Merge branch 'develop' into 'master'

Fixed internal issues with wrong conversions of speeds and turns.

See merge request !18

docs/entity.md

@@ -63,14 +63,14 @@ As described in `robofish.io`, Files and Entities have useful properties.
 
 <small>
 
-| Entity function                                  | Description                                                              |
-| ------------------------------------------------ | ------------------------------------------------------------------------ |
-| `robofish.io.entity.Entity.positions`            | Positions as a `(timesteps, 2 (x, y))` array.                            |
-| `robofish.io.entity.Entity.orientations`         | Orientations as a `(timesteps, 2 (ori_x, ori_y))` array.                 |
-| `robofish.io.entity.Entity.orientations_rad`     | Orientations as a `(timesteps, 1 (ori_rad))` array.                      |
-| `robofish.io.entity.Entity.poses`                | Poses as a `(timesteps, 4 (x, y, x_ori, y_ori))` array.                  |
-| `robofish.io.entity.Entity.poses_rad`            | Poses as a `(timesteps, 3(x, y, ori_rad))` array.                        |
-| `robofish.io.entity.Entity.actions_speeds_turns` | Speed and turn as a `(timesteps - 1, 2 (speed_cm/s, turn_rad/s))` array. |
+| Entity function                                  | Description                                                                            |
+| ------------------------------------------------ | -------------------------------------------------------------------------------------- |
+| `robofish.io.entity.Entity.positions`            | Positions as a `(timesteps, 2 (x, y))` array.                                          |
+| `robofish.io.entity.Entity.orientations`         | Orientations as a `(timesteps, 2 (ori_x, ori_y))` array.                               |
+| `robofish.io.entity.Entity.orientations_rad`     | Orientations as a `(timesteps, 1 (ori_rad))` array.                                    |
+| `robofish.io.entity.Entity.poses`                | Poses as a `(timesteps, 4 (x, y, x_ori, y_ori))` array.                                |
+| `robofish.io.entity.Entity.poses_rad`            | Poses as a `(timesteps, 3(x, y, ori_rad))` array.                                      |
+| `robofish.io.entity.Entity.actions_speeds_turns` | Speed and turn as a `(timesteps - 1, 2 (speed in cm/frame, turn in rad/frame))` array. |
 
 </small>
 

docs/index.md

@@ -124,14 +124,14 @@ In the same scheme the following properties are available:
 
 <small>
 
-| File/ Entity function         | Description                                                                          |
-| ----------------------------- | ------------------------------------------------------------------------------------ |
-| *entity_*positions            | Positions as a `(*entities*, timesteps, 2 (x, y))` arary.                            |
-| *entity_*orientations         | Orientations as a `(*entities*, timesteps, 2 (ori_x, ori_y))` arary.                 |
-| *entity_*orientations_rad     | Orientations as a `(*entities*, timesteps, 1 (ori_rad))` arary.                      |
-| *entity_*poses                | Poses as a `(*entities*, timesteps, 4 (x, y, x_ori, y_ori))` array.                  |
-| *entity_*poses_rad            | Poses as a `(*entities*, timesteps, 3(x, y, ori_rad))` array.                        |
-| *entity_*actions_speeds_turns | Speed and turn as a `(*entities*, timesteps - 1, 2 (speed_cm/s, turn_rad/s))` array. |
+| File/ Entity function         | Description                                                                                        |
+| ----------------------------- | -------------------------------------------------------------------------------------------------- |
+| *entity_*positions            | Positions as a `(*entities*, timesteps, 2 (x, y))` array.                                          |
+| *entity_*orientations         | Orientations as a `(*entities*, timesteps, 2 (ori_x, ori_y))` array.                               |
+| *entity_*orientations_rad     | Orientations as a `(*entities*, timesteps, 1 (ori_rad))` array.                                    |
+| *entity_*poses                | Poses as a `(*entities*, timesteps, 4 (x, y, x_ori, y_ori))` array.                                |
+| *entity_*poses_rad            | Poses as a `(*entities*, timesteps, 3(x, y, ori_rad))` array.                                      |
+| *entity_*actions_speeds_turns | Speed and turn as a `(*entities*, timesteps - 1, 2 (speed in cm/frame, turn in rad/frame))` array. |
 
