def get_estimator(epochs=10, batch_size=32, alpha=1.0, warmup=0, model_dir=tempfile.mkdtemp()):
(x_train, y_train), (x_eval, y_eval) = tf.keras.datasets.cifar10.load_data()
data = {"train": {"x": x_train, "y": y_train}, "eval": {"x": x_eval, "y": y_eval}}
num_classes = 10
pipeline = fe.Pipeline(batch_size=batch_size, data=data, ops=Minmax(inputs="x", outputs="x"))
model = FEModel(model_def=lambda: LeNet(input_shape=x_train.shape[1:], classes=num_classes),
model_name="LeNet",
optimizer="adam")
mixup_map = {warmup: MixUpBatch(inputs="x", outputs=["x", "lambda"], alpha=alpha, mode="train")}
mixup_loss = {
0: SparseCategoricalCrossentropy(y_true="y", y_pred="y_pred", mode="train"),
warmup: MixUpLoss(KerasCrossentropy(), lam="lambda", y_true="y", y_pred="y_pred", mode="train")
}
network = fe.Network(ops=[
Scheduler(mixup_map),
ModelOp(inputs="x", model=model, outputs="y_pred"),
Scheduler(mixup_loss),
SparseCategoricalCrossentropy(y_true="y", y_pred="y_pred", mode="eval")
])
traces = [
Accuracy(true_key="y", pred_key="y_pred"),
ConfusionMatrix(true_key="y", pred_key="y_pred", num_classes=num_classes),
ModelSaver(model_name="LeNet", save_dir=model_dir, save_best=True)
]
estimator = fe.Estimator(network=network, pipeline=pipeline, epochs=epochs, traces=traces)
return estimator
def get_estimator(style_img_path=None,
data_path=None,
style_weight=5.0,
content_weight=1.0,
tv_weight=1e-4,
steps_per_epoch=None,
validation_steps=None,
model_dir=tempfile.mkdtemp()):
train_csv, _, path = load_data(data_path, load_object=False)
if style_img_path is None:
style_img_path = tf.keras.utils.get_file(
'kandinsky.jpg',
'https://storage.googleapis.com/download.tensorflow.org/example_images/Vassily_Kandinsky%2C_1913_'
'-_Composition_7.jpg')
style_img = cv2.imread(style_img_path)
assert (style_img is not None), "Invalid style reference image"
tfr_save_dir = os.path.join(path, 'tfrecords')
style_img = (style_img.astype(np.float32) / 127.5) / 127.5
style_img_t = tf.convert_to_tensor(np.expand_dims(style_img, axis=0))
writer = RecordWriter(train_data=train_csv,
save_dir=tfr_save_dir,
ops=[
ImageReader(inputs="image",
parent_path=path,
outputs="image"),
Resize(inputs="image",
target_size=(256, 256),
outputs="image")
])
pipeline = fe.Pipeline(batch_size=4,
data=writer,
ops=[Rescale(inputs="image", outputs="image")])
model = fe.build(model_def=styleTransferNet,
model_name="style_transfer_net",
loss_name="loss",
optimizer=tf.keras.optimizers.Adam(1e-3))
network = fe.Network(ops=[
ModelOp(inputs="image", model=model, outputs="image_out"),
ExtractVGGFeatures(inputs=lambda: style_img_t, outputs="y_style"),
ExtractVGGFeatures(inputs="image", outputs="y_content"),
ExtractVGGFeatures(inputs="image_out", outputs="y_pred"),
StyleContentLoss(style_weight=style_weight,
content_weight=content_weight,
tv_weight=tv_weight,
inputs=('y_pred', 'y_style', 'y_content',
'image_out'),
outputs='loss')
])
estimator = fe.Estimator(network=network,
pipeline=pipeline,
epochs=2,
steps_per_epoch=steps_per_epoch,
validation_steps=validation_steps,
traces=ModelSaver(model_name="style_transfer_net",
save_dir=model_dir))
return estimator
def get_estimator(epochs=2, batch_size=32, model_dir=tempfile.mkdtemp()):
# step 1. prepare data
(x_train, y_train), (x_eval, y_eval) = tf.keras.datasets.mnist.load_data()
train_data = {"x": np.expand_dims(x_train, -1), "y": y_train}
eval_data = {"x": np.expand_dims(x_eval, -1), "y": y_eval}
data = {"train": train_data, "eval": eval_data}
pipeline = fe.Pipeline(batch_size=batch_size,
data=data,
ops=Minmax(inputs="x", outputs="x"))
# step 2. prepare model
model = fe.FEModel(model_def=LeNet, model_name="lenet", optimizer="adam")
network = fe.Network(ops=[
ModelOp(inputs="x", model=model, outputs="y_pred"),
SparseCategoricalCrossentropy(inputs=("y", "y_pred"))
])
# step 3.prepare estimator
traces = [
Accuracy(true_key="y", pred_key="y_pred", output_name='acc'),
ModelSaver(model_name="lenet", save_dir=model_dir, save_best=True)
]
estimator = fe.Estimator(network=network,
