Merge pull request #547 from sg-s/no-getfullstatesize

No getfullstatesize
sg-s · Dec 12, 2020 · 8358165 · 8358165
2 parents 99dc6b5 + 80ae5c0
commit 8358165
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Showing 192 changed files with 687 additions and 1,160 deletions.
diff --git a/+xolotl/version.m b/+xolotl/version.m
@@ -1,2 +1,2 @@
 function version()
-disp('v20.12.11');
+disp('v20.12.12');
diff --git a/@xtest/xtest.m b/@xtest/xtest.m
@@ -4,9 +4,9 @@
 properties
 
     % xolotl objects
-    single_comp@xolotl
+    single_comp (1,1) xolotl
 
-    stg_network@xolotl
+    stg_network (1,1) xolotl
 
 
 

diff --git a/c++/compartment.hpp b/c++/compartment.hpp
@@ -436,7 +436,7 @@ It does the following things:
 1. Adds a pointer to the conductance to a vector of pointers called `mech`
 2. Updates various attributes of the conductance like verbosity, etc.
 3. Tells the mechanism what its ordering in `mech` is by updating `mechanism_idx` in that mechanism object
-4. Determines the data frame size of this object by calling `getFullStateSize` and storing this in `mechanism_sizes`
+4. Determines the data frame size of this object by reading out `fullStateSize` and storing this in `mechanism_sizes`
 
 **See Also**
 
@@ -453,7 +453,7 @@ void compartment::addMechanism(mechanism *mech_) {
     n_mech++;
 
     // also store the mechanism's full state size
-    mechanism_sizes.push_back(mech_->getFullStateSize());
+    mechanism_sizes.push_back(mech_->fullStateSize);
 }
 
 /*
@@ -473,7 +473,7 @@ void compartment::addSynapse(synapse *syn_) {
     n_syn ++;
 
     // also store the synapse's full state size
-    synapse_sizes.push_back(syn_->getFullStateSize());
+    synapse_sizes.push_back(syn_->fullStateSize);
 }
 
 /*
@@ -569,7 +569,7 @@ conductance* compartment::getConductancePointer(const char* cond_class) {
     conductance* req_cond = NULL;
 
     for (int i = 0; i < n_cond; i ++) {
-        if ((cond[i]->getClass()) == cond_class) {
+        if ((cond[i]->name) == cond_class) {
             req_cond = cond[i];
         }
     }
@@ -640,7 +640,7 @@ what their data dimension is, and adding up all those numbers.
 int compartment::getFullMechanismSize(void) {
     int full_size = 0;
     for (int i=0; i<n_mech; i++) {
-        full_size += mech[i]->getFullStateSize();
+        full_size += mech[i]->fullStateSize;
     }
     return full_size;
 }
@@ -687,7 +687,7 @@ what their data dimension is, and adding up all those numbers.
 int compartment::getFullSynapseSize(void) {
     int full_size = 0;
     for (int i=0; i<n_syn; i++) {
-        full_size += syn[i]->getFullStateSize();
+        full_size += syn[i]->fullStateSize;
     }
     return full_size;
 }

diff --git a/c++/conductance.hpp b/c++/conductance.hpp
@@ -111,6 +111,8 @@ class conductance {
     double m = 0;
     double h = 1;
 
+    string name = "unset";
+
     int verbosity = -1;
 
     int p = 1;
@@ -162,7 +164,6 @@ class conductance {
     virtual void integrateLangevin(double, double);
 
     virtual void connect(compartment*); 
-    virtual string getClass(void) = 0;
     virtual double getState(int);
     virtual double getCurrent(double);
     void checkSolvers(int);
@@ -222,7 +223,7 @@ void conductance::buildLUT(double approx_channels) {
 
 
         if (verbosity==0) {
-            mexPrintf("%s NOT using approximate activation functions because approx_channels is set to 0.\n", getClass().c_str());  
+            mexPrintf("%s NOT using approximate activation functions because approx_channels is set to 0.\n", name.c_str());  
         }
 
         return;
@@ -237,7 +238,7 @@ void conductance::buildLUT(double approx_channels) {
 
     if (UseMInfApproximation == 1) {
         if (verbosity==0) {
-            mexPrintf("%s using approximate activation functions\n", getClass().c_str());  
+            mexPrintf("%s using approximate activation functions\n", name.c_str());  
         }
 
