Merge remote-tracking branch 'upstream/master'

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

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

research/astronet/light_curve_util/cc/normalize.h → research/astronet/light_curve/fast_ops/normalize.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_NORMALIZE_H_
-#define TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_UTIL_CC_NORMALIZE_H_
+#ifndef TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_NORMALIZE_H_
+#define TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_NORMALIZE_H_
 
 #include <iostream>
 
@@ -41,4 +41,4 @@ bool NormalizeMedianAndMinimum(const std::vector<double>& x,
 
 }  // namespace astronet
 
-#endif  // TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_UTIL_CC_NORMALIZE_H_
+#endif  // TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_NORMALIZE_H_

research/astronet/light_curve_util/cc/normalize_test.cc → research/astronet/light_curve/fast_ops/normalize_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/normalize.h"
+#include "light_curve/fast_ops/normalize.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/phase_fold.cc → research/astronet/light_curve/fast_ops/phase_fold.cc

@@ -12,7 +12,7 @@ See the License for the specific language governing permissions and
 limitations under the License.
 ==============================================================================*/
 
-#include "light_curve_util/cc/phase_fold.h"
+#include "light_curve/fast_ops/phase_fold.h"
 
 #include <math.h>
 #include <algorithm>

research/astronet/light_curve_util/cc/phase_fold.h → research/astronet/light_curve/fast_ops/phase_fold.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_PHASE_FOLD_H_
-#define TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_UTIL_CC_PHASE_FOLD_H_
+#ifndef TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_PHASE_FOLD_H_
+#define TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_PHASE_FOLD_H_
 
 #include <iostream>
 
@@ -65,4 +65,4 @@ bool PhaseFoldAndSortLightCurve(std::vector<double> time,
 
 }  // namespace astronet
 
-#endif  // TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_UTIL_CC_PHASE_FOLD_H_
+#endif  // TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_PHASE_FOLD_H_

research/astronet/light_curve_util/cc/phase_fold_test.cc → research/astronet/light_curve/fast_ops/phase_fold_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/phase_fold.h"
+#include "light_curve/fast_ops/phase_fold.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/python/median_filter.clif → research/astronet/light_curve/fast_ops/python/median_filter.clif

@@ -16,9 +16,9 @@
 #
 # See https://github.com/google/clif
 
-from light_curve_util.cc.python.postproc import ValueErrorOnFalse
+from light_curve.fast_ops.python.postproc import ValueErrorOnFalse
 
-from "third_party/tensorflow_models/astronet/light_curve_util/cc/median_filter.h":
+from "third_party/tensorflow_models/astronet/light_curve/fast_ops/median_filter.h":
   namespace `astronet`:
     def `MedianFilter` as median_filter (x: list<float>,
                                          y: list<float>,

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

@@ -21,7 +21,7 @@ from __future__ import print_function
 from absl.testing import absltest
 import numpy as np
 
-from light_curve_util.cc.python import median_filter
+from light_curve.fast_ops.python import median_filter
 
 
 class MedianFilterTest(absltest.TestCase):

research/astronet/light_curve_util/cc/python/phase_fold.clif → research/astronet/light_curve/fast_ops/python/phase_fold.clif

@@ -16,9 +16,9 @@
 #
 # See https://github.com/google/clif
 
-from light_curve_util.cc.python.postproc import ValueErrorOnFalse
+from light_curve.fast_ops.python.postproc import ValueErrorOnFalse
 
-from "third_party/tensorflow_models/astronet/light_curve_util/cc/phase_fold.h":
+from "third_party/tensorflow_models/astronet/light_curve/fast_ops/phase_fold.h":
   namespace `astronet`:
     def `PhaseFoldTime` as phase_fold_time (time: list<float>,
                                             period: float,

research/astronet/light_curve_util/cc/python/phase_fold_test.py → research/astronet/light_curve/fast_ops/python/phase_fold_test.py

@@ -21,7 +21,7 @@ from __future__ import print_function
 from absl.testing import absltest
 import numpy as np
 
-from light_curve_util.cc.python import phase_fold
+from light_curve.fast_ops.python import phase_fold
 
 
 class PhaseFoldTimeTest(absltest.TestCase):

research/astronet/light_curve_util/cc/python/postproc.py → research/astronet/light_curve/fast_ops/python/postproc.py

@@ -12,7 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""Postprocessing utility function for CLIF."""
+"""Postprocessing utility functions for CLIF."""
 
