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Commit 707ab97e authored by lucas_miranda's avatar lucas_miranda
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Ran PyCharm code cleaner 


Former-commit-id: bb286fec
parent 4c71282e
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deepof/data.py
View file @ 707ab97e
......@@ -14,29 +14,30 @@ Contains methods for generating training and test sets ready for model training.
"""
import os
import warnings
from collections import defaultdict
from joblib import delayed, Parallel, parallel_backend
from typing import Dict, List, Tuple, Union
from multiprocessing import cpu_count
from typing import Dict, List, Tuple, Union
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import tensorflow as tf
from joblib import delayed, Parallel, parallel_backend
from pkg_resources import resource_filename
from sklearn import random_projection
from sklearn.decomposition import KernelPCA
from sklearn.experimental import enable_iterative_imputer
from sklearn.impute import IterativeImputer
from sklearn.manifold import TSNE
from sklearn.preprocessing import MinMaxScaler, StandardScaler, LabelEncoder
from tqdm import tqdm
import deepof.models
import deepof.pose_utils
import deepof.train_utils
import deepof.utils
import deepof.visuals
import deepof.train_utils
import matplotlib.pyplot as plt
import numpy as np
import os
import pandas as pd
import tensorflow as tf
import warnings
# Remove excessive logging from tensorflow
os.environ["TF_CPP_MIN_LOG_LEVEL"] = "2"
......@@ -58,23 +59,23 @@ class project:
"""
def __init__(
self,
animal_ids: List = tuple([""]),
arena: str = "circular",
arena_detection: str = "cnn",
arena_dims: tuple = (1,),
enable_iterative_imputation: bool = None,
exclude_bodyparts: List = tuple([""]),
exp_conditions: dict = None,
interpolate_outliers: bool = True,
interpolation_limit: int = 5,
interpolation_std: int = 5,
likelihood_tol: float = 0.25,
model: str = "mouse_topview",
path: str = deepof.utils.os.path.join("."),
smooth_alpha: float = 0.99,
table_format: str = "autodetect",
video_format: str = ".mp4",
self,
animal_ids: List = tuple([""]),
arena: str = "circular",
arena_detection: str = "cnn",
arena_dims: tuple = (1,),
enable_iterative_imputation: bool = None,
exclude_bodyparts: List = tuple([""]),
exp_conditions: dict = None,
interpolate_outliers: bool = True,
interpolation_limit: int = 5,
interpolation_std: int = 5,
likelihood_tol: float = 0.25,
model: str = "mouse_topview",
path: str = deepof.utils.os.path.join("."),
smooth_alpha: float = 0.99,
table_format: str = "autodetect",
video_format: str = ".mp4",
):
# Set working paths
......@@ -115,7 +116,6 @@ class project:
self.arena_dims = arena_dims
self.ellipse_detection = None
if arena == "circular" and arena_detection == "cnn":
self.ellipse_detection = tf.keras.models.load_model(
[
os.path.join(self.trained_path, i)
......@@ -286,8 +286,8 @@ class project:
).T.index.remove_unused_levels()
tab = value.loc[
:, [i for i in value.columns.levels[0] if i not in lablist]
]
:, [i for i in value.columns.levels[0] if i not in lablist]
]
tab.columns = tabcols
......@@ -361,14 +361,14 @@ class project:
for key in distance_dict.keys():
distance_dict[key] = distance_dict[key].loc[
:, [np.all([i in nodes for i in j]) for j in distance_dict[key].columns]
]
:, [np.all([i in nodes for i in j]) for j in distance_dict[key].columns]
]
if self.ego:
for key, val in distance_dict.items():
distance_dict[key] = val.loc[
:, [dist for dist in val.columns if self.ego in dist]
]
:, [dist for dist in val.columns if self.ego in dist]
]
return distance_dict
......@@ -471,20 +471,20 @@ class coordinates:
"""
def __init__(
self,
arena: str,
arena_detection: str,
arena_dims: np.array,
path: str,
quality: dict,
scales: np.array,
tables: dict,
videos: list,
angles: dict = None,
animal_ids: List = tuple([""]),
distances: dict = None,
exp_conditions: dict = None,
ellipse_detection: tf.keras.models.Model = None,
self,
arena: str,
arena_detection: str,
arena_dims: np.array,
path: str,
quality: dict,
scales: np.array,
tables: dict,
videos: list,
angles: dict = None,
animal_ids: List = tuple([""]),
distances: dict = None,
exp_conditions: dict = None,
ellipse_detection: tf.keras.models.Model = None,
):
self._animal_ids = animal_ids
self._arena = arena
......@@ -509,15 +509,15 @@ class coordinates:
return "deepof analysis of {} videos".format(len(self._videos))
def get_coords(
self,
center: str = "arena",
polar: bool = False,
speed: int = 0,
length: str = None,
align: bool = False,
align_inplace: bool = False,
propagate_labels: bool = False,
propagate_annotations: Dict = False,
self,
center: str = "arena",
polar: bool = False,
speed: int = 0,
length: str = None,
align: bool = False,
align_inplace: bool = False,
propagate_labels: bool = False,
propagate_annotations: Dict = False,
) -> Table_dict:
"""
Returns a table_dict object with the coordinates of each animal as values.
