Update SI-GUI from SpikeInterface

Author: alejoe91

Dockerfile

@@ -23,9 +23,9 @@ RUN wget "https://www.wavpack.com/wavpack-${WAVPACK_VERSION}.tar.bz2" && \
 RUN pip install wavpack-numcodecs
 
 # Install spikeinterface-gui from source
-RUN git clone https://github.com/alejoe91/spikeinterface-gui.git && \
+RUN git clone https://github.com/SpikeInterface/spikeinterface-gui.git && \
     cd spikeinterface-gui && \
-    git checkout a616ff653eea37632cac013bf21a39cdea18c0c1 && \
+    git checkout e7c37434169df1ad107acdc2b7a6b4d3fd18821a && \
     pip install . && cd ..
 
 

src/aind_ephys_portal/panel/ephys_gui.py

@@ -1,6 +1,8 @@
 import sys
 import param
 import boto3
+import time
+from copy import deepcopy
 
 import panel as pn
 
@@ -15,6 +17,19 @@
 from .utils import Tee
 
 
+displayed_unit_properties = ["decoder_label", "firing_rate", "y", "snr", "amplitude_median", "isi_violation_ratio"]
+default_curation_dict = {
+    "label_definitions": {
+        "quality":{
+            "label_options": ["good", "MUA", "noise"],
+            "exclusive": True,
+        }, 
+    },
+    "manual_labels": [],
+    "merge_unit_groups": [],
+    "removed_units": [],
+}
+
 class EphysGuiView(param.Parameterized):
 
     def __init__(self, analyzer_path, recording_path, **params):
@@ -53,6 +68,7 @@ def __init__(self, analyzer_path, recording_path, **params):
 
     def _initialize(self):
         if self.analyzer_input.value != "":
+            t_start = time.perf_counter()
             spinner = pn.indicators.LoadingSpinner(value=True, sizing_mode="stretch_width")
             # Create a TextArea widget to display logs
             log_output = pn.widgets.TextAreaInput(value="", sizing_mode="stretch_both")
@@ -75,6 +91,8 @@ def _initialize(self):
             self.win = self._create_main_window()
             self.layout[1] = self.win
             print("Ephys GUI initialized successfully!")
+            t_stop = time.perf_counter()
+            print(f"Initialization time: {t_stop - t_start:.2f} seconds")
             sys.stdout = sys.__stdout__  # Reset stdout
             sys.stderr = sys.__stderr__  # Reset stderr
 
@@ -115,10 +133,22 @@ def _check_if_s3_folder_exists(self, location):
 
     def _create_main_window(self):
         if self.analyzer is not None:
+            # prepare the curation data using decoder labels
+            curation_dict = deepcopy(default_curation_dict)
+            curation_dict["unit_ids"] = self.analyzer.unit_ids
+            if "decoder_label" in self.analyzer.sorting.get_property_keys():
+                decoder_labels = self.analyzer.get_sorting_property("decoder_label")
+                noise_units = self.analyzer.unit_ids[decoder_labels == "noise"]
+                curation_dict["removed_units"] = list(noise_units)
+                for unit_id in noise_units:
+                    curation_dict["manual_labels"].append({"unit_id": unit_id, "quality": ["noise"]})
+
             win = run_mainwindow(
                 analyzer=self.analyzer,
                 curation=True,
                 skip_extensions=["waveforms"],
+                displayed_unit_properties=displayed_unit_properties,
+                curation_dict=curation_dict,
                 backend="panel",
                 start_app=False,
                 make_servable=False,

src/aind_ephys_portal/panel/ephys_portal.py

@@ -1,10 +1,12 @@
 """Main Panel application for the AIND SIGUI Portal."""
 
 import param
-import threading
 import panel as pn
 import pandas as pd
 import boto3
+from botocore import UNSIGNED
+from botocore.config import Config
+
 
 from aind_ephys_portal.docdb.database import get_raw_asset_by_name, get_all_ecephys_derived
 from aind_ephys_portal.panel.utils import format_link, OUTER_STYLE, EPHYSGUI_LINK_PREFIX
@@ -113,7 +115,12 @@ def update_streams(self, event):
                 links_url = []
                 for stream_name in stream_names:
                     raw_stream_name = stream_name[: stream_name.find("_recording")]
-                    recording_path = f"{raw_asset['location']}/ecephys/ecephys_compressed/{raw_stream_name}.zarr"
+                    raw_asset_prefix = self.get_raw_asset_location(raw_asset["location"])
+                    print(f"Raw asset prefix: {raw_asset_prefix}")
+                    if raw_asset_prefix is None:
+                        recording_path=""
+                    else:
+                        recording_path = f"{raw_asset_prefix}/{raw_stream_name}.zarr"
                     analyzer_path = f"{analyzer_base_location}/postprocessed/{stream_name}"
                     print("Raw path:", recording_path)
                     print("Analyzer path:", analyzer_path)
@@ -140,6 +147,27 @@ def update_streams(self, event):
     #     # Schedule next run in 1 hour (3600 seconds)
     #     threading.Timer(3600, self.auto_update_datasets).start()
 
+    def get_raw_asset_location(self, asset_location):
+        asset_without_s3 = asset_location[asset_location.find("s3://") + 5:]
+        asset_split = asset_without_s3.split("/")
+        bucket_name = asset_split[0]
+        session_name = "/".join(asset_split[1:])
+        possible_locations = ["ecephys/ecephys_compressed", "ecephys_compressed"]
+        raw_asset_location = None
+        for location in possible_locations:
+            prefix = f"{session_name}/{location}/"
+            try:
+                response = s3_client.list_objects_v2(Bucket=bucket_name, Prefix=prefix, MaxKeys=1)
+            except Exception as e:
+                print(f"Error listing objects with unsigned client from {bucket_name}/{prefix}: {e}")
+                continue
+            if "Contents" in response:
+                raw_asset_location = f"s3://{bucket_name}/{prefix}"
+                break
+        if raw_asset_location is not None and raw_asset_location.endswith("/"):
+            raw_asset_location = raw_asset_location[:-1]
+        return raw_asset_location
+
     def panel(self):
         """Build a Panel object representing the Ephys Portal."""
         # Create a layout with the search bar at the top, results panel in the middle,