 </small>
 

pyproject.toml

@@ -8,7 +8,7 @@ extend-ignore = "E203"
 
 [tool.black]
 line-length = 88
-include =''
+include ='\.py'
 
 [tool.pytest.ini_options]
 filterwarnings = ["error"]
\ No newline at end of file

src/robofish/evaluate/evaluate.py

@@ -73,11 +73,18 @@ def evaluate_speed(
     """
     files_per_path = [robofish.io.read_multiple_files(p) for p in paths]
     speeds = []
+    frequency = None
+
     for k, files in enumerate(files_per_path):
         path_speeds = []
         for p, file in files.items():
+            assert frequency is None or frequency == file.frequency
+            frequency = file.frequency
+
             for e_speeds_turns in file.entity_actions_speeds_turns:
-                path_speeds = np.concatenate([path_speeds, e_speeds_turns[:, 0]])
+                path_speeds = np.concatenate(
+                    [path_speeds, e_speeds_turns[:, 0] * frequency]
+                )
         speeds.append(path_speeds)
 
     if labels is None:
@@ -91,7 +98,7 @@ def evaluate_speed(
     plt.title("Agent speeds")
     plt.xlabel("Speed [cm/s]")
     plt.ylabel("Frequency")
-    plt.ticklabel_format(useOffset=False)
+    plt.ticklabel_format(useOffset=False, style="plain")
     plt.legend()
     plt.tight_layout()
 
@@ -130,14 +137,14 @@ def evaluate_turn(
             frequency = file.frequency
 
             for e_speeds_turns in file.entity_actions_speeds_turns:
-                path_turns.extend(e_speeds_turns[:, 1])
+                path_turns.extend(np.rad2deg(e_speeds_turns[:, 1]))
         turns.append(path_turns)
 
     if labels is None:
         labels = paths
 
-    left_quantile = np.min(np.quantile(np.array(turns), 0.001, axis=1))
-    right_quantile = np.max(np.quantile(np.array(turns), 0.999, axis=1))
+    left_quantile = np.min(np.quantile(np.array(turns), 0.005, axis=1))
+    right_quantile = np.max(np.quantile(np.array(turns), 0.995, axis=1))
     plt.hist(
         turns,
         bins=41,
@@ -148,7 +155,7 @@ def evaluate_turn(
     plt.title("Agent turns")
     plt.xlabel("Change in orientation [Degree / timestep at %dhz]" % frequency)
     plt.ylabel("Frequency")
-    plt.ticklabel_format(useOffset=False)
+    plt.ticklabel_format(useOffset=False, style="plain")
     plt.legend()
     # plt.tight_layout()
 

src/robofish/io/entity.py

@@ -241,15 +241,12 @@ class Entity(h5py.Group):
     def actions_speeds_turns(self):
         """Calculate the speed, turn and from the recorded positions and orientations.
 
-        The turn is calculated by the change of orientation.
+        The turn is calculated by the change of orientation between frames.
         The speed is calculated by the distance between the points, projected on the new orientation vector.
         The sideway change of position cannot be represented with this method.
 
         Returns:
-            An array with shape (number_of_positions -1, 3).
-            The first column is the speed (distance projected on new orientation).
-            The second column is the turning angle.
-
+            An array with shape (number_of_positions -1, 2 (speed in cm/frame, turn in rad/frame).
         """
 
         ori = self.orientations

src/robofish/io/file.py

@@ -463,6 +463,15 @@ class File(h5py.File):
 
     @property
     def entity_actions_speeds_turns(self):
+        """Calculate the speed, turn and from the recorded positions and orientations.
+
+        The turn is calculated by the change of orientation between frames.
+        The speed is calculated by the distance between the points, projected on the new orientation vector.
+        The sideway change of position cannot be represented with this method.
+
+        Returns:
+            An array with shape (number_of_entities, number_of_positions -1, 2 (speed in cm/frame, turn in rad/frame).
+        """
         return self.select_entity_property(
             None, entity_property=Entity.actions_speeds_turns
         )