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Commit 3234508f authored by lucas_miranda's avatar lucas_miranda
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Reformatted files using last version of Black; fixed seaborn update issues

parent 9db84390
Pipeline #88235 passed with stage
in 24 minutes and 22 seconds
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deepof/data.py
View file @ 3234508f
......@@ -138,7 +138,7 @@ class project:
@property
def angles(self):
"""Bool. Toggles angle computation. True by default. If turned off,
enhances performance for big datasets"""
enhances performance for big datasets"""
return self._angles
@property
......@@ -274,7 +274,7 @@ class project:
def get_distances(self, tab_dict: dict, verbose: bool = False) -> dict:
"""Computes the distances between all selected body parts over time.
If ego is provided, it only returns distances to a specified bodypart"""
If ego is provided, it only returns distances to a specified bodypart"""
if verbose:
print("Computing distances...")
......@@ -290,7 +290,11 @@ class project:
scales = self.scales[:, 2:]
distance_dict = {
key: deepof.utils.bpart_distance(tab, scales[i, 1], scales[i, 0],)
key: deepof.utils.bpart_distance(
tab,
scales[i, 1],
scales[i, 0],
)
for i, (key, tab) in enumerate(tab_dict.items())
}
......@@ -782,7 +786,7 @@ class table_dict(dict):
def filter_videos(self, keys: list) -> Table_dict:
"""Returns a subset of the original table_dict object, containing only the specified keys. Useful, for example,
for selecting data coming from videos of a specified condition."""
for selecting data coming from videos of a specified condition."""
assert np.all([k in self.keys() for k in keys]), "Invalid keys selected"
......@@ -825,7 +829,9 @@ class table_dict(dict):
return heatmaps
def get_training_set(
self, test_videos: int = 0, encode_labels: bool = True,
self,
test_videos: int = 0,
encode_labels: bool = True,
) -> Tuple[np.ndarray, list, Union[np.ndarray, list], list]:
"""Generates training and test sets as numpy.array objects for model training"""
......
deepof/hypermodels.py
View file @ 3234508f
......@@ -30,18 +30,40 @@ class SEQ_2_SEQ_AE(HyperModel):
"""Retrieve hyperparameters to tune"""
conv_filters = hp.Int(
"units_conv", min_value=32, max_value=256, step=32, default=256,
"units_conv",
min_value=32,
max_value=256,
step=32,
default=256,
)
lstm_units_1 = hp.Int(
"units_lstm", min_value=128, max_value=512, step=32, default=256,
"units_lstm",
min_value=128,
max_value=512,
step=32,
default=256,
)
dense_2 = hp.Int(
"units_dense2", min_value=32, max_value=256, step=32, default=64,
"units_dense2",
min_value=32,
max_value=256,
step=32,
default=64,
)
dropout_rate = hp.Float(
"dropout_rate", min_value=0.0, max_value=0.5, default=0.25, step=0.05,
"dropout_rate",
min_value=0.0,
max_value=0.5,
default=0.25,
step=0.05,
)
encoding = hp.Int(
"encoding",
min_value=16,
max_value=64,
step=8,
default=24,
)
encoding = hp.Int("encoding", min_value=16, max_value=64, step=8, default=24,)
return conv_filters, lstm_units_1, dense_2, dropout_rate, encoding
......
deepof/model_utils.py
View file @ 3234508f
......@@ -141,16 +141,16 @@ def compute_kernel(x: tf.Tensor, y: tf.Tensor) -> tf.Tensor:
def compute_mmd(tensors: Tuple[Any, Any]) -> tf.Tensor:
"""
Computes the MMD between the two specified vectors using a gaussian kernel.
Computes the MMD between the two specified vectors using a gaussian kernel.
Parameters:
- tensors (tuple): tuple containing two tf.Tensor objects
Parameters:
- tensors (tuple): tuple containing two tf.Tensor objects
Returns
- mmd (tf.Tensor): returns the maximum mean discrepancy for each
training instance
Returns
- mmd (tf.Tensor): returns the maximum mean discrepancy for each
training instance
"""
"""
x = tensors[0]
y = tensors[1]
......@@ -339,8 +339,8 @@ class DenseTranspose(Layer):
class KLDivergenceLayer(tfpl.KLDivergenceAddLoss):
"""
Identity transform layer that adds KL Divergence
to the final model loss.
