Fixed deprecation warning

Removed buggy quiver from standard evaluation.

src/robofish/evaluate/app.py

@@ -36,20 +36,21 @@ def function_dict() -> dict:
         "follow_iid": base.evaluate_follow_iid,
         "individual_speed": base.evaluate_individual_speed,
         "individual_iid": base.evaluate_individual_iid,
-        "quiver": base.evaluate_quiver,
+        # "quiver": base.evaluate_quiver, # Quiver has issues with multiple paths and raises exceptions. The function is not used for now.
         "all": base.evaluate_all,
     }
 
 
-def evaluate(args=None):
+def evaluate(args: dict = None) -> None:
     """This function can be called from the commandline to evaluate files.
 
     The function is called with robofish-io-evaluate. Different evaluation
     methods can be called, which generate graphs from the given files
 
     Args:
-        args: a dictionary to overwrite the argument parser
-        (robofish-io-evaluate --help for more info)
+        args (dict, optional): a dictionary to overwrite the argument parser (robofish-io-evaluate --help for more info)
+    Raises:
+        ValueError: When the analysis type is all, and no save_path is given.
     """
 
     fdict = function_dict()
@@ -104,7 +105,7 @@ def evaluate(args=None):
         args = parser.parse_args()
 
     if args.analysis_type == "all" and args.save_path is None:
-        raise Exception("When the analysis type is all, a --save_path must be given.")
+        raise ValueError("When the analysis type is all, a --save_path must be given.")
 
     if args.analysis_type in fdict:
         if args.labels is None:

src/robofish/evaluate/evaluate.py

@@ -515,13 +515,17 @@ def evaluate_quiver(
     #    )
     #    print(speeds_turns_from_paths)
     try:
-        speeds_turns_from_paths = np.array(speeds_turns_from_paths)
+        print(speeds_turns_from_paths)
+        speeds_turns_from_paths = np.stack(
+            [np.array(st, dtype=np.float32) for st in speeds_turns_from_paths]
+        )
     except Exception as e:
         warnings.warn(
-            f"The conversion to numpy array failed:\nspeeds_turns_from_path.shape was {speeds_turns_from_paths.shape}. Exception was {e}"
+            f"The conversion to numpy array failed:\nlen(speeds_turns_from_path) was {len(speeds_turns_from_paths)}. Exception was {e}"
         )
         return
-
+    print(speeds_turns_from_paths.dtype)
+    print(speeds_turns_from_paths)
     all_poses = torch.tensor(poses_from_paths)[0, :, :, :-1].reshape((-1, 4))
     speed = torch.tensor(speeds_turns_from_paths)[0, ..., 0].flatten()
     all_poses_speed = torch.clone(all_poses)

src/robofish/io/file.py

@@ -16,7 +16,6 @@
 # -----------------------------------------------------------
 
 from __future__ import annotations
-from pytest import skip
 import robofish.io
 from robofish.io.entity import Entity
 import h5py
@@ -36,11 +35,10 @@ import warnings
 from textwrap import wrap
 import platform
 
-import matplotlib as mpl
+import matplotlib
 import matplotlib.pyplot as plt
 from matplotlib import animation
 from matplotlib import patches
-from matplotlib import cm
 
 from tqdm.auto import tqdm
 
@@ -850,19 +848,19 @@ class File(h5py.File):
 
     def plot(
         self,
-        ax: mpl.axes = None,
+        ax: matplotlib.axes = None,
         lw_distances: bool = False,
         lw: int = 2,
         ms: int = 32,
         figsize: Tuple[int] = None,
         step_size: int = 4,
         c: List = None,
-        cmap: mpl.colors.Colormap = "Set1",
+        cmap: matplotlib.colors.Colormap = "Set1",
         skip_timesteps=0,
         max_timesteps=None,
         show=False,
         legend=True,
-    ) -> mpl.axes:
+    ) -> matplotlib.axes:
         """Plot the file using matplotlib.pyplot
 
         The tracks in the file are plotted using matplotlib.plot().
@@ -910,7 +908,7 @@ class File(h5py.File):
         else:
             step_size = poses.shape[1]
 
-        cmap = cm.get_cmap(cmap)
+        cmap = matplotlib.colormaps[cmap]
 
         x_world, y_world = self.world_size
         if figsize is None:
@@ -1260,10 +1258,10 @@ class File(h5py.File):
                     )
 
                     current_pose = entity_poses[i_entity, file_frame]
-                    t = mpl.transforms.Affine2D().translate(
+                    t = matplotlib.transforms.Affine2D().translate(
                         current_pose[0], current_pose[1]
                     )
-                    r = mpl.transforms.Affine2D().rotate(current_pose[2])
+                    r = matplotlib.transforms.Affine2D().rotate(current_pose[2])
                     tra = r + t + ax.transData
                     entity_polygons[i_entity].set_transform(tra)
             else: