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Merge pull request #5862 from cshallue/master 

Move tensorflow_models/research/astronet to google-research/exoplanet-ml
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# Ignore all bazel-* symlinks.
/bazel-*
get_kepler.sh
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research/astronet/README.md
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# Exoplanet ML # AstroNet has moved!
Machine learning models and utilities for exoplanet science. The code is now located at https://github.com/google-research/exoplanet-ml
## Code Author
Chris Shallue: [@cshallue](https://github.com/cshallue)
## Quick Start
Jump to the [AstroNet walkthrough](astronet/README.md#walkthrough).
## Citation
If you find this code useful, please cite our paper:
Shallue, C. J., & Vanderburg, A. (2018). Identifying Exoplanets with Deep
Learning: A Five-planet Resonant Chain around Kepler-80 and an Eighth Planet
around Kepler-90. *The Astronomical Journal*, 155(2), 94.
Full text available at [*The Astronomical Journal*](http://iopscience.iop.org/article/10.3847/1538-3881/aa9e09/meta).
## Directories
[astronet/](astronet/)
* A neural network for identifying exoplanets in light curves. Contains code for:
* Downloading and preprocessing Kepler light curves.
* Building different types of neural network classification models.
* Training and evaluating a new model.
* Using a trained model to generate new predictions.
[astrowavenet/](astrowavenet/)
* A generative model for light curves.
[light_curve/](light_curve)
* Utilities for operating on light curves. These include:
* Reading Kepler data from `.fits` files.
* Applying a median filter to smooth and normalize a light curve.
* Phase folding, splitting, removing periodic events, etc.
* [light_curve/fast_ops/](light_curve/fast_ops) contains optimized C++ light
curve operations.
[tf_util/](tf_util)
* Shared TensorFlow utilities.
[third_party/](third_party/)
* Utilities derived from third party code.
# Setup
## 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))
## Run Unit Tests
Verify that all dependencies are satisfied by running the unit tests:
```bash
bazel test astronet/... astrowavenet/... light_curve/... tf_util/... third_party/...
```
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# Abseil C++ libraries.
http_archive(
name = "com_google_absl",
urls = ["https://github.com/abseil/abseil-cpp/archive/master.zip"],
strip_prefix = "abseil-cpp-master",
)
# GoogleTest/GoogleMock framework. Used by C++ unit-tests.
http_archive(
name = "com_google_googletest",
urls = ["https://github.com/google/googletest/archive/master.zip"],
strip_prefix = "googletest-master",
)
research/astronet/astronet/BUILD deleted 100644 → 0
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package(default_visibility = ["//visibility:public"])
licenses(["notice"]) # Apache 2.0
py_library(
name = "models",
srcs = ["models.py"],
srcs_version = "PY2AND3",
deps = [
"//astronet/astro_cnn_model",
"//astronet/astro_cnn_model:configurations",
"//astronet/astro_fc_model",
"//astronet/astro_fc_model:configurations",
"//astronet/astro_model",
"//astronet/astro_model:configurations",
"//tf_util:configdict",
],
)
py_binary(
name = "train",
srcs = ["train.py"],
srcs_version = "PY2AND3",
deps = [
":models",
"//astronet/util:estimator_util",
"//tf_util:config_util",
"//tf_util:configdict",
"//tf_util:estimator_runner",
],
)
py_binary(
name = "evaluate",
srcs = ["evaluate.py"],
srcs_version = "PY2AND3",
deps = [
":models",
"//astronet/util:estimator_util",
"//tf_util:config_util",
"//tf_util:configdict",
"//tf_util:estimator_runner",
],
)
py_binary(
name = "predict",
srcs = ["predict.py"],
srcs_version = "PY2AND3",
deps = [
":models",
"//astronet/data:preprocess",
"//astronet/util:estimator_util",
"//tf_util:config_util",
"//tf_util:configdict",
],
)
research/astronet/astronet/README.md deleted 100644 → 0
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# AstroNet: A Neural Network for Identifying Exoplanets in Light Curves
![Transit Animation](docs/transit.gif)
## Code Author
Chris Shallue: [@cshallue](https://github.com/cshallue)
## Background
This directory contains TensorFlow models and data processing code for
identifying exoplanets in astrophysical light curves. For complete background,
see [our paper](http://adsabs.harvard.edu/abs/2018AJ....155...94S) in
*The Astronomical Journal*.
For shorter summaries, see:
* ["Earth to Exoplanet"](https://www.blog.google/topics/machine-learning/hunting-planets-machine-learning/) on the Google blog
* [This blog post](https://www.cfa.harvard.edu/~avanderb/page1.html#kepler90) by Andrew Vanderburg
* [This great article](https://milesobrien.com/artificial-intelligence-gains-intuition-hunting-exoplanets/) by Fedor Kossakovski
* [NASA's press release](https://www.nasa.gov/press-release/artificial-intelligence-nasa-data-used-to-discover-eighth-planet-circling-distant-star) article
## Citation
If you find this code useful, please cite our paper:
Shallue, C. J., & Vanderburg, A. (2018). Identifying Exoplanets with Deep
Learning: A Five-planet Resonant Chain around Kepler-80 and an Eighth Planet
around Kepler-90. *The Astronomical Journal*, 155(2), 94.
Full text available at [*The Astronomical Journal*](http://iopscience.iop.org/article/10.3847/1538-3881/aa9e09/meta).
## Walkthrough
### Required Packages
First, ensure that you have installed the
[required packages](../README.md#required-packages) and that the
[unit tests](../README.md#run-unit-tests) pass.
### Download Kepler Data
A *light curve* is a plot of the brightness of a star over time. We will be
focusing on light curves produced by the Kepler space telescope, which monitored
the brightness of 200,000 stars in our milky way galaxy for 4 years. An example
light curve produced by Kepler is shown below.
![Kepler-934](docs/kepler-943.png)
To train a model to identify planets in Kepler light curves, you will need a
training set of labeled *Threshold Crossing Events* (TCEs). A TCE is a periodic
signal that has been detected in a Kepler light curve, and is associated with a
*period* (the number of days between each occurrence of the detected signal),
a *duration* (the time taken by each occurrence of the signal), an *epoch* (the
time of the first observed occurrence of the signal), and possibly additional
metadata like the signal-to-noise ratio. An example TCE is shown below. The
labels are ground truth classifications (decided by humans) that indicate which
TCEs in the training set are actual planets signals and which are caused by
other phenomena.
![Kepler-934 Transits](docs/kepler-943-transits.png)
You can download the DR24 TCE Table in CSV format from the [NASA Exoplanet
Archive](https://exoplanetarchive.ipac.caltech.edu/cgi-bin/TblView/nph-tblView?app=ExoTbls&config=q1_q17_dr24_tce). Ensure the following columns are selected:
* `rowid`: Integer ID of the row in the TCE table.
* `kepid`: Kepler ID of the target star.
* `tce_plnt_num`: TCE number within the target star.
* `tce_period`: Period of the detected event, in days.
* `tce_time0bk`: The time corresponding to the center of the first detected
event in Barycentric Julian Day (BJD) minus a constant offset of
2,454,833.0 days.
* `tce_duration`: Duration of the detected event, in hours.
* `av_training_set`: Autovetter training set label; one of PC (planet candidate),
AFP (astrophysical false positive), NTP (non-transiting phenomenon),
UNK (unknown).
Next, you will need to download the light curves of the stars corresponding to
the TCEs in the training set. These are available at the
[Mikulski Archive for Space Telescopes](https://archive.stsci.edu/). However,
you almost certainly don't want all of the Kepler data, which consists of almost
3 million files, takes up over a terabyte of space, and may take several weeks
to download! To train our model, we only need to download the subset of light
curves that are associated with TCEs in the DR24 file. To download just those
light curves, follow these steps:
**NOTE:** Even though we are only downloading a subset of the entire Kepler
dataset, the files downloaded by the following script take up about **90 GB**.
```bash
# Filename containing the CSV file of TCEs in the training set.
TCE_CSV_FILE="${HOME}/astronet/dr24_tce.csv"
# Directory to download Kepler light curves into.
KEPLER_DATA_DIR="${HOME}/astronet/kepler/"
# Generate a bash script that downloads the Kepler light curves in the training set.
python astronet/data/generate_download_script.py \
--kepler_csv_file=${TCE_CSV_FILE} \
--download_dir=${KEPLER_DATA_DIR}
# Run the download script to download Kepler light curves.
./get_kepler.sh
```
The final line should read: `Finished downloading 12669 Kepler targets to
${KEPLER_DATA_DIR}`
Let's explore the downloaded light curve of the Kepler-90 star! Note that Kepler
light curves are divided into
[four quarters each year](https://keplerscience.arc.nasa.gov/data-products.html#kepler-data-release-notes), which are separated by the quarterly rolls that the spacecraft
made to reorient its solar panels. In the downloaded light curves, each `.fits`
file corresponds to a specific Kepler quarter, but some quarters are divided
into multiple `.fits` files.
```python
# Launch iPython (or Python) from the tensorflow_models/astronet/ directory.
ipython
In[1]:
from light_curve import kepler_io
import matplotlib.pyplot as plt
import numpy as np
In[2]:
KEPLER_DATA_DIR = "/path/to/kepler/"
KEPLER_ID = 11442793 # Kepler-90.
In[3]:
# Read the light curve.
file_names = kepler_io.kepler_filenames(KEPLER_DATA_DIR, KEPLER_ID)
assert file_names, "Failed to find .fits files in {}".format(KEPLER_DATA_DIR)
all_time, all_flux = kepler_io.read_kepler_light_curve(file_names)
print("Read light curve with {} segments".format(len(all_time)))
In[4]:
# Plot the fourth segment.
plt.plot(all_time[3], all_flux[3], ".")
plt.show()
In[5]:
# Plot all light curve segments. We first divide by the median flux in each
# segment, because the segments are on different scales.
for f in all_flux:
f /= np.median(f)
plt.plot(np.concatenate(all_time), np.concatenate(all_flux), ".")
plt.show()
```
The output plots should look something like this:
![Kepler 90 Q4](docs/kep90-q4-raw.png)
![Kepler 90 All](docs/kep90-all.png)
The first plot is a single segment of approximately 20 days. You can see a
planet transit --- that's Kepler-90 g! Also, notice that the brightness of the
star is not flat over time --- there is natural variation in the brightness,
even away from the planet transit.
The second plot is the full light curve over the entire Kepler mission
(aproximately 4 years). You can easily see two transiting planets by eye ---
they are Kepler-90 h (the biggest known planet in the system with the deepest
transits) and Kepler-90 g (the second biggest known planet in the system with
the second deepest transits).
### Process Kepler Data
To train a model to identify exoplanets, you will need to provide TensorFlow
with training data in
[TFRecord](https://www.tensorflow.org/programmers_guide/datasets) format. The
TFRecord format consists of a set of sharded files containing serialized
`tf.Example` [protocol buffers](https://developers.google.com/protocol-buffers/).
The command below will generate a set of sharded TFRecord files for the TCEs in
the training set. Each `tf.Example` proto will contain the following light curve
representations:
* `global_view`: Vector of length 2001: a "global view" of the TCE.
* `local_view`: Vector of length 201: a "local view" of the TCE.
In addition, each `tf.Example` will contain the value of each column in the
input TCE CSV file. The columns include:
* `rowid`: Integer ID of the row in the TCE table.
* `kepid`: Kepler ID of the target star.
* `tce_plnt_num`: TCE number within the target star.
* `av_training_set`: Autovetter training set label.
* `tce_period`: Period of the detected event, in days.
```bash
# Use Bazel to create executable Python scripts.
#
# Alternatively, since all code is pure Python and does not need to be compiled,
# we could invoke the source scripts with the following addition to PYTHONPATH:
# export PYTHONPATH="/path/to/source/dir/:${PYTHONPATH}"
bazel build astronet/...
# Directory to save output TFRecord files into.
TFRECORD_DIR="${HOME}/astronet/tfrecord"
# Preprocess light curves into sharded TFRecord files using 5 worker processes.
bazel-bin/astronet/data/generate_input_records \
--input_tce_csv_file=${TCE_CSV_FILE} \
--kepler_data_dir=${KEPLER_DATA_DIR} \
--output_dir=${TFRECORD_DIR} \
--num_worker_processes=5
```
When the script finishes you will find 8 training files, 1 validation file and
1 test file in `TFRECORD_DIR`. The files will match the patterns
`train-0000?-of-00008`, `val-00000-of-00001` and `test-00000-of-00001`
respectively.
Here's a quick description of what the script does. For a full description, see
Section 3 of [our paper](http://iopscience.iop.org/article/10.3847/1538-3881/aa9e09/meta).
For each light curve, we first fit a normalization spline to remove any
low-frequency variability (that is, the natural variability in light from star)
without removing any deviations caused by planets or other objects. For example,
the following image shows the normalization spline for the segment of Kepler-90
that we considered above:
![Kepler 90 Q4 Spline](docs/kep90-q4-spline.png)
Next, we divide by the spline to make the star's baseline brightness
approximately flat. Notice that after normalization the transit of Kepler-90 g
is still preserved:
![Kepler 90 Q4 Normalized](docs/kep90-q4-normalized.png)
Finally, for each TCE in the input CSV table, we generate two representations of
the light curve of that star. Both representations are *phase-folded*, which
means that we combine all periods of the detected TCE into a single curve, with
the detected event centered.
Let's explore the generated representations of Kepler-90 g in the output.
```python
# Launch iPython (or Python) from the tensorflow_models/astronet/ directory.
ipython
In[1]:
import matplotlib.pyplot as plt
import numpy as np
import os.path
import tensorflow as tf
In[2]:
KEPLER_ID = 11442793 # Kepler-90
TFRECORD_DIR = "/path/to/tfrecords/dir"
In[3]:
# Helper function to find the tf.Example corresponding to a particular TCE.
def find_tce(kepid, tce_plnt_num, filenames):
for filename in filenames:
for record in tf.python_io.tf_record_iterator(filename):
ex = tf.train.Example.FromString(record)
if (ex.features.feature["kepid"].int64_list.value[0] == kepid and
ex.features.feature["tce_plnt_num"].int64_list.value[0] == tce_plnt_num):
print("Found {}_{} in file {}".format(kepid, tce_plnt_num, filename))
return ex
raise ValueError("{}_{} not found in files: {}".format(kepid, tce_plnt_num, filenames))
In[4]:
# Find Kepler-90 g.
filenames = tf.gfile.Glob(os.path.join(TFRECORD_DIR, "*"))
assert filenames, "No files found in {}".format(TFRECORD_DIR)
ex = find_tce(KEPLER_ID, 1, filenames)
In[5]:
# Plot the global and local views.
global_view = np.array(ex.features.feature["global_view"].float_list.value)
local_view = np.array(ex.features.feature["local_view"].float_list.value)
fig, axes = plt.subplots(1, 2, figsize=(20, 6))
axes[0].plot(global_view, ".")
axes[1].plot(local_view, ".")
plt.show()
```
The output should look something like this:
![Kepler 90 g Processed](docs/kep90h-localglobal.png)
### Train an AstroNet Model
This directory contains several types of neural network architecture and various
configuration options. To train a convolutional neural network to classify
Kepler TCEs as either "planet" or "not planet", using the best configuration
from
[our paper](http://iopscience.iop.org/article/10.3847/1538-3881/aa9e09/meta),
run the following training script:
```bash
# Directory to save model checkpoints into.
MODEL_DIR="${HOME}/astronet/model/"
# Run the training script.
bazel-bin/astronet/train \
--model=AstroCNNModel \
--config_name=local_global \
--train_files=${TFRECORD_DIR}/train* \
--eval_files=${TFRECORD_DIR}/val* \
--model_dir=${MODEL_DIR}
```
Optionally, you can also run a [TensorBoard](https://www.tensorflow.org/programmers_guide/summaries_and_tensorboard)
server in a separate process for real-time
monitoring of training progress and evaluation metrics.
```bash
# Launch TensorBoard server.
tensorboard --logdir ${MODEL_DIR}
```
The TensorBoard server will show a page like this:
![TensorBoard](docs/tensorboard.png)
### Evaluate an AstroNet Model
Run the following command to evaluate a model on the test set. The result will
be printed on the screen, and a summary file will also be written to the model
directory, which will be visible in TensorBoard.
