tests pass

Author: neuromusic

tests/conftest.py

@@ -181,23 +181,6 @@ def exemplar_extended_trials_fixture():
 @pytest.fixture(scope="module")
 def trials_df_fixture():
     trials = pd.read_pickle(os.path.join(TESTING_RES_DIR, "trials.pkl"))
-    trials["scheduled_change_time"] = trials.apply(
-        lambda row: row["scheduled_change_time"] - row["starttime"],
-        axis=1
-    )  # change scheduled_change_time from time relative to experiment start to time relative to trial start
-    del trials['stim_on_frames']
-    del trials['publish_time']
-    trials['endframe'] = trials['startframe'].shift(periods=-1)
-    trials.at[trials.index[-1],'endframe']=94157
-
-    def nan_to_empty_string(val):
-        if pd.isnull(val):
-            return ''
-        return val
-    trials["change_image_category"] = trials["change_image_category"].apply(nan_to_empty_string)  # use empty string instead of NoneType
-    trials["change_image_name"] = trials["change_image_name"].apply(nan_to_empty_string)  # use empty string instead of NoneType
-    trials["initial_image_category"] = trials["initial_image_category"].apply(nan_to_empty_string)  # use empty string instead of NoneType
-    trials["initial_image_name"] = trials["initial_image_name"].apply(nan_to_empty_string)  # use empty string instead of NoneType
     return trials
 
 

tests/res/trials.pkl

@@ -26,6 +26,7 @@ def test_load_time(behavioral_session_output_fixture):
 
 def test_load_trials(behavioral_session_output_fixture, trials_df_fixture):
     trials = foraging.load_trials(behavioral_session_output_fixture)
+
     pd.testing.assert_frame_equal(
         trials,
         trials_df_fixture,
@@ -96,6 +97,13 @@ def test_load_running_speed(behavioral_session_output_fixture):
             #     3: -100.3045892838318,
             #     4: -218.06477955362016
             # },
+            'frame': {
+                0: 0,
+                1: 1,
+                2: 2,
+                3: 3,
+                4: 4
+            },
             'speed': {
                 0: 0.0,
                 1: 0.14556417360329282,
@@ -111,10 +119,6 @@ def test_load_running_speed(behavioral_session_output_fixture):
                 4: 0.2000794094055891
             }
         },
-        columns=[
-            u'speed',
-            u'time',
-        ]
     )
 
     pd.testing.assert_frame_equal(

tests/translator/foraging/test_foraging_translator.py

@@ -283,10 +283,11 @@ def test_get_licks(monkeypatch, foraging2_data_fixture):
     (
         {},
         pd.DataFrame(data={
-            "time": np.array([0.0, 0.016, 0.032, 0.048, 0.064, ]),
-            "speed (cm/s)": np.array([0, 0, 0, 0, 0, ]),
-            "acceleration (cm/s^2)": np.array([0, 0, 0, 0, 0, ]),
-            "jerk (cm/s^3)": np.array([0, 0, 0, 0, 0, ]),
+            "time": [0.0, 0.016, 0.032, 0.048, 0.064, ],
+            "speed": [0, 0, 0, 0, 0, ],
+            "frame": [0, 1, 2, 3, 4, ]
+            # "acceleration (cm/s^2)": np.array([0, 0, 0, 0, 0, ]),
+            # "jerk (cm/s^3)": np.array([0, 0, 0, 0, 0, ]),
         }),
     ),
 ])

tests/translator/foraging2/test_foraging2_extract.py

@@ -216,17 +216,8 @@ def data_to_running(data):
     -----
     - the index of each time is the frame number
     """
-    speed_df = get_running_speed(data)[["speed (cm/s)", "time"]]  # yeah...it's dumb i kno...
-
-    n_frames = len(speed_df)
-
-    frames_df = pd.DataFrame(data={"frame": range(n_frames)})
-
-    return pd.DataFrame(data={
-        "speed": speed_df["speed (cm/s)"],
-        "frame": frames_df["frame"],
-        "time": speed_df["time"],
-    })
+    speed_df = get_running_speed(data)
+    return speed_df
 
 
 def data_to_time(data):

visual_behavior/translator/foraging2/__init__.py

@@ -724,7 +724,8 @@ def get_running_speed(exp_data, smooth=False, time=None):
 
     running_speed = pd.DataFrame({
         'time': time,
-        'speed (cm/s)': speed,
+        'frame': range(len(time)),
+        'speed': speed,
         # 'acceleration (cm/s^2)': accel,
         # 'jerk (cm/s^3)': jerk,
     })