set_tstop_oct25

hnn_core/dipole.py

@@ -467,16 +467,11 @@ def savgol_filter(self, h_freq):
                                             self.sfreq)
         return self
 
-    def plot(self, tmin=None, tmax=None, layer='agg', decim=None, ax=None,
-             color='k', show=True):
+    def plot(self, layer='agg', decim=None, ax=None, color='k', show=True):
         """Simple layer-specific plot function.
 
         Parameters
         ----------
-        tmin : float or None
-            Start time of plot (in ms). If None, plot entire simulation.
-        tmax : float or None
-            End time of plot (in ms). If None, plot entire simulation.
         layer : str
             The layer to plot. Can be one of 'agg', 'L2', and 'L5'
         decimate : int
@@ -493,8 +488,8 @@ def plot(self, tmin=None, tmax=None, layer='agg', decim=None, ax=None,
         fig : instance of plt.fig
             The matplotlib figure handle.
         """
-        return plot_dipole(self, tmin=tmin, tmax=tmax, ax=ax, layer=layer,
-                           decim=decim, color=color, show=show)
+        return plot_dipole(self, ax=ax, layer=layer, decim=decim, color=color,
+                           show=show)
 
     def plot_psd(self, fmin=0, fmax=None, tmin=None, tmax=None, layer='agg',
                  color=None, label=None, ax=None, show=True):

hnn_core/extracellular.py

@@ -421,9 +421,9 @@ def smooth(self, window_len):
 
         return self
 
-    def plot_lfp(self, *, trial_no=None, contact_no=None, tmin=None, tmax=None,
-                 ax=None, decim=None, color='cividis', voltage_offset=50,
-                 voltage_scalebar=200, show=True):
+    def plot_lfp(self, *, trial_no=None, contact_no=None, ax=None, decim=None,
+                 color='cividis', voltage_offset=50, voltage_scalebar=200,
+                 show=True):
         """Plot laminar local field potential time series.
 
         One plot is created for each trial. Multiple trials can be overlaid
@@ -435,11 +435,6 @@ def plot_lfp(self, *, trial_no=None, contact_no=None, tmin=None, tmax=None,
             Trial number(s) to plot
         contact_no : int | list of int | slice
             Electrode contact number(s) to plot
-        tmin : float | None
-            Start time of plot in milliseconds. If None, plot entire
-            simulation.
-        tmax : float | None
-            End time of plot in milliseconds. If None, plot entire simulation.
         ax : instance of matplotlib figure | None
             The matplotlib axis
         decim : int | list of int | None (default)
@@ -486,7 +481,7 @@ def plot_lfp(self, *, trial_no=None, contact_no=None, tmin=None, tmax=None,
 
         for trial_data in plot_data:
             fig = plot_laminar_lfp(
-                self.times, trial_data, tmin=tmin, tmax=tmax, ax=ax,
+                self.times, trial_data, ax=ax,
                 decim=decim, color=color,
                 voltage_offset=voltage_offset,
                 voltage_scalebar=voltage_scalebar,
@@ -534,6 +529,7 @@ class _ExtracellularArrayBuilder(object):
         The instance of :class:`hnn_core.extracellular.ExtracellularArray` to
         build in NEURON-Python
     """
+
     def __init__(self, array):
         self.array = array
         self.n_contacts = array.n_contacts

hnn_core/viz.py

@@ -78,9 +78,9 @@ def plt_show(show=True, fig=None, **kwargs):
         (fig or plt).show(**kwargs)
 
 
-def plot_laminar_lfp(times, data, contact_labels, tmin=None, tmax=None,
-                     ax=None, decim=None, color='cividis',
-                     voltage_offset=50, voltage_scalebar=200, show=True):
+def plot_laminar_lfp(times, data, contact_labels, ax=None, decim=None,
+                     color='cividis', voltage_offset=50, voltage_scalebar=200,
+                     show=True):
     """Plot laminar extracellular electrode array voltage time series.
 
     Parameters
@@ -89,10 +89,6 @@ def plot_laminar_lfp(times, data, contact_labels, tmin=None, tmax=None,
         Sampling times (in ms).
     data : Two-dimensional Numpy array
         The extracellular voltages as an (n_contacts, n_times) array.
-    tmin : float | None
-        Start time of plot in milliseconds. If None, plot entire simulation.
-    tmax : float | None
-        End time of plot in milliseconds. If None, plot entire simulation.
     ax : instance of matplotlib figure | None
         The matplotlib axis
     decim : int | list of int | None (default)
@@ -168,11 +164,11 @@ def plot_laminar_lfp(times, data, contact_labels, tmin=None, tmax=None,
         trace_offsets = np.arange(n_offsets)[:, np.newaxis] * voltage_offset
 
     for contact_no, trace in enumerate(np.atleast_2d(data)):
-        plot_data, plot_times = _get_plot_data_trange(times, trace, tmin, tmax)
+        plot_data = trace
+        plot_times = times
 
         if decim is not None:
-            plot_data, plot_times = _decimate_plot_data(decim, plot_data,
-                                                        plot_times)
+            plot_data, plot_times = _decimate_plot_data(decim, trace, times)
 
         if isinstance(color, np.ndarray):
             col = color[contact_no]
@@ -182,6 +178,7 @@ def plot_laminar_lfp(times, data, contact_labels, tmin=None, tmax=None,
             col = color
         ax.plot(plot_times, plot_data + trace_offsets[contact_no],
                 label=f'C{contact_no}', color=col)
+        ax.set_xlim(right=plot_times[-1])
 
     if voltage_offset is not None:
         ax.set_ylim(-voltage_offset, n_offsets * voltage_offset)
@@ -220,18 +217,14 @@ def plot_laminar_lfp(times, data, contact_labels, tmin=None, tmax=None,
     return ax.get_figure()
 
 
-def plot_dipole(dpl, tmin=None, tmax=None, ax=None, layer='agg', decim=None,
+def plot_dipole(dpl, ax=None, layer='agg', decim=None,
                 color='k', label="average", average=False, show=True):
     """Simple layer-specific plot function.
 
     Parameters
     ----------
     dpl : instance of Dipole | list of Dipole instances
         The Dipole object.
-    tmin : float or None
-        Start time of plot in milliseconds. If None, plot entire simulation.
-    tmax : float or None
-        End time of plot in milliseconds. If None, plot entire simulation.
     ax : instance of matplotlib figure | None
         The matplotlib axis
     layer : str
@@ -288,19 +281,19 @@ def plot_dipole(dpl, tmin=None, tmax=None, ax=None, layer='agg', decim=None,
             if layer in dpl_trial.data.keys():
 
                 # extract scaled data and times
-                data, times = _get_plot_data_trange(dpl_trial.times,
-                                                    dpl_trial.data[layer],
-                                                    tmin, tmax)
+                data = dpl_trial.data[layer]
+                times = dpl_trial.times
                 if decim is not None:
-                    data, times = _decimate_plot_data(decim, data, times)
+                    data, times = _decimate_plot_data(
+                        decim, dpl_trial.data[layer], dpl_trial.times)
                 if idx == len(dpl) - 1 and average:
                     # the average dpl
                     ax.plot(times, data, color=color, label=label, lw=1.5)
                 else:
                     alpha = 0.5 if average else 1.
                     ax.plot(times, data, color=_lighten_color(color, 0.5),
                             alpha=alpha, lw=1.)
-
+            ax.set_xlim(right=dpl_trial.times[-1])
         if average:
             ax.legend()
 
@@ -477,6 +470,7 @@ def plot_spikes_hist(cell_response, trial_idx=None, ax=None, spike_types=None,
 
     ax.set_ylabel("Counts")
     ax.legend()
+    ax.set_xlim(right=cell_response.times[-1])
 
     plt_show(show)
     return ax.get_figure()
@@ -558,7 +552,7 @@ def plot_spikes_raster(cell_response, trial_idx=None, tmin=None, tmax=None,
     ax.set_facecolor('k')
     ax.set_xlabel('Time (ms)')
     ax.get_yaxis().set_visible(False)
-    ax.set_xlim(left=0)
+    ax.set_xlim(left=0, right=cell_response.times[-1])
 
     plt_show(show)
     return ax.get_figure()
@@ -1229,6 +1223,7 @@ def plot_laminar_csd(times, data, contact_labels, tmin=None, tmax=None,
 
     ax.set_xlabel('Time (ms)')
     ax.set_ylabel('Electrode depth')
+    ax.set_xlim(right=times[-1])
     plt.tight_layout()
     plt_show(show)