Fix raster plot handling of segment times where t_start is not zero.

playing.py

@@ -0,0 +1,92 @@
+"""
+Generate a multi-segment recording whose segments start at non-zero times,
+then plot a raster of the segments.
+"""
+
+import matplotlib
+
+matplotlib.use("QtAgg")
+import matplotlib.pyplot as plt
+
+from spikeinterface.core import append_recordings, append_sortings, create_sorting_analyzer, generate_ground_truth_recording
+from spikeinterface.generation import generate_drifting_recording
+from spikeinterface.preprocessing import compute_motion
+import spikeinterface.widgets as sw
+
+
+def make_multi_segment_recording(num_segments=3, seed=2205):
+    """Build a multi-segment recording and sorting with non-zero segment start times."""
+
+    common_kwargs = dict(
+        durations=[10.0],
+        sampling_frequency=30000.0,
+        num_channels=64,
+        num_units=60,
+    )
+
+    recordings = []
+    sortings = []
+    # Offsets so segments do NOT start at time zero.
+    start_time_offsets = [5.0, 120.0, 260.0]
+
+    for seg in range(num_segments):
+        recording, sorting = generate_ground_truth_recording(seed=seed + seg, **common_kwargs)
+        # Give this segment a non-zero start time.
+        recording.shift_times(shift=start_time_offsets[seg % len(start_time_offsets)])
+        recordings.append(recording)
+        sortings.append(sorting)
+
+    multi_segment_recording = append_recordings(recordings)
+    multi_segment_sorting = append_sortings(sortings)
+    return multi_segment_recording, multi_segment_sorting
+
+
+def plot_amplitudes_output(recording, sorting):
+    """Plot spike amplitudes for a few units across all recording segments."""
+
+    analyzer = create_sorting_analyzer(sorting=sorting, recording=recording, format="memory")
+    analyzer.compute(["random_spikes", "waveforms", "templates", "spike_amplitudes"])
+
+    amplitude_widget = sw.plot_amplitudes(
+        analyzer,
+        unit_ids=sorting.unit_ids[:6],
+        segment_indices=list(range(sorting.get_num_segments())),
+        plot_histograms=True,
+    )
+    amplitude_widget.figure.canvas.manager.set_window_title("Amplitude output")
+    amplitude_widget.axes.flatten()[0].set_title("Spike amplitudes")
+
+
+def main():
+    recording, sorting = make_multi_segment_recording()
+    sorting.register_recording(recording)
+
+    for seg in range(recording.get_num_segments()):
+        print(f"  segment {seg}: start={recording.get_start_time(seg):.1f}s end={recording.get_end_time(seg):.1f}s")
+
+    # Plot a raster of all segments.
+    segment_indices = list(range(sorting.get_num_segments()))
+    # sw.plot_rasters(sorting, segment_indices=segment_indices)
+    # plot_amplitudes_output(recording, sorting)
+
+
+    motion_recording = recording.select_segments([0])
+    motion, motion_info = compute_motion(
+        motion_recording,
+        preset="rigid_fast",
+        estimate_motion_kwargs=dict(method="decentralized", conv_engine="numpy"),
+        n_jobs=-1,
+        progress_bar=True,
+        output_motion_info=True,
+    )
+    print(motion)
+    motion_widget = sw.plot_motion_info(motion_info, recording=motion_recording)
+    motion_widget.figure.canvas.manager.set_window_title("Motion output")
+    motion_widget.figure.canvas.draw()
+    motion_widget.figure.show()
+
+    plt.show(block=True)
+
+
+if __name__ == "__main__":
+    main()

src/spikeinterface/core/sorting_tools.py

@@ -447,7 +447,7 @@ def random_spikes_selection(
                 if maximum_rate is None:
                     raise ValueError(f"maximum_rate must be defined")
 