 
 # CLIF postprocessor for a C++ function with signature:

research/astronet/light_curve_util/cc/python/view_generator.clif → research/astronet/light_curve/fast_ops/python/view_generator.clif

@@ -16,10 +16,10 @@
 #
 # See https://github.com/google/clif
 
-from light_curve_util.cc.python.postproc import ValueErrorOnFalse
-from light_curve_util.cc.python.postproc import ValueErrorOnNull
+from light_curve.fast_ops.python.postproc import ValueErrorOnFalse
+from light_curve.fast_ops.python.postproc import ValueErrorOnNull
 
-from "third_party/tensorflow_models/astronet/light_curve_util/cc/view_generator.h":
+from "third_party/tensorflow_models/astronet/light_curve/fast_ops/view_generator.h":
   namespace `astronet`:
     class ViewGenerator:
       def `GenerateView` as generate_view (self,

research/astronet/light_curve_util/cc/python/view_generator_test.py → research/astronet/light_curve/fast_ops/python/view_generator_test.py

@@ -21,7 +21,7 @@ from __future__ import print_function
 from absl.testing import absltest
 import numpy as np
 
-from light_curve_util.cc.python import view_generator
+from light_curve.fast_ops.python import view_generator
 
 
 class ViewGeneratorTest(absltest.TestCase):

research/astronet/light_curve_util/cc/test_util.h → research/astronet/light_curve/fast_ops/test_util.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_TEST_UTIL_H_
-#define TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_UTIL_CC_TEST_UTIL_H_
+#ifndef TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_TEST_UTIL_H_
+#define TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_TEST_UTIL_H_
 
 #include <vector>
 
@@ -42,4 +42,4 @@ inline std::vector<double> range(double start, double stop, double step) {
 
 }  // namespace astronet
 
-#endif  // TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_UTIL_CC_TEST_UTIL_H_
+#endif  // TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_TEST_UTIL_H_

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

@@ -12,12 +12,12 @@ See the License for the specific language governing permissions and
 limitations under the License.
 ==============================================================================*/
 
-#include "light_curve_util/cc/view_generator.h"
+#include "light_curve/fast_ops/view_generator.h"
 
 #include "absl/memory/memory.h"
-#include "light_curve_util/cc/median_filter.h"
-#include "light_curve_util/cc/normalize.h"
-#include "light_curve_util/cc/phase_fold.h"
+#include "light_curve/fast_ops/median_filter.h"
+#include "light_curve/fast_ops/normalize.h"
+#include "light_curve/fast_ops/phase_fold.h"
 
 using std::vector;
 

research/astronet/light_curve_util/cc/view_generator.h → research/astronet/light_curve/fast_ops/view_generator.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_VIEW_GENERATOR_H_
-#define TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_UTIL_CC_VIEW_GENERATOR_H_
+#ifndef TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_VIEW_GENERATOR_H_
+#define TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_VIEW_GENERATOR_H_
 
 #include <memory>
 #include <string>
@@ -24,9 +24,10 @@ namespace astronet {
 // Helper class for phase-folding a light curve and then generating "views" of
 // the light curve using a median filter.
 //
-// This class wraps the functions in light_curve_util.h for intended use as a
-// a Python extension. It keeps the phase-folded light curve in the class state
-// to minimize expensive copies between the language barrier.
+// This class wraps functions for phase folding, median filtering, and
+// normalizing for efficient use as a Python extension. It keeps the
+// phase-folded light curve in the class state to minimize expensive copies
+// between the language barrier.
 class ViewGenerator {
  public:
   // Factory function to create a new ViewGenerator.
@@ -96,4 +97,4 @@ class ViewGenerator {
 
 }  // namespace astronet
 
-#endif  // TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_UTIL_CC_VIEW_GENERATOR_H_
+#endif  // TENSORFLOW_MODELS_ASTRONET_LIGHT_CURVE_FAST_OPS_VIEW_GENERATOR_H_

research/astronet/light_curve_util/cc/view_generator_test.cc → research/astronet/light_curve/fast_ops/view_generator_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/view_generator.h"
+#include "light_curve/fast_ops/view_generator.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;
@@ -49,7 +49,7 @@ TEST(ViewGenerator, GenerateViews) {
   vector<double> result;
 
   // Error: t_max <= t_min. We do not test all failure cases here since they
-  // are tested in light_curve_util_test.cc.
+  // are covered by the median filter's tests.
   EXPECT_FALSE(generator->GenerateView(10, 1, -1, -1, false, &result, &error));
   EXPECT_FALSE(error.empty());
   error.clear();

research/astronet/light_curve_util/kepler_io.py → research/astronet/light_curve/kepler_io.py

