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Commit 156f1af2 authored by Lucas Miranda's avatar Lucas Miranda
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Implemented rotation alignment in preprocess.py

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main.ipynb
+ 11670
− 472
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model_training.py
+ 22
− 8
View file @ 156f1af2
......@@ -232,7 +232,7 @@ DLC_social_1_coords = DLC_social_1.run(verbose=True)
DLC_social_2_coords = DLC_social_2.run(verbose=True)
# Coordinates for training data
coords1 = DLC_social_1_coords.get_coords(center="B_Center", polar=False)
coords1 = DLC_social_1_coords.get_coords(center="B_Center", align="B_Nose")
distances1 = DLC_social_1_coords.get_distances()
angles1 = DLC_social_1_coords.get_angles()
coords_distances1 = merge_tables(coords1, distances1)
......@@ -241,7 +241,7 @@ dists_angles1 = merge_tables(distances1, angles1)
coords_dist_angles1 = merge_tables(coords1, distances1, angles1)
# Coordinates for validation data
coords2 = DLC_social_2_coords.get_coords(center="B_Center", polar=False)
coords2 = DLC_social_2_coords.get_coords(center="B_Center", align="B_Nose")
distances2 = DLC_social_2_coords.get_distances()
angles2 = DLC_social_2_coords.get_angles()
coords_distances2 = merge_tables(coords2, distances2)
......@@ -258,6 +258,7 @@ input_dict_train = {
random_state=42,
filter="gaussian",
sigma=55,
align=True,
),
"dists": distances1.preprocess(
window_size=11,
......@@ -266,6 +267,7 @@ input_dict_train = {
random_state=42,
filter="gaussian",
sigma=55,
align=True,
),
"angles": angles1.preprocess(
window_size=11,
......@@ -274,6 +276,7 @@ input_dict_train = {
random_state=42,
filter="gaussian",
sigma=55,
align=True,
),
"coords+dist": coords_distances1.preprocess(
window_size=11,
......@@ -282,6 +285,7 @@ input_dict_train = {
random_state=42,
filter="gaussian",
sigma=55,
align=True,
),
"coords+angle": coords_angles1.preprocess(
window_size=11,
......@@ -290,6 +294,7 @@ input_dict_train = {
random_state=42,
filter="gaussian",
sigma=55,
align=True,
),
"dists+angle": dists_angles1.preprocess(
window_size=11,
......@@ -298,6 +303,7 @@ input_dict_train = {
random_state=42,
filter="gaussian",
sigma=55,
align=True,
),
"coords+dist+angle": coords_dist_angles1.preprocess(
window_size=11,
......@@ -306,54 +312,60 @@ input_dict_train = {
random_state=42,
filter="gaussian",
sigma=55,
align=True,
),
}
input_dict_val = {
"coords": coords2.preprocess(
window_size=11,
window_step=1,
window_step=10,
scale=True,
random_state=42,
filter="gaussian",
sigma=55,
shuffle=True,
align=True,
),
"dists": distances2.preprocess(
window_size=11,
window_step=1,
window_step=10,
scale=True,
random_state=42,
filter="gaussian",
sigma=55,
shuffle=True,
align=True,
),
"angles": angles2.preprocess(
window_size=11,
window_step=1,
window_step=10,
scale=True,
random_state=42,
filter="gaussian",
sigma=55,
shuffle=True,
align=True,
),
"coords+dist": coords_distances2.preprocess(
window_size=11,
window_step=1,
window_step=10,
scale=True,
random_state=42,
filter="gaussian",
sigma=55,
shuffle=True,
align=True,
),
"coords+angle": coords_angles2.preprocess(
window_size=11,
window_step=1,
window_step=10,
scale=True,
random_state=42,
filter="gaussian",
sigma=55,
shuffle=True,
align=True,
),
"dists+angle": dists_angles2.preprocess(
window_size=11,
......@@ -363,15 +375,17 @@ input_dict_val = {
filter="gaussian",
sigma=55,
shuffle=True,
align=True,
),
"coords+dist+angle": coords_dist_angles2.preprocess(
window_size=11,
window_step=1,
window_step=10,
scale=True,
random_state=42,
filter="gaussian",
sigma=55,
shuffle=True,
align=True,
),
}
......
