Project import generated by Copybara.

PiperOrigin-RevId: 217341274

research/astronet/README.md

@@ -40,6 +40,10 @@ Full text available at [*The Astronomical Journal*](http://iopscience.iop.org/ar
   * Training and evaluating a new model.
   * Using a trained model to generate new predictions.
 
+[astrowavenet/](astrowavenet/)
+
+* A generative model for light curves.
+
 [light_curve_util/](light_curve_util)
 
 * Utilities for operating on light curves. These include:
@@ -63,11 +67,11 @@ First, ensure that you have installed the following required packages:
 * **TensorFlow** ([instructions](https://www.tensorflow.org/install/))
 * **Pandas** ([instructions](http://pandas.pydata.org/pandas-docs/stable/install.html))
 * **NumPy** ([instructions](https://docs.scipy.org/doc/numpy/user/install.html))
+* **SciPy** ([instructions](https://scipy.org/install.html))
 * **AstroPy** ([instructions](http://www.astropy.org/))
 * **PyDl** ([instructions](https://pypi.python.org/pypi/pydl))
 * **Bazel** ([instructions](https://docs.bazel.build/versions/master/install.html))
 * **Abseil Python Common Libraries** ([instructions](https://github.com/abseil/abseil-py))
-    * Optional: only required for unit tests.
 
 ### Optional: Run Unit Tests
 

research/astronet/astronet/util/config_util.py

@@ -63,6 +63,14 @@ def parse_json(json_string_or_file):
   return json_dict
 
 
+def to_json(config):
+  """Converts a JSON-serializable configuration object to a JSON string."""
+  if hasattr(config, "to_json") and callable(config.to_json):
+    return config.to_json(indent=2)
+  else:
+    return json.dumps(config, indent=2)
+
+
 def log_and_save_config(config, output_dir):
   """Logs and writes a JSON-serializable configuration object.
 
@@ -70,10 +78,7 @@ def log_and_save_config(config, output_dir):
     config: A JSON-serializable object.
     output_dir: Destination directory.
   """
-  if hasattr(config, "to_json") and callable(config.to_json):
-    config_json = config.to_json(indent=2)
-  else:
-    config_json = json.dumps(config, indent=2)
+  config_json = to_json(config)
   tf.logging.info("config: %s", config_json)
 
   tf.gfile.MakeDirs(output_dir)

research/astronet/astrowavenet/BUILD

@@ -4,6 +4,22 @@ package(default_visibility = ["//visibility:public"])
 
 licenses(["notice"])  # Apache 2.0
 
+py_binary(
+    name = "trainer",
+    srcs = ["trainer.py"],
+    srcs_version = "PY2AND3",
+    deps = [
+        ":astrowavenet_model",
+        ":configurations",
+        "//astronet/util:config_util",
+        "//astronet/util:configdict",
+        "//astronet/util:estimator_runner",
+        "//astrowavenet/data:kepler_light_curves",
+        "//astrowavenet/data:synthetic_transits",
+        "//astrowavenet/util:estimator_util",
+    ],
+)
+
 py_library(
     name = "configurations",
     srcs = ["configurations.py"],
@@ -11,22 +27,22 @@ py_library(
 )
 
 py_library(
-    name = "astrowavenet",
+    name = "astrowavenet_model",
     srcs = [
-        "astrowavenet.py",
+        "astrowavenet_model.py",
     ],
     srcs_version = "PY2AND3",
 )
 
 py_test(
-    name = "astrowavenet_test",
+    name = "astrowavenet_model_test",
     size = "small",
     srcs = [
-        "astrowavenet_test.py",
+        "astrowavenet_model_test.py",
     ],
     srcs_version = "PY2AND3",
     deps = [
-        ":astrowavenet",
+        ":astrowavenet_model",
         ":configurations",
         "//astronet/util:configdict",
     ],

research/astronet/astrowavenet/README.md

+# AstroWaveNet: A generative model for light curves.
+
+Implementation based on "WaveNet: A Generative Model of Raw Audio":
+https://arxiv.org/abs/1609.03499
+
+## Code Authors
+
+Alex Tamkin: [@atamkin](https://github.com/atamkin)
+
+Chris Shallue: [@cshallue](https://github.com/cshallue)
+
+## Pull Requests / Issues
+
+Chris Shallue: [@cshallue](https://github.com/cshallue)
+
+## Additional Dependencies
+
+This package requires TensorFlow 1.12 or greater. As of October 2018, this
+requires the **TensorFlow nightly build**
+([instructions](https://www.tensorflow.org/install/pip)).
+
+In addition to the dependencies listed in the top-level README, this package
+requires:
+
+* **TensorFlow Probability** ([instructions](https://www.tensorflow.org/probability/install))
+* **Six** ([instructions](https://pypi.org/project/six/))
+
+## Basic Usage
+
+To train a model on synthetic transits:
+
+```bash
+bazel build astrowavenet/...
+```
+
+```bash
+bazel-bin/astrowavenet/trainer \
+--dataset=synthetic_transits \
+--model_dir=/tmp/astrowavenet/ \
+--config_overrides='{"hparams": {"batch_size": 16, "num_residual_blocks": 2}}' \
+--schedule=train_and_eval \
+--eval_steps=100 \
+--save_checkpoints_steps=1000
+```

research/astronet/astrowavenet/__init__.py

+# Copyright 2018 The TensorFlow Authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+

research/astronet/astrowavenet/astrowavenet.py → research/astronet/astrowavenet/astrowavenet_model.py

@@ -23,6 +23,7 @@ from __future__ import division
 from __future__ import print_function
 
 import tensorflow as tf
+import tensorflow_probability as tfp
 
 
 def _shift_right(x):
@@ -64,18 +65,21 @@ class AstroWaveNet(object):
         tf.estimator.ModeKeys.PREDICT
     ]
     if mode not in valid_modes:
-      raise ValueError('Expected mode in {}. Got: {}'.format(valid_modes, mode))
+      raise ValueError("Expected mode in {}. Got: {}".format(valid_modes, mode))
     self.hparams = hparams
     self.mode = mode
 
-    self.autoregressive_input = features['autoregressive_input']
-    self.conditioning_stack = features['conditioning_stack']
-    self.weights = features.get('weights')
+    self.autoregressive_input = features["autoregressive_input"]
+    self.conditioning_stack = features["conditioning_stack"]
+    self.weights = features.get("weights")
 
     self.network_output = None  # Sum of skip connections from dilation stack.
+    self.dist_params = None  # Dict of predicted distribution parameters.
     self.predicted_distributions = None  # Predicted distribution for examples.
+    self.autoregressive_target = None  # Autoregressive target predictions.
     self.batch_losses = None  # Loss for each predicted distribution in batch.
     self.per_example_loss = None  # Loss for each example in batch.
+    self.num_nonzero_weight_examples = None  # Number of examples in batch.
     self.total_loss = None  # Overall loss for the batch.
     self.global_step = None  # Global step Tensor.
 
