Merge branch 'develop' into 'master'

Changed the "soft validation error" in form of a warning, Refined evaluation code

Closes #9

See merge request !12

src/robofish/evaluate/app.py

@@ -84,13 +84,14 @@ def evaluate(args=None):
         default=None,
     )
 
-    # TODO: ignore fish/ concider_names
+    # TODO: ignore fish/ consider_names
 
     if args is None:
         args = parser.parse_args()
 
     if args.analysis_type in fdict:
-        params = (args.paths, args.names, Path(args.save_path))
+        save_path = None if args.save_path is None else Path(args.save_path)
+        params = (args.paths, args.names, save_path)
         if args.analysis_type == "all":
             normal_functions = function_dict()
             normal_functions.pop("all")

src/robofish/evaluate/evaluate.py

@@ -363,8 +363,9 @@ def evaluate_distanceToWall(
         range=[0, min(worldBoundsX / 2, worldBoundsY / 2)],
     )
     plt.title("Distance to closest wall")
-    plt.xlabel("Distance in cm")
+    plt.xlabel("Distance [cm]")
     plt.ylabel("Frequency")
+    plt.tight_layout()
     plt.ticklabel_format(useOffset=False)
     plt.legend()
     # plt.tight_layout()
@@ -462,7 +463,7 @@ def evaluate_trajectories(
             )
             world_bounds.append(file.attrs["world_size_cm"])
             path_poses.append(poses[:, :, :2])
-        poses = np.concatenate(path_poses, axis = 1)
+        poses = np.concatenate(path_poses, axis=1)
 
         path_pos = {
             fish: pd.DataFrame({"x": poses[fish, :, 0], "y": poses[fish, :, 1]})
@@ -470,7 +471,7 @@ def evaluate_trajectories(
         }
         combined = pd.concat(
             [
-                path_pos[fish].assign(Agent=f"Agent {fish}")
+                path_pos[fish].assign(Agent=f"{file.entity_names[fish]}")
                 for fish in path_pos.keys()
             ]
         )
@@ -488,10 +489,11 @@ def evaluate_trajectories(
         sns.scatterplot(
             x="x", y="y", hue="Agent", linewidth=0, s=4, data=pos[i][1], ax=ax[i]
         )
-        ax[i].set_title("Trajectories (%s)" % labels[i])
+        ax[i].set_title(f"Trajectories\n{labels[i]}")
         ax[i].set_xlim(-world_bounds[i][0] / 2, world_bounds[i][0] / 2)
         ax[i].set_ylim(-world_bounds[i][1] / 2, world_bounds[i][1] / 2)
-        # ax[i].invert_yaxis()
+        ax[i].set_xlabel("x [cm]")
+        ax[i].set_ylabel("y [cm]")
         ax[i].xaxis.set_ticks_position("top")
         ax[i].xaxis.set_label_position("top")
         ax[i].yaxis.set_ticks_position("left")

src/robofish/io/validation.py

@@ -9,7 +9,7 @@ import logging
 def assert_validate(
     statement: bool, message: str, location: str = None, strict_validate=True
 ) -> None:
-    """ Assert the statement and attach the entity name to the error message.
+    """Assert the statement and attach the entity name to the error message.
 
     Args:
         statement: The statement, which should be tested.
@@ -31,7 +31,7 @@ def assert_validate(
 def assert_validate_type(
     object, expected_type, object_name: str, location: str = None
 ) -> None:
-    """ Assert the statement and attach the entity name to the error message.
+    """Assert the statement and attach the entity name to the error message.
 
     Args:
         statement: The statement, which should be tested.
@@ -291,7 +291,7 @@ def validate(iofile: File, strict_validate: bool = True) -> (bool, str):
             #     e_name,
             # )
 
-    except Exception as e:
+    except AssertionError as e:
         if strict_validate:
             raise e
         else: