diff --git a/examples/example_basic.ipynb b/examples/example_basic.ipynb
index 7fa65910b9078944cef3d566248c6978558e99cb..23005dbf8504108e1b47076fed5b73bb5ce051f9 100644
--- a/examples/example_basic.ipynb
+++ b/examples/example_basic.ipynb
@@ -12,7 +12,7 @@
"\n",
"def create_example_file(path):\n",
" # Create a new io file object with a 100x100cm world\n",
- " f = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25.0)\n",
+ " f = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25.0, world_shape=\"rectangle\")\n",
"\n",
" # create a robofish with 1000 timesteps. If we would not give a name, the name would be generated to be robot_1.\n",
" robofish_timesteps = 1000\n",
diff --git a/examples/example_basic.py b/examples/example_basic.py
index f37d0cc253053f8e5ffa06000d79dea38d80f927..a8257746399d3aa461a55e5cfbf4061d4ffa7f4e 100755
--- a/examples/example_basic.py
+++ b/examples/example_basic.py
@@ -5,7 +5,9 @@ import numpy as np
def create_example_file(path):
# Create a new io file object with a 100x100cm world.
# Mode "w" means that the file should be opened with write access.
- f = robofish.io.File(path, "w", world_size_cm=[100, 100], frequency_hz=25.0)
+ f = robofish.io.File(
+ path, "w", world_size_cm=[100, 100], frequency_hz=25.0, world_shape="rectangle"
+ )
# create a robofish with 1000 timesteps. If we would not give a name, the name would be generated to be robot_1.
robofish_timesteps = 1000
diff --git a/examples/example_readme.py b/examples/example_readme.py
index 7b2e22c66fbdb08d9520c0a23deac58ed65f9184..cf77488b96577c557d5e3f1bafa26e9f39bd5583 100644
--- a/examples/example_readme.py
+++ b/examples/example_readme.py
@@ -5,7 +5,9 @@ import numpy as np
def create_example_file(path):
# Create a new robofish io file
# Mode "w" means that the file should be opened with write access.
- f = robofish.io.File(path, "w", world_size_cm=[100, 100], frequency_hz=25.0)
+ f = robofish.io.File(
+ path, "w", world_size_cm=[100, 100], frequency_hz=25.0, world_shape="rectangle"
+ )
f.attrs["experiment_setup"] = "This is a simple example with made up data."
# Create a new robot entity with 10 timesteps.
diff --git a/src/robofish/io/app.py b/src/robofish/io/app.py
index 2f4091db6ac1a0c51d40b42a3bb31ddd5086be14..0efc84c86cf9f4a4fd986da6ba8d4ca863e47665 100644
--- a/src/robofish/io/app.py
+++ b/src/robofish/io/app.py
@@ -430,7 +430,9 @@ def update_world_shape(args: dict = None) -> None:
for file in pbar:
pbar.set_description(f"Updating {file.name}")
- with robofish.io.File(file, "r+") as f:
+ with robofish.io.File(
+ file, "r+", validate_when_saving=False, calculate_data_on_close=False
+ ) as f:
f.attrs["world_shape"] = args.world_shape
pbar.update(1)
diff --git a/tests/resources/invalid.hdf5 b/tests/resources/invalid.hdf5
index 18e2361c58dce4478a173e40f9c998cda90beac7..e76736436cc0d0499e8a95a031bccc449a07fc50 100755
Binary files a/tests/resources/invalid.hdf5 and b/tests/resources/invalid.hdf5 differ
diff --git a/tests/resources/nan_test.hdf5 b/tests/resources/nan_test.hdf5
index 92c3050e3b5204721b0eb0a0543adf0c4d5f65c0..daabe3c98a442a0f35bfe834d9c09cae6cd8ad59 100644
Binary files a/tests/resources/nan_test.hdf5 and b/tests/resources/nan_test.hdf5 differ
diff --git a/tests/resources/valid_1.hdf5 b/tests/resources/valid_1.hdf5
index 664e40a39b908364ac70cf99dc11715a6ecd2abc..cb5d38c857def87d8719ef309c189fe4374bc308 100644
Binary files a/tests/resources/valid_1.hdf5 and b/tests/resources/valid_1.hdf5 differ
diff --git a/tests/resources/valid_2.hdf5 b/tests/resources/valid_2.hdf5
index eb8c69e1a01f1704c29c94b7c85590c5443275dd..a080dda64d6ba7d59d2505482757249725376005 100644