@@ -94,9 +98,9 @@ class AstroWaveNet(object):
     causal_conv_op = tf.keras.layers.Conv1D(
         output_size,
         kernel_width,
-        padding='causal',
+        padding="causal",
         dilation_rate=dilation_rate,
-        name='causal_conv')
+        name="causal_conv")
     return causal_conv_op(x)
 
   def conv_1x1_layer(self, x, output_size, activation=None):
@@ -111,7 +115,7 @@ class AstroWaveNet(object):
       Resulting tf.Tensor after applying the 1x1 convolution.
     """
     conv_1x1_op = tf.keras.layers.Conv1D(
-        output_size, 1, activation=activation, name='conv1x1')
+        output_size, 1, activation=activation, name="conv1x1")
     return conv_1x1_op(x)
 
   def gated_residual_layer(self, x, dilation_rate):
@@ -125,24 +129,26 @@ class AstroWaveNet(object):
       skip_connection: tf.Tensor; Skip connection to network_output layer.
       residual_connection: tf.Tensor; Sum of learned residual and input tensor.
     """
-    with tf.variable_scope('filter'):
-      x_filter_conv = self.causal_conv_layer(x, int(
-          x.shape[-1]), self.hparams.dilation_kernel_width, dilation_rate)
+    with tf.variable_scope("filter"):
+      x_filter_conv = self.causal_conv_layer(x, x.shape[-1].value,
+                                             self.hparams.dilation_kernel_width,
+                                             dilation_rate)
       cond_filter_conv = self.conv_1x1_layer(self.conditioning_stack,
-                                             int(x.shape[-1]))
-    with tf.variable_scope('gate'):
-      x_gate_conv = self.causal_conv_layer(x, int(
-          x.shape[-1]), self.hparams.dilation_kernel_width, dilation_rate)
+                                             x.shape[-1].value)
+    with tf.variable_scope("gate"):
+      x_gate_conv = self.causal_conv_layer(x, x.shape[-1].value,
+                                           self.hparams.dilation_kernel_width,
+                                           dilation_rate)
       cond_gate_conv = self.conv_1x1_layer(self.conditioning_stack,
-                                           int(x.shape[-1]))
+                                           x.shape[-1].value)
 
     gated_activation = (
         tf.tanh(x_filter_conv + cond_filter_conv) *
         tf.sigmoid(x_gate_conv + cond_gate_conv))
 
-    with tf.variable_scope('residual'):
-      residual = self.conv_1x1_layer(gated_activation, int(x.shape[-1]))
-    with tf.variable_scope('skip'):
+    with tf.variable_scope("residual"):
+      residual = self.conv_1x1_layer(gated_activation, x.shape[-1].value)
+    with tf.variable_scope("skip"):
       skip_connection = self.conv_1x1_layer(gated_activation,
                                             self.hparams.skip_output_dim)
 
@@ -167,13 +173,13 @@ class AstroWaveNet(object):
     """
     skip_connections = []
     x = _shift_right(self.autoregressive_input)
-    with tf.variable_scope('preprocess'):
+    with tf.variable_scope("preprocess"):
       x = self.causal_conv_layer(x, self.hparams.preprocess_output_size,
                                  self.hparams.preprocess_kernel_width)
     for i in range(self.hparams.num_residual_blocks):
-      with tf.variable_scope('block_{}'.format(i)):
+      with tf.variable_scope("block_{}".format(i)):
         for dilation_rate in self.hparams.dilation_rates:
-          with tf.variable_scope('dilation_{}'.format(dilation_rate)):
+          with tf.variable_scope("dilation_{}".format(dilation_rate)):
             skip_connection, x = self.gated_residual_layer(x, dilation_rate)
             skip_connections.append(skip_connection)
 
@@ -192,7 +198,7 @@ class AstroWaveNet(object):
       The parameters of each distribution, a tensor of shape [batch_size,
         time_series_length, outputs_size].
     """
-    with tf.variable_scope('dist_params'):
+    with tf.variable_scope("dist_params"):
       conv_outputs = self.conv_1x1_layer(x, outputs_size)
     return conv_outputs
 
@@ -212,36 +218,40 @@ class AstroWaveNet(object):
       self.network_outputs
 
     Outputs:
+      self.dist_params
       self.predicted_distributions
 
     Raises:
       ValueError: If distribution type is neither 'categorical' nor 'normal'.
     """
-    with tf.variable_scope('postprocess'):
+    with tf.variable_scope("postprocess"):
       network_output = tf.keras.activations.relu(self.network_output)
       network_output = self.conv_1x1_layer(
           network_output,
-          output_size=int(network_output.shape[-1]),
-          activation='relu')
-    num_dists = int(self.autoregressive_input.shape[-1])
+          output_size=network_output.shape[-1].value,
+          activation="relu")
+    num_dists = self.autoregressive_input.shape[-1].value
 
-    if self.hparams.output_distribution.type == 'categorical':
+    if self.hparams.output_distribution.type == "categorical":
       num_classes = self.hparams.output_distribution.num_classes
-      dist_params = self.dist_params_layer(network_output,
-                                           num_dists * num_classes)
-      dist_shape = tf.concat(
+      logits = self.dist_params_layer(network_output, num_dists * num_classes)
+      logits_shape = tf.concat(
           [tf.shape(network_output)[:-1], [num_dists, num_classes]], 0)
-      dist_params = tf.reshape(dist_params, dist_shape)
-      dist = tf.distributions.Categorical(logits=dist_params)
-    elif self.hparams.output_distribution.type == 'normal':
-      dist_params = self.dist_params_layer(network_output, num_dists * 2)
-      loc, scale = tf.split(dist_params, 2, axis=-1)
+      logits = tf.reshape(logits, logits_shape)
+      dist = tfp.distributions.Categorical(logits=logits)
+      dist_params = {"logits": logits}
+    elif self.hparams.output_distribution.type == "normal":
+      loc_scale = self.dist_params_layer(network_output, num_dists * 2)
+      loc, scale = tf.split(loc_scale, 2, axis=-1)
       # Ensure scale is positive.
       scale = tf.nn.softplus(scale) + self.hparams.output_distribution.min_scale
-      dist = tf.distributions.Normal(loc, scale)
+      dist = tfp.distributions.Normal(loc, scale)
+      dist_params = {"loc": loc, "scale": scale}
     else:
-      raise ValueError('Unsupported distribution type {}'.format(
+      raise ValueError("Unsupported distribution type {}".format(
           self.hparams.output_distribution.type))
+
+    self.dist_params = dist_params
     self.predicted_distributions = dist
 
   def build_losses(self):
@@ -257,7 +267,7 @@ class AstroWaveNet(object):
     autoregressive_target = self.autoregressive_input
 
     # Quantize the target if the output distribution is categorical.
-    if self.hparams.output_distribution.type == 'categorical':
+    if self.hparams.output_distribution.type == "categorical":
       min_val = self.hparams.output_distribution.min_quantization_value
       max_val = self.hparams.output_distribution.max_quantization_value
       num_classes = self.hparams.output_distribution.num_classes
@@ -270,7 +280,7 @@ class AstroWaveNet(object):
       # final quantized bucket a closed interval while all the other quantized
       # buckets are half-open intervals.
       quantized_target = tf.where(
-          quantized_target == num_classes,
+          quantized_target >= num_classes,
           tf.ones_like(quantized_target) * (num_classes - 1), quantized_target)
       autoregressive_target = quantized_target
 
@@ -280,22 +290,24 @@ class AstroWaveNet(object):
     if weights is None:
       weights = tf.ones_like(log_prob)
     weights_dim = len(weights.shape)
-    per_example_weight = tf.reduce_sum(weights, axis=range(1, weights_dim))
+    per_example_weight = tf.reduce_sum(
+        weights, axis=list(range(1, weights_dim)))
     per_example_indicator = tf.to_float(tf.greater(per_example_weight, 0))
-    num_examples = tf.reduce_sum(
-        per_example_indicator, name='num_nonzero_weight_examples')
+    num_examples = tf.reduce_sum(per_example_indicator)
 
     batch_losses = -log_prob * weights
-    losses_dim = len(batch_losses.shape)
+    losses_ndims = batch_losses.shape.ndims
     per_example_loss_sum = tf.reduce_sum(
-        batch_losses, axis=range(1, losses_dim))
+        batch_losses, axis=list(range(1, losses_ndims)))
     per_example_loss = tf.where(per_example_weight > 0,
                                 per_example_loss_sum / per_example_weight,
                                 tf.zeros_like(per_example_weight))
     total_loss = tf.reduce_sum(per_example_loss) / num_examples
 
+    self.autoregressive_target = autoregressive_target
     self.batch_losses = batch_losses
     self.per_example_loss = per_example_loss
+    self.num_nonzero_weight_examples = num_examples
     self.total_loss = total_loss
 
   def build(self):

research/astronet/astrowavenet/data/BUILD

@@ -2,6 +2,48 @@ package(default_visibility = ["//visibility:public"])
 
 licenses(["notice"])  # Apache 2.0
 
+py_library(
+    name = "base",
+    srcs = [
+        "base.py",
+    ],
+    deps = [
+        "//astronet/ops:dataset_ops",
+        "//astronet/util:configdict",
+    ],
+)
+
+py_test(
+    name = "base_test",
+    srcs = ["base_test.py"],
+    data = ["test_data/test-dataset.tfrecord"],
+    srcs_version = "PY2AND3",
+    deps = [":base"],
+)
+
+py_library(
+    name = "kepler_light_curves",
+    srcs = [
+        "kepler_light_curves.py",
+    ],
+    deps = [
+        ":base",
+        "//astronet/util:configdict",
+    ],
+)
+
+py_library(
+    name = "synthetic_transits",
+    srcs = [
+        "synthetic_transits.py",
+    ],
+    deps = [
+        ":base",
+        ":synthetic_transit_maker",
+        "//astronet/util:configdict",
+    ],
+)
+
 py_library(
     name = "synthetic_transit_maker",
     srcs = [

research/astronet/astrowavenet/data/__init__.py

+# Copyright 2018 The TensorFlow Authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+

research/astronet/astrowavenet/data/base.py

+# Copyright 2018 The TensorFlow Authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Base dataset builder classes for AstroWaveNet input pipelines."""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+
+import abc
+import six
+
+import tensorflow as tf
+
+from astronet.util import configdict
+from astronet.ops import dataset_ops
+
+
+@six.add_metaclass(abc.ABCMeta)
+class DatasetBuilder(object):
+  """Base class for building a dataset input pipeline for AstroWaveNet."""
+
+  def __init__(self, config_overrides=None):
+    """Initializes the dataset builder.
+
+    Args:
+      config_overrides: Dict or ConfigDict containing overrides to the default
+        configuration.
+    """
+    self.config = configdict.ConfigDict(self.default_config())
+    if config_overrides is not None:
+      self.config.update(config_overrides)
+
+  @staticmethod
+  def default_config():
+    """Returns the default configuration as a ConfigDict or Python dict."""
+    return {}
+
+  @abc.abstractmethod
+  def build(self, batch_size):
+    """Builds the dataset input pipeline.
+
+    Args:
+      batch_size: The number of input examples in each batch.
+
+    Returns:
+      A tf.data.Dataset object.
+    """
+    raise NotImplementedError
+
+
+@six.add_metaclass(abc.ABCMeta)
+class _ShardedDatasetBuilder(DatasetBuilder):
+  """Abstract base class for a dataset consisting of sharded files."""
+
+  def __init__(self, file_pattern, mode, config_overrides=None, use_tpu=False):
+    """Initializes the dataset builder.
+
+    Args:
+      file_pattern: File pattern matching input file shards, e.g.
+        "/tmp/train-?????-of-00100". May also be a comma-separated list of file
+        patterns.
+      mode: A tf.estimator.ModeKeys.
+      config_overrides: Dict or ConfigDict containing overrides to the default
+        configuration.
+      use_tpu: Whether to build the dataset for TPU.
+    """
+    super(_ShardedDatasetBuilder, self).__init__(config_overrides)
+    self.file_pattern = file_pattern
+    self.mode = mode
+    self.use_tpu = use_tpu
+
+  @staticmethod
+  def default_config():
+    config = super(_ShardedDatasetBuilder,
+                   _ShardedDatasetBuilder).default_config()
+    config.update({
+        "max_length": 1024,
+        "shuffle_values_buffer": 1000,
+        "num_parallel_parser_calls": 4,
+        "batches_buffer_size": None,  # Defaults to max(1, 256 / batch_size).
+    })
+    return config
+
+  @abc.abstractmethod
+  def file_reader(self):
+    """Returns a function that reads a single sharded file."""
+    raise NotImplementedError
+
+  @abc.abstractmethod
+  def create_example_parser(self):
+    """Returns a function that parses a single tf.Example proto."""
+    raise NotImplementedError
+
+  def _batch_and_pad(self, dataset, batch_size):
+    """Combines elements into batches of the same length, padding if needed."""
+    if self.use_tpu:
+      padded_length = self.config.max_length
+      if not padded_length:
+        raise ValueError("config.max_length is required when using TPU")
+      # Pad with zeros up to padded_length. Note that this will pad the
+      # "weights" Tensor with zeros as well, which ensures that padded elements
+      # do not contribute to the loss.
+      padded_shapes = {}
+      for name, shape in dataset.output_shapes.iteritems():
+        shape.assert_is_compatible_with([None, None])  # Expect a 2D sequence.
+        dims = shape.as_list()
+        dims[0] = padded_length
+        shape = tf.TensorShape(dims)
+        shape.assert_is_fully_defined()
+        padded_shapes[name] = shape
+    else:
+      # Pad each batch up to the maximum size of each dimension in the batch.
+      padded_shapes = dataset.output_shapes
+
+    return dataset.padded_batch(batch_size, padded_shapes)
+
+  def build(self, batch_size):
+    """Builds the dataset input pipeline.
+
+    Args:
+      batch_size:
+
+    Returns:
+      A tf.data.Dataset.
+
+    Raises:
+      ValueError: If no files match self.file_pattern.
+    """
+    file_patterns = self.file_pattern.split(",")
+    filenames = []
+    for p in file_patterns:
+      matches = tf.gfile.Glob(p)
+      if not matches:
+        raise ValueError("Found no input files matching {}".format(p))
+      filenames.extend(matches)
+    tf.logging.info(
+        "Building input pipeline from %d files matching patterns: %s",
+        len(filenames), file_patterns)
+
+    is_training = self.mode == tf.estimator.ModeKeys.TRAIN
+
+    # Create a string dataset of filenames, and possibly shuffle.
+    filename_dataset = tf.data.Dataset.from_tensor_slices(filenames)
+    if is_training and len(filenames) > 1:
+      filename_dataset = filename_dataset.shuffle(len(filenames))
+
+    # Read serialized Example protos.
+    dataset = filename_dataset.apply(
+        tf.contrib.data.parallel_interleave(
+            self.file_reader(), cycle_length=8, block_length=8, sloppy=True))
+
+    if is_training:
+      # Shuffle and repeat. Note that shuffle() is before repeat(), so elements
+      # are shuffled among each epoch of data, and not between epochs of data.
+      if self.config.shuffle_values_buffer > 0:
+        dataset = dataset.shuffle(self.config.shuffle_values_buffer)
+      dataset = dataset.repeat()
+
+    # Map the parser over the dataset.
+    dataset = dataset.map(
+        self.create_example_parser(),
+        num_parallel_calls=self.config.num_parallel_parser_calls)
+
+    def _prepare_wavenet_inputs(features):
+      """Validates features, and clips lengths and adds weights if needed."""
+      # Validate feature names.
+      required_features = {"autoregressive_input", "conditioning_stack"}
+      allowed_features = required_features | {"weights"}
+      feature_names = features.keys()
+      if not required_features.issubset(feature_names):
+        raise ValueError("Features must contain all of: {}. Got: {}".format(
+            required_features, feature_names))
+      if not allowed_features.issuperset(feature_names):
+        raise ValueError("Features can only contain: {}. Got: {}".format(
+            allowed_features, feature_names))
+
+      output = {}
+      for name, value in features.items():
+        # Validate shapes. The output dimension is [num_samples, dim].
+        ndims = len(value.shape)
+        if ndims == 1:
+          # Add an extra dimension: [num_samples] -> [num_samples, 1].
+          value = tf.expand_dims(value, -1)
+        elif ndims != 2:
+          raise ValueError(
+              "Features should be 1D or 2D sequences. Got '{}' = {}".format(
+                  name, value))
+        if self.config.max_length:
+          value = value[:self.config.max_length]
+        output[name] = value
+
+      if "weights" not in output:
+        output["weights"] = tf.ones_like(output["autoregressive_input"])
+
+      return output
+
+    dataset = dataset.map(_prepare_wavenet_inputs)
+
+    # Batch results by up to batch_size.
+    dataset = self._batch_and_pad(dataset, batch_size)
+
+    if is_training:
+      # The dataset repeats infinitely before batching, so each batch has the
+      # maximum number of elements.
+      dataset = dataset_ops.set_batch_size(dataset, batch_size)
+    elif self.use_tpu and self.mode == tf.estimator.ModeKeys.EVAL:
+      # Pad to ensure that each batch has the same number of elements.
+      dataset = dataset_ops.pad_dataset_to_batch_size(dataset, batch_size)
+
+    # Prefetch batches.
+    buffer_size = (
+        self.config.batches_buffer_size or max(1, int(256 / batch_size)))
+    dataset = dataset.prefetch(buffer_size)
+
+    return dataset
+
+
+def tfrecord_reader(filename):
+  """Returns a tf.data.Dataset that reads a single TFRecord file shard."""
+  return tf.data.TFRecordDataset(filename, buffer_size=16 * 1000 * 1000)
+
+
+class TFRecordDataset(_ShardedDatasetBuilder):
+  """Builder for a dataset consisting of TFRecord files."""
+
+  def file_reader(self):
+    """Returns a function that reads a single file shard."""
+    return tfrecord_reader

