Main channel template

docs/source/generate_view_page.py

@@ -10,6 +10,8 @@
 import re
 from pathlib import Path
 
+from spikeinterface_gui.viewlist import get_all_possible_views
+
 
 def markdown_to_rst(markdown_text):
     """Convert markdown text to RST format."""
@@ -66,28 +68,12 @@ def generate_views_rst():
 
     # Add GUI directory to Python path
     sys.path.insert(0, str(gui_dir.absolute()))
+
+    all_possible_class_views = get_all_possible_views()
 
     # Define view information by parsing files directly (avoiding import issues)
     view_files = {
-        'probe': 'probeview.py',
-        'unitlist': 'unitlistview.py',
-        'spikelist': 'spikelistview.py', 
-        'merge': 'mergeview.py',
-        'trace': 'traceview.py',
-        'waveform': 'waveformview.py',
-        'waveformheatmap': 'waveformheatmapview.py',
-        'isi': 'isiview.py',
-        'correlogram': 'crosscorrelogramview.py',
-        'ndscatter': 'ndscatterview.py',
-        'similarity': 'similarityview.py',
-        'spikeamplitude': 'spikeamplitudeview.py',
-        'spikedepth': 'spikedepthview.py',
-        'amplitudescalings': 'amplitudescalingsview.py',
-        'tracemap': 'tracemapview.py',
-        'curation': 'curationview.py',
-        'spikerate': 'spikerateview.py',
-        'metrics': 'metricsview.py',        
-        'mainsettings': 'mainsettingsview.py',
+        p: f"{p}view.py" for p in all_possible_class_views.keys()
     }
 
     # Extract help text from each view file

docs/source/views.rst

@@ -29,6 +29,26 @@ Screenshots
      - .. image:: images/views/web/probe.png
           :width: 100%
 
+Main settings
+-------------
+
+Overview and main controls.
+Can save current settings for entire GUI as the default user settings using the "Save as default settings" button.
+
+Screenshots
+~~~~~~~~~~~
+
+.. list-table::
+   :widths: 50 50
+   :header-rows: 1
+
+   * - Desktop (Qt)
+     - Web (Panel)
+   * - .. image:: images/views/desktop/mainsettings.png
+          :width: 100%
+     - .. image:: images/views/web/mainsettings.png
+          :width: 100%
+
 Unit List
 ---------
 
@@ -64,17 +84,10 @@ Screenshots
      - .. image:: images/views/web/unitlist.png
           :width: 100%
 
-Spike list View
----------------
-
-Show all spikes of the visible units. When spikes are selected, they are highlighted in the Spike Amplitude View and the ND SCatter View.
-When a single spike is selected, the Trace and TraceMap Views are centered on it.
+SpikeRateView View
+------------------
 
-Controls
-~~~~~~~~
-* **↻ spikes**: refresh the spike list
-* **clear**: clear the selected spikes
-* **shift + arrow up/down** : select next/previous spike and make it visible alone
+This view shows firing rate for spikes per `bin_s`.
 
 Screenshots
 ~~~~~~~~~~~
@@ -85,19 +98,17 @@ Screenshots
 
    * - Desktop (Qt)
      - Web (Panel)
-   * - .. image:: images/views/desktop/spikelist.png
+   * - .. image:: images/views/desktop/spikerate.png
           :width: 100%
-     - .. image:: images/views/web/spikelist.png
+     - .. image:: images/views/web/spikerate.png
           :width: 100%
 
 Merge View
 ----------
 
 This view allows you to compute potential merges between units based on their similarity or using the auto merge function.
-Select the method to use for merging units.
-The available methods are:
-- similarity: Computes the similarity between units based on their features.
-- automerge: uses the auto merge function in SpikeInterface to find potential merges.
+Select the preset to use for merging units.
+The available presets are inherited from spikeinterface.
 
 Click "Calculate merges" to compute the potential merges. When finished, the table will be populated
 with the potential merges.
@@ -133,6 +144,7 @@ Controls
 * **auto scale**: Automatically adjust the scale of the traces.
 * **time (s)**: Set the time point to display traces.
 * **mouse wheel**: change the scale of the traces.
+* **double click**: select the nearest spike and center the view on it.
 
 Screenshots
 ~~~~~~~~~~~
@@ -148,6 +160,33 @@ Screenshots
      - .. image:: images/views/web/trace.png
           :width: 100%
 
