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Commit 0d9fc5e5 authored by lucas_miranda's avatar lucas_miranda
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Implementation of elliptic recognition (for videos with tilted cameras)

parent de772f44
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......@@ -21,7 +21,6 @@ tensorflow-probability = "*"
tensorflow = "*"
tqdm = "*"
umap-learn = "*"
scikit-image = "*"
[dev-packages]
coverage = "*"
......
Pipfile.lock
View file @ 0d9fc5e5
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......@@ -221,13 +221,6 @@
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......@@ -313,34 +306,34 @@
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......@@ -668,42 +661,6 @@
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......@@ -781,28 +738,6 @@
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......@@ -971,14 +906,6 @@
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......@@ -1359,11 +1286,11 @@
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......
deepof/data.py
View file @ 0d9fc5e5
......@@ -149,16 +149,16 @@ class project:
scales = []
for vid_index, _ in enumerate(self.videos):
ellipse = deepof.utils.recognize_arena(
self.videos,
vid_index,
path=self.video_path,
arena_type=self.arena,
)[0]
scales.append(
list(
deepof.utils.recognize_arena(
self.videos,
vid_index,
path=self.video_path,
arena_type=self.arena,
)[0]
* 2
)
list(np.array([ellipse[0][0], ellipse[0][1], ellipse[1][1]]) * 2)
+ list(self.arena_dims)
)
......@@ -686,7 +686,7 @@ class coordinates:
# noinspection PyDefaultArgument
def rule_based_annotation(
self, hparams: Dict = {}, video_output: bool = False, frame_limit: int = np.inf
self, hparams: Dict = {}, video_output: bool = False, frame_limit: int = np.inf, debug: bool = False,
) -> Table_dict:
"""Annotates coordinates using a simple rule-based pipeline"""
......@@ -724,6 +724,7 @@ class coordinates:
self._videos,
list(self._tables.keys()).index(idx),
tag_dict[idx],
debug=debug,
frame_limit=frame_limit,
recog_limit=1,
path=os.path.join(self._path, "Videos"),
......
deepof/pose_utils.py
View file @ 0d9fc5e5
......@@ -133,10 +133,34 @@ def climb_wall(
nose = pos_dict[nose]
def rotate(origin, point, angle):
ox, oy = origin
px, py = point
qx = ox + np.cos(angle) * (px - ox) - np.sin(angle) * (py - oy)
qy = oy + np.sin(angle) * (px - ox) + np.cos(angle) * (py - oy)
return qx, qy
def outside_ellipse(x, y, e_center, e_axes, e_angle, threshold=0.):
x, y = rotate(e_center, (x, y), np.radians(e_angle))
term_x = (x - e_center[0]) ** 2 / (e_axes[0] + threshold) ** 2
term_y = (y - e_center[1]) ** 2 / (e_axes[1] + threshold) ** 2
return term_x + term_y > 1
if arena_type == "circular":
center = np.zeros(2) if centered_data else np.array(arena[:2])
radius = arena[2]
climbing = np.linalg.norm(nose - center, axis=1) > (radius + tol)
center = np.zeros(2) if centered_data else np.array(arena[0])
axes = arena[1]
angle = arena[2]
climbing = outside_ellipse(
x=nose["x"],
y=nose["y"],
e_center=center,
e_axes=axes,
e_angle=-angle,
threshold=tol,
)
else:
raise NotImplementedError("Supported values for arena_type are ['circular']")
......@@ -381,6 +405,7 @@ def get_hparameters(hparams: dict = {}) -> dict:
defaults = {
"speed_pause": 3,
"climb_tol": 10,
"close_contact_tol": 35,
"side_contact_tol": 80,
"follow_frames": 10,
......@@ -548,7 +573,7 @@ def rule_based_tagging(
for _id in animal_ids:
tag_dict[_id + undercond + "climbing"] = deepof.utils.smooth_boolean_array(
climb_wall(arena_type, arena, coords, 1, _id + undercond + "Nose")
climb_wall(arena_type, arena, coords, hparams["climb_tol"], _id + undercond + "Nose")
)
tag_dict[_id + undercond + "speed"] = speeds[_id + undercond + "Center"]
tag_dict[_id + undercond + "huddle"] = deepof.utils.smooth_boolean_array(
......@@ -579,6 +604,7 @@ def tag_rulebased_frames(
undercond,
hparams,
arena,
debug,
):
"""Helper function for rule_based_video. Annotates a given frame with on-screen information
about the recognised patterns"""
......@@ -616,7 +642,8 @@ def tag_rulebased_frames(
if len(animal_ids) > 1:
cv2.circle(frame, (arena[0], arena[1]), arena[2], thickness=2, color=(0, 0, 255))
if debug:
cv2.ellipse(frame, arena[0], arena[1], arena[2], 0, 360, (0, 255, 0), 3)
if tag_dict["nose2nose"][fnum] and not tag_dict["sidebyside"][fnum]:
write_on_frame("Nose-Nose", conditional_pos())
......@@ -690,6 +717,7 @@ def rule_based_video(
recog_limit: int = 1,
path: str = os.path.join("."),
hparams: dict = {},
debug: bool = False,
) -> True:
"""Renders a version of the input video with all rule-based taggings in place.