pipeline=pipeline,
epochs=epochs,
traces=traces)
return estimator
def get_estimator(batch_size=256, epochs=50, model_dir=tempfile.mkdtemp()):
# prepare data
(x_train, _), (_, _) = tf.keras.datasets.mnist.load_data()
data = {"train": {"x": np.expand_dims(x_train, -1)}}
pipeline = fe.Pipeline(batch_size=batch_size,
data=data,
ops=Myrescale(inputs="x", outputs="x"))
# prepare model
g_femodel = FEModel(model_def=make_generator_model,
model_name="gen",
loss_name="gloss",
optimizer=tf.optimizers.Adam(1e-4))
d_femodel = FEModel(model_def=make_discriminator_model,
model_name="disc",
loss_name="dloss",
optimizer=tf.optimizers.Adam(1e-4))
network = fe.Network(ops=[
ModelOp(inputs=lambda: tf.random.normal([batch_size, 100]),
model=g_femodel),
ModelOp(model=d_femodel, outputs="pred_fake"),
ModelOp(inputs="x", model=d_femodel, outputs="pred_true"),
GLoss(inputs=("pred_fake"), outputs="gloss"),
DLoss(inputs=("pred_true", "pred_fake"), outputs="dloss")
])
# prepare estimator
traces = [ModelSaver(model_name='gen', save_dir=model_dir, save_freq=5)]
estimator = fe.Estimator(network=network,
pipeline=pipeline,
epochs=epochs,
traces=traces)
return estimator
def get_estimator(batch_size=32, epochs=25, model_dir=tempfile.mkdtemp()):
# load CUB200 dataset.
csv_path, path = cub200.load_data()
writer = RecordWriter(
save_dir=os.path.join(path, "FEdata"),
train_data=csv_path,
validation_data=0.2,
ops=[
ImageReader(inputs='image', parent_path=path),
Resize(target_size=(128, 128), keep_ratio=True, outputs='image'),
MatReader(inputs='annotation', parent_path=path),
SelectDictKey(),
Resize((128, 128), keep_ratio=True),
Reshape(shape=(128, 128, 1), outputs="annotation")
])
# data pipeline
pipeline = fe.Pipeline(batch_size=batch_size, data=writer, ops=Minmax(inputs='image', outputs='image'))
# Network
model = FEModel(model_def=UNet, model_name="unet_cub", optimizer=tf.optimizers.Adam())
network = fe.Network(ops=[
ModelOp(inputs='image', model=model, outputs='mask_pred'),
BinaryCrossentropy(y_true='annotation', y_pred='mask_pred')
])
# estimator
traces = [
Dice(true_key="annotation", pred_key='mask_pred'),
ModelSaver(model_name="unet_cub", save_dir=model_dir, save_best=True)
]
estimator = fe.Estimator(network=network, pipeline=pipeline, traces=traces, epochs=epochs, log_steps=50)
return estimator
def get_estimator(batch_size=4, epochs=25, model_dir=tempfile.mkdtemp()):
csv_path, path = montgomery.load_data()
writer = RecordWriter(save_dir=os.path.join(path, "FEdata"),
train_data=csv_path,
validation_data=0.2,
ops=[
ImageReader(grey_scale=True,
inputs="image",
parent_path=path,
outputs="image"),
ImageReader(grey_scale=True,
inputs="mask_left",
parent_path=path,
outputs="mask_left"),
ImageReader(grey_scale=True,
inputs="mask_right",
parent_path=path,
outputs="mask_right"),
CombineLeftRightMask(inputs=("mask_left",
"mask_right")),
Resize(target_size=(512, 512)),
Reshape(shape=(512, 512, 1), outputs="mask"),
Resize(inputs="image", target_size=(512, 512)),
Reshape(shape=(512, 512, 1), outputs="image"),
],
write_feature=["image", "mask"])
pipeline = fe.Pipeline(batch_size=batch_size,
data=writer,
ops=[
Augmentation2D(inputs=["image", "mask"],
outputs=["image", "mask"],
mode="train",
rotation_range=10,
flip_left_right=True),
Minmax(inputs="image", outputs="image"),
Minmax(inputs="mask", outputs="mask")
])
model = FEModel(model_def=lambda: UNet(input_size=(512, 512, 1)),
model_name="lungsegmentation",
optimizer=tf.keras.optimizers.Adam(learning_rate=0.0001))
network = fe.Network(ops=[
ModelOp(inputs="image", model=model, outputs="pred_segment"),
BinaryCrossentropy(y_true="mask", y_pred="pred_segment")
])
traces = [
Dice(true_key="mask", pred_key="pred_segment"),
ModelSaver(model_name="lungsegmentation",
save_dir=model_dir,
save_best=True)
]
estimator = fe.Estimator(network=network,
pipeline=pipeline,
epochs=epochs,
log_steps=20,
traces=traces)
return estimator
def get_estimator(batch_size=8, epochs=25, steps_per_epoch=None, validation_steps=None, model_dir=tempfile.mkdtemp()):