+Trace Map View
+--------------
+
+This view shows the trace map of all the channels.
+
+Controls
+~~~~~~~~
+* **x size (s)**: Set the time window size for the traces.
+* **auto scale**: Automatically adjust the scale of the traces.
+* **time (s)**: Set the time point to display traces.
+* **mouse wheel**: change the scale of the traces.
+* **double click**: select the nearest spike and center the view on it.
+
+Screenshots
+~~~~~~~~~~~
+
+.. list-table::
+   :widths: 50 50
+   :header-rows: 1
+
+   * - Desktop (Qt)
+     - Web (Panel)
+   * - .. image:: images/views/desktop/tracemap.png
+          :width: 100%
+     - .. image:: images/views/web/tracemap.png
+          :width: 100%
+
 Waveform View
 -------------
 
@@ -163,9 +202,11 @@ Controls
 ~~~~~~~~
 * **mode** : change displaye mode (geometry or flatten)
 * **ctrl + o** : toggle overlap mode
+* **ctrl + p** : toggle plot waveform samples
 * **mouse wheel** : scale waveform amplitudes
 * **alt + mouse wheel** : widen/narrow x axis
 * **shift + mouse wheel** : zoom
+* **shift + alt + mouse wheel** : scale vertical spacing between channels
 
 Screenshots
 ~~~~~~~~~~~
@@ -304,6 +345,7 @@ comparing the distribution of ampltidues to the noise levels.
 Controls
 ~~~~~~~~
 - **select** : activate lasso selection to select individual spikes
+- **split** or **ctrl+s** : split the selected spikes into a new unit (only if one unit is visible)
 
 Screenshots
 ~~~~~~~~~~~
@@ -327,6 +369,7 @@ Check deppth of spikes across the recording time or in a histogram.
 Controls
 ~~~~~~~~
 - **select** : activate lasso selection to select individual spikes
+- **split** or **ctrl+s** : split the selected spikes into a new unit (only if one unit is visible)
 
 Screenshots
 ~~~~~~~~~~~
@@ -342,32 +385,6 @@ Screenshots
      - .. image:: images/views/web/spikedepth.png
           :width: 100%
 
-Trace Map View
---------------
-
-This view shows the trace map of all the channels.
-
-Controls
-~~~~~~~~
-* **x size (s)**: Set the time window size for the traces.
-* **auto scale**: Automatically adjust the scale of the traces.
-* **time (s)**: Set the time point to display traces.
-* **mouse wheel**: change the scale of the traces.
-
-Screenshots
-~~~~~~~~~~~
-
-.. list-table::
-   :widths: 50 50
-   :header-rows: 1
-
-   * - Desktop (Qt)
-     - Web (Panel)
-   * - .. image:: images/views/desktop/tracemap.png
-          :width: 100%
-     - .. image:: images/views/web/tracemap.png
-          :width: 100%
-
 Curation View
 -------------
 
@@ -399,10 +416,10 @@ Screenshots
      - .. image:: images/views/web/curation.png
           :width: 100%
 
-SpikeRateView View
-------------------
+Metrics View
+------------
 
-This view shows firing rate for spikes per `bin_s`.
+View and explore unit metrics in a customizable grid of plots.
 
 Screenshots
 ~~~~~~~~~~~
@@ -413,15 +430,22 @@ Screenshots
 
    * - Desktop (Qt)
      - Web (Panel)
-   * - .. image:: images/views/desktop/spikerate.png
+   * - .. image:: images/views/desktop/metrics.png
           :width: 100%
-     - .. image:: images/views/web/spikerate.png
+     - .. image:: images/views/web/metrics.png
           :width: 100%
 
-Metrics View
-------------
+Spike list View
+---------------
 
-View and explore unit metrics in a customizable grid of plots.
+Show all spikes of the visible units. When spikes are selected, they are highlighted in the Spike Amplitude View and the ND SCatter View.
+When a single spike is selected, the Trace and TraceMap Views are centered on it.
+
+Controls
+~~~~~~~~
+* **↻ spikes**: refresh the spike list
+* **clear**: clear the selected spikes
+* **shift + arrow up/down** : select next/previous spike and make it visible alone
 
 Screenshots
 ~~~~~~~~~~~
@@ -432,15 +456,34 @@ Screenshots
 
