Various fixes

pyproject.toml

@@ -20,6 +20,7 @@ dependencies = [
     "neuroconv>=0.4.6",
     "pyopenephys>=1.2.0",
     "spikeinterface[full,widgets]>=0.100.0",
+    "scikit-learn<1.5.0",
     "pynwb>=2.5.0",
     "neuroconv>=0.4.6",
     "ipywidgets>=8.1.1",

requirements.txt

@@ -7,4 +7,4 @@ pyopenephys>=1.2.0
 tbb>=2021.11.0
 spikeinterface[full,widgets]>=0.100.0
 pynwb>=2.6.0
-neuroconv>=0.4.6
+neuroconv>=0.4.6

src/expipe_plugin_cinpla/cli/register.py

@@ -8,9 +8,6 @@
 from expipe_plugin_cinpla.cli.utils import validate_depth, validate_position, validate_angle, validate_adjustment
 
 
-import spikeinterface.sorters as ss
-
-
 def attach_to_register(cli):
     ### OpenEphys ###
     @cli.command("openephys", short_help="Register an open-ephys recording-action to database.")

src/expipe_plugin_cinpla/scripts/data_processing.py → src/expipe_plugin_cinpla/data_loader.py

@@ -6,8 +6,7 @@
 import spikeinterface as si
 import spikeinterface.extractors as se
 
-from pynwb import NWBHDF5IO
-from .utils import _get_data_path
+from .scripts.utils import _get_data_path
 
 
 def get_data_path(action):
@@ -92,6 +91,8 @@ def load_leds(data_path):
     x1, y1, t1, x2, y2, t2, stop_time: tuple
         The x and y positions of the red and green LEDs, the timestamps and the stop time
     """
+    from pynwb import NWBHDF5IO
+
     io = NWBHDF5IO(str(data_path), "r")
     nwbfile = io.read()
 
@@ -130,6 +131,10 @@ def load_lfp(data_path, channel_group=None, lim=None):
     LFP: neo.AnalogSignal
         The LFP signal
     """
+    from pynwb import NWBHDF5IO
+    # get the session start time
+    io = NWBHDF5IO(str(data_path), "r")
+    nwbfile = io.read()
     recording_lfp = se.read_nwb_recording(
         str(data_path), electrical_series_path="processing/ecephys/LFP/ElectricalSeriesLFP"
     )
@@ -190,10 +195,11 @@ def load_epochs(data_path, label_column=None):
     epochs: neo.Epoch
         The trials as NEO epochs
     """
+    from pynwb import NWBHDF5IO
+
     with NWBHDF5IO(str(data_path), "r") as io:
         nwbfile = io.read()
         trials = nwbfile.trials.to_dataframe()
-
         start_times = trials["start_time"].values * pq.s
         stop_times = trials["stop_time"].values * pq.s
         durations = stop_times - start_times
@@ -248,6 +254,10 @@ def load_spiketrains(data_path, channel_group=None, lim=None):
     spiketrains: list of NEO spike trains
         The spike trains
     """
+    from pynwb import NWBHDF5IO
+    # get the session start time
+    io = NWBHDF5IO(str(data_path), "r")
+    nwbfile = io.read()
     recording = se.read_nwb_recording(str(data_path), electrical_series_path="acquisition/ElectricalSeries")
     sorting = se.read_nwb_sorting(str(data_path), electrical_series_path="acquisition/ElectricalSeries")
 
@@ -260,22 +270,25 @@ def load_spiketrains(data_path, channel_group=None, lim=None):
             unit_id for unit_index, unit_id in enumerate(sorting.unit_ids) if groups[unit_index] == channel_group
         ]
     sptr = []
-    # build neo pbjects
+    # build neo objects
     for unit in unit_ids:
-        times = sorting.get_unit_spike_train(unit, return_times=True) * pq.s
+        spike_times = sorting.get_unit_spike_train(unit, return_times=True) 
+        # subtract the session start time
+        spike_times = spike_times * pq.s
         if lim is None:
             times = recording.get_times() * pq.s
             t_start = times[0]
             t_stop = times[-1]
         else:
             t_start = pq.Quantity(lim[0], "s")
             t_stop = pq.Quantity(lim[1], "s")
-        mask = (times >= t_start) & (times <= t_stop)
-        times = times[mask]
+        mask = (spike_times >= t_start) & (spike_times <= t_stop)
+        spike_times = spike_times[mask]
 
