Merge branch 'master' into release

src/spyglass/__init__.py

@@ -7,6 +7,3 @@
 # Important to do this so that we add the franklab namespace for pynwb
 # Note: This is franklab-specific
 import ndx_franklab_novela
-
-from .data_import.insert_sessions import insert_sessions
-from .data_import.storage_dirs import base_dir, check_env, kachery_storage_dir

src/spyglass/common/common_ephys.py

@@ -148,7 +148,7 @@ def make(self, key):
         interval_dict['nwb_file_name'] = key['nwb_file_name']
         interval_dict['interval_list_name'] = raw_interval_name
         if rawdata.rate is not None:
-            interval_dict['valid_times'] = np.array([[0, len(rawdata.data)*rawdata.rate]])
+            interval_dict['valid_times'] = np.array([[0, len(rawdata.data)/rawdata.rate]])
         else:
             # get the list of valid times given the specified sampling rate.
             interval_dict['valid_times'] = get_valid_intervals(np.asarray(rawdata.timestamps), key['sampling_rate'],
@@ -159,7 +159,7 @@ def make(self, key):
         key['raw_object_id'] = rawdata.object_id
         key['sampling_rate'] = sampling_rate
         print(
-            f'Importing raw data: Estimated sampling rate:\t{key["sampling_rate"]} Hz')
+            f'Importing raw data: Sampling rate:\t{key["sampling_rate"]} Hz')
         print(
             f'Number of valid intervals:\t{len(interval_dict["valid_times"])}')
         key['interval_list_name'] = raw_interval_name

src/spyglass/common/common_lab.py

@@ -56,8 +56,9 @@ def insert_from_name(cls, full_name):
         """
         labmember_dict = dict()
         labmember_dict['lab_member_name'] = full_name
-        labmember_dict['first_name'] = str.split(full_name)[:-1]
-        labmember_dict['last_name'] = str.split(full_name)[-1]
+        full_name_split = str.split(full_name)
+        labmember_dict['first_name'] = " ".join(full_name_split[:-1])
+        labmember_dict['last_name'] = full_name_split[-1]
         cls.insert1(labmember_dict, skip_duplicates=True)
 
 

src/spyglass/common/populate_all_common.py

@@ -14,21 +14,27 @@ def populate_all_common(nwb_file_name):
     # Insert session one by one
     fp = [(Nwbfile & {'nwb_file_name': nwb_file_name}).proj()]
     print('Populate Session...')
-    # Session().populate()
     Session.populate(fp)
+
     # If we use Kachery for data sharing we can uncomment the following two lines. TBD
     # print('Populate NwbfileKachery...')
     # NwbfileKachery.populate()
+
     print('Populate ExperimenterList...')
     ExperimenterList.populate(fp)
+
     print('Populate ElectrodeGroup...')
     ElectrodeGroup.populate(fp)
+
     print('Populate Electrode...')
     Electrode.populate(fp)
+
     print('Populate Raw...')
     Raw.populate(fp)
+
     print('Populate SampleCount...')
     SampleCount.populate(fp)
+
     print('Populate DIOEvents...')
     DIOEvents.populate(fp)
     # sensor data (from analog ProcessingModule) is temporarily removed from NWBFile

src/spyglass/data_import/__init__.py

@@ -1,2 +1,2 @@
 from .insert_sessions import insert_sessions
-from .storage_dirs import base_dir, check_env, kachery_storage_dir
+from .storage_dirs import base_dir, check_env

src/spyglass/data_import/insert_sessions.py

@@ -1,3 +1,4 @@
+from typing import Union, List
 import os
 import stat
 import warnings
@@ -8,14 +9,14 @@
 from .storage_dirs import check_env
 
 
-def insert_sessions(nwb_file_names):
+def insert_sessions(nwb_file_names: Union[str, List[str]]):
     """
     Populate the dj database with new sessions.
 
     Parameters
     ----------
-    nwb_file_names : string or List of strings
-        nwb_file_names is a list of relative file paths, relative to $SPYGLASS_BASE_DIR, pointing to
+    nwb_file_names : str or List of str
+        File paths (relative to $SPYGLASS_BASE_DIR) pointing to
         existing .nwb files. Each file represents a session.
     """
     check_env()

src/spyglass/data_import/storage_dirs.py

@@ -6,7 +6,6 @@ def check_env():
     Raise an exception if not.
     """
     base_dir()
-    # kachery_storage_dir()
 
 
 def base_dir():
@@ -18,36 +17,6 @@ def base_dir():
     p = os.getenv('SPYGLASS_BASE_DIR', None)
     assert p is not None, '''
     You must set the SPYGLASS_BASE_DIR environment variable.
-    You MUST also set the $KACHERY_STORAGE_DIR environment variable
-    to be equal to $SPYGLASS_BASE_DIR/kachery-storage
     '''
     return p
 
-
-def kachery_storage_dir():
-    """Get the kachery storage directory from $KACHERY_STORAGE_DIR
-    And verifies that it is equal to $SPYGLASS_BASE_DIR/kachery-storage
-    Raise an exception if not.
-
-    Returns:
-        str: The kachery storage directory
-    """
-    base = base_dir()
-    p = os.getenv('KACHERY_STORAGE_DIR', None)
-    assert p is not None, '''
-    You must set the KACHERY_STORAGE_DIR environment variable.
-    And it should be equal to $SPYGLASS_BASE_DIR/kachery-storage
-    '''
-
-    assert p == os.path.join(base, 'kachery-storage'), f'''
-    Although KACHERY_STORAGE_DIR is set, it is not equal to $SPYGLASS_BASE_DIR/kachery-storage
-
-    Current values:
-    SPYGLASS_BASE_DIR={base}
-    KACHERY_STORAGE_DIR={p}
-
-    You must update these variables before proceeding
-    '''
-    if not os.path.exists(p):
-        os.mkdir(p)
-    return p