Merge remote-tracking branch 'upstream/master'

research/astronet/astronet/ops/input_ops_test.py

@@ -21,7 +21,7 @@ from __future__ import print_function
 import tensorflow as tf
 
 from astronet.ops import input_ops
-from astronet.util import configdict
+from tf_util import configdict
 
 
 class InputOpsTest(tf.test.TestCase):

research/astronet/astronet/predict.py

@@ -27,9 +27,9 @@ import tensorflow as tf
 
 from astronet import models
 from astronet.data import preprocess
-from astronet.util import config_util
-from astronet.util import configdict
 from astronet.util import estimator_util
+from tf_util import config_util
+from tf_util import configdict
 
 parser = argparse.ArgumentParser()
 
@@ -102,8 +102,9 @@ def _process_tce(feature_config):
         "Only 'global_view' and 'local_view' features are supported.")
 
   # Read and process the light curve.
-  time, flux = preprocess.read_and_process_light_curve(FLAGS.kepler_id,
-                                                       FLAGS.kepler_data_dir)
+  all_time, all_flux = preprocess.read_light_curve(FLAGS.kepler_id,
+                                                   FLAGS.kepler_data_dir)
+  time, flux = preprocess.process_light_curve(all_time, all_flux)
   time, flux = preprocess.phase_fold_and_sort_light_curve(
       time, flux, FLAGS.period, FLAGS.t0)
 
@@ -158,11 +159,7 @@ def main(_):
 
   # Create an input function.
   def input_fn():
-    return {
-        "time_series_features":
-            tf.estimator.inputs.numpy_input_fn(
-                features, batch_size=1, shuffle=False, queue_capacity=1)()
-    }
+    return tf.data.Dataset.from_tensors({"time_series_features": features})
 
   # Generate the predictions.
   for predictions in estimator.predict(input_fn):

research/astronet/astronet/train.py

@@ -24,10 +24,10 @@ import sys
 import tensorflow as tf
 
 from astronet import models
-from astronet.util import config_util
-from astronet.util import configdict
-from astronet.util import estimator_runner
 from astronet.util import estimator_util
+from tf_util import config_util
+from tf_util import configdict
+from tf_util import estimator_runner
 
 parser = argparse.ArgumentParser()
 
@@ -68,7 +68,7 @@ parser.add_argument(
 parser.add_argument(
     "--train_steps",
     type=int,
-    default=10000,
+    default=625,
     help="Total number of steps to train the model for.")
 
 parser.add_argument(

research/astronet/astronet/util/BUILD

@@ -2,42 +2,6 @@ package(default_visibility = ["//visibility:public"])
 
 licenses(["notice"])  # Apache 2.0
 
-py_library(
-    name = "configdict",
-    srcs = ["configdict.py"],
-    srcs_version = "PY2AND3",
-    deps = [
-    ],
-)
-
-py_test(
-    name = "configdict_test",
-    size = "small",
-    srcs = ["configdict_test.py"],
-    srcs_version = "PY2AND3",
-    deps = [":configdict"],
-)
-
-py_library(
-    name = "config_util",
-    srcs = ["config_util.py"],
-    srcs_version = "PY2AND3",
-)
-
-py_test(
-    name = "config_util_test",
-    size = "small",
-    srcs = ["config_util_test.py"],
-    srcs_version = "PY2AND3",
-    deps = [":config_util"],
-)
-
-py_library(
-    name = "estimator_runner",
-    srcs = ["estimator_runner.py"],
-    srcs_version = "PY2AND3",
-)
-
 py_library(
     name = "estimator_util",
     srcs = ["estimator_util.py"],
@@ -48,18 +12,3 @@ py_library(
         "//astronet/ops:training",
     ],
 )
-
-py_library(
-    name = "example_util",
-    srcs = ["example_util.py"],
-    srcs_version = "PY2AND3",
-    visibility = ["//visibility:public"],
-)
-
-py_test(
-    name = "example_util_test",
-    size = "small",
-    srcs = ["example_util_test.py"],
-    srcs_version = "PY2AND3",
-    deps = [":example_util"],
-)

research/astronet/astrowavenet/BUILD

@@ -11,12 +11,12 @@ py_binary(
     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",
+        "//tf_util:config_util",
+        "//tf_util:configdict",
+        "//tf_util:estimator_runner",
     ],
 )
 
@@ -44,6 +44,6 @@ py_test(
     deps = [
         ":astrowavenet_model",
         ":configurations",
-        "//astronet/util:configdict",
+        "//tf_util:configdict",
     ],
 )

research/astronet/astrowavenet/README.md

@@ -15,13 +15,10 @@ 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:
+In addition to the [required packages](../README.md#required-packages) listed in
+the top-level README, this package requires:
 
+* **TensorFlow 1.12 or greater** ([instructions](https://www.tensorflow.org/install/))
 * **TensorFlow Probability** ([instructions](https://www.tensorflow.org/probability/install))
 * **Six** ([instructions](https://pypi.org/project/six/))
 

research/astronet/astrowavenet/astrowavenet_model_test.py

@@ -21,8 +21,8 @@ from __future__ import print_function
 import numpy as np
 import tensorflow as tf
 
