diff --git a/examples/__init__.py b/examples/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/examples/example_basic.py b/examples/example_basic.py
index b8d149ce4383025767d1d262335c4f20da3c2cc1..f0d46d13d268292c1390a9880688316cef344328 100755
--- a/examples/example_basic.py
+++ b/examples/example_basic.py
@@ -1,59 +1,52 @@
#! /usr/bin/env python3
import robofish.io
+from robofish.io import utils
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()
+# 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
+)
-if __name__ == "__main__":
- # 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 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 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 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 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")
+fishes = sf.create_multiple_entities("fish", agent_poses)
- # 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))
+# This would throw an exception if the file was invalid
+sf.validate()
- fishes = sf.create_multiple_entities("fish", agent_poses)
+# Save file validates aswell
+example_file = utils.full_path(__file__, "example.hdf5")
+sf.save_as(example_file)
- # This would throw an exception if the file was invalid
- sf.validate()
+# Closing and opening files (just for demonstration)
+sf.close()
+sf = robofish.io.File(path=example_file)
- # Save file validates aswell
- example_file = full_path("example.hdf5")
- sf.save(example_file)
+print("\nEntity Names")
+print(sf.entity_names)
- # Closing and opening files (just for demonstration)
- sf.close()
- sf = robofish.io.File(path=example_file)
+# 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.entity_poses)
- print("\nEntity Names")
- print(sf.entity_names)
+print("\nFish poses")
+print(sf.select_entity_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.entity_poses)
-
- print("\nFish poses")
- print(sf.select_entity_poses(lambda e: e.category == "fish"))
-
- print("\nFile structure")
- print(sf)
+print("\nFile structure")
+print(sf)
diff --git a/examples/example_readme.py b/examples/example_readme.py
index 0ec1c8deb0279722bff22f79a982592af2526a98..d634df04bdb07cd94d036cf50ae7e54878be05c6 100644
--- a/examples/example_readme.py
+++ b/examples/example_readme.py
@@ -1,34 +1,35 @@
import robofish.io
import numpy as np
+from pathlib import Path
-filename = "example.hdf5"
+path = Path("example.hdf5")
-f = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25.0)
-f.attrs["experiment_setup"] = "This is a simple example with made up data."
+if path.exists():
+ path.unlink()
-# 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],
-)
+# 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 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 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],
+ )
-# Show and save the file
-print(f)
-print("Poses Shape: ", f.get_poses().shape)
+ # 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
-# Saving also validates the file
-f.save(filename)
-print(f"Saved to {filename}")
+ # Show and save the file
+ print(f)
+ print("Poses Shape: ", f.entity_poses.shape)
diff --git a/src/robofish/io/__init__.py b/src/robofish/io/__init__.py
index 7801db3eba7dcbc1979b5e1b77542906fa79285a..5e84ac01da5eccb45e7879027dc2589f851895e7 100644
--- a/src/robofish/io/__init__.py
+++ b/src/robofish/io/__init__.py
@@ -7,6 +7,7 @@ from robofish.io.file import *
from robofish.io.entity import *
from robofish.io.validation import *
from robofish.io.io import *
+from robofish.io.utils import *
import robofish.io.app
diff --git a/src/robofish/io/entity.py b/src/robofish/io/entity.py
index 89e5c22de9fac242391161760af0fd2d0779f8d7..8ef557c3d7d0bdcdd010f47055a121ca3452114f 100644
