assays/Assay1/dataset/CPlantBox-isp/examples/PSP_infiltrationRedistribution1D/soil_sand.txt

+upperDepth,	lowerDepth,	Campbell_he,	Campbell_b,	VG_he,	VG_alpha, 	VG_n, 	VG_alpha_mod,	VG_n_mod, 	thetaR, thetaS, Ksat
+0.0, 		1.0, 		-4.2, 			3.58, 		-3.8,  	0.15, 		1.35, 	0.3,  			1.33,		0.01, 	0.46, 	0.001

assays/Assay1/dataset/CPlantBox-isp/examples/analysis_write_rootsystem.vtp

+<?xml version="1.0"?><VTKFile type="PolyData" version="0.1" byte_order="LittleEndian">
+<PolyData>
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+<CellData Scalars=" CellData">
+
+</CellData>
+<Points>
+<DataArray type="Float32" Name="Coordinates" NumberOfComponents="3" format="ascii" >
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+</Points>
+<Lines>
+<DataArray type="Int32" Name="connectivity" NumberOfComponents="1" format="ascii" >
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+</DataArray>
+<DataArray type="Int32" Name="offsets" NumberOfComponents="1" format="ascii" >
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+</DataArray>
+
+</Lines>
+</Piece>
+</PolyData>
+</VTKFile>

assays/Assay1/dataset/CPlantBox-isp/examples/benchmarks.h

+/**
+
+namespace CPlantBox {
+
+ * Benchmarks
+
+namespace CPlantBox {
+
+ *
+
+namespace CPlantBox {
+
+ * Compare root system lengths with the exact solution (see also the Python script singleroot.py)
+
+namespace CPlantBox {
+
+ *
+
+namespace CPlantBox {
+
+ * Benchmark 1a
+
+namespace CPlantBox {
+
+ * Single root, no laterals: defined as apical zone
+
+namespace CPlantBox {
+
+ *
+
+namespace CPlantBox {
+
+ * Benchmark 1a
+
+namespace CPlantBox {
+
+ * Single root, no laterals: defined as root with laterals (lb, ln, la, nob), but laterals have 0 length
+
+namespace CPlantBox {
+
+ *
+
+namespace CPlantBox {
+
+ * Benchmark 2
+
+namespace CPlantBox {
+
+ * Single root, with laterals
+
+namespace CPlantBox {
+
+ *
+
+namespace CPlantBox {
+
+ */
+
+namespace CPlantBox {
+
+using namespace std;
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+void benchmark(string name, vector<double> times, vector<double> dt_, double dx,
+
+namespace CPlantBox {
+
+               vector<double>& l0, vector<double>& l1, vector<double>& lt,
+
+namespace CPlantBox {
+
+               string bm_name)
+
+namespace CPlantBox {
+
+{
+
+namespace CPlantBox {
+
+  RootSystem rs1;
+
+namespace CPlantBox {
+
+  rs1.openFile(name,"modelparameter_bu/");
+
+namespace CPlantBox {
+
+  rs1.getRootTypeParameter(1)->dx=dx; // apply axial resolution
+
+namespace CPlantBox {
+
+  rs1.getRootTypeParameter(2)->dx=dx; // apply axial resolution
+
+namespace CPlantBox {
+
+  rs1.initialize();
+
+namespace CPlantBox {
+
+  int i =0;
+
+namespace CPlantBox {
+
+  for (auto dt : dt_) {
+
+namespace CPlantBox {
+
+      rs1.simulate(dt);
+
+namespace CPlantBox {
+
+      SegmentAnalyser analysis0(rs1);
+
+namespace CPlantBox {
+
+      lt[i] = analysis0.getSummed(RootSystem::st_length);
+
+namespace CPlantBox {
+
+      analysis0.filter(RootSystem::st_type,1);
+
+namespace CPlantBox {
+
+      l0[i] = analysis0.getSummed(RootSystem::st_length);
+
+namespace CPlantBox {
+
+      SegmentAnalyser analysis1(rs1);
+
+namespace CPlantBox {
+
+      analysis1.filter(RootSystem::st_type,2);
+
+namespace CPlantBox {
+
+      l1[i] = analysis1.getSummed(RootSystem::st_length);
+
+namespace CPlantBox {
+
+      i++;
+
+namespace CPlantBox {
+
+  }
+
+namespace CPlantBox {
+
+  cout << bm_name <<"\ntimes              [\t";
+
+namespace CPlantBox {
+
+  for (auto t : times) { cout << t << "\t"; }
+
+namespace CPlantBox {
+
+  cout << "]\nzero order length  [\t";
+
+namespace CPlantBox {
+
+  for (auto l : l0) { cout << l << "\t"; }
+
+namespace CPlantBox {
+
+  cout << "]\nfirst order length [\t";
+
+namespace CPlantBox {
+
+  for (auto l : l1) { cout << l << "\t"; }
+
+namespace CPlantBox {
+
+  cout << "]\ntotal length       [\t";
+
+namespace CPlantBox {
+
+  for (auto l : lt) { cout << l << "\t"; }
+
+namespace CPlantBox {
+
+  cout << "]\n\n";
+
+namespace CPlantBox {
+
+}
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+void benchmarks()
+
+namespace CPlantBox {
+
+{
+
+namespace CPlantBox {
+
+  vector<double> times = { 7 ,15, 30, 60 };
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  vector<double> dt_(times.size());
+
+namespace CPlantBox {
+
+  dt_[0] = times[0];
+
+namespace CPlantBox {
+
+  for (size_t i=1; i<times.size(); i++) {
+
+namespace CPlantBox {
+
+      dt_[i] = times.at(i)-times.at(i-1);
+
+namespace CPlantBox {
+
+  }
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  vector<double> l0(times.size()); // zero order lengths
+
+namespace CPlantBox {
+
+  vector<double> l1(times.size()); // first order lengths
+
+namespace CPlantBox {
+
+  vector<double> lt(times.size()); // total lengths
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  double dx = 0.1;
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  benchmark("bm_singleroot_nl",times,dt_,dx,l0,l1,lt,"Benchmark 1a"); // single root, no laterals, default tap root system
+
+namespace CPlantBox {
+
+  benchmark("bm_singleroot_nl2",times,dt_,dx,l0,l1,lt,"Benchmark 1b"); // single root,  0-lenght laterals, pparam file
+
+namespace CPlantBox {
+
+  benchmark("bm_singleroot",times,dt_,dx,l0,l1,lt,"Benchmark 2"); // single root, laterals
+
+namespace CPlantBox {
+
+  benchmark("bm_monocot_nl",times,dt_,dx,l0,l1,lt,"Benchmark 3a"); // multiple roots of type benchmark 1a
+
+namespace CPlantBox {
+
+  benchmark("bm_monocot_nl2",times,dt_,dx,l0,l1,lt,"Benchmark 3b"); // multiple roots of type benchmark 1b
+
+namespace CPlantBox {
+
+  benchmark("bm_monocot",times,dt_,dx,l0,l1,lt,"Benchmark 4"); // multiple roots of type benchmark 2
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+}
+
+namespace CPlantBox {
+

assays/Assay1/dataset/CPlantBox-isp/examples/example1.h

+/**
+
+
+
+ * Example 1
+
+
+
+ *
+
+
+
+ * 1) Opens plant and root parameters from a file
+
+
+
+ * 2) Simulates root growth
+
+
+
+ * 3) Outputs a VTP (for vizualisation in ParaView)
+
+
+
+ *    In Paraview: use tubePLot.py script for fancy visualisation (Macro/Add new macro...), apply after opening file
+
+
+
+ *
+
+
+
+ *  Additionally, exports the line segments as .txt file to import into Matlab for postprocessing
+
+
+
+ */
+
+
+
+using namespace std;
+
+
+
+namespace CPlantBox {
+
+
+
+void example1()
+
+
+
+{
+
+
+
+    Plant plant;
+
+
+
+
+
+
+
+    string name = "PMA2018";
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Open plant and root parameter from a file
+
+
+
+     */
+
+
+
+    plant.openXML(name);
+
+
+
+    //plant.openFile(name);
+
+
+
+//    plant.writeAlltoXML(name);
+
+
+
+
+
+
+
+//     plant.writeParameters(std::cout);
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Initialize
+
+
+
+     */
+
+
+
+    plant.initialize();
+
+
+
+    std::cout << "finished initialize\n";
+
+
+
+    /*
+
+
+
+     * Simulate
+
+
+
+     */
+
+
+
+    double simtime =3; // 60; // 20, 40, 60 days
+
+
+
+    double dt = 1; // try other values here
+
+
+
+    int N = round(simtime/dt);
+
+
+
+
+
+
+
+    for (int i=0; i<N; i++) {
+
+
+
+        plant.simulate(dt);
+
+
+
+    }
+
+
+
+    cout << "fin (with " << plant.getNumberOfNodes() << " nodes) \n";
+
+
+
+    auto o_ = plant.getOrgans(Organ::ot_organ);
+
+
+
+    cout << o_.size() << " organs \n";
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Export final result (as vtp)
+
+
+
+     */
+
+
+
+//    auto t1 = std::chrono::high_resolution_clock::now();
+
+
+
+//      plant.write("plant_write_rootsystem.vtp");
+
+
+
+//    auto t2 = std::chrono::high_resolution_clock::now();
+
+
+
+//    std::cout << "test function took "
+
+
+
+//              << std::chrono::duration_cast<std::chrono::milliseconds>(t2-t1).count()
+
+
+
+//              << " milliseconds\n";
+
+
+
+
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Export segments for Matlab analysis
+
+
+
+     */
+
+
+
+    SegmentAnalyser analysis(plant);
+
+
+
+//    analysis.write("rootsystem.txt");
+
+
+
+      analysis.write("analysis_write_rootsystem.vtp");
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Export dgf file
+
+
+
+     */
+
+
+
+    // analysis.write("rootsystem.dgf");
+
+
+
+
+
+
+
+    /*
+
+
+
+      Total length and surface
+
+
+
+     */
+
+
+
+//    double l = analysis.getSummed(Plant::st_length);
+
+
+
+//    std::cout << "Root system length " << l << " cm \n";
+
+
+
+
+
+
+
+    cout << "Finished with a total of " << plant.getNumberOfNodes()<< " nodes\n";
+
+
+
+
+
+
+
+}
+
+ }
+

assays/Assay1/dataset/CPlantBox-isp/examples/example2.h

+/**
+
+
+
+ * Example 2
+
+
+
+ *
+
+
+
+ * Same as Example 1, but with a plant container confining root growth
+
+
+
+ *
+
+
+
+ * Example container are:
+
+
+
+ * 1. Cylindrical soil core,
+
+
+
+ * 2. Flat square rhizotron,
+
+
+
+ * 3. Rotated square rhizotron
+
+
+
+ *
+
+
+
+ * Additionally, exports the confining geometry as paraview pyhton script
+
+
+
+ * (run file in Paraview by Tools->Python Shell, Run Script)
+
+
+
+ */
+
+namespace CPlantBox {
+
+using namespace std;
+
+
+
+
+
+
+
+void example2()
+
+
+
+{
+
+
+
+    Plant rootsystem;
+
+
+
+
+
+
+
+    string name = "Zea_mays_5_Leitner_2014";
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Plant and root parameter from a file
+
+
+
+     */
+
+
+
+    rootsystem.openFile(name);
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Set geometry
+
+
+
+     */
+
+
+
+
+
+
+
+    // 1.creates a cylindrical soil core with top radius 5 cm, bot radius 5 cm, height 50cm, not square but circular
+
+
+
+    SDF_PlantContainer soilcore(5,5,40,false);
+
+
+
+
+
+
+
+    //2. creates a square 27*27 cm containter with height 1.5 cm (used in parametrisation experiment)
+
+
+
+    SDF_PlantBox rhizotron(1.4,27,27);
+
+
+
+
+
+
+
+    //3. creates a square rhizotron r*r, with height h, rotated around the x-axis for angle alpha
+
+
+
+    double r = 20;
+
+
+
+    double h = 4;
+
+
+
+    double alpha = 45.;
+
+
+
+    SDF_PlantContainer rhizotron2(r,r,h,true);
+
+
+
+    Vector3d posA = Vector3d(0,r,-h/2); // origin before rotation
+
+
+
+    Matrix3d A = Matrix3d::rotX(alpha/180.*3.14);
+
+
+
+    posA = A.times(posA); // origin after rotation
+
+
+
+    SDF_RotateTranslate rotatedRhizotron(&rhizotron2,alpha,0,posA.times(-1));
+
+
+
+
+
+
+
+    //rootsystem.setGeometry(&soilcore); // pick one of the geometries
+
+
+
+	rootsystem.setGeometry(&rhizotron); // pick one of the geometries
+
+
+
+    //rootsystem.setGeometry(&rotatedRhizotron); // pick one of the geometries
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Initialize
+
+
+
+     */
+
+
+
+    rootsystem.initialize(); //it is important to call initialize() after setGeometry()
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Simulate
+
+
+
+     */
+
+
+
+    double simtime = 60;
+
+
+
+    double dt = 1;
+
+
+
+    int N = round(simtime/dt);
+
+
+
+    for (int i=0; i<N; i++) {
+
+
+
+        rootsystem.simulate(dt);
+
+
+
+    }
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Export results (as vtp)
+
+
+
+     */
+
+
+
+    rootsystem.write(name+std::string(".vtp"));
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Export container geometry as Paraview Python script (run file in Paraview by Tools->Python Shell, Run Script)
+
+
+
+     */
+
+
+
+    rootsystem.write(name+ std::string(".py"));
+
+
+
+
+
+
+
+    cout << "Finished with a total of " << rootsystem.getNumberOfNodes()<< " nodes\n";
+
+
+
+
+
+
+
+}
+}
+
+