-from astronet.util import configdict
 from astrowavenet import astrowavenet_model
+from tf_util import configdict
 
 
 class AstrowavenetTest(tf.test.TestCase):

research/astronet/astrowavenet/data/BUILD

@@ -9,7 +9,7 @@ py_library(
     ],
     deps = [
         "//astronet/ops:dataset_ops",
-        "//astronet/util:configdict",
+        "//tf_util:configdict",
     ],
 )
 
@@ -28,7 +28,7 @@ py_library(
     ],
     deps = [
         ":base",
-        "//astronet/util:configdict",
+        "//tf_util:configdict",
     ],
 )
 
@@ -40,7 +40,7 @@ py_library(
     deps = [
         ":base",
         ":synthetic_transit_maker",
-        "//astronet/util:configdict",
+        "//tf_util:configdict",
     ],
 )
 

research/astronet/astrowavenet/data/base.py

@@ -23,7 +23,7 @@ import six
 
 import tensorflow as tf
 
-from astronet.util import configdict
+from tf_util import configdict
 from astronet.ops import dataset_ops
 
 

research/astronet/astrowavenet/data/synthetic_transits.py

@@ -21,7 +21,7 @@ from __future__ import print_function
 import numpy as np
 import tensorflow as tf
 
-from astronet.util import configdict
+from tf_util import configdict
 from astrowavenet.data import base
 from astrowavenet.data import synthetic_transit_maker
 

research/astronet/astrowavenet/trainer.py

@@ -24,15 +24,14 @@ 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
-
+from tf_util import config_util
+from tf_util import configdict
+from tf_util import estimator_runner
 
 FLAGS = flags.FLAGS
 

research/astronet/light_curve/README.md

+# Light Curve Operations
+
+## Code Author
+
+Chris Shallue: [@cshallue](https://github.com/cshallue)
+
+## Python modules
+
+* `kepler_io`: Functions for reading Kepler data.
+* `median_filter`: Utility for smoothing data using a median filter.
+* `periodic_event`: Event class, which represents a periodic event in a light curve.
+* `util`: Light curve utility functions.
+
+## Fast ops
+
+The [fast_ops](fast_ops/) subdirectory contains optimized C++ light curve
+operations. These operations can be compiled for Python using
+[CLIF](https://github.com/google/clif). The [fast_ops/python](fast_ops/python/)
+directory contains CLIF API description files.

research/astronet/light_curve_util/cc/median.h → research/astronet/light_curve/fast_ops/median.h

@@ -12,8 +12,8 @@ See the License for the specific language governing permissions and
 limitations under the License.
 ==============================================================================*/
 
-#ifndef TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_UTIL_CC_MEDIAN_H_
-#define TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_UTIL_CC_MEDIAN_H_
+#ifndef TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_MEDIAN_H_
+#define TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_MEDIAN_H_
 
 #include <algorithm>
 #include <iterator>
@@ -70,4 +70,4 @@ typename std::iterator_traits<ForwardIterator>::value_type Median(
 
 }  // namespace astronet
 
-#endif  // TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_UTIL_CC_MEDIAN_H_
+#endif  // TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_MEDIAN_H_

research/astronet/light_curve_util/cc/median_filter.cc → research/astronet/light_curve/fast_ops/median_filter.cc

@@ -12,10 +12,10 @@ See the License for the specific language governing permissions and
 limitations under the License.
 ==============================================================================*/
 
-#include "light_curve_util/cc/median_filter.h"
+#include "light_curve/fast_ops/median_filter.h"
 
 #include "absl/strings/substitute.h"
-#include "light_curve_util/cc/median.h"
+#include "light_curve/fast_ops/median.h"
 
 using absl::Substitute;
 using std::min;

research/astronet/light_curve_util/cc/median_filter.h → research/astronet/light_curve/fast_ops/median_filter.h

@@ -12,8 +12,8 @@ See the License for the specific language governing permissions and
 limitations under the License.
 ==============================================================================*/
 
-#ifndef TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_UTIL_CC_MEDIAN_FILTER_H_
-#define TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_UTIL_CC_MEDIAN_FILTER_H_
+#ifndef TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_MEDIAN_FILTER_H_
+#define TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_MEDIAN_FILTER_H_
 
 #include <iostream>
 
@@ -56,4 +56,4 @@ bool MedianFilter(const std::vector<double>& x, const std::vector<double>& y,
 
 }  // namespace astronet
 
-#endif  // TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_UTIL_CC_MEDIAN_FILTER_H_
+#endif  // TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_MEDIAN_FILTER_H_

research/astronet/light_curve_util/cc/median_filter_test.cc → research/astronet/light_curve/fast_ops/median_filter_test.cc

@@ -12,11 +12,11 @@ See the License for the specific language governing permissions and
 limitations under the License.
 ==============================================================================*/
 
-#include "light_curve_util/cc/median_filter.h"
+#include "light_curve/fast_ops/median_filter.h"
 
 #include "gmock/gmock.h"
 #include "gtest/gtest.h"
-#include "light_curve_util/cc/test_util.h"
+#include "light_curve/fast_ops/test_util.h"
 
 using std::vector;
 using testing::Pointwise;

research/astronet/light_curve_util/cc/median_test.cc → research/astronet/light_curve/fast_ops/median_test.cc

@@ -12,7 +12,7 @@ See the License for the specific language governing permissions and
 limitations under the License.
 ==============================================================================*/
 
-#include "light_curve_util/cc/median.h"
+#include "light_curve/fast_ops/median.h"
 
 #include "gmock/gmock.h"
 #include "gtest/gtest.h"