Identity transform layer that adds KL Divergence
to the final model loss.
"""
def __init__(self, *args, **kwargs):
......@@ -360,7 +360,9 @@ class KLDivergenceLayer(tfpl.KLDivergenceAddLoss):
kl_batch = self._regularizer(distribution_a)
self.add_loss(kl_batch, inputs=[distribution_a])
self.add_metric(
kl_batch, aggregation="mean", name="kl_divergence",
kl_batch,
aggregation="mean",
name="kl_divergence",
)
# noinspection PyProtectedMember
self.add_metric(self._regularizer._weight, aggregation="mean", name="kl_rate")
......
deepof/models.py
View file @ 3234508f
......@@ -33,7 +33,9 @@ class SEQ_2_SEQ_AE:
""" Simple sequence to sequence autoencoder implemented with tf.keras """
def __init__(
self, architecture_hparams: Dict = {}, huber_delta: float = 1.0,
self,
architecture_hparams: Dict = {},
huber_delta: float = 1.0,
):
self.hparams = self.get_hparams(architecture_hparams)
self.CONV_filters = self.hparams["units_conv"]
......@@ -118,13 +120,19 @@ class SEQ_2_SEQ_AE:
# Decoder layers
Model_D0 = deepof.model_utils.DenseTranspose(
Model_E5, activation="elu", output_dim=self.ENCODING,
Model_E5,
activation="elu",
output_dim=self.ENCODING,
)
Model_D1 = deepof.model_utils.DenseTranspose(
Model_E4, activation="elu", output_dim=self.DENSE_2,
Model_E4,
activation="elu",
output_dim=self.DENSE_2,
)
Model_D2 = deepof.model_utils.DenseTranspose(
Model_E3, activation="elu", output_dim=self.DENSE_1,
Model_E3,
activation="elu",
output_dim=self.DENSE_1,
)
Model_D3 = RepeatVector(input_shape[1])
Model_D4 = Bidirectional(
......@@ -161,7 +169,10 @@ class SEQ_2_SEQ_AE:
Model_D5,
)
def build(self, input_shape: tuple,) -> Tuple[Any, Any, Any]:
def build(
self,
input_shape: tuple,
) -> Tuple[Any, Any, Any]:
"""Builds the tf.keras model"""
(
......@@ -213,7 +224,10 @@ class SEQ_2_SEQ_AE:
model.compile(
loss=Huber(delta=self.delta),
optimizer=Nadam(lr=self.learn_rate, clipvalue=0.5,),
optimizer=Nadam(
lr=self.learn_rate,
clipvalue=0.5,
),
metrics=["mae"],
)
......@@ -298,7 +312,10 @@ class SEQ_2_SEQ_GMVAE:
),
components=[
tfd.Independent(
tfd.Normal(loc=init_means[k], scale=1,),
tfd.Normal(
loc=init_means[k],
scale=1,
),
reinterpreted_batch_ndims=1,
)
for k in range(self.number_of_components)
......@@ -537,7 +554,10 @@ class SEQ_2_SEQ_GMVAE:
encoder = BatchNormalization()(encoder)
# encoding_shuffle = deepof.model_utils.MCDropout(self.DROPOUT_RATE)(encoder)
z_cat = Dense(self.number_of_components, activation="softmax",)(encoder)
z_cat = Dense(
self.number_of_components,
activation="softmax",
)(encoder)
z_cat = deepof.model_utils.Entropy_regulariser(self.entropy_reg_weight)(z_cat)
z_gauss = Dense(
deepof.model_utils.tfpl.IndependentNormal.params_size(
......@@ -553,12 +573,16 @@ class SEQ_2_SEQ_GMVAE:
if self.overlap_loss:
z_gauss = deepof.model_utils.Gaussian_mixture_overlap(
self.ENCODING, self.number_of_components, loss=self.overlap_loss,
self.ENCODING,
self.number_of_components,
loss=self.overlap_loss,
)(z_gauss)
z = deepof.model_utils.tfpl.DistributionLambda(
lambda gauss: tfd.mixture.Mixture(
cat=tfd.categorical.Categorical(probs=gauss[0],),
