Merge cec9415 into 32f5459

docs/metadata.rst

@@ -610,9 +610,8 @@ Rectified Area Under the Curve (RAUC)
 -------------------------------------
 
 One way to simplify a high-frequency signal is by plotted a time series of the
-rectified area under the curve (RAUC). Note that RAUCs are calculated
-automatically only in the standalone application and only if fast loading is
-off (``lazy=False``).
+rectified area under the curve (RAUC). Note that RAUCs are calculated only if
+fast loading is off (``lazy=False``).
 
 For each signal, the baseline (mean or median) is optionally subtracted off.
 The signal is then rectified (absolute value) and divided into non-overlapping

neurotic/datasets/data.py

@@ -36,8 +36,10 @@ def load_dataset(metadata, lazy=False, signal_group_mode='split-all', filter_eve
     ``epoch_encoder_file`` and spike trains loaded from ``tridesclous_file``
     are added to the Neo Block.
 
-    If ``lazy=False``, filters given in ``metadata`` are applied to the
-    signals and amplitude discriminators are run to detect spikes.
+    If ``lazy=False``, parameters given in ``metadata`` are used to apply
+    filters to the signals, to detect spikes using amplitude discriminators, to
+    detect bursts of spikes, and to calculate the rectified area under the
+    curve (RAUC) for each signal.
     """
 
     # read in the electrophysiology data
@@ -83,6 +85,22 @@ def load_dataset(metadata, lazy=False, signal_group_mode='split-all', filter_eve
     blk.segments[0].epochs.sort(key=lambda ep: ep.name)
     blk.segments[0].events.sort(key=lambda ev: ev.name)
 
+    # compute rectified area under the curve (RAUC) for each signal if not
+    # using lazy loading of signals
+    if not lazy:
+        for sig in blk.segments[0].analogsignals:
+            rauc_sig = _elephant_tools.rauc(
+                signal=sig,
+                baseline=metadata['rauc_baseline'],
+                bin_duration=metadata['rauc_bin_duration']*pq.s,
+            )
+            rauc_sig.name = sig.name + ' RAUC'
+            sig.annotate(
+                rauc_sig=rauc_sig,
+                rauc_baseline=metadata['rauc_baseline'],
+                rauc_bin_duration=metadata['rauc_bin_duration']*pq.s,
+            )
+
     return blk
 
 def _get_io(metadata):
@@ -610,7 +628,7 @@ def _run_burst_detectors(metadata, blk):
 
         spikeTrainNameToIndex = {st.name:i for i, st in enumerate(blk.segments[0].spiketrains)}
 
-        # detect bursts spikes using frequency thresholds
+        # detect bursts of spikes using frequency thresholds
         for detector in metadata['burst_detectors']:
 
             index = spikeTrainNameToIndex.get(detector['spiketrain'], None)

neurotic/example/example-notebook.ipynb

@@ -173,23 +173,13 @@
     "# - this decreases loading time and consumes much less memory, especially\n",
     "#   for large files\n",
     "# - to take advantage of these benefits, signal filtering, amplitude\n",
-    "#   window spike discrimination, and rauc computation must be disabled\n",
+    "#   window spike discrimination, and RAUC computation must be disabled\n",
     "# - spike markers on signals are currently incompatible with lazy loading\n",
     "lazy = False\n",
     "\n",
     "blk = neurotic.load_dataset(metadata, lazy=lazy)\n",
     "\n",
-    "# compute rectified area under the curve (RAUC) for each signal\n",
-    "# - these computations require loading the entire file now, so only\n",
-    "#   perform them if we're not using lazy loading\n",
-    "rauc_sigs = []\n",
-    "if not lazy:\n",
-    "    for sig in blk.segments[0].analogsignals:\n",
-    "        rauc = neurotic._elephant_tools.rauc(sig, baseline=metadata['rauc_baseline'], bin_duration=metadata['rauc_bin_duration']*pq.s)\n",
-    "        rauc.name = sig.name + ' RAUC'\n",
-    "        rauc_sigs.append(rauc)\n",
-    "\n",
-    "ephyviewer_config = neurotic.EphyviewerConfiguratorWidget(metadata, blk, rauc_sigs, lazy)\n",
+    "ephyviewer_config = neurotic.EphyviewerConfiguratorWidget(metadata, blk, lazy)\n",
     "ephyviewer_config.show_all()\n",
     "display(ephyviewer_config)"
    ]

neurotic/gui/config.py

@@ -56,14 +56,13 @@ class EphyviewerConfigurator():
     and should be used if there is already a Qt app running.
     """
 