```bash
# Run the evaluation script.
bazel-bin/astronet/evaluate \
--model=AstroCNNModel \
--config_name=local_global \
--eval_files=${TFRECORD_DIR}/test* \
--model_dir=${MODEL_DIR}
```
The output should look something like this:
```bash
INFO:tensorflow:Saving dict for global step 10000: accuracy/accuracy = 0.9625159, accuracy/num_correct = 1515.0, auc = 0.988882, confusion_matrix/false_negatives = 10.0, confusion_matrix/false_positives = 49.0, confusion_matrix/true_negatives = 1165.0, confusion_matrix/true_positives = 350.0, global_step = 10000, loss = 0.112445444, losses/weighted_cross_entropy = 0.11295206, num_examples = 1574.
```
### Make Predictions
Suppose you detect a weak TCE in the light curve of the Kepler-90 star, with
period 14.44912 days, duration 2.70408 hours (0.11267 days) beginning 2.2 days
after 12:00 on 1/1/2009 (the year the Kepler telescope launched). To run this
TCE though your trained model, execute the following command:
```bash
# Generate a prediction for a new TCE.
bazel-bin/astronet/predict \
--model=AstroCNNModel \
--config_name=local_global \
--model_dir=${MODEL_DIR} \
--kepler_data_dir=${KEPLER_DATA_DIR} \
--kepler_id=11442793 \
--period=14.44912 \
--t0=2.2 \
--duration=0.11267 \
--output_image_file="${HOME}/astronet/kepler-90i.png"
```
The output should look like this:
```Prediction: 0.9480018```
This means the model is about 95% confident that the input TCE is a planet.
Of course, this is only a small step in the overall process of discovering and
validating an exoplanet: the model’s prediction is not proof one way or the
other. The process of validating this signal as a real exoplanet requires
significant follow-up work by an expert astronomer --- see Sections 6.3 and 6.4
of [our paper](http://iopscience.iop.org/article/10.3847/1538-3881/aa9e09/meta)
for the full details. In this particular case, our follow-up analysis validated
this signal as a bona fide exoplanet: it’s now called
[Kepler-90 i](https://www.nasa.gov/press-release/artificial-intelligence-nasa-data-used-to-discover-eighth-planet-circling-distant-star),
and is the record-breaking eighth planet discovered around the Kepler-90 star!
In addition to the output prediction, the script will also produce a plot of the
input representations. For Kepler-90 i, the plot should look something like
this:
![Kepler 90 h Processed](docs/kep90i-localglobal.png)
research/astronet/astronet/__init__.py deleted 100644 → 0
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# 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/astronet/astro_cnn_model/BUILD deleted 100644 → 0
View file @ caafb6d1
package(default_visibility = ["//visibility:public"])
licenses(["notice"]) # Apache 2.0
py_library(
name = "configurations",
srcs = ["configurations.py"],
srcs_version = "PY2AND3",
deps = [
"//astronet/astro_model:configurations",
],
)
py_library(
name = "astro_cnn_model",
srcs = [
"astro_cnn_model.py",
],
srcs_version = "PY2AND3",
deps = ["//astronet/astro_model"],
)
py_test(
name = "astro_cnn_model_test",
size = "small",
srcs = [
"astro_cnn_model_test.py",
],
srcs_version = "PY2AND3",
deps = [
":astro_cnn_model",
":configurations",
"//astronet/ops:input_ops",
"//astronet/ops:testing",
"//tf_util:configdict",
],
)
research/astronet/astronet/astro_cnn_model/__init__.py deleted 100644 → 0
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# 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/astronet/astro_cnn_model/astro_cnn_model.py deleted 100644 → 0
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# 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.
"""A model for classifying light curves using a convolutional neural network.
See the base class (in astro_model.py) for a description of the general
framework of AstroModel and its subclasses.
The architecture of this model is:
predictions
^
|
logits
^
|
(fully connected layers)
^
|
pre_logits_concat
^
|
(concatenate)
^ ^ ^
| | |
(convolutional blocks 1) (convolutional blocks 2) ... |
^ ^ |
| | |
time_series_feature_1 time_series_feature_2 ... aux_features
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import tensorflow as tf
from astronet.astro_model import astro_model
class AstroCNNModel(astro_model.AstroModel):
"""A model for classifying light curves using a convolutional neural net."""
def _build_cnn_layers(self, inputs, hparams, scope="cnn"):
"""Builds convolutional layers.
The layers are defined by convolutional blocks with pooling between blocks
(but not within blocks). Within a block, all layers have the same number of
filters, which is a constant multiple of the number of filters in the
previous block. The kernel size is fixed throughout.
Args:
inputs: A Tensor of shape [batch_size, length].
hparams: Object containing CNN hyperparameters.
scope: Name of the variable scope.
Returns:
A Tensor of shape [batch_size, output_size], where the output size depends
on the input size, kernel size, number of filters, number of layers,
convolution padding type and pooling.
"""
with tf.variable_scope(scope):
net = tf.expand_dims(inputs, -1) # [batch, length, channels]
for i in range(hparams.cnn_num_blocks):
num_filters = int(hparams.cnn_initial_num_filters *
hparams.cnn_block_filter_factor**i)
with tf.variable_scope("block_{}".format(i + 1)):
for j in range(hparams.cnn_block_size):
net = tf.layers.conv1d(
inputs=net,
filters=num_filters,
kernel_size=int(hparams.cnn_kernel_size),
padding=hparams.convolution_padding,
activation=tf.nn.relu,
name="conv_{}".format(j + 1))
if hparams.pool_size > 1: # pool_size 0 or 1 denotes no pooling
net = tf.layers.max_pooling1d(
inputs=net,
pool_size=int(hparams.pool_size),
strides=int(hparams.pool_strides),
name="pool")
# Flatten.
net.get_shape().assert_has_rank(3)
net_shape = net.get_shape().as_list()
output_dim = net_shape[1] * net_shape[2]
net = tf.reshape(net, [-1, output_dim], name="flatten")
return net
def build_time_series_hidden_layers(self):
"""Builds hidden layers for the time series features.
Inputs:
self.time_series_features
Outputs:
self.time_series_hidden_layers
"""
time_series_hidden_layers = {}
for name, time_series in self.time_series_features.items():
time_series_hidden_layers[name] = self._build_cnn_layers(
inputs=time_series,
hparams=self.hparams.time_series_hidden[name],
scope=name + "_hidden")
self.time_series_hidden_layers = time_series_hidden_layers
research/astronet/astronet/astro_cnn_model/astro_cnn_model_test.py deleted 100644 → 0
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# 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.
"""Tests for astro_cnn_model.AstroCNNModel."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import tensorflow as tf
from astronet.astro_cnn_model import astro_cnn_model
from astronet.astro_cnn_model import configurations
from astronet.ops import input_ops
from astronet.ops import testing
from tf_util import configdict
class AstroCNNModelTest(tf.test.TestCase):
def assertShapeEquals(self, shape, tensor_or_array):
"""Asserts that a Tensor or Numpy array has the expected shape.
Args:
shape: Numpy array or anything that can be converted to one.
tensor_or_array: tf.Tensor, tf.Variable, or Numpy array.
