Merge branch 'main' into fix_ylabel

Author: alexpiet

pyproject.toml

@@ -27,7 +27,8 @@ dependencies = [
     'pathlib',
     'numpy',
     'pydantic',
-    'hdmf_zarr'
+    'hdmf_zarr',
+    'aind-dynamic-foraging-data-utils >= 0.1.25'
 ]
 
 [project.optional-dependencies]

src/aind_dynamic_foraging_basic_analysis/licks/annotation.py

@@ -32,7 +32,7 @@ def annotate_licks(nwb):
     nwb is an object that has df_events as an attribute
     """
     if not hasattr(nwb, "df_events"):
-        print("You need to compute df_events: nwb_utils.create_events_df(nwb)")
+        print("You need to compute df_events: nwb_utils.create_df_events(nwb)")
         return
     nwb.df_licks = annotate_lick_bouts(nwb)
     nwb.df_licks = annotate_artifacts(nwb)
@@ -57,7 +57,7 @@ def annotate_lick_bouts(nwb):
     """
 
     if not hasattr(nwb, "df_events"):
-        print("You need to compute df_events: nwb_utils.create_events_df(nwb)")
+        print("You need to compute df_events: nwb_utils.create_df_events(nwb)")
         return
     df_licks = nwb.df_events.query('event in ["right_lick_time","left_lick_time"]').copy()
     df_licks.reset_index(drop=True, inplace=True)
@@ -90,7 +90,7 @@ def annotate_artifacts(nwb):
     nwb, an object with attributes: df_licks, df_events
     """
     if not hasattr(nwb, "df_events"):
-        print("You need to compute df_events: nwb_utils.create_events_df(nwb)")
+        print("You need to compute df_events: nwb_utils.create_df_events(nwb)")
         return
 
     if not hasattr(nwb, "df_licks"):
@@ -122,7 +122,7 @@ def annotate_rewards(nwb):
     """
 
     if not hasattr(nwb, "df_events"):
-        print("You need to compute df_events: nwb_utils.create_events_df(nwb)")
+        print("You need to compute df_events: nwb_utils.create_df_events(nwb)")
         return
 
     # ensure we have df_licks
@@ -183,7 +183,7 @@ def annotate_cue_response(nwb):
     """
 
     if not hasattr(nwb, "df_events"):
-        print("You need to compute df_events: nwb_utils.create_events_df(nwb)")
+        print("You need to compute df_events: nwb_utils.create_df_events(nwb)")
         return
 
     # ensure we have df_licks
@@ -232,7 +232,7 @@ def annotate_intertrial_choices(nwb):
     """
     # Add lick_bout annotation, and cue_response if not already added
     if not hasattr(nwb, "df_events"):
-        print("You need to compute df_events: nwb_utils.create_events_df(nwb)")
+        print("You need to compute df_events: nwb_utils.create_df_events(nwb)")
         return
     if not hasattr(nwb, "df_licks"):
         nwb.df_licks = annotate_lick_bouts(nwb)
@@ -267,7 +267,7 @@ def annotate_switches(nwb):
     """
     # Add lick_bout annotation, and cue_response if not already added
     if not hasattr(nwb, "df_events"):
-        print("You need to compute df_events: nwb_utils.create_events_df(nwb)")
+        print("You need to compute df_events: nwb_utils.create_df_events(nwb)")
         return
     if not hasattr(nwb, "df_licks"):
         nwb.df_licks = annotate_lick_bouts(nwb)
@@ -337,7 +337,7 @@ def annotate_within_session(nwb):
     """
 
     if not hasattr(nwb, "df_events"):
-        print("You need to compute df_events: nwb_utils.create_events_df(nwb)")
+        print("You need to compute df_events: nwb_utils.create_df_events(nwb)")
         return
 
     # ensure we have df_licks

src/aind_dynamic_foraging_basic_analysis/metrics/trial_metrics.py

@@ -35,7 +35,7 @@ def compute_trial_metrics(nwb):
     """
     if not hasattr(nwb, "df_events"):
         print("computing df_events first")
-        nwb.df_events = nu.create_events_df(nwb)
+        nwb.df_events = nu.create_df_events(nwb)
 
     if not hasattr(nwb, "df_trials"):
         print("computing df_trials")
@@ -340,7 +340,7 @@ def get_average_signal_window(
         raise ValueError("You need to compute df_trials: nwb_utils.create_trials_df(nwb)")
 
     if not hasattr(nwb, "df_fip"):
-        raise ValueError("You need to compute df_fip: nwb_utils.create_fib_df(nwb)")
+        raise ValueError("You need to compute df_fip: nwb_utils.create_df_fip(nwb)")
 
