Adding curation panel during merge focus

spikeinterface_gui/layout_presets.py

@@ -93,12 +93,12 @@ def get_layout_description(preset_name, layout=None):
 
 merge_focus_layout = dict(
     zone1=['merge', 'unitlist'],
-    zone2=['waveform'],
+    zone2=['curation'],
     zone3=['spikeamplitude'],
     zone4=['ndscatter'],
     zone5=['probe'],
     zone6=[],
-    zone7=['spikerate'],
+    zone7=['waveform'],
     zone8=['correlogram'],
 )
 

spikeinterface_gui/tests/test_mainwindow_merge_focus.py

@@ -0,0 +1,186 @@
+from argparse import ArgumentParser
+from spikeinterface_gui import run_mainwindow, run_launcher
+
+from spikeinterface_gui.tests.testingtools import clean_all, make_analyzer_folder, make_curation_dict
+
+from spikeinterface import load_sorting_analyzer
+
+
+from pathlib import Path
+
+import numpy as np
+import sys
+
+
+# yep is for testing
+yep_layout = dict(
+    zone1=['curation', 'spikelist'],
+    zone2=['unitlist', 'mergelist'],
+    zone3=['trace', 'tracemap', 'spikeamplitude'],
+    zone4=['similarity'],
+    zone5=['probe'],
+    zone6=['ndscatter', ],
+    zone7=['waveform', 'waveformheatmap', ],
+    zone8=['correlogram', 'isi'],
+)
+
+
+def setup_module():
+    global test_folder
+    case = test_folder.stem.split('_')[-1]
+    make_analyzer_folder(test_folder, case=case, unit_dtype="int")
+
+
+def teardown_module():
+    clean_all(test_folder)
+
+
+def test_mainwindow(start_app=False, verbose=True, curation=False, only_some_extensions=False, events=False):
+
+    analyzer = load_sorting_analyzer(test_folder / "sorting_analyzer")
+    # analyzer = load_analyzer(test_folder / "sorting_analyzer.zarr")
+
+    tm = analyzer.get_extension("template_metrics").get_data().iloc[0, :]
+    # print(tm)
+    # return
+
+    print(analyzer)
+
+    if curation:
+        curation_dict = make_curation_dict(analyzer)
+    else:
+        curation_dict = None
+
+    if only_some_extensions:
+        analyzer = analyzer.copy()
+        # analyzer._recording = None
+        for k in ("principal_components", "template_similarity", "spike_amplitudes"):
+            analyzer.delete_extension(k)
+        print(analyzer)
+
+    n = analyzer.unit_ids.size
+    analyzer.sorting.set_property(
+        key='yep', values=np.array([f"yep{i}" for i in range(n)]))
+
+    extra_unit_properties = dict(
+        yop=np.array([f"yop{i}" for i in range(n)]),
+        yip=np.array([f"yip{i}" for i in range(n)]),
+    )
+
+    for segment_index in range(analyzer.get_num_segments()):
+        shift = (segment_index + 1) * 100
+        # add a gap to times
+        gap = 5
+        times = analyzer.recording.get_times(segment_index)
+        times = times + shift
+        times[len(times)//2:] += gap  # add a gap in the middle
+        analyzer.recording.set_times(
+            times,
+            segment_index=segment_index
+        )
+
+    events_dict = None
+    if events:
+        events_dict = {"event1": {"times": []}, "event2": {"times": []}}
+        for segment_index in range(analyzer.get_num_segments()):
+            times = analyzer.recording.get_times(segment_index)
+            events_dict["event1"]["times"].append(
+                np.random.choice(times, 30)
+            )
+            events_dict["event2"]["times"].append(
+                np.random.choice(times, 50)
+            )
+            # add some events outside of recording times to test filtering
+            events_dict["event1"]["times"][-1] = np.concatenate(
+                [events_dict["event1"]["times"][-1],
+                    [times[0] - 10, times[-1] + 20]]
+            )
