NWB to dataframe tools

examples/make_dataframes.py

@@ -0,0 +1,32 @@
+"""
+    This is an example script to extract dataframes
+    from an NWB file
+"""
+
+import glob
+from aind_dynamic_foraging_data_utils import nwb_utils
+
+# List of filepaths to NWBs
+NWB_FILES = glob.glob("../tests/nwb/**.nwb")
+
+# Load a single NWB file
+nwb = nwb_utils.load_nwb_from_filename(NWB_FILES[0])
+
+# Make dataframe of sessions, each row is a session
+# Accepts: NWB objects, NWB files, list of NWB files
+df_session = nwb_utils.create_df_session(NWB_FILES)
+
+# Dataframe of trials, each row is a trial
+# Accepts NWB filepath or object
+df_trials = nwb_utils.create_df_trials(nwb)
+df_trials = nwb_utils.create_df_trials(NWB_FILES[0])
+
+# tidy data frame of all events in the session
+# Accepts NWB filepath or object
+df_events = nwb_utils.create_events_df(nwb)
+df_events = nwb_utils.create_events_df(NWB_FILES[0])
+
+# Data frame of FIB data
+# Accepts NWB filepath or object
+fib_df = nwb_utils.create_fib_df(nwb)
+fib_df = nwb_utils.create_fib_df(NWB_FILES[0])

pyproject.toml

@@ -19,7 +19,8 @@ dynamic = ["version"]
 dependencies = [
     'pandas',
     'numpy',
-    'pynwb'
+    'pynwb',
+    'hdmf_zarr'
 ]
 
 [project.optional-dependencies]