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bioroboticslab
robofish
io
Commits
2a9ddb37
Commit
2a9ddb37
authored
Mar 3, 2021
by
marc131183
Browse files
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Plain Diff
removed consider_ and added predicate, to select fishes
parent
7753e7c1
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Pipeline
#36195
failed
Mar 3, 2021
Stage: package
Stage: test
Changes
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1 changed file
src/robofish/evaluate/evaluate.py
+47
-152
47 additions, 152 deletions
src/robofish/evaluate/evaluate.py
with
47 additions
and
152 deletions
src/robofish/evaluate/evaluate.py
+
47
−
152
View file @
2a9ddb37
...
@@ -19,13 +19,8 @@ from typing import Iterable
...
@@ -19,13 +19,8 @@ from typing import Iterable
from
scipy
import
stats
from
scipy
import
stats
<<<<<<<
HEAD
# def get_all_poses_from_paths(paths: Iterable(str)):
# """This function reads all poses from given paths.
=======
def
get_all_poses_from_paths
(
paths
:
Iterable
[
str
]):
def
get_all_poses_from_paths
(
paths
:
Iterable
[
str
]):
"""
This function reads all poses from given paths.
"""
This function reads all poses from given paths.
>>>
>>>>
master
# Args:
# Args:
# paths: An array of strings, with files or folders
# paths: An array of strings, with files or folders
...
@@ -35,13 +30,9 @@ def get_all_poses_from_paths(paths: Iterable[str]):
...
@@ -35,13 +30,9 @@ def get_all_poses_from_paths(paths: Iterable[str]):
# # Open all files, shape (paths, files)
# # Open all files, shape (paths, files)
# files_per_path = [robofish.io.read_multiple_files(p) for p in paths]
# files_per_path = [robofish.io.read_multiple_files(p) for p in paths]
<<<<<<<
HEAD
# # Read all poses from the files, shape (paths, files)
# poses_per_path = [[f.get_poses() for f in files] for files in files_per_path]
=======
# Read all poses from the files, shape (paths, files)
# Read all poses from the files, shape (paths, files)
poses_per_path
=
[[
f
.
entity_poses
for
f
in
files
]
for
files
in
files_per_path
]
poses_per_path
=
[[
f
.
entity_poses
for
f
in
files
]
for
files
in
files_per_path
]
>>>>>>>
master
# # close all files
# # close all files
# for p in files_per_path:
# for p in files_per_path:
...
@@ -51,20 +42,14 @@ def get_all_poses_from_paths(paths: Iterable[str]):
...
@@ -51,20 +42,14 @@ def get_all_poses_from_paths(paths: Iterable[str]):
# return poses_per_path
# return poses_per_path
def
evaluate_speed
(
def
evaluate_speed
(
paths
,
names
=
None
,
save_path
=
None
,
predicate
=
None
):
paths
,
names
=
None
,
save_path
=
None
,
consider_names
=
None
,
consider_categories
=
None
):
files_per_path
=
[
robofish
.
io
.
read_multiple_files
(
p
)
for
p
in
paths
]
files_per_path
=
[
robofish
.
io
.
read_multiple_files
(
p
)
for
p
in
paths
]
speeds
=
[]
speeds
=
[]
for
k
,
files
in
enumerate
(
files_per_path
):
for
k
,
files
in
enumerate
(
files_per_path
):
path_speeds
=
[]
path_speeds
=
[]
for
p
,
file
in
files
.
items
():
for
p
,
file
in
files
.
items
():
# TODO: Change to select_poses()
poses
=
file
.
select_entity_poses
(
poses
=
file
.
get_poses
(
None
if
predicate
is
None
else
predicate
[
k
]
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
if
consider_categories
is
None
else
consider_categories
[
k
],
)
)
for
e_poses
in
poses
:
for
e_poses
in
poses
:
e_speeds
=
np
.
linalg
.
norm
(
np
.
diff
(
e_poses
[:,
:
2
],
axis
=
0
),
axis
=
1
)
e_speeds
=
np
.
linalg
.
norm
(
np
.
diff
(
e_poses
[:,
:
2
],
axis
=
0
),
axis
=
1
)
...
@@ -90,20 +75,14 @@ def evaluate_speed(
...
@@ -90,20 +75,14 @@ def evaluate_speed(
plt
.
close
()
plt
.
close
()
def
evaluate_turn
(
def
evaluate_turn
(
paths
,
names
=
None
,
save_path
=
None
,
predicate
=
None
):
paths
,
names
=
None
,
save_path
=
None
,
consider_names
=
None
,
consider_categories
=
None
):
files_per_path
=
[
robofish
.
io
.
read_multiple_files
(
p
)
for
p
in
paths
]
files_per_path
=
[
robofish
.
io
.
read_multiple_files
(
p
)
for
p
in
paths
]
turns
=
[]
turns
=
[]
for
k
,
files
in
enumerate
(
files_per_path
):
for
k
,
files
in
enumerate
(
files_per_path
):
path_turns
=
[]
path_turns
=
[]
for
p
,
file
in
files
.
items
():
for
p
,
file
in
files
.
items
():
# TODO: Change to select_poses()
poses
=
file
.
select_entity_poses
(
poses
=
file
.
get_poses
(
None
if
predicate
is
None
else
predicate
[
k
]
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
if
consider_categories
is
None
else
consider_categories
[
k
],
)
)
# Todo check if all frequencies are the same
# Todo check if all frequencies are the same
...
@@ -140,19 +119,13 @@ def evaluate_turn(
...
@@ -140,19 +119,13 @@ def evaluate_turn(
plt
.
close
()
plt
.
close
()
def
evaluate_orientation
(
def
evaluate_orientation
(
paths
,
names
=
None
,
save_path
=
None
,
predicate
=
None
):
paths
,
names
=
None
,
save_path
=
None
,
consider_names
=
None
,
consider_categories
=
None
):
files_per_path
=
[
robofish
.
io
.
read_multiple_files
(
p
)
for
p
in
paths
]
files_per_path
=
[
robofish
.
io
.
read_multiple_files
(
p
)
for
p
in
paths
]
orientations
=
[]
orientations
=
[]
for
k
,
files
in
enumerate
(
files_per_path
):
for
k
,
files
in
enumerate
(
files_per_path
):
for
p
,
file
in
files
.
items
():
for
p
,
file
in
files
.
items
():
# TODO: Change to select_poses()
poses
=
file
.
select_entity_poses
(
poses
=
file
.
get_poses
(
None
if
predicate
is
None
else
predicate
[
k
]
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
if
consider_categories
is
None
else
consider_categories
[
k
],
)
)
poses
=
poses
.
reshape
((
len
(
poses
)
*
len
(
poses
[
0
]),
4
))
poses
=
poses
.
reshape
((
len
(
poses
)
*
len
(
poses
[
0
]),
4
))
world_size
=
file
.
attrs
[
"
world_size_cm
"
]
world_size
=
file
.
attrs
[
"
world_size_cm
"
]
...
@@ -211,20 +184,14 @@ def evaluate_orientation(
...
@@ -211,20 +184,14 @@ def evaluate_orientation(
plt
.
close
()
plt
.
close
()
def
evaluate_relativeOrientation
(
def
evaluate_relativeOrientation
(
paths
,
names
=
None
,
save_path
=
None
,
predicate
=
None
):
paths
,
names
=
None
,
save_path
=
None
,
consider_names
=
None
,
consider_categories
=
None
):
files_per_path
=
[
robofish
.
io
.
read_multiple_files
(
p
)
for
p
in
paths
]
files_per_path
=
[
robofish
.
io
.
read_multiple_files
(
p
)
for
p
in
paths
]
orientations
=
[]
orientations
=
[]
for
k
,
files
in
enumerate
(
files_per_path
):
for
k
,
files
in
enumerate
(
files_per_path
):
path_orientations
=
[]
path_orientations
=
[]
for
p
,
file
in
files
.
items
():
for
p
,
file
in
files
.
items
():
# TODO: Change to select_poses()
poses
=
file
.
select_entity_poses
(
poses
=
file
.
get_poses
(
None
if
predicate
is
None
else
predicate
[
k
]
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
if
consider_categories
is
None
else
consider_categories
[
k
],
)
)
all_poses
=
file
.
entity_poses
all_poses
=
file
.
entity_poses
for
i
in
range
(
len
(
poses
)):
for
i
in
range
(
len
(
poses
)):
...