Binary files a/tests/resources/valid_2.hdf5 and b/tests/resources/valid_2.hdf5 differ
diff --git a/tests/robofish/evaluate/test_app_evaluate.py b/tests/robofish/evaluate/test_app_evaluate.py
index d8b1d69947a7e6208b085303cb521c95b9a8ec60..4b1332f7dad72d268e1c6f59a571731f2ca06159 100644
--- a/tests/robofish/evaluate/test_app_evaluate.py
+++ b/tests/robofish/evaluate/test_app_evaluate.py
@@ -14,46 +14,43 @@ h5py_file_2 = utils.full_path(__file__, "../../resources/valid_2.hdf5")
nan_file_path = utils.full_path(__file__, "../../resources/nan_test.hdf5")
+class DummyArgs:
+ def __init__(self, analysis_type, paths, save_path, add_train_data):
+ self.paths = paths
+ self.names = None
+ self.analysis_type = analysis_type
+ self.save_path = save_path
+ self.labels = None
+ self.add_train_data = add_train_data
+
+
def test_app_validate(tmp_path):
"""This tests the function of the robofish-io-validate command"""
- class DummyArgs:
- def __init__(self, analysis_type, paths, save_path):
- self.paths = paths
- self.names = None
- self.analysis_type = analysis_type
- self.save_path = save_path
- self.labels = None
-
for mode in app.function_dict().keys():
if mode == "all":
- app.evaluate(DummyArgs(mode, [h5py_file_1], tmp_path))
- app.evaluate(DummyArgs(mode, [h5py_file_2, h5py_file_2], tmp_path))
- app.evaluate(DummyArgs(mode, [nan_file_path], tmp_path))
+ app.evaluate(DummyArgs(mode, [h5py_file_1], tmp_path, False))
+ app.evaluate(DummyArgs(mode, [h5py_file_2, h5py_file_2], tmp_path, False))
+ app.evaluate(DummyArgs(mode, [nan_file_path], tmp_path, False))
else:
- app.evaluate(DummyArgs(mode, [h5py_file_1], tmp_path / "image.png"))
+ app.evaluate(DummyArgs(mode, [h5py_file_1], tmp_path / "image.png", False))
app.evaluate(
- DummyArgs(mode, [h5py_file_2, h5py_file_2], tmp_path / "image.png")
+ DummyArgs(
+ mode, [h5py_file_2, h5py_file_2], tmp_path / "image.png", False
+ )
)
def test_app_validate(tmp_path):
"""This tests the function of the robofish-io-validate command"""
-
- class DummyArgs:
- def __init__(self, analysis_type, paths, save_path):
- self.paths = paths
- self.names = None
- self.analysis_type = analysis_type
- self.save_path = save_path
- self.labels = None
-
for mode in app.function_dict().keys():
if mode == "all":
- app.evaluate(DummyArgs(mode, [h5py_file_1], tmp_path))
- app.evaluate(DummyArgs(mode, [h5py_file_2, h5py_file_2], tmp_path))
+ app.evaluate(DummyArgs(mode, [h5py_file_1], tmp_path, False))
+ app.evaluate(DummyArgs(mode, [h5py_file_2, h5py_file_2], tmp_path, False))
else:
- app.evaluate(DummyArgs(mode, [h5py_file_1], tmp_path / "image.png"))
+ app.evaluate(DummyArgs(mode, [h5py_file_1], tmp_path / "image.png", False))
app.evaluate(
- DummyArgs(mode, [h5py_file_2, h5py_file_2], tmp_path / "image.png")
+ DummyArgs(
+ mode, [h5py_file_2, h5py_file_2], tmp_path / "image.png", False
+ )
)
diff --git a/tests/robofish/io/test_entity.py b/tests/robofish/io/test_entity.py
index 0d843bb2829b40b9b0df4b8a05afd27c43b219db..38d50dea85d464b39a4a5958f80e00231a032500 100644
--- a/tests/robofish/io/test_entity.py
+++ b/tests/robofish/io/test_entity.py
@@ -4,7 +4,9 @@ import numpy as np
def test_entity_object():
- sf = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25)
+ sf = robofish.io.File(
+ world_size_cm=[100, 100], frequency_hz=25, world_shape="rectangle"
+ )
f = sf.create_entity("fish", positions=[[10, 10]])
assert type(f) == robofish.io.Entity, "Type of entity was wrong"
assert f.name == "fish_1", "Name of entity was wrong"
@@ -40,7 +42,9 @@ def test_entity_turns_speeds():
There is an open issue, to check this test again: https://git.imp.fu-berlin.de/bioroboticslab/robofish/io/-/issues/14
"""
- f = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25)
+ f = robofish.io.File(
+ world_size_cm=[100, 100], frequency_hz=25, world_shape="rectangle"
+ )
circle_rad = np.linspace(0, 2 * np.pi, num=100)
circle_size = 40
poses_rad = np.stack(
diff --git a/tests/robofish/io/test_file.py b/tests/robofish/io/test_file.py
index 04d4b988148fe4c44304deac663e1bb5d6422098..927f44ff4d30f44b84bb396529b4d31c0a563698 100644
--- a/tests/robofish/io/test_file.py
+++ b/tests/robofish/io/test_file.py
@@ -15,33 +15,37 @@ nan_file_path = utils.full_path(__file__, "../../resources/nan_test.hdf5")
def test_constructor():
- sf = robofish.io.File(world_size_cm=[100, 100])
+ sf = robofish.io.File(world_size_cm=[100, 100], world_shape="rectangle")
sf.validate()
sf.close()
def test_context():
- with robofish.io.File(world_size_cm=[10, 10]) as f:
+ with robofish.io.File(world_size_cm=[10, 10], world_shape="rectangle") as f:
pass
def test_new_file_w_path(tmp_path):
f = tmp_path / "file.hdf5"
- sf = robofish.io.File(f, "w", world_size_cm=[100, 100], frequency_hz=25)
+ sf = robofish.io.File(
+ f, "w", world_size_cm=[100, 100], frequency_hz=25, world_shape="rectangle"
+ )
sf.create_entity("fish")
sf.validate()
sf.close()
def test_missing_attribute():
- sf = robofish.io.File(world_size_cm=[10, 10])
+ sf = robofish.io.File(world_size_cm=[10, 10], world_shape="rectangle")
sf.attrs.pop("world_size_cm")
assert not sf.validate(strict_validate=False)[0]
sf.close()
def test_single_entity_frequency_hz():
- sf = robofish.io.File(world_size_cm=[100, 100], frequency_hz=(1000 / 40))
+ sf = robofish.io.File(
+ world_size_cm=[100, 100], frequency_hz=(1000 / 40), world_shape="rectangle"
+ )
test_poses = np.ones(shape=(10, 4))
test_poses[:, 3] = 0 # All Fish pointing right
sf.create_entity("robofish", poses=test_poses)
@@ -54,7 +58,9 @@ def test_single_entity_frequency_hz():
def test_single_entity_monotonic_time_points_us():
with pytest.warns(Warning):
sf = robofish.io.File(
- world_size_cm=[100, 100], monotonic_time_points_us=np.ones(10)
+ world_size_cm=[100, 100],
+ monotonic_time_points_us=np.ones(10),
+ world_shape="rectangle",
)
test_poses = np.ones(shape=(10, 4))
test_poses[:, 3] = 0 # All Fish pointing right
@@ -76,7 +82,9 @@ def test_multiple_entities():
with pytest.warns(Warning):
sf = robofish.io.File(
- world_size_cm=[100, 100], monotonic_time_points_us=m_points
+ world_size_cm=[100, 100],
+ monotonic_time_points_us=m_points,
+ world_shape="rectangle",
)
returned_entities = sf.create_multiple_entities("fish", poses)
returned_names = [entity.name for entity in returned_entities]
@@ -146,7 +154,9 @@ def test_multiple_entities():
def test_actions_speeds_turns_angles():
- with robofish.io.File(world_size_cm=[100, 100], frequency_hz=25) as f:
+ with robofish.io.File(
+ world_size_cm=[100, 100], frequency_hz=25, world_shape="rectangle"
+ ) as f:
poses = np.zeros((10, 100, 3))
f.create_multiple_entities("fish", poses=poses)
@@ -155,7 +165,9 @@ def test_actions_speeds_turns_angles():
def test_entity_poses_rad(caplog):
- with robofish.io.File(world_size_cm=[100, 100], frequency_hz=25) as f:
+ with robofish.io.File(
+ world_size_cm=[100, 100], frequency_hz=25, world_shape="rectangle"
+ ) as f:
# Create an entity, using radians
f.create_entity("fish", poses=np.ones((100, 3)))
@@ -169,7 +181,9 @@ def test_entity_poses_rad(caplog):
def test_entity_positions_no_orientation():
- with robofish.io.File(world_size_cm=[100, 100], frequency_hz=25) as f:
+ with robofish.io.File(
+ world_size_cm=[100, 100], frequency_hz=25, world_shape="rectangle"
+ ) as f:
# Create an entity, using radians
f.create_entity("fish", positions=np.ones((100, 2)))