-    def __init__(self, metadata, blk, rauc_sigs = None, lazy = False):
+    def __init__(self, metadata, blk, lazy = False):
         """
         Initialize a new EphyviewerConfigurator.
         """
 
         self.metadata = metadata
         self.blk = blk
-        self.rauc_sigs = rauc_sigs
         self.lazy = lazy
 
         self.viewer_settings = {
@@ -100,10 +99,10 @@ def __init__(self, metadata, blk, rauc_sigs = None, lazy = False):
         }
 
         # hide and disable viewers for which inputs are missing
-        if not self.rauc_sigs:
+        if not [sig.annotations['rauc_sig'] for sig in blk.segments[0].analogsignals if 'rauc_sig' in sig.annotations]:
             self.viewer_settings['traces_rauc']['show'] = False
             self.viewer_settings['traces_rauc']['disabled'] = True
-            self.viewer_settings['traces_rauc']['reason'] = 'Cannot enable because rauc_sigs is empty'
+            self.viewer_settings['traces_rauc']['reason'] = 'Cannot enable because there are no RAUC signals'
         if not self.blk.segments[0].spiketrains:
             self.viewer_settings['spike_trains']['show'] = False
             self.viewer_settings['spike_trains']['disabled'] = True
@@ -424,54 +423,58 @@ def create_ephyviewer_window(self, theme='light', support_increased_line_width=F
         ########################################################################
         # TRACES OF RAUC
 
-        if self.is_shown('traces_rauc') and self.rauc_sigs is not None:
-
-            sig_rauc_source = ephyviewer.InMemoryAnalogSignalSource(
-                signals = np.concatenate([self.rauc_sigs[p['index']].as_array() for p in self.metadata['plots']], axis = 1),
-                sample_rate = self.rauc_sigs[0].sampling_rate, # assuming all AnalogSignals have the same sampling rate
-                t_start = self.rauc_sigs[0].t_start,           # assuming all AnalogSignals start at the same time
-                channel_names = [p['ylabel'] + ' RAUC' for p in self.metadata['plots']],
-            )
-            sources['signal_rauc'] = [sig_rauc_source]
-
-            trace_rauc_view = ephyviewer.TraceViewer(source = sources['signal_rauc'][0], name = 'signals rauc')
-
-            if 'signals' in win.viewers:
-                win.add_view(trace_rauc_view, tabify_with = 'signals')
-            else:
-                win.add_view(trace_rauc_view)
-
-            trace_rauc_view.params['line_width'] = line_width
-            trace_rauc_view.params['display_labels'] = True
-            trace_rauc_view.params['display_offset'] = True
-            trace_rauc_view.params['antialias'] = True
-
-            # set the theme
-            if theme != 'original':
-                trace_rauc_view.params['background_color'] = self.themes[theme]['background_color']
-                trace_rauc_view.params['vline_color'] = self.themes[theme]['vline_color']
-                trace_rauc_view.params['label_fill_color'] = self.themes[theme]['label_fill_color']
-                trace_rauc_view.params_controller.combo_cmap.setCurrentText(self.themes[theme]['cmap'])
-                trace_rauc_view.params_controller.on_automatic_color()
-
-            # set explicitly assigned signal colors
-            for name, color in sig_colors.items():
-                try:
-                    index = [p['channel'] for p in self.metadata['plots']].index(name)
-                    trace_rauc_view.by_channel_params['ch{}'.format(index), 'color'] = color
-                except ValueError:
-                    # sig name may not have been found in the rauc trace list
-                    pass
-
-            # adjust plot range
-            trace_rauc_view.params['ylim_max'] = 0.5
-            trace_rauc_view.params['ylim_min'] = -trace_rauc_view.source.nb_channel + 0.5
-            trace_rauc_view.params['scale_mode'] = 'by_channel'
-            for i, p in enumerate(self.metadata['plots']):
-                ylim_span = np.median(self.rauc_sigs[p['index']].magnitude) * 10
-                ylim_center = ylim_span / 2
-                trace_rauc_view.by_channel_params['ch{}'.format(i), 'gain'] = 1/ylim_span # rescale [ymin,ymax] across a unit
-                trace_rauc_view.by_channel_params['ch{}'.format(i), 'offset'] = -i - ylim_center/ylim_span # center [ymin,ymax] within the unit
+        if self.is_shown('traces_rauc'):
+
+            rauc_sigs = [sig.annotations['rauc_sig'] for sig in sigs if 'rauc_sig' in sig.annotations]
+
+            if rauc_sigs:
+
+                sig_rauc_source = ephyviewer.InMemoryAnalogSignalSource(
+                    signals = np.concatenate([rauc_sigs[p['index']].as_array() for p in self.metadata['plots']], axis = 1),
+                    sample_rate = rauc_sigs[0].sampling_rate, # assuming all AnalogSignals have the same sampling rate
+                    t_start = rauc_sigs[0].t_start,           # assuming all AnalogSignals start at the same time
+                    channel_names = [p['ylabel'] + ' RAUC' for p in self.metadata['plots']],
+                )
+                sources['signal_rauc'] = [sig_rauc_source]
+
+                trace_rauc_view = ephyviewer.TraceViewer(source = sources['signal_rauc'][0], name = 'signals rauc')
+
+                if 'signals' in win.viewers:
+                    win.add_view(trace_rauc_view, tabify_with = 'signals')
+                else:
+                    win.add_view(trace_rauc_view)
+
+                trace_rauc_view.params['line_width'] = line_width
+                trace_rauc_view.params['display_labels'] = True
+                trace_rauc_view.params['display_offset'] = True
+                trace_rauc_view.params['antialias'] = True
+
+                # set the theme
+                if theme != 'original':
+                    trace_rauc_view.params['background_color'] = self.themes[theme]['background_color']
+                    trace_rauc_view.params['vline_color'] = self.themes[theme]['vline_color']
+                    trace_rauc_view.params['label_fill_color'] = self.themes[theme]['label_fill_color']
+                    trace_rauc_view.params_controller.combo_cmap.setCurrentText(self.themes[theme]['cmap'])
+                    trace_rauc_view.params_controller.on_automatic_color()
+
+                # set explicitly assigned signal colors
+                for name, color in sig_colors.items():
+                    try:
+                        index = [p['channel'] for p in self.metadata['plots']].index(name)
+                        trace_rauc_view.by_channel_params['ch{}'.format(index), 'color'] = color
+                    except ValueError:
+                        # sig name may not have been found in the rauc trace list
+                        pass
+
+                # adjust plot range
+                trace_rauc_view.params['ylim_max'] = 0.5
+                trace_rauc_view.params['ylim_min'] = -trace_rauc_view.source.nb_channel + 0.5
+                trace_rauc_view.params['scale_mode'] = 'by_channel'
+                for i, p in enumerate(self.metadata['plots']):
+                    ylim_span = np.median(rauc_sigs[p['index']].magnitude) * 10
+                    ylim_center = ylim_span / 2
+                    trace_rauc_view.by_channel_params['ch{}'.format(i), 'gain'] = 1/ylim_span # rescale [ymin,ymax] across a unit
+                    trace_rauc_view.by_channel_params['ch{}'.format(i), 'offset'] = -i - ylim_center/ylim_span # center [ymin,ymax] within the unit
 