@@ -255,9 +222,7 @@ def evaluate_relativeOrientation(
...
@@ -255,9 +222,7 @@ def evaluate_relativeOrientation(
plt
.
close
()
plt
.
close
()
def
evaluate_distanceToWall
(
def
evaluate_distanceToWall
(
paths
,
names
=
None
,
save_path
=
None
,
predicate
=
None
):
paths
,
names
=
None
,
save_path
=
None
,
consider_names
=
None
,
consider_categories
=
None
):
"""
"""
only works for rectangular tanks
only works for rectangular tanks
"""
"""
...
@@ -269,12 +234,8 @@ def evaluate_distanceToWall(
...
@@ -269,12 +234,8 @@ def evaluate_distanceToWall(
for
p
,
file
in
files
.
items
():
for
p
,
file
in
files
.
items
():
worldBoundsX
.
append
(
file
.
attrs
[
"
world_size_cm
"
][
0
])
worldBoundsX
.
append
(
file
.
attrs
[
"
world_size_cm
"
][
0
])
worldBoundsY
.
append
(
file
.
attrs
[
"
world_size_cm
"
][
1
])
worldBoundsY
.
append
(
file
.
attrs
[
"
world_size_cm
"
][
1
])
# TODO: Change to select_poses()
poses
=
file
.
select_entity_poses
(
poses
=
file
.
get_poses
(
None
if
predicate
is
None
else
predicate
[
k
]
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
if
consider_categories
is
None
else
consider_categories
[
k
],
)
)
world_size
=
file
.
attrs
[
"
world_size_cm
"
]
world_size
=
file
.
attrs
[
"
world_size_cm
"
]
world_bounds
=
[
world_bounds
=
[
...
@@ -328,9 +289,7 @@ def evaluate_distanceToWall(
...
@@ -328,9 +289,7 @@ def evaluate_distanceToWall(
plt
.
close
()
plt
.
close
()
def
evaluate_tankpositions
(
def
evaluate_tankpositions
(
paths
,
names
=
None
,
save_path
=
None
,
predicate
=
None
):
paths
,
names
=
None
,
save_path
=
None
,
consider_names
=
None
,
consider_categories
=
None
):
"""
"""
Heatmap of fishpositions
Heatmap of fishpositions
By Moritz Maxeiner
By Moritz Maxeiner
...
@@ -341,12 +300,8 @@ def evaluate_tankpositions(
...
@@ -341,12 +300,8 @@ def evaluate_tankpositions(
for
k
,
files
in
enumerate
(
files_per_path
):
for
k
,
files
in
enumerate
(
files_per_path
):
path_x_pos
,
path_y_pos
=
[],
[]
path_x_pos
,
path_y_pos
=
[],
[]
for
p
,
file
in
files
.
items
():
for
p
,
file
in
files
.
items
():
# TODO: Change to select_poses()
poses
=
file
.
select_entity_poses
(
poses
=
file
.
get_poses
(
None
if
predicate
is
None
else
predicate
[
k
]
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
if
consider_categories
is
None
else
consider_categories
[
k
],
)
)
world_bounds
.
append
(
file
.
attrs
[
"
world_size_cm
"
])
world_bounds
.
append
(
file
.
attrs
[
"
world_size_cm
"
])
for
e_poses
in
poses
:
for
e_poses
in
poses
:
...
@@ -375,9 +330,7 @@ def evaluate_tankpositions(
...
