fixed #535

uses regex to convert a^b -> pow(a,b)
sg-s · Jul 11, 2020 · f79e685 · f79e685
1 parent c9684f0
commit f79e685
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Showing 2 changed files with 39 additions and 45 deletions.
diff --git a/+xolotl/conductance.m b/+xolotl/conductance.m
@@ -70,14 +70,23 @@ function generateCPPFile(self, name)
 						f = func2str(self.(props{i}));
 						f = strrep(f,'@(V,Ca)',' ');
 					else
-						error('Unrecognised function signature.')
+						error('Unrecognized function signature.')
 					end
 
 					if any(strfind(f,'NaN'))
 						f = '  1';
 					end
 
 
+					% remove ^ and convert to pow
+					if any(strfind(f,'^'))
+						caretpos = strfind(f,'^');
+						basepos = max(regexpi(f(1:caretpos-1),'\W'))+1:caretpos-1;
+						temp = regexp(f(caretpos+1:end),'[^0-9.]')-1;
+						exponentpos =  (caretpos+1:caretpos+temp(1));
+						f = strrep(f,f(basepos(1):exponentpos(end)),['pow(',f(basepos),',',f(exponentpos),')']);
+					end
+
 					this_line = strrep(this_line,['$' props{i}], f);
 
 				else

diff --git a/examples/demo_conductance.m b/examples/demo_conductance.m
@@ -12,59 +12,38 @@
 end
 
 
-channels = x.AB.find('conductance');
+% construct a new ACurrent based on the Liu ACurrent
+[m_inf, h_inf, tau_m, tau_h] =  xolotl.getGatingFunctions(x.AB.ACurrent.cpp_class_path);
 
-%       A  CaS  CaT H KCa Kd leak NaV
-all_p = [3  3   3   1  4  4   0    3];
-all_q = [1  1   1   0  0  0   0    1];
-is_Ca = [0  1   1   0  0  0   0    0];
 
-for i = 1:length(channels)
+% specify a conductance using the function we read out
+conductance = xolotl.conductance;
+conductance.m_inf = m_inf;
+conductance.h_inf = h_inf;
+conductance.tau_m = tau_m;
+conductance.tau_h = tau_h;
+conductance.default_E = x.AB.ACurrent.E;
+conductance.p = 3;
+conductance.q = 1;
 
-	if strcmp(channels{i},'Leak')
-		continue
-	end
+% make a new C++ file
+conductance.generateCPPFile('ACurrent');
 
 
-	[m_inf, h_inf, tau_m, tau_h] =  xolotl.getGatingFunctions(x.AB.(channels{i}).cpp_class_path);
 
-	temp = xolotl.conductance;
-	temp.m_inf = m_inf;
-	temp.h_inf = h_inf;
-	temp.tau_m = tau_m;
-	temp.tau_h = tau_h;
+% now construct a new object using this channels
 
-	temp.default_E = x.AB.(channels{i}).E;
+x2 = xolotl.examples.neurons.BurstingNeuron('prefix','liu');
+x2.AB.ACurrent.destroy;
+x2.AB.add('custom/ACurrent','gbar',246);
 
-	temp.p = all_p(i);
-	temp.q = all_q(i);
-	temp.is_Ca = logical(is_Ca(i));
-
-	temp.generateCPPFile(channels{i});
-
-
-end
-
-% now construct a new object using these channels
-
-x2 = xolotl;
-x2.add('compartment','AB','A',x.AB.A);
-x2.AB.add('prinz/CalciumMech','f',1.496);
-
-x2.AB.add('custom/NaV','gbar',@() 115/x.AB.A,'E',30);
-x2.AB.add('custom/CaT','gbar',@() 1.44/x.AB.A,'E',30);
-x2.AB.add('custom/CaS','gbar',@() 1.7/x.AB.A,'E',30);
-x2.AB.add('custom/ACurrent','gbar',@() 15.45/x.AB.A,'E',-80);
-x2.AB.add('custom/KCa','gbar',@() 61.54/x.AB.A,'E',-80);
-x2.AB.add('custom/Kd','gbar',@() 38.31/x.AB.A,'E',-80);
-x2.AB.add('custom/HCurrent','gbar',@() .6343/x.AB.A,'E',-20);
-x2.AB.add('Leak','gbar',@() 0.0622/x.AB.A,'E',-50);
 
 x.sim_dt = .1;
 x.dt = .1;
 x.reset;
 x.approx_channels = 0;
 V = x.integrate;
+time = (1:length(V))*x.dt*1e-3;
 
 x2.t_end = x.t_end;
 x2.sim_dt = .1;
@@ -73,10 +52,16 @@
 x2.reset;
 V2 = x2.integrate;
 
-figure, hold on
-plot(V)
-plot(V2)
+figure('outerposition',[300 300 1200 600],'PaperUnits','points','PaperSize',[1200 600]); hold on
+subplot(2,1,1); hold on
+plot(time,V,'k')
+title('Using original ACurrent channel')
+ylabel('Voltage (mV)')
 
-figlib.pretty()
+subplot(2,1,2); hold on
+plot(time,V2,'r')
+title('Using generated ACurrent channel')
+xlabel('Time (s)')
+ylabel('Voltage (mV)')
 
-% corelib.assert(sum(V2 - V)==0,'Something went wrong')
+figlib.pretty()