remove sortingview

src/expipe_plugin_cinpla/scripts/curation.py

@@ -1,5 +1,4 @@
 # -*- coding: utf-8 -*-
-import json
 import shutil
 import warnings
 
@@ -200,37 +199,6 @@ def get_phy_run_command(self, sorter):
         phy_run_command = f"phy template-gui {phy_path}"
         return phy_run_command
 
-    def get_sortingview_link(self, sorter):
-        visualization_json = self.si_path / sorter / "sortingview_links.json"
-        if not visualization_json.is_file():
-            return "Sorting view link not found."
-        with open(visualization_json) as f:
-            sortingview_links = json.load(f)
-        return sortingview_links["raw"]
-
-    def apply_sortingview_curation(self, sorter, curated_link):
-        import spikeinterface.curation as sc
-
-        sorting_raw = self.load_raw_sorting(sorter)
-        assert sorting_raw is not None, f"Could not load raw sorting for {sorter}."
-        sorting_raw = sorting_raw.save(format="memory")
-
-        # delete NWB-specific properties: id, waveform_mean, and waveform_sd properties
-        sorting_raw.delete_property("waveform_mean")
-        sorting_raw.delete_property("waveform_sd")
-        sorting_raw.delete_property("electrodes")
-
-        curated_link_ = curated_link.replace("%22", '"')
-        curation_str = curated_link_[curated_link_.find("sortingCuration") :]
-        uri = curation_str[curation_str.find("sha1://") : -2]
-        sorting_curated = sc.apply_sortingview_curation(sorting_raw, uri_or_json=uri)
-        # exclude noise
-        good_units = sorting_curated.unit_ids[sorting_curated.get_property("noise") == False]  # noqa E712
-        # create single property for SUA and MUA
-        sorting_curated = sorting_curated.select_units(good_units)
-        self.apply_curation(sorter, sorting_curated)
-        self.curation_description = f"Curation manually performed in Sortingview\nLink: {curated_link}"
-
     def apply_qc_curator(self, sorter, query):
         raw_we = self.load_raw_waveforms(sorter)
         qm_table = raw_we.load_extension("quality_metrics").get_data()

src/expipe_plugin_cinpla/scripts/process.py

@@ -28,7 +28,6 @@ def process_ecephys(
     overwrite=False,
     singularity_image=None,
     n_components=3,
-    plot_sortingview=True,
     verbose=True,
 ):
     import warnings
@@ -41,7 +40,6 @@ def process_ecephys(
     import spikeinterface.preprocessing as spre
     import spikeinterface.qualitymetrics as sqm
     import spikeinterface.sorters as ss
-    import spikeinterface.widgets as sw
     from neuroconv.tools.spikeinterface import add_recording
     from pynwb import NWBHDF5IO
 
@@ -279,7 +277,7 @@ def process_ecephys(
         _ = spost.compute_template_metrics(we)
         if verbose:
             print("\tComputing QC metrics")
-        qm = sqm.compute_quality_metrics(we, metric_names=metric_names)
+        _ = sqm.compute_quality_metrics(we, metric_names=metric_names)
 
         if verbose:
             print("\tExporting to phy")
@@ -296,43 +294,6 @@ def process_ecephys(
         # generate files to be used with restore
         utils.generate_phy_restore_files(phy_folder)
 
-        if plot_sortingview:
-            if verbose:
-                print("\tGenerating sortingview link")
-            unit_table_properties = ["group"]
-            if "firing_rate" in qm:
-                we.sorting.set_property("firing_rate", np.round(qm["firing_rate"], 2))
-                unit_table_properties.append("firing_rate")
-            if "amplitude_median" in qm:
-                we.sorting.set_property("amplitude", np.round(qm["amplitude_median"]))
-                unit_table_properties.append("firing_rate")
-            try:
-                w = sw.plot_sorting_summary(
-                    we,
-                    backend="sortingview",
-                    curation=True,
-                    unit_table_properties=["group", "firing_rate", "amplitude"],
-                    label_choices=["SUA", "MUA", "noise"],
-                    figlabel=f"{action_id}-{sorter}",
-                )
-                sorting_summary_url = w.url
-                visualization_dict = dict(raw=sorting_summary_url)
-                # save params in output
-                with open(si_folder / sorter / "sortingview_links.json", "w") as f:
-                    json.dump(visualization_dict, f, indent=4)
-            except Exception as e:
-                print(
-                    f"Could not generate sortingview link, probably due to a wrong configuration. "
-                    f"You can setup sortingview using the following instructions:\n"
-                    "https://spikeinterface.readthedocs.io/en/latest/modules/widgets.html#sorting-view"
-                    f"\nError:\n{e}"
-                )
-                w = None
-            if "firing_rate" in qm:
-                we.sorting.delete_property("firing_rate")
-            if "amplitude_median" in qm:
-                we.sorting.delete_property("amplitude")
-
     if verbose:
         print("\nWriting to NWB")
     nwb_path.unlink()

src/expipe_plugin_cinpla/widgets/curation.py

@@ -87,9 +87,8 @@ def __init__(self, project):
 
