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Commit 685a3136 authored by Andi Gerken's avatar Andi Gerken
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Adapted ipynb example 

Added test for ipynb example
Added testbook dependency
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Stage: test
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.gitlab-ci.yml
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− 0
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...@@ -24,6 +24,7 @@ stages: ...@@ -24,6 +24,7 @@ stages:
artifacts: artifacts:
paths: paths:
- report.xml - report.xml
- htmlcov
expire_in: 1 day expire_in: 1 day
script: script:
- ./ci/test.py - ./ci/test.py
......
ci/test.py
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...@@ -34,7 +34,7 @@ if __name__ == "__main__": ...@@ -34,7 +34,7 @@ if __name__ == "__main__":
"--prompt", "--prompt",
"ci", "ci",
".venv", ".venv",
], ]
) )
check_call( check_call(
...@@ -44,9 +44,16 @@ if __name__ == "__main__": ...@@ -44,9 +44,16 @@ if __name__ == "__main__":
"pip", "pip",
"install", "install",
str(sorted(Path("dist").glob("*.whl"))[-1].resolve()), str(sorted(Path("dist").glob("*.whl"))[-1].resolve()),
], ]
) )
check_call( check_call(
[python_venv_executable(), "-m", "pytest", "--junitxml=report.xml"], [
python_venv_executable(),
"-m",
"pytest",
"--junitxml=report.xml",
"--cov=src",
"--cov-report=html",
]
) )
examples/example_basic.ipynb
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%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
#! /usr/bin/env python3
import robofish.io import robofish.io
import numpy as np import numpy as np
from pathlib import Path
import os
# Helper function to enable relative paths from this file
def full_path(path):
return (Path(os.path.abspath("__file__")).parent / path).resolve()
if __name__ == "__main__": def create_example_file(path):
# Create a new io file object with a 100x100cm world # Create a new io file object with a 100x100cm world
sf = robofish.io.File(world_size=[100, 100]) sf = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25.0)
# create a simple obstacle, fixed in place, fixed outline # create a simple obstacle, fixed in place, fixed outline
obstacle_pose = [[50, 50, 0, 0]]
obstacle_outline = [[[-10, -10], [-10, 0], [0, 0], [0, -10]]] obstacle_outline = [[[-10, -10], [-10, 0], [0, 0], [0, -10]]]
obstacle_name = sf.create_entity( obstacle_name = sf.create_entity(
"obstacle", poses=obstacle_pose, outlines=obstacle_outline "obstacle", positions=[[50, 50]], orientations=[[0]], outlines=obstacle_outline
) )
# create a robofish with 100 timesteps and 40ms between the timesteps. If we would not give a name, the name would be generated to be robot_1. # create a robofish with 1000 timesteps. If we would not give a name, the name would be generated to be robot_1.
robofish_timesteps = 4 robofish_timesteps = 1000
robofish_poses = np.zeros((robofish_timesteps, 4)) robofish_poses = np.ones((robofish_timesteps, 4)) * 50
sf.create_entity("robot", robofish_poses, name="robot", monotonic_step=40) robot = sf.create_entity("robot", robofish_poses, name="robot")
# create multiple fishes with timestamps. Since we don't specify names, but only the type "fish" the fishes will be named ["fish_1", "fish_2", "fish_3"] # create multiple fishes with timestamps. Since we don't specify names, but only the type "fish" the fishes will be named ["fish_1", "fish_2", "fish_3"]
agents = 3 agents = 3
timesteps = 5 timesteps = 1000
timestamps = np.linspace(0, timesteps + 1, timesteps) # timestamps = np.linspace(0, timesteps + 1, timesteps)
agent_poses = np.random.random((agents, timesteps, 4)) agent_poses = np.random.random((agents, timesteps, 4))
fish_names = sf.create_multiple_entities( fishes = sf.create_multiple_entities("fish", agent_poses)
"fish", agent_poses, monotonic_points=timestamps
)
# This would throw an exception if the file was invalid # This would throw an exception if the file was invalid
sf.validate() sf.validate()
# Save file validates aswell # Save file validates aswell
example_file = full_path("example.hdf5")
sf.save(example_file) sf.save_as(path)
# Closing and opening files (just for demonstration) # Closing and opening files (just for demonstration)
sf.close() sf.close()
sf = robofish.io.File(path=example_file) sf = robofish.io.File(path=path)
print("\nEntity Names") print("\nEntity Names")
print(sf.entity_names) print(sf.entity_names)
# Get an array with all poses. As the length of poses varies per agent, it # Get an array with all poses. As the length of poses varies per agent, it is filled up with nans.