cat=tfd.categorical.Categorical(
probs=gauss[0],
),
components=[
tfd.Independent(
tfd.Normal(
......@@ -663,7 +687,11 @@ class SEQ_2_SEQ_GMVAE:
grouper = Model(x, z_cat, name="Deep_Gaussian_Mixture_clustering")
# noinspection PyUnboundLocalVariable
gmvaep = Model(inputs=x, outputs=model_outs, name="SEQ_2_SEQ_GMVAE",)
gmvaep = Model(
inputs=x,
outputs=model_outs,
name="SEQ_2_SEQ_GMVAE",
)
# Build generator as a separate entity
g = Input(shape=self.ENCODING)
......@@ -682,7 +710,10 @@ class SEQ_2_SEQ_GMVAE:
if self.compile:
gmvaep.compile(
loss=model_losses,
optimizer=Nadam(lr=self.learn_rate, clipvalue=self.clipvalue,),
optimizer=Nadam(
lr=self.learn_rate,
clipvalue=self.clipvalue,
),
metrics=model_metrics,
loss_weights=loss_weights,
)
......
deepof/pose_utils.py
View file @ 3234508f
......@@ -33,18 +33,18 @@ def close_single_contact(
) -> np.array:
"""Returns a boolean array that's True if the specified body parts are closer than tol.
Parameters:
- pos_dframe (pandas.DataFrame): DLC output as pandas.DataFrame; only applicable
to two-animal experiments.
- left (string): First member of the potential contact
- right (string): Second member of the potential contact
- tol (float): maximum distance for which a contact is reported
- arena_abs (int): length in mm of the diameter of the real arena
- arena_rel (int): length in pixels of the diameter of the arena in the video
Parameters:
- pos_dframe (pandas.DataFrame): DLC output as pandas.DataFrame; only applicable
to two-animal experiments.
- left (string): First member of the potential contact
- right (string): Second member of the potential contact
- tol (float): maximum distance for which a contact is reported
- arena_abs (int): length in mm of the diameter of the real arena
- arena_rel (int): length in pixels of the diameter of the arena in the video
Returns:
- contact_array (np.array): True if the distance between the two specified points
is less than tol, False otherwise"""
Returns:
- contact_array (np.array): True if the distance between the two specified points
is less than tol, False otherwise"""
close_contact = (
np.linalg.norm(pos_dframe[left] - pos_dframe[right], axis=1) * arena_abs
......@@ -66,21 +66,21 @@ def close_double_contact(
) -> np.array:
"""Returns a boolean array that's True if the specified body parts are closer than tol.
Parameters:
- pos_dframe (pandas.DataFrame): DLC output as pandas.DataFrame; only applicable
to two-animal experiments.
- left1 (string): First contact point of animal 1
- left2 (string): Second contact point of animal 1
- right1 (string): First contact point of animal 2
- right2 (string): Second contact point of animal 2
- tol (float): maximum distance for which a contact is reported
- arena_abs (int): length in mm of the diameter of the real arena
- arena_rel (int): length in pixels of the diameter of the arena in the video
- rev (bool): reverses the default behaviour (nose2tail contact for both mice)
Parameters:
- pos_dframe (pandas.DataFrame): DLC output as pandas.DataFrame; only applicable
to two-animal experiments.
- left1 (string): First contact point of animal 1
- left2 (string): Second contact point of animal 1
- right1 (string): First contact point of animal 2
- right2 (string): Second contact point of animal 2
- tol (float): maximum distance for which a contact is reported
- arena_abs (int): length in mm of the diameter of the real arena
- arena_rel (int): length in pixels of the diameter of the arena in the video
- rev (bool): reverses the default behaviour (nose2tail contact for both mice)
Returns:
- double_contact (np.array): True if the distance between the two specified points
is less than tol, False otherwise"""
Returns:
- double_contact (np.array): True if the distance between the two specified points
is less than tol, False otherwise"""
if rev:
double_contact = (
......@@ -117,19 +117,19 @@ def climb_wall(
) -> np.array:
"""Returns True if the specified mouse is climbing the wall
Parameters:
- arena_type (str): arena type; must be one of ['circular']
- arena (np.array): contains arena location and shape details
- pos_dict (table_dict): position over time for all videos in a project
- tol (float): minimum tolerance to report a hit
- nose (str): indicates the name of the body part representing the nose of
the selected animal
- arena_dims (int): indicates radius of the real arena in mm
- centered_data (bool): indicates whether the input data is centered
Parameters:
- arena_type (str): arena type; must be one of ['circular']
- arena (np.array): contains arena location and shape details
- pos_dict (table_dict): position over time for all videos in a project
- tol (float): minimum tolerance to report a hit
- nose (str): indicates the name of the body part representing the nose of
the selected animal
- arena_dims (int): indicates radius of the real arena in mm
- centered_data (bool): indicates whether the input data is centered
Returns:
- climbing (np.array): boolean array. True if selected animal
is climbing the walls of the arena"""
Returns:
- climbing (np.array): boolean array. True if selected animal
is climbing the walls of the arena"""
nose = pos_dict[nose]
......@@ -166,7 +166,7 @@ def huddle(
Returns:
hudd (np.array): True if the animal is huddling, False otherwise
"""
"""
if animal_id != "":
animal_id += "_"
......@@ -254,7 +254,8 @@ def following_path(
)
follow = np.all(
np.array([(dist_df.min(axis=1) < tol), right_orient1, right_orient2]), axis=0,
np.array([(dist_df.min(axis=1) < tol), right_orient1, right_orient2]),
axis=0,
)
return follow
......@@ -270,28 +271,27 @@ def single_behaviour_analysis(
ylim: float = None,
) -> list:
"""Given the name of the behaviour, a dictionary with the names of the groups to compare, and a dictionary
with the actual tags, outputs a box plot and a series of significance tests amongst the groups
with the actual tags, outputs a box plot and a series of significance tests amongst the groups
Parameters:
- behaviour_name (str): name of the behavioural trait to analize
- treatment_dict (dict): dictionary containing video names as keys and experimental conditions as values
- behavioural_dict (dict): tagged dictionary containing video names as keys and annotations as values
- plot (int): Silent if 0; otherwise, indicates the dpi of the figure to plot
- stat_tests (bool): performs FDR corrected Mann-U non-parametric tests among all groups if True
- save (str): Saves the produced figure to the specified file
- ylim (float): y-limit for the boxplot. Ignored if plot == False
Parameters:
- behaviour_name (str): name of the behavioural trait to analize
- treatment_dict (dict): dictionary containing video names as keys and experimental conditions as values
- behavioural_dict (dict): tagged dictionary containing video names as keys and annotations as values
- plot (int): Silent if 0; otherwise, indicates the dpi of the figure to plot
- stat_tests (bool): performs FDR corrected Mann-U non-parametric tests among all groups if True
- save (str): Saves the produced figure to the specified file
- ylim (float): y-limit for the boxplot. Ignored if plot == False
Returns:
- beh_dict (dict): dictionary containing experimental conditions as keys and video names as values
- stat_dict (dict): dictionary containing condition pairs as keys and stat results as values"""
Returns:
- beh_dict (dict): dictionary containing experimental conditions as keys and video names as values
- stat_dict (dict): dictionary containing condition pairs as keys and stat results as values"""
beh_dict = {condition: [] for condition in treatment_dict.keys()}
for condition in beh_dict.keys():
for ind in treatment_dict[condition]:
beh_dict[condition].append(
np.sum(behavioural_dict[ind][behaviour_name])
/ len(behavioural_dict[ind][behaviour_name])
beh_dict[condition] += np.sum(behavioural_dict[ind][behaviour_name]) / len(
behavioural_dict[ind][behaviour_name]
)
return_list = [beh_dict]
......@@ -301,7 +301,10 @@ def single_behaviour_analysis(
fig, ax = plt.subplots(dpi=plot)
sns.boxplot(
list(beh_dict.keys()), list(beh_dict.values()), orient="vertical", ax=ax
x=list(beh_dict.keys()),
y=list(beh_dict.values()),
orient="vertical",
ax=ax,
)
ax.set_title("{} across groups".format(behaviour_name))
......@@ -343,16 +346,16 @@ def max_behaviour(
) -> np.array:
"""Returns the most frequent behaviour in a window of window_size frames
Parameters:
- behaviour_dframe (pd.DataFrame): boolean matrix containing occurrence
of tagged behaviours per frame in the video
- window_size (int): size of the window to use when computing
the maximum behaviour per time slot
- stepped (bool): sliding windows don't overlap if True. False by default
Parameters:
- behaviour_dframe (pd.DataFrame): boolean matrix containing occurrence
of tagged behaviours per frame in the video
- window_size (int): size of the window to use when computing
the maximum behaviour per time slot
- stepped (bool): sliding windows don't overlap if True. False by default
Returns:
- max_array (np.array): string array with the most common behaviour per instance
of the sliding window"""
Returns:
- max_array (np.array): string array with the most common behaviour per instance
of the sliding window"""
speeds = [col for col in behaviour_dframe.columns if "speed" in col.lower()]
......@@ -369,12 +372,12 @@ def max_behaviour(
def get_hparameters(hparams: dict = {}) -> dict:
"""Returns the most frequent behaviour in a window of window_size frames
Parameters:
- hparams (dict): dictionary containing hyperparameters to overwrite
Parameters:
- hparams (dict): dictionary containing hyperparameters to overwrite
Returns:
- defaults (dict): dictionary with overwriten parameters. Those not
specified in the input retain their default values"""
Returns:
- defaults (dict): dictionary with overwriten parameters. Those not
specified in the input retain their default values"""
defaults = {
"speed_pause": 3,
......@@ -398,14 +401,14 @@ def get_hparameters(hparams: dict = {}) -> dict:
def frame_corners(w, h, corners: dict = {}):
"""Returns a dictionary with the corner positions of the video frame
Parameters:
- w (int): width of the frame in pixels
- h (int): height of the frame in pixels
- corners (dict): dictionary containing corners to overwrite
Parameters:
- w (int): width of the frame in pixels
- h (int): height of the frame in pixels
- corners (dict): dictionary containing corners to overwrite
Returns:
- defaults (dict): dictionary with overwriten parameters. Those not
specified in the input retain their default values"""
Returns:
- defaults (dict): dictionary with overwriten parameters. Those not
specified in the input retain their default values"""
defaults = {
"downleft": (int(w * 0.3 / 10), int(h / 1.05)),
......@@ -614,11 +617,13 @@ def tag_rulebased_frames(
write_on_frame("Nose-Tail", corners["downright"])
if tag_dict["sidebyside"][fnum]:
write_on_frame(
"Side-side", conditional_pos(),
"Side-side",
conditional_pos(),
)
if tag_dict["sidereside"][fnum]:
write_on_frame(
"Side-Rside", conditional_pos(),
"Side-Rside",
conditional_pos(),
)
for _id, down_pos, up_pos in zipped_pos:
if (
......@@ -626,7 +631,9 @@ def tag_rulebased_frames(
and not tag_dict[_id + "_climbing"][fnum]
):
write_on_frame(
"*f", (int(w * 0.3 / 10), int(h / 10)), conditional_col(),
"*f",
(int(w * 0.3 / 10), int(h / 10)),
conditional_col(),
)
for _id, down_pos, up_pos in zipped_pos:
......