         # 1. Load from Phy
         # 2. Use Quality metrics
-        # 3. Use sortingview
         strategy = ipywidgets.RadioButtons(
-            options=["Phy", "Sortingview", "Quality Metrics"],
+            options=["Phy", "Quality Metrics"],
             description="Curation strategy:",
             disabled=False,
             value="Phy",
@@ -114,24 +113,6 @@ def __init__(self, project):
             layout={"width": "initial"},
         )
 
-        # Sortingview
-        sv_visualization_link = ipywidgets.Text(
-            value="",
-            placeholder="The Sortingview link will appear here",
-            description="Curation link:",
-            disabled=True,
-            layout={"width": "500px"},
-        )
-        sv_curated_link = ipywidgets.Text(
-            value="",
-            placeholder="Enter the link to the curated sorting here",
-            description="Curated link:",
-            disabled=False,
-            layout={"width": "500px"},
-        )
-        apply_sv_curation = ipywidgets.Button(description="Apply", layout={"width": "200px"})
-        apply_sv_curation.style.button_color = "pink"
-
         # Quality metrics
         qm_thresholds = []
         standard_qms = project.config.get("custom_qms") if project.config.get("custom_qms") is not None else default_qms
@@ -159,8 +140,6 @@ def __init__(self, project):
             ]
         )
 
-        sortingview_panel = ipywidgets.VBox([sv_visualization_link, sv_curated_link, apply_sv_curation])
-
         qm_panel = ipywidgets.VBox(
             [
                 qc_controls,
@@ -214,9 +193,7 @@ def on_action(change):
                 if units_main is not None:
                     w = nwb2widget(units_main, custom_main_unit_vis)
                     units_viewers["main"] = w
-                if strategy.value == "Sortingview":
-                    sv_visualization_link.value = self.sorting_curator.get_sortingview_link(sorter_list.value[0])
-                elif strategy.value == "Phy":
+                if strategy.value == "Phy":
                     run_phy_command.value = self.sorting_curator.get_phy_run_command(sorter_list.value[0])
                 units_dropdown.value = "Raw"
                 on_choose_units(None)
@@ -235,10 +212,7 @@ def on_sorter(change):
                     if units_main is not None:
                         w = nwb2widget(units_main, custom_main_unit_vis)
                         units_viewers["main"] = w
-                    if strategy.value == "Sortingview":
-                        # load visualization link
-                        sv_visualization_link.value = self.sorting_curator.get_sortingview_link(sorter_list.value[0])
-                    elif strategy.value == "Phy":
+                    if strategy.value == "Phy":
                         run_phy_command.value = self.sorting_curator.get_phy_run_command(sorter_list.value[0])
                     units_dropdown.value = "Raw"
                     on_choose_units(None)
@@ -253,23 +227,6 @@ def on_change_strategy(change):
                 # check if metrics apply
                 if len(sorter_list.value) == 1:
                     check_metrics(project, actions_list, sorter_list.value[0], qc_metrics)
-            elif change["new"] == "Sortingview":
-                curation_panel.children = [strategy, sortingview_panel]
-                if len(sorter_list.value) == 1:
-                    sv_visualization_link.value = self.sorting_curator.get_sortingview_link(sorter_list.value[0])
-
-        @self.output.capture()
-        def on_curated_link(change):
-            required_values_filled(actions_list, sorter_list, sv_curated_link)
-            if len(sorter_list.value) > 1:
-                print("Select one spike sorting output at a time")
-            else:
-                print(f"Applying curation from {sv_curated_link.value}")
-                self.sorting_curator.apply_sortingview_curation(sorter_list.value[0], sv_curated_link.value)
-                units = self.sorting_curator.construct_curated_units()
-                if units:
-                    w = nwb2widget(units, custom_curated_unit_vis)
-                    units_viewers["curated"] = w
 
         def on_add_metric(change):
             action = project.actions[actions_list.value]
@@ -358,7 +315,6 @@ def on_save_to_nwb(change):
         sorter_list.observe(on_sorter)
         set_default_qms.on_click(on_set_default_qms)
         apply_qm_curation.on_click(on_apply_qm_curation)
-        apply_sv_curation.on_click(on_curated_link)
         units_dropdown.observe(on_choose_units)
 
         add_metric_button.on_click(on_add_metric)