# is filled up with nans. The result is not interpolated and the time scales
# per agent are different. It is planned to create a warning in the case of
# different time scales and have another function, which generates an
# interpolated array.
print("\nAll poses") print("\nAll poses")
print(sf.select_poses()) print(sf.entity_poses)
print("\nFish poses") print("\nFish poses")
print(sf.select_poses(lambda e: e.category == "fish")) print(sf.select_entity_poses(lambda e: e.category == "fish"))
print("\nFile structure") print("\nFile structure")
print(sf) print(sf)
if __name__ == "__main__":
create_example_file("example.hdf5")
``` ```
%% Output %% Output
Entity Names Entity Names
['fish_1', 'fish_2', 'fish_3', 'obstacle_1', 'robot'] ['fish_1', 'fish_2', 'fish_3', 'obstacle_1', 'robot']
All poses All poses
[[[8.86584103e-01 2.35670820e-01 5.41754842e-01 4.49850202e-01] [[[5.56598067e-01 2.42021829e-01 2.45265663e-01 2.95294344e-01]
[8.15511882e-01 4.78223324e-01 6.29803419e-01 1.12592392e-01] [9.83367860e-01 4.36241180e-01 5.68063319e-01 8.96367550e-01]
[1.53732300e-01 7.24954247e-01 9.38574493e-01 4.65665817e-01] [8.71030211e-01 9.32705551e-02 8.51928890e-01 9.48658109e-01]
[9.10354614e-01 4.47880208e-01 3.81429136e-01 9.67544317e-01] ...
[6.07822955e-01 5.20158827e-01 8.17965686e-01 8.42760384e-01]] [6.94550753e-01 6.52826130e-01 6.08456850e-01 4.88614887e-01]
[4.84500438e-01 1.14949882e-01 6.08556986e-01 7.93362781e-02]
[[2.29353935e-01 8.80753636e-01 7.94585168e-01 2.22074524e-01] [9.54909027e-01 3.18913072e-01 4.58294243e-01 7.45387852e-01]]
[6.13970399e-01 1.33511815e-02 2.89155185e-01 2.65219092e-01]
[6.62197351e-01 6.47982001e-01 9.46004018e-02 6.59599364e-01] [[7.51943365e-02 9.95502114e-01 5.04003823e-01 8.36720586e-01]
[4.86104101e-01 4.23153102e-01 1.39821902e-01 3.11809748e-01] [8.18848014e-01 4.04324770e-01 5.49858093e-01 3.51742476e-01]
[8.03322852e-01 9.52799857e-01 3.89638603e-01 6.43237352e-01]] [1.66903093e-01 1.78061739e-01 2.81622916e-01 8.88221264e-01]
...
[[9.70978260e-01 6.75936878e-01 6.23196602e-01 8.42264950e-01] [7.69020915e-01 6.33118331e-01 4.15713340e-01 4.24170971e-01]
[4.07079160e-01 8.46290290e-01 5.64092159e-01 3.56871307e-01] [7.64205098e-01 7.78579533e-01 7.44598091e-01 3.30398619e-01]
[4.84096229e-01 8.60232174e-01 1.39015794e-01 7.82253265e-01] [4.45223182e-01 9.25011218e-01 2.36187894e-02 7.62242600e-02]]
[1.24170482e-01 2.21511930e-01 8.88282284e-02 4.53450561e-01]
[1.28404438e-01 2.87771430e-02 4.57022637e-01 9.80571806e-01]] [[7.73669600e-01 3.54849041e-01 4.21867281e-01 9.16552365e-01]
[4.73650604e-01 1.79305673e-01 8.38760436e-01 3.96051705e-01]
[2.01547332e-02 8.12301695e-01 2.78097481e-01 8.67732406e-01]
...