    * - Desktop (Qt)
      - Web (Panel)
-   * - .. image:: images/views/desktop/metrics.png
+   * - .. image:: images/views/desktop/spikelist.png
           :width: 100%
-     - .. image:: images/views/web/metrics.png
+     - .. image:: images/views/web/spikelist.png
           :width: 100%
 
-Main settings
--------------
+Amplitude Scalings View
+-----------------------
 
-Overview and main controls
+Amplitude scalings measure the optimal scaling which should be applied to the template so that
+it best matches each spike waveform.
+
+Controls
+~~~~~~~~
+- **select** : activate lasso selection to select individual spikes
+- **split** or **ctrl+s** : split the selected spikes into a new unit (only if one unit is visible)
+
+*Screenshots not available for this view.*
+
+Main Template View
+------------------
+
+Display average template on main channel.
+If the `template_metrics` are computed, it also displayed the template signal
+used to compute metrics (usually upsampled) and the trough/peak_before/peak_after
+positions and widths.
+
+- troughs are negative extrema and are displayed with a downward triangle symbol
+- peaks are positive extrema and are displayed with an upward triangle symbol
 
 Screenshots
 ~~~~~~~~~~~
@@ -451,8 +494,8 @@ Screenshots
 
    * - Desktop (Qt)
      - Web (Panel)
-   * - .. image:: images/views/desktop/mainsettings.png
+   * - .. image:: images/views/desktop/maintemplate.png
           :width: 100%
-     - .. image:: images/views/web/mainsettings.png
+     - .. image:: images/views/web/maintemplate.png
           :width: 100%
 

spikeinterface_gui/controller.py

@@ -255,7 +255,8 @@ def __init__(
 
         t0 = time.perf_counter()
 
-        self._extremum_channel = get_template_extremum_channel(self.analyzer, peak_sign='neg', outputs='index')
+        self._extremum_channel = get_template_extremum_channel(self.analyzer,
+                                    mode="extremum", peak_sign='both', outputs='index')
 
         # some direct attribute
         self.num_segments = self.analyzer.get_num_segments()
@@ -722,6 +723,26 @@ def get_waveforms(self, unit_id):
             # sparse waveforms
             chan_inds = self.analyzer.sparsity.unit_id_to_channel_indices[unit_id]
         return wfs, chan_inds
+
+    def get_template_upsampling_factor(self):
+        template_metrics_ext = self.analyzer.get_extension("template_metrics")
+        if template_metrics_ext is None or template_metrics_ext.params.get('upsampling_factor') is None:
+            return 1
+        else:
+            return template_metrics_ext.params['upsampling_factor']
+
+    def get_upsampled_templates(self, unit_id):
+        template_metrics_ext = self.analyzer.get_extension("template_metrics")
+        unit_index = list(self.unit_ids).index(unit_id)
+        chan_ind = self.get_extremum_channel(unit_id)
+        template = self.templates_average[unit_index, :, chan_ind]
+        if template_metrics_ext is None or "peaks_data" not in template_metrics_ext.data:
+            return template, None, None
+        else:
+            peaks_data = template_metrics_ext.data['peaks_data']
+            template_high = template_metrics_ext.data['main_channel_templates'][unit_index]
+            return template, template_high, peaks_data.loc[unit_id]
+
 
     def get_common_sparse_channels(self, unit_ids):
         sparsity_mask = self.get_sparsity_mask()

spikeinterface_gui/layout_presets.py

@@ -61,7 +61,7 @@ def get_layout_description(preset_name, layout=None):
     zone5=['probe'],
     zone6=['ndscatter', 'similarity'],
     zone7=['waveform', 'waveformheatmap', ],
-    zone8=['correlogram', 'isi', 'metrics', 'mainsettings'],
+    zone8=['correlogram', 'isi', 'metrics', 'maintemplate', 'mainsettings'],
 )
 _presets['default'] = default_layout