Added buffer for poses_rad and actions_speeds_turns so that they don't have to...

Added buffer for poses_rad and actions_speeds_turns so that they don't have to be recalculated every time.

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",
     ]

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

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.
 

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

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