research/astronet/astrowavenet/data/kepler_light_curves.py

+# Copyright 2018 The TensorFlow Authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Kepler light curve inputs to the AstroWaveNet model."""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+
+import tensorflow as tf
+
+from astrowavenet.data import base
+
+COND_INPUT_KEY = "mask"
+AR_INPUT_KEY = "flux"
+
+
+class KeplerLightCurves(base.TFRecordDataset):
+  """Kepler light curve inputs to the AstroWaveNet model."""
+
+  def create_example_parser(self):
+
+    def _example_parser(serialized):
+      """Parses a single tf.Example proto."""
+      features = tf.parse_single_example(
+          serialized,
+          features={
+              AR_INPUT_KEY: tf.VarLenFeature(tf.float32),
+              COND_INPUT_KEY: tf.VarLenFeature(tf.int64),
+          })
+      # Extract values from SparseTensor objects.
+      autoregressive_input = features[AR_INPUT_KEY].values
+      conditioning_stack = tf.to_float(features[COND_INPUT_KEY].values)
+      return {
+          "autoregressive_input": autoregressive_input,
+          "conditioning_stack": conditioning_stack,
+      }
+
+    return _example_parser

research/astronet/astrowavenet/data/synthetic_transit_maker.py

@@ -43,8 +43,8 @@ class SyntheticTransitMaker(object):
       would translate the sine wave by half of the period. The most common
       reason to override this would be to generate light curves
       deterministically (with e.g. (0,0)).
-    noise_sd_range: A tuple of values in [0, 1) specifying the range of
-      standard deviations for the Gaussian noise applied to the sine wave.
+    noise_sd_range: A tuple of values in [0, 1) specifying the range of standard
+      deviations for the Gaussian noise applied to the sine wave.
   """
 
   def __init__(self,
@@ -125,7 +125,7 @@ class SyntheticTransitMaker(object):
     Args:
        time: An np.array of x-values to sample from the thresholded sine wave.
        mask_prob: Value in [0,1], probability an individual datapoint is set to
-        zero.
+         zero.
 
     Returns:
       A generator yielding random light curves.

research/astronet/astrowavenet/data/synthetic_transit_maker_test.py

@@ -29,30 +29,30 @@ class SyntheticTransitMakerTest(absltest.TestCase):
   def testBadRangesRaiseExceptions(self):
 
     # Period range cannot contain negative values.
-    with self.assertRaisesRegexp(ValueError, 'Period'):
+    with self.assertRaisesRegexp(ValueError, "Period"):
       synthetic_transit_maker.SyntheticTransitMaker(period_range=(-1, 10))
 
     # Amplitude range cannot contain negative values.
-    with self.assertRaisesRegexp(ValueError, 'Amplitude'):
+    with self.assertRaisesRegexp(ValueError, "Amplitude"):
       synthetic_transit_maker.SyntheticTransitMaker(amplitude_range=(-10, -1))
 
     # Threshold ratio range must be contained in the half-open interval [0, 1).
-    with self.assertRaisesRegexp(ValueError, 'Threshold ratio'):
+    with self.assertRaisesRegexp(ValueError, "Threshold ratio"):
       synthetic_transit_maker.SyntheticTransitMaker(
           threshold_ratio_range=(0, 1))
 
     # Noise standard deviation range must only contain nonnegative values.
-    with self.assertRaisesRegexp(ValueError, 'Noise standard deviation'):
+    with self.assertRaisesRegexp(ValueError, "Noise standard deviation"):
       synthetic_transit_maker.SyntheticTransitMaker(noise_sd_range=(-1, 1))
 
     # End of range may not be less than start.
     invalid_range = (0.2, 0.1)
     range_args = [
-        'period_range', 'threshold_ratio_range', 'amplitude_range',
-        'noise_sd_range', 'phase_range'
+        "period_range", "threshold_ratio_range", "amplitude_range",
+        "noise_sd_range", "phase_range"
     ]
     for range_arg in range_args:
-      with self.assertRaisesRegexp(ValueError, 'may not be less'):
+      with self.assertRaisesRegexp(ValueError, "may not be less"):
         synthetic_transit_maker.SyntheticTransitMaker(
             **{range_arg: invalid_range})
 
@@ -106,5 +106,5 @@ class SyntheticTransitMakerTest(absltest.TestCase):
       self.assertEqual(len(mask), 100)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
   absltest.main()

research/astronet/astrowavenet/data/synthetic_transits.py

+# Copyright 2018 The TensorFlow Authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Synthetic transit inputs to the AstroWaveNet model."""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+
+import numpy as np
+import tensorflow as tf
+
+from astronet.util import configdict
+from astrowavenet.data import base
+from astrowavenet.data import synthetic_transit_maker
+
+
+def _prepare_wavenet_inputs(light_curve, mask):
+  """Gathers synthetic transits into the format expected by AstroWaveNet."""
+  return {
+      "autoregressive_input": tf.expand_dims(light_curve, -1),
+      "conditioning_stack": tf.expand_dims(mask, -1),
+  }
+
+
+class SyntheticTransits(base.DatasetBuilder):
+  """Synthetic transit inputs to the AstroWaveNet model."""
+
+  @staticmethod
+  def default_config():
+    return configdict.ConfigDict({
+        "period_range": (0.5, 4),
+        "amplitude_range": (1, 1),
+        "threshold_ratio_range": (0, 0.99),
+        "phase_range": (0, 1),
+        "noise_sd_range": (0.1, 0.1),
+        "mask_probability": 0.1,
+        "light_curve_time_range": (0, 100),
+        "light_curve_num_points": 1000
+    })
+
+  def build(self, batch_size):
+    transit_maker = synthetic_transit_maker.SyntheticTransitMaker(
+        period_range=self.config.period_range,
+        amplitude_range=self.config.amplitude_range,
+        threshold_ratio_range=self.config.threshold_ratio_range,
+        phase_range=self.config.phase_range,
+        noise_sd_range=self.config.noise_sd_range)
+    t_start, t_end = self.config.light_curve_time_range
+    time = np.linspace(t_start, t_end, self.config.light_curve_num_points)
+    dataset = tf.data.Dataset.from_generator(
+        transit_maker.random_light_curve_generator(
+            time, mask_prob=self.config.mask_probability),
+        output_types=(tf.float32, tf.float32),
+        output_shapes=(tf.TensorShape((self.config.light_curve_num_points,)),
+                       tf.TensorShape((self.config.light_curve_num_points,))))
+    dataset = dataset.map(_prepare_wavenet_inputs)
+    dataset = dataset.batch(batch_size, drop_remainder=True)
+    dataset = dataset.prefetch(-1)
+
+    return dataset