         st = neo.SpikeTrain(
-            times=times, t_start=t_start, t_stop=t_stop, sampling_rate=sorting.sampling_frequency * pq.Hz
+            times=spike_times, t_start=t_start, t_stop=t_stop, sampling_rate=sorting.sampling_frequency * pq.Hz
         )
+        st.annotations.update({"name": unit})
         for p in sorting.get_property_keys():
             st.annotations.update({p: sorting.get_unit_property(unit, p)})
         sptr.append(st)
@@ -313,7 +326,7 @@ def load_unit_annotations(data_path, channel_group=None):
         ]
 
     for unit in unit_ids:
-        annotations = {}
+        annotations = {"name": unit}
         for p in sorting.get_property_keys():
             annotations.update({p: sorting.get_unit_property(unit, p)})
         units.append(annotations)

src/expipe_plugin_cinpla/imports.py

@@ -1,18 +1,6 @@
-# import click
-# from expipe.cliutils.misc import lazy_import
-
 import expipe
 from pathlib import Path
 
-# @lazy_import
-# def expipe():
-#     import expipe
-#     return expipe
-
-# @lazy_import
-# def pathlib():
-#     import pathlib
-#     return pathlib
 
 local_root, _ = expipe.config._load_local_config(Path.cwd())
 if local_root is not None:
@@ -23,171 +11,3 @@ class P:
         config = {}
 
     project = P
-
-
-# @lazy_import
-# def pd():
-#     import pandas as pd
-#     return pd
-
-# @lazy_import
-# def dt():
-#     import datetime as dt
-#     return dt
-
-# @lazy_import
-# def yaml():
-#     import yaml
-#     return yaml
-
-# @lazy_import
-# def ipywidgets():
-#     import ipywidgets
-#     return ipywidgets
-
-# @lazy_import
-# def pyopenephys():
-#     import pyopenephys
-#     return pyopenephys
-
-# # @lazy_import
-# # def openephys_io():
-# #     from expipe_io_neuro.openephys import openephys as openephys_io
-# #     return openephys_io
-
-# @lazy_import
-# def pyintan():
-#     import pyintan
-#     return pyintan
-
-# @lazy_import
-# def pyxona():
-#     import pyxona
-#     return pyxona
-
-# @lazy_import
-# def platform():
-#     import platform
-#     return platform
-
-# @lazy_import
-# def csv():
-#     import csv
-#     return csv
-
-# @lazy_import
-# def json():
-#     import json
-#     return json
-
-# # @lazy_import
-# # def axona():
-# #     from expipe_io_neuro import axona
-# #     return axona
-
-# @lazy_import
-# def os():
-#     import os
-#     return os
-
-# @lazy_import
-# def shutil():
-#     import shutil
-#     return shutil
-
-# @lazy_import
-# def datetime():
-#     import datetime
-#     return datetime
-
-# @lazy_import
-# def subprocess():
-#     import subprocess
-#     return subprocess
-
-# @lazy_import
-# def tarfile():
-#     import tarfile
-#     return tarfile
-
-# @lazy_import
-# def paramiko():
-#     import paramiko
-#     return paramiko
-
-# @lazy_import
-# def getpass():
-#     import getpass
-#     return getpass
-
-# @lazy_import
-# def tqdm():
-#     from tqdm import tqdm
-#     return tqdm
-
-# @lazy_import
-# def scp():
-#     import scp
-#     return scp
-
-# @lazy_import
-# def neo():
-#     import neo
-#     return neo
-
-# @lazy_import
-# def exdir():
-#     import exdir
-#     import exdir.plugins.quantities
-#     return exdir
-
-# @lazy_import
-# def pq():
-#     import quantities as pq
-#     return pq
-
-# @lazy_import
-# def logging():
-#     import logging
-#     return logging
-
-# @lazy_import
-# def np():
-#     import numpy as np
-#     return np
-
-# @lazy_import
-# def copy():
-#     import copy
-#     return copy
-
-# @lazy_import
-# def scipy():
-#     import scipy
-#     import scipy.io
-#     return scipy
-
-# @lazy_import
-# def glob():
-#     import glob
-#     return glob
-
-# @lazy_import
-# def el():
-#     import elephant as el
-#     return el
-
-# @lazy_import
-# def sys():
-#     import sys
-#     return sys
-
-# @lazy_import
-# def pprint():
-#     import pprint
-#     return pprint
-
-# @lazy_import
-# def collections():
-#     import collections
-#     return collections