assays/Assay1/dataset/CPlantBox-isp/examples/example3.h

+///**
+
+
+
+// * Example 3
+
+
+
+// *
+
+
+
+// * Creates N*N root systems at different locations, no confining geometry
+
+
+
+// *
+
+
+
+// */
+
+
+
+//using namespace std;
+
+
+
+//
+
+
+
+//void example3()
+
+
+
+//{
+
+
+
+//  auto gen = default_random_engine(chrono::system_clock::now().time_since_epoch().count());
+
+
+
+//  auto UD = uniform_real_distribution<double>(0,1); // random stuff
+
+
+
+//
+
+
+
+//  char * name = "Zea_mays_5_Leitner_2014";
+
+
+
+//
+
+
+
+//  /*
+
+
+
+//   * Creates N*N root systems
+
+
+
+//   */
+
+
+
+//  int N=3;
+
+
+
+//  double dist = 40; // [cm]
+
+
+
+//  vector<Plant*> allRS;
+
+
+
+//  for (int i=0; i<N; i++) {
+
+
+
+//      for (int j=0;j<N; j++) {
+
+
+
+//          Plant* rs = new Plant();
+
+
+
+//          allRS.push_back(rs);
+
+
+
+//          rs->openFile(name);
+
+
+
+//        //  rs->getRootSystemParameter()->seedPos = Vector3d(dist*i,dist*j,-3); // set position of seed [cm] TODO
+
+
+
+//      }
+
+
+
+//  }
+
+
+
+//
+
+
+
+//  /*
+
+
+
+//   * Simulate
+
+
+
+//   */
+
+
+
+//  double simtime = 120; // days
+
+
+
+//  for (auto rs : allRS) { // simulate all
+
+
+
+//      double s = UD(gen);
+
+
+
+//      rs->setSeed(s); // randomly select a seed
+
+
+
+//      rs->initialize();
+
+
+
+//      rs->simulate(simtime);
+
+
+
+//      cout << "Finished with a total of " << rs->getNumberOfNodes()<< " nodes\n";
+
+
+
+////  }
+
+
+
+//
+
+
+
+//  /*
+
+
+
+//   * Export results as single vtp files
+
+
+
+//   */
+
+
+
+//  int c=0;
+
+
+
+//  for (auto rs : allRS) {
+
+
+
+//      c++; // root system number
+
+
+
+//      string vtpname = "results/"+name+std::to_string(c)+".vtp";
+
+
+
+//      rs->write(vtpname);
+
+
+
+//  }
+
+
+
+//
+
+
+
+//}
+
+
+

assays/Assay1/dataset/CPlantBox-isp/examples/example4.h

+/**
+
+
+
+ * Example 4
+
+
+
+ *
+
+
+
+ * More complex geometries
+
+
+
+ *
+
+
+
+ * 1. a split pot experiment
+
+
+
+ * 2. rhizotubes as obstacles (from Example_Rhizotubes.m)
+
+
+
+ *
+
+
+
+ * Additionally, exports the confining geometry as paraview pyhton script
+
+
+
+ * (run file in Paraview by Tools->Python Shell, Run Script)
+
+
+
+ */
+
+namespace CPlantBox {
+
+using namespace std;
+
+
+
+
+
+
+
+void example4()
+
+
+
+{
+
+
+
+    RootSystem rootsystem;
+
+
+
+
+
+
+
+    string name = "Zea_mays_5_Leitner_2014";
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Plant and root parameter from a file
+
+
+
+     */
+
+
+
+    rootsystem.openFile(name);
+
+
+
+
+
+
+
+    /*
+
+
+
+     * 1. A split pot experiment
+
+
+
+     */
+
+
+
+    SDF_PlantBox topBox(22,20,5);
+
+
+
+    SDF_PlantBox sideBox(10,20,35);
+
+
+
+
+
+
+
+    SDF_RotateTranslate left(&sideBox, Vector3d(-6,0,-5));
+
+
+
+    SDF_RotateTranslate right(&sideBox, Vector3d(6,0,-5));
+
+
+
+
+
+
+
+    vector<SignedDistanceFunction*> box_;
+
+
+
+    box_.push_back(&topBox);
+
+
+
+    box_.push_back(&left);
+
+
+
+    box_.push_back(&right);
+
+
+
+    SDF_Union splitBox(box_);
+
+
+
+
+
+
+
+    /*
+
+
+
+     * 2. Rhizotubes as obstacles
+
+
+
+     */
+
+
+
+    // Box
+
+
+
+    double boxX = 96.;
+
+
+
+    double boxY = 126.;
+
+
+
+    double boxZ = 130.;
+
+
+
+    SDF_PlantBox box(boxX,boxY,boxZ);
+
+
+
+
+
+
+
+    // A single Rhizotube
+
+
+
+    double r = 2.*3.2; // cm
+
+
+
+    SDF_PlantContainer rhizotube(r,r,96.,false);
+
+
+
+    SDF_RotateTranslate rhizoX(&rhizotube, 90., SDF_RotateTranslate::yaxis, Vector3d(boxX/2.,0.,0));
+
+
+
+
+
+
+
+    // The experimental setting
+
+
+
+    vector<SignedDistanceFunction*> rhizotubes_;
+
+
+
+    const int tubeN=6;
+
+
+
+    double y_[tubeN] = { -30, -18, -6, 6, 18, 30 };
+
+
+
+    double z_[tubeN]= { -10, -20, -40, -60, -80, -120 };
+
+
+
+    for (int i=0; i<tubeN; i++) {
+
+
+
+        rhizotubes_.push_back(new SDF_RotateTranslate(&rhizoX, 0, SDF_RotateTranslate::xaxis, Vector3d(0,y_[i],z_[i])));
+
+
+
+    }
+
+
+
+
+
+
+
+    // Final geometry
+
+
+
+    SDF_Union rhizotubes(rhizotubes_);
+
+
+
+    SDF_Difference rhizoTubes(&box, &rhizotubes);
+
+
+
+
+
+
+
+    rootsystem.setGeometry(&rhizoTubes); // &splitBox, or &rhizoTubes
+
+
+
+
+
+
+
+    /**
+
+
+
+     * Initialize
+
+
+
+     */
+
+
+
+    rootsystem.initialize(); //it is important to call initialize() after setGeometry()
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Simulate
+
+
+
+     */
+
+
+
+    double simtime = 100; // e.g. 30 or 60 days
+
+
+
+    double dt = 1;
+
+
+
+    int N = round(simtime/dt);
+
+
+
+    for (int i=0; i<N; i++) {
+
+
+
+        rootsystem.simulate(dt);
+
+
+
+    }
+
+
+
+
+
+
+
+    /**
+
+
+
+     * Export results (as vtp)
+
+
+
+     */
+
+
+
+    rootsystem.write(name+".vtp");
+
+
+
+
+
+
+
+    /**
+
+
+
+     * Export container geometry as Paraview Python script (run file in Paraview by Tools->Python Shell, Run Script)
+
+
+
+     */
+
+
+
+    rootsystem.write(name+".py");
+
+
+
+
+
+
+
+    cout << "Finished with a total of " << rootsystem.getNumberOfNodes()<< " nodes\n";
+
+
+
+
+
+
+
+}
+}
+
+

assays/Assay1/dataset/CPlantBox-isp/examples/example5.h

+/**
+
+
+
+ * Example 5
+
+
+
+ *
+
+
+
+ * Hydrotropism ,
+
+
+
+ * proof of concept, with a static soil water content
+
+
+
+ *
+
+
+
+ */
+
+
+
+namespace CPlantBox {
+using namespace std;
+
+
+
+
+
+
+
+void example5()
+
+
+
+{
+
+
+
+    RootSystem rootsystem;
+
+
+
+
+
+
+
+    string name = "Zea_mays_5_Leitner_2014";
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Plant and root parameter from a file
+
+
+
+     */
+
+
+
+    rootsystem.openFile(name);
+
+
+
+
+
+
+
+    // "manually" set tropism to hydrotropism
+
+
+
+    for (int i=1; i<7; i++) {
+
+
+
+        rootsystem.getRootTypeParameter(i)->tropismT = RootSystem::tt_hydro;
+
+
+
+        rootsystem.getRootTypeParameter(i)->tropismN = 1; //N
+
+
+
+        rootsystem.getRootTypeParameter(i)->tropismS = 0.4; //sigma
+
+
+
+    }
+
+
+
+
+
+
+
+    /**
+
+
+
+     * Static soil property
+
+
+
+     */
+
+
+
+    SDF_PlantBox sideBox(10,20,50);
+
+
+
+    SDF_RotateTranslate left(&sideBox, Vector3d(-4.99,0,0));
+
+
+
+    SDF_RotateTranslate right(&sideBox, Vector3d(4.99,0,0));
+
+
+
+    SDF_Union leftright(&left,&right);
+
+
+
+    rootsystem.setGeometry(&leftright);  //for vizualisation
+
+
+
+
+
+
+
+    double maxS = 0.7; // maximal saturation
+
+
+
+    double minS = 0.1; // minimal saturation
+
+
+
+    double slope = 20; // [cm] linear gradient between min and max
+
+
+
+    SoilLookUpSDF soilprop(&left, maxS, minS, slope);
+
+
+
+
+
+
+
+    // set the soil properties before calling initialize
+
+
+
+    rootsystem.setSoil(&soilprop);
+
+
+
+
+
+
+
+    /**
+
+
+
+     * Initialize
+
+
+
+     */
+
+
+
+    rootsystem.initialize(); //it is important to call initialize() after setGeometry()
+
+
+
+
+
+
+
+    /*
+
+
+
+     * Simulate
+
+
+
+     */
+
+
+
+    double simtime = 30; // e.g. 30 or 60 days
+
+
+
+    double dt = 1;
+
+
+
+    int N = round(simtime/dt);
+
+
+
+    for (int i=0; i<N; i++) {
+
+
+
+        rootsystem.simulate(dt);
+
+
+
+    }
+
+
+
+
+
+
+
+    /**
+
+
+
+     * Export results (as vtp)
+
+
+
+     */
+
+
+
+    rootsystem.write(name+".vtp");
+
+
+
+
+
+
+
+    /**
+
+
+
+     * Export container geometry as Paraview Python script (run file in Paraview by Tools->Python Shell, Run Script)
+
+
+
+     */
+
+
+
+    rootsystem.write(name+".py");
+
+
+
+
+
+
+
+    cout << "Finished with a total of " << rootsystem.getNumberOfNodes()<< " nodes\n";
+
+
+
+}
+
+}
+