@@ -23,7 +23,7 @@ import os.path
 from astropy.io import fits
 import numpy as np
 
-from light_curve_util import util
+from light_curve import util
 from tensorflow import gfile
 
 # Quarter index to filename prefix for long cadence Kepler data.

research/astronet/light_curve_util/kepler_io_test.py → research/astronet/light_curve/kepler_io_test.py

@@ -24,16 +24,17 @@ from absl import flags
 from absl.testing import absltest
 import numpy as np
 
-from light_curve_util import kepler_io
+from light_curve import kepler_io
 
 FLAGS = flags.FLAGS
 
-_DATA_DIR = "light_curve_util/test_data/"
+_DATA_DIR = "light_curve/test_data/"
 
 
 class KeplerIoTest(absltest.TestCase):
 
   def setUp(self):
+    super(KeplerIoTest, self).setUp()
     self.data_dir = os.path.join(FLAGS.test_srcdir, _DATA_DIR)
 
   def testScrambleLightCurve(self):
@@ -49,8 +50,8 @@ class KeplerIoTest(absltest.TestCase):
     gold_flux = [[41, 42], [np.nan, np.nan, 33], [11, 12], [21]]
     gold_time = [[101, 102], [201, 301, 302], [303, 401], [402]]
 
-    self.assertEqual(len(gold_flux), len(scr_flux))
-    self.assertEqual(len(gold_time), len(scr_time))
+    self.assertLen(gold_flux, len(scr_flux))
+    self.assertLen(gold_time, len(scr_time))
 
     for i in range(len(gold_flux)):
       np.testing.assert_array_equal(gold_flux[i], scr_flux[i])
@@ -60,7 +61,7 @@ class KeplerIoTest(absltest.TestCase):
     # All quarters.
     filenames = kepler_io.kepler_filenames(
         "/my/dir/", 1234567, check_existence=False)
-    self.assertItemsEqual([
+    self.assertCountEqual([
         "/my/dir/0012/001234567/kplr001234567-2009131105131_llc.fits",
         "/my/dir/0012/001234567/kplr001234567-2009166043257_llc.fits",
         "/my/dir/0012/001234567/kplr001234567-2009259160929_llc.fits",
@@ -85,7 +86,7 @@ class KeplerIoTest(absltest.TestCase):
     # Subset of quarters.
     filenames = kepler_io.kepler_filenames(
         "/my/dir/", 1234567, quarters=[3, 4], check_existence=False)
-    self.assertItemsEqual([
+    self.assertCountEqual([
         "/my/dir/0012/001234567/kplr001234567-2009350155506_llc.fits",
         "/my/dir/0012/001234567/kplr001234567-2010078095331_llc.fits",
         "/my/dir/0012/001234567/kplr001234567-2010009091648_llc.fits"
@@ -99,7 +100,7 @@ class KeplerIoTest(absltest.TestCase):
         injected_group="inj1",
         check_existence=False)
     # pylint:disable=line-too-long
-    self.assertItemsEqual([
+    self.assertCountEqual([
         "/my/dir/0012/001234567/kplr001234567-2009350155506_INJECTED-inj1_llc.fits",
         "/my/dir/0012/001234567/kplr001234567-2010078095331_INJECTED-inj1_llc.fits",
         "/my/dir/0012/001234567/kplr001234567-2010009091648_INJECTED-inj1_llc.fits"
@@ -113,7 +114,7 @@ class KeplerIoTest(absltest.TestCase):
         long_cadence=False,
         quarters=[0, 1],
         check_existence=False)
-    self.assertItemsEqual([
+    self.assertCountEqual([
         "/my/dir/0012/001234567/kplr001234567-2009131110544_slc.fits",
         "/my/dir/0012/001234567/kplr001234567-2009166044711_slc.fits"
     ], filenames)
@@ -126,7 +127,7 @@ class KeplerIoTest(absltest.TestCase):
                      "0114/011442793/kplr011442793-{}_llc.fits".format(q))
         for q in ["2009350155506", "2010009091648", "2010174085026"]
     ]
-    self.assertItemsEqual(expected_filenames, filenames)
+    self.assertCountEqual(expected_filenames, filenames)
 
   def testReadKeplerLightCurve(self):
     filenames = [