Export to nwb

element_session/export/nwb.py

@@ -0,0 +1,107 @@
+import datetime
+from uuid import uuid4
+import pynwb
+
+from .. import session
+
+assert session.schema.is_activated()
+
+
+def session_to_nwb(
+        session_key: dict,
+        lab_key=None,
+        project_key=None,
+        protocol_key=None,
+        additional_nwbfile_kwargs=None,
+):
+    """Gather session- and subject-level metadata and use it to create an NWBFile. If
+    there is no subject_to_nwb export function in the current namespace, subject_id will
+    be inferred from the set of primary attributes in the Subject table upstream of Session.
+
+    Parameters
+    ----------
+    session_key: dict,
+        e.g.,
+        {
+            'subject': 'subject5',
+            'session_datetime': datetime.datetime(2020, 5, 12, 4, 13, 7),
+        }
+    lab_key, project_key, protocol_key: dict, optional
+        Used to gather additional optional metadata.
+    additional_nwbfile_kwargs: dict, optional
+        Optionally overwrite or add fields to NWBFile.
+
+    Returns
+    -------
+    pynwb.NWBFile
+
+    mappings:
+        session.Session::KEY -> NWBFile.session_id
+        session.Session::session_datetime -> NWBFile.session_start_time
+        session.SessionNote::session_note -> NWBFile.session_description
+        session.SessionExperimenter::user -> NWBFile.experimenter
+
+        subject.Subject::subject -> NWBFile.subject.subject_id
+        subject.Subject::sex -> NWBFile.subject.sex
+
+        lab.Lab::institution -> NWBFile.institution
+        lab.Lab::lab_name -> NWBFile.lab
+
+        lab.Protocol::protocol -> NWBFile.protocol
+        lab.Protocol::protocol_description -> NWBFile.notes
+
+        lab.Project::project_description -> NWBFile.experiment_description
+        lab.ProjectKeywords.keyword -> NWBFile.keywords
+        lab.ProjectPublication.publication -> NWBFile.related_publications
+
+    """
+
+    # ensure only one session key is entered
+    session_key = (session.Session & session_key).fetch1("KEY")
+
+    session_identifier = {
+        k: v.isoformat() if isinstance(v, datetime.datetime) else v
+        for k, v in session_key.items()
+    }
+
+    nwbfile_kwargs = dict(
+        session_id="_".join(session_identifier.values()), identifier=str(uuid4()),
+    )
+
+    session_info = (session.Session & session_key).join(session.SessionNote, left=True).fetch1()
+
+    nwbfile_kwargs.update(
+        session_start_time=session_info["session_datetime"].astimezone(
+            datetime.timezone.utc
+        )
+    )
+
+    nwbfile_kwargs.update(session_description=session_info.get("session_note", ""))
+
+    experimenters =(session.SessionExperimenter & session_key).fetch("user")
+
+    nwbfile_kwargs.update(experimenter=list(experimenters) or None)
+
+    subject_to_nwb = getattr(session._linking_module, "subject_to_nwb", False)
+
+    if subject_to_nwb:
+        nwbfile_kwargs.update(subject=subject_to_nwb(session_key))
+    else:
+        subject_id = '_'.join((getattr(session._linking_module, 'Subject') & session_key).fetch1('KEY').values())
+        nwbfile_kwargs.update(subject=pynwb.file.Subject(subject_id=subject_id))
+
+    if any([lab_key, project_key, protocol_key]):
+        element_lab_to_nwb_dict = getattr(session._linking_module, "element_lab_to_nwb_dict", {})
+
+        nwbfile_kwargs.update(
+            element_lab_to_nwb_dict(
+                lab_key=lab_key,
+                project_key=project_key,
+                protocol_key=protocol_key,
+            )
+        )
+
+    if additional_nwbfile_kwargs is not None:
+        nwbfile_kwargs.update(additional_nwbfile_kwargs)
+
+    return pynwb.NWBFile(**nwbfile_kwargs)

element_session/session_with_id.py

@@ -3,7 +3,6 @@
 import inspect
 
 schema = dj.schema()
-
 _linking_module = None
 
 
@@ -46,7 +45,7 @@ class Session(dj.Manual):
     ---
     session_datetime: datetime
     """
-    
+
 
 @schema
 class SessionDirectory(dj.Manual):
@@ -72,6 +71,7 @@ class SessionNote(dj.Manual):
     -> Session
     ---
     session_note: varchar(1024)
+
     """
 
 

requirements.txt

@@ -1 +1,2 @@
-datajoint>=0.13.0
+datajoint>=0.13.0
+pynwb