"""
if isinstance(tensor_or_array, (np.ndarray, np.generic)):
self.assertAllEqual(shape, tensor_or_array.shape)
elif isinstance(tensor_or_array, (tf.Tensor, tf.Variable)):
self.assertAllEqual(shape, tensor_or_array.shape.as_list())
else:
raise TypeError("tensor_or_array must be a Tensor or Numpy ndarray")
def testOneTimeSeriesFeature(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 20,
"is_time_series": True,
}
}
hidden_spec = {
"time_feature_1": {
"cnn_num_blocks": 2,
"cnn_block_size": 2,
"cnn_initial_num_filters": 4,
"cnn_block_filter_factor": 1.5,
"cnn_kernel_size": 3,
"convolution_padding": "same",
"pool_size": 2,
"pool_strides": 2,
}
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config["hparams"]["time_series_hidden"] = hidden_spec
config = configdict.ConfigDict(config)
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_cnn_model.AstroCNNModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate Tensor shapes.
block_1_conv_1 = testing.get_variable_by_name(
"time_feature_1_hidden/block_1/conv_1/kernel")
self.assertShapeEquals((3, 1, 4), block_1_conv_1)
block_1_conv_2 = testing.get_variable_by_name(
"time_feature_1_hidden/block_1/conv_2/kernel")
self.assertShapeEquals((3, 4, 4), block_1_conv_2)
block_2_conv_1 = testing.get_variable_by_name(
"time_feature_1_hidden/block_2/conv_1/kernel")
self.assertShapeEquals((3, 4, 6), block_2_conv_1)
block_2_conv_2 = testing.get_variable_by_name(
"time_feature_1_hidden/block_2/conv_2/kernel")
self.assertShapeEquals((3, 6, 6), block_2_conv_2)
self.assertItemsEqual(["time_feature_1"],
model.time_series_hidden_layers.keys())
self.assertShapeEquals((None, 30),
model.time_series_hidden_layers["time_feature_1"])
self.assertEqual(len(model.aux_hidden_layers), 0)
self.assertIs(model.time_series_hidden_layers["time_feature_1"],
model.pre_logits_concat)
# Execute the TensorFlow graph.
scaffold = tf.train.Scaffold()
scaffold.finalize()
with self.test_session() as sess:
sess.run([scaffold.init_op, scaffold.local_init_op])
step = sess.run(model.global_step)
self.assertEqual(0, step)
# Fetch predictions.
features = testing.fake_features(feature_spec, batch_size=16)
labels = testing.fake_labels(config.hparams.output_dim, batch_size=16)
feed_dict = input_ops.prepare_feed_dict(model, features, labels)
predictions = sess.run(model.predictions, feed_dict=feed_dict)
self.assertShapeEquals((16, 1), predictions)
def testTwoTimeSeriesFeatures(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 20,
"is_time_series": True,
},
"time_feature_2": {
"length": 5,
"is_time_series": True,
},
"aux_feature_1": {
"length": 1,
"is_time_series": False,
},
}
hidden_spec = {
"time_feature_1": {
"cnn_num_blocks": 2,
"cnn_block_size": 2,
"cnn_initial_num_filters": 4,
"cnn_block_filter_factor": 1.5,
"cnn_kernel_size": 3,
"convolution_padding": "same",
"pool_size": 2,
"pool_strides": 2,
},
"time_feature_2": {
"cnn_num_blocks": 1,
"cnn_block_size": 1,
"cnn_initial_num_filters": 5,
"cnn_block_filter_factor": 1,
"cnn_kernel_size": 2,
"convolution_padding": "same",
"pool_size": 0,
"pool_strides": 0,
}
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config["hparams"]["time_series_hidden"] = hidden_spec
config = configdict.ConfigDict(config)
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_cnn_model.AstroCNNModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate Tensor shapes.
feature_1_block_1_conv_1 = testing.get_variable_by_name(
"time_feature_1_hidden/block_1/conv_1/kernel")
self.assertShapeEquals((3, 1, 4), feature_1_block_1_conv_1)
feature_1_block_1_conv_2 = testing.get_variable_by_name(
"time_feature_1_hidden/block_1/conv_2/kernel")
self.assertShapeEquals((3, 4, 4), feature_1_block_1_conv_2)
feature_1_block_2_conv_1 = testing.get_variable_by_name(
"time_feature_1_hidden/block_2/conv_1/kernel")
self.assertShapeEquals((3, 4, 6), feature_1_block_2_conv_1)
feature_1_block_2_conv_2 = testing.get_variable_by_name(
"time_feature_1_hidden/block_2/conv_2/kernel")
self.assertShapeEquals((3, 6, 6), feature_1_block_2_conv_2)
feature_2_block_1_conv_1 = testing.get_variable_by_name(
"time_feature_2_hidden/block_1/conv_1/kernel")
self.assertShapeEquals((2, 1, 5), feature_2_block_1_conv_1)
self.assertItemsEqual(["time_feature_1", "time_feature_2"],
model.time_series_hidden_layers.keys())
self.assertShapeEquals((None, 30),
model.time_series_hidden_layers["time_feature_1"])
self.assertShapeEquals((None, 25),
model.time_series_hidden_layers["time_feature_2"])
self.assertItemsEqual(["aux_feature_1"], model.aux_hidden_layers.keys())
self.assertIs(model.aux_features["aux_feature_1"],
model.aux_hidden_layers["aux_feature_1"])
self.assertShapeEquals((None, 56), model.pre_logits_concat)
# Execute the TensorFlow graph.
scaffold = tf.train.Scaffold()
scaffold.finalize()
with self.test_session() as sess:
sess.run([scaffold.init_op, scaffold.local_init_op])
step = sess.run(model.global_step)
self.assertEqual(0, step)
# Fetch predictions.
features = testing.fake_features(feature_spec, batch_size=16)
labels = testing.fake_labels(config.hparams.output_dim, batch_size=16)
feed_dict = input_ops.prepare_feed_dict(model, features, labels)
predictions = sess.run(model.predictions, feed_dict=feed_dict)
self.assertShapeEquals((16, 1), predictions)
if __name__ == "__main__":
tf.test.main()
research/astronet/astronet/astro_cnn_model/configurations.py deleted 100644 → 0
View file @ caafb6d1
# 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.
"""Configurations for model building, training and evaluation.
Available configurations:
* base: One time series feature per input example. Default is "global_view".
* local_global: Two time series features per input example.
- A "global" view of the entire orbital period.
- A "local" zoomed-in view of the transit event.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from astronet.astro_model import configurations as parent_configs
def base():
"""Base configuration for a CNN model with a single global view."""
config = parent_configs.base()
# Add configuration for the convolutional layers of the global_view feature.
config["hparams"]["time_series_hidden"] = {
"global_view": {
"cnn_num_blocks": 5,
"cnn_block_size": 2,
"cnn_initial_num_filters": 16,
"cnn_block_filter_factor": 2,
"cnn_kernel_size": 5,
"convolution_padding": "same",
"pool_size": 5,
"pool_strides": 2,
},
}
config["hparams"]["num_pre_logits_hidden_layers"] = 4
config["hparams"]["pre_logits_hidden_layer_size"] = 1024
return config
def local_global():
"""Base configuration for a CNN model with separate local/global views."""
config = parent_configs.base()
# Override the model features to be local_view and global_view time series.
config["inputs"]["features"] = {
"local_view": {
"length": 201,
"is_time_series": True,
},
"global_view": {
"length": 2001,
"is_time_series": True,
},
}
# Add configurations for the convolutional layers of time series features.
config["hparams"]["time_series_hidden"] = {
"local_view": {
"cnn_num_blocks": 2,
"cnn_block_size": 2,
"cnn_initial_num_filters": 16,
"cnn_block_filter_factor": 2,
"cnn_kernel_size": 5,
"convolution_padding": "same",
"pool_size": 7,
"pool_strides": 2,
},
"global_view": {
"cnn_num_blocks": 5,
"cnn_block_size": 2,
"cnn_initial_num_filters": 16,
"cnn_block_filter_factor": 2,
"cnn_kernel_size": 5,
"convolution_padding": "same",
"pool_size": 5,
"pool_strides": 2,
},
}
config["hparams"]["num_pre_logits_hidden_layers"] = 4
config["hparams"]["pre_logits_hidden_layer_size"] = 512
return config
research/astronet/astronet/astro_fc_model/BUILD deleted 100644 → 0
View file @ caafb6d1
package(default_visibility = ["//visibility:public"])
licenses(["notice"]) # Apache 2.0
py_library(
name = "configurations",
srcs = ["configurations.py"],
srcs_version = "PY2AND3",
deps = [
"//astronet/astro_model:configurations",
],
)
py_library(
name = "astro_fc_model",
srcs = [
"astro_fc_model.py",
],
srcs_version = "PY2AND3",
deps = ["//astronet/astro_model"],
)
py_test(
name = "astro_fc_model_test",
size = "small",
srcs = [
"astro_fc_model_test.py",
],
srcs_version = "PY2AND3",
deps = [
":astro_fc_model",
":configurations",
"//astronet/ops:input_ops",
"//astronet/ops:testing",
"//tf_util:configdict",
],
)
research/astronet/astronet/astro_fc_model/__init__.py deleted 100644 → 0
View file @ caafb6d1
# 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/astronet/astro_fc_model/astro_fc_model.py deleted 100644 → 0
View file @ caafb6d1
# 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.
"""A model for classifying light curves using (locally) fully connected layers.