# load CUB200 dataset.
csv_path, path = cub200.load_data()
writer = RecordWriter(
save_dir=os.path.join(path, "tfrecords"),
train_data=csv_path,
validation_data=0.2,
ops=[
ImageReader(inputs='image', parent_path=path),
Resize(target_size=(512, 512), keep_ratio=True, outputs='image'),
MatReader(inputs='annotation', parent_path=path),
SelectDictKey(),
Resize((512, 512), keep_ratio=True),
Reshape(shape=(512, 512, 1), outputs="annotation")
])
#step 1, pipeline
pipeline = fe.Pipeline(
batch_size=batch_size,
data=writer,
ops=[
Augmentation2D(inputs=("image", "annotation"),
outputs=("image", "annotation"),
mode="train",
rotation_range=15.0,
zoom_range=[0.8, 1.2],
flip_left_right=True),
Rescale(inputs='image', outputs='image')
])
#step 2, network
opt = tf.optimizers.Adam(learning_rate=0.0001)
resunet50 = fe.build(model_def=ResUnet50, model_name="resunet50", optimizer=opt, loss_name="total_loss")
uncertainty = fe.build(model_def=UncertaintyLoss, model_name="uncertainty", optimizer=opt, loss_name="total_loss")
network = fe.Network(ops=[
ModelOp(inputs='image', model=resunet50, outputs=["label_pred", "mask_pred"]),
SparseCategoricalCrossentropy(inputs=["label", "label_pred"], outputs="cls_loss"),
BinaryCrossentropy(inputs=["annotation", "mask_pred"], outputs="seg_loss"),
ModelOp(inputs=("cls_loss", "seg_loss"), model=uncertainty, outputs="total_loss"),
Loss(inputs="total_loss", outputs="total_loss")
])
#step 3, estimator
traces = [
Dice(true_key="annotation", pred_key='mask_pred'),
Accuracy(true_key="label", pred_key="label_pred"),
ModelSaver(model_name="resunet50", save_dir=model_dir, save_best=True),
LRController(model_name="resunet50", lr_schedule=CyclicLRSchedule())
]
estimator = fe.Estimator(network=network,
pipeline=pipeline,
traces=traces,
epochs=epochs,
steps_per_epoch=steps_per_epoch,
validation_steps=validation_steps)
return estimator
def get_estimator(epochs=10,
batch_size=64,
max_len=500,
steps_per_epoch=None,
validation_steps=None,
model_dir=tempfile.mkdtemp()):
# step 1. prepare data
(x_train,
y_train), (x_eval,
y_eval) = tf.keras.datasets.imdb.load_data(maxlen=max_len,
num_words=MAX_WORDS)
data = {
"train": {
"x": np.array([pad(x, max_len, 0) for x in x_train]),
"y": y_train
},
"eval": {
"x": np.array([pad(x, max_len, 0) for x in x_eval]),
"y": y_eval
}
}
pipeline = fe.Pipeline(batch_size=batch_size,
data=data,
ops=Reshape([1], inputs="y", outputs="y"))
# step 2. prepare model
model = fe.build(model_def=lambda: create_lstm(max_len),
model_name="lstm_imdb",
optimizer="adam",
loss_name="loss")
network = fe.Network(ops=[
ModelOp(inputs="x", model=model, outputs="y_pred"),
BinaryCrossentropy(y_true="y", y_pred="y_pred", outputs="loss")
])
traces = [
Accuracy(true_key="y", pred_key="y_pred"),
ModelSaver(model_name="lstm_imdb", save_dir=model_dir, save_best=True)
]
# step 3.prepare estimator
estimator = fe.Estimator(network=network,
pipeline=pipeline,
epochs=epochs,
traces=traces,
steps_per_epoch=steps_per_epoch,
validation_steps=validation_steps)
return estimator
def get_estimator(epochs=50,
batch_size=64,
steps_per_epoch=None,
validation_steps=None,
model_dir=tempfile.mkdtemp()):
# step 1. prepare data
(x_train, y_train), (x_eval,
y_eval) = tf.keras.datasets.cifar10.load_data()
data = {
"train": {
"x": x_train,
"y": y_train
},
"eval": {
"x": x_eval,
"y": y_eval
}
}
pipeline = fe.Pipeline(batch_size=batch_size,
data=data,
ops=Minmax(inputs="x", outputs="x"))
# step 2. prepare model
model = fe.build(model_def=DenseNet121_cifar10,
model_name="densenet121",
optimizer="adam",
loss_name="loss")
network = fe.Network(ops=[
ModelOp(inputs="x", model=model, outputs="y_pred"),
SparseCategoricalCrossentropy(
y_true="y", y_pred="y_pred", outputs="loss")
])
