Merge 0f57aed into a692c58

docs/metadata.rst

@@ -341,7 +341,9 @@ Plot Parameters
 ---------------
 
 Use the ``plots`` parameter to specify which signal channels from ``data_file``
-you want plotted and how to scale them.
+you want plotted and how to scale them. Optionally, a color may be specified
+for channels using a single letter color code (e.g., ``'b'`` for blue or
+``'k'`` for black) or a hexadecimal color code (e.g., ``'1b9e77'``).
 
 Consider the following example, and notice the use of hyphens and indentation
 for each channel.
@@ -357,11 +359,13 @@ for each channel.
               ylabel: Buccal nerve 2 (BN2)
               units: uV
               ylim: [-150, 150]
+              color: r
 
             - channel: Intracellular
               ylabel: B3 neuron
               units: mV
               ylim: [-100, 50]
+              color: '666666'
 
             - channel: Force
               units: mN
@@ -564,7 +568,8 @@ burst detection algorithm that relies on firing rate thresholds can be run to
 detect periods of intense activity. Note that burst detectors are only applied
 if fast loading is off (``lazy=False``).
 
-Detected bursts are plotted as epochs.
+Detected bursts are plotted as epochs. Colors are inherited from
+``amplitude_discriminators``, if they are provided there.
 
 Burst detectors are specified in metadata like this:
 
@@ -614,7 +619,8 @@ The signal is then rectified (absolute value) and divided into non-overlapping
 bins of fixed duration. Finally, the integral is calculated within each bin.
 The result is a new time series that represents the overall activity of the
 original signal. RAUC time series are plotted separately from the original
-signals in a second tab.
+signals in a second tab. Colors are inherited from ``plots``, if they are
+provided there.
 
 The choice of baseline is controlled by the ``rauc_baseline`` metadata
 parameter, which may have the value ``None`` (default), ``'mean'``, or

neurotic/datasets/metadata.py

@@ -388,7 +388,7 @@ def _defaults_for_key(key):
         'video_rate_correction': None,
 
         # list the channels in the order they should be plotted
-        # - e.g. [{'channel': 'Channel A', 'ylabel': 'My channel', 'ylim': [-120, 120], 'units': 'uV'}, ...]
+        # - e.g. [{'channel': 'Channel A', 'ylabel': 'My channel', 'ylim': [-120, 120], 'units': 'uV', 'color': 'ff0000'}, ...]
         'plots': None,
 
         # amount of time in seconds to plot initially

neurotic/gui/config.py

@@ -272,6 +272,21 @@ def create_ephyviewer_window(self, theme='light', support_increased_line_width=F
         # delete on close so that memory and file resources are released
         win.setAttribute(ephyviewer.QT.WA_DeleteOnClose, True)
 
+        ########################################################################
+        # COLORS
+
+        # colors for signals given explicitly in plots, used for raw signals
+        # and RAUC
+        sig_colors = {}
+        if self.metadata['plots'] is not None:
+            sig_colors = {p['channel']: p['color'] for p in self.metadata['plots'] if 'color' in p}
+
+        # colors for units given explicitly in amplitude_discriminators, used
+        # for scatter markers, spike trains, and burst epochs
+        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}
+
         ########################################################################
         # TRACES WITH SCATTER PLOTS
 
@@ -347,11 +362,8 @@ def create_ephyviewer_window(self, theme='light', support_increased_line_width=F
                 # 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}
+                # override colors for units that have been explicitly set in
+                # amplitude_discriminators (done here)
                 sources['signal'][-1].scatter_colors.update(unit_colors)
 
             # useOpenGL=True eliminates the extremely poor performance associated
@@ -382,6 +394,15 @@ def create_ephyviewer_window(self, theme='light', support_increased_line_width=F
                 trace_view.params_controller.combo_cmap.setCurrentText(self.themes[theme]['cmap'])
                 trace_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_view.by_channel_params['ch{}'.format(index), 'color'] = color
+                except ValueError:
+                    # sig name may not have been found in the trace list
+                    pass
+
             # adjust plot range, scaling, and positioning
             trace_view.params['ylim_max'] = 0.5
             trace_view.params['ylim_min'] = -trace_view.source.nb_channel + 0.5
@@ -428,6 +449,15 @@ def create_ephyviewer_window(self, theme='light', support_increased_line_width=F
                 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
@@ -486,17 +516,14 @@ 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
+            # set explicitly assigned unit colors
+            for name, color in unit_colors.items():
+                try:
+                    index = [st.name for st in seg.spiketrains].index(name)
+                    spike_train_view.by_channel_params['ch{}'.format(index), 'color'] = color
+                except ValueError:
+                    # unit name may not have been found in the spike train list
+                    pass
 
         ########################################################################
         # EPOCHS
@@ -514,6 +541,15 @@ def create_ephyviewer_window(self, theme='light', support_increased_line_width=F
                 epoch_view.params_controller.combo_cmap.setCurrentText(self.themes[theme]['cmap'])
                 epoch_view.params_controller.on_automatic_color()
 
+            # set explicitly assigned unit colors
+            for name, color in unit_colors.items():
+                try:
+                    index = [ep['name'] for ep in sources['epoch'][0].all].index(name + ' burst')
+                    epoch_view.by_channel_params['ch{}'.format(index), 'color'] = color
+                except ValueError:
+                    # unit burst name may not have been found in the epoch list
+                    pass
+
         ########################################################################
         # EPOCH ENCODER