......@@ -557,23 +557,23 @@ class coordinates:
try:
value.loc[:, (slice("coords"), ["x"])] = (
value.loc[:, (slice("coords"), ["x"])]
- self._scales[i][0] / 2
value.loc[:, (slice("coords"), ["x"])]
- self._scales[i][0] / 2
)
value.loc[:, (slice("coords"), ["y"])] = (
value.loc[:, (slice("coords"), ["y"])]
- self._scales[i][1] / 2
value.loc[:, (slice("coords"), ["y"])]
- self._scales[i][1] / 2
)
except KeyError:
value.loc[:, (slice("coords"), ["rho"])] = (
value.loc[:, (slice("coords"), ["rho"])]
- self._scales[i][0] / 2
value.loc[:, (slice("coords"), ["rho"])]
- self._scales[i][0] / 2
)
value.loc[:, (slice("coords"), ["phi"])] = (
value.loc[:, (slice("coords"), ["phi"])]
- self._scales[i][1] / 2
value.loc[:, (slice("coords"), ["phi"])]
- self._scales[i][1] / 2
)
elif isinstance(center, str) and center != "arena":
......@@ -582,24 +582,24 @@ class coordinates:
try:
value.loc[:, (slice("coords"), ["x"])] = value.loc[
:, (slice("coords"), ["x"])
].subtract(value[center]["x"], axis=0)
:, (slice("coords"), ["x"])
].subtract(value[center]["x"], axis=0)
value.loc[:, (slice("coords"), ["y"])] = value.loc[
:, (slice("coords"), ["y"])
].subtract(value[center]["y"], axis=0)
:, (slice("coords"), ["y"])
].subtract(value[center]["y"], axis=0)
except KeyError:
value.loc[:, (slice("coords"), ["rho"])] = value.loc[
:, (slice("coords"), ["rho"])
].subtract(value[center]["rho"], axis=0)
:, (slice("coords"), ["rho"])
].subtract(value[center]["rho"], axis=0)
value.loc[:, (slice("coords"), ["phi"])] = value.loc[
:, (slice("coords"), ["phi"])
].subtract(value[center]["phi"], axis=0)
:, (slice("coords"), ["phi"])
].subtract(value[center]["phi"], axis=0)
tabs[key] = value.loc[
:, [tab for tab in value.columns if tab[0] != center]
]
:, [tab for tab in value.columns if tab[0] != center]
]
if speed:
for key, tab in tabs.items():
......@@ -614,16 +614,16 @@ class coordinates:
if align:
assert (
align in list(tabs.values())[0].columns.levels[0]
align in list(tabs.values())[0].columns.levels[0]
), "align must be set to the name of a bodypart"
for key, tab in tabs.items():
# Bring forward the column to align
columns = [i for i in tab.columns if align not in i]
columns = [
(align, ("phi" if polar else "x")),
(align, ("rho" if polar else "y")),
] + columns
(align, ("phi" if polar else "x")),
(align, ("rho" if polar else "y")),
] + columns
tab = tab[columns]
tabs[key] = tab
......@@ -658,11 +658,11 @@ class coordinates:
)
def get_distances(
self,
speed: int = 0,
length: str = None,
propagate_labels: bool = False,
propagate_annotations: Dict = False,
self,
speed: int = 0,
length: str = None,
propagate_labels: bool = False,
propagate_annotations: Dict = False,
) -> Table_dict:
"""
Returns a table_dict object with the distances between body parts animal as values.
......@@ -719,12 +719,12 @@ class coordinates:
) # pragma: no cover
def get_angles(
self,
degrees: bool = False,
speed: int = 0,
length: str = None,
propagate_labels: bool = False,
propagate_annotations: Dict = False,
self,
degrees: bool = False,
speed: int = 0,
length: str = None,
propagate_labels: bool = False,
propagate_annotations: Dict = False,
) -> Table_dict:
"""
Returns a table_dict object with the angles between body parts animal as values.