+            events_dict["event2"]["times"][-1] = np.concatenate(
+                [events_dict["event2"]["times"][-1],
+                    [times[0] - 5, times[-1] + 15]]
+            )
+
+    win = run_mainwindow(
+        analyzer,
+        mode="desktop",
+        start_app=start_app,
+        verbose=verbose,
+        curation=curation, curation_dict=curation_dict,
+        displayed_unit_properties=None,
+        extra_unit_properties=extra_unit_properties,
+        layout_preset='default',
+        events=events_dict
+        # user_settings={"mainsettings": {"color_mode": "color_by_visibility", "max_visible_units": 5}}
+    )
+
+
+def test_launcher(verbose=True):
+
+    # case 1
+    analyzer_folders = None
+    root_folder = None
+
+    # case 2 : explore parent
+    analyzer_folders = None
+    root_folder = Path(__file__).parent
+
+    # case 3 : list
+    # analyzer_folders = [
+    #     Path(__file__).parent / 'my_dataset_small/sorting_analyzer',
+    #     Path(__file__).parent / 'my_dataset_big/sorting_analyzer',
+    # ]
+    # root_folder = None
+
+    # case 4 : dict
+    # analyzer_folders = {
+    #     'small' : Path(__file__).parent / 'my_dataset_small/sorting_analyzer',
+    #     'big' : Path(__file__).parent / 'my_dataset_big/sorting_analyzer',
+    # }
+    # root_folder = None
+
+    win = run_launcher(mode="desktop", analyzer_folders=analyzer_folders,
+                       root_folder=root_folder,  verbose=verbose)
+
+
+def test_main_window_merge_focus(start_app=False, Verbose=True):
+    analyzer = load_sorting_analyzer(test_folder/"sorting_analyzer")
+    if not analyzer.has_extension("template_similarity"):
+        analyzer.compute_one_extension("template_similarity")
+    merge_unit_groups = sc.compute_merge_unit_groups(
+        analyzer,
+        preset="slay",
+    )
+    print("Computed merge unit groups:", merge_unit_groups)
+    win = run_mainwindow(
+        analyzer,
+        mode="desktop",
+        start_app=start_app,
+        verbose=verbose,
+        curation=True,
+        layout_preset="merge_focus",
+        merge_unit_groups=merge_unit_groups,
+    )
+    return win
+
+
+parser = ArgumentParser()
+parser.add_argument('--dataset', default="small",
+                    help='Path to the dataset folder')
+parser.add_argument('--events', action="store_true",
+                    help='Simulate and add events')
+
+if __name__ == '__main__':
+    args = parser.parse_args()
+    dataset = args.dataset
+    global test_folder
+    if dataset is not None:
+        test_folder = Path(__file__).parents[2] / f"my_dataset_{dataset}"
+
+    if not test_folder.is_dir():
+        setup_module()
+
+    win = test_mainwindow(start_app=True, verbose=True,
+                          curation=True, events=args.events)
+    # win = test_mainwindow(start_app=True, verbose=True, curation=False)
+
+    # test_launcher(verbose=True)

spikeinterface_gui/tests/testingtools.py

@@ -138,9 +138,9 @@ def make_analyzer_folder(test_folder, case="small", unit_dtype="str"):
     sorting_analyzer.compute("correlograms", window_ms=50., bin_ms=1.)
     sorting_analyzer.compute("template_similarity", method="l1")
     sorting_analyzer.compute("principal_components", n_components=3, mode='by_channel_global', whiten=True, **job_kwargs)
+    sorting_analyzer.compute(["spike_amplitudes", "spike_locations"], **job_kwargs)
     sorting_analyzer.compute("quality_metrics", metric_names=["snr", "firing_rate"])
     sorting_analyzer.compute("template_metrics")
-    sorting_analyzer.compute(["spike_amplitudes", "spike_locations"], **job_kwargs)
 
 
 def make_curation_dict(analyzer):