     # Check alignment_event is in df_trials columns
     if alignment_event not in nwb.df_trials.columns:

src/aind_dynamic_foraging_basic_analysis/plot/plot_fip.py

@@ -56,12 +56,12 @@ def plot_fip_psth_compare_alignments(  # NOQA C901
     for nwb_i in nwb_list:
         if not hasattr(nwb_i, "df_fip"):
             print("You need to compute the df_fip first")
-            print("running `nwb.df_fip = create_fib_df(nwb,tidy=True)`")
-            nwb_i.df_fip = nu.create_fib_df(nwb_i, tidy=True)
+            print("running `nwb.df_fip = create_df_fip(nwb,tidy=True)`")
+            nwb_i.df_fip = nu.create_df_fip(nwb_i, tidy=True)
         if not hasattr(nwb_i, "df_events"):
             print("You need to compute the df_events first")
-            print("run `nwb.df_events = create_events_df(nwb)`")
-            nwb_i.df_events = nu.create_events_df(nwb_i)
+            print("run `nwb.df_events = create_df_events(nwb)`")
+            nwb_i.df_events = nu.create_df_events(nwb_i)
         if channel not in nwb_i.df_fip["event"].values:
             print("channel {} not in df_fip".format(channel))
 
@@ -222,12 +222,12 @@ def plot_fip_psth_compare_channels(  # NOQA C901
     for nwb_i in nwb_list:
         if not hasattr(nwb_i, "df_fip"):
             print("You need to compute the df_fip first")
-            print("running `nwb.df_fip = create_fib_df(nwb,tidy=True)`")
-            nwb_i.df_fip = nu.create_fib_df(nwb_i, tidy=True)
+            print("running `nwb.df_fip = create_df_fip(nwb,tidy=True)`")
+            nwb_i.df_fip = nu.create_df_fip(nwb_i, tidy=True)
         if not hasattr(nwb_i, "df_events"):
             print("You need to compute the df_events first")
-            print("run `nwb.df_events = create_events_df(nwb)`")
-            nwb_i.df_events = nu.create_events_df(nwb_i)
+            print("run `nwb.df_events = create_df_events(nwb)`")
+            nwb_i.df_events = nu.create_df_events(nwb_i)
 
         # Add warning if channels are missing
         missing_channels = [c for c in channels if c not in nwb_i.df_fip["event"].values]
@@ -434,8 +434,8 @@ def plot_histogram(nwb, preprocessed=True, edge_percentile=2, data_column="data"
     """
     if not hasattr(nwb, "df_fip"):
         print("You need to compute the df_fip first")
-        print("running `nwb.df_fip = create_fib_df(nwb,tidy=True)`")
-        nwb.df_fip = nu.create_fib_df(nwb, tidy=True)
+        print("running `nwb.df_fip = create_df_fip(nwb,tidy=True)`")
+        nwb.df_fip = nu.create_df_fip(nwb, tidy=True)
         return
 
     fig, ax = plt.subplots(3, 2, sharex=True)

src/aind_dynamic_foraging_basic_analysis/plot/plot_foraging_session_plotly.py

@@ -16,13 +16,13 @@ def plot_session_in_time_plotly(  # noqa: C901 pragma: no cover
     df_events: A tidy dataframe of session events.
 
     fip_df is a tidy dataframe of FIP measurements generated by
-        aind_dynamic_foraging_data_utils.nwb_utils.create_fib_df(tidy=True)
+        aind_dynamic_foraging_data_utils.nwb_utils.create_df_fip(tidy=True)
 
     adjust_time (bool): If True, resets time=0 to the first event of the session.
 
     EXAMPLE:
-    df_events = nwb_utils.create_events_df(nwb_object)
-    fip_df = nwb_utils.create_fib_df(nwb_object, tidy=True)
+    df_events = nwb_utils.create_df_events(nwb_object)
+    fip_df = nwb_utils.create_df_fip(nwb_object, tidy=True)
     plot_foraging_session_plotly.plot_session_events_plotly(df_events)
     """
 

src/aind_dynamic_foraging_basic_analysis/plot/plot_session_scroller.py

@@ -84,7 +84,7 @@ def plot_session_scroller(  # noqa: C901 pragma: no cover
 
     if not hasattr(nwb, "df_events"):
         print("computing df_events first")
-        nwb.df_events = nu.create_events_df(nwb)
+        nwb.df_events = nu.create_df_events(nwb)
         df_events = nwb.df_events
     else:
         df_events = nwb.df_events