Merge pull request #91 from CardiacModelling/js_fix_subtraction_plots

Simplify subtraction plot code

Author: joeyshuttleworth

pcpostprocess/subtraction_plots.py

@@ -52,7 +52,7 @@ def do_subtraction_plot(fig, times, sweeps, before_currents, after_currents,
         ax.plot(times*1e-3, voltages, color='black')
         ax.set_title(f'Well {well}, sweep {sweeps[i]}', fontweight='bold')
         ax.tick_params(axis='x', labelbottom=False)
-        # ax.set_xlabel('time (s)')
+
     protocol_axs[0].set_ylabel(r'$V_\mathrm{cmd}$ (mV)', fontsize=16)
 
     all_leak_params_before = []
@@ -62,32 +62,22 @@ def do_subtraction_plot(fig, times, sweeps, before_currents, after_currents,
     style_of_zero = '-'
     range_of_zero = [times[0]*1e-3, times[-1]*1e-3]
 
-    for i in range(len(sweeps)):
-        before_params, _ = fit_linear_leak(before_currents[i], voltages, times,
-                                           *ramp_bounds)
-        all_leak_params_before.append(before_params)
-
-        after_params, _ = fit_linear_leak(after_currents[i], voltages, times,
-                                          *ramp_bounds)
-        all_leak_params_after.append(after_params)
-
     # Compute and store leak currents
     before_leak_currents = np.full((nsweeps, voltages.shape[0]),
                                    np.nan)
     after_leak_currents = np.full((nsweeps, voltages.shape[0]),
                                   np.nan)
-    for i, sweep in enumerate(sweeps):
-
-        b0, b1 = all_leak_params_before[i]
-        gleak = b1
-        Eleak = -b0/b1
-        before_leak_currents[i, :] = gleak * (voltages - Eleak)
 
-        b0, b1 = all_leak_params_after[i]
-        gleak = b1
-        Eleak = -b0/b1
+    for i in range(len(sweeps)):
+        before_params, before_leak_current = fit_linear_leak(before_currents[i], voltages, times,
+                                                             *ramp_bounds)
+        before_leak_currents[i, :] = before_leak_current
+        all_leak_params_before.append(before_params)
 
-        after_leak_currents[i, :] = gleak * (voltages - Eleak)
+        after_params, after_leak_current = fit_linear_leak(after_currents[i], voltages, times,
+                                                           *ramp_bounds)
+        all_leak_params_after.append(after_params)
+        after_leak_currents[i, :] = after_leak_current
 
     for i, (sweep, ax) in enumerate(zip(sweeps, before_axs)):
         b0, b1 = all_leak_params_before[i]
@@ -101,13 +91,10 @@ def do_subtraction_plot(fig, times, sweeps, before_currents, after_currents,
         ax.legend()
         ax.tick_params(axis='x', labelbottom=False)
 
-        # ax.set_xlabel('time (s)')
     before_axs[0].set_ylabel(r'Pre-drug trace', fontsize=16)
-    # ax.yaxis.set_major_formatter(mtick.FormatStrFormatter('%.1e'))
-    # ax.tick_params(axis='y', rotation=90)
 
     for i, (sweep, ax) in enumerate(zip(sweeps, after_axs)):
-        b0, b1 = all_leak_params_before[i]
+        b0, b1 = all_leak_params_after[i]
         gleak = b1
         Eleak = -b0/b1
 
@@ -117,11 +104,7 @@ def do_subtraction_plot(fig, times, sweeps, before_currents, after_currents,
         ax.plot(range_of_zero, [0, 0], color='black', linestyle=style_of_zero, alpha=alpha_of_zero)
         ax.legend()
         ax.tick_params(axis='x', labelbottom=False)
-
-        # ax.set_xlabel('$t$ (s)')
     after_axs[0].set_ylabel(r'Post-drug trace', fontsize=16)
-    # ax.yaxis.set_major_formatter(mtick.FormatStrFormatter('%.1e'))
-    # ax.tick_params(axis='y', rotation=90)
 
     for i, (sweep, ax) in enumerate(zip(sweeps, corrected_axs)):
         corrected_before_currents = before_currents[i, :] - before_leak_currents[i, :]
@@ -134,33 +117,20 @@ def do_subtraction_plot(fig, times, sweeps, before_currents, after_currents,
         ax.set_xlabel(r'Time (s)')
         ax.legend()
     corrected_axs[0].set_ylabel(r'Leak-corrected traces', fontsize=16)
-    # ax.tick_params(axis='y', rotation=90)
-    # ax.yaxis.set_major_formatter(mtick.FormatStrFormatter('%.1e'))
 
     for i, sweep in enumerate(sweeps):
-        before_trace = before_currents[i, :].flatten()
-        after_trace = after_currents[i, :].flatten()
-        before_params, before_leak = fit_linear_leak(before_trace, voltages, times,
-                                                     *ramp_bounds)
-        after_params, after_leak = fit_linear_leak(after_trace, voltages, times,
-                                                   *ramp_bounds)
-
         subtracted_currents = before_currents[i, :] - before_leak_currents[i, :] - \
             (after_currents[i, :] - after_leak_currents[i, :])
 
         subtracted_ax.plot(times*1e-3, subtracted_currents, label=f"sweep {sweep}", alpha=.5)
 
-        #  Cycle to next colour
-        # subtracted_ax.plot([np.nan], [np.nan], label=f"sweep {sweep}", alpha=.5)
-
     subtracted_ax.legend()
     subtracted_ax.plot(range_of_zero, [0, 0], color='black',
                        linestyle=style_of_zero, alpha=alpha_of_zero)
     subtracted_ax.set_ylabel('Final subtracted traces', fontsize=16)
     subtracted_ax.set_xlabel('Time (s)', fontsize=16)
 
     long_protocol_ax.plot(times*1e-3, voltages, color='black')
-    # long_protocol_ax.set_xlabel('time (s)')
     long_protocol_ax.set_ylabel(r'$V_\mathrm{cmd}$ (mV)', fontsize=16)
     long_protocol_ax.tick_params(axis='x', labelbottom=False)