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bioroboticslab
robofish
io
Commits
e42758bb
Commit
e42758bb
authored
4 years ago
by
Andi Gerken
Browse files
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Patches
Plain Diff
Fixed evaluate functions and corresponding tests
parent
4417d8ed
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Changes
2
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2 changed files
src/robofish/evaluate/evaluate.py
+16
-7
16 additions, 7 deletions
src/robofish/evaluate/evaluate.py
tests/robofish/evaluate/test_app_evaluate.py
+13
-6
13 additions, 6 deletions
tests/robofish/evaluate/test_app_evaluate.py
with
29 additions
and
13 deletions
src/robofish/evaluate/evaluate.py
+
16
−
7
View file @
e42758bb
...
@@ -31,7 +31,7 @@ def get_all_poses_from_paths(paths: Iterable[str]):
...
@@ -31,7 +31,7 @@ def get_all_poses_from_paths(paths: Iterable[str]):
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
]
# Read all poses from the files, shape (paths, files)
# 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
]
poses_per_path
=
[[
f
.
poses
for
f
in
files
]
for
files
in
files_per_path
]
# close all files
# close all files
for
p
in
files_per_path
:
for
p
in
files_per_path
:
...
@@ -49,6 +49,7 @@ def evaluate_speed(
...
@@ -49,6 +49,7 @@ def evaluate_speed(
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
.
get_poses
(
poses
=
file
.
get_poses
(
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
category
=
None
...
@@ -57,7 +58,7 @@ def evaluate_speed(
...
@@ -57,7 +58,7 @@ def evaluate_speed(
)
)
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
)
e_speeds
*=
file
.
get_
frequency
()
e_speeds
*=
file
.
frequency
path_speeds
.
extend
(
e_speeds
)
path_speeds
.
extend
(
e_speeds
)
speeds
.
append
(
path_speeds
)
speeds
.
append
(
path_speeds
)
...
@@ -87,6 +88,7 @@ def evaluate_turn(
...
@@ -87,6 +88,7 @@ def evaluate_turn(
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
.
get_poses
(
poses
=
file
.
get_poses
(
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
category
=
None
...
@@ -95,7 +97,7 @@ def evaluate_turn(
...
@@ -95,7 +97,7 @@ def evaluate_turn(
)
)
# Todo check if all frequencies are the same
# Todo check if all frequencies are the same
frequency
=
file
.
get_
frequency
()
frequency
=
file
.
frequency
for
e_poses
in
poses
:
for
e_poses
in
poses
:
# convert ori_x, ori_y to radians
# convert ori_x, ori_y to radians
...
@@ -104,7 +106,7 @@ def evaluate_turn(
...
@@ -104,7 +106,7 @@ def evaluate_turn(
e_turns
=
ori_rad
[
1
:]
-
ori_rad
[:
-
1
]
e_turns
=
ori_rad
[
1
:]
-
ori_rad
[:
-
1
]
e_turns
=
np
.
where
(
e_turns
<
-
np
.
pi
,
e_turns
+
2
*
np
.
pi
,
e_turns
)
e_turns
=
np
.
where
(
e_turns
<
-
np
.
pi
,
e_turns
+
2
*
np
.
pi
,
e_turns
)
e_turns
=
np
.
where
(
e_turns
>
np
.
pi
,
e_turns
-
2
*
np
.
pi
,
e_turns
)
e_turns
=
np
.
where
(
e_turns
>
np
.
pi
,
e_turns
-
2
*
np
.
pi
,
e_turns
)
# e_turns *= file.
get_
frequency
()
# e_turns *= file.frequency
e_turns
*=
180
/
np
.
pi
e_turns
*=
180
/
np
.
pi
path_turns
.
extend
(
e_turns
)
path_turns
.
extend
(
e_turns
)
turns
.
append
(
path_turns
)
turns
.
append
(
path_turns
)
...
@@ -135,6 +137,7 @@ def evaluate_orientation(
...
@@ -135,6 +137,7 @@ def evaluate_orientation(
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
.
get_poses
(
poses
=
file
.
get_poses
(
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
category
=
None
...
@@ -206,13 +209,14 @@ def evaluate_relativeOrientation(
...