-                t_duration = np.sum(get_segment_durations(sorting))
+                t_duration = np.sum(get_segment_durations(sorting)[0])
                 rng_size = min(int(t_duration * maximum_rate), max_spikes_per_unit, all_unit_indices.size)
                 selected_unit_indices = rng.choice(all_unit_indices, size=rng_size, replace=False, shuffle=False)
 

src/spikeinterface/widgets/amplitudes.py

@@ -122,14 +122,14 @@ def __init__(
             bins = 100
 
         # Calculate durations for all segments for x-axis limits
-        durations = get_segment_durations(sorting, segment_indices)
+        _, segment_start_stop_times = get_segment_durations(sorting, segment_indices)
 
         # Build the plot data with the full dict of dicts structure
         plot_data = dict(
             unit_colors=unit_colors,
             plot_histograms=plot_histograms,
             bins=bins,
-            durations=durations,
+            segment_start_stop_times=segment_start_stop_times,
             unit_ids=unit_ids,
             hide_unit_selector=hide_unit_selector,
             plot_legend=plot_legend,
@@ -180,9 +180,14 @@ def plot_figpack(self, data_plot, **backend_kwargs):
             for u in unit_ids
         ]
 
+        segment_times = dp.segment_start_stop_times.values()
+
+        start_time_sec = min(start for start, _ in segment_times)
+        end_time_sec = max(stop for _, stop in segment_times)
+
         self.view = vv_views.SpikeAmplitudes(
-            start_time_sec=0,
-            end_time_sec=np.sum(dp.durations),
+            start_time_sec=start_time_sec,
+            end_time_sec=end_time_sec,
             plots=sa_items,
             # hide_unit_selector=dp.hide_unit_selector,
         )

src/spikeinterface/widgets/motion.py

@@ -4,6 +4,7 @@
 
 from spikeinterface.core import BaseRecording, SortingAnalyzer
 from .rasters import BaseRasterWidget
+from .utils import compute_segment_durations_from_spike_vector
 from spikeinterface.core.motion import Motion
 
 
@@ -155,7 +156,6 @@ def __init__(
         color: str = "Gray",
         clim: tuple[float, float] | None = None,
         alpha: float = 1,
-        segment_index: int | list[int] | None = None,
         backend: str | None = None,
         **backend_kwargs,
     ):
@@ -229,7 +229,10 @@ def __init__(
             segment_locations = filtered_locations[segment_mask]
 
             # Convert peak times to seconds
-            spike_times = segment_peaks["sample_index"] / sampling_frequency
+            if recording is None:
+                spike_times = segment_peaks["sample_index"] / sampling_frequency
+            else:
+                spike_times = recording.sample_index_to_time(segment_peaks["sample_index"], segment_index=seg_idx)
 
             # Store in dict of dicts format (using 0 as the "unit" id)
             spike_train_data[seg_idx] = {0: spike_times}
@@ -257,19 +260,17 @@ def __init__(
         else:
             color_kwargs = dict(color=color, c=None, alpha=alpha)
 
-        # Calculate segment durations for x-axis limits
+        # Calculate segment start/stop times for x-axis limits
         if recording is not None:
-            durations = [recording.get_duration(seg_idx) for seg_idx in segment_indices]
+            segment_start_stop_times = {
+                seg_idx: (recording.get_start_time(seg_idx), recording.get_end_time(seg_idx))
+                for seg_idx in segment_indices
+            }
         else:
             # Find boundaries between segments using searchsorted
-            segment_boundaries = [
-                np.searchsorted(filtered_peaks["segment_index"], [seg_idx, seg_idx + 1]) for seg_idx in segment_indices
-            ]
-
-            # Calculate durations from max sample in each segment
-            durations = [
-                (filtered_peaks["sample_index"][end - 1] + 1) / sampling_frequency for (_, end) in segment_boundaries
-            ]
+            _, segment_start_stop_times = compute_segment_durations_from_spike_vector(
+                filtered_peaks, segment_indices, sampling_frequency
+            )
 
         plot_data = dict(
             spike_train_data=spike_train_data,
@@ -280,7 +281,7 @@ def __init__(
             scatter_decimate=scatter_decimate,
             title="Peak depth",
             y_label="Depth [um]",
-            durations=durations,
+            segment_start_stop_times=segment_start_stop_times,
         )
 