assays/Assay1/dataset/CPlantBox-isp/examples/example_scenegraph.h

+///**
+
+namespace CPlantBox {
+
+// * Example
+
+namespace CPlantBox {
+
+// *
+
+namespace CPlantBox {
+
+// * defines a minimal organ from the base organ class
+
+namespace CPlantBox {
+
+// *
+
+namespace CPlantBox {
+
+// */
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+///**
+
+namespace CPlantBox {
+
+// * example organ, having two nodes, from (0,0,0) and (0,0,1)
+
+namespace CPlantBox {
+
+// */
+
+namespace CPlantBox {
+
+//class MyOrgan : public Organ {
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//public:
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//	MyOrgan(Plant* plant, Organ* parent, int subtype, double delay): Organ(plant, parent, subtype, delay) {
+
+namespace CPlantBox {
+
+//		r_nodes.push_back(Vector3d(0,0,0));
+
+namespace CPlantBox {
+
+//	    nodeIDs.push_back(0);
+
+namespace CPlantBox {
+
+//	    nctimes.push_back(0.);
+
+namespace CPlantBox {
+
+//		r_nodes.push_back(Vector3d(0,0,1));
+
+namespace CPlantBox {
+
+//	    nodeIDs.push_back(0);
+
+namespace CPlantBox {
+
+//	    nctimes.push_back(0.);
+
+namespace CPlantBox {
+
+//	}
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//	virtual void setRelativeOrigin(const Vector3d& o) override { this->o = o; }
+
+namespace CPlantBox {
+
+//    virtual Vector3d getRelativeOrigin() const override { return o;  }
+
+namespace CPlantBox {
+
+//	virtual void setRelativeHeading(const Matrix3d& m) override { this->A = m; }
+
+namespace CPlantBox {
+
+//    virtual Matrix3d getRelativeHeading() const override { return A; }
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//	Vector3d o;
+
+namespace CPlantBox {
+
+//	Matrix3d A;
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//};
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//void example_scenegraph()
+
+namespace CPlantBox {
+
+//{
+
+namespace CPlantBox {
+
+//	Plant* plant = new Plant(); // we use the plant only for the vtp export
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//	Seed* seed = new Seed(plant);
+
+namespace CPlantBox {
+
+//	MyOrgan* base = new MyOrgan(plant, nullptr, 0, 0);
+
+namespace CPlantBox {
+
+//	MyOrgan* branch1 = new MyOrgan(plant, nullptr, 0, 0); // at top of base
+
+namespace CPlantBox {
+
+//	MyOrgan* branch2 = new MyOrgan(plant, nullptr, 0, 0); // half way base
+
+namespace CPlantBox {
+
+//	MyOrgan* branch3 = new MyOrgan(plant, nullptr, 0, 0); // at top of branch 1
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//	seed->setRelativeOrigin(Vector3d(0.,0.,2));
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//	base->setRelativeOrigin(Vector3d(0.,0.,0.));
+
+namespace CPlantBox {
+
+//	base->setRelativeHeading(Matrix3d::rotX(30./180.*3.1415)); // rotated 30 degrees
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//	branch1->setRelativeOrigin(Vector3d(0.,0.,1.)); // at top
+
+namespace CPlantBox {
+
+//	branch1->setRelativeHeading(Matrix3d::rotX(30./180.*3.1415)); // rotated 30 degrees
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//	branch2->setRelativeOrigin(Vector3d(0.,0.,0.5)); // half way
+
+namespace CPlantBox {
+
+//	branch2->setRelativeHeading(Matrix3d::rotX(30./180.*3.1415)); // X rotated 30 degrees
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//	branch3->setRelativeOrigin(Vector3d(0.,0.,1.)); // at top
+
+namespace CPlantBox {
+
+//	branch3->setRelativeHeading(Matrix3d::rotY(30./180.*3.1415)); // Y rotated 30 degrees
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//	// make tree by hand
+
+namespace CPlantBox {
+
+//	seed->children.push_back(base);
+
+namespace CPlantBox {
+
+//	base->children.push_back(branch1);
+
+namespace CPlantBox {
+
+//	base->children.push_back(branch2);
+
+namespace CPlantBox {
+
+//	branch1->children.push_back(branch3);
+
+namespace CPlantBox {
+
+//	base->parent = seed;
+
+namespace CPlantBox {
+
+//	branch1->parent = base;
+
+namespace CPlantBox {
+
+//	branch2->parent = base;
+
+namespace CPlantBox {
+
+//	branch3->parent = branch1;
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//	plant->seed = seed;
+
+namespace CPlantBox {
+
+//	plant->write("example_scenegraph.vtp", Organ::ot_organ);
+
+namespace CPlantBox {
+
+//
+
+namespace CPlantBox {
+
+//}
+
+namespace CPlantBox {
+

assays/Assay1/dataset/CPlantBox-isp/examples/main.cpp

+// Copyright (C) 2016 Daniel Leitner and Andrea Schnepf. See //license.txt for details.
+///This is an under developed version with a simple stem growth.
+#include <istream>
+#include "Plant.h"
+#include "Organ.h"
+#include "analysis.h"
+
+#include <iostream>
+#include <fstream>
+//#include <unistd.h>
+#include "tinyxml2.h"
+
+
+#include "example1.h"
+#include "example2.h"
+//#include "example3.h"
+//#include "example_scenegraph.h"
+
+
+
+
+
+/**
+ * Starts an examples (from the examples folder)
+ */
+int main(int argc, char* argv[])
+{
+	string name = "PMA2018";
+
+	if (argc>1) {
+		name= argv[1];
+	}
+
+	CPlantBox::example1(); // open parameter file, and output VTP
+	// example2(); // like example 1, but with put geometry
+	// example3(); // more than 1 plant
+
+	// example_scenegraph();
+
+	return(0);
+
+}
+
+
+
+
+

assays/Assay1/dataset/CPlantBox-isp/examples/modelparameter

+/mnt/c/cpb1/modelparameter
\ No newline at end of file

assays/Assay1/dataset/CPlantBox-isp/examples/shehan_RhizoTubes.h

+/**
+
+namespace CPlantBox {
+
+ * Shehans experimental set-up
+
+namespace CPlantBox {
+
+ *
+
+namespace CPlantBox {
+
+ * (B) Virtual analysis using rhizo tubes
+
+namespace CPlantBox {
+
+ *
+
+namespace CPlantBox {
+
+ * simulates the growing root systems (6*37) in the field
+
+namespace CPlantBox {
+
+ * uses trenches to analyse the number of roots in a coarse grid
+
+namespace CPlantBox {
+
+ * *
+
+namespace CPlantBox {
+
+ */
+
+namespace CPlantBox {
+
+using namespace std;
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+/*
+
+namespace CPlantBox {
+
+ * Creates the geometry of the rhizo tubes
+
+namespace CPlantBox {
+
+ *
+
+namespace CPlantBox {
+
+ * @param r     radius of the rhizo tubes
+
+namespace CPlantBox {
+
+ * \return union of the rhizo tubes
+
+namespace CPlantBox {
+
+ */
+
+namespace CPlantBox {
+
+SignedDistanceFunction* fieldRhizoTubes(double r)
+
+namespace CPlantBox {
+
+{
+
+namespace CPlantBox {
+
+  double l = 90; // cm tube length
+
+namespace CPlantBox {
+
+  SDF_PlantContainer* rhizotube = new SDF_PlantContainer(r,r,l,false);
+
+namespace CPlantBox {
+
+  SDF_RotateTranslate* rhizoX = new SDF_RotateTranslate(rhizotube, l, SDF_RotateTranslate::yaxis, Vector3d(l,0.,0.));
+
+namespace CPlantBox {
+
+  vector<SignedDistanceFunction*> rhizotubes_;
+
+namespace CPlantBox {
+
+  const int tubeN=6;
+
+namespace CPlantBox {
+
+  double y_[tubeN] = { 35, 45, 55, 65, 75, 85 };
+
+namespace CPlantBox {
+
+  double z_[tubeN] = { -10, -20, -40, -60, -80, -120 };
+
+namespace CPlantBox {
+
+  for (int i=0; i<tubeN; i++) {
+
+namespace CPlantBox {
+
+      rhizotubes_.push_back(new SDF_RotateTranslate(rhizoX, 0, SDF_RotateTranslate::xaxis, Vector3d(0,y_[i],z_[i])));
+
+namespace CPlantBox {
+
+  }
+
+namespace CPlantBox {
+
+  SDF_Union* rhizotubes = new SDF_Union(rhizotubes_);
+
+namespace CPlantBox {
+
+  return rhizotubes;
+
+namespace CPlantBox {
+
+}
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+/*
+
+namespace CPlantBox {
+
+ * The positions in the rhizotubes were fotos are taken
+
+namespace CPlantBox {
+
+ *
+
+namespace CPlantBox {
+
+ * \return Positions of the fotos
+
+namespace CPlantBox {
+
+ */
+
+namespace CPlantBox {
+
+vector<Vector3d> fotoPos() {
+
+namespace CPlantBox {
+
+  double l = 90; // cm
+
+namespace CPlantBox {
+
+  vector<Vector3d> fP;
+
+namespace CPlantBox {
+
+  const int tubeN=6;
+
+namespace CPlantBox {
+
+  double y_[tubeN] = { 35, 45, 55, 65, 75, 85 };
+
+namespace CPlantBox {
+
+  double z_[tubeN]= { -10, -20, -40, -60, -80, -120 };
+
+namespace CPlantBox {
+
+  int nf = 7; // number of foto positions per tube
+
+namespace CPlantBox {
+
+  double dist = l/double(nf+2);  // = 10 cm
+
+namespace CPlantBox {
+
+  for (int i=0; i<tubeN; i++) {
+
+namespace CPlantBox {
+
+      for (int j=0; j<nf; j++) {
+
+namespace CPlantBox {
+
+          fP.push_back(Vector3d((j+1)*dist,y_[i],z_[i]));
+
+namespace CPlantBox {
+
+      }
+
+namespace CPlantBox {
+
+  }
+
+namespace CPlantBox {
+
+  return fP;
+
+namespace CPlantBox {
+
+}
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+/**
+
+namespace CPlantBox {
+
+ * Rhizo tube analysis in the virtual field experiment
+
+namespace CPlantBox {
+
+ */
+
+namespace CPlantBox {
+
+void shehan_RhizoTubes(string name = "wheat", bool exportVTP = false)
+
+namespace CPlantBox {
+
+{
+
+namespace CPlantBox {
+
+  /*
+
+namespace CPlantBox {
+
+   * Initialize
+
+namespace CPlantBox {
+
+   */
+
+namespace CPlantBox {
+
+  double r = 3.2;
+
+namespace CPlantBox {
+
+  SignedDistanceFunction* geometry = new SDF_Complement(fieldRhizoTubes(r));
+
+namespace CPlantBox {
+
+  auto allRS = initializeRootSystems(name,geometry);
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  /*
+
+namespace CPlantBox {
+
+   * Simulate
+
+namespace CPlantBox {
+
+   */
+
+namespace CPlantBox {
+
+  vector<double> times = {0, 30, 60, 90, 120, 150, 180, 210, 240};
+
+namespace CPlantBox {
+
+  //vector<double> times = {0, 7, 14, 21, 30, 37, 44, 51, 60, 67, 74, 81, 90, 97, 104, 111, 120, 127, 134, 141, 150, 157, 164, 171, 180, 187, 194, 201, 210,
+
+namespace CPlantBox {
+
+  //		217, 223, 231, 240}; // test...
+
+namespace CPlantBox {
+
+  simulateRS(times, allRS);
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  /*
+
+namespace CPlantBox {
+
+   * Analysis: crop to the segments visible from the rhizotubes
+
+namespace CPlantBox {
+
+   */
+
+namespace CPlantBox {
+
+  double dx = 0.3; //cm
+
+namespace CPlantBox {
+
+  SignedDistanceFunction* visible = fieldRhizoTubes(3.2+dx);
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  vector<SegmentAnalyser> croppedTubes;
+
+namespace CPlantBox {
+
+  for (size_t i=1; i<times.size(); i++) {
+
+namespace CPlantBox {
+
+      std::cout << "\nANALYSE TIME " << times.at(i) <<"\n\n";
+
+namespace CPlantBox {
+
+      SegmentAnalyser analyser = getResult(allRS,times.at(i));
+
+namespace CPlantBox {
+
+      analyser.crop(visible); // throw segments away
+
+namespace CPlantBox {
+
+      analyser.pack(); // throw nodes away
+
+namespace CPlantBox {
+
+      if (exportVTP) {
+
+namespace CPlantBox {
+
+          string vtpname = name + "_tube_cropped"+ std::to_string(i)+".vtp"; // export cropped segments for visualization
+
+namespace CPlantBox {
+
+          analyser.write(vtpname);
+
+namespace CPlantBox {
+
+      }
+
+namespace CPlantBox {
+
+      croppedTubes.push_back(analyser); // copies into the vector
+
+namespace CPlantBox {
+
+  }
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  /*
+
+namespace CPlantBox {
+
+   * Foto
+
+namespace CPlantBox {
+
+   */
+
+namespace CPlantBox {
+
+  vector<vector<double>> finalmatrixC(times.size()-1);
+
+namespace CPlantBox {
+
+  vector<vector<double>> finalmatrixL(times.size()-1);
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  vector<Vector3d> fpos = fotoPos();
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  vector<SegmentAnalyser> fotos; // not real fotos, but slices of the croopedTube
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  double xx = 1.4; // cm slice thickness
+
+namespace CPlantBox {
+
+  double a1 = 8./180.*M_PI;
+
+namespace CPlantBox {
+
+  double a2 = 22./180.*M_PI;
+
+namespace CPlantBox {
+
+  double r_ = r+dx; // 3.5
+
+namespace CPlantBox {
+
+  double zz = sin(a1)*r_ + sin(a2)*r_;
+
+namespace CPlantBox {
+
+  cout << " foto box " << xx << ", 100, "<<zz<< "\n";
+
+namespace CPlantBox {
+
+  SDF_PlantBox fotoBox(xx,100.,zz);
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  vector<SignedDistanceFunction*> allcameras;
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  for (size_t t=0; t<times.size()-1; t++) {
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+      int c = 0;
+
+namespace CPlantBox {
+
+      cout << "Time: " << times.at(t) << "\n";
+
+namespace CPlantBox {
+
+      SegmentAnalyser empty = SegmentAnalyser();
+
+namespace CPlantBox {
+
+      fotos.push_back(empty); // fill in this time step
+
+namespace CPlantBox {
+
+      SegmentAnalyser f = croppedTubes.at(t);
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+      for (auto& p :fpos) {
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+          int j = floor(double(c)/7.);
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+          if (int(finalmatrixC[t].size())<=j) {
+
+namespace CPlantBox {
+
+              finalmatrixC[t].push_back(0.);
+
+namespace CPlantBox {
+
+              finalmatrixL[t].push_back(0.);
+
+namespace CPlantBox {
+
+          }
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+          // foto 1 + 2
+
+namespace CPlantBox {
+
+          SDF_RotateTranslate* foto = new SDF_RotateTranslate(&fotoBox,
+
+namespace CPlantBox {
+
+                                                              Vector3d(p.x,p.y,p.z+r_*sin(a2)));
+
+namespace CPlantBox {
+
+          SegmentAnalyser foto12 = f;
+
+namespace CPlantBox {
+
+          foto12.crop(foto);
+
+namespace CPlantBox {
+
+          foto12.pack();
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+          finalmatrixC[t][j] += double(foto12.getNumberOfRoots())/7.;
+
+namespace CPlantBox {
+
+          // number of segments is not feasible, since a root might grow around the tube
+
+namespace CPlantBox {
+
+          finalmatrixL[t][j] += double(foto12.getSummed(RootSystem::st_length))/7.;
+
+namespace CPlantBox {
+
+//          finalmatrixC[t][j] += 1./7.; // for debugging
+
+namespace CPlantBox {
+
+//          finalmatrixL[t][j] += 1./7.;
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+          std::cout << "#" << c << " foto at location: "<< p.toString() << " tube " << j  << "\n";
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+          allcameras.push_back(foto); // save geometry for later vizualisation
+
+namespace CPlantBox {
+
+          fotos.back().addSegments(foto12); // save segments for vizualisation
+
+namespace CPlantBox {
+
+          c++;
+
+namespace CPlantBox {
+
+      }
+
+namespace CPlantBox {
+
+  }
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  /*
+
+namespace CPlantBox {
+
+   * export fotos
+
+namespace CPlantBox {
+
+   */
+
+namespace CPlantBox {
+
+  int c=0;
+
+namespace CPlantBox {
+
+  for (auto& ft : fotos) {
+
+namespace CPlantBox {
+
+    string vtpname = name +  "_tube_fotos"+std::to_string(++c) +".vtp";
+
+namespace CPlantBox {
+
+    ft.write(vtpname);
+
+namespace CPlantBox {
+
+  }
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  int n = finalmatrixC[0].size(); // 32
+
+namespace CPlantBox {
+
+  int m = times.size()-1; // 8
+
+namespace CPlantBox {
+
+  string matname = name+"_tube_matrix1.txt";
+
+namespace CPlantBox {
+
+  std::ofstream fos;
+
+namespace CPlantBox {
+
+  fos.open(matname.c_str());
+
+namespace CPlantBox {
+
+  for (int j=0; j<n; j++) {
+
+namespace CPlantBox {
+
+      for (int i=0; i<m; i++) {
+
+namespace CPlantBox {
+
+          std::cout << std::fixed << std::setprecision(4)<< finalmatrixC[i][j] << "\t";
+
+namespace CPlantBox {
+
+          fos << std::fixed << std::setprecision(4)<< finalmatrixC[i][j] << "\t";
+
+namespace CPlantBox {
+
+      }
+
+namespace CPlantBox {
+
+      std::cout << "\n";
+
+namespace CPlantBox {
+
+      fos << "\n";
+
+namespace CPlantBox {
+
+  }
+
+namespace CPlantBox {
+
+  fos.close();
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  n = finalmatrixL[0].size(); // 32
+
+namespace CPlantBox {
+
+  m = times.size()-1; // 8
+
+namespace CPlantBox {
+
+  matname = name+"_tube_matrix2.txt";
+
+namespace CPlantBox {
+
+  fos.open(matname.c_str());
+
+namespace CPlantBox {
+
+  for (int j=0; j<n; j++) {
+
+namespace CPlantBox {
+
+      for (int i=0; i<m; i++) {
+
+namespace CPlantBox {
+
+          std::cout << std::fixed << std::setprecision(4)<< finalmatrixL[i][j] << "\t";
+
+namespace CPlantBox {
+
+          fos << std::fixed << std::setprecision(4)<< finalmatrixL[i][j] << "\t";
+
+namespace CPlantBox {
+
+      }
+
+namespace CPlantBox {
+
+      std::cout << "\n";
+
+namespace CPlantBox {
+
+      fos << "\n";
+
+namespace CPlantBox {
+
+  }
+
+namespace CPlantBox {
+
+  fos.close();
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+  /**
+
+namespace CPlantBox {
+
+   * Export rhizotube geometry
+
+namespace CPlantBox {
+
+   */
+
+namespace CPlantBox {
+
+  if (exportVTP) {
+
+namespace CPlantBox {
+
+      string gname = name + "_tube.py";
+
+namespace CPlantBox {
+
+      allRS[0]->write(gname);
+
+namespace CPlantBox {
+
+      string gname2 = name + "_tubeCamera.py";
+
+namespace CPlantBox {
+
+      SDF_Union cam(allcameras);
+
+namespace CPlantBox {
+
+      allRS[0]->setGeometry(&cam);
+
+namespace CPlantBox {
+
+      allRS[0]->write(gname2);
+
+namespace CPlantBox {
+
+  }
+
+namespace CPlantBox {
+
+}
+
+namespace CPlantBox {
+