 
@@ -248,13 +249,13 @@ void conductance::buildLUT(double approx_channels) {
         }
     } else {
         if (verbosity==0) {
-            mexPrintf("%s NOT USING approximate activation functions\n", getClass().c_str());  
+            mexPrintf("%s NOT USING approximate activation functions\n", name.c_str());  
         }
     }
 
     if (UseHInfApproximation == 1) {
         if (verbosity==0) {
-           mexPrintf("%s using approximate in-activation functions\n", getClass().c_str()); 
+           mexPrintf("%s using approximate in-activation functions\n", name.c_str()); 
         }
 
         for (int V_int = -999; V_int < 1001; V_int++) {
@@ -342,7 +343,7 @@ void conductance::checkSolvers(int solver_order) {
     } else if (solver_order == 4) {
         return;
     } else {
-        mexPrintf("Error using %s", getClass().c_str());
+        mexPrintf("Error using %s", name.c_str());
         mexErrMsgTxt("Unsupported solver order \n");
     }
 }

diff --git a/c++/conductances/GenericKdLike.hpp b/c++/conductances/GenericKdLike.hpp
@@ -51,14 +51,15 @@ class GenericKdLike: public conductance {
 
         p = 4;
 
+        name = "GenericKdLike";
+
     }
 
     double m_inf(double, double);
     double tau_m(double, double);
-    string getClass(void);
+
 };
 
-string GenericKdLike::getClass(){return "GenericKdLike";}
 
 
 double GenericKdLike::m_inf(double V, double Ca) {return 1.0/(1.0+exp((V-m_V_half)/m_V_slope));}

diff --git a/c++/conductances/GenericNaVLike.hpp b/c++/conductances/GenericNaVLike.hpp
@@ -76,17 +76,17 @@ class GenericNaVLike: public conductance {
         p = 3;
         q = 1;
 
+        name = "GenericNaVLike";
+
     }
 
     double m_inf(double, double);
     double h_inf(double, double);
     double tau_m(double, double);
     double tau_h(double, double);
-    string getClass(void);
+
 };
 
-string GenericNaVLike::getClass(){return "GenericNaVLike";}
-
 
 double GenericNaVLike::m_inf(double V, double Ca) {return 1.0/(1.0+exp((V-m_V_half)/m_V_slope));}
 double GenericNaVLike::h_inf(double V, double Ca) {return 1.0/(1.0+exp((V-h_V_half)/h_V_slope));}

diff --git a/c++/conductances/Leak.hpp b/c++/conductances/Leak.hpp
@@ -22,18 +22,19 @@ class Leak: public conductance {
 
         if (isnan (E)) { E = -55; }
 
+        name = "Leak";
+
     }
 
 
     void integrate(double, double);
     void integrateMS(int, double, double);
     void integrateLangevin(double, double);
 
-    string getClass(void);
+
 
 };
 
-string Leak::getClass(){return "Leak";}
 
 void Leak::integrate(double V, double Ca) {
     // do nothing

diff --git a/c++/conductances/bronk/EAGes.hpp b/c++/conductances/bronk/EAGes.hpp
@@ -26,15 +26,16 @@ class EAGes: public conductance {
 
         p = 1;
 
+        name = "EAGes";
+
     }
 
     double m_inf(double V, double Ca);
     double tau_m(double, double);
-    string getClass(void);
+
 
 };
 
-string EAGes::getClass(){return "EAG";}
 
 
 double EAGes::m_inf(double V, double Ca) { return (9.29e-4/(Ca+9.29e-4))/(1.0+exp((V+23.12)/-16.94)); }

diff --git a/c++/conductances/bronk/EAGmut.hpp b/c++/conductances/bronk/EAGmut.hpp
@@ -27,19 +27,19 @@ class EAGmut: public conductance {
 
         if (isnan (E)) { E = -80; }
 
+        name = "EAGmut";
+
         p = 1;
 
     }
 
 
     double m_inf(double V, double Ca);
     double tau_m(double, double);
-    string getClass(void);
+
 
 };
 
-string EAGmut::getClass(){return "EAG";}
-
 
 double EAGmut::m_inf(double V, double Ca) { return (.92*(1-.05)/(Ca+.92) + .05)/(1.0+exp((V+23.12)/-16.94)); }
 double EAGmut::tau_m(double V, double Ca) {return 5497 - 5500/(1.0+exp((V+251.5 )/-51.5));}

diff --git a/c++/conductances/bronk/EAGwt.hpp b/c++/conductances/bronk/EAGwt.hpp
@@ -23,21 +23,21 @@ class EAGwt: public conductance {
 