# step 3.prepare estimator
estimator = fe.Estimator(network=network,
pipeline=pipeline,
epochs=epochs,
steps_per_epoch=steps_per_epoch,
validation_steps=validation_steps,
traces=[
Accuracy(true_key="y", pred_key="y_pred"),
ModelSaver(model_name="densenet121",
save_dir=model_dir,
save_best=True),
LRController(model_name="densenet121",
reduce_on_eval=True)
])
return estimator
def get_estimator(batch_size=100,
epochs=100,
steps_per_epoch=None,
validation_steps=None,
model_dir=tempfile.mkdtemp()):
# prepare data
(x_train, _), (x_eval, _) = tf.keras.datasets.mnist.load_data()
x_train = x_train.reshape(x_train.shape[0], 28, 28, 1).astype('float32')
x_eval = x_eval.reshape(x_eval.shape[0], 28, 28, 1).astype('float32')
data = {"train": {"x": x_train}, "eval": {"x": x_eval}}
pipeline = fe.Pipeline(batch_size=batch_size,
data=data,
ops=[
Myrescale(inputs="x", outputs="x"),
Mybinarize(inputs="x", outputs="x")
])
# prepare model
infer_model = fe.build(model_def=inference_net,
model_name="encoder",
loss_name="loss",
optimizer=tf.optimizers.Adam(1e-4))
gen_model = fe.build(model_def=generative_net,
model_name="decoder",
loss_name="loss",
optimizer=tf.optimizers.Adam(1e-4))
network = fe.Network(ops=[
ModelOp(inputs="x", model=infer_model, outputs="meanlogvar",
mode=None),
SplitOp(inputs="meanlogvar", outputs=("mean", "logvar"), mode=None),
ReparameterizepOp(inputs=("mean", "logvar"), outputs="z", mode=None),
ModelOp(inputs="z", model=gen_model, outputs="x_logit"),
CVAELoss(inputs=("x", "mean", "logvar", "z", "x_logit"),
mode=None,
outputs="loss")
])
estimator = fe.Estimator(network=network,
pipeline=pipeline,
epochs=epochs,
steps_per_epoch=steps_per_epoch,
validation_steps=validation_steps,
traces=ModelSaver(model_name="decoder",
save_dir=model_dir,
save_best=True))
return estimator
def get_estimator(batch_size=4, epochs=1000, steps_per_epoch=1000, validation_steps=None, model_dir=tempfile.mkdtemp(), imagenet_path=None):
"""Args:
imagenet_path: folder path of ImageNet dataset, containing train and val subdirs .
"""
assert imagenet_path is not None, 'Pass valid folder path of Imagenet dataset'
# Ensure ImageNet dataset is downloaded. Pass the folder contianing train and val subdirectories.
# currently the script doesn't download the ImageNet data.
train_csv, val_csv, path = srgan.load_data(path_imgnet= imagenet_path)
writer = fe.RecordWriter(
save_dir=os.path.join(path, "sr_tfrecords"),
train_data=train_csv,
validation_data=val_csv,
ops=[ImageReader(inputs="lowres", outputs="lowres"), ImageReader(inputs="highres", outputs="highres")],
compression="GZIP",
write_feature=['lowres', 'highres'])
pipeline = fe.Pipeline(
max_shuffle_buffer_mb=3000,
batch_size=batch_size,
data=writer,
ops=[
LowresRescale(inputs='lowres', outputs='lowres'),
Rescale(inputs='highres', outputs='highres'), ])
# prepare model
model = fe.build(model_def=lambda: get_generator(input_shape=(24, 24, 3)),
model_name="srresnet_gen",
optimizer=tf.optimizers.Adam(learning_rate=0.0001),
loss_name="mse_loss")
network = fe.Network(ops=[
ModelOp(inputs='lowres', model=model, outputs='superres'),
PixelMeanSquaredError(inputs=('superres', 'highres'), outputs="mse_loss")
])
model_dir = os.path.join(path)
estimator = fe.Estimator(network=network,
pipeline=pipeline,
steps_per_epoch=steps_per_epoch,
epochs=epochs,
traces=[
ModelSaver(model_name="srresnet_gen", save_dir=model_dir, save_best=True), ])
return estimator
def get_estimator(batch_size=128, epochs=15, model_dir=tempfile.mkdtemp()):
# prepare data in disk
train_csv, val_csv, path = svhn.load_data()
writer = RecordWriter(
save_dir=os.path.join(path, "FEdata"),
train_data=train_csv,
validation_data=val_csv,
ops=[
ImageReader(inputs="image", parent_path=path, outputs="image"),