Note that the first layer of each fully connected stack is optionally
implemented as a convolution with a wide kernel followed by pooling. This causes
invariance to small translations.
See the base class (in astro_model.py) for a description of the general
framework of AstroModel and its subclasses.
The architecture of this model is:
predictions
^
|
logits
^
|
(fully connected layers)
^
|
pre_logits_concat
^
|
(concatenate)
^ ^ ^
| | |
(locally fully connected 1) (locally fully connected 2) ... |
^ ^ |
| | |
time_series_feature_1 time_series_feature_2 ... aux_features
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import tensorflow as tf
from astronet.astro_model import astro_model
class AstroFCModel(astro_model.AstroModel):
"""A model for classifying light curves using fully connected layers."""
def _build_local_fc_layers(self, inputs, hparams, scope):
"""Builds locally fully connected layers.
Note that the first layer of the fully connected stack is optionally
implemented as a convolution with a wide kernel followed by pooling. This
makes the fully connected stack invariant to small translations of its
input.
Args:
inputs: A Tensor of shape [batch_size, length].
hparams: Object containing hyperparameters.
scope: Name of the variable scope.
Returns:
A Tensor of shape [batch_size, hparams.local_layer_size].
Raises:
ValueError: If hparams.pooling_type is unrecognized.
"""
if hparams.num_local_layers == 0:
return inputs
net = inputs
with tf.variable_scope(scope):
# First layer is optionally implemented as a wide convolution for
# invariance to small translations.
if hparams.translation_delta > 0:
kernel_size = inputs.shape.as_list()[1] - 2 * hparams.translation_delta
net = tf.expand_dims(net, -1) # [batch, length, channels=1]
net = tf.layers.conv1d(
inputs=net,
filters=hparams.local_layer_size,
kernel_size=kernel_size,
padding="valid",
activation=tf.nn.relu,
name="conv1d")
# net is [batch, length, num_filters], where length = 1 +
# 2 * translation_delta. Pool along the length dimension.
if hparams.pooling_type == "max":
net = tf.reduce_max(net, axis=1, name="max_pool")
elif hparams.pooling_type == "avg":
net = tf.reduce_mean(net, axis=1, name="avg_pool")
else:
raise ValueError("Unrecognized pooling_type: {}".format(
hparams.pooling_type))
remaining_layers = hparams.num_local_layers - 1
else:
remaining_layers = hparams.num_local_layers
# Remaining fully connected layers.
for i in range(remaining_layers):
net = tf.contrib.layers.fully_connected(
inputs=net,
num_outputs=hparams.local_layer_size,
activation_fn=tf.nn.relu,
scope="fully_connected_{}".format(i + 1))
if hparams.dropout_rate > 0:
net = tf.layers.dropout(
net, hparams.dropout_rate, training=self.is_training)
return net
def build_time_series_hidden_layers(self):
"""Builds hidden layers for the time series features.
Inputs:
self.time_series_features
Outputs:
self.time_series_hidden_layers
"""
time_series_hidden_layers = {}
for name, time_series in self.time_series_features.items():
time_series_hidden_layers[name] = self._build_local_fc_layers(
inputs=time_series,
hparams=self.hparams.time_series_hidden[name],
scope=name + "_hidden")
self.time_series_hidden_layers = time_series_hidden_layers
research/astronet/astronet/astro_fc_model/astro_fc_model_test.py deleted 100644 → 0
View file @ caafb6d1
# 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.
"""Tests for astro_fc_model.AstroFCModel."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import tensorflow as tf
from astronet.astro_fc_model import astro_fc_model
from astronet.astro_fc_model import configurations
from astronet.ops import input_ops
from astronet.ops import testing
from tf_util import configdict
class AstroFCModelTest(tf.test.TestCase):
def assertShapeEquals(self, shape, tensor_or_array):
"""Asserts that a Tensor or Numpy array has the expected shape.
Args:
shape: Numpy array or anything that can be converted to one.
tensor_or_array: tf.Tensor, tf.Variable, or Numpy array.
"""
if isinstance(tensor_or_array, (np.ndarray, np.generic)):
self.assertAllEqual(shape, tensor_or_array.shape)
elif isinstance(tensor_or_array, (tf.Tensor, tf.Variable)):
self.assertAllEqual(shape, tensor_or_array.shape.as_list())
else:
raise TypeError("tensor_or_array must be a Tensor or Numpy ndarray")
def testOneTimeSeriesFeature(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 14,
"is_time_series": True,
}
}
hidden_spec = {
"time_feature_1": {
"num_local_layers": 2,
"local_layer_size": 20,
"translation_delta": 2,
"pooling_type": "max",
"dropout_rate": 0.5,
}
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config["hparams"]["time_series_hidden"] = hidden_spec
config = configdict.ConfigDict(config)
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_fc_model.AstroFCModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate Tensor shapes.
conv = testing.get_variable_by_name("time_feature_1_hidden/conv1d/kernel")
self.assertShapeEquals((10, 1, 20), conv)
fc_1 = testing.get_variable_by_name(
"time_feature_1_hidden/fully_connected_1/weights")
self.assertShapeEquals((20, 20), fc_1)
self.assertItemsEqual(["time_feature_1"],
model.time_series_hidden_layers.keys())
self.assertShapeEquals((None, 20),
model.time_series_hidden_layers["time_feature_1"])
self.assertEqual(len(model.aux_hidden_layers), 0)
self.assertIs(model.time_series_hidden_layers["time_feature_1"],
model.pre_logits_concat)
# Execute the TensorFlow graph.
scaffold = tf.train.Scaffold()
scaffold.finalize()
with self.test_session() as sess:
sess.run([scaffold.init_op, scaffold.local_init_op])
step = sess.run(model.global_step)
self.assertEqual(0, step)
# Fetch predictions.
features = testing.fake_features(feature_spec, batch_size=16)
labels = testing.fake_labels(config.hparams.output_dim, batch_size=16)
feed_dict = input_ops.prepare_feed_dict(model, features, labels)
predictions = sess.run(model.predictions, feed_dict=feed_dict)
self.assertShapeEquals((16, 1), predictions)
def testTwoTimeSeriesFeatures(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 20,
"is_time_series": True,
},
"time_feature_2": {
"length": 5,
"is_time_series": True,
},
"aux_feature_1": {
"length": 1,
"is_time_series": False,
},
}
hidden_spec = {
"time_feature_1": {
"num_local_layers": 1,
"local_layer_size": 20,
"translation_delta": 1,
"pooling_type": "max",
"dropout_rate": 0.5,
},
"time_feature_2": {
"num_local_layers": 2,
"local_layer_size": 7,
"translation_delta": 0,
"dropout_rate": 0,
}
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config["hparams"]["time_series_hidden"] = hidden_spec
config = configdict.ConfigDict(config)
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_fc_model.AstroFCModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate Tensor shapes.
conv = testing.get_variable_by_name("time_feature_1_hidden/conv1d/kernel")
self.assertShapeEquals((18, 1, 20), conv)
fc_1 = testing.get_variable_by_name(
"time_feature_2_hidden/fully_connected_1/weights")
self.assertShapeEquals((5, 7), fc_1)
fc_2 = testing.get_variable_by_name(
"time_feature_2_hidden/fully_connected_2/weights")
self.assertShapeEquals((7, 7), fc_2)
self.assertItemsEqual(["time_feature_1", "time_feature_2"],
model.time_series_hidden_layers.keys())
self.assertShapeEquals((None, 20),
model.time_series_hidden_layers["time_feature_1"])
self.assertShapeEquals((None, 7),
model.time_series_hidden_layers["time_feature_2"])
self.assertItemsEqual(["aux_feature_1"], model.aux_hidden_layers.keys())
self.assertIs(model.aux_features["aux_feature_1"],
model.aux_hidden_layers["aux_feature_1"])
self.assertShapeEquals((None, 28), model.pre_logits_concat)
# Execute the TensorFlow graph.
scaffold = tf.train.Scaffold()
scaffold.finalize()
with self.test_session() as sess:
sess.run([scaffold.init_op, scaffold.local_init_op])
step = sess.run(model.global_step)
self.assertEqual(0, step)
# Fetch predictions.
features = testing.fake_features(feature_spec, batch_size=16)
labels = testing.fake_labels(config.hparams.output_dim, batch_size=16)
feed_dict = input_ops.prepare_feed_dict(model, features, labels)
predictions = sess.run(model.predictions, feed_dict=feed_dict)
self.assertShapeEquals((16, 1), predictions)
if __name__ == "__main__":
tf.test.main()
research/astronet/astronet/astro_fc_model/configurations.py deleted 100644 → 0
View file @ caafb6d1
# 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.
"""Configurations for model building, training and evaluation.