src/expipe_plugin_cinpla/nwbutils/interfaces/openephystrackinginterface.py

@@ -78,14 +78,15 @@ def add_to_nwbfile(
                             rising = rising[:-1]
 
                         if len(rising) == len(falling):
-                            nwbfile.add_trial_column(
-                                name="channel",
-                                description="Open Ephys channel",
-                            )
-                            nwbfile.add_trial_column(
-                                name="processor",
-                                description="Open Ephys processor that recorded the event",
-                            )
+                            if nwbfile.trials is None:
+                                nwbfile.add_trial_column(
+                                    name="channel",
+                                    description="Open Ephys channel",
+                                )
+                                nwbfile.add_trial_column(
+                                    name="processor",
+                                    description="Open Ephys processor that recorded the event",
+                                )
                             start_times = times[rising].rescale("s").magnitude
                             stop_times = times[falling].rescale("s").magnitude
                             for start, stop in zip(start_times, stop_times):

src/expipe_plugin_cinpla/nwbutils/nwbwidgetsunitviewer.py

@@ -2,21 +2,17 @@
 import numpy as np
 import ipywidgets as widgets
 from ipywidgets import Layout, interactive_output
-from pynwb.misc import Units
-from pynwb.behavior import SpatialSeries
 
 import matplotlib.pyplot as plt
 
-from nwbwidgets.view import default_neurodata_vis_spec
-
 
 color_wheel = plt.rcParams["axes.prop_cycle"].by_key()["color"]
 
 
 class UnitWaveformsWidget(widgets.VBox):
     def __init__(
         self,
-        units: Units,
+        units: "pynwb.misc.Units",
     ):
         super().__init__()
 
@@ -55,7 +51,7 @@ def on_unit_change(self, change):
         self.unit_group_text.value = f"Group: {unit_group}"
 
 
-def show_unit_waveforms(units: Units, unit_index=None, ax=None):
+def show_unit_waveforms(units: "pynwb.mis.Units", unit_index=None, ax=None):
     """
     TODO: add docstring
 
@@ -105,8 +101,8 @@ def show_unit_waveforms(units: Units, unit_index=None, ax=None):
 class UnitRateMapWidget(widgets.VBox):
     def __init__(
         self,
-        units: Units,
-        spatial_series: SpatialSeries = None,
+        units: "pynwb.mis.Units",
+        spatial_series: "SpatialSeries" = None,
     ):
         super().__init__()
 
@@ -186,6 +182,8 @@ def on_unit_change(self, change):
         self.unit_group_text.value = f"Group: {unit_group}"
 
     def get_spatial_series(self):
+        from pynwb.behavior import SpatialSeries
+
         spatial_series = dict()
         nwbfile = self.units.get_ancestor("NWBFile")
         for item in nwbfile.all_children():
@@ -265,6 +263,9 @@ def show_unit_rate_maps(self, unit_index=None, spatial_series_selector=None, num
 
 
 def get_custom_spec():
+    from pynwb.misc import Units
+    from nwbwidgets.view import default_neurodata_vis_spec
+
     custom_neurodata_vis_spec = default_neurodata_vis_spec.copy()
 
     # remove irrelevant widgets