......@@ -810,11 +810,11 @@ class coordinates:
# noinspection PyDefaultArgument
def rule_based_annotation(
self,
params: Dict = {},
video_output: bool = False,
frame_limit: int = np.inf,
debug: bool = False,
self,
params: Dict = {},
video_output: bool = False,
frame_limit: int = np.inf,
debug: bool = False,
) -> Table_dict:
"""Annotates coordinates using a simple rule-based pipeline"""
......@@ -882,29 +882,29 @@ class coordinates:
@staticmethod
def deep_unsupervised_embedding(
preprocessed_object: Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray],
batch_size: int = 256,
encoding_size: int = 4,
epochs: int = 35,
hparams: dict = None,
kl_warmup: int = 0,
log_history: bool = True,
log_hparams: bool = False,
loss: str = "ELBO",
mmd_warmup: int = 0,
montecarlo_kl: int = 10,
n_components: int = 25,
output_path: str = ".",
phenotype_class: float = 0,
predictor: float = 0,
pretrained: str = False,
save_checkpoints: bool = False,
save_weights: bool = True,
variational: bool = True,
reg_cat_clusters: bool = False,
reg_cluster_variance: bool = False,
entropy_samples: int = 10000,
entropy_knn: int = 100,
preprocessed_object: Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray],
batch_size: int = 256,
encoding_size: int = 4,
epochs: int = 35,
hparams: dict = None,
kl_warmup: int = 0,
log_history: bool = True,
log_hparams: bool = False,
loss: str = "ELBO",
mmd_warmup: int = 0,
montecarlo_kl: int = 10,
n_components: int = 25,
output_path: str = ".",
phenotype_class: float = 0,
predictor: float = 0,
pretrained: str = False,
save_checkpoints: bool = False,
save_weights: bool = True,
variational: bool = True,
reg_cat_clusters: bool = False,
reg_cluster_variance: bool = False,
entropy_samples: int = 10000,
entropy_knn: int = 100,
) -> Tuple:
"""
Annotates coordinates using an unsupervised autoencoder.
......@@ -982,15 +982,15 @@ class table_dict(dict):
"""
def __init__(
self,
tabs: Dict,
typ: str,
arena: str = None,
arena_dims: np.array = None,
center: str = None,
polar: bool = None,
propagate_labels: bool = False,
propagate_annotations: Dict = False,
self,
tabs: Dict,
typ: str,
arena: str = None,
arena_dims: np.array = None,
center: str = None,
polar: bool = None,
propagate_labels: bool = False,
propagate_annotations: Dict = False,
):
super().__init__(tabs)
self._type = typ
......@@ -1013,13 +1013,13 @@ class table_dict(dict):
# noinspection PyTypeChecker
def plot_heatmaps(
self,
bodyparts: list,
xlim: float = None,
ylim: float = None,
save: bool = False,
i: int = 0,
dpi: int = 100,
self,
bodyparts: list,
xlim: float = None,
ylim: float = None,
save: bool = False,
i: int = 0,
dpi: int = 100,
) -> plt.figure:
"""Plots heatmaps of the specified body parts (bodyparts) of the specified animal (i)"""
......@@ -1045,9 +1045,9 @@ 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"""
......@@ -1106,17 +1106,17 @@ class table_dict(dict):
# noinspection PyTypeChecker,PyGlobalUndefined
def preprocess(
self,
window_size: int = 1,
window_step: int = 1,
scale: str = "standard",
test_videos: int = 0,
verbose: bool = False,
conv_filter: bool = None,
sigma: float = 1.0,
shift: float = 0.0,
shuffle: bool = False,
align: str = False,
self,
window_size: int = 1,
window_step: int = 1,
scale: str = "standard",
test_videos: int = 0,
verbose: bool = False,
conv_filter: bool = None,
sigma: float = 1.0,
shift: float = 0.0,
shuffle: bool = False,
align: str = False,
) -> np.ndarray:
"""
......@@ -1243,7 +1243,7 @@ class table_dict(dict):
return X_train, y_train, np.array(X_test), np.array(y_test)
def random_projection(
self, n_components: int = None, sample: int = 1000
self, n_components: int = None, sample: int = 1000
) -> deepof.utils.Tuple[deepof.utils.Any, deepof.utils.Any]:
"""Returns a training set generated from the 2D original data (time x features) and a random projection
to a n_components space. The sample parameter allows the user to randomly pick a subset of the data for
......@@ -1265,7 +1265,7 @@ class table_dict(dict):
return X, rproj
def pca(
self, n_components: int = None, sample: int = 1000, kernel: str = "linear"
self, n_components: int = None, sample: int = 1000, kernel: str = "linear"
) -> deepof.utils.Tuple[deepof.utils.Any, deepof.utils.Any]:
"""Returns a training set generated from the 2D original data (time x features) and a PCA projection
to a n_components space. The sample parameter allows the user to randomly pick a subset of the data for
......@@ -1287,7 +1287,7 @@ class table_dict(dict):
return X, pca
def tsne(
self, n_components: int = None, sample: int = 1000, perplexity: int = 30
self, n_components: int = None, sample: int = 1000, perplexity: int = 30
) -> deepof.utils.Tuple[deepof.utils.Any, deepof.utils.Any]:
"""Returns a training set generated from the 2D original data (time x features) and a PCA projection
to a n_components space. The sample parameter allows the user to randomly pick a subset of the data for
......@@ -1331,7 +1331,6 @@ def merge_tables(*args):
return merged_tables
# TODO:
# - Generate ragged training array using a metric (acceleration, maybe?)
# - Use something like Dynamic Time Warping to put all instances in the same length
......