String2List(inputs=["label", "x1", "y1", "x2", "y2"],
outputs=["label", "x1", "y1", "x2", "y2"]),
RelativeCoordinate(inputs=("image", "x1", "y1", "x2", "y2"),
outputs=("x1", "y1", "x2", "y2")),
Resize(inputs="image", target_size=(64, 128), outputs="image"),
GenerateTarget(inputs=("label", "x1", "y1", "x2", "y2"),
outputs=("target_cls", "target_loc"))
])
# prepare pipeline
pipeline = Pipeline(batch_size=batch_size,
data=writer,
ops=Minmax(inputs="image", outputs="image"),
read_feature=["image", "target_cls", "target_loc"])
# prepare model
model = FEModel(
model_def=lambda: RetinaNet(input_shape=(64, 128, 3), num_classes=10),
model_name="retinanet",
optimizer=tf.optimizers.Adam(learning_rate=0.0001))
network = Network(ops=[
ModelOp(inputs="image", model=model, outputs=["pred_cls", "pred_loc"]),
PredictBox(outputs=("cls_selected", "loc_selected", "valid_outputs"),
mode="eval"),
RetinaLoss(inputs=("target_cls", "target_loc", "pred_cls", "pred_loc"),
outputs="loss"),
])
# prepare estimator
estimator = Estimator(network=network,
pipeline=pipeline,
epochs=epochs,
log_steps=20,
traces=ModelSaver(model_name="retinanet",
save_dir=model_dir,
save_best=True))
return estimator
def get_estimator(epochs=50, batch_size=32, model_dir=tempfile.mkdtemp()):
(x_train, y_train), (x_eval, y_eval) = tf.keras.datasets.boston_housing.load_data()
# step 1. prepare data
scaler = StandardScaler()
x_train = scaler.fit_transform(x_train)
x_eval = scaler.transform(x_eval)
data = {"train": {"x": x_train, "y": y_train}, "eval": {"x": x_eval, "y": y_eval}}
pipeline = fe.Pipeline(batch_size=batch_size, data=data)
# step 2. prepare model
model = FEModel(model_def=create_dnn, model_name="dnn", optimizer="adam")
network = fe.Network(
ops=[ModelOp(inputs="x", model=model, outputs="y_pred"), MeanSquaredError(y_true="y", y_pred="y_pred")])
# step 3.prepare estimator
traces = [ModelSaver(model_name="dnn", save_dir=model_dir, save_best=True)]
estimator = fe.Estimator(network=network, pipeline=pipeline, epochs=epochs, log_steps=10, traces=traces)
return estimator
def get_estimator(epochs=50,
batch_size=32,
steps_per_epoch=None,
validation_steps=None,
model_dir=tempfile.mkdtemp()):
(X, y) = load_breast_cancer(True)
x_train, x_eval, y_train, y_eval = train_test_split(X, y, test_size=0.2)
# step 1. prepare data
scaler = StandardScaler()
x_train = scaler.fit_transform(x_train)
x_eval = scaler.transform(x_eval)
train_data = {"x": x_train, "y": np.expand_dims(y_train, -1)}
eval_data = {"x": x_eval, "y": np.expand_dims(y_eval, -1)}
data = {"train": train_data, "eval": eval_data}
pipeline = fe.Pipeline(batch_size=batch_size, data=data)
# step 2. prepare model
model = fe.build(model_def=create_dnn,
model_name="dnn",
optimizer="adam",
loss_name="loss")
network = fe.Network(ops=[
ModelOp(inputs="x", model=model, outputs="y_pred"),
MeanSquaredError(inputs=("y", "y_pred"), outputs="loss")
])
# step 3.prepare estimator
traces = [ModelSaver(model_name="dnn", save_dir=model_dir, save_best=True)]
estimator = fe.Estimator(network=network,
pipeline=pipeline,
epochs=epochs,
steps_per_epoch=steps_per_epoch,
validation_steps=validation_steps,
log_steps=10,
traces=traces)
return estimator
def get_estimator(batch_size=4,
epochs=200,
steps_per_epoch=1000,
validation_steps=None,
model_dir=tempfile.mkdtemp(),
imagenet_path=None,
srresnet_model_path=None):
"""Args:
imagenet_path: folder path of ImageNet dataset, containing train and val subdirs .
srresnet_model_path: srresnet model weights, srgan generator gets initialized with the weights.
"""
assert imagenet_path is not None, 'Pass valid folder path of Imagenet dataset'
assert srresnet_model_path is not None, 'srresnet model is needed to initialize srgan generator model'