research/astronet/astrowavenet/trainer.py

+# Copyright 2018 The TensorFlow Authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Script for training and evaluating AstroWaveNet models."""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+
+import json
+import os.path
+
+from absl import flags
+import tensorflow as tf
+
+from astronet.util import config_util
+from astronet.util import configdict
+from astronet.util import estimator_runner
+from astrowavenet import astrowavenet_model
+from astrowavenet import configurations
+from astrowavenet.data import kepler_light_curves
+from astrowavenet.data import synthetic_transits
+from astrowavenet.util import estimator_util
+
+
+FLAGS = flags.FLAGS
+
+flags.DEFINE_enum("dataset", None,
+                  ["synthetic_transits", "kepler_light_curves"],
+                  "Dataset for training and/or evaluation.")
+
+flags.DEFINE_string("model_dir", None, "Base output directory.")
+
+flags.DEFINE_string(
+    "train_files", None,
+    "Comma-separated list of file patterns matching the TFRecord files in the "
+    "training dataset.")
+
+flags.DEFINE_string(
+    "eval_files", None,
+    "Comma-separated list of file patterns matching the TFRecord files in the "
+    "evaluation dataset.")
+
+flags.DEFINE_string("config_name", "base",
+                    "Name of the AstroWaveNet configuration.")
+
+flags.DEFINE_string(
+    "config_overrides", "{}",
+    "JSON string or JSON file containing overrides to the base configuration.")
+
+flags.DEFINE_enum("schedule", None,
+                  ["train", "train_and_eval", "continuous_eval"],
+                  "Schedule for running the model.")
+
+flags.DEFINE_string("eval_name", "val", "Name of the evaluation task.")
+
+flags.DEFINE_integer("train_steps", None, "Total number of steps for training.")
+
+flags.DEFINE_integer("eval_steps", None, "Number of steps for each evaluation.")
+
+flags.DEFINE_integer(
+    "local_eval_frequency", 1000,
+    "The number of training steps in between evaluation runs. Only applies "
+    "when schedule == 'train_and_eval'.")
+
+flags.DEFINE_integer("save_summary_steps", None,
+                     "The frequency at which to save model summaries.")
+
+flags.DEFINE_integer("save_checkpoints_steps", None,
+                     "The frequency at which to save model checkpoints.")
+
+flags.DEFINE_integer("save_checkpoints_secs", None,
+                     "The frequency at which to save model checkpoints.")
+
+flags.DEFINE_integer("keep_checkpoint_max", 1,
+                     "The maximum number of model checkpoints to keep.")
+
+# ------------------------------------------------------------------------------
+# TPU-only flags
+# ------------------------------------------------------------------------------
+
+flags.DEFINE_boolean("use_tpu", False, "Whether to execute on TPU.")
+
+flags.DEFINE_string("master", None, "Address of the TensorFlow TPU master.")
+
+flags.DEFINE_integer("tpu_num_shards", 8, "Number of TPU shards.")
+
+flags.DEFINE_integer("tpu_iterations_per_loop", 1000,
+                     "Number of iterations per TPU training loop.")
+
+flags.DEFINE_integer(
+    "eval_batch_size", None,
+    "Batch size for TPU evaluation. Defaults to the training batch size.")
+
+
+def _create_run_config():
+  """Creates a TPU RunConfig if FLAGS.use_tpu is True, else a RunConfig."""
+  session_config = tf.ConfigProto(allow_soft_placement=True)
+  run_config_kwargs = {
+      "save_summary_steps": FLAGS.save_summary_steps,
+      "save_checkpoints_steps": FLAGS.save_checkpoints_steps,
+      "save_checkpoints_secs": FLAGS.save_checkpoints_secs,
+      "session_config": session_config,
+      "keep_checkpoint_max": FLAGS.keep_checkpoint_max
+  }
+
+  if FLAGS.use_tpu:
+    if not FLAGS.master:
+      raise ValueError("FLAGS.master must be set for TPUEstimator.")
+
+    tpu_config = tf.contrib.tpu.TPUConfig(
+        iterations_per_loop=FLAGS.tpu_iterations_per_loop,
+        num_shards=FLAGS.tpu_num_shards,
+        per_host_input_for_training=(FLAGS.tpu_num_shards <= 8))
+    run_config = tf.contrib.tpu.RunConfig(
+        tpu_config=tpu_config, master=FLAGS.master, **run_config_kwargs)
+  else:
+    if FLAGS.master:
+      raise ValueError("FLAGS.master should only be set for TPUEstimator.")
+
+    run_config = tf.estimator.RunConfig(**run_config_kwargs)
+
+  return run_config
+
+
+def _get_file_pattern(mode):
+  """Gets the value of the file pattern flag for the specified mode."""
+  flag_name = ("train_files"
+               if mode == tf.estimator.ModeKeys.TRAIN else "eval_files")
+  file_pattern = FLAGS[flag_name].value
+  if file_pattern is None:
+    raise ValueError("--{} is required for mode '{}'".format(flag_name, mode))
+  return file_pattern
+
+
