Changeset 1249

Timestamp:

05/21/23 23:16:51 (19 months ago)

Author:

Maciej Komosinski

Message:

Multiple issues fixed when calculating bending range for the '|' bending muscle (earlier it was always 1.0 despite the code that supposedly calculated this)

Location:

cpp/frams/genetics

Files:

• f4/f4_conv.cpp (modified) (9 diffs)
• f4/f4_conv.h (modified) (1 diff)
• f4/f4_general.cpp (modified) (12 diffs)
• f4/f4_general.h (modified) (3 diffs)
• geneprops.h (modified) (1 diff)

cpp/frams/genetics/f4/f4_conv.cpp

@@ -124 +124 @@
         // reset recursive traverse flags
         for (int i = 0; i < cells->cell_count; i++)
-                cells->C[i]->recProcessedFlag = 0;
+                cells->C[i]->recurProcessedFlag = false;
 
         open(using_checkpoints); // begin model build
@@ -131 +131 @@
         for (int i = 0; i < cells->cell_count; i++)
         {
-                int res = buildModelRec(cells->C[i]);
+                int res = buildModelRecur(cells->C[i]);
                 if (res)
                 {
@@ -166 +166 @@
 
 
-int f4_Model::buildModelRec(f4_Cell *C)
-{
-        int partidx;
-        int j, res;
-        MultiRange range;
-
-        if (C->recProcessedFlag)
+int f4_Model::buildModelRecur(f4_Cell *C)
+{
+        if (C->recurProcessedFlag)
                 // already processed
                 return 0;
 
         // mark it processed
-        C->recProcessedFlag = 1;
+        C->recurProcessedFlag = true;
 
         // make sure parent is a stick
-        if (NULL != C->dadlink)
+        if (C->dadlink != NULL)
                 if (C->dadlink->type != CELL_STICK)
                 {
@@ -187 +183 @@
 
         // make sure its parent is processed first
-        if (NULL != C->dadlink)
-        {
-                res = buildModelRec(C->dadlink);
+        if (C->dadlink != NULL)
+        {
+                int res = buildModelRecur(C->dadlink);
                 if (res) return res;
         }
 
         char tmpLine[100];
-
-        range = C->genoRange;
+        MultiRange range = C->genoRange;
+
         if (C->type == CELL_STICK)
         {
@@ -208 +204 @@
                                 //C->firstend.x, C->firstend.y, C->firstend.z
                         );
-                        partidx = addFromString(PartType, tmpLine, &range);
-                        if (partidx < 0) return -1;
+                        jj_p1_refno = addFromString(PartType, tmpLine, &range);
+                        if (jj_p1_refno < 0) return -1;
                         this->checkpoint();
-                        jj_p1_refno = partidx;
                 }
                 else {
@@ -225 +220 @@
                         /*"vol=" 1.0/C->P.mass,*/ C->P.friction, C->P.ingestion, C->P.assimilation
                 );
-                partidx = addFromString(PartType, tmpLine, &range);
-                if (partidx < 0) return -2;
-                C->p2_refno = partidx;
+                C->p2_refno = addFromString(PartType, tmpLine, &range);
+                if (C->p2_refno < 0) return -2;
 
                 // new joint object
@@ -245 +239 @@
                         C->P.stamina
                 );
-                partidx = addFromString(JointType, tmpLine, &range);
-                if (partidx < 0) return -13;
+                C->joint_refno = addFromString(JointType, tmpLine, &range);
+                if (C->joint_refno < 0) return -13;
                 this->checkpoint();
-                C->joint_refno = partidx;
         }
 