# Ensure ImageNet dataset is downloaded. Pass the folder contianing train and val subdirectories.
# currently the script doesn't download the ImageNet data.
train_csv, val_csv, path = srgan.load_data(path_imgnet=imagenet_path)
writer = fe.RecordWriter(save_dir=os.path.join(path, "sr_tfrecords"),
train_data=train_csv,
validation_data=val_csv,
ops=[
ImageReader(inputs="lowres",
outputs="lowres"),
ImageReader(inputs="highres",
outputs="highres")
],
compression="GZIP",
write_feature=['lowres', 'highres'])
pipeline = fe.Pipeline(max_shuffle_buffer_mb=3000,
batch_size=batch_size,
data=writer,
ops=[
LowresRescale(inputs='lowres',
outputs='lowres'),
Rescale(inputs='highres', outputs='highres'),
])
# prepare model
model_gen = fe.build(model_def=srresnet_model_path,
model_name="srgan_gen",
optimizer=tf.optimizers.Adam(learning_rate=0.0001),
loss_name="mse_adv_loss",
custom_objects={'SubPixelConv2D': SubPixelConv2D})
model_desc = fe.build(
model_def=lambda: get_discriminator(input_shape=(96, 96, 3)),
model_name="srgan_desc",
optimizer=tf.optimizers.Adam(learning_rate=0.0001),
loss_name="desc_loss")
network = fe.Network(ops=[
ModelOp(inputs='lowres', model=model_gen, outputs='superres'),
ModelOp(inputs='superres', model=model_desc, outputs='pred_fake'),
ModelOp(inputs='highres', model=model_desc, outputs='pred_true'),
DLoss(inputs=("pred_true", "pred_fake"),
outputs=("desc_loss", "real_loss", "fake_loss")),
GLoss(inputs=('superres', 'highres', 'pred_fake'),
outputs=("mse_adv_loss", "mse_loss", "adv_loss"),
vgg_content=True)
])
model_dir = os.path.join(path)
estimator = fe.Estimator(
network=network,
pipeline=pipeline,
steps_per_epoch=steps_per_epoch,
epochs=epochs,
traces=[
ModelSaver(model_name="srgan_gen",
save_dir=model_dir,
save_best=True),
ModelSaver(model_name="srgan_desc",
save_dir=model_dir,
save_best=True),
LRController(model_name="srgan_gen",
lr_schedule=MyLRSchedule(schedule_mode='step')),
LRController(model_name="srgan_desc",
lr_schedule=MyLRSchedule(schedule_mode='step'))
])
return estimator
def get_estimator(batch_size=1,
epochs=500,
steps_per_epoch=128,
model_dir=tempfile.mkdtemp(),
path_brats=os.path.join(os.getenv('HOME'),
'fastestimator_data', 'BraTs')):
"""Args:
path_brats: folder path of BraTs 2018 dataset, containing data subdir inturn having LGG and HGG data.
Expected folder structure path_brats
path_brats/
|----------data/
|----LGG/
|----HGG/
"""
assert path_brats is not None, 'Pass valid folder path of BraTs 2018 dataset'
# Ensure Brats 2018 dataset is downloaded. Pass the folder contianing train and val subdirectories.
# currently the script doesn't download the BraTs data.
train_csv, val_csv, path_brats = brats.load_data(path_brats=path_brats,
resized_img_shape=(128,
128,
128),
bias_correction=False)
writer = fe.RecordWriter(save_dir=os.path.join(path_brats, "tfrecords"),
train_data=train_csv,
validation_data=val_csv,
ops=[
NIBImageReader(inputs="mod_img",
outputs="mod_img"),
NIBImageReader(inputs="seg_mask",
outputs="seg_mask")
],
compression="GZIP",
write_feature=['mod_img', 'seg_mask'])
pipeline = fe.Pipeline(data=writer,
batch_size=batch_size,
ops=[
SplitMaskLabelwise(inputs="seg_mask",
outputs="seg_mask"),
Augmentation3D(inputs=("mod_img", "seg_mask"),
outputs=("mod_img", "seg_mask"),
mode='train')
])
model_unet3d_is = fe.build(
model_def=lambda: UNet3D_Isensee(input_shape=(4, 64, 64, 64)),
model_name="brats_unet3d_is",
optimizer=tf.optimizers.Adam(learning_rate=5e-4),
loss_name="wdice_loss")
network = fe.Network(ops=[
ModelOp(
inputs="mod_img", model=model_unet3d_is, outputs="pred_seg_mask"),
WeightedDiceLoss(inputs=("seg_mask", "pred_seg_mask"),
outputs=("wdice_loss"))
])
model_dir = path_brats
estimator = fe.Estimator(network=network,
pipeline=pipeline,
steps_per_epoch=steps_per_epoch,
epochs=epochs,
traces=[
ModelSaver(model_name="brats_unet3d_is",
save_dir=model_dir,
save_best=True),
LRController(model_name="brats_unet3d_is",
reduce_patience=10,
reduce_factor=0.5,
reduce_on_eval=True,
min_lr=1e-07)
],
log_steps=steps_per_epoch)
return estimator
def get_estimator(data_path=None, model_dir=tempfile.mkdtemp(), batch_size=2):
