Adds plots module and plot_realtime_fulldata capability in run_sequence

ohmpi.py

@@ -24,6 +24,7 @@ import threading
 from logging_setup import setup_loggers
 from config import MQTT_CONTROL_CONFIG, OHMPI_CONFIG, EXEC_LOGGING_CONFIG
 from logging import DEBUG
+from plots import *
 
 # finish import (done only when class is instantiated as some libs are only available on arm64 platform)
 try:
@@ -1235,7 +1236,7 @@ class OhmPi(object):
         self.thread = threading.Thread(target=func)
         self.thread.start()
 
-    def run_sequence(self, cmd_id=None, **kwargs):
+    def run_sequence(self, cmd_id=None, plot_realtime_fulldata=False, **kwargs):
         """Runs sequence synchronously (=blocking on main thread).
            Additional arguments are passed to run_measurement().
 
@@ -1314,7 +1315,6 @@ class OhmPi(object):
 
             # switch mux off
             self.switch_mux_off(quad)
-
             # add command_id in dataset
             acquired_data.update({'cmd_id': cmd_id})
             # log data to the data logger
@@ -1323,6 +1323,20 @@ class OhmPi(object):
             self.append_and_save(filename, acquired_data)
             self.exec_logger.debug(f'quadrupole {i + 1:d}/{n:d}')
 
+            if plot_realtime_fulldata:
+                realtime_plot_window = 10
+                plt.ion()
+                last_measurement = acquired_data["fulldata"][~np.isnan(acquired_data["fulldata"][:, 2])]
+                if i==0:
+                    xlim = [last_measurement[:, 2][-1] - realtime_plot_window, last_measurement[:, 2][-1]]
+                    fig, (ax1,ax2), (line1,line2) = plot_fulldata(last_measurement, realtime=True,xlim=xlim)
+                    acquired_dataset = last_measurement
+                else:
+                    fig,(ax1,ax2), (line1,line2), acquired_dataset = \
+                        update_realtime_fulldata_plot(last_measurement, acquired_dataset, (line1,line2),(ax1,ax2), fig, x_window=realtime_plot_window )
+
+        if plot_realtime_fulldata:
+            return fig,(ax1,ax2), (line1,line2), acquired_dataset
         self.switch_dps('off')
         self.status = 'idle'
 

plots.py

+import matplotlib.pyplot as plt
+import numpy as np
+
+
+def plot_fulldata(fulldata, axes=None, fig=None, save=False, output="fulldata.png", show=False, realtime=False, xlim=None):
+
+    if axes is None:
+        fig, (ax1,ax2) = plt.subplots(2, sharex=True)
+    else:
+        (ax1,ax2) = axes
+
+    line1, = ax1.plot(fulldata[:, 2], fulldata[:, 0], 'r.-', label='current [mA]')
+    ax1.set_ylabel('Current (mA)')
+    ax1.set_title('Current')
+    line2, = ax2.plot(fulldata[:, 2], fulldata[:, 1], '.-', label='Voltage [mV]',alpha=.5)
+    ax2.set_xlabel('Time (s)')
+    ax2.set_ylabel('Voltage (mV)')
+    ax2.set_title('Voltage')
+
+    if xlim is not None:
+        ax1.set_xlim(xlim)
+        ax2.set_xlim(xlim)
+
+    if save:
+        fig.savefig(output,dpi=300,bbox_inches='tight')
+    if show:
+        plt.show()
+    
+    if realtime:
+        fig.canvas.draw()
+        fig.canvas.flush_events()
+        return fig, (ax1,ax2), (line1,line2)
+    else:
+        return fig, (ax1, ax2)
+
+
+def update_realtime_fulldata_plot(last_measurement, acquired_dataset, lines, axes, fig, x_window=10):
+    (line1, line2) = lines
+    (ax1,ax2) = axes
+    t = np.append(acquired_dataset[:,2], last_measurement[:, 2][~np.isnan(last_measurement[:, 2])] + acquired_dataset[:,2][-1])
+    i_rt = np.append(acquired_dataset[:,0], last_measurement[:, 0][~np.isnan(last_measurement[:, 2])])
+    u_rt = np.append(acquired_dataset[:,1], last_measurement[:, 1][~np.isnan(last_measurement[:, 2])])
+    line1.set_ydata(i_rt)
+    line1.set_xdata(t)
+    line2.set_ydata(u_rt)
+    line2.set_xdata(t)
+    ax1.relim()
+    ax2.relim()
+    ax1.autoscale_view(scalex=False)
+    ax2.autoscale_view(scalex=False)
+    ax1.set_xlim([t[-1] - x_window, t[-1]])
+    ax2.set_xlim([t[-1] - x_window, t[-1]])
+
+    fig.canvas.draw()
+    fig.canvas.flush_events()
+    
+    return fig,(ax1,ax2), (line1,line2), np.array([i_rt,u_rt,t]).T
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