assays/Assay1/dataset/CPlantBox-isp/examples/shehan_SoilCore.h

+/**
+ * Shehans experimental set-up
+ *
+ * (A) Virtual soil core analysis
+ *
+ * Simulates the growing root systems (6*37) in the field
+ * uses the soil coring method to analyse the root systems.
+ *
+ */
+using namespace std;
+#include <iostream>
+
+namespace CPlantBox {
+
+} // namespace CPlantBox
+
+#include <iomanip>
+
+/**
+ * Creates a field of multiply root system (6*37)
+ *
+ * @param name     filename of the parameter file
+ * @param geom     confining geometry
+ */
+vector<RootSystem*> initializeRootSystems(string name, SignedDistanceFunction* geom = new SignedDistanceFunction())
+{
+	auto gen = mt19937(chrono::system_clock::now().time_since_epoch().count());
+	auto UID = std::uniform_int_distribution<unsigned int>(); // random stuff, does it work now?
+	int M=6;
+	int N=37;
+	double dist1 = 18; // [cm] (M-1)*18 = 90
+	double dist2 = 3; // [cm] (N-1)*3 = 108
+	vector<RootSystem*> allRS;
+	for (int i=0; i<M; i++) {
+		for (int j=0;j<N; j++) {
+			RootSystem* rs = new RootSystem();
+			allRS.push_back(rs);
+			rs->openFile(name);
+			rs->setGeometry(geom);
+			rs->getRootTypeParameter(4)->theta = 80./180.*M_PI; // fix insertion angle of the basal roots
+			rs->getRootSystemParameter()->seedPos = Vector3d(dist1*i,dist2*j,-3); // set position of seed [cm]
+			unsigned int s = UID(gen);
+			rs->setSeed(s); // randomly select a seed
+			rs->initialize();
+		}
+	}
+	return allRS;
+}
+
+/**
+ * Simulates all root systems and stores the results in one analyser class per time step
+ *
+ * @param times     simulation times we want to simulate (starting with 0)
+ * @param allRS     root systems to simulate
+ */
+void simulateRS(vector<double> times, vector<RootSystem*>& allRS)
+{
+	int N_ = allRS.size();
+	for (size_t i=0; i<times.size()-1; i++) {
+		std::cout << "\nTIME " << times.at(i+1) <<"\n\n";
+		double dt = times.at(i+1)-times.at(i);
+		for (int r=0; r<N_; r++) { // simulate all
+			allRS.at(r)->simulate(dt,true);
+		}
+	}
+}
+
+/**
+ * Retrieves a the state of the root systems at a certain time in a SegmentAnalyser object
+ */
+SegmentAnalyser getResult(vector<RootSystem*>& allRS, double time) {
+  SegmentAnalyser a = SegmentAnalyser();
+  for (const auto& rs : allRS) { // merge all into one analyser object
+      //cout << "Analyser " << a.segments.size()<< ", " << a.nodes.size() << "\n";
+      //cout << "Root system: " << rs->getNumberOfNodes() <<"\n";
+	  auto news = SegmentAnalyser(*rs);
+	  news.filter(RootSystem::st_time,0,time);
+	  news.pack(); // delete unused nodes
+      a.addSegments(news);
+  }
+  return a;
+}
+
+/**
+ * The geometry of the 15 soil cores with fixed location in the field
+ *
+ * @param r     radius of the soil core
+ * @param h     height of the soil core
+ */
+vector<SignedDistanceFunction*> soilCores(double r,double h)
+{
+	SDF_PlantContainer* core =  new SDF_PlantContainer(r,r,h,false);
+	vector<double> x = {27, 27, 27, 27, 27, 45, 45, 45, 45, 45, 63, 63, 63, 63, 63};
+	vector<double> y = {30, 42, 54, 66, 78, 30, 42, 54, 66, 78, 30, 42, 54, 66, 78};
+	vector<SignedDistanceFunction*> cores_;
+	for (size_t i=0; i<x.size(); i++) {
+		cores_.push_back(new SDF_RotateTranslate(core, 0, SDF_RotateTranslate::xaxis, Vector3d(x[i],y[i],0)));
+	}
+	// SDF_Union* cores = new SDF_Union(cores_);
+	return cores_;
+}
+
+
+
+/**
+ * Soil core analysis in the virtual field experiment
+ */
+void shehan_SoilCore(string name = "wheat", bool exportVTP = false)
+{
+	/*
+	 * Initialize
+	 */
+	auto allRS = initializeRootSystems(name);
+
+	/*
+	 * Simulate
+	 */
+	vector<double> times = {0, 30, 60, 90};
+	simulateRS(times, allRS);
+
+	/*
+	 * Analysis: vertical distribution within the soil cores
+	 */
+	double r = 2.1; // radius of the soil core (cm)
+	double h = 160; // depth of the soil core (cm)
+	double dz = 5; // width of layer (cm)
+	vector<SignedDistanceFunction*> coregeometry = soilCores(r,h);
+
+	vector<vector<double>> finalmatrix(15*(times.size()-1));
+	for (size_t i=1; i<times.size(); i++) {
+		for (size_t j=0; j<15; j++) {
+
+			std::cout << "\nANALYSE TIME " << times.at(i) <<"\n\n";
+			SegmentAnalyser coreanalyser = getResult(allRS, times.at(i));
+			std::cout << "crop\n";
+			coreanalyser.crop(coregeometry[j]); // throw segments away
+			std::cout << "pack\n";
+			coreanalyser.pack(); // throw unused nodes away
+			std::cout << "get distribution\n";
+			vector<double> tl = coreanalyser.distribution(RootSystem::st_length,0,h,round(h/dz),true);  // vertical distribution
+			for (double& d :tl) {
+				d = d/(15*r*r*M_PI*dz); // 15 soil cores
+			}
+			finalmatrix.at((i-1)*15+j) = tl; // store length density in the finalmatrix
+			if (exportVTP) {
+				string vtpname = name + "_core_cropped"+ std::to_string(i)+".vtp"; // export cropped segments for vizualisaten
+				coreanalyser.write(vtpname);
+			}
+
+		}
+	}
+
+	/*
+	 * Export the final matrix
+	 */
+	int n = finalmatrix[0].size(); // h/dz = 32
+	int m = finalmatrix.size();
+	string matname = name+"_core_matrix.txt";
+	std::ofstream fos;
+	fos.open(matname.c_str());
+	for (int j=0; j<n; j++) {
+		for (int i=0; i<m; i++) {
+			std::cout << std::fixed << std::setprecision(4)<< finalmatrix[i][j] << "\t";
+			fos << std::fixed << std::setprecision(4)<< finalmatrix[i][j] << "\t";
+		}
+		std::cout << "\n";
+		fos << "\n";
+	}
+	fos.close();
+
+//	/*
+//	 * Export rootsystems (around 4.5GB)
+//	 */
+//	SegmentAnalyser analyser;
+//	for (const auto& rs : allRS) {
+//	    analyser.addSegments(*rs);
+//	}
+//	string vtpname = name +".vtp";
+//	analyser.write(vtpname);
+
+
+	/**
+	 * Export core geometry
+	 */
+	if (exportVTP) {
+		string gname = name + "_core.py";
+		SDF_Union* cores = new SDF_Union(coregeometry);
+		allRS[0]->setGeometry(cores); // just for writing
+		allRS[0]->write(gname);
+	}
+
+}