         BaseRasterWidget.__init__(self, **plot_data, backend=backend, **backend_kwargs)

src/spikeinterface/widgets/rasters.py

@@ -3,7 +3,11 @@
 
 from spikeinterface.core import SortingAnalyzer, BaseSorting
 from .base import BaseWidget, to_attr, default_backend_kwargs
-from .utils import get_some_colors, validate_segment_indices, get_segment_durations
+from .utils import (
+    get_some_colors,
+    validate_segment_indices,
+    get_segment_durations,
+)
 
 
 class BaseRasterWidget(BaseWidget):
@@ -67,7 +71,7 @@ def __init__(
         sort_by_depth: bool = False,
         unit_ids: list | None = None,
         segment_indices: list | None = None,
-        durations: list | None = None,
+        segment_start_stop_times: dict[int, tuple[float, float]] | None = None,
         plot_histograms: bool = False,
         bins: int | None = None,
         scatter_decimate: int = 1,
@@ -84,7 +88,6 @@ def __init__(
         backend: str | None = None,
         **backend_kwargs,
     ):
-
         # Set default segment boundary kwargs if not provided
         if segment_boundary_kwargs is None:
             segment_boundary_kwargs = {"color": "gray", "linestyle": "--", "alpha": 0.7}
@@ -113,16 +116,15 @@ def __init__(
                 all_units.update(spike_train_data[seg_idx].keys())
             unit_ids = list(all_units)
 
-        # Calculate cumulative durations for segment boundaries
-        segment_boundaries = np.cumsum(durations)
-        cumulative_durations = np.concatenate([[0], segment_boundaries])
+        # Drop segment times we don't want to use
+        if segment_start_stop_times is not None:
+            segment_start_stop_times = {seg: segment_start_stop_times[seg] for seg in segments_to_use}
 
         # Concatenate data across segments with proper time offsets
         concatenated_spike_trains = {unit_id: np.array([]) for unit_id in unit_ids}
         concatenated_y_axis = {unit_id: np.array([]) for unit_id in unit_ids}
 
-        for offset, spike_train_segment, y_axis_segment in zip(
-            cumulative_durations,
+        for spike_train_segment, y_axis_segment in zip(
             [spike_train_data[idx] for idx in segments_to_use],
             [y_axis_data[idx] for idx in segments_to_use],
         ):
@@ -134,13 +136,8 @@ def __init__(
                 # Get y-axis values for this unit
                 y_values = y_axis_segment[unit_id]
 
-                # Apply offset to spike times
-                adjusted_times = spike_times + offset
-
                 # Add to concatenated data
-                concatenated_spike_trains[unit_id] = np.concatenate(
-                    [concatenated_spike_trains[unit_id], adjusted_times]
-                )
+                concatenated_spike_trains[unit_id] = np.concatenate([concatenated_spike_trains[unit_id], spike_times])
                 concatenated_y_axis[unit_id] = np.concatenate([concatenated_y_axis[unit_id], y_values])
 
         plot_data = dict(
@@ -157,12 +154,11 @@ def __init__(
             unit_colors=unit_colors,
             y_label=y_label,
             title=title,
-            durations=durations,
+            segment_start_stop_times=segment_start_stop_times,
             plot_legend=plot_legend,
             bins=bins,
             y_ticks=y_ticks,
             hide_unit_selector=hide_unit_selector,
-            segment_boundaries=segment_boundaries,
             segment_boundary_kwargs=segment_boundary_kwargs,
         )
 
@@ -233,11 +229,6 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
                 count, bins = np.histogram(unit_y_data, bins=bins)
                 ax_hist.plot(count, bins[:-1], color=unit_colors[unit_id], alpha=0.8)
 