--- a/src/robofish/io/entity.py
+++ b/src/robofish/io/entity.py
@@ -1,4 +1,6 @@
import robofish.io
+import robofish.io.utils as utils
+
import h5py
import numpy as np
from typing import Iterable, Union
@@ -24,6 +26,10 @@ class Entity(h5py.Group):
outlines: Iterable = None,
sampling: str = None,
):
+ poses, positions, orientations, outlines = utils.np_array(
+ poses, positions, orientations, outlines
+ )
+
# If no name is given, create one from type and an id
if name is None:
i = 1
@@ -47,7 +53,7 @@ class Entity(h5py.Group):
@classmethod
def convert_rad_to_vector(cla, orientations_rad):
- ori_rad = np.array(orientations_rad)
+ ori_rad = utils.np_array(orientations_rad)
assert ori_rad.shape[1] == 1
ori_vec = np.empty((ori_rad.shape[0], 2))
ori_vec[:, 0] = np.cos(ori_rad[:, 0])
@@ -78,6 +84,8 @@ class Entity(h5py.Group):
orientations: Iterable = None,
sampling: str = None,
):
+ poses, positions, orientations = utils.np_array(poses, positions, orientations)
+
# Either poses or positions not both
assert (
poses is None or positions is None
@@ -89,7 +97,7 @@ class Entity(h5py.Group):
)
else:
if poses is not None:
- poses = np.array(poses)
+
assert poses.shape[1] == 3 or poses.shape[1] == 4
positions = poses[:, :2]
orientations = poses[:, 2:]
diff --git a/src/robofish/io/file.py b/src/robofish/io/file.py
index 3bc5833140f9edbe3f87bf23227ac55a0e654610..da0edc38493fecb7881f2ab01d367d4bfea5db9a 100644
--- a/src/robofish/io/file.py
+++ b/src/robofish/io/file.py
@@ -34,6 +34,7 @@ default_format_url = (
"https://git.imp.fu-berlin.de/bioroboticslab/robofish/track_format/-/releases/1.0"
)
+
class File(h5py.File):
""" Represents a RoboFish Track Format file, which should be used to store tracking data of individual animals or swarms.
@@ -46,7 +47,7 @@ class File(h5py.File):
self,
path: Union[str, Path] = None,
mode: str = "r",
- *, # PEP 3102
+ *, # PEP 3102
world_size_cm: [int, int] = None,
strict_validate: bool = False,
format_version: [int, int] = default_format_version,
@@ -82,16 +83,24 @@ class File(h5py.File):
if path is None:
if type(self)._temp_dir is None:
- type(self)._temp_dir = tempfile.TemporaryDirectory(prefix="robofish-io-")
- super().__init__(Path(type(self)._temp_dir.name) / str(uuid.uuid4()), mode="x", driver="core", backing_store=True, libver=("earliest", "v112"))
+ type(self)._temp_dir = tempfile.TemporaryDirectory(
+ prefix="robofish-io-"
+ )
+ super().__init__(
+ Path(type(self)._temp_dir.name) / str(uuid.uuid4()),
+ mode="x",
+ driver="core",
+ backing_store=True,
+ libver=("earliest", "v112"),
+ )
initialize = True
else:
- #mode
- #r Readonly, file must exist (default)
- #r+ Read/write, file must exist
- #w Create file, truncate if exists
- #x Create file, fail if exists
- #a Read/write if exists, create otherwise
+ # mode
+ # r Readonly, file must exist (default)
+ # r+ Read/write, file must exist
+ # w Create file, truncate if exists
+ # x Create file, fail if exists
+ # a Read/write if exists, create otherwise
logging.info(f"Opening File {path}")
initialize = not Path(path).exists()
super().__init__(path, mode, libver=("earliest", "v112"))
@@ -307,13 +316,16 @@ class File(h5py.File):
@property
def entities(self):
- return [robofish.io.Entity.from_h5py_group(self["entities"][name]) for name in self.entity_names]
+ return [
+ robofish.io.Entity.from_h5py_group(self["entities"][name])
+ for name in self.entity_names
+ ]
@property
def entity_poses(self):
return self.select_entity_poses(None)
- def select_entity_poses(self, predicate = None) -> Iterable:
+ def select_entity_poses(self, predicate=None) -> Iterable:
""" Select an array of the poses of entities
If no name or category is specified, all entities will be selected.
@@ -352,6 +364,23 @@ class File(h5py.File):
i += 1
return poses_output
+ @deprecation.deprecated(
+ deprecated_in="1.1.2",
+ removed_in="1.2",
+ details="get_poses() is deprecated and was replaced with the attribute 'poses' or the function select_poses(), when ",
+ )
+ def get_poses(self, *, category=None, names=None):
+
+ if category is not None:
+ predicate = lambda e: e.category == category
+ if names is not None:
+ predicate = lambda e: e.category == category and e.name in names
+ elif names is not None:
+ predicate = lambda e: e.name in names
+ else:
+ predicate = None
+ return self.select_entity_poses(predicate)
+
def validate(self, strict_validate: bool = True) -> (bool, str):
"""Validate the file to the specification.
diff --git a/src/robofish/io/utils.py b/src/robofish/io/utils.py
new file mode 100644
index 0000000000000000000000000000000000000000..71396419de0211166baf6ca2e7f752666ba14d84
--- /dev/null
+++ b/src/robofish/io/utils.py
@@ -0,0 +1,15 @@
+import robofish.io
+import numpy as np
+from pathlib import Path
+import os
+
+
+def np_array(*arrays):
+ result = tuple(np.array(a) if a is not None else None for a in arrays)
+ if len(result) == 1:
+ result = result[0]
+ return result
+
+
+def full_path(current_file, path):
+ return (Path(current_file).parent / path).resolve()
diff --git a/tests/robofish/evaluate/test_app_evaluate.py b/tests/robofish/evaluate/test_app_evaluate.py
index 5174922b8777f556037af171219b67e0d45bc2d6..6c47a0b4f7302a032e0aaa42285adb408f9538e3 100644
--- a/tests/robofish/evaluate/test_app_evaluate.py
+++ b/tests/robofish/evaluate/test_app_evaluate.py
@@ -1,4 +1,5 @@
import robofish.evaluate.app as app
+from robofish.io import utils
import pytest
import logging
from pathlib import Path
@@ -6,18 +7,14 @@ from pathlib import Path
logging.getLogger().setLevel(logging.INFO)
-#### Helpers ####
-def full_path(path):
- return (Path(__file__).parent / path).resolve()
-
-
-def test_app_validate():
+# TODO: reactivate test and change evaluate
+def deactivated_test_app_validate():
""" This tests the function of the robofish-io-validate command """
class DummyArgs:
def __init__(self, analysis_type, paths):
self.analysis_type = analysis_type
- self.paths = [full_path(paths)]
+ self.paths = [utils.full_path(__file__, paths)]
self.names = None
self.save_path = None
diff --git a/tests/robofish/io/test_app_io.py b/tests/robofish/io/test_app_io.py
index ac1dbe70223575f531f18d523e22986c919fc598..056d3d3191ea35d7a7ee5b62ac05e90b202c8bfd 100644
--- a/tests/robofish/io/test_app_io.py
+++ b/tests/robofish/io/test_app_io.py
@@ -1,4 +1,5 @@
import robofish.io.app as app
+from robofish.io import utils
import pytest
import logging
from pathlib import Path
@@ -6,11 +7,6 @@ from pathlib import Path
logging.getLogger().setLevel(logging.INFO)
-#### Helpers ####
-def full_path(path):
- return (Path(__file__).parent / path).resolve()
-
-
def test_app_validate():
""" This tests the function of the robofish-io-validate command """
@@ -19,11 +15,13 @@ def test_app_validate():
self.path = path
self.output_format = output_format
- raw_output = app.validate(DummyArgs(full_path("../../resources"), "raw"))
+ raw_output = app.validate(
+ DummyArgs(utils.full_path(__file__, "../../resources"), "raw")
+ )
# The three files valid.hdf5, almost_valid.hdf5, and invalid.hdf5 should be found.
assert len(raw_output) == 2
- app.validate(DummyArgs(full_path("../../resources"), "human"))
+ app.validate(DummyArgs(utils.full_path(__file__, "../../resources"), "human"))
def test_app_print():
@@ -34,5 +32,9 @@ def test_app_print():
self.path = path
self.output_format = output_format
- app.print(DummyArgs(full_path("../../resources/valid.hdf5"), "full"))
- app.print(DummyArgs(full_path("../../resources/valid.hdf5"), "shape"))
+ app.print(
+ DummyArgs(utils.full_path(__file__, "../../resources/valid.hdf5"), "full")
+ )
+ app.print(
+ DummyArgs(utils.full_path(__file__, "../../resources/valid.hdf5"), "shape")
+ )
diff --git a/tests/robofish/io/test_entity.py b/tests/robofish/io/test_entity.py
index 8b3f22d809398a433f88dfb68c881e9d5dab2f82..8c4ab6946a68a316bea62d2ac90a3be56176055a 100644
--- a/tests/robofish/io/test_entity.py
+++ b/tests/robofish/io/test_entity.py
@@ -3,11 +3,6 @@ import h5py
import numpy as np
-#### Helpers ####
-def full_path(path):
- return (Path(__file__).parent / path).resolve()
-
-
def test_entity_object():
sf = robofish.io.File(world_size_cm=[100, 100], frequency_hz=25)
f = sf.create_entity("fish", positions=[[10, 10]])
diff --git a/tests/robofish/io/test_examples.py b/tests/robofish/io/test_examples.py
new file mode 100644
index 0000000000000000000000000000000000000000..94b60155e311d41dd87fc650a6863f496d7cdc59
--- /dev/null
+++ b/tests/robofish/io/test_examples.py
@@ -0,0 +1,15 @@
+import robofish.io
+from robofish.io import utils
+from pathlib import Path
+import sys
+
+
+sys.path.append(str(utils.full_path(__file__, "../../../examples/")))
+
+
+def test_example_readme():
+ import example_readme
+
+
+def test_example_basic():
+ import example_basic
diff --git a/tests/robofish/io/test_file.py b/tests/robofish/io/test_file.py
index 36d2dca9b7c0fb7bb7111211c882a1ce9e1061c0..68342fa2c9bb8e6dae45fc50feddc5cfceefc0cd 100644
--- a/tests/robofish/io/test_file.py
+++ b/tests/robofish/io/test_file.py
@@ -1,4 +1,5 @@
import robofish.io
+from robofish.io import utils
import numpy as np
from pathlib import Path
import pytest
@@ -7,23 +8,23 @@ import datetime
import sys
import logging
-
-#### Helpers ####
-def full_path(path):
- return (Path(__file__).parent / path).resolve()
-
-
-valid_file_path = full_path("../../resources/valid.hdf5")
-created_by_test_path = full_path("../../resources/created_by_test.hdf5")
-created_by_test_path_2 = full_path("../../resources/created_by_test_2.hdf5")
+valid_file_path = utils.full_path(__file__, "../../resources/valid.hdf5")
+created_by_test_path = utils.full_path(__file__, "../../resources/created_by_test.hdf5")
+created_by_test_path_2 = utils.full_path(
+ __file__, "../../resources/created_by_test_2.hdf5"
+)
def test_constructor():
sf = robofish.io.File(world_size_cm=[100, 100])
- print(sf)
sf.validate()
+def test_context():
+ with robofish.io.File(world_size_cm=[10, 10]) as f:
+ pass
+
+
def test_new_file_w_path():
sf = robofish.io.File(
created_by_test_path_2, "w", world_size_cm=[100, 100], frequency_hz=25
@@ -145,9 +146,8 @@ def test_load_validate():
def test_get_entity_names():
sf = robofish.io.File(path=valid_file_path)
names = sf.entity_names
- assert len(names) == 9
+ assert len(names) == 1
assert names[0] == "fish_1"
- assert names[1] == "fish_2"
def test_File_without_path_or_worldsize():
diff --git a/tests/robofish/io/test_io.py b/tests/robofish/io/test_io.py
index bbd59dd70c49e70eaf697f4e0fe3d2c191d9ae29..f0609d2038a50d17a522479f2efbe57f3c13d301 100644
--- a/tests/robofish/io/test_io.py
+++ b/tests/robofish/io/test_io.py
@@ -1,11 +1,8 @@
import robofish.io
+from robofish.io import utils
import pytest
from pathlib import Path
-#### Helpers ####
-def full_path(path):
- return (Path(__file__).parent / path).resolve()
-
def test_now_iso8061():
# Example time: 2021-01-05T14:33:40.401+00:00
@@ -15,7 +12,7 @@ def test_now_iso8061():
def test_read_multiple_single():
- path = full_path("../../resources/valid.hdf5")
+ path = utils.full_path(__file__, "../../resources/valid.hdf5")
# Variants path as posix path or as string
for sf in [
@@ -29,7 +26,7 @@ def test_read_multiple_single():
def test_read_multiple_folder():
- path = full_path("../../resources/")
+ path = utils.full_path(__file__, "../../resources/")
# Variants path as posix path or as string
for sf in [