......@@ -697,6 +725,8 @@ def rule_based_video(
- tracks (list): list containing experiment IDs as strings
- videos (list): list of videos to load, in the same order as tracks
- coordinates (deepof.preprocessing.coordinates): coordinates object containing the project information
- debug (bool): if True, several debugging attributes (such as used body parts and arena) are plotted in
the output video
- vid_index (int): index in videos of the experiment to annotate
- fps (float): frames per second of the analysed video. Same as input by default
- path (str): directory in which the experimental data is stored
......@@ -777,7 +807,8 @@ def rule_based_video(
(w, h),
undercond,
hparams,
(arena, h, w)
(arena, h, w),
debug
)
if writer is None:
......@@ -800,7 +831,5 @@ def rule_based_video(
return True
# TODO:
# - Relativise default contact parameters
# (right now they only work if 'arena_dims' is correctly set in the project object
# - Is border sniffing anything you might consider interesting?
deepof/utils.py
View file @ 0d9fc5e5
......@@ -19,7 +19,8 @@ import regex as re
from copy import deepcopy
from itertools import combinations, product
from joblib import Parallel, delayed
#from skimage.transform import hough_ellipse
# from skimage.transform import hough_ellipse
from sklearn import mixture
from tqdm import tqdm
from typing import Tuple, Any, List, Union, NewType
......@@ -409,10 +410,14 @@ def circular_arena_recognition(frame: np.array) -> np.array:
# Convert image to greyscale, threshold it, blur it and apply open-close operations
gray_image = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
ret, thresh = cv2.threshold(gray_image, 100, 255, 0)
ret, thresh = cv2.threshold(gray_image, 80, 255, 0)
frame = cv2.medianBlur(thresh, 9)
frame = cv2.morphologyEx(frame, cv2.MORPH_CLOSE, cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (80, 80)))
frame = cv2.morphologyEx(frame, cv2.MORPH_OPEN, cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (80, 80)))
frame = cv2.morphologyEx(
frame, cv2.MORPH_CLOSE, cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (80, 80))
)
frame = cv2.morphologyEx(
frame, cv2.MORPH_OPEN, cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (80, 80))
)
# Find contours in the processed image
cnts, _ = cv2.findContours(frame, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
......@@ -423,31 +428,9 @@ def circular_arena_recognition(frame: np.array) -> np.array:
axes_length = tuple([int(i) // 2 for i in ellipse_params[1]])
angle = ellipse_params[2]
# circle = cv2.HoughCircles(
# frame,
# # accuracy=20,
# # threshold=250,
# # min_size=frame.shape[0] // 6,
# # max_size=frame.shape[0] // 2,
# cv2.HOUGH_GRADIENT,
# 1,
# 300,
# param1=50,
# param2=10,
# minRadius=0,
# maxRadius=frame.shape[0] // 2,
# )
# #result.sort(order='accumulator')
#
# circles = []
#
# if circle is not None:
# circle = np.uint16(np.around(circle[0]))
# circles.append(circle)
# return circles[0]
return center_coordinates, axes_length, angle
def rolling_speed(
dframe: pd.DatetimeIndex,
window: int = 5,
......
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