+ num_examples : int or None
+ The number of examples to try.
+ batch_size : int
+ The size of evaluation batch.
+
+ This function requires the ``from __future__ import division`` import.
+
+ Returns
+ -------
+ int
+ 0 for success, anything else for fail.
+
+ """
+ with tf.Session() as sess:
+ sess.run(tf.local_variables_initializer())
+ sess.run(tf.global_variables_initializer())
+
+ if model_checkpoint_path:
+ # Restores from checkpoint
+ saver.restore(sess, model_checkpoint_path)
+ else:
+ print('No checkpoint file found')
+ return -1
+
+ # Start the queue runners.
+ coord = tf.train.Coordinator()
+ try:
+ threads = []
+ for qr in tf.get_collection(tf.GraphKeys.QUEUE_RUNNERS):
+ threads.extend(qr.create_threads(sess, coord=coord, daemon=True,
+ start=True))
+
+ if num_examples is None:
+ num_iter = float("inf")
+ else:
+ num_iter = int(math.ceil(num_examples / batch_size))
+ true_count = 0 # Counts the number of correct predictions.
+ total_sample_count = 0
+ step = 0
+ while step < num_iter and not coord.should_stop():
+ predictions = sess.run([prediction_op])
+ true_count += np.sum(predictions)
+ total_sample_count += np.asarray(predictions).size
+ step += 1
+
+ # Compute precision @ 1.
+ precision = true_count / total_sample_count
+ print('%s: precision @ 1 = %.3f' % (datetime.now(), precision))
+
+ summary = tf.Summary()
+ summary.ParseFromString(sess.run(summary_op))
+ summary.value.add(tag='Precision @ 1', simple_value=precision)
+ summary_writer.add_summary(summary, global_step)
+ return 0
+ except Exception as e: # pylint: disable=broad-except
+ coord.request_stop(e)
+ return -1
+ finally:
+ coord.request_stop()
+ coord.join(threads, stop_grace_period_secs=10)
diff --git a/bob/learn/tensorflow/utils/hooks.py b/bob/learn/tensorflow/utils/hooks.py
new file mode 100644
index 00000000..fe15d519
--- /dev/null
+++ b/bob/learn/tensorflow/utils/hooks.py
@@ -0,0 +1,35 @@
+import tensorflow as tf
+import time
+from datetime import datetime
+
+
+class LoggerHook(tf.train.SessionRunHook):
+ """Logs loss and runtime."""
+
+ def __init__(self, loss, batch_size, log_frequency):
+ self.loss = loss
+ self.batch_size = batch_size
+ self.log_frequency = log_frequency
+
+ def begin(self):
+ self._step = -1
+ self._start_time = time.time()
+
+ def before_run(self, run_context):
+ self._step += 1
+ return tf.train.SessionRunArgs(self.loss) # Asks for loss value.
+
+ def after_run(self, run_context, run_values):
+ if self._step % self.log_frequency == 0:
+ current_time = time.time()
+ duration = current_time - self._start_time
+ self._start_time = current_time
+
+ loss_value = run_values.results
+ examples_per_sec = self.log_frequency * self.batch_size / duration
+ sec_per_batch = float(duration / self.log_frequency)
+
+ format_str = ('%s: step %d, loss = %.2f (%.1f examples/sec; %.3f '
+ 'sec/batch)')
+ print(format_str % (datetime.now(), self._step, loss_value,
+ examples_per_sec, sec_per_batch))
diff --git a/bob/learn/tensorflow/utils/reproducible.py b/bob/learn/tensorflow/utils/reproducible.py
new file mode 100644
index 00000000..87c4ce87
--- /dev/null
+++ b/bob/learn/tensorflow/utils/reproducible.py
@@ -0,0 +1,37 @@
+import os
+import numpy as np
+import tensorflow as tf
+import random as rn
+from tensorflow.contrib import keras
+
+# reproducible networks
+# The below is necessary in Python 3.2.3 onwards to
+# have reproducible behavior for certain hash-based operations.
+# See these references for further details:
+# https://docs.python.org/3.4/using/cmdline.html#envvar-PYTHONHASHSEED
+# https://github.com/fchollet/keras/issues/2280#issuecomment-306959926
+os.environ['PYTHONHASHSEED'] = '0'
+
+# The below is necessary for starting Numpy generated random numbers
+# in a well-defined initial state.
+np.random.seed(42)
+
+# The below is necessary for starting core Python generated random numbers
+# in a well-defined state.
+rn.seed(12345)
+
+# Force TensorFlow to use single thread.
+# Multiple threads are a potential source of
+# non-reproducible results.
+# For further details, see:
+# https://stackoverflow.com/questions/42022950/which-seeds-have-to-be-set-where-to-realize-100-reproducibility-of-training-res
+session_conf = tf.ConfigProto(intra_op_parallelism_threads=1,
+ inter_op_parallelism_threads=1)
+
+# The below tf.set_random_seed() will make random number generation
+# in the TensorFlow backend have a well-defined initial state.
+# For further details, see:
+# https://www.tensorflow.org/api_docs/python/tf/set_random_seed
+tf.set_random_seed(1234)
+# sess = tf.Session(graph=tf.get_default_graph(), config=session_conf)
+# keras.backend.set_session(sess)
diff --git a/bob/learn/tensorflow/utils/sequences.py b/bob/learn/tensorflow/utils/sequences.py
new file mode 100644
index 00000000..fa16cb82
--- /dev/null
+++ b/bob/learn/tensorflow/utils/sequences.py
@@ -0,0 +1,143 @@
+from __future__ import division
+import numpy
+from keras.utils import Sequence
+# documentation imports
+from bob.dap.base.database import PadDatabase, PadFile
+from bob.bio.base.preprocessor import Preprocessor
+
+
+class PadSequence(Sequence):
+ """A data shuffler for bob.dap.base database interfaces.