Available configurations:
* base: One time series feature per input example. Default is "global_view".
* local_global: Two time series features per input example.
- A "global" view of the entire orbital period.
- A "local" zoomed-in view of the transit event.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from astronet.astro_model import configurations as parent_configs
def base():
"""Base config for a fully connected model with a single global view."""
config = parent_configs.base()
# Add configuration for the fully-connected layers of the global_view feature.
config["hparams"]["time_series_hidden"] = {
"global_view": {
"num_local_layers": 0,
"local_layer_size": 128,
# If > 0, the first layer is implemented as a wide convolutional layer
# for invariance to small translations.
"translation_delta": 0,
# Pooling type following the wide convolutional layer.
"pooling_type": "max",
# Dropout rate for the fully connected layers.
"dropout_rate": 0.0,
},
}
return config
def local_global():
"""Base config for a locally fully connected model with local/global views."""
config = parent_configs.base()
# Override the model features to be local_view and global_view time series.
config["inputs"]["features"] = {
"local_view": {
"length": 201,
"is_time_series": True,
},
"global_view": {
"length": 2001,
"name_in_proto": "light_curve",
"is_time_series": True,
"data_source": "",
},
}
# Add configurations for the fully-connected layers of time series features.
config["hparams"]["time_series_hidden"] = {
"local_view": {
"num_local_layers": 0,
"local_layer_size": 128,
"translation_delta": 0, # For wide convolution.
"pooling_type": "max", # For wide convolution.
"dropout_rate": 0.0,
},
"global_view": {
"num_local_layers": 0,
"local_layer_size": 128,
"translation_delta": 0, # For wide convolution.
"pooling_type": "max", # For wide convolution.
"dropout_rate": 0.0,
},
}
return config
research/astronet/astronet/astro_model/BUILD deleted 100644 → 0
View file @ caafb6d1
package(default_visibility = ["//visibility:public"])
licenses(["notice"]) # Apache 2.0
py_library(
name = "configurations",
srcs = ["configurations.py"],
srcs_version = "PY2AND3",
)
py_library(
name = "astro_model",
srcs = [
"astro_model.py",
],
srcs_version = "PY2AND3",
)
py_test(
name = "astro_model_test",
size = "small",
srcs = [
"astro_model_test.py",
],
srcs_version = "PY2AND3",
deps = [
":astro_model",
":configurations",
"//astronet/ops:input_ops",
"//astronet/ops:testing",
"//tf_util:configdict",
],
)
research/astronet/astronet/astro_model/__init__.py deleted 100644 → 0
View file @ caafb6d1
# 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/astronet/astro_model/astro_model.py deleted 100644 → 0
View file @ caafb6d1
# 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.
"""A TensorFlow model for identifying exoplanets in astrophysical light curves.
AstroModel is a concrete base class for models that identify exoplanets in
astrophysical light curves. This class implements a simple linear model that can
be extended by subclasses.
The general framework for AstroModel and its subclasses is as follows:
* Model inputs:
- Zero or more time_series_features (e.g. astrophysical light curves)
- Zero or more aux_features (e.g. orbital period, transit duration)
* Labels:
- An integer feature with 2 or more values (eg. 0 = Not Planet, 1 = Planet)
* Model outputs:
- The predicted probabilities for each label
* Architecture:
predictions
^
|
logits
^
|
(pre_logits_hidden_layers)
^
|
pre_logits_concat
^
|
(concatenate)
^ ^
| |
(time_series_hidden_layers) (aux_hidden_layers)
^ ^
| |
time_series_features aux_features
Subclasses will typically override the build_time_series_hidden_layers()
and/or build_aux_hidden_layers() functions. For example, a subclass could
override build_time_series_hidden_layers() to apply convolutional layers to the
time series features. In this class, those functions are simple concatenations
of the input features.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import operator
import tensorflow as tf
class AstroModel(object):
"""A TensorFlow model for classifying astrophysical light curves."""
def __init__(self, features, labels, hparams, mode):
"""Basic setup.
The actual TensorFlow graph is constructed in build().
Args:
features: A dictionary containing "time_series_features" and
"aux_features", each of which is a dictionary of named input Tensors.
All features have dtype float32 and shape [batch_size, length].
labels: An int64 Tensor with shape [batch_size]. May be None if mode is
tf.estimator.ModeKeys.PREDICT.
hparams: A ConfigDict of hyperparameters for building the model.
mode: A tf.estimator.ModeKeys to specify whether the graph should be built
for training, evaluation or prediction.
Raises:
ValueError: If mode is invalid.
"""
valid_modes = [
tf.estimator.ModeKeys.TRAIN, tf.estimator.ModeKeys.EVAL,
tf.estimator.ModeKeys.PREDICT
]
if mode not in valid_modes:
raise ValueError("Expected mode in {}. Got: {}".format(valid_modes, mode))
self.hparams = hparams
self.mode = mode
# A dictionary of input Tensors. Values have dtype float32 and shape
# [batch_size, length].
self.time_series_features = features.get("time_series_features", {})
# A dictionary of input Tensors. Values have dtype float32 and shape
# [batch_size, length].
self.aux_features = features.get("aux_features", {})
# An int32 Tensor with shape [batch_size]. May be None if mode is
# tf.estimator.ModeKeys.PREDICT.
self.labels = labels
# Optional Tensor; the weights corresponding to self.labels.
self.weights = features.get("weights")
# A Python boolean or a scalar boolean Tensor. Indicates whether the model
# is in training mode for the purpose of graph ops, such as dropout. (Since
# this might be a Tensor, its value is defined in build()).
self.is_training = None
# Global step Tensor.
self.global_step = None
# A dictionary of float32 Tensors with shape [batch_size, layer_size]; the
# outputs of the time series hidden layers.
self.time_series_hidden_layers = {}
# A dictionary of float32 Tensors with shape [batch_size, layer_size]; the
# outputs of the auxiliary hidden layers.
self.aux_hidden_layers = {}
# A float32 Tensor with shape [batch_size, layer_size]; the concatenation of
# outputs from the hidden layers.
self.pre_logits_concat = None
# A float32 Tensor with shape [batch_size, output_dim].
self.logits = None
# A float32 Tensor with shape [batch_size, output_dim].
self.predictions = None
# A float32 Tensor with shape [batch_size]; the cross-entropy losses for the
# current batch.
self.batch_losses = None
# Scalar Tensor; the total loss for the trainer to optimize.
self.total_loss = None
def build_time_series_hidden_layers(self):
"""Builds hidden layers for the time series features.
Inputs:
self.time_series_features
Outputs:
self.time_series_hidden_layers
"""
# No hidden layers.
self.time_series_hidden_layers = self.time_series_features
def build_aux_hidden_layers(self):
"""Builds hidden layers for the auxiliary features.
Inputs:
self.aux_features
Outputs:
self.aux_hidden_layers
"""
# No hidden layers.
self.aux_hidden_layers = self.aux_features
def build_logits(self):
"""Builds the model logits.
Inputs:
self.aux_hidden_layers
self.time_series_hidden_layers
Outputs:
self.pre_logits_concat
self.logits
Raises:
ValueError: If self.time_series_hidden_layers and self.aux_hidden_layers
are both empty.