@@ -375,9 +330,7 @@ def evaluate_tankpositions(
plt
.
close
()
plt
.
close
()
def
evaluate_trajectories
(
def
evaluate_trajectories
(
paths
,
names
=
None
,
save_path
=
None
,
predicate
=
None
):
paths
,
names
=
None
,
save_path
=
None
,
consider_names
=
None
,
consider_categories
=
None
):
"""
"""
trajectories of fishes
trajectories of fishes
By Moritz Maxeiner
By Moritz Maxeiner
...
@@ -387,12 +340,8 @@ def evaluate_trajectories(
...
@@ -387,12 +340,8 @@ def evaluate_trajectories(
world_bounds
=
[]
world_bounds
=
[]
for
k
,
files
in
enumerate
(
files_per_path
):
for
k
,
files
in
enumerate
(
files_per_path
):
for
p
,
file
in
files
.
items
():
for
p
,
file
in
files
.
items
():
# TODO: Change to select_poses()
poses
=
file
.
select_entity_poses
(
poses
=
file
.
get_poses
(
None
if
predicate
is
None
else
predicate
[
k
]
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
if
consider_categories
is
None
else
consider_categories
[
k
],
)
)
world_bounds
.
append
(
file
.
attrs
[
"
world_size_cm
"
])
world_bounds
.
append
(
file
.
attrs
[
"
world_size_cm
"
])
path_pos
=
{
path_pos
=
{
...
@@ -451,9 +400,7 @@ def evaluate_trajectories(
...
@@ -451,9 +400,7 @@ def evaluate_trajectories(
plt
.
close
()
plt
.
close
()
def
evaluate_positionVec
(
def
evaluate_positionVec
(
paths
,
names
=
None
,
save_path
=
None
,
predicate
=
None
):
paths
,
names
=
None
,
save_path
=
None
,
consider_names
=
None
,
consider_categories
=
None
):
files_per_path
=
[
robofish
.
io
.
read_multiple_files
(
p
)
for
p
in
paths
]
files_per_path
=
[
robofish
.
io
.
read_multiple_files
(
p
)
for
p
in
paths
]
posVec
=
[]
posVec
=
[]
worldBoundsX
,
worldBoundsY
=
[],
[]
worldBoundsX
,
worldBoundsY
=
[],
[]
...
@@ -462,12 +409,8 @@ def evaluate_positionVec(
...
@@ -462,12 +409,8 @@ def evaluate_positionVec(
for
p
,
file
in
files
.
items
():
for
p
,
file
in
files
.
items
():
worldBoundsX
.
append
(
file
.
attrs
[
"
world_size_cm
"
][
0
])
worldBoundsX
.
append
(
file
.
attrs
[
"
world_size_cm
"
][
0
])
worldBoundsY
.
append
(
file
.
attrs
[
"
world_size_cm
"
][
1
])
worldBoundsY
.
append
(
file
.
attrs
[
"
world_size_cm
"
][
1
])
# TODO: Change to select_poses()
poses
=
file
.
select_entity_poses
(
poses
=
file
.
get_poses
(
None
if
predicate
is
None
else
predicate
[
k
]
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
if
consider_categories
is
None
else
consider_categories
[
k
],
)
)
all_poses
=
file
.
entity_poses
all_poses
=
file
.
entity_poses
# calculate posVec for every fish combination
# calculate posVec for every fish combination
...
@@ -512,9 +455,7 @@ def evaluate_positionVec(
...
@@ -512,9 +455,7 @@ def evaluate_positionVec(
plt
.
close
()
plt
.
close
()
def
evaluate_follow_iid
(
def
evaluate_follow_iid
(
paths
,
names
=
None
,
save_path
=
None
,
predicate
=
None
):
paths
,
names
=
None
,
save_path
=
None
,
consider_names
=
None
,
consider_categories
=
None
):
files_per_path
=
[
robofish
.
io
.
read_multiple_files
(
p
)
for
p
in
paths
]
files_per_path
=
[
robofish
.
io
.
read_multiple_files
(
p
)
for
p
in
paths
]
follow
,
iid
=
[],
[]
follow
,
iid
=
[],
[]
worldBoundsX
,
worldBoundsY
=
[],
[]
worldBoundsX
,
worldBoundsY
=
[],
[]
...