+def _create_dataset_builder(mode, config_overrides=None):
+  """Creates a dataset builder for the input pipeline."""
+  if FLAGS.dataset == "synthetic_transits":
+    return synthetic_transits.SyntheticTransits(config_overrides)
+
+  file_pattern = _get_file_pattern(mode)
+  if FLAGS.dataset == "kepler_light_curves":
+    builder_class = kepler_light_curves.KeplerLightCurves
+  else:
+    raise ValueError("Unsupported dataset: {}".format(FLAGS.dataset))
+
+  return builder_class(
+      file_pattern,
+      mode,
+      config_overrides=config_overrides,
+      use_tpu=FLAGS.use_tpu)
+
+
+def _create_input_fn(mode, config_overrides=None):
+  """Creates an Estimator input_fn."""
+  builder = _create_dataset_builder(mode, config_overrides)
+  tf.logging.info("Dataset config for mode '%s': %s", mode,
+                  config_util.to_json(builder.config))
+  return estimator_util.create_input_fn(builder)
+
+
+def _create_eval_args(config_overrides=None):
+  """Builds eval_args for estimator_runner.evaluate()."""
+  if FLAGS.dataset == "synthetic_transits" and not FLAGS.eval_steps:
+    raise ValueError("Dataset '{}' requires --eval_steps for evaluation".format(
+        FLAGS.dataset))
+  input_fn = _create_input_fn(tf.estimator.ModeKeys.EVAL, config_overrides)
+  return {FLAGS.eval_name: (input_fn, FLAGS.eval_steps)}
+
+
+def main(argv):
+  del argv  # Unused.
+
+  config = configdict.ConfigDict(configurations.get_config(FLAGS.config_name))
+  config_overrides = json.loads(FLAGS.config_overrides)
+  for key in config_overrides:
+    if key not in ["dataset", "hparams"]:
+      raise ValueError("Unrecognized config override: {}".format(key))
+  config.hparams.update(config_overrides.get("hparams", {}))
+
+  # Log configs.
+  configs_json = [
+      ("config_overrides", config_util.to_json(config_overrides)),
+      ("config", config_util.to_json(config)),
+  ]
+  for config_name, config_json in configs_json:
+    tf.logging.info("%s: %s", config_name, config_json)
+
+  # Create the estimator.
+  run_config = _create_run_config()
+  estimator = estimator_util.create_estimator(
+      astrowavenet_model.AstroWaveNet, config.hparams, run_config,
+      FLAGS.model_dir, FLAGS.eval_batch_size)
+
+  if FLAGS.schedule in ["train", "train_and_eval"]:
+    # Save configs.
+    tf.gfile.MakeDirs(FLAGS.model_dir)
+    for config_name, config_json in configs_json:
+      filename = os.path.join(FLAGS.model_dir, "{}.json".format(config_name))
+      with tf.gfile.Open(filename, "w") as f:
+        f.write(config_json)
+
+    train_input_fn = _create_input_fn(tf.estimator.ModeKeys.TRAIN,
+                                      config_overrides.get("dataset"))
+
+    train_hooks = []
+    if FLAGS.schedule == "train":
+      estimator.train(
+          train_input_fn, hooks=train_hooks, max_steps=FLAGS.train_steps)
+    else:
+      assert FLAGS.schedule == "train_and_eval"
+
+      eval_args = _create_eval_args(config_overrides.get("dataset"))
+      for _ in estimator_runner.continuous_train_and_eval(
+          estimator=estimator,
+          train_input_fn=train_input_fn,
+          eval_args=eval_args,
+          local_eval_frequency=FLAGS.local_eval_frequency,
+          train_hooks=train_hooks,
+          train_steps=FLAGS.train_steps):
+        # continuous_train_and_eval() yields evaluation metrics after each
+        # FLAGS.local_eval_frequency. It also saves and logs them, so we don't
+        # do anything here.
+        pass
+
+  else:
+    assert FLAGS.schedule == "continuous_eval"
+
+    eval_args = _create_eval_args(config_overrides.get("dataset"))
+    for _ in estimator_runner.continuous_eval(
+        estimator=estimator, eval_args=eval_args,
+        train_steps=FLAGS.train_steps):
+      # continuous_train_and_eval() yields evaluation metrics after each
+      # checkpoint. It also saves and logs them, so we don't do anything here.
+      pass
+
+
+if __name__ == "__main__":
+  tf.logging.set_verbosity(tf.logging.INFO)
+
+  flags.mark_flags_as_required(["dataset", "model_dir", "schedule"])
+
+  def _validate_schedule(flag_values):
+    """Validates the --schedule flag and the flags it interacts with."""
+    schedule = flag_values["schedule"]
+    save_checkpoints_steps = flag_values["save_checkpoints_steps"]
+    save_checkpoints_secs = flag_values["save_checkpoints_secs"]
+
+    if schedule in ["train", "train_and_eval"]:
+      if not (save_checkpoints_steps or save_checkpoints_secs):
+        raise flags.ValidationError(
+            "--schedule='%s' requires --save_checkpoints_steps or "
+            "--save_checkpoints_secs." % schedule)
+
+    return True
+
+  flags.register_multi_flags_validator(
+      ["schedule", "save_checkpoints_steps", "save_checkpoints_secs"],
+      _validate_schedule)
+
+  tf.app.run()