+
+ Attributes
+ ----------
+ batch_size : int
+ The number of samples to return in every batch.
+ files : list of :any:`PadFile`
+ List of file objects for a particular group and protocol.
+ labels : list of bool
+ List of labels for the files. ``True`` if bona-fide, ``False`` if
+ attack.
+ preprocessor : :any:`Preprocessor`
+ The preprocessor to be used to load and process the data.
+ """
+
+ def __init__(self, files, labels, batch_size, preprocessor,
+ original_directory, original_extension):
+ super(PadSequence, self).__init__()
+ self.files = files
+ self.labels = labels
+ self.batch_size = int(batch_size)
+ self.preprocessor = preprocessor
+ self.original_directory = original_directory
+ self.original_extension = original_extension
+
+ def __len__(self):
+ """Number of batch in the Sequence.
+
+ Returns
+ -------
+ int
+ The number of batches in the Sequence.
+ """
+ return int(numpy.ceil(len(self.files) / self.batch_size))
+
+ def __getitem__(self, idx):
+ files = self.files[idx * self.batch_size:(idx + 1) * self.batch_size]
+ labels = self.labels[idx * self.batch_size:(idx + 1) * self.batch_size]
+ return self.load_batch(files, labels)
+
+ def load_batch(self, files, labels):
+ """Loads a batch of files and processes them.
+
+ Parameters
+ ----------
+ files : list of :any:`PadFile`
+ List of files to load.
+ labels : list of bool
+ List of labels corresponding to the files.
+
+ Returns
+ -------
+ tuple of :any:`numpy.array`
+ A tuple of (x, y): the data and their targets.
+ """
+ data, targets = [], []
+ for file_object, target in zip(files, labels):
+ loaded_data = self.preprocessor.read_original_data(
+ file_object,
+ self.original_directory,
+ self.original_extension)
+ preprocessed_data = self.preprocessor(loaded_data)
+ data.append(preprocessed_data)
+ targets.append(target)
+ return numpy.array(data), numpy.array(targets)
+
+ def on_epoch_end(self):
+ pass
+
+
+def shuffle_data(files, labels):
+ indexes = numpy.arange(len(files))
+ numpy.random.shuffle(indexes)
+ return [files[i] for i in indexes], [labels[i] for i in indexes]
+
+
+def get_pad_files_labels(database, groups):
+ """Returns the pad files and their labels.
+
+ Parameters
+ ----------
+ database : :any:`PadDatabase`
+ The database to be used. The database should have a proper
+ ``database.protocol`` attribute.
+ groups : str
+ The group to be used to return the data. One of ('world', 'dev',
+ 'eval'). 'world' means training data and 'dev' means validation data.
+
+ Returns
+ -------
+ tuple
+ A tuple of (files, labels) for that particular group and protocol.
+ """
+ files = database.samples(
+ groups=groups, protocol=database.protocol)
+ labels = ((f.attack_type is None) for f in files)
+ labels = numpy.fromiter(labels, bool, len(files))
+ return files, labels
+
+
+def get_pad_sequences(database, preprocessor, batch_size,
+ groups=('world', 'dev', 'eval'), shuffle=False,
+ limit=None):
+ """Returns a list of :any:`Sequence` objects for the database.
+
+ Parameters
+ ----------
+ database : :any:`PadDatabase`
+ The database to be used. The database should have a proper
+ ``database.protocol`` attribute.
+ preprocessor : :any:`Preprocessor`
+ The preprocessor to be used to load and process the data.
+ batch_size : int
+ The number of samples to return in every batch.
+ groups : str
+ The group to be used to return the data. One of ('world', 'dev',
+ 'eval'). 'world' means training data and 'dev' means validation data.
+
+ Returns
+ -------
+ list of :any:`Sequence`
+ The requested sequences to be used.
+ """
+ seqs = []
+ for grp in groups:
+ files, labels = get_pad_files_labels(database, grp)
+ if shuffle:
+ files, labels = shuffle_data(files, labels)
+ if limit is not None:
+ files, labels = files[:limit], labels[:limit]
+ seqs.append(PadSequence(files, labels, batch_size, preprocessor,
+ database.original_directory,
+ database.original_extension))
+ return seqs
diff --git a/bob/learn/tensorflow/utils/tfrecords.py b/bob/learn/tensorflow/utils/tfrecords.py
new file mode 100644
index 00000000..309575a2
--- /dev/null
+++ b/bob/learn/tensorflow/utils/tfrecords.py
@@ -0,0 +1,25 @@
+import tensorflow as tf
+
+
+def example_parser(serialized_example, feature, data_shape):
+ """Parses a single tf.Example into image and label tensors."""
+ # Decode the record read by the reader
+ features = tf.parse_single_example(serialized_example, features=feature)
+ # Convert the image data from string back to the numbers
+ image = tf.decode_raw(features['train/data'], tf.float32)
+ # Cast label data into int64
+ label = tf.cast(features['train/label'], tf.int64)
+ # Reshape image data into the original shape
+ image = tf.reshape(image, data_shape)
+ return image, label
+
+
+def read_and_decode(filename_queue, data_shape, feature=None):
+
+ if feature is None:
+ feature = {'train/data': tf.FixedLenFeature([], tf.string),
+ 'train/label': tf.FixedLenFeature([], tf.int64)}
+ # Define a reader and read the next record
+ reader = tf.TFRecordReader()
+ _, serialized_example = reader.read(filename_queue)
+ return example_parser(serialized_example, feature, data_shape)
--
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