[8.12627971e-01 6.28660858e-01 2.13196307e-01 6.49513781e-01]
[5.58035910e-01 4.63277161e-01 8.21570277e-01 6.79726541e-01]
[7.10023165e-01 5.45146585e-01 8.51007760e-01 9.56029415e-01]]
[[5.00000000e+01 5.00000000e+01 0.00000000e+00 0.00000000e+00] [[5.00000000e+01 5.00000000e+01 1.00000000e+00 0.00000000e+00]
[ nan nan nan nan]
[ nan nan nan nan] [ nan nan nan nan]
...
[ nan nan nan nan] [ nan nan nan nan]
[ nan nan nan nan] [ nan nan nan nan]
[ nan nan nan nan]] [ nan nan nan nan]]
[[0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00] [[5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]
[0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00] [5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]
[0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00] [5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]
[0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00] ...
[ nan nan nan nan]]] [5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]
[5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]
[5.00000000e+01 5.00000000e+01 5.00000000e+01 5.00000000e+01]]]
Fish poses Fish poses
[[[0.8865841 0.23567082 0.54175484 0.4498502 ] [[[0.55659807 0.24202183 0.24526566 0.29529434]
[0.81551188 0.47822332 0.62980342 0.11259239] [0.98336786 0.43624118 0.56806332 0.89636755]
[0.1537323 0.72495425 0.93857449 0.46566582] [0.87103021 0.09327056 0.85192889 0.94865811]
[0.91035461 0.44788021 0.38142914 0.96754432] ...
[0.60782295 0.52015883 0.81796569 0.84276038]] [0.69455075 0.65282613 0.60845685 0.48861489]
[0.48450044 0.11494988 0.60855699 0.07933628]
[[0.22935393 0.88075364 0.79458517 0.22207452] [0.95490903 0.31891307 0.45829424 0.74538785]]
[0.6139704 0.01335118 0.28915519 0.26521909]
[0.66219735 0.647982 0.0946004 0.65959936] [[0.07519434 0.99550211 0.50400382 0.83672059]
[0.4861041 0.4231531 0.1398219 0.31180975] [0.81884801 0.40432477 0.54985809 0.35174248]
[0.80332285 0.95279986 0.3896386 0.64323735]] [0.16690309 0.17806174 0.28162292 0.88822126]
...
[[0.97097826 0.67593688 0.6231966 0.84226495] [0.76902092 0.63311833 0.41571334 0.42417097]
[0.40707916 0.84629029 0.56409216 0.35687131] [0.7642051 0.77857953 0.74459809 0.33039862]
[0.48409623 0.86023217 0.13901579 0.78225327] [0.44522318 0.92501122 0.02361879 0.07622426]]
[0.12417048 0.22151193 0.08882823 0.45345056]
[0.12840444 0.02877714 0.45702264 0.98057181]]] [[0.7736696 0.35484904 0.42186728 0.91655236]
[0.4736506 0.17930567 0.83876044 0.3960517 ]
[0.02015473 0.8123017 0.27809748 0.86773241]
...
[0.81262797 0.62866086 0.21319631 0.64951378]
[0.55803591 0.46327716 0.82157028 0.67972654]
[0.71002316 0.54514658 0.85100776 0.95602942]]]
File structure File structure
version: [1 0] format_url: https://git.imp.fu-berlin.de/bioroboticslab/robofish/track_format/-/releases/1.0
world size: [100. 100.] format_version: [1 0]
world_size_cm: [100. 100.]
| entities | entities
|---| fish_1 |---| fish_1
|---|--- type: fish |---|--- category: fish
|---|--- poses: Shape (5, 4) |---|--- orientations: Shape (1000, 2)
|---|---| time |---|--- positions: Shape (1000, 2)
|---|---|--- monotonic points: Shape (5,)
|---| fish_2 |---| fish_2
|---|--- type: fish |---|--- category: fish
|---|--- poses: Shape (5, 4) |---|--- orientations: Shape (1000, 2)
|---|---| time |---|--- positions: Shape (1000, 2)
|---|---|--- monotonic points: Shape (5,)
|---| fish_3 |---| fish_3
|---|--- type: fish |---|--- category: fish
|---|--- poses: Shape (5, 4) |---|--- orientations: Shape (1000, 2)
|---|---| time |---|--- positions: Shape (1000, 2)
|---|---|--- monotonic points: Shape (5,)
|---| obstacle_1 |---| obstacle_1
|---|--- type: obstacle |---|--- category: obstacle
|---|--- orientations: Shape (1, 2)
|---|--- outlines: Shape (1, 4, 2) |---|--- outlines: Shape (1, 4, 2)
|---|--- poses: Shape (1, 4) |---|--- positions: Shape (1, 2)
|---|---| time
|---| robot |---| robot
|---|--- type: robot |---|--- category: robot
|---|--- poses: Shape (4, 4) |---|--- orientations: Shape (1000, 2)
|---|---| time |---|--- positions: Shape (1000, 2)
|---|---|--- monotonic step: 40 | samplings
|--- default: 25 hz
|---| 25 hz
|---|--- frequency_hz: 25.0
......
examples/example_basic.py
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#! /usr/bin/env python3 #! /usr/bin/env python3
import robofish.io import robofish.io
from robofish.io import utils
import numpy as np import numpy as np
......
setup.py
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...@@ -14,9 +14,15 @@ entry_points = { ...@@ -14,9 +14,15 @@ entry_points = {
] ]
} }
def source_version(): def source_version():
version_parts = ( version_parts = (
run(["git", "describe", "--tags", "--dirty"], check=True, stdout=PIPE, encoding="utf-8") run(
["git", "describe", "--tags", "--dirty"],
check=True,
stdout=PIPE,
encoding="utf-8",
)
.stdout.strip() .stdout.strip()
.split("-") .split("-")
) )
...@@ -36,12 +42,20 @@ def source_version(): ...@@ -36,12 +42,20 @@ def source_version():
return version return version
setup( setup(
name="robofish-io", name="robofish-io",
version=source_version(), version=source_version(),
author="", author="",
author_email="", author_email="",
install_requires=["h5py>=3", "numpy", "seaborn", "pandas", "deprecation"], install_requires=[
"h5py>=3",
"numpy",
"seaborn",
"pandas",
"deprecation",
"testbook",
],
classifiers=[ classifiers=[
"Development Status :: 3 - Alpha", "Development Status :: 3 - Alpha",
"Intended Audience :: Science/Research", "Intended Audience :: Science/Research",
......
src/robofish/io/entity.py
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...@@ -98,7 +98,7 @@ class Entity(h5py.Group): ...@@ -98,7 +98,7 @@ class Entity(h5py.Group):
else: else:
if poses is not None: if poses is not None:
assert poses.shape[1] == 3 or poses.shape[1] == 4 assert poses.shape[1] in [3, 4]
positions = poses[:, :2] positions = poses[:, :2]
orientations = poses[:, 2:] orientations = poses[:, 2:]
if orientations is not None and orientations.shape[1] == 1: if orientations is not None and orientations.shape[1] == 1:
......
tests/robofish/evaluate/test_app_evaluate.py
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...@@ -22,7 +22,7 @@ def test_app_validate(): ...@@ -22,7 +22,7 @@ def test_app_validate():
self.names = None self.names = None
self.save_path = graphics_out self.save_path = graphics_out
# TODO: Get rid of deprecated get_poses function # TODO: Get rid of deprecation
with pytest.warns(DeprecationWarning): with pytest.warns(DeprecationWarning):
app.evaluate(DummyArgs("speed")) app.evaluate(DummyArgs("speed"))
graphics_out.unlink() graphics_out.unlink()
tests/robofish/io/test_examples.py
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import robofish.io import robofish.io
from robofish.io import utils from robofish.io import utils
from pathlib import Path from pathlib import Path
from testbook import testbook
import sys import sys
sys.path.append(str(utils.full_path(__file__, "../../../examples/"))) sys.path.append(str(utils.full_path(__file__, "../../../examples/")))
ipynb_path = utils.full_path(__file__, "../../../examples/example_basic.ipynb")
path = utils.full_path(__file__, "../../../examples/tmp_example.hdf5") path = utils.full_path(__file__, "../../../examples/tmp_example.hdf5")
if path.exists(): if path.exists():
path.unlink() path.unlink()
...@@ -24,3 +25,9 @@ def test_example_basic(): ...@@ -24,3 +25,9 @@ def test_example_basic():
example_basic.create_example_file(path) example_basic.create_example_file(path)
path.unlink() path.unlink()
def test_example_basic_ipynb():
# Executing the notebook should not lead to an exception
with testbook(str(ipynb_path), execute=True) as tb:
pass
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