diff --git a/.gitignore b/.gitignore
index 764c5ec57cd932bc024ae62cff117e517559d4a3..0cd5109888fa7ddcebdb5a6386249d8b1aed7110 100644
--- a/.gitignore
+++ b/.gitignore
@@ -21,3 +21,4 @@ env
feature_requests.md
output_graph.png
+.testmondata
diff --git a/src/robofish/evaluate/evaluate.py b/src/robofish/evaluate/evaluate.py
index d46d2a643b5b1faebf3f373bf5f2ba297e691c32..fe48edbeeea0c0d22ba06cd3229f4487225e4562 100644
--- a/src/robofish/evaluate/evaluate.py
+++ b/src/robofish/evaluate/evaluate.py
@@ -705,6 +705,8 @@ def evaluate_all(
fdict: A dictionary of strings and evaluation functions
predicate: a lambda function, selecting entities
(example: lambda e: e.category == "fish")
+ Returns:
+ An array of all paths to the created images.
"""
assert (
save_folder is not None and save_folder != ""
@@ -712,6 +714,7 @@ def evaluate_all(
save_folder.mkdir(exist_ok=True)
+ save_paths = []
if fdict is None:
fdict = robofish.evaluate.app.function_dict()
fdict.pop("all")
@@ -720,7 +723,11 @@ def evaluate_all(
for f_name, f_callable in t:
t.set_description(f_name)
t.refresh() # to show immediately the update
- f_callable(paths, labels, save_folder / (f_name + ".png"), predicate)
+ save_path = save_folder / (f_name + ".png")
+ f_callable(paths, labels, save_path, predicate)
+ save_paths.append(save_path)
+
+ return save_paths
def calculate_follow(a, b):
@@ -745,6 +752,20 @@ def calculate_iid(a, b):
return np.linalg.norm(b[:, :2] - a[:, :2], axis=-1)
+def calc_tlvc(a, b, tau_min, tau_max):
+ """
+ Given two velocity series and both minimum and maximum time lag return the
+ time lagged velocity correlation from the first to the second series.
+ """
+ length = tau_max - tau_min
+ return np.float32(
+ [
+ (a[t] @ b[t + tau_min :][:length].T).mean()
+ for t in range(min(len(a), len(b) - tau_max + 1))
+ ]
+ )
+
+
def normalize_series(x):
"""Normalize series.
diff --git a/src/robofish/io/file.py b/src/robofish/io/file.py
index 14272418e2ad968f57b562255fe4cd429bce4388..82cfefcad880788bf6d79895acf02ea7c344aaf2 100644
--- a/src/robofish/io/file.py
+++ b/src/robofish/io/file.py
@@ -37,6 +37,8 @@ import matplotlib.pyplot as plt
from matplotlib import animation
from matplotlib import patches
+from subprocess import run
+
# Remember: Update docstring when updating these two global variables
default_format_version = np.array([1, 0], dtype=np.int32)
@@ -66,6 +68,7 @@ class File(h5py.File):
frequency_hz: int = None,
monotonic_time_points_us: Iterable = None,
calendar_time_points: Iterable = None,
+ open_copy: bool = False,
):
"""Create a new RoboFish Track Format object.
@@ -126,15 +129,35 @@ class File(h5py.File):
refer to explanation of `sampling_name`
calendar_time_points: Iterable of str, optional
refer to explanation of `sampling_name`
+ open_copy: bool, optional
+ a temporary copy of the file will be opened instead of the file itself.
"""
- if path is None:
- if type(self)._temp_dir is None:
- type(self)._temp_dir = tempfile.TemporaryDirectory(
- prefix="robofish-io-"
- )
+ if open_copy:
+ assert (
+ path is not None
+ ), "A path has to be given if a copy should be opened."
+
+ temp_file = self.temp_dir / str(uuid.uuid4())
+ logging.info(
+ f"Copying file to temporary file and opening it:\n{path} -> {temp_file}"
+ )
+
+ shutil.copyfile(path, temp_file)
+ super().__init__(
+ temp_file,
+ mode="r+",
+ driver="core",
+ backing_store=True,
+ libver=("earliest", "v110"),
+ )
+ initialize = False
+
+ elif path is None:
+ temp_file = self.temp_dir / str(uuid.uuid4())
+ logging.info(f"Opening New temporary file {temp_file}")
super().__init__(
- Path(type(self)._temp_dir.name) / str(uuid.uuid4()),
+ temp_file,
mode="x",
driver="core",
backing_store=True,
@@ -182,7 +205,12 @@ class File(h5py.File):
self.validate()
super().__exit__(type, value, traceback)
- def save_as(self, path: Union[str, Path], strict_validate: bool = True, no_warning: bool=False):
+ def save_as(
+ self,
+ path: Union[str, Path],
+ strict_validate: bool = True,
+ no_warning: bool = False,
+ ):
"""Save a copy of the file
Args:
@@ -269,6 +297,13 @@ class File(h5py.File):
self["samplings"].attrs["default"] = name
return name
+ @property
+ def temp_dir(self):
+ cla = type(self)
+ if cla._temp_dir is None:
+ cla._temp_dir = tempfile.TemporaryDirectory(prefix="robofish-io-")
+ return Path(cla._temp_dir.name)
+
@property
def world_size(self):
return self.attrs["world_size_cm"]
@@ -462,8 +497,8 @@ class File(h5py.File):
@deprecation.deprecated(
deprecated_in="0.2",
removed_in="0.2.4",
- details="We found that our calculation of 'speed_turn' is flawed and replaced it "
- "with 'actions_speeds_turns'. The difference in calculation is, that the tracked "
+ details="We found that our calculation of 'entity_speeds_turns' is flawed and replaced it "
+ "with 'entity_actions_speeds_turns'. The difference in calculation is, that the tracked "
"orientation is used now which gives the fish the ability to swim backwards. "
"If you see this message and you don't know what to do, update all packages and if nothing helps, contact Andi.\n"
"Don't ignore this warning, it's a serious issue.",
@@ -613,6 +648,14 @@ class File(h5py.File):
As there are render functions in gym_guppy and robofish.trackviewer, this function is a temporary addition.
The goal should be to bring together the rendering tools."""
+ if video_path is not None:
+ try:
+ run(["ffmpeg"], capture_output=True)
+ except Exception as e:
+ raise Exception(
+ f"ffmpeg is required to store videos. Please install it.\n{e}"
+ )
+
def shape_vertices(scale=1) -> np.ndarray:
base_shape = np.array(
[
diff --git a/tests/robofish/io/test_file.py b/tests/robofish/io/test_file.py
index 2ec1f26b2d0804f20c70d685c7576a3fe4a6bc05..601657d173f643d62502e5732c4ae5acb0a28166 100644
--- a/tests/robofish/io/test_file.py
+++ b/tests/robofish/io/test_file.py
@@ -16,6 +16,7 @@ valid_file_path = utils.full_path(__file__, "../../resources/valid_1.hdf5")
def test_constructor():
sf = robofish.io.File(world_size_cm=[100, 100])
sf.validate()
+ sf.close()
def test_context():
@@ -28,12 +29,14 @@ def test_new_file_w_path(tmp_path):
sf = robofish.io.File(f, "w", world_size_cm=[100, 100], frequency_hz=25)
sf.create_entity("fish")
sf.validate()
+ sf.close()
def test_missing_attribute():
sf = robofish.io.File(world_size_cm=[10, 10])
sf.attrs.pop("world_size_cm")
assert not sf.validate(strict_validate=False)[0]
+ sf.close()
def test_single_entity_monotonic_step():
@@ -44,6 +47,7 @@ def test_single_entity_monotonic_step():
sf.create_entity("object_without_poses")
print(sf)
sf.validate()
+ sf.close()
def test_single_entity_monotonic_time_points_us():
@@ -55,6 +59,7 @@ def test_single_entity_monotonic_time_points_us():
sf.create_entity("robofish", poses=test_poses)
print(sf)
sf.validate()
+ sf.close()
def test_multiple_entities():
@@ -174,6 +179,7 @@ def test_entity_positions_no_orientation():
def test_load_validate():
sf = robofish.io.File(path=valid_file_path)
sf.validate()
+ sf.close()
def test_get_entity_names():
@@ -181,6 +187,19 @@ def test_get_entity_names():
names = sf.entity_names
assert len(names) == 2
assert names == ["fish_1", "robot"]
+ sf.close()
+
+
+def test_load_copy():
+ # Open a copy of a file and change an attribute
+ sf = robofish.io.File(path=valid_file_path, open_copy=True)
+ sf.attrs["test"] = "test"
+ sf.close()
+
+ # When reopening the file, the attribute should be not saved.
+ sf = robofish.io.File(valid_file_path, "r")
+ assert "test" not in sf.attrs
+ sf.close()
def test_File_without_path_or_worldsize():
@@ -210,6 +229,7 @@ def test_loading_saving(tmp_path):
entity.poses
sf.validate()
+ sf.close()
if __name__ == "__main__":