deepof/hypermodels.py
View file @ 707ab97e
......@@ -8,10 +8,11 @@ keras hypermodels for hyperparameter tuning of deep autoencoders
"""
import tensorflow_probability as tfp
from kerastuner import HyperModel
import deepof.models
import deepof.model_utils
import tensorflow_probability as tfp
import deepof.models
tfd = tfp.distributions
tfpl = tfp.layers
......@@ -92,18 +93,18 @@ class SEQ_2_SEQ_GMVAE(HyperModel):
"""Hyperparameter tuning pipeline for deepof.models.SEQ_2_SEQ_GMVAE"""
def __init__(
self,
input_shape: tuple,
encoding: int,
kl_warmup_epochs: int = 0,
learn_rate: float = 1e-3,
loss: str = "ELBO+MMD",
mmd_warmup_epochs: int = 0,
number_of_components: int = 10,
overlap_loss: float = False,
phenotype_predictor: float = 0.0,
predictor: float = 0.0,
prior: str = "standard_normal",
self,
input_shape: tuple,
encoding: int,
kl_warmup_epochs: int = 0,
learn_rate: float = 1e-3,
loss: str = "ELBO+MMD",
mmd_warmup_epochs: int = 0,
number_of_components: int = 10,
overlap_loss: float = False,
phenotype_predictor: float = 0.0,
predictor: float = 0.0,
prior: str = "standard_normal",
):
super().__init__()
self.input_shape = input_shape
......@@ -119,7 +120,7 @@ class SEQ_2_SEQ_GMVAE(HyperModel):
self.prior = prior
assert (
"ELBO" in self.loss or "MMD" in self.loss
"ELBO" in self.loss or "MMD" in self.loss
), "loss must be one of ELBO, MMD or ELBO+MMD (default)"
def get_hparams(self, hp):
......@@ -191,7 +192,6 @@ class SEQ_2_SEQ_GMVAE(HyperModel):
return gmvaep
# TODO:
# - We can add as many parameters as we want to the hypermodel!
# with this implementation, predictor, warmup, loss and even number of components can be tuned using BayOpt
......
deepof/model_utils.py
View file @ 707ab97e
......@@ -10,15 +10,16 @@ Functions and general utilities for the deepof tensorflow models. See documentat
from itertools import combinations
from typing import Any, Tuple
import matplotlib.pyplot as plt
import numpy as np
import tensorflow as tf
import tensorflow_probability as tfp
from scipy.stats import entropy
from sklearn.neighbors import NearestNeighbors
from tensorflow.keras import backend as K
from tensorflow.keras.constraints import Constraint
from tensorflow.keras.layers import Layer
import matplotlib.pyplot as plt
import numpy as np
import tensorflow as tf
import tensorflow_probability as tfp
tfd = tfp.distributions
tfpl = tfp.layers
......@@ -44,7 +45,7 @@ class exponential_learning_rate(tf.keras.callbacks.Callback):
def find_learning_rate(
model, X, y, epochs=1, batch_size=32, min_rate=10 ** -5, max_rate=10
model, X, y, epochs=1, batch_size=32, min_rate=10 ** -5, max_rate=10
):
"""Trains the provided model for an epoch with an exponentially increasing learning rate"""
......@@ -123,9 +124,9 @@ def compute_mmd(tensors: Tuple[Any]) -> tf.Tensor:
y_kernel = compute_kernel(y, y)
xy_kernel = compute_kernel(x, y)
mmd = (
tf.reduce_mean(x_kernel)
+ tf.reduce_mean(y_kernel)
- 2 * tf.reduce_mean(xy_kernel)
tf.reduce_mean(x_kernel)
+ tf.reduce_mean(y_kernel)
- 2 * tf.reduce_mean(xy_kernel)
)
return mmd
......@@ -140,13 +141,13 @@ class one_cycle_scheduler(tf.keras.callbacks.Callback):
"""
def __init__(
self,
iterations: int,
max_rate: float,
start_rate: float = None,
last_iterations: int = None,
last_rate: float = None,
log_dir: str = ".",
self,
iterations: int,
max_rate: float,
start_rate: float = None,
last_iterations: int = None,
last_rate: float = None,
log_dir: str = ".",
):
super().__init__()
self.iterations = iterations
......@@ -212,13 +213,13 @@ class neighbor_latent_entropy(tf.keras.callbacks.Callback):
"""
def __init__(
self,
encoding_dim: int,
variational: bool = True,