assays/Assay1/dataset/CPlantBox-isp/examples/shehan_Trenches.h

+/**
+
+namespace CPlantBox {
+
+ * Shehans experimental set-up
+
+namespace CPlantBox {
+
+ *
+
+namespace CPlantBox {
+
+ * (C) Virtual analysis of trenches
+
+namespace CPlantBox {
+
+ *
+
+namespace CPlantBox {
+
+ * simulates the growing root systems (6*37) in the field
+
+namespace CPlantBox {
+
+ * uses trenches to analyse the number of roots in a coarse grid
+
+namespace CPlantBox {
+
+ *
+
+namespace CPlantBox {
+
+ */
+
+namespace CPlantBox {
+
+using namespace std;
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+/**
+
+namespace CPlantBox {
+
+ * Creates the geometry of the trenches
+
+namespace CPlantBox {
+
+ *
+
+namespace CPlantBox {
+
+ * \return a vector of 9 infinitely large trenches
+
+namespace CPlantBox {
+
+ */
+
+namespace CPlantBox {
+
+vector<SDF_HalfPlane*> fieldTrenches() {
+
+namespace CPlantBox {
+
+	int N = 9; // number of trenches
+
+namespace CPlantBox {
+
+	vector<SDF_HalfPlane*> trenches;
+
+namespace CPlantBox {
+
+	double dist1 = 18; // cm horizontal distance between plants
+
+namespace CPlantBox {
+
+	double dist2 = 6; 	// cm vertical distance between the trenches
+
+namespace CPlantBox {
+
+	for (int i=0; i<N; i++) {
+
+namespace CPlantBox {
+
+		Vector3d o(1.5*dist1, 5.*dist2+i*dist2,  -160);
+
+namespace CPlantBox {
+
+		std::cout << o.toString() << "\n";
+
+namespace CPlantBox {
+
+		Vector3d p1(1.5*dist1, 5.*dist2+i*dist2,  0);
+
+namespace CPlantBox {
+
+		Vector3d p2(3.5*dist1, 5.*dist2+i*dist2,  -160);
+
+namespace CPlantBox {
+
+		trenches.push_back(new SDF_HalfPlane(o,p1,p2));
+
+namespace CPlantBox {
+
+	}
+
+namespace CPlantBox {
+
+	return trenches;
+
+namespace CPlantBox {
+
+}
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+/**
+
+namespace CPlantBox {
+
+ * Creates a field of multiply root system relevant for the trenches (4*21)
+
+namespace CPlantBox {
+
+ *
+
+namespace CPlantBox {
+
+ * @param name     filename of the parameter file
+
+namespace CPlantBox {
+
+ * @param geom     confining geometry
+
+namespace CPlantBox {
+
+ */
+
+namespace CPlantBox {
+
+vector<RootSystem*> initializeRootSystems2(string name, SignedDistanceFunction* geom = new SignedDistanceFunction())
+
+namespace CPlantBox {
+
+						{
+
+namespace CPlantBox {
+
+	// auto gen = mt19937(chrono::system_clock::now().time_since_epoch().count());
+
+namespace CPlantBox {
+
+	// auto UD = uniform_real_distribution<double>(0,1); // random stuff, does it work now?
+
+namespace CPlantBox {
+
+	int M=6;
+
+namespace CPlantBox {
+
+	int N=37;
+
+namespace CPlantBox {
+
+	double dist1 = 18; // [cm] (M-1)*18 = 90
+
+namespace CPlantBox {
+
+	double dist2 = 3; // [cm] (N-1)*3 = 108
+
+namespace CPlantBox {
+
+	vector<RootSystem*> allRS;
+
+namespace CPlantBox {
+
+	for (int i=1; i<(M-1); i++) {
+
+namespace CPlantBox {
+
+		for (int j=8;j<(N-8); j++) {
+
+namespace CPlantBox {
+
+			RootSystem* rs = new RootSystem();
+
+namespace CPlantBox {
+
+			// double s = UD(gen);
+
+namespace CPlantBox {
+
+			// rs->setSeed(s); // randomly select a seed
+
+namespace CPlantBox {
+
+			allRS.push_back(rs);
+
+namespace CPlantBox {
+
+			rs->openFile(name);
+
+namespace CPlantBox {
+
+			rs->setGeometry(geom);
+
+namespace CPlantBox {
+
+			rs->getRootTypeParameter(4)->theta = 80./180.*M_PI; // fix insertion angle of the basal roots
+
+namespace CPlantBox {
+
+			auto pos = Vector3d(dist1*i,dist2*j,-3);
+
+namespace CPlantBox {
+
+			std::cout << pos.toString() << "\n";
+
+namespace CPlantBox {
+
+			rs->getRootSystemParameter()->seedPos = pos; // set position of seed [cm]
+
+namespace CPlantBox {
+
+			rs->initialize();
+
+namespace CPlantBox {
+
+		}
+
+namespace CPlantBox {
+
+	}
+
+namespace CPlantBox {
+
+	return allRS;
+
+namespace CPlantBox {
+
+}
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+/**
+
+namespace CPlantBox {
+
+ * Trench analysis in the virtual field experiment
+
+namespace CPlantBox {
+
+ */
+
+namespace CPlantBox {
+
+void shehan_Trenches(string name = "wheat", bool exportVTP = false)
+
+namespace CPlantBox {
+
+{
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+	/*
+
+namespace CPlantBox {
+
+	 * Initialize
+
+namespace CPlantBox {
+
+	 */
+
+namespace CPlantBox {
+
+	auto allRS = initializeRootSystems2(name); // no geometry, trenches are destructive and created after roots are grown
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+	/*
+
+namespace CPlantBox {
+
+	 * Simulate
+
+namespace CPlantBox {
+
+	 */
+
+namespace CPlantBox {
+
+	vector<double> times = {0, 30}; //, 60, 90, 120, 150, 180, 210, 240};
+
+namespace CPlantBox {
+
+	simulateRS(times, allRS);
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+	/*
+
+namespace CPlantBox {
+
+	 * Analysis: cut the roots along the trenches
+
+namespace CPlantBox {
+
+	 */
+
+namespace CPlantBox {
+
+	double dist1 = 18; // cm
+
+namespace CPlantBox {
+
+	int m = 4;
+
+namespace CPlantBox {
+
+	int n = 32;
+
+namespace CPlantBox {
+
+	SDF_PlantBox box_(36.,1.e9,160.);
+
+namespace CPlantBox {
+
+	//SDF_RotateTranslate box(&box_, Vector3d(18.+ 27., 0., 0.) );
+
+namespace CPlantBox {
+
+	vector<SDF_HalfPlane*> trenches = fieldTrenches();
+
+namespace CPlantBox {
+
+	vector<vector<vector<double>>> finalMT;
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+	for (size_t t=0; t<times.size()-1; t++) {
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+		std::cout<<"create empty matrix";
+
+namespace CPlantBox {
+
+		// create empty n*m matrix
+
+namespace CPlantBox {
+
+		vector<vector<double>> finalmatrix(n);
+
+namespace CPlantBox {
+
+		for (int i=0; i<n; i++) {
+
+namespace CPlantBox {
+
+			for (int j=0; j<m; j++) {
+
+namespace CPlantBox {
+
+				finalmatrix[i].push_back(0.);
+
+namespace CPlantBox {
+
+			}
+
+namespace CPlantBox {
+
+		}
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+		// loop over trenches
+
+namespace CPlantBox {
+
+		int ii=0;
+
+namespace CPlantBox {
+
+		for (auto& tr : trenches) {
+
+namespace CPlantBox {
+
+		//auto& tr = trenches[0];
+
+namespace CPlantBox {
+
+			std::string s;
+
+namespace CPlantBox {
+
+			std::ostringstream os;
+
+namespace CPlantBox {
+
+			os << "trench_" << ++ii;
+
+namespace CPlantBox {
+
+			std::cout << os.str() <<"\n";
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+			// cut along the trench
+
+namespace CPlantBox {
+
+			std::cout << "cut \n";
+
+namespace CPlantBox {
+
+			SegmentAnalyser analyser = getResult(allRS,times.at(t+1));
+
+namespace CPlantBox {
+
+			SegmentAnalyser cut = analyser.cut(*tr);
+
+namespace CPlantBox {
+
+			// cut.crop(&box); // cut with bounding box
+
+namespace CPlantBox {
+
+			// cut.write(os.str()+".vtp");
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+			// split into grid
+
+namespace CPlantBox {
+
+			std::cout <<"grid \n";
+
+namespace CPlantBox {
+
+			//			vector<vector<SegmentAnalyser>> anamatrix1 = cut.distribution2(0,160, 1.5*dist1, 2.5*dist1,n,m);
+
+namespace CPlantBox {
+
+			//			vector<vector<SegmentAnalyser>> anamatrix2 = cut.distribution2(0,160, 2.5*dist1, 3.5*dist1,n,m);
+
+namespace CPlantBox {
+
+			vector<vector<SegmentAnalyser>> anamatrix = cut.distribution2(0,160, 1.5*dist1, 3.5*dist1,n,2*m); // grid of 8 * 32
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+			// save root count into matrix
+
+namespace CPlantBox {
+
+			std::cout<<"count \n";
+
+namespace CPlantBox {
+
+			for (int i=0; i<n; i++) {
+
+namespace CPlantBox {
+
+				for (int j=0; j<m; j++) {
+
+namespace CPlantBox {
+
+					//					finalmatrix[i][j] += anamatrix[i][j].segments.size();
+
+namespace CPlantBox {
+
+					//					finalmatrix[i][j] += anamatrix[i][j+m].segments.size();
+
+namespace CPlantBox {
+
+					finalmatrix[i][j] += anamatrix[i][j].getSummed(RootSystem::st_length);
+
+namespace CPlantBox {
+
+					finalmatrix[i][j] += anamatrix[i][j+m].getSummed(RootSystem::st_length);;
+
+namespace CPlantBox {
+
+				}
+
+namespace CPlantBox {
+
+			}
+
+namespace CPlantBox {
+
+		}
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+		finalMT.push_back(finalmatrix); // a lot of finals we have here (one matrix per time step)
+
+namespace CPlantBox {
+
+	}
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+	/*
+
+namespace CPlantBox {
+
+	 * Export the final matrix (one file per matrix)
+
+namespace CPlantBox {
+
+	 */
+
+namespace CPlantBox {
+
+	double N = double(trenches.size())*2.*(4.5*5.);
+
+namespace CPlantBox {
+
+	// to calculate the mean number of roots per cm^2 over the trenches
+
+namespace CPlantBox {
+
+	for (int j=0; j<m; j++) {
+
+namespace CPlantBox {
+
+		string matname = name+"_trench_matrix"+std::to_string(j+1)+".txt"; // grid number
+
+namespace CPlantBox {
+
+		std::ofstream fos;
+
+namespace CPlantBox {
+
+		fos.open(matname.c_str());
+
+namespace CPlantBox {
+
+		for (int i=0; i<n ; i++) {
+
+namespace CPlantBox {
+
+			for (size_t t=0; t<times.size()-1; t++) {
+
+namespace CPlantBox {
+
+				std::cout << std::fixed << std::setprecision(4)<< finalMT.at(t)[i][j]/N << "\t";
+
+namespace CPlantBox {
+
+				fos << std::fixed << std::setprecision(4)<< finalMT.at(t)[i][j]/N << "\t";
+
+namespace CPlantBox {
+
+			}
+
+namespace CPlantBox {
+
+			std::cout << "\n";
+
+namespace CPlantBox {
+
+			fos << "\n";
+
+namespace CPlantBox {
+
+		}
+
+namespace CPlantBox {
+
+		fos.close();
+
+namespace CPlantBox {
+
+		std::cout << "\n\n";
+
+namespace CPlantBox {
+
+	}
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+	/*
+
+namespace CPlantBox {
+
+	 * Export rootsystems (around 4.5GB)
+
+namespace CPlantBox {
+
+	 */
+
+namespace CPlantBox {
+
+	if (exportVTP) {
+
+namespace CPlantBox {
+
+		for (size_t i=0; i<times.size()-1; i++) {
+
+namespace CPlantBox {
+
+			string vtpname = name + std::to_string(i+1)+".vtp";
+
+namespace CPlantBox {
+
+			getResult(allRS,times.at(i+1)).write(vtpname);
+
+namespace CPlantBox {
+
+		}
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+		// export trench geometry
+
+namespace CPlantBox {
+
+		vector<SignedDistanceFunction*> tr_;
+
+namespace CPlantBox {
+
+		for (const auto& tr : trenches) { // copy vector
+
+namespace CPlantBox {
+
+			tr_.push_back(tr);
+
+namespace CPlantBox {
+
+		}
+
+namespace CPlantBox {
+
+		string gname = name + "_trench.py";
+
+namespace CPlantBox {
+
+		SDF_Union trenchgeometry = SDF_Union(tr_);
+
+namespace CPlantBox {
+
+		allRS[0]->setGeometry(&trenchgeometry); // just for writing
+
+namespace CPlantBox {
+
+		allRS[0]->write(gname);
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+//		allRS[0]->setGeometry(&box); // just for writing
+
+namespace CPlantBox {
+
+//		allRS[0]->write("boundingbox.py");
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+	}
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+}
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+
+
+
+namespace CPlantBox {
+

assays/Assay1/dataset/CPlantBox-isp/modelparameter/0.xml

+<Plant filetype="parameters" name="Juncus_squarrosus_Clausnitzer_1994">
+<organ name="true" subType="0" type="seed">
+    <parameter name="seedPos.x" value="0" />
+    <parameter name="seedPos.y" value="0" />
+    <parameter name="seedPos.z" value="-3" />
+    <parameter name="plantingdepth" value="3" />
+    <parameter dev="0" name="firstB" value="0" />
+    <parameter dev="0" name="delayB" value="0" />
+    <parameter dev="0" name="maxB" value="47" />
+    <parameter dev="0" name="maxTi" value="20" />
+    <parameter name="nC" value="0" />
+    <parameter name="nz" value="0" />
+    <parameter dev="0" name="firstSB" value="1000" />
+    <parameter dev="0" name="delaySB" value="1000" />
+    <parameter dev="0" name="delayRC" value="1000" />
+    <parameter dev="0" name="simulationTime" value="30" />
+</organ>
+
+<organ name="taproot" subType="1" type="root">
+    <parameter dev="0" name="lb" value="3" />
+    
+    <parameter dev="0" name="la" value="12" />
+    
+    <parameter dev="0" name="ln" value="1" />
+    
+    <parameter dev="19.600000000000001" name="lmax" value="196.69999999999999" />
+    
+    <parameter dev="19.600000000000001" name="nob" value="182.69999999999999" />
+    <parameter dev="0" name="r" value="2.0880000000000001" />
+    <parameter dev="0" name="a" value="0.14999999999999999" />
+    <parameter name="RotBeta" value="0" />
+    <parameter name="BetaDev" value="0" />
+    <parameter name="InitBeta" value="205" />
+    <parameter name="tropismT" value="1" />
+    <parameter name="tropismN" value="0.20000000000000001" />
+    <parameter name="tropismS" value="0.20000000000000001" />
+    <parameter name="dx" value="0.5" />
+    <parameter dev="0" name="theta" value="0.5" />
+    <parameter dev="0" name="rlt" value="1000000000" />
+    <parameter name="gf" value="1" />
+    <parameter name="successor" number="0" percentage="1" type="2" />
+</organ>
+
+<organ name="lateral1" subType="2" type="root">
+    <parameter dev="0" name="lb" value="0.29999999999999999" />
+    
+    <parameter dev="0" name="la" value="1.9199999999999999" />
+    
+    <parameter dev="0" name="ln" value="0.14999999999999999" />
+    
+    <parameter dev="0.27000000000000002" name="lmax" value="2.6699999999999999" />
+    
+    <parameter dev="1.8000000000000003" name="nob" value="4" />
+    <parameter dev="0" name="r" value="0.23999999999999999" />
+    <parameter dev="0" name="a" value="0.050000000000000003" />
+    <parameter name="RotBeta" value="238" />
+    <parameter name="BetaDev" value="0" />
+    <parameter name="InitBeta" value="0" />
+    <parameter name="tropismT" value="1" />
+    <parameter name="tropismN" value="1.5" />
+    <parameter name="tropismS" value="0.20000000000000001" />
+    <parameter name="dx" value="0.5" />
+    <parameter dev="0" name="theta" value="1.5708" />
+    <parameter dev="0" name="rlt" value="1000000000" />
+    <parameter name="gf" value="1" />
+</organ>
+
+<organ name="mainstem" subType="1" type="stem">
+    <parameter dev="0" name="lb" value="70" />
+    
+    <parameter dev="0" name="la" value="0.2" />
+    
+    <parameter dev="0" functiontype="0" name="ln" value="0" />
+    
+    <parameter dev="0" name="lmax" value="100" />
+    
+    <parameter dev="0" name="nob" value="0" />
+    <parameter dev="0.45000000000000001" name="r" value="4" />
+    <parameter dev="0.02" name="a" value="0.20000000000000001" />
+    <parameter name="RotBeta" value="1" />
+    <parameter name="BetaDev" value="0" />
+    <parameter name="InitBeta" value="0" />
+    <parameter name="tropismT" value="1" />
+    <parameter name="tropismN" value="1" />
+    <parameter name="tropismS" value="0" />
+    <parameter name="dx" value="0.25" />
+    <parameter dev="0" name="theta" value="0" />
+    <parameter dev="0" name="rlt" value="1000000000" />
+    <parameter name="gf" value="1" />
+    <parameter name="successor" number="0" percentage="1" type="2" />
+</organ>
+
+
+
+<organ name="1stbranch" subType="2" type="stem">
+    <parameter dev="0" name="lb" value="0" />
+    
+    <parameter dev="0" name="la" value="0" />
+    
+    <parameter dev="0" functiontype="1" name="ln" value="0" />
+    
+    <parameter dev="0" name="lmax" value="1" />
+    
+    <parameter dev="0" name="nob" value="0" />
+    <parameter dev="0.035000000000000003" name="r" value="2" />
+    <parameter dev="0.00125" name="a" value="0.29999999999999999" />
+    <parameter name="RotBeta" value="0" />
+    <parameter name="BetaDev" value="0" />
+    <parameter name="InitBeta" value="0" />
+    <parameter name="tropismT" value="1" />
+    <parameter name="tropismN" value="2" />
+    <parameter name="tropismS" value="0.10000000000000001" />
+    <parameter name="dx" value="0.25" />
+    <parameter dev="0" name="theta" value="0" />
+    <parameter dev="0" name="rlt" value="1000000000" />
+    <parameter name="gf" value="1" />
+</organ>
+
+<organ name="2ndbranch" subType="3" type="stem">
+    <parameter dev="0" name="lb" value="1" />
+    
+    <parameter dev="0" name="la" value="30" />
+    
+    <parameter dev="0" functiontype="1" name="ln" value="8" />
+    
+    <parameter dev="0" name="lmax" value="140" />
+    
+    <parameter dev="0" name="nob" value="14.625" />
+    <parameter dev="0.45000000000000001" name="r" value="2" />
+    <parameter dev="0.02" name="a" value="0.20000000000000001" />
+    <parameter name="RotBeta" value="0.5" />
+    <parameter name="BetaDev" value="0.10000000000000001" />
+    <parameter name="InitBeta" value="0" />
+    <parameter name="tropismT" value="1" />
+    <parameter name="tropismN" value="1" />
+    <parameter name="tropismS" value="0" />
+    <parameter name="dx" value="0.25" />
+    <parameter dev="0" name="theta" value="0.29999999999999999" />
+    <parameter dev="0" name="rlt" value="1000000000" />
+    <parameter name="gf" value="1" />
+    <parameter name="successor" number="0" percentage="1" type="2" />
+</organ>
+
+<organ name="lateral1" subType="2" type="leaf">
+    <parameter dev="6" name="lb" value="20" />
+    
+    <parameter dev="6" name="la" value="4" />
+    
+    <parameter dev="6" functiontype="3" name="ln" value="14" />
+    
+    <parameter dev="6" name="lmax" value="21" />
+    
+    <parameter dev="0" name="nob" value="4.5" />
+    <parameter dev="3" name="r" value="0.59999999999999998" />
+    <parameter dev="0.002" name="a" value="2" />
+    <parameter name="RotBeta" value="0.69999999999999996" />
+    <parameter name="BetaDev" value="0.29999999999999999" />
+    <parameter name="InitBeta" value="0" />
+    <parameter name="tropismT" value="1" />
+    <parameter name="tropismN" value="18" />
+    <parameter name="tropismS" value="0.01" />
+    <parameter name="dx" value="0.25" />
+    <parameter dev="0.3" name="theta" value="0.1" />
+    <parameter dev="0" name="rlt" value="1000000000" />
+    <parameter name="gf" value="1" />
+</organ>
+
+
+<organ name="tiller" subType="4" type="stem">
+    <parameter dev="0" name="lb" value="1" />
+    
+    <parameter dev="0" name="la" value="0" />
+    
+    <parameter dev="0" functiontype="0" name="ln" value="4" />
+    
+    <parameter dev="3" name="lmax" value="5" />
+    
+    <parameter dev="0" name="nob" value="0" />
+    <parameter dev="0.035000000000000003" name="r" value="1" />
+    <parameter dev="0.00125" name="a" value="0.29999999999999999" />
+    <parameter name="RotBeta" value="0.3" />
+    <parameter name="BetaDev" value="0" />
+    <parameter name="InitBeta" value="0" />
+    <parameter name="tropismT" value="1" />
+    <parameter name="tropismN" value="0.5" />
+    <parameter name="tropismS" value="0.05" />
+    <parameter name="dx" value="0.25" />
+    <parameter dev="0.02" name="theta" value="0.05" />
+
+    <parameter dev="0" name="rlt" value="1000000000" />
+    <parameter name="gf" value="1" />
+	<parameter name="successor" number="0" percentage="1" type="2" />
+</organ>
+</Plant>
\ No newline at end of file