#prepare dataset
train_csv, val_csv, path = load_data(path=data_path)
writer = fe.RecordWriter(
save_dir=os.path.join(path, "retinanet_coco_1024"),
train_data=train_csv,
validation_data=val_csv,
ops=[
ImageReader(inputs="image", parent_path=path, outputs="image"),
String2List(inputs=["x1", "y1", "width", "height", "obj_label"],
outputs=["x1", "y1", "width", "height", "obj_label"]),
ResizeImageAndBbox(
target_size=(1024, 1024),
keep_ratio=True,
inputs=["image", "x1", "y1", "width", "height"],
outputs=["image", "x1", "y1", "width", "height"]),
FlipImageAndBbox(inputs=[
"image", "x1", "y1", "width", "height", "obj_label", "id"
],
outputs=[
"image", "x1", "y1", "width", "height",
"obj_label", "id"
]),
GenerateTarget(inputs=("obj_label", "x1", "y1", "width", "height"),
outputs=("cls_gt", "x1_gt", "y1_gt", "w_gt",
"h_gt"))
],
expand_dims=True,
compression="GZIP",
write_feature=[
"image", "id", "cls_gt", "x1_gt", "y1_gt", "w_gt", "h_gt",
"obj_label", "x1", "y1", "width", "height"
])
# prepare pipeline
pipeline = fe.Pipeline(batch_size=batch_size,
data=writer,
ops=[
Rescale(inputs="image", outputs="image"),
Pad(padded_shape=[2051],
inputs=[
"x1_gt", "y1_gt", "w_gt", "h_gt",
"obj_label", "x1", "y1", "width",
"height"
],
outputs=[
"x1_gt", "y1_gt", "w_gt", "h_gt",
"obj_label", "x1", "y1", "width",
"height"
])
])
# prepare network
model = fe.build(model_def=lambda: RetinaNet(input_shape=(1024, 1024, 3),
num_classes=90),
model_name="retinanet",
optimizer=tf.optimizers.SGD(momentum=0.9),
loss_name="total_loss")
network = fe.Network(ops=[
ModelOp(inputs="image", model=model, outputs=["cls_pred", "loc_pred"]),
RetinaLoss(inputs=("cls_gt", "x1_gt", "y1_gt", "w_gt", "h_gt",
"cls_pred", "loc_pred"),
outputs=("total_loss", "focal_loss", "l1_loss")),
PredictBox(inputs=[
"cls_pred", "loc_pred", "obj_label", "x1", "y1", "width", "height"
],
outputs=("pred", "gt"),
mode="eval",
input_shape=(1024, 1024, 3))
])
# prepare estimator
estimator = fe.Estimator(
network=network,
pipeline=pipeline,
epochs=7,
traces=[
MeanAvgPrecision(90, (1024, 1024, 3),
'pred',
'gt',
output_name=("mAP", "AP50", "AP75")),
ModelSaver(model_name="retinanet",
save_dir=model_dir,
save_best='mAP',
save_best_mode='max'),
LRController(model_name="retinanet",
lr_schedule=MyLRSchedule(schedule_mode="step"))
])
return estimator
def get_estimator(weight=10.0, epochs=200, model_dir=tempfile.mkdtemp()):
trainA_csv, trainB_csv, _, _, parent_path = load_data()
tfr_save_dir = os.path.join(parent_path, 'FEdata')
# Step 1: Define Pipeline
writer = RecordWriter(train_data=(trainA_csv, trainB_csv),
save_dir=tfr_save_dir,
ops=([
ImageReader(inputs="imgA",
outputs="imgA",
parent_path=parent_path)
], [
ImageReader(inputs="imgB",
outputs="imgB",
parent_path=parent_path)
]))
pipeline = fe.Pipeline(data=writer,
batch_size=1,
ops=[
Myrescale(inputs="imgA", outputs="imgA"),
RandomJitter(inputs="imgA", outputs="real_A"),
Myrescale(inputs="imgB", outputs="imgB"),
RandomJitter(inputs="imgB", outputs="real_B")
])
# Step2: Define Network
g_AtoB = FEModel(model_def=build_generator,
model_name="g_AtoB",
loss_name="g_AtoB_loss",
optimizer=tf.keras.optimizers.Adam(2e-4, 0.5))
g_BtoA = FEModel(model_def=build_generator,
model_name="g_BtoA",
loss_name="g_BtoA_loss",
optimizer=tf.keras.optimizers.Adam(2e-4, 0.5))
d_A = FEModel(model_def=build_discriminator,
model_name="d_A",
loss_name="d_A_loss",
optimizer=tf.keras.optimizers.Adam(2e-4, 0.5))
d_B = FEModel(model_def=build_discriminator,
model_name="d_B",
loss_name="d_B_loss",
optimizer=tf.keras.optimizers.Adam(2e-4, 0.5))
network = fe.Network(ops=[
ModelOp(inputs="real_A", model=g_AtoB, outputs="fake_B"),
ModelOp(inputs="real_B", model=g_BtoA, outputs="fake_A"),
ModelOp(inputs="real_A", model=d_A, outputs="d_real_A"),
ModelOp(inputs="fake_A", model=d_A, outputs="d_fake_A"),
ModelOp(inputs="real_B", model=d_B, outputs="d_real_B"),
ModelOp(inputs="fake_B", model=d_B, outputs="d_fake_B"),
ModelOp(inputs="real_A", model=g_BtoA, outputs="same_A"),
ModelOp(inputs="fake_B", model=g_BtoA, outputs="cycled_A"),
ModelOp(inputs="real_B", model=g_AtoB, outputs="same_B"),