research/astronet/astrowavenet/util/BUILD

+package(default_visibility = ["//visibility:public"])
+
+licenses(["notice"])  # Apache 2.0
+
+py_library(
+    name = "estimator_util",
+    srcs = ["estimator_util.py"],
+    srcs_version = "PY2AND3",
+    deps = ["//astronet/ops:training"],
+)

research/astronet/astrowavenet/util/estimator_util.py

+# Copyright 2018 The TensorFlow Authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Helper functions for creating a TensorFlow Estimator."""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+
+import copy
+
+import tensorflow as tf
+
+from astronet.ops import training
+
+
+class _InputFn(object):
+  """Class that acts as a callable input function for Estimator train / eval."""
+
+  def __init__(self, dataset_builder):
+    """Initializes the input function.
+
+    Args:
+      dataset_builder: Instance of DatasetBuilder.
+    """
+    self._builder = dataset_builder
+
+  def __call__(self, params):
+    """Builds the input pipeline."""
+    return self._builder.build(batch_size=params["batch_size"])
+
+
+def create_input_fn(dataset_builder):
+  """Creates an input_fn that that builds an input pipeline.
+
+  Args:
+    dataset_builder: Instance of DatasetBuilder.
+
+  Returns:
+    A callable that builds an input pipeline and returns a tf.data.Dataset
+    object.
+  """
+  return _InputFn(dataset_builder)
+
+
+class _ModelFn(object):
+  """Class that acts as a callable model function for Estimator train / eval."""
+
+  def __init__(self, model_class, hparams, use_tpu=False):
+    """Initializes the model function.
+
+    Args:
+      model_class: Model class.
+      hparams: A HParams object containing hyperparameters for building and
+        training the model.
+      use_tpu: If True, a TPUEstimator will be returned. Otherwise an Estimator
+        will be returned.
+    """
+    self._model_class = model_class
+    self._base_hparams = hparams
+    self._use_tpu = use_tpu
+
+  def __call__(self, features, mode, params):
+    """Builds the model and returns an EstimatorSpec or TPUEstimatorSpec."""
+    hparams = copy.deepcopy(self._base_hparams)
+    if "batch_size" in params:
+      hparams.batch_size = params["batch_size"]
+
+    model = self._model_class(features, hparams, mode)
+    model.build()
+
+    # Possibly create train_op.
+    use_tpu = self._use_tpu
+    train_op = None
+    if mode == tf.estimator.ModeKeys.TRAIN:
+      learning_rate = training.create_learning_rate(hparams, model.global_step)
+      optimizer = training.create_optimizer(hparams, learning_rate, use_tpu)
+      train_op = training.create_train_op(model, optimizer)
+
+    if use_tpu:
+      estimator = tf.contrib.tpu.TPUEstimatorSpec(
+          mode=mode, loss=model.total_loss, train_op=train_op)
+    else:
+      estimator = tf.estimator.EstimatorSpec(
+          mode=mode, loss=model.total_loss, train_op=train_op)
+
+    return estimator
+
+
+def create_model_fn(model_class, hparams, use_tpu=False):
+  """Wraps model_class as an Estimator or TPUEstimator model_fn.
+
+  Args:
+    model_class: AstroModel or a subclass.
+    hparams: ConfigDict of configuration parameters for building the model.
+    use_tpu: If True, a TPUEstimator model_fn is returned. Otherwise an
+      Estimator model_fn is returned.
+
+  Returns:
+    model_fn: A callable that constructs the model and returns a
+      TPUEstimatorSpec if use_tpu is True, otherwise an EstimatorSpec.
+  """
+  return _ModelFn(model_class, hparams, use_tpu)
+
+
+def create_estimator(model_class,
+                     hparams,
+                     run_config=None,
+                     model_dir=None,
+                     eval_batch_size=None):
+  """Wraps model_class as an Estimator or TPUEstimator.
+
+  If run_config is None or a tf.estimator.RunConfig, an Estimator is returned.
+  If run_config is a tf.contrib.tpu.RunConfig, a TPUEstimator is returned.
+
+  Args:
+    model_class: AstroWaveNet or a subclass.
+    hparams: ConfigDict of configuration parameters for building the model.
+    run_config: Optional tf.estimator.RunConfig or tf.contrib.tpu.RunConfig.
+    model_dir: Optional directory for saving the model. If not passed
+      explicitly, it must be specified in run_config.
+    eval_batch_size: Optional batch size for evaluation on TPU. Only applicable
+      if run_config is a tf.contrib.tpu.RunConfig. Defaults to
+      hparams.batch_size.
+
+  Returns:
+    An Estimator object if run_config is None or a tf.estimator.RunConfig, or a
+    TPUEstimator object if run_config is a tf.contrib.tpu.RunConfig.
+
+  Raises:
+    ValueError:
+      If model_dir is not passed explicitly or in run_config.model_dir, or if
+      eval_batch_size is specified and run_config is not a
+      tf.contrib.tpu.RunConfig.
+  """
+  if run_config is None:
+    run_config = tf.estimator.RunConfig()
+  else:
+    run_config = copy.deepcopy(run_config)
+
+  if not model_dir and not run_config.model_dir:
+    raise ValueError(
+        "model_dir must be passed explicitly or specified in run_config")
+
+  use_tpu = isinstance(run_config, tf.contrib.tpu.RunConfig)
+  model_fn = create_model_fn(model_class, hparams, use_tpu)
+
+  if use_tpu:
+    eval_batch_size = eval_batch_size or hparams.batch_size
+    estimator = tf.contrib.tpu.TPUEstimator(
+        model_fn=model_fn,
+        model_dir=model_dir,
+        config=run_config,
+        train_batch_size=hparams.batch_size,
+        eval_batch_size=eval_batch_size)
+
+  else:
+    if eval_batch_size is not None:
+      raise ValueError("eval_batch_size can only be specified for TPU.")
+
+    estimator = tf.estimator.Estimator(
+        model_fn=model_fn,
+        model_dir=model_dir,
+        config=run_config,
+        params={"batch_size": hparams.batch_size})
+
+  return estimator

research/astronet/light_curve_util/util.py

@@ -220,14 +220,13 @@ def reshard_arrays(xs, ys):
   return np.split(concat_x, boundaries)
 
 
-def uniform_cadence_light_curve(all_cadence_no, all_time, all_flux):
+def uniform_cadence_light_curve(cadence_no, time, flux):
   """Combines data into a single light curve with uniform cadence numbers.
 
   Args:
-    all_cadence_no: A list of numpy arrays; the cadence numbers of the light
-      curve.
-    all_time: A list of numpy arrays; the time values of the light curve.
-    all_flux: A list of numpy arrays; the flux values of the light curve.
+    cadence_no: numpy array; the cadence numbers of the light curve.
+    time: numpy array; the time values of the light curve.
+    flux: numpy array; the flux values of the light curve.
 
   Returns:
     cadence_no: numpy array; the cadence numbers of the light curve with no
@@ -245,24 +244,23 @@ def uniform_cadence_light_curve(all_cadence_no, all_time, all_flux):
   Raises:
     ValueError: If there are duplicate cadence numbers in the input.
   """
-  min_cadence_no = np.min([np.min(c) for c in all_cadence_no])
-  max_cadence_no = np.max([np.max(c) for c in all_cadence_no])
+  min_cadence_no = np.min(cadence_no)
+  max_cadence_no = np.max(cadence_no)
 
   out_cadence_no = np.arange(
-      min_cadence_no, max_cadence_no + 1, dtype=all_cadence_no[0].dtype)
-  out_time = np.zeros_like(out_cadence_no, dtype=all_time[0].dtype)
-  out_flux = np.zeros_like(out_cadence_no, dtype=all_flux[0].dtype)
+      min_cadence_no, max_cadence_no + 1, dtype=cadence_no.dtype)
+  out_time = np.zeros_like(out_cadence_no, dtype=time.dtype)
+  out_flux = np.zeros_like(out_cadence_no, dtype=flux.dtype)
   out_mask = np.zeros_like(out_cadence_no, dtype=np.bool)
 
-  for cadence_no, time, flux in zip(all_cadence_no, all_time, all_flux):
-    for c, t, f in zip(cadence_no, time, flux):
-      if np.isfinite(c) and np.isfinite(t) and np.isfinite(f):
-        i = int(c - min_cadence_no)
-        if out_mask[i]:
-          raise ValueError("Duplicate cadence number: {}".format(c))
-        out_time[i] = t
-        out_flux[i] = f
-        out_mask[i] = True
+  for c, t, f in zip(cadence_no, time, flux):
+    if np.isfinite(c) and np.isfinite(t) and np.isfinite(f):
+      i = int(c - min_cadence_no)
+      if out_mask[i]:
+        raise ValueError("Duplicate cadence number: {}".format(c))
+      out_time[i] = t
+      out_flux[i] = f
+      out_mask[i] = True
 
   return out_cadence_no, out_time, out_flux, out_mask