"""
# Sort the hidden layers by name because the order of dictionary items is
# nondeterministic between invocations of Python.
time_series_hidden_layers = sorted(
self.time_series_hidden_layers.items(), key=operator.itemgetter(0))
aux_hidden_layers = sorted(
self.aux_hidden_layers.items(), key=operator.itemgetter(0))
hidden_layers = time_series_hidden_layers + aux_hidden_layers
if not hidden_layers:
raise ValueError("At least one time series hidden layer or auxiliary "
"hidden layer is required.")
# Concatenate the hidden layers.
if len(hidden_layers) == 1:
pre_logits_concat = hidden_layers[0][1]
else:
pre_logits_concat = tf.concat([layer[1] for layer in hidden_layers],
axis=1,
name="pre_logits_concat")
net = pre_logits_concat
with tf.variable_scope("pre_logits_hidden"):
for i in range(self.hparams.num_pre_logits_hidden_layers):
net = tf.layers.dense(
inputs=net,
units=self.hparams.pre_logits_hidden_layer_size,
activation=tf.nn.relu,
name="fully_connected_{}".format(i + 1))
if self.hparams.pre_logits_dropout_rate > 0:
net = tf.layers.dropout(
net,
self.hparams.pre_logits_dropout_rate,
training=self.is_training)
# Identify the final pre-logits hidden layer as "pre_logits_hidden/final".
tf.identity(net, "final")
logits = tf.layers.dense(
inputs=net, units=self.hparams.output_dim, name="logits")
self.pre_logits_concat = pre_logits_concat
self.logits = logits
def build_predictions(self):
"""Builds the output predictions and losses.
Inputs:
self.logits
Outputs:
self.predictions
"""
# Use sigmoid activation function for binary classification, or softmax for
# multi-class classification.
prediction_fn = (
tf.sigmoid if self.hparams.output_dim == 1 else tf.nn.softmax)
predictions = prediction_fn(self.logits, name="predictions")
self.predictions = predictions
def build_losses(self):
"""Builds the training losses.
Inputs:
self.logits
self.labels
Outputs:
self.batch_losses
self.total_loss
"""
if self.hparams.output_dim == 1:
# Binary classification.
batch_losses = tf.nn.sigmoid_cross_entropy_with_logits(
labels=tf.to_float(self.labels), logits=tf.squeeze(self.logits, [1]))
else:
# Multi-class classification.
batch_losses = tf.nn.sparse_softmax_cross_entropy_with_logits(
labels=self.labels, logits=self.logits)
# Compute the weighted mean cross entropy loss and add it to the LOSSES
# collection.
weights = self.weights if self.weights is not None else 1.0
tf.losses.compute_weighted_loss(
losses=batch_losses,
weights=weights,
reduction=tf.losses.Reduction.MEAN)
# Compute the total loss, including any other losses added to the LOSSES
# collection (e.g. regularization losses).
total_loss = tf.losses.get_total_loss()
self.batch_losses = batch_losses
self.total_loss = total_loss
def build(self):
"""Creates all ops for training, evaluation or inference."""
self.global_step = tf.train.get_or_create_global_step()
if self.mode == tf.estimator.ModeKeys.TRAIN:
# This is implemented as a placeholder Tensor, rather than a constant, to
# allow its value to be feedable during training (e.g. to disable dropout
# when performing in-process validation set evaluation).
self.is_training = tf.placeholder_with_default(True, [], "is_training")
else:
self.is_training = False
self.build_time_series_hidden_layers()
self.build_aux_hidden_layers()
self.build_logits()
self.build_predictions()
if self.mode in [tf.estimator.ModeKeys.TRAIN, tf.estimator.ModeKeys.EVAL]:
self.build_losses()
research/astronet/astronet/astro_model/astro_model_test.py deleted 100644 → 0
View file @ caafb6d1
# 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.
"""Tests for astro_model.AstroModel."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import tensorflow as tf
from astronet.astro_model import astro_model
from astronet.astro_model import configurations
from astronet.ops import input_ops
from astronet.ops import testing
from tf_util import configdict
class AstroModelTest(tf.test.TestCase):
def assertShapeEquals(self, shape, tensor_or_array):
"""Asserts that a Tensor or Numpy array has the expected shape.
Args:
shape: Numpy array or anything that can be converted to one.
tensor_or_array: tf.Tensor, tf.Variable, or Numpy array.
"""
if isinstance(tensor_or_array, (np.ndarray, np.generic)):
self.assertAllEqual(shape, tensor_or_array.shape)
elif isinstance(tensor_or_array, (tf.Tensor, tf.Variable)):
self.assertAllEqual(shape, tensor_or_array.shape.as_list())
else:
raise TypeError("tensor_or_array must be a Tensor or Numpy ndarray")
def testInvalidModeRaisesError(self):
# Build config.
config = configdict.ConfigDict(configurations.base())
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
with self.assertRaises(ValueError):
_ = astro_model.AstroModel(features, labels, config.hparams, "training")
def testZeroFeaturesRaisesError(self):
# Build config.
config = configurations.base()
config["inputs"]["features"] = {}
config = configdict.ConfigDict(config)
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_model.AstroModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
with self.assertRaises(ValueError):
# Raises ValueError because at least one feature is required.
model.build()
def testOneTimeSeriesFeature(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 10,
"is_time_series": True,
}
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config = configdict.ConfigDict(config)
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_model.AstroModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate hidden layers.
self.assertItemsEqual(["time_feature_1"],
model.time_series_hidden_layers.keys())
self.assertIs(model.time_series_features["time_feature_1"],
model.time_series_hidden_layers["time_feature_1"])
self.assertEqual(len(model.aux_hidden_layers), 0)
self.assertIs(model.time_series_features["time_feature_1"],
model.pre_logits_concat)
def testOneAuxFeature(self):
# Build config.
feature_spec = {
"aux_feature_1": {
"length": 1,
"is_time_series": False,
}
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config = configdict.ConfigDict(config)
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_model.AstroModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate hidden layers.
self.assertEqual(len(model.time_series_hidden_layers), 0)
self.assertItemsEqual(["aux_feature_1"], model.aux_hidden_layers.keys())
self.assertIs(model.aux_features["aux_feature_1"],
model.aux_hidden_layers["aux_feature_1"])
self.assertIs(model.aux_features["aux_feature_1"], model.pre_logits_concat)
def testTwoTimeSeriesFeatures(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 10,
"is_time_series": True,
},
"time_feature_2": {
"length": 10,
"is_time_series": True,
}
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config = configdict.ConfigDict(config)
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_model.AstroModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate hidden layers.
self.assertItemsEqual(["time_feature_1", "time_feature_2"],
model.time_series_hidden_layers.keys())
self.assertIs(model.time_series_features["time_feature_1"],
model.time_series_hidden_layers["time_feature_1"])
self.assertIs(model.time_series_features["time_feature_2"],
model.time_series_hidden_layers["time_feature_2"])
self.assertEqual(len(model.aux_hidden_layers), 0)
self.assertShapeEquals((None, 20), model.pre_logits_concat)
def testOneTimeSeriesOneAuxFeature(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 10,
"is_time_series": True,
},
"aux_feature_1": {
"length": 1,
"is_time_series": False,
},
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config = configdict.ConfigDict(config)
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_model.AstroModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate hidden layers.
self.assertItemsEqual(["time_feature_1"],
model.time_series_hidden_layers.keys())
self.assertIs(model.time_series_features["time_feature_1"],
model.time_series_hidden_layers["time_feature_1"])
self.assertItemsEqual(["aux_feature_1"], model.aux_hidden_layers.keys())
self.assertIs(model.aux_features["aux_feature_1"],
model.aux_hidden_layers["aux_feature_1"])
self.assertShapeEquals((None, 11), model.pre_logits_concat)
def testOneTimeSeriesTwoAuxFeatures(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 10,
"is_time_series": True,
},
"aux_feature_1": {
"length": 1,
"is_time_series": False,
},
"aux_feature_2": {
"length": 2,
"is_time_series": False,
},
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config = configdict.ConfigDict(config)
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_model.AstroModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate hidden layers.
