fixed acceleration

Author: yeshaokai

amadeusgpt/analysis_objects/animal.py

@@ -122,7 +122,7 @@ def get_keypoint_names(self):
     def query_states(self, query: str) -> ndarray:
         assert query in [
             "speed",
-            "acceleration",
+            "acceleration_mag",
             "bodypart_pairwise_distance",
         ], f"{query} is not supported"
 
@@ -172,8 +172,9 @@ def get_acceleration_mag(self) -> ndarray:
         Returns the magnitude of the acceleration vector    
         """
         accelerations = self.get_acceleration()
-        acceleration_mag = np.linalg.norm(accelerations, axis=-1)    
-        assert len(acceleration_mag.shape) == 2
+        acceleration_mag = np.linalg.norm(accelerations, axis=-1)  
+        acceleration_mag = np.expand_dims(acceleration_mag, axis=-1)
+        assert len(acceleration_mag.shape) == 3
         return acceleration_mag
 
     def get_bodypart_wise_relation(self):
@@ -230,5 +231,18 @@ def calc_head_cs(self):
     # unit testing the shape of kinematics data
     # acceleration, acceleration_mag, velocity, speed, and keypoints
 
+    from amadeusgpt.config import Config
+    from amadeusgpt.main import AMADEUS
+    config = Config("/Users/shaokaiye/AmadeusGPT-dev/amadeusgpt/configs/MausHaus_template.yaml")
+    amadeus = AMADEUS(config)
+    analysis = amadeus.get_analysis()
+    # get an instance of animal
+    animal = analysis.animal_manager.get_animals()[0]
 
+    print ("velocity shape", animal.get_velocity().shape)
+    print ("speed shape", animal.get_speed().shape)
+    print ("acceleration shape", animal.get_acceleration().shape)
+    print ("acceleration_mag shape", animal.get_acceleration_mag().shape)
+
+    print(animal.query_states("acceleration_mag").shape)
 

amadeusgpt/analysis_objects/relationship.py

@@ -6,7 +6,8 @@
 from scipy.spatial.distance import cdist
 
 from .base import AnalysisObject
-from .object import AnimalSeq, Object
+from .object import Object
+from .animal import AnimalSeq
 
 
 class Orientation(IntEnum):

amadeusgpt/managers/animal_manager.py

@@ -7,7 +7,7 @@
 import pandas as pd
 from numpy import ndarray
 
-from amadeusgpt.analysis_objects.object import AnimalSeq
+from amadeusgpt.analysis_objects.animal import AnimalSeq
 from amadeusgpt.programs.api_registry import (register_class_methods,
                                               register_core_api)
 

amadeusgpt/managers/visual_manager.py

@@ -8,7 +8,7 @@
 from matplotlib.patches import Wedge
 
 from amadeusgpt.analysis_objects.event import BaseEvent
-from amadeusgpt.analysis_objects.object import AnimalSeq
+from amadeusgpt.analysis_objects.animal import AnimalSeq
 from amadeusgpt.analysis_objects.visualization import (EventVisualization,
                                                        GraphVisualization,
                                                        KeypointVisualization,