         // defaults
         if (isnan(gbar)) { gbar = 0; }
-
         if (isnan (E)) { E = -80; }
 
+        name = "EAGwt";
+
         p = 1;
 
 
     }
 
     double m_inf(double V, double Ca);
     double tau_m(double, double);
-    string getClass(void);
+
 
 };
 
-string EAGwt::getClass(){return "EAG";}
 
 double EAGwt::m_inf(double V, double Ca) { return (9.29e-2/(Ca+9.29e-2))/(1.0+exp((V+23.12)/-16.94)); }
 double EAGwt::tau_m(double V, double Ca) {return 5497 - 5500/(1.0+exp((V+251.5 )/-51.5));}

diff --git a/c++/conductances/brookings/ACurrent.hpp b/c++/conductances/brookings/ACurrent.hpp
@@ -28,21 +28,20 @@ class ACurrent: public conductance {
 
         p = 3;
 
+        name = "ACurrent";
+
     }
 
 
     double m_inf(double V, double Ca);
     double h_inf(double V, double Ca);
     double tau_m(double V, double Ca);
     double tau_h(double V, double Ca);
-    string getClass(void);
 
 };
 
 
-string ACurrent::getClass(){
-    return "ACurrent";
-}
+
 
 
 double ACurrent::m_inf(double V, double Ca) {return (1.0/(1.0+exp(((V)+12.3)/-11.8))); }

diff --git a/c++/conductances/caplan/MICurrent.hpp b/c++/conductances/caplan/MICurrent.hpp
@@ -24,22 +24,21 @@ class MICurrent: public conductance {
 
         // defaults
         if (isnan(gbar)) { gbar = 0; }
-
         if (isnan (E)) { E = 30; }
 
         p = 1;
+
+        name = "MICurrent";
     }
 
     double m_inf(double V, double Ca);
     double h_inf(double V, double Ca);
     double tau_m(double V, double Ca);
     double tau_h(double V, double Ca);
-    string getClass(void);
+
 
 };
 
-string MICurrent::getClass(){return "MICurrent";}
-
 
 
 double MICurrent::m_inf(double V, double Ca) {return 1.0/(1.0+exp((V+12.0)/-5));}

diff --git a/c++/conductances/chow/Kd.hpp b/c++/conductances/chow/Kd.hpp
@@ -22,28 +22,25 @@ class Kd: public conductance {
 
         // defaults 
         if (isnan(gbar)) { gbar = 0; }
-
         if (isnan (E)) { E = -77; }
 
         unitary_conductance = 20e-6; // uS
 
+        name = "Kd";
+
         p = 4;
 
     }
 
     double m_inf(double, double);
     double tau_m(double, double);
-    string getClass(void);
+
 
     double Alpha(double);
     double Beta(double);
 
 };
 
-string Kd::getClass(){
-    return "Kd";
-}
-
 
 double Kd::Alpha(double V) {
     return 0.01 * (V+55) / (1-exp((V+55)/(-10)));

diff --git a/c++/conductances/chow/NaV.hpp b/c++/conductances/chow/NaV.hpp
@@ -23,15 +23,15 @@ class NaV: public conductance {
 
         // defaults 
         if (isnan(gbar)) { gbar = 0; }
-
-
         if (isnan (E)) { E = 50; }
 
         unitary_conductance = 20e-6; // uS
 
         p = 3;
         q = 1;
 
+        name = "NaV";
+
     }
 
     double m_inf(double, double);
@@ -45,10 +45,10 @@ class NaV: public conductance {
     double BetaM(double);
     double BetaH(double);
 
-    string getClass(void);
+
 };
 
-string NaV::getClass(){return "NaV";}
+
 
 
 double NaV::AlphaM(double V) {

diff --git a/c++/conductances/clay00/Kd2.hpp b/c++/conductances/clay00/Kd2.hpp
@@ -39,19 +39,17 @@ class Kd2: public conductance {
         // need to set E to zero to linearize. Don't worry,
         // this is not the reversal potential
         E = 0;
+
+        name = "Kd2";
     }
 
-    string getClass(void);
+
 
     void integrate(double, double);
 
 
 };
 
-string Kd2::getClass(){
-    return "Kd2";
-}
-
 
 void Kd2::integrate(double V_, double Ca_){