self.assertItemsEqual(["time_feature_1"],
model.time_series_hidden_layers.keys())
self.assertIs(model.time_series_features["time_feature_1"],
model.time_series_hidden_layers["time_feature_1"])
self.assertItemsEqual(["aux_feature_1", "aux_feature_2"],
model.aux_hidden_layers.keys())
self.assertIs(model.aux_features["aux_feature_1"],
model.aux_hidden_layers["aux_feature_1"])
self.assertIs(model.aux_features["aux_feature_2"],
model.aux_hidden_layers["aux_feature_2"])
self.assertShapeEquals((None, 13), model.pre_logits_concat)
def testZeroHiddenLayers(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 10,
"is_time_series": True,
},
"time_feature_2": {
"length": 10,
"is_time_series": True,
},
"aux_feature_1": {
"length": 1,
"is_time_series": False,
},
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config = configdict.ConfigDict(config)
config.hparams.output_dim = 1
config.hparams.num_pre_logits_hidden_layers = 0
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_model.AstroModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate Tensor shapes.
self.assertShapeEquals((None, 21), model.pre_logits_concat)
logits_w = testing.get_variable_by_name("logits/kernel")
self.assertShapeEquals((21, 1), logits_w)
def testOneHiddenLayer(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 10,
"is_time_series": True,
},
"time_feature_2": {
"length": 10,
"is_time_series": True,
},
"aux_feature_1": {
"length": 1,
"is_time_series": False,
},
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config = configdict.ConfigDict(config)
config.hparams.output_dim = 1
config.hparams.num_pre_logits_hidden_layers = 1
config.hparams.pre_logits_hidden_layer_size = 5
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_model.AstroModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate Tensor shapes.
self.assertShapeEquals((None, 21), model.pre_logits_concat)
fc1 = testing.get_variable_by_name(
"pre_logits_hidden/fully_connected_1/kernel")
self.assertShapeEquals((21, 5), fc1)
logits_w = testing.get_variable_by_name("logits/kernel")
self.assertShapeEquals((5, 1), logits_w)
def testTwoHiddenLayers(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 10,
"is_time_series": True,
},
"time_feature_2": {
"length": 10,
"is_time_series": True,
},
"aux_feature_1": {
"length": 1,
"is_time_series": False,
},
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config = configdict.ConfigDict(config)
config.hparams.output_dim = 1
config.hparams.num_pre_logits_hidden_layers = 2
config.hparams.pre_logits_hidden_layer_size = 5
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_model.AstroModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate Tensor shapes.
self.assertShapeEquals((None, 21), model.pre_logits_concat)
fc1 = testing.get_variable_by_name(
"pre_logits_hidden/fully_connected_1/kernel")
self.assertShapeEquals((21, 5), fc1)
fc2 = testing.get_variable_by_name(
"pre_logits_hidden/fully_connected_2/kernel")
self.assertShapeEquals((5, 5), fc2)
logits_w = testing.get_variable_by_name("logits/kernel")
self.assertShapeEquals((5, 1), logits_w)
def testBinaryClassification(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 10,
"is_time_series": True,
},
"time_feature_2": {
"length": 10,
"is_time_series": True,
},
"aux_feature_1": {
"length": 1,
"is_time_series": False,
},
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config = configdict.ConfigDict(config)
config.hparams.output_dim = 1
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_model.AstroModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate Tensor shapes.
self.assertShapeEquals((None, 1), model.logits)
self.assertShapeEquals((None, 1), model.predictions)
self.assertShapeEquals((None,), model.batch_losses)
self.assertShapeEquals((), model.total_loss)
# Execute the TensorFlow graph.
scaffold = tf.train.Scaffold()
scaffold.finalize()
with self.test_session() as sess:
sess.run([scaffold.init_op, scaffold.local_init_op])
step = sess.run(model.global_step)
self.assertEqual(0, step)
# Fetch total loss.
features = testing.fake_features(feature_spec, batch_size=16)
labels = testing.fake_labels(config.hparams.output_dim, batch_size=16)
feed_dict = input_ops.prepare_feed_dict(model, features, labels)
total_loss = sess.run(model.total_loss, feed_dict=feed_dict)
self.assertShapeEquals((), total_loss)
def testMultiLabelClassification(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 10,
"is_time_series": True,
},
"time_feature_2": {
"length": 10,
"is_time_series": True,
},
"aux_feature_1": {
"length": 1,
"is_time_series": False,
},
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config = configdict.ConfigDict(config)
config.hparams.output_dim = 3
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_model.AstroModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate Tensor shapes.
self.assertShapeEquals((None, 3), model.logits)
self.assertShapeEquals((None, 3), model.predictions)
self.assertShapeEquals((None,), model.batch_losses)
self.assertShapeEquals((), model.total_loss)
# Execute the TensorFlow graph.
scaffold = tf.train.Scaffold()
scaffold.finalize()
with self.test_session() as sess:
sess.run([scaffold.init_op, scaffold.local_init_op])
step = sess.run(model.global_step)
self.assertEqual(0, step)
# Fetch total loss.
features = testing.fake_features(feature_spec, batch_size=16)
labels = testing.fake_labels(config.hparams.output_dim, batch_size=16)
feed_dict = input_ops.prepare_feed_dict(model, features, labels)
total_loss = sess.run(model.total_loss, feed_dict=feed_dict)
self.assertShapeEquals((), total_loss)
def testEvalMode(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 10,
"is_time_series": True,
},
"time_feature_2": {
"length": 10,
"is_time_series": True,
},
"aux_feature_1": {
"length": 1,
"is_time_series": False,
},
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config = configdict.ConfigDict(config)
config.hparams.output_dim = 1
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
labels = input_ops.build_labels_placeholder()
model = astro_model.AstroModel(features, labels, config.hparams,
tf.estimator.ModeKeys.TRAIN)
model.build()
# Validate Tensor shapes.
self.assertShapeEquals((None, 21), model.pre_logits_concat)
self.assertShapeEquals((None, 1), model.logits)
self.assertShapeEquals((None, 1), model.predictions)
self.assertShapeEquals((None,), model.batch_losses)
self.assertShapeEquals((), model.total_loss)
# Execute the TensorFlow graph.
scaffold = tf.train.Scaffold()
scaffold.finalize()
with self.test_session() as sess:
sess.run([scaffold.init_op, scaffold.local_init_op])
step = sess.run(model.global_step)
self.assertEqual(0, step)
# Fetch total loss.
features = testing.fake_features(feature_spec, batch_size=16)
labels = testing.fake_labels(config.hparams.output_dim, batch_size=16)
feed_dict = input_ops.prepare_feed_dict(model, features, labels)
total_loss = sess.run(model.total_loss, feed_dict=feed_dict)
self.assertShapeEquals((), total_loss)
def testPredictMode(self):
# Build config.
feature_spec = {
"time_feature_1": {
"length": 10,
"is_time_series": True,
},
"time_feature_2": {
"length": 10,
"is_time_series": True,
},
"aux_feature_1": {
"length": 1,
"is_time_series": False,
},
}
config = configurations.base()
config["inputs"]["features"] = feature_spec
config = configdict.ConfigDict(config)
config.hparams.output_dim = 1
# Build model.
features = input_ops.build_feature_placeholders(config.inputs.features)
model = astro_model.AstroModel(features, None, config.hparams,
tf.estimator.ModeKeys.PREDICT)
model.build()
# Validate Tensor shapes.
self.assertIsNone(model.labels)
self.assertShapeEquals((None, 21), model.pre_logits_concat)
self.assertShapeEquals((None, 1), model.logits)
self.assertShapeEquals((None, 1), model.predictions)
self.assertIsNone(model.batch_losses)
self.assertIsNone(model.total_loss)
# Execute the TensorFlow graph.
scaffold = tf.train.Scaffold()
scaffold.finalize()
with self.test_session() as sess:
sess.run([scaffold.init_op, scaffold.local_init_op])
step = sess.run(model.global_step)
self.assertEqual(0, step)
# Fetch predictions.
features = testing.fake_features(feature_spec, batch_size=16)
feed_dict = input_ops.prepare_feed_dict(model, features)
predictions = sess.run(model.predictions, feed_dict=feed_dict)
self.assertShapeEquals((16, 1), predictions)
if __name__ == "__main__":
tf.test.main()
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