deepof/train_model.py
View file @ 3234508f
......@@ -310,7 +310,12 @@ if not tune:
tf.keras.backend.clear_session()
run_ID, tensorboard_callback, onecycle, cp_callback = get_callbacks(
X_train, batch_size, True, variational, predictor, loss,
X_train,
batch_size,
True,
variational,
predictor,
loss,
)
if not variational:
......@@ -393,7 +398,10 @@ if not tune:
epochs=250,
batch_size=batch_size,
verbose=1,
validation_data=(Xvals, yvals,),
validation_data=(
Xvals,
yvals,
),
callbacks=callbacks_,
)
......
deepof/train_utils.py
View file @ 3234508f
......@@ -69,10 +69,10 @@ def get_callbacks(
loss: str,
) -> List[Union[Any]]:
"""Generates callbacks for model training, including:
- run_ID: run name, with coarse parameter details;
- tensorboard_callback: for real-time visualization;
- cp_callback: for checkpoint saving,
- onecycle: for learning rate scheduling"""
- run_ID: run name, with coarse parameter details;
- tensorboard_callback: for real-time visualization;
- cp_callback: for checkpoint saving,
- onecycle: for learning rate scheduling"""
run_ID = "{}{}{}_{}".format(
("GMVAE" if variational else "AE"),
......@@ -83,11 +83,14 @@ def get_callbacks(
log_dir = os.path.abspath("logs/fit/{}".format(run_ID))
tensorboard_callback = tf.keras.callbacks.TensorBoard(
log_dir=log_dir, histogram_freq=1, profile_batch=2,
log_dir=log_dir,
histogram_freq=1,
profile_batch=2,
)
onecycle = deepof.model_utils.one_cycle_scheduler(
X_train.shape[0] // batch_size * 250, max_rate=0.005,
X_train.shape[0] // batch_size * 250,
max_rate=0.005,
)
callbacks = [run_ID, tensorboard_callback, onecycle]
......@@ -124,30 +127,30 @@ def tune_search(
) -> Union[bool, Tuple[Any, Any]]:
"""Define the search space using keras-tuner and bayesian optimization
Parameters:
- train (np.array): dataset to train the model on
- test (np.array): dataset to validate the model on
- hypertun_trials (int): number of Bayesian optimization iterations to run
- hpt_type (str): specify one of Bayesian Optimization (bayopt) and Hyperband (hyperband)
- hypermodel (str): hypermodel to load. Must be one of S2SAE (plain autoencoder)
or S2SGMVAE (Gaussian Mixture Variational autoencoder).
- k (int) number of components of the Gaussian Mixture
- loss (str): one of [ELBO, MMD, ELBO+MMD]
- overlap_loss (float): assigns as weight to an extra loss term which
penalizes overlap between GM components
- pheno_class (float): adds an extra regularizing neural network to the model,
which tries to predict the phenotype of the animal from which the sequence comes
- predictor (float): adds an extra regularizing neural network to the model,
which tries to predict the next frame from the current one
- project_name (str): ID of the current run
- callbacks (list): list of callbacks for the training loop
- n_epochs (int): optional. Number of epochs to train each run for
- n_replicas (int): optional. Number of replicas per parameter set. Higher values
will yield more robust results, but will affect performance severely
Returns:
- best_hparams (dict): dictionary with the best retrieved hyperparameters
- best_run (tf.keras.Model): trained instance of the best model found
Parameters:
- train (np.array): dataset to train the model on
- test (np.array): dataset to validate the model on
- hypertun_trials (int): number of Bayesian optimization iterations to run
- hpt_type (str): specify one of Bayesian Optimization (bayopt) and Hyperband (hyperband)
- hypermodel (str): hypermodel to load. Must be one of S2SAE (plain autoencoder)
or S2SGMVAE (Gaussian Mixture Variational autoencoder).
- k (int) number of components of the Gaussian Mixture
- loss (str): one of [ELBO, MMD, ELBO+MMD]
- overlap_loss (float): assigns as weight to an extra loss term which
penalizes overlap between GM components
- pheno_class (float): adds an extra regularizing neural network to the model,
which tries to predict the phenotype of the animal from which the sequence comes
- predictor (float): adds an extra regularizing neural network to the model,
which tries to predict the next frame from the current one
- project_name (str): ID of the current run