ModelOp(inputs="fake_A", model=g_AtoB, outputs="cycled_B"),
GLoss(inputs=("real_A", "d_fake_B", "cycled_A", "same_A"),
weight=weight,
outputs="g_AtoB_loss"),
GLoss(inputs=("real_B", "d_fake_A", "cycled_B", "same_B"),
weight=weight,
outputs="g_BtoA_loss"),
DLoss(inputs=("d_real_A", "d_fake_A"), outputs="d_A_loss"),
DLoss(inputs=("d_real_B", "d_fake_B"), outputs="d_B_loss")
])
# Step3: Define Estimator
traces = [
ModelSaver(model_name="g_AtoB", save_dir=model_dir, save_freq=10),
ModelSaver(model_name="g_BtoA", save_dir=model_dir, save_freq=10)
]
estimator = fe.Estimator(network=network,
pipeline=pipeline,
epochs=epochs,
traces=traces)
return estimator
def get_estimator(epochs=200, batch_size=128, steps_per_epoch=500, validation_steps=100, model_dir=tempfile.mkdtemp()):
# step 1. prepare pipeline
train_path, eval_path = load_data()
data = {
"train": lambda: get_batch(train_path, batch_size=batch_size),
"eval": lambda: get_batch(eval_path, batch_size=batch_size, is_train=False)
}
pipeline = fe.Pipeline(
data=data,
batch_size=batch_size,
ops=[
Probability(
tensor_op=Augmentation2D(inputs="x_a",
outputs="x_a",
mode="train",
rotation_range=10.0,
shear_range=-0.3 * 180 / np.pi,
zoom_range=[0.8, 1.2],
width_shift_range=0.05,
height_shift_range=0.05),
prob=0.89),
Probability(
tensor_op=Augmentation2D(inputs="x_b",
outputs="x_b",
mode="train",
rotation_range=10.0,
shear_range=-0.3 * 180 / np.pi,
zoom_range=[0.8, 1.2],
width_shift_range=0.05,
height_shift_range=0.05),
prob=0.89),
Minmax(inputs="x_a", outputs="x_a"),
Minmax(inputs="x_b", outputs="x_b")
])
# step 2. prepare model
model = fe.build(model_def=siamese_network,
model_name="siamese_net",
optimizer=Adam(learning_rate=1e-4),
loss_name="loss")
network = fe.Network(ops=[
ModelOp(inputs=["x_a", "x_b"], model=model, outputs="y_pred"),
BinaryCrossentropy(inputs=("y", "y_pred"), outputs="loss")
])
# Defining learning rate schedule
lr_scheduler = LRDecaySchedule(decay_rate=0.99)
# Loading images for validation one-shot accuracy
val_img_list = load_eval_data(path=eval_path, is_test=False)
# step 3.prepare estimator
traces = [
LRController(model_name="siamese_net", lr_schedule=lr_scheduler),
OneShotAccuracy(model=model, img_list=val_img_list, output_name='one_shot_accuracy'),
ModelSaver(model_name="siamese_net", save_dir=model_dir, save_best='one_shot_accuracy', save_best_mode='max'),
EarlyStopping(monitor="one_shot_accuracy", patience=20, compare='max', mode="eval")
]
estimator = fe.Estimator(network=network,
pipeline=pipeline,
epochs=epochs,
traces=traces,
steps_per_epoch=steps_per_epoch,
validation_steps=validation_steps)
return estimator
def get_estimator(epochs=10,
batch_size=32,
epsilon=0.01,
warmup=0,
model_dir=tempfile.mkdtemp()):
(x_train, y_train), (x_eval,
y_eval) = tf.keras.datasets.cifar10.load_data()
data = {
"train": {
"x": x_train,
"y": y_train
},
"eval": {
"x": x_eval,
"y": y_eval
}
}
num_classes = 10
pipeline = Pipeline(batch_size=batch_size,
data=data,
ops=Minmax(inputs="x", outputs="x"))
model = FEModel(model_def=lambda: LeNet(input_shape=x_train.shape[1:],
classes=num_classes),
model_name="LeNet",
optimizer="adam")
adv_img = {
warmup:
AdversarialSample(inputs=("loss", "x"),
outputs="x_adverse",
epsilon=epsilon,
mode="train")
}
adv_eval = {
warmup:
ModelOp(inputs="x_adverse",
model=model,
outputs="y_pred_adverse",
mode="train")
}
adv_loss = {
warmup:
SparseCategoricalCrossentropy(y_true="y",
y_pred="y_pred_adverse",
outputs="adverse_loss",
mode="train")
}
adv_avg = {
warmup:
Average(inputs=("loss", "adverse_loss"), outputs="loss", mode="train")
}
network = Network(ops=[
ModelOp(inputs="x", model=model, outputs="y_pred", track_input=True),
SparseCategoricalCrossentropy(
y_true="y", y_pred="y_pred", outputs="loss"),
Scheduler(adv_img),
Scheduler(adv_eval),
Scheduler(adv_loss),
Scheduler(adv_avg)
])
traces = [
Accuracy(true_key="y", pred_key="y_pred"),
ConfusionMatrix(true_key="y",
pred_key="y_pred",
num_classes=num_classes),
ModelSaver(model_name="LeNet", save_dir=model_dir, save_freq=2)
]
estimator = Estimator(network=network,
pipeline=pipeline,
epochs=epochs,
traces=traces)
return estimator