Merge pull request #166 from jpgill86/spike-colors

Add color option for amplitude_discriminators

docs/metadata.rst

@@ -450,7 +450,9 @@ the basis of amplitude alone. Note that amplitude discriminators are only
 applied if fast loading is off (``lazy=False``).
 
 Detected spikes are indicated on the signals with markers, and spike trains are
-displayed in a raster plot.
+displayed in a raster plot. Optionally, a color may be specified for an
+amplitude discriminator using a single letter color code (e.g., ``'b'`` for
+blue or ``'k'`` for black) or a hexadecimal color code (e.g., ``'1b9e77'``).
 
 In addition to restricting spike detection for a given unit to an amplitude
 window, detection can also be limited in time to overlap with epochs with a
@@ -471,12 +473,14 @@ for each amplitude discriminator.
               channel: Extracellular
               units: uV
               amplitude: [50, 150]
+              color: r
 
             - name: Unit 2
               channel: Extracellular
               units: uV
               amplitude: [20, 50]
               epoch: Unit 2 activity
+              color: 'e6ab02'
 
 Here two units are detected on the same channel with different amplitude
 windows. Any peaks between 50 and 150 microvolts on the "Extracellular" channel

neurotic/datasets/metadata.py

@@ -332,8 +332,8 @@ def _defaults_for_key(key):
         # list of labels for epoch encoder
         'epoch_encoder_possible_labels': ['Type 1', 'Type 2', 'Type 3'],
 
-        # list of dicts giving name, channel, units, amplitude window, epoch window for each unit
-        # - e.g. [{'name': 'Unit X', 'channel': 'Channel A', 'units': 'uV', 'amplitude': [75, 150], 'epoch': 'Type 1'}, ...]
+        # list of dicts giving name, channel, units, amplitude window, epoch window, color for each unit
+        # - e.g. [{'name': 'Unit X', 'channel': 'Channel A', 'units': 'uV', 'amplitude': [75, 150], 'epoch': 'Type 1', 'color': 'ff0000'}, ...]
         'amplitude_discriminators': None,
 
         # list of dicts giving name of a spiketrain, start and stop firing rate

neurotic/example/metadata.yml

@@ -50,17 +50,20 @@ example dataset:
           channel: BN2
           units: uV
           amplitude: [50, 150]
+          color: '1b9e77'
 
         - name: B38
           channel: BN2
           units: uV
           amplitude: [17, 26]
           epoch: B38 activity
+          color: '7570b3'
 
         - name: B4/B5
           channel: BN3
           units: uV
           amplitude: [85, 200]
+          color: 'e6ab02'
 
     burst_detectors:  # used only if fast loading is off (lazy=False)
 

neurotic/gui/config.py

@@ -338,6 +338,16 @@ def create_ephyviewer_window(self, theme='light', support_increased_line_width=F
                     scatter_channels = spike_channels,
                 ))
 
+                # instead of passing colors into AnalogSignalSourceWithScatter
+                # constructor with scatter_colors, first let the constructor
+                # choose reasonable default colors (done above), and only then
+                # override colors for spike trains that have been explicitly
+                # set in amplitude_discriminators (done here)
+                unit_colors = {}
+                if self.metadata['amplitude_discriminators'] is not None:
+                    unit_colors = {d['name']: d['color'] for d in self.metadata['amplitude_discriminators'] if 'color' in d}
+                sources['signal'][-1].scatter_colors.update(unit_colors)
+
             # useOpenGL=True eliminates the extremely poor performance associated
             # with TraceViewer's line_width > 1.0, but it also degrades overall
             # performance somewhat and is reportedly unstable
@@ -470,6 +480,18 @@ def create_ephyviewer_window(self, theme='light', support_increased_line_width=F
                 spike_train_view.params_controller.combo_cmap.setCurrentText(self.themes[theme]['cmap'])
                 spike_train_view.params_controller.on_automatic_color()
 
+            # set explicitly assigned spike train colors
+            if self.metadata['amplitude_discriminators'] is not None:
+                for d in self.metadata['amplitude_discriminators']:
+                    if 'color' in d:
+                        try:
+                            index = [st.name for st in seg.spiketrains].index(d['name'])
+                            spike_train_view.by_channel_params['ch{}'.format(index), 'color'] = d['color']
+                        except ValueError:
+                            # the amplitude discriminator name may not have
+                            # been found in the spike train list
+                            pass
+
         ########################################################################
         # EPOCHS