Psth use intervals

nwbwidgets/allen.py

@@ -19,10 +19,6 @@ def make_group_and_sort(self, group_by=None, control_order=False):
         )
 
 
-class AllenPSTHWidget(TimeIntervalsSelector):
-    InnerWidget = PSTHWidget
-
-
 class AllenRasterGridWidget(TimeIntervalsSelector):
     InnerWidget = RasterGridWidget
 
@@ -85,7 +81,6 @@ def allen_show_electrodes(node: DynamicTable):
 
 def load_allen_widgets():
     default_neurodata_vis_spec[Units]["Session Raster"] = AllenRasterWidget
-    default_neurodata_vis_spec[Units]["Grouped PSTH"] = AllenPSTHWidget
     default_neurodata_vis_spec[Units]["Raster Grid"] = AllenRasterGridWidget
     default_neurodata_vis_spec[Units]["Tuning Curves"] = AllenTuningCurveWidget
     # default_neurodata_vis_spec[DynamicTable] = allen_show_dynamic_table

nwbwidgets/base.py

@@ -12,6 +12,7 @@
 from nwbwidgets import view
 from pynwb import ProcessingModule
 from pynwb.core import NWBDataInterface, MultiContainerInterface
+from pynwb.epoch import TimeIntervals
 
 from ipywidgets.widgets.interaction import show_inline_matplotlib_plots
 
@@ -371,46 +372,61 @@ def row_to_hover_text(row):
     return "<br>".join(text_rows)
 
 
-class TimeIntervalsSelector(widgets.VBox):
-    InnerWidget = None
-
-    def __init__(self, input_data, **kwargs):
+class TimeIntervalsSelectorMixin:
+    """
+    Sister class must have intervals_selector_callback
+    """
+    def set_interval_selector(self, intervals, nwbfile=None):
         """
-        Creates a TimeInterval controller that controls InnerWidget.
+        If a string is given, look up that table in nwb.intervals
+        If a pynwb.epoch.TimeIntervals object is given, use that
+        If a Dropdown is given, use that as a selector
+        If there is no input for intervals, look at nwb.intervals
+            If nwb.intervals has 0 entries, render a placeholder
+            If nwb.intervals has 1 entry, use it
+            If nwb.intervals has more than one entry, create a dropdown of all available intervals
 
         Parameters
         ----------
-        input_data: pynwb object
-            Pynwb object (e.g. pynwb.misc.Units) belonging to a nwbfile 
-            that will be filtered by the TimeIntervalSelector controller. 
+        intervals: str or pynwb.epoch.TimeIntervals or ipywidgets.DropDown or None
+        nwbfile: pynwb.NWBFile
+
+        Returns
+        -------
+
         """
-        super().__init__()
-        self.input_data = input_data
-        self.kwargs = kwargs
-        self.intervals_tables = input_data.get_ancestor("NWBFile").intervals
-        self.stimulus_type_dd = widgets.Dropdown(
-            options=list(self.intervals_tables.keys()), 
-            description="stimulus type"
-        )
-        self.stimulus_type_dd.observe(self.stimulus_type_dd_callback)
-
-        trials = list(self.intervals_tables.values())[0]
-        inner_widget = self.InnerWidget(
-            units=self.input_data,
-            trials=trials, 
-            **kwargs
-        )
-        self.children = [self.stimulus_type_dd, inner_widget]
-
-    def stimulus_type_dd_callback(self, change):
-        self.children = [self.stimulus_type_dd, widgets.HTML("Rendering...")]
-        trials = self.intervals_tables[self.stimulus_type_dd.value]
-        inner_widget = self.InnerWidget(
-            input_data=self.input_data, 
-            trials=trials, 
-            **self.kwargs
-        )
-        self.children = [self.stimulus_type_dd, inner_widget]
+        self.intervals_dropdown = None
+
+        if isinstance(intervals, str):
+            if intervals == "trials":
+                self.intervals = nwbfile.trials
+            elif intervals not in nwbfile.intervals:
+                raise ValueError("'{intervals}' not in NWBFile.intervals")
+                self.intervals = nwbfile.intervals[intervals]
+        elif isinstance(intervals, widgets.Dropdown):
+            self.intervals = nwbfile.intervals[self.intervals_dropdown.value]
+            self.intervals_dropdown.observe(self.intervals_selector_callback)
+        elif isinstance(intervals, TimeIntervals):
+            self.intervals = intervals
+        elif intervals is None:
+            all_intervals_tables = nwbfile.intervals
+            trials = nwbfile.trials
+            if trials is not None:
+                all_intervals_tables.add(trials)
+            if len(all_intervals_tables) == 0:
+                self.children = [HTML("could not find intervals")]
+                return
+            elif len(all_intervals_tables) == 1:
+                self.intervals = list(all_intervals_tables.values())[0]
+            else:
+                self.intervals_dropdown = widgets.Dropdown(
+                    options=list(all_intervals_tables),
+                    description="intervals",
+                )
+                self.intervals_dropdown.observe(self.intervals_selector_callback)
+                self.intervals = list(all_intervals_tables.values())[0]
+        else:
+            raise ValueError("intervals is not an allowable type")
 