@@ -254 +247 @@
         {
                 const char* nclass = C->neuclass->name.c_str();
-                int partno, jointno;
                 if (C->neuclass->getPreferredLocation() == 0)
                 {
-                        if (strcmp(nclass, "N") == 0)
-                        {
-                                partno = C->dadlink->p2_refno;
-                                if ((partno < 0) || (partno >= getPartCount())) return -21;
-                                else sprintf(tmpLine, "p=%d,d=\"N:in=%g,fo=%g,si=%g\"", partno, C->inertia, C->force, C->sigmo);
-                        }
+                        if (strcmp(nclass, "N") == 0) //special case just to specify the only neuron properties supported by f4, i.e., the properties for neuron class 'N'
+                                sprintf(tmpLine, "d=\"N:in=%g,fo=%g,si=%g\"", C->inertia, C->force, C->sigmo);
                         else
-                        {
                                 sprintf(tmpLine, "d=\"%s\"", nclass);
-                        }
-                        partidx = addFromString(NeuronType, tmpLine, &range);
-                        if (partidx < 0) return -22;
+
+                        C->neuro_refno = addFromString(NeuronType, tmpLine, &range);
+                        if (C->neuro_refno < 0) return -22;
                         this->checkpoint();
-                        C->neuro_refno = partidx;
                 }
                 else if (C->neuclass->getPreferredLocation() == 1) // attached to Part or have no required attachment - also part
                 {
-                        partno = C->dadlink->p2_refno;
+                        int partno = C->dadlink->p2_refno;
                         if ((partno < 0) || (partno >= getPartCount())) return -21;
 
-                        if (strcmp(nclass, "N") == 0)
-                                sprintf(tmpLine, "p=%d,d=\"N:in=%g,fo=%g,si=%g\"", partno, C->inertia, C->force, C->sigmo);
-                        else
-                                sprintf(tmpLine, "p=%d,d=\"%s\"", partno, nclass);
-
-                        partidx = addFromString(NeuronType, tmpLine, &range);
-                        if (partidx < 0) return -22;
+                        sprintf(tmpLine, "p=%d,d=\"%s\"", partno, nclass);
+
+                        C->neuro_refno = addFromString(NeuronType, tmpLine, &range);
+                        if (C->neuro_refno < 0) return -22;
                         this->checkpoint();
-                        C->neuro_refno = partidx;
                 }
                 else // attached to Joint, assume there are only three possibilities of getPreferredLocation()
                 {
-                        jointno = C->dadlink->joint_refno;
+                        int jointno = C->dadlink->joint_refno;
 
                         if (strcmp(nclass, "@") == 0)
                                 sprintf(tmpLine, "j=%d,d=\"@:p=%g\"", jointno, C->P.muscle_power);
                         else if (strcmp(nclass, "|") == 0)
-                                sprintf(tmpLine, "j=%d,d=\"|:p=%g,r=%g\"", jointno, C->P.muscle_power, C->mz);
+                        {
+                                sprintf(tmpLine, "j=%d,d=\"|:p=%g,r=%g\"", jointno, C->P.muscle_power, C->dadlink->P.muscle_bend_range); //Macko 2023-05 change: we take muscle_bend_range from dadlink, not from C, because we also assign this neuron to C->dadlink->joint_refno. Without this, for example in /*4*/<<X><<<<X>N:|>X>X>X>X the muscle is attached to the junction with 3 sticks, but gets range=33% as in a four-stick junction. f1 correctly sets range=0.5 for the analogous phenotype: X(X[|],X(X,X,X))
+                        }
                         else
                                 sprintf(tmpLine, "j=%d,d=\"%s\"", jointno, nclass);
 
-                        partidx = addFromString(NeuronType, tmpLine, &range);
-                        if (partidx < 0) return -32;
+                        C->neuro_refno = addFromString(NeuronType, tmpLine, &range);
+                        if (C->neuro_refno < 0) return -32;
                         this->checkpoint();
                 }
-                C->neuro_refno = partidx;
-                int n_refno = C->neuro_refno;
-
-                for (j = 0; j < C->conns_count; j++)
+                for (int j = 0; j < C->conns_count; j++)
                 {
                         if (C->conns[j]->from != NULL)
-                                buildModelRec(C->conns[j]->from);
+                                buildModelRecur(C->conns[j]->from);
 
                         tmpLine[0] = 0;
@@ -320 +301 @@
                         if (from >= 0)
                         {
-                                sprintf(tmpLine, "%d,%d,%g", n_refno, from, C->conns[j]->weight);
+                                sprintf(tmpLine, "%d,%d,%g", C->neuro_refno, from, C->conns[j]->weight);
                                 if (addFromString(NeuronConnectionType, tