diff --git a/setup.py b/setup.py
index fd67f2ed2906a91b878e31b1a5754202034ce591..48573d8af70ab56fc4c1098994c2b9b3b4e7014f 100644
--- a/setup.py
+++ b/setup.py
@@ -10,6 +10,7 @@ entry_points = {
"robofish-io-validate=robofish.io.app:validate",
"robofish-io-print=robofish.io.app:print_file",
"robofish-io-render=robofish.io.app:render",
+ "robofish-io-clear-calculated-data=robofish.io.app:clear_calculated_data",
# TODO: This should be called robofish-evaluate which is not possible because of the package name (guess) ask moritz
"robofish-io-evaluate=robofish.evaluate.app:evaluate",
]
diff --git a/src/robofish/io/__init__.py b/src/robofish/io/__init__.py
index 5b054c2fb71018dd23ceb315d83bf83f51cc1cac..b14b319e8e1899321e1140140d0846dcee92662e 100644
--- a/src/robofish/io/__init__.py
+++ b/src/robofish/io/__init__.py
@@ -20,3 +20,9 @@ import robofish.io.app
if not ((3, 7) <= sys.version_info < (4, 0)):
logging.warning("Unsupported Python version")
+
+warn_when_unable_to_store = True
+
+
+def disable_warning_when_unable_to_store():
+ robofish.io.warn_when_unable_to_store = False
diff --git a/src/robofish/io/app.py b/src/robofish/io/app.py
index be1690d62049354a292a0d06627affd2c410d397..15b6ebe15cb09eac6bf38b901b86184bf0da5077 100644
--- a/src/robofish/io/app.py
+++ b/src/robofish/io/app.py
@@ -53,6 +53,33 @@ def print_file(args=None):
return not valid
+def clear_calculated_data(args=None):
+ parser = argparse.ArgumentParser(
+ description="This function clears calculated data from robofish.io files."
+ )
+
+ parser.add_argument(
+ "path",
+ type=str,
+ nargs="+",
+ help="The path to one or multiple files and/or folders.",
+ )
+ if args is None:
+ args = parser.parse_args()
+
+ files_per_path = utils.get_all_files_from_paths(args.path)
+ files = [
+ f for f_in_path in files_per_path for f in f_in_path
+ ] # Concatenate all files to one list
+
+ assert len(files) > 0, f"No files found in path {args.path}."
+
+ for fp in files:
+ print(f"File {fp}")
+ with robofish.io.File(fp, "r+") as f:
+ f.clear_calculated_data()
+
+
def validate(args=None):
"""This function can be used to validate hdf5 files.
diff --git a/src/robofish/io/entity.py b/src/robofish/io/entity.py
index 85c9c926ae7acc333759375d3039015b30c66454..fb0b1a209ec070aab86b9e44b02d1829bb0be417 100644
--- a/src/robofish/io/entity.py
+++ b/src/robofish/io/entity.py
@@ -143,11 +143,33 @@ class Entity(h5py.Group):
@property
def orientations_rad(self):
- ori_rad = utils.limit_angle_range(
- np.arctan2(self.orientations[:, 1], self.orientations[:, 0]),
- _range=(0, 2 * np.pi),
- )
- return ori_rad[:, np.newaxis]
+ # If actions_speeds_turns does not exist yet or the poses hash is not correct
+ if (
+ "calculated_orientations_rad" not in self
+ or "poses_hash" not in self.attrs
+ or self.poses_hash != self.attrs["poses_hash"]
+ ):
+
+ ori_rad = utils.limit_angle_range(
+ np.arctan2(self.orientations[:, 1], self.orientations[:, 0]),
+ _range=(0, 2 * np.pi),
+ )[:, np.newaxis]
+
+ try:
+
+ self.attrs["poses_hash"] = self.poses_hash
+ self["calculated_orientations_rad"] = ori_rad.astype(np.float64)
+ except RuntimeError as e:
+ if robofish.io.warn_when_unable_to_store:
+ print(
+ "Trying to store calculated orientations_rad in file to reuse it but the file was opened as read-only.\n"
+ "If you open the file with mode 'r+' (or 'w' if it is still open from creation time) the information can be stored and reused.\n"
+ "To disable this message execute robofish.io.disable_warning_when_unable_to_store().\n"
+ )
+ else:
+ ori_rad = self["calculated_orientations_rad"]
+
+ return ori_rad
@property
@deprecation.deprecated(
@@ -196,6 +218,14 @@ class Entity(h5py.Group):
return poses_with_calculated_orientation
+ @property
+ def poses_hash(self):
+ if "orientations" in self:
+ h = (hash(self["positions"]) + hash(self["orientations"])) // 2
+ else:
+ h = hash(self["positions"])
+ return int(h)
+
@property
def poses(self):
return np.concatenate([self.positions, self.orientations], axis=1)
@@ -249,13 +279,35 @@ class Entity(h5py.Group):
An array with shape (number_of_positions -1, 2 (speed in cm/frame, turn in rad/frame).
"""
- ori = self.orientations
- ori_rad = self.orientations_rad
- pos = self.positions
- turn = utils.limit_angle_range(np.diff(ori_rad, axis=0)[:, 0])
- pos_diff = np.diff(pos, axis=0)
- speed = np.array(
- [np.dot(pos_diff[i], ori[i + 1]) for i in range(pos_diff.shape[0])]
- )
+ # If actions_speeds_turns does not exist yet or the poses hash is not correct
+ if (
+ "calculated_actions_speeds_turns" not in self
+ or "poses_hash" not in self.attrs
+ or self.poses_hash != self.attrs["poses_hash"]
+ ):
+ ori = self.orientations
+ ori_rad = self.orientations_rad
+ pos = self.positions
+ turn = utils.limit_angle_range(np.diff(ori_rad, axis=0)[:, 0])
+ pos_diff = np.diff(pos, axis=0)
+ speed = np.array(
+ [np.dot(pos_diff[i], ori[i + 1]) for i in range(pos_diff.shape[0])]
+ )
+ actions_speeds_turns = np.stack([speed, turn], axis=-1)
- return np.stack([speed, turn], axis=-1)
+ try:
+ self.attrs["poses_hash"] = self.poses_hash
+ self["calculated_actions_speeds_turns"] = actions_speeds_turns.astype(
+ np.float64
+ )
+ except RuntimeError as e:
+ if robofish.io.warn_when_unable_to_store:
+ print(
+ "Trying to store calculated actions_speeds_turns in file to reuse it but the file was opened as read-only.\n"
+ "If you open the file with mode 'r+' (or 'w' if it is still open from creation time) the information can be stored and reused.\n"
+ "To disable this message execute robofish.io.disable_warning_when_unable_to_store().\n"
+ )
+ else:
+ actions_speeds_turns = self["calculated_actions_speeds_turns"]
+
+ return actions_speeds_turns
diff --git a/src/robofish/io/file.py b/src/robofish/io/file.py
index 1bf1ed173f0a25f84963a9f7e90f477d2c7e44e7..cdb2aedbbe52ab3c81f99590b1a992c20cff0b9b 100644
--- a/src/robofish/io/file.py
+++ b/src/robofish/io/file.py
@@ -470,6 +470,24 @@ class File(h5py.File):
)
return entity_names
+ def clear_calculated_data(self, verbose=True):
+ """Delete all calculated data from the files."""
+ txt = ""
+ for e in self.entities:
+ txt += f"Deleting from {e}. Attrs: ["
+ for a in ["poses_hash"]:
+ if a in e.attrs:
+ del e.attrs[a]
+ txt += f"{a}, "
+ txt = txt[:-2] + "] Datasets: ["
+ for g in ["calculated_actions_speeds_turns", "calculated_orientations_rad"]:
+ if g in e:
+ del e[g]
+ txt += f"{g}, "
+ txt = txt[:-2] + "]\n"
+ if verbose:
+ print(txt[:-1])
+
@property
def entity_names(self) -> Iterable[str]:
"""Getter for the names of all entities