source/preprocess.py
+ 31
− 7
View file @ 156f1af2
......@@ -309,7 +309,9 @@ class coordinates:
else:
return "DLC analysis of {} videos".format(len(self._videos))
def get_coords(self, center="arena", polar=False, speed=0, length=None):
def get_coords(
self, center="arena", polar=False, speed=0, length=None, align=False
):
tabs = deepcopy(self._tables)
if polar:
......@@ -384,6 +386,21 @@ class coordinates:
"00:00:00", length, periods=tab.shape[0] + 1, closed="left"
)
if align:
assert (
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
tabs[key] = tab[columns]
return table_dict(
tabs,
"coords",
......@@ -524,17 +541,17 @@ class table_dict(dict):
self,
window_size=1,
window_step=1,
scale=True,
scale="standard",
test_proportion=0,
random_state=None,
verbose=False,
filter=None,
sigma=None,
shift=0,
standard_scaler=True,
shuffle=False,
align=False,
):
"""Builds a sliding window. If desired, splits train and test and
"""Builds a sliding window. If specified, splits train and test and
Z-scores the data using sklearn's standard scaler"""
X_train = self.get_training_set()
......@@ -550,16 +567,20 @@ class table_dict(dict):
if verbose:
print("Scaling data...")
if standard_scaler:
if scale == "standard":
scaler = StandardScaler()
else:
elif scale == "minmax":
scaler = MinMaxScaler()
else:
raise ValueError(
"Invalid scaler. Select one of standard, minmax or None"
)
X_train = scaler.fit_transform(
X_train.reshape(-1, X_train.shape[-1])
).reshape(X_train.shape)
if standard_scaler:
if scale == "standard":
assert np.allclose(np.mean(X_train), 0)
assert np.allclose(np.std(X_train), 1)
......@@ -573,6 +594,9 @@ class table_dict(dict):
X_train = rolling_window(X_train, window_size, window_step)
if align:
X_train = align_trajectories(X_train)
if filter == "gaussian":
r = range(-int(window_size / 2), int(window_size / 2) + 1)
r = [i - shift for i in r]
......
source/utils.py
+ 27
− 0
View file @ 156f1af2
......@@ -11,6 +11,7 @@ import pims
import re
import scipy
import seaborn as sns
from copy import deepcopy
from itertools import cycle, combinations, product
from joblib import Parallel, delayed
from numba import jit
......@@ -87,6 +88,32 @@ def angle_trio(array, degrees=False):
return np.array([angle(a, b, c), angle(a, c, b), angle(b, a, c),])
def rotate(p, angles, origin=np.array([0, 0])):
R = np.array([[np.cos(angles), -np.sin(angles)], [np.sin(angles), np.cos(angles)]])
o = np.atleast_2d(origin)
p = np.atleast_2d(p)
return np.squeeze((R @ (p.T - o.T) + o.T).T)
def align_trajectories(data):
data = deepcopy(data)
center_time = (data.shape[1] - 1) // 2
angles = np.arctan2(data[:, center_time, 0], data[:, center_time, 1])
aligned_trajs = np.zeros(data.shape)
for frame in range(data.shape[0]):
aligned_trajs[frame] = rotate(
data[frame].reshape([data.shape[1] * data.shape[2] // 2, 2]), angles[frame],
).reshape(data.shape[1:])
return aligned_trajs
def smooth_boolean_array(a):
"""Returns a boolean array in which isolated appearances of a feature are smoothened"""
for i in range(1, len(a) - 1):
......
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