         ########################################################################
         # FREQUENCY (EXPERIMENTAL AND COMPUTATIONALLY EXPENSIVE!)

neurotic/gui/notebook.py

@@ -153,7 +153,7 @@ class EphyviewerConfiguratorWidget(EphyviewerConfigurator):
     ephyviewer.
     """
 
-    def __init__(self, metadata, blk, rauc_sigs = None, lazy = False):
+    def __init__(self, metadata, blk, lazy = False):
         """
         Initialize a new EphyviewerConfiguratorWidget.
         """
@@ -165,7 +165,6 @@ def __init__(self, metadata, blk, rauc_sigs = None, lazy = False):
             self,
             metadata=metadata,
             blk=blk,
-            rauc_sigs=rauc_sigs,
             lazy=lazy)
 
         self.viewer_settings['traces'].update({       'icon': 'line-chart',   'description': 'Traces'})

neurotic/gui/standalone.py

@@ -281,14 +281,7 @@ def launch(self):
 
             blk = load_dataset(metadata, lazy=self.lazy)
 
-            rauc_sigs = []
-            if not self.lazy:
-                for sig in blk.segments[0].analogsignals:
-                    rauc = _elephant_tools.rauc(sig, baseline=metadata['rauc_baseline'], bin_duration=metadata['rauc_bin_duration']*pq.s)
-                    rauc.name = sig.name + ' RAUC'
-                    rauc_sigs.append(rauc)
-
-            ephyviewer_config = EphyviewerConfigurator(metadata, blk, rauc_sigs, self.lazy)
+            ephyviewer_config = EphyviewerConfigurator(metadata, blk, self.lazy)
             ephyviewer_config.show_all()
 
             win = ephyviewer_config.create_ephyviewer_window(theme=self.theme, support_increased_line_width=self.support_increased_line_width, show_datetime=self.show_datetime)