diff --git a/examples/example_basic.py b/examples/example_basic.py
index 70c39b6b862543abba085657a339d4588b8cb67c..359e4d01983bbf67b125ffd34f1d7a97f11e5c05 100755
--- a/examples/example_basic.py
+++ b/examples/example_basic.py
@@ -5,48 +5,53 @@ from robofish.io import utils
import numpy as np
-# Create a new io file object with a 100x100cm world
-sf = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25.0)
+def create_example_file(path):
+ # Create a new io file object with a 100x100cm world
+ sf = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25.0)
-# create a simple obstacle, fixed in place, fixed outline
-obstacle_outline = [[[-10, -10], [-10, 0], [0, 0], [0, -10]]]
-obstacle_name = sf.create_entity(
- "obstacle", positions=[[50, 50]], orientations=[[0]], outlines=obstacle_outline
-)
+ # create a simple obstacle, fixed in place, fixed outline
+ obstacle_outline = [[[-10, -10], [-10, 0], [0, 0], [0, -10]]]
+ obstacle_name = sf.create_entity(
+ "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.
-robofish_timesteps = 1000
-robofish_poses = np.ones((robofish_timesteps, 4)) * 50
-robot = sf.create_entity("robot", robofish_poses, name="robot")
+ # 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
+ robofish_poses = np.ones((robofish_timesteps, 4)) * 50
+ 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"]
-agents = 3
-timesteps = 1000
-# timestamps = np.linspace(0, timesteps + 1, timesteps)
-agent_poses = np.random.random((agents, timesteps, 4))
+ # 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
+ timesteps = 1000
+ # timestamps = np.linspace(0, timesteps + 1, timesteps)
+ agent_poses = np.random.random((agents, timesteps, 4))
-fishes = sf.create_multiple_entities("fish", agent_poses)
+ fishes = sf.create_multiple_entities("fish", agent_poses)
-# This would throw an exception if the file was invalid
-sf.validate()
+ # This would throw an exception if the file was invalid
+ sf.validate()
-# Save file validates aswell
-example_file = utils.full_path(__file__, "example.hdf5")
-sf.save_as(example_file)
+ # Save file validates aswell
-# Closing and opening files (just for demonstration)
-sf.close()
-sf = robofish.io.File(path=example_file)
+ sf.save_as(path)
-print("\nEntity Names")
-print(sf.entity_names)
+ # Closing and opening files (just for demonstration)
+ sf.close()
+ sf = robofish.io.File(path=path)
-# Get an array with all poses. As the length of poses varies per agent, it is filled up with nans.
-print("\nAll poses")
-print(sf.poses)
+ print("\nEntity Names")
+ print(sf.entity_names)
-print("\nFish poses")
-print(sf.select_poses(lambda e: e.category == "fish"))
+ # Get an array with all poses. As the length of poses varies per agent, it is filled up with nans.
+ print("\nAll poses")
+ print(sf.poses)
-print("\nFile structure")
-print(sf)
+ print("\nFish poses")
+ print(sf.select_poses(lambda e: e.category == "fish"))
+
+ print("\nFile structure")
+ print(sf)
+
+
+if __name__ == "__main__":
+ create_example_file("example.hdf5")
diff --git a/examples/example_readme.py b/examples/example_readme.py
index 71442e29faac159ffc739a10340ea65ecc64e005..cec24cf35dfe83115e16cfd317f01d4a9078ef9a 100644
--- a/examples/example_readme.py
+++ b/examples/example_readme.py
@@ -2,34 +2,35 @@ import robofish.io
import numpy as np
from pathlib import Path
-path = Path("example.hdf5")
-if path.exists():
- path.unlink()
+def create_example_file(path):
+ # By using the context, the file will be automatically validated
+ with robofish.io.File(path, "w", world_size_cm=[100, 100], frequency_hz=25.0) as f:
+ f.attrs["experiment_setup"] = "This is a simple example with made up data."
-# By using the context, the file will be automatically validated
-with robofish.io.File(path, "w", world_size_cm=[100, 100], frequency_hz=25.0) as f:
- f.attrs["experiment_setup"] = "This is a simple example with made up data."
+ # Create a single robot with 30 timesteps
+ # positions are passed separately
+ # orientations are passed as with two columns -> orientation_x and orientation_y
+ f.create_entity(
+ category="robot",
+ name="robot",
+ positions=np.zeros((100, 2)),
+ orientations=np.ones((100, 2)) * [0, 1],
+ )
- # Create a single robot with 30 timesteps
- # positions are passed separately
- # orientations are passed as with two columns -> orientation_x and orientation_y
- f.create_entity(
- category="robot",
- name="robot",
- positions=np.zeros((100, 2)),
- orientations=np.ones((100, 2)) * [0, 1],
- )
+ # Create fishes with 30 poses (x, y, orientation_rad)
+ poses = np.zeros((100, 3))
+ poses[:, 0] = np.arange(-50, 50)
+ poses[:, 1] = np.arange(-50, 50)
+ poses[:, 2] = np.arange(0, 2 * np.pi, step=2 * np.pi / 100)
+ fish = f.create_entity("fish", poses=poses)
+ fish.attrs["species"] = "My rotating spaghetti fish"
+ fish.attrs["fish_standard_length_cm"] = 10
- # Create fishes with 30 poses (x, y, orientation_rad)
- poses = np.zeros((100, 3))
- poses[:, 0] = np.arange(-50, 50)
- poses[:, 1] = np.arange(-50, 50)
- poses[:, 2] = np.arange(0, 2 * np.pi, step=2 * np.pi / 100)
- fish = f.create_entity("fish", poses=poses)
- fish.attrs["species"] = "My rotating spaghetti fish"
- fish.attrs["fish_standard_length_cm"] = 10
+ # Show and save the file
+ print(f)
+ print("Poses Shape: ", f.poses.shape)
- # Show and save the file
- print(f)
- print("Poses Shape: ", f.poses.shape)
+
+if __name__ == "__main__":
+ path = create_example_file("example.hdf5")
diff --git a/src/robofish/io/file.py b/src/robofish/io/file.py
index 2a9392743892c72cd3b4e72c3c45774681e5e553..3e3b0121794a968d3d84bee488200f817f6127bb 100644
--- a/src/robofish/io/file.py
+++ b/src/robofish/io/file.py
@@ -129,8 +129,10 @@ class File(h5py.File):
return self
def __exit__(self, type, value, traceback):
- self.validate()
- self.close()
+ # Check if the context was left under normal circumstances
+ if (type, value, traceback) is (None, None, None):
+ self.validate()
+ self.close()
def save_as(self, path: Union[str, Path], strict_validate: bool = True):
""" Save a copy of the file
diff --git a/tests/robofish/io/test_examples.py b/tests/robofish/io/test_examples.py
index 94b60155e311d41dd87fc650a6863f496d7cdc59..1d0379fb1b06448e5f733c3690ff48a4f623592c 100644
--- a/tests/robofish/io/test_examples.py
+++ b/tests/robofish/io/test_examples.py
@@ -7,9 +7,20 @@ import sys
sys.path.append(str(utils.full_path(__file__, "../../../examples/")))
+path = utils.full_path(__file__, "../../../examples/tmp_example.hdf5")
+if path.exists():
+ path.unlink()
+
+
def test_example_readme():
import example_readme
+ example_readme.create_example_file(path)
+ path.unlink()
+
def test_example_basic():
import example_basic
+
+ example_basic.create_example_file(path)
+ path.unlink()