Merge pull request #27 from openworm/test_neuroml_apdp_1

Test neuroml apdp 1

Author: pgleeson

.github/workflows/ci-make.yml

@@ -72,7 +72,7 @@ jobs:
 
     - name: Test Python command line script
       run: |
-        python run_main.py -R 1233 -p 6 --doEvol --folderName exampleRun2  # Note: small population of 6 for quick runtime
+        python run_main.py -R 1233 -p 6 --doEvol --outputFolderName exampleRun2  # Note: small population of 6 for quick runtime
 
     - name: Test using test_all.sh
       run: |

.test.example.mep

@@ -3,4 +3,4 @@ system: Testing activity of some neurons
 experiments:
     Test:
         expected:
-            spike times: [0.605, 4.955, 10.055, 14.805, 19.605, 24.405, 29.155]
+            spike times: [0.605, 4.955, 10.055, 14.805, 19.605, 24.405, 29.155]

.test.example.omt

@@ -15,4 +15,4 @@ experiments:
         spike detection: 
           method: threshold
           threshold: 2
-        tolerance: 0
+        tolerance: 0

.test.nmlNS.omt

@@ -15,4 +15,4 @@ experiments:
         spike detection: 
           method: threshold
           threshold: 2
-        tolerance: 0.008264462809917363
+        tolerance: 0.04027846842366976

Mainvars.h

@@ -25,8 +25,8 @@ extern const int SR_B;
 
 // Size of genotype
 extern int	VectSize;
-extern string output_dir_name;
+//extern string output_dir_name;
 //extern int nn(int, int);
-extern string nervousSystemName;
-extern string nervousSystemNameForSim;
-extern string nervousSystemNameForEvol;
+//extern string nervousSystemName;
+//extern string nervousSystemNameForSim;
+//extern string nervousSystemNameForEvol;

Makefile

@@ -27,7 +27,7 @@ random.o: random.cpp random.h VectorMatrix.h
 TSearch.o: TSearch.cpp TSearch.h
 	g++ -c -O3 -flto TSearch.cpp
 
-jsonUtils.o: jsonUtils.cpp jsonUtils.h Worm.h
+jsonUtils.o: jsonUtils.cpp jsonUtils.h
 	g++ -c -O3 -std=c++11 -I/opt/homebrew/Cellar/nlohmann-json/3.11.3/include  -flto $(CXXFLAGS) $(LDFLAGS) jsonUtils.cpp	
 
 utils.o: utils.cpp utils.h
@@ -49,7 +49,7 @@ StretchReceptor.o: StretchReceptor.cpp StretchReceptor.h
 Muscles.o: Muscles.cpp Muscles.h VectorMatrix.h random.h
 	g++ -c -O3 -flto Muscles.cpp
 main.o: main.cpp Worm.h WormBody.h StretchReceptor.h Muscles.h TSearch.h
-	g++ -c -O3 -flto $(CXXFLAGS) $(LDFLAGS) main.cpp
+	g++ -c -O3 -std=c++11 -flto $(CXXFLAGS) $(LDFLAGS) main.cpp
 tests.o: tests.cpp NervousSystem.o random.o
 	g++ -c -O3 -flto tests.cpp
 tests: info tests.o 

Worm.cpp

@@ -7,21 +7,13 @@
 //
 
 #include "Worm.h"
-
+#include "utils.h"
 
 int nn(int neuronNumber, int unitNumber)
 {
   return neuronNumber+((unitNumber-1)*N_neuronsperunit);
 }
 
-string nervousSystemName = "NervousSystem";
-string nervousSystemNameForSim = "nmlNervousSystem";
-string nervousSystemNameForEvol = "NervousSystem";
-
-bool checkNervousSystemForJson(){
-return (strcmp(nervousSystemName.c_str(),"NervousSystem") == 0);
-}
-
 NervousSystemBase* makeNervousSystem()
 {  
 if (checkNervousSystemForJson()) return new NervousSystem();

Worm.h

@@ -5,7 +5,7 @@
 //  Created by Eduardo Izquierdo on 9/25/15.
 //  Copyright © 2015 Eduardo Izquierdo. All rights reserved.
 //
-
+#pragma once
 #include "VectorMatrix.h"
 #include "random.h"
 #include "WormBody.h"

exampleRun/simulation_pars.json

@@ -0,0 +1,5 @@
+{
+    "doNML": 0,
+    "seed": 1233,
+    "Duration": 24
+}

exampleRun/worm_data.json

@@ -61,6 +61,20 @@
             "value": 0.41666666666666663
         }
     },
+    "Evolutionary Optimization Parameters": {
+        "Duration": {
+            "message": "optimization simulation duration",
+            "value": 24
+        },
+        "pop_size": {
+            "message": "population size",
+            "value": 96
+        },
+        "randomseed": {
+            "message": "seed",
+            "value": 1233
+        }
+    },
     "Fitness traj": {
         "AvgSpeed": {
             "message": "Average speed of the worm in meters per second",

jsonUtils.cpp

@@ -5,7 +5,7 @@
 #include <functional>
 #include <vector>
 #include <nlohmann/json.hpp>
-//#include "utils.h"
+#include "utils.h"
 #include "jsonUtils.h"
 #include "Mainvars.h"
 
@@ -682,10 +682,10 @@ n.InternalSetElectricalSynapseWeight(elec_weights[i].w.from, elec_weights[i].to,
 }
 
 
-void writeParsToJson(wormForJson & w, string file_name)
+
+void writeParsToJson(json & j, wormForJson & w, string file_name)
 {
 
-json j;
 {Params<double> par = getBodyParams(w.b);
 appendToJson<double>(j["Body"],par);}
 
@@ -760,6 +760,27 @@ void writeParsToJson(wormForJson & w)
 writeParsToJson(w, "worm_data.json");
 }
 
+
+void writeParsToJson(wormForJson & w, string file_name)
+{
+json j;
+writeParsToJson(j,w,file_name);
+}
+
+void writeParsToJson(wormForJson & w, string file_name, vector<doubIntParamsHead> & parvec)
+{
+json j;
+
+for (size_t i=0;i<parvec.size(); i++) {
+if (strcmp(parvec[i].parDoub.head.c_str(),"NULL")!=0)
+appendToJson<double>(j[parvec[i].parDoub.head],parvec[i].parDoub);
+if (strcmp(parvec[i].parInt.head.c_str(),"NULL")!=0)
+appendToJson<long>(j[parvec[i].parInt.head],parvec[i].parInt);
+}
+writeParsToJson(j,w,file_name);
+}
+
+
 void readJson(json j, ifstream & ifs)
 {
 ifs >> j;

jsonUtils.h

@@ -1,10 +1,11 @@
+#pragma once
 #include "Worm.h"
 #include <vector>
 #include <string>
 #include "utils.h"
+//#include <nlohmann/json.hpp>
 
-//#pragma once
-
+//using json = nlohmann::json;
 using namespace std;
 using wormForJson = Worm;
 
@@ -20,10 +21,16 @@ vector<string> messages;
 template <class T>
 struct ParamsHead : Params<T> {
 ParamsHead(string head_val, Params<T> par_val):Params<T>(par_val){head=head_val;}
-ParamsHead():Params<T>(){}
+ParamsHead():Params<T>(){head = "NULL";}
 string head;
 };
 
+struct doubIntParamsHead
+{
+ParamsHead<double> parDoub;
+ParamsHead<long> parInt;
+};
+
 
 //ifstream & setParamsFromDump(ifstream &ifs, Worm<NervousSystem> &);
 ifstream & setParamsFromDump(ifstream &ifs, wormForJson &);
@@ -40,7 +47,8 @@ void setNSFromJsonFile(ifstream & ifs, NervousSystem & n);
 
 
 void writeWormParams(wormForJson & w);
-
+void writeParsToJson(wormForJson & w, string file_name, vector<doubIntParamsHead> & parvec);
+//void writeParsToJson(json & j, wormForJson & w, string file_name);
 void writeParsToJson(wormForJson &, string);
 void writeParsToJson(wormForJson &);
 void testNervousSystemJson(string, NervousSystem &);