 
 def show_multi_container_interface(

nwbwidgets/misc.py

@@ -6,12 +6,13 @@
 import plotly.graph_objects as go
 import pynwb
 import scipy
-from ipywidgets import widgets, fixed, FloatProgress, Layout
+from ipywidgets import widgets, fixed, FloatProgress, Layout, HTML
 from matplotlib.collections import PatchCollection
 from matplotlib.patches import Rectangle
 from pynwb.misc import AnnotationSeries, Units, DecompositionSeries
 
 from .analysis.spikes import compute_smoothed_firing_rate
+from .base import TimeIntervalsSelectorMixin
 from .controllers import (
     make_trial_event_controller,
     GroupAndSortController,
@@ -267,27 +268,39 @@ def control_plot(x0, x1, ch0, ch1):
     return vbox
 
 
-class PSTHWidget(widgets.VBox):
+class PSTHWidget(widgets.VBox, TimeIntervalsSelectorMixin):
     def __init__(
-            self,
-            input_data: Units,
-            trials: pynwb.epoch.TimeIntervals = None,
-            unit_index=0,
-            unit_controller=None,
-            ntt=1000,
+        self,
+        units: Units,
+        intervals: str = None,
+        unit_index=0,
+        unit_controller=None,
+        ntt=1000,
     ):
+        """
+
+        Parameters
+        ----------
+        input_data: pynwb.Units
+        intervals: str, optional
+            If a string is given, look up that table in nwb.intervals
+            If a TimeIntervals object is given, use that
+            If a Dropdown is given, use that as a selector
+            If there is no input for intervals, look at nwb.intervals
+                If nwb.intervals has 0 entries, render a placeholder
+                If nwb.intervals has 1 entry, use it
+                If nwb.intervals has more than one entry, create a dropdown of all available intervals
+        unit_index: int
+        unit_controller
+        ntt: int
+        """
 
-        self.units = input_data
+        self.units = units
+        self.ntt = ntt
 
         super().__init__()
 
-        if trials is None:
-            self.trials = self.get_trials()
-            if self.trials is None:
-                self.children = [widgets.HTML("No trials present")]
-                return
-        else:
-            self.trials = trials
+        self.set_interval_selector(intervals, units.get_ancestor("NWBFile"))
 
         if unit_controller is None:
             self.unit_ids = self.units.id.data[:]
@@ -301,8 +314,16 @@ def __init__(
         else:
             self.unit_controller = unit_controller
 
+        self.refresh_intervals()
+
+    def make_group_and_sort(self, window=None, control_order=False):
+        return GroupAndSortController(
+            self.intervals, window=window, control_order=control_order
+        )
+
+    def refresh_intervals(self):
         self.trial_event_controller = make_trial_event_controller(
-            self.trials, layout=Layout(width="200px"), multiple=True
+            self.intervals, layout=Layout(width="200px"), multiple=True
         )
         self.start_ft = widgets.FloatText(
             -0.5, step=0.1, description="start (s)", layout=Layout(width="200px"),
@@ -332,7 +353,7 @@ def __init__(
         self.gas = self.make_group_and_sort(window=False, control_order=False)
 
         self.controls = dict(
-            ntt=fixed(ntt),
+            ntt=fixed(self.ntt),
             index=self.unit_controller,
             end=self.end_ft,
             start=self.start_ft,
@@ -346,7 +367,7 @@ def __init__(
 
         out_fig = interactive_output(self.update, self.controls)
 
-        self.children = [
+        children = [
             widgets.HBox(
                 [
                     widgets.VBox(
@@ -373,13 +394,16 @@ def __init__(
             out_fig,
         ]
 
-    def get_trials(self):
-        return self.units.get_ancestor("NWBFile").trials
+        if self.intervals_dropdown is not None:
+            children.insert(0, self.intervals_dropdown)
 
-    def make_group_and_sort(self, window=None, control_order=False):
-        return GroupAndSortController(
-            self.trials, window=window, control_order=control_order
-        )
+        self.children = children
+
+
+    def intervals_selector_callback(self, change):
+        self.children = [self.intervals_dropdown, widgets.HTML("Rendering...")]
+        self.intervals = self.units.get_ancestor("NWBFile").intervals[self.intervals_dropdown.value]
+        self.refresh_intervals()
 
     def update(
             self,
@@ -441,7 +465,7 @@ def update(
             data = align_by_time_intervals(
                 self.units,
                 index,
-                self.trials,
+                self.intervals,
                 start_label,
                 start_label,
                 start,
@@ -485,7 +509,7 @@ def update(
                 expanded_data = align_by_time_intervals(
                     units=self.units,
                     index=index,
-                    intervals=self.trials,
+                    intervals=self.intervals,
                     start_label=start_label,
                     stop_label=start_label,
                     start=start - sigma_in_secs * 4,
@@ -514,6 +538,7 @@ def update(
                 )
 