-        # Add segment boundary lines if provided
-        if getattr(dp, "segment_boundaries", None) is not None:
-            for boundary in dp.segment_boundaries:
-                scatter_ax.axvline(boundary, **dp.segment_boundary_kwargs)
-
         if dp.plot_histograms:
             ax_hist = self.axes.flatten()[1]
             ax_hist.set_ylim(scatter_ax.get_ylim())
@@ -253,9 +244,20 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
         if dp.y_lim is not None:
             scatter_ax.set_ylim(*dp.y_lim)
         x_lim = dp.x_lim
-        if x_lim is None:
-            x_lim = [0, np.sum(dp.durations)]
-        scatter_ax.set_xlim(x_lim)
+
+        # Add segment boundary lines if provided and handle x limits
+        if dp.segment_start_stop_times is not None:
+
+            # We only plot boundaries for sequential segments.
+            segment_boundaries = np.array(list(dp.segment_start_stop_times.values())).ravel()
+
+            if np.all(np.diff(segment_boundaries) > 0):
+                for boundary in segment_boundaries:
+                    scatter_ax.axvline(boundary, **dp.segment_boundary_kwargs)
+
+            if x_lim is None:
+                x_lim = (segment_boundaries.min(), segment_boundaries.max())
+                scatter_ax.set_xlim(x_lim)
 
         if dp.sort_by_depth and dp.depth_dict is not None:
             scatter_ax.set_yticks(ticks=list(range(len(dp.depth_dict))), labels=list(dp.depth_dict.keys()))
@@ -455,24 +457,39 @@ def __init__(
         # Create a lookup dictionary for unit indices
         unit_indices_map = {unit_id: i for i, unit_id in enumerate(unit_ids)}
 
-        # Estimate segment duration from max spike time in each segment
-        durations = get_segment_durations(sorting, segment_indices)
-
         # Extract spike data for all segments and units at once
         spike_train_data = {seg_idx: {} for seg_idx in segment_indices}
         y_axis_data = {seg_idx: {} for seg_idx in segment_indices}
 
+        segment_start_stop_times = {}
+
+        # Get the spikes for this segment. Also, if the sorting does not have a recording,
+        # build the segment start / stop times from the spike times. This is not done
+        # with get_segment_durations to avoid the conversion to spike_vector.
         for seg_idx in segment_indices:
+
+            min_spiketime = np.inf
+            max_spiketime = -np.inf
+
             for unit_id in unit_ids:
                 # Get spikes for this segment and unit
-                spike_times = (
-                    sorting.get_unit_spike_train(unit_id=unit_id, segment_index=seg_idx) / sorting.sampling_frequency
-                )
-
+                spike_times = sorting.get_unit_spike_train_in_seconds(unit_id=unit_id, segment_index=seg_idx)
                 # Store data
                 spike_train_data[seg_idx][unit_id] = spike_times
                 y_axis_data[seg_idx][unit_id] = unit_indices_map[unit_id] * np.ones(len(spike_times))
 
+                if not sorting.has_recording() and len(spike_times) > 0:
+                    min_spiketime = min(min_spiketime, spike_times[0])
+                    max_spiketime = max(max_spiketime, spike_times[-1])
+
+            if sorting.has_recording():
+                segment_start_stop_times[seg_idx] = (
+                    sorting.get_start_time(seg_idx),
+                    sorting.get_end_time(seg_idx),
+                )
+            else:
+                segment_start_stop_times[seg_idx] = (min_spiketime, max_spiketime)
+
         # Apply time range filtering if specified
         if time_range is not None:
             assert len(time_range) == 2, "'time_range' should be a list with start and end time in seconds"
@@ -498,7 +515,7 @@ def __init__(
             unit_colors=unit_colors,
             plot_histograms=None,
             y_ticks=y_ticks,
-            durations=durations,
+            segment_start_stop_times=segment_start_stop_times,
         )
 
         BaseRasterWidget.__init__(self, **plot_data, backend=backend, **backend_kwargs)