@@ -206,13 +209,14 @@ def evaluate_relativeOrientation(
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
.
get_poses
(
poses
=
file
.
get_poses
(
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
category
=
None
if
consider_categories
is
None
if
consider_categories
is
None
else
consider_categories
[
k
],
else
consider_categories
[
k
],
)
)
all_poses
=
file
.
get_
poses
()
all_poses
=
file
.
poses
for
i
in
range
(
len
(
poses
)):
for
i
in
range
(
len
(
poses
)):
for
j
in
range
(
len
(
all_poses
)):
for
j
in
range
(
len
(
all_poses
)):
if
(
poses
[
i
]
!=
all_poses
[
j
]).
any
():
if
(
poses
[
i
]
!=
all_poses
[
j
]).
any
():
...
@@ -255,6 +259,7 @@ def evaluate_distanceToWall(
...
@@ -255,6 +259,7 @@ 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
.
get_poses
(
poses
=
file
.
get_poses
(
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
category
=
None
...
@@ -326,6 +331,7 @@ def evaluate_tankpositions(
...
@@ -326,6 +331,7 @@ 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
.
get_poses
(
poses
=
file
.
get_poses
(
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
category
=
None
...
@@ -371,6 +377,7 @@ def evaluate_trajectories(
...
@@ -371,6 +377,7 @@ 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
.
get_poses
(
poses
=
file
.
get_poses
(
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
category
=
None
...
@@ -445,13 +452,14 @@ def evaluate_positionVec(
...
@@ -445,13 +452,14 @@ 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
.
get_poses
(
poses
=
file
.
get_poses
(
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
category
=
None
if
consider_categories
is
None
if
consider_categories
is
None
else
consider_categories
[
k
],
else
consider_categories
[
k
],
)
)
all_poses
=
file
.
get_
poses
()
all_poses
=
file
.
poses
# calculate posVec for every fish combination
# calculate posVec for every fish combination
for
i
in
range
(
len
(
poses
)):
for
i
in
range
(
len
(
poses
)):
for
j
in
range
(
len
(
all_poses
)):
for
j
in
range
(
len
(
all_poses
)):
...
@@ -505,13 +513,14 @@ def evaluate_follow_iid(
...
@@ -505,13 +513,14 @@ 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
.
get_poses
(
poses
=
file
.
get_poses
(
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
names
=
None
if
consider_names
is
None
else
consider_names
[
k
],
category
=
None
category
=
None
if
consider_categories
is
None
if
consider_categories
is
None
else
consider_categories
[
k
],
else
consider_categories
[
k
],
)
)
all_poses
=
file
.
get_
poses
()
all_poses
=
file
.
poses
for
i
in
range
(
len
(
poses
)):
for
i
in
range
(
len
(
poses
)):
for
j
in
range
(
len
(
all_poses
)):
for
j
in
range
(
len
(
all_poses
)):
if
(
poses
[
i
]
!=
all_poses
[
j
]).
any
():
if
(
poses
[
i
]
!=
all_poses
[
j
]).
any
():
...
...
This diff is collapsed.
Click to expand it.
tests/robofish/evaluate/test_app_evaluate.py
+
13
−
6
View file @
e42758bb
...
@@ -6,16 +6,23 @@ from pathlib import Path
...
@@ -6,16 +6,23 @@ from pathlib import Path
logging
.
getLogger
().
setLevel
(
logging
.
INFO
)
logging
.
getLogger
().
setLevel
(
logging
.
INFO
)
h5py_files
=
[
utils
.
full_path
(
__file__
,
"
../../resources/valid.hdf5
"
)]
graphics_out
=
utils
.
full_path
(
__file__
,
"
output_graph.png
"
)
if
graphics_out
.
exists
():
graphics_out
.
unlink
()
# TODO: reactivate test and change evaluate
def
deactivated_
test_app_validate
():
def
test_app_validate
():
"""
This tests the function of the robofish-io-validate command
"""
"""
This tests the function of the robofish-io-validate command
"""
class
DummyArgs
:
class
DummyArgs
:
def
__init__
(
self
,
analysis_type
,
paths
):
def
__init__
(
self
,
analysis_type
):
self
.
analysis_type
=
analysis_type
self
.
analysis_type
=
analysis_type
self
.
paths
=
[
utils
.
full_path
(
__file__
,
paths
)]
self
.
paths
=
h5py_files
self
.
names
=
None
self
.
names
=
None
self
.
save_path
=
None
self
.
save_path
=
graphics_out
app
.
evaluate
(
DummyArgs
(
"
speed
"
,
"
../../resources/valid.hdf5
"
))
# TODO: Get rid of deprecated get_poses function
with
pytest
.
warns
(
DeprecationWarning
):
app
.
evaluate
(
DummyArgs
(
"
speed
"
))
graphics_out
.
unlink
()
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