             ax1.set_xlim([start, end])
+            ax1.set_xticks([start, end])
             if i_s == 0:
                 ax1.set_ylabel("firing rate (Hz)", fontsize=12)
             ax1.set_xlabel("time (s)", fontsize=12)
@@ -1167,7 +1192,7 @@ class RasterGridWidget(widgets.VBox):
     def __init__(
             self,
             units: Units,
-            trials: pynwb.epoch.TimeIntervals = None,
+            intervals: pynwb.epoch.TimeIntervals = None,
             unit_index=0,
             units_trials_controller=None,
     ):
@@ -1177,7 +1202,7 @@ def __init__(
         if not units_trials_controller:
             units_trials_controller = UnitsAndTrialsControllerWidget(
                 units=units,
-                trials=trials,
+                trials=intervals,
                 unit_index=unit_index
             )
             self.children = [units_trials_controller]
@@ -1195,7 +1220,7 @@ class TuningCurveWidget(widgets.VBox):
     def __init__(
             self,
             units: Units,
-            trials: pynwb.epoch.TimeIntervals = None,
+            intervals: pynwb.epoch.TimeIntervals = None,
             unit_index=0,
             units_trials_controller=None,
     ):
@@ -1206,7 +1231,7 @@ def __init__(
         if not units_trials_controller:
             units_trials_controller = UnitsAndTrialsControllerWidget(
                 units=units,
-                trials=trials,
+                trials=intervals,
                 unit_index=unit_index
             )
             self.children = [units_trials_controller]
@@ -1239,15 +1264,15 @@ def __init__(
         # Tuning curve widget
         self.tuning_curve = TuningCurveWidget(
             units=units,
-            trials=trials,
+            intervals=trials,
             unit_index=unit_index,
             units_trials_controller=self.units_trials_controller,
         )
 
         # Raster grid widget
         self.raster_grid = RasterGridWidget(
             units=units,
-            trials=trials,
+            intervals=trials,
             unit_index=unit_index,
             units_trials_controller=self.units_trials_controller,
         )

nwbwidgets/utils/units.py

@@ -116,7 +116,7 @@ def align_by_time_intervals(
     index,
     intervals,
     start_label="start_time",
-    stop_label="stop_time",
+    stop_label=None,
     start=0.0,
     end=0.0,
     rows_select=(),

test/test_misc.py

@@ -18,7 +18,7 @@
 )
 from pynwb import NWBFile
 from pynwb.misc import DecompositionSeries, AnnotationSeries
-
+from pynwb.epoch import TimeIntervals
 
 def test_show_psth():
     data = np.random.random([6, 50])
@@ -93,11 +93,34 @@ def test_psth_widget(self):
 
     def test_multipsth_widget(self):
         psth_widget = PSTHWidget(self.nwbfile.units)
-        assert isinstance(psth_widget, widgets.Widget)
         start_labels = ('start_time', 'stop_time')
         fig = psth_widget.update(index=0, start_labels=start_labels)
         assert len(fig.axes) == 2 * len(start_labels)
-
+
+    def test_multiple_intervals(self):
+        time_intervals = TimeIntervals("custom_intervals_table")
+        time_intervals.add_row(start_time=1., stop_time=2.)
+        time_intervals.add_row(start_time=2.5, stop_time=3.5)
+        self.nwbfile.intervals.add(time_intervals)
+        widget = PSTHWidget(self.nwbfile.units)
+        assert widget.intervals_dropdown is not None
+
+    def test_input_intervals_trials_name(self):
+
+        widget = PSTHWidget(self.nwbfile.units, intervals="trials")
+        assert widget.intervals.name == "trials"
+        assert widget.intervals_dropdown is None
+
+    def test_input_intervals_object(self):
+
+        time_intervals = TimeIntervals("custom_intervals_table")
+        time_intervals.add_row(start_time=1., stop_time=2.)
+        time_intervals.add_row(start_time=2.5, stop_time=3.5)
+        widget = PSTHWidget(self.nwbfile.units, intervals=time_intervals)
+        assert widget.intervals.name == "custom_intervals_table"
+        assert widget.intervals_dropdown is None
+
+
     def test_raster_widget(self):
         assert isinstance(RasterWidget(self.nwbfile.units), widgets.Widget)
 

test/test_utils_units.py

@@ -114,7 +114,7 @@ def setUp(self):
         super().setUp()
         self.widget = TuningCurveWidget(
             units=self.nwbfile.units,
-            trials=self.nwbfile.trials
+            intervals=self.nwbfile.trials
         )
         # rows controller triggers drawing of graphic
         self.widget.children[0].children[1].value = 'stim'