assays/Assay1/dataset/CPlantBox-isp/modelparameter/0_new.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<Plant name="0_new" filetype="parameters">
+<organ type="seed" name="true" subType="0">
+    <parameter name="seedPos.x" value="0"/>
+    <parameter name="seedPos.y" value="0"/>
+    <parameter name="seedPos.z" value="-3"/>
+    <parameter name="plantingdepth" value="3"/>
+    <parameter name="firstB" value="0" dev="0"/>
+    <parameter name="delayB" value="0" dev="0"/>
+    <parameter name="maxB" value="47" dev="0"/>
+    <parameter name="maxTi" value="20" dev="0"/>
+    <parameter name="nC" value="0"/>
+    <parameter name="nz" value="0"/>
+    <parameter name="firstSB" value="1000" dev="0"/>
+    <parameter name="delaySB" value="1000" dev="0"/>
+    <parameter name="delayRC" value="1000" dev="0"/>
+    <parameter name="simulationTime" value="30" dev="0"/>
+</organ>
+
+<organ type="root" name="taproot" subType="1">
+    <parameter name="lb" value="3" dev="0"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="12" dev="0"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="1" dev="0"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="196.69999999999999" dev="19.600000000000001"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="182.69999999999999" dev="19.600000000000001"/>
+    <parameter name="r" value="2.0880000000000001" dev="0"/>
+    <parameter name="a" value="0.14999999999999999" dev="0"/>
+    <parameter name="RotBeta" value="0"/>
+    <parameter name="BetaDev" value="0"/>
+    <parameter name="InitBeta" value="205"/>
+    <parameter name="tropismT" value="1"/>
+    <parameter name="tropismN" value="0.20000000000000001"/>
+    <parameter name="tropismS" value="0.20000000000000001"/>
+    <parameter name="dx" value="0.5"/>
+    <parameter name="theta" value="0.5" dev="0"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+    <parameter name="successor" number="0" type="2" percentage="1"/>
+</organ>
+
+<organ type="root" name="lateral1" subType="2">
+    <parameter name="lb" value="0.29999999999999999" dev="0"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="1.9199999999999999" dev="0"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="0.14999999999999999" dev="0"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="2.6699999999999999" dev="0.27000000000000002"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="4" dev="1.8000000000000003"/>
+    <parameter name="r" value="0.23999999999999999" dev="0"/>
+    <parameter name="a" value="0.050000000000000003" dev="0"/>
+    <parameter name="RotBeta" value="238"/>
+    <parameter name="BetaDev" value="0"/>
+    <parameter name="InitBeta" value="0"/>
+    <parameter name="tropismT" value="1"/>
+    <parameter name="tropismN" value="1.5"/>
+    <parameter name="tropismS" value="0.20000000000000001"/>
+    <parameter name="dx" value="0.5"/>
+    <parameter name="theta" value="1.5708" dev="0"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+</organ>
+
+<organ type="stem" name="mainstem" subType="1">
+    <parameter name="lb" value="70" dev="0"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="0.20000000000000001" dev="0"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="0" dev="0" functiontype="0"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="100" dev="0"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="0" dev="0"/>
+    <parameter name="r" value="4" dev="0.45000000000000001"/>
+    <parameter name="a" value="0.20000000000000001" dev="0.02"/>
+    <parameter name="RotBeta" value="1"/>
+    <parameter name="BetaDev" value="0"/>
+    <parameter name="InitBeta" value="0"/>
+    <parameter name="tropismT" value="1"/>
+    <parameter name="tropismN" value="1"/>
+    <parameter name="tropismS" value="0"/>
+    <parameter name="dx" value="0.25"/>
+    <parameter name="theta" value="0" dev="0"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+    <parameter name="successor" number="0" type="2" percentage="1"/>
+</organ>
+
+<organ type="stem" name="1stbranch" subType="2">
+    <parameter name="lb" value="0" dev="0"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="0" dev="0"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="0" dev="0" functiontype="1"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="1" dev="0"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="0" dev="0"/>
+    <parameter name="r" value="2" dev="0.035000000000000003"/>
+    <parameter name="a" value="0.29999999999999999" dev="0.00125"/>
+    <parameter name="RotBeta" value="0"/>
+    <parameter name="BetaDev" value="0"/>
+    <parameter name="InitBeta" value="0"/>
+    <parameter name="tropismT" value="1"/>
+    <parameter name="tropismN" value="2"/>
+    <parameter name="tropismS" value="0.10000000000000001"/>
+    <parameter name="dx" value="0.25"/>
+    <parameter name="theta" value="0" dev="0"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+</organ>
+
+<organ type="stem" name="2ndbranch" subType="3">
+    <parameter name="lb" value="1" dev="0"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="30" dev="0"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="8" dev="0" functiontype="1"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="140" dev="0"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="14.625" dev="0"/>
+    <parameter name="r" value="2" dev="0.45000000000000001"/>
+    <parameter name="a" value="0.20000000000000001" dev="0.02"/>
+    <parameter name="RotBeta" value="0.5"/>
+    <parameter name="BetaDev" value="0.10000000000000001"/>
+    <parameter name="InitBeta" value="0"/>
+    <parameter name="tropismT" value="1"/>
+    <parameter name="tropismN" value="1"/>
+    <parameter name="tropismS" value="0"/>
+    <parameter name="dx" value="0.25"/>
+    <parameter name="theta" value="0.29999999999999999" dev="0"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+    <parameter name="successor" number="0" type="2" percentage="1"/>
+</organ>
+
+<organ type="stem" name="otherbranch1" subType="4">
+    <parameter name="lb" value="1" dev="0"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="0" dev="0"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="4" dev="0" functiontype="0"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="5" dev="3"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="2" dev="0.75"/>
+    <parameter name="r" value="1" dev="0.035000000000000003"/>
+    <parameter name="a" value="0.29999999999999999" dev="0.00125"/>
+    <parameter name="RotBeta" value="0.29999999999999999"/>
+    <parameter name="BetaDev" value="0"/>
+    <parameter name="InitBeta" value="0"/>
+    <parameter name="tropismT" value="1"/>
+    <parameter name="tropismN" value="0.5"/>
+    <parameter name="tropismS" value="0.050000000000000003"/>
+    <parameter name="dx" value="0.25"/>
+    <parameter name="theta" value="0.050000000000000003" dev="0.02"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+    <parameter name="successor" number="0" type="2" percentage="1"/>
+</organ>
+
+<organ type="leaf" name="lateral1" subType="2">
+    <parameter name="lb" value="20" dev="6"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="4" dev="6"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="14" dev="6" functiontype="3"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="21" dev="6"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="0.7857142857142857" dev="0"/>
+    <parameter name="r" value="0.59999999999999998" dev="3"/>
+    <parameter name="a" value="2" dev="0.002"/>
+    <parameter name="RotBeta" value="0.69999999999999996"/>
+    <parameter name="BetaDev" value="0.29999999999999999"/>
+    <parameter name="InitBeta" value="0"/>
+    <parameter name="tropismT" value="1"/>
+    <parameter name="tropismN" value="18"/>
+    <parameter name="tropismS" value="0.01"/>
+    <parameter name="dx" value="0.25"/>
+    <parameter name="theta" value="0.10000000000000001" dev="0.29999999999999999"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+</organ>
+
+
+</Plant>

assays/Assay1/dataset/CPlantBox-isp/modelparameter/1.xml

+<Plant filetype="parameters" name="maize">
+<organ name="maize" subType="0" type="seed">
+    <parameter name="seedPos.x" value="0" />
+	
+    <parameter name="seedPos.y" value="100" />
+    <parameter name="seedPos.z" value="-3" />
+    <parameter name="plantingdepth" value="3" />
+	
+    <parameter dev="0" name="firstB" value="1" />
+	
+    <parameter dev="0" name="delayB" value="1" />
+	
+    <parameter dev="0" name="maxB" value="0" />
+		
+	<parameter dev="0" name="maxTi" value="2" />
+		
+    <parameter name="nC" value="0" />
+	
+    <parameter name="nz" value="0" />
+	
+    <parameter dev="0" name="firstSB" value="1000" />
+    <parameter dev="0" name="delaySB" value="1000" />
+    <parameter dev="0" name="delayRC" value="1000" />
+    <parameter dev="0" name="simulationTime" value="15" />
+	
+</organ>
+
+<organ name="taproot" subType="1" type="root">
+    <parameter dev="0" name="lb" value="1" />
+    
+    <parameter dev="0" name="la" value="1.2" />
+    
+    <parameter dev="0" name="ln" value="0.80000000000000004" />
+    
+    <parameter dev="3.2999999999999998" name="lmax" value="33.399999999999999" />
+    
+    <parameter dev="4.1249999999999991" name="nob" value="39.999999999999993" />
+	 
+    <parameter dev="0" name="r" value="4" />
+	
+    <parameter dev="0" name="a" value="0.050000000000000003" />
+	 
+    <parameter name="RotBeta" value="0.43137300000000001" />
+	
+    <parameter name="BetaDev" value="0.39215699999999998" />
+	
+    <parameter name="InitBeta" value="0.196078" />
+	
+    <parameter name="tropismT" value="1" />
+	
+    <parameter name="tropismN" value="4" />
+	
+    <parameter name="tropismS" value="1.5708" />
+		
+    <parameter name="dx" value="1" />
+	
+    <parameter dev="0" name="theta" value="0" />
+		
+    <parameter dev="0" name="rlt" value="1000000000" />
+	
+    <parameter name="gf" value="1" />
+		
+    <parameter name="successor" number="0" percentage="1" type="2" />
+</organ>
+
+<organ name="lateral1" subType="2" type="root">
+    <parameter dev="0.10000000000000001" name="lb" value="0.40000000000000002" />
+    
+    <parameter dev="0.20000000000000001" name="la" value="0.80000000000000004" />
+    
+    <parameter dev="0.10000000000000001" name="ln" value="0.5" />
+    
+    <parameter dev="10" name="lmax" value="7.7000000000000002" />
+    
+    <parameter dev="16.800000000000004" name="nob" value="14" />
+    <parameter dev="0.14999999999999999" name="r" value="1.5" />
+    <parameter dev="0" name="a" value="0.029999999999999999" />
+    <parameter name="RotBeta" value="0.54901999999999995" />
+    <parameter name="BetaDev" value="0.49019600000000002" />
+    <parameter name="InitBeta" value="0.156863" />
+    <parameter name="tropismT" value="0" />
+    <parameter name="tropismN" value="2" />
+    <parameter name="tropismS" value="0.52359900000000004" />
+    <parameter name="dx" value="1" />
+    <parameter dev="0.052359900000000001" name="theta" value="1.22173" />
+    <parameter dev="0" name="rlt" value="1000000000" />
+    <parameter name="gf" value="1" />
+    <parameter name="successor" number="0" percentage="1" type="3" />
+</organ>
+
+<organ name="lateral2" subType="3" type="root">
+    <parameter dev="0.01" name="lb" value="0.10000000000000001" />
+    
+    <parameter dev="0.01" name="la" value="0.10000000000000001" />
+    
+    <parameter dev="0" name="ln" value="0.23999999999999999" />
+    
+    <parameter dev="0.040000000000000001" name="lmax" value="0.44" />
+    
+    <parameter dev="0.083333333333333329" name="nob" value="2" />
+    <parameter dev="0.20000000000000001" name="r" value="2" />
+    <parameter dev="0" name="a" value="0.02" />
+    <parameter name="RotBeta" value="0.62745099999999998" />
+    <parameter name="BetaDev" value="0.58823499999999995" />
+    <parameter name="InitBeta" value="0.117647" />
+    <parameter name="tropismT" value="1" />
+    <parameter name="tropismN" value="2" />
+    <parameter name="tropismS" value="0.78539800000000004" />
+    <parameter name="dx" value="1" />
+    <parameter dev="0.052359900000000001" name="theta" value="1.18682" />
+    <parameter dev="0" name="rlt" value="1000000000" />
+    <parameter name="gf" value="1" />
+    <parameter name="successor" number="0" percentage="1" type="4" />
+</organ>
+
+<organ name="nodal_root" subType="4" type="root">
+    <parameter dev="0" name="lb" value="0" />
+    
+    <parameter dev="0.029999999999999999" name="la" value="0.40000000000000002" />
+    
+    <parameter dev="0" name="ln" value="0" />
+    
+    <parameter dev="0.040000000000000001" name="lmax" value="0.40000000000000002" />
+    
+    <parameter dev="0" name="nob" value="0" />
+    <parameter dev="0.20000000000000001" name="r" value="2" />
+    <parameter dev="0" name="a" value="0.02" />
+    <parameter name="RotBeta" value="0.78431399999999996" />
+    <parameter name="BetaDev" value="0.78431399999999996" />
+    <parameter name="InitBeta" value="0.039215699999999999" />
+    <parameter name="tropismT" value="0" />
+    <parameter name="tropismN" value="0" />
+    <parameter name="tropismS" value="0.31415900000000002" />
+    <parameter name="dx" value="1" />
+    <parameter dev="0.052359900000000001" name="theta" value="1.18682" />
+    <parameter dev="0" name="rlt" value="1000000000" />
+    <parameter name="gf" value="1" />
+</organ>
+
+<organ name="mainstem" subType="1" type="stem">
+    <parameter dev="0" name="lb" value="1" />
+    
+    <parameter dev="0" name="la" value="0" />
+    
+    <parameter dev="0" functiontype="3" name="ln" value="2" />
+    
+    <parameter dev="0" name="lmax" value="30" />
+    
+    <parameter dev="0" name="nob" value="0" />
+    <parameter dev="0.45000000000000001" name="r" value="1" />
+    <parameter dev="0.02" name="a" value="0.20000000000000001" />
+    <parameter name="RotBeta" value="1" />
+    <parameter name="BetaDev" value="0" />
+    <parameter name="InitBeta" value="0" />
+    <parameter name="tropismT" value="1" />
+    <parameter name="tropismN" value="1" />
+    <parameter name="tropismS" value="0" />
+    <parameter name="dx" value="0.25" />
+    <parameter dev="0" name="theta" value="0" />
+    <parameter dev="0" name="rlt" value="1000000000" />
+    <parameter name="gf" value="1" />
+
+</organ>
+
+
+
+<organ name="bud" subType="2" type="stem">
+    <parameter dev="0" name="lb" value="1" />
+    
+    <parameter dev="0" name="la" value="0" />
+    
+    <parameter dev="0" functiontype="5" name="ln" value="5" />
+    
+    <parameter dev="0" name="lmax" value="70" />
+    
+    <parameter dev="0" name="nob" value="0" />
+    <parameter dev="0.035000000000000003" name="r" value="0.1" />
+    <parameter dev="0.00125" name="a" value="0.29999999999999999" />
+    <parameter name="RotBeta" value="1" />
+    <parameter name="BetaDev" value="0" />
+    <parameter name="InitBeta" value="0.5" />
+    <parameter name="tropismT" value="4" />
+    <parameter name="tropismN" value="8" />
+    <parameter name="tropismS" value="0.05" />
+    <parameter name="dx" value="0.25" />
+    <parameter dev="0" name="theta" value="0.3" />
+    <parameter dev="0" name="rlt" value="1000000000" />
+    <parameter name="gf" value="1" />
+
+</organ>
+
+
+<organ name="tiller" subType="4" type="stem">
+    <parameter dev="0" name="lb" value="1" />
+    
+    <parameter dev="0" name="la" value="0" />
+    
+    <parameter dev="0" functiontype="3" name="ln" value="2" />
+    
+    <parameter dev="0" name="lmax" value="20" />
+    
+    <parameter dev="0" name="nob" value="0" />
+    <parameter dev="0.035000000000000003" name="r" value="1" />
+    <parameter dev="0.00125" name="a" value="0.13" />
+    <parameter name="RotBeta" value="1" />
+    <parameter name="BetaDev" value="0" />
+    <parameter name="InitBeta" value="0.5" />
+    <parameter name="tropismT" value="4" />
+    <parameter name="tropismN" value="8" />
+    <parameter name="tropismS" value="0.02" />
+    <parameter name="dx" value="0.25" />
+    <parameter dev="0" name="theta" value="0.3" />
+
+    <parameter dev="0" name="rlt" value="1000000000" />
+    <parameter name="gf" value="1" />
+
+</organ>
+
+
+
+<organ name="lateral2" subType="2" type="leaf">
+    <parameter dev="0" name="lb" value="2" />
+    
+    <parameter dev="0" name="la" value="0.2" />
+    
+    <parameter dev="0" functiontype="5" name="ln" value="0" />
+    
+    <parameter dev="0" name="lmax" value="2" />
+    
+    <parameter dev="0" name="nob" value="0" />
+    <parameter dev="0" name="r" value="1" />
+    <parameter dev="0.002" name="a" value="0.02" />
+    <parameter name="RotBeta" value="0.5" />
+    <parameter name="BetaDev" value="0.1" />
+    <parameter name="InitBeta" value="0.5" />
+
+    <parameter name="tropismT" value="1" />
+    <parameter name="tropismN" value="2" />
+    <parameter name="tropismS" value="0" />
+    <parameter name="dx" value="0.25" />
+    <parameter dev="0" name="theta" value="0.4" />
+    <parameter dev="0" name="rlt" value="1000000000" />
+    <parameter name="gf" value="1" />
+</organ>
+
+</Plant>
\ No newline at end of file