@@ -523,12 +464,8 @@ def evaluate_follow_iid(
...
@@ -523,12 +464,8 @@ def evaluate_follow_iid(
for
p
,
file
in
files
.
items
():
for
p
,
file
in
files
.
items
():
worldBoundsX
.
append
(
file
.
attrs
[
"
world_size_cm
"
][
0
])
worldBoundsX
.
append
(
file
.
attrs
[
"
world_size_cm
"
][
0
])
worldBoundsY
.
append
(
file
.
attrs
[
"
world_size_cm
"
][
1
])
worldBoundsY
.
append
(
file
.
attrs
[
"
world_size_cm
"
][
1
])
# TODO: Change to select_poses()
poses
=
file
.
select_entity_poses
(
poses
=
file
.
get_poses
(
None
if
predicate
is
None
else
predicate
[
k
]
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
if
consider_categories
is
None
else
consider_categories
[
k
],
)
)
all_poses
=
file
.
entity_poses
all_poses
=
file
.
entity_poses
for
i
in
range
(
len
(
poses
)):
for
i
in
range
(
len
(
poses
)):
...
@@ -586,60 +523,18 @@ def evaluate_follow_iid(
...
@@ -586,60 +523,18 @@ def evaluate_follow_iid(
plt
.
close
()
plt
.
close
()
def
evaluate_all
(
def
evaluate_all
(
paths
,
names
=
None
,
save_folder
=
None
,
predicate
=
None
):
paths
,
names
=
None
,
save_folder
=
None
,
consider_names
=
None
,
consider_categories
=
None
evaluate_speed
(
paths
,
names
,
save_folder
+
"
speed.png
"
,
predicate
)
):
evaluate_turn
(
paths
,
names
,
save_folder
+
"
turn.png
"
,
predicate
)
evaluate_speed
(
evaluate_orientation
(
paths
,
names
,
save_folder
+
"
orientation.png
"
,
predicate
)
paths
,
names
,
save_folder
+
"
speed.png
"
,
consider_names
,
consider_categories
)
evaluate_turn
(
paths
,
names
,
save_folder
+
"
turn.png
"
,
consider_names
,
consider_categories
)
evaluate_orientation
(
paths
,
names
,
save_folder
+
"
orientation.png
"
,
consider_names
,
consider_categories
,
)
evaluate_relativeOrientation
(
evaluate_relativeOrientation
(
paths
,
paths
,
names
,
save_folder
+
"
relativeOrientation.png
"
,
predicate
names
,
save_folder
+
"
relativeOrientation.png
"
,
consider_names
,
consider_categories
,
)
evaluate_distanceToWall
(
paths
,
names
,
save_folder
+
"
distanceToWall.png
"
,
consider_names
,
consider_categories
,
)
evaluate_tankpositions
(
paths
,
names
,
save_folder
+
"
tankpositions.png
"
,
consider_names
,
consider_categories
,
)
evaluate_trajectories
(
paths
,
names
,
save_folder
+
"
trajectories.png
"
,
consider_names
,
consider_categories
,
)
evaluate_positionVec
(
paths
,
names
,
save_folder
+
"
posVec.png
"
,
consider_names
,
consider_categories
)
evaluate_follow_iid
(
paths
,
names
,
save_folder
+
"
follow_iid.png
"
,
consider_names
,
consider_categories
,
)
)
evaluate_distanceToWall
(
paths
,
names
,
save_folder
+
"
distanceToWall.png
"
,
predicate
)
evaluate_tankpositions
(
paths
,
names
,
save_folder
+
"
tankpositions.png
"
,
predicate
)
evaluate_trajectories
(
paths
,
names
,
save_folder
+
"
trajectories.png
"
,
predicate
)
evaluate_positionVec
(
paths
,
names
,
save_folder
+
"
posVec.png
"
,
predicate
)
evaluate_follow_iid
(
paths
,
names
,
save_folder
+
"
follow_iid.png
"
,
predicate
)
def
calculate_follow
(
a
,
b
):
def
calculate_follow
(
a
,
b
):
...
...
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