assays/Assay1/dataset/CPlantBox-isp/modelparameter/1_new.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<Plant name="1_new" filetype="parameters">
+<organ type="seed" name="true" subType="0">
+    <parameter name="seedPos.x" value="0"/>
+    <parameter name="seedPos.y" value="100"/>
+    <parameter name="seedPos.z" value="-3"/>
+    <parameter name="plantingdepth" value="3"/>
+    <parameter name="firstB" value="1" dev="0"/>
+    <parameter name="delayB" value="1" dev="0"/>
+    <parameter name="maxB" value="0" dev="0"/>
+    <parameter name="maxTi" value="2" dev="0"/>
+    <parameter name="nC" value="0"/>
+    <parameter name="nz" value="0"/>
+    <parameter name="firstSB" value="1000" dev="0"/>
+    <parameter name="delaySB" value="1000" dev="0"/>
+    <parameter name="delayRC" value="1000" dev="0"/>
+    <parameter name="simulationTime" value="15" dev="0"/>
+</organ>
+
+<organ type="root" name="taproot" subType="1">
+    <parameter name="lb" value="1" dev="0"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="1.2" dev="0"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="0.80000000000000004" dev="0"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="33.399999999999999" dev="3.2999999999999998"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="39.999999999999993" dev="4.1249999999999991"/>
+    <parameter name="r" value="4" dev="0"/>
+    <parameter name="a" value="0.050000000000000003" dev="0"/>
+    <parameter name="RotBeta" value="0.43137300000000001"/>
+    <parameter name="BetaDev" value="0.39215699999999998"/>
+    <parameter name="InitBeta" value="0.196078"/>
+    <parameter name="tropismT" value="1"/>
+    <parameter name="tropismN" value="4"/>
+    <parameter name="tropismS" value="1.5708"/>
+    <parameter name="dx" value="1"/>
+    <parameter name="theta" value="0" dev="0"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+    <parameter name="successor" number="0" type="2" percentage="1"/>
+</organ>
+
+<organ type="root" name="lateral1" subType="2">
+    <parameter name="lb" value="0.40000000000000002" dev="0.10000000000000001"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="0.80000000000000004" dev="0.20000000000000001"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="0.5" dev="0.10000000000000001"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="7.7000000000000002" dev="10"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="14" dev="16.800000000000004"/>
+    <parameter name="r" value="1.5" dev="0.14999999999999999"/>
+    <parameter name="a" value="0.029999999999999999" dev="0"/>
+    <parameter name="RotBeta" value="0.54901999999999995"/>
+    <parameter name="BetaDev" value="0.49019600000000002"/>
+    <parameter name="InitBeta" value="0.156863"/>
+    <parameter name="tropismT" value="0"/>
+    <parameter name="tropismN" value="2"/>
+    <parameter name="tropismS" value="0.52359900000000004"/>
+    <parameter name="dx" value="1"/>
+    <parameter name="theta" value="1.22173" dev="0.052359900000000001"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+    <parameter name="successor" number="0" type="3" percentage="1"/>
+</organ>
+
+<organ type="root" name="lateral2" subType="3">
+    <parameter name="lb" value="0.10000000000000001" dev="0.01"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="0.10000000000000001" dev="0.01"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="0.23999999999999999" dev="0"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="0.44" dev="0.040000000000000001"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="2" dev="0.083333333333333329"/>
+    <parameter name="r" value="2" dev="0.20000000000000001"/>
+    <parameter name="a" value="0.02" dev="0"/>
+    <parameter name="RotBeta" value="0.62745099999999998"/>
+    <parameter name="BetaDev" value="0.58823499999999995"/>
+    <parameter name="InitBeta" value="0.117647"/>
+    <parameter name="tropismT" value="1"/>
+    <parameter name="tropismN" value="2"/>
+    <parameter name="tropismS" value="0.78539800000000004"/>
+    <parameter name="dx" value="1"/>
+    <parameter name="theta" value="1.18682" dev="0.052359900000000001"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+    <parameter name="successor" number="0" type="4" percentage="1"/>
+</organ>
+
+<organ type="root" name="nodal_root" subType="4">
+    <parameter name="lb" value="0" dev="0"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="0.40000000000000002" dev="0.029999999999999999"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="0" dev="0"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="0.40000000000000002" dev="0.040000000000000001"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="0" dev="0"/>
+    <parameter name="r" value="2" dev="0.20000000000000001"/>
+    <parameter name="a" value="0.02" dev="0"/>
+    <parameter name="RotBeta" value="0.78431399999999996"/>
+    <parameter name="BetaDev" value="0.78431399999999996"/>
+    <parameter name="InitBeta" value="0.039215699999999999"/>
+    <parameter name="tropismT" value="0"/>
+    <parameter name="tropismN" value="0"/>
+    <parameter name="tropismS" value="0.31415900000000002"/>
+    <parameter name="dx" value="1"/>
+    <parameter name="theta" value="1.18682" dev="0.052359900000000001"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+</organ>
+
+<organ type="stem" name="mainstem" subType="1">
+    <parameter name="lb" value="1" dev="0"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="0" dev="0"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="2" dev="0" functiontype="3"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="30" dev="0"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="15.5" dev="0"/>
+    <parameter name="r" value="1" dev="0.45000000000000001"/>
+    <parameter name="a" value="0.20000000000000001" dev="0.02"/>
+    <parameter name="RotBeta" value="1"/>
+    <parameter name="BetaDev" value="0"/>
+    <parameter name="InitBeta" value="0"/>
+    <parameter name="tropismT" value="1"/>
+    <parameter name="tropismN" value="1"/>
+    <parameter name="tropismS" value="0"/>
+    <parameter name="dx" value="0.25"/>
+    <parameter name="theta" value="0" dev="0"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+</organ>
+
+<organ type="stem" name="1stbranch" subType="2">
+    <parameter name="lb" value="1" dev="0"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="0" dev="0"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="5" dev="0" functiontype="5"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="70" dev="0"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="14.800000000000001" dev="0"/>
+    <parameter name="r" value="0.10000000000000001" dev="0.035000000000000003"/>
+    <parameter name="a" value="0.29999999999999999" dev="0.00125"/>
+    <parameter name="RotBeta" value="1"/>
+    <parameter name="BetaDev" value="0"/>
+    <parameter name="InitBeta" value="0.5"/>
+    <parameter name="tropismT" value="4"/>
+    <parameter name="tropismN" value="8"/>
+    <parameter name="tropismS" value="0.050000000000000003"/>
+    <parameter name="dx" value="0.25"/>
+    <parameter name="theta" value="0.29999999999999999" dev="0"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+</organ>
+
+<organ type="stem" name="otherbranch1" subType="4">
+    <parameter name="lb" value="1" dev="0"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="0" dev="0"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="2" dev="0" functiontype="3"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="20" dev="0"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="10.5" dev="0"/>
+    <parameter name="r" value="1" dev="0.035000000000000003"/>
+    <parameter name="a" value="0.13" dev="0.00125"/>
+    <parameter name="RotBeta" value="1"/>
+    <parameter name="BetaDev" value="0"/>
+    <parameter name="InitBeta" value="0.5"/>
+    <parameter name="tropismT" value="4"/>
+    <parameter name="tropismN" value="8"/>
+    <parameter name="tropismS" value="0.02"/>
+    <parameter name="dx" value="0.25"/>
+    <parameter name="theta" value="0.29999999999999999" dev="0"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+</organ>
+
+<organ type="leaf" name="lateral2" subType="2">
+    <parameter name="lb" value="2" dev="0"/>
+    <!--Basal zone [cm]-->
+    <parameter name="la" value="0.20000000000000001" dev="0"/>
+    <!--Apical zone [cm];-->
+    <parameter name="ln" value="0" dev="0" functiontype="5"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="lmax" value="2" dev="0"/>
+    <!--Inter-lateral distance [cm];-->
+    <parameter name="nob" value="0" dev="0"/>
+    <parameter name="r" value="1" dev="0"/>
+    <parameter name="a" value="0.02" dev="0.002"/>
+    <parameter name="RotBeta" value="0.5"/>
+    <parameter name="BetaDev" value="0.10000000000000001"/>
+    <parameter name="InitBeta" value="0.5"/>
+    <parameter name="tropismT" value="1"/>
+    <parameter name="tropismN" value="2"/>
+    <parameter name="tropismS" value="0"/>
+    <parameter name="dx" value="0.25"/>
+    <parameter name="theta" value="0.40000000000000002" dev="0"/>
+    <parameter name="rlt" value="1000000000" dev="0"/>
+    <parameter name="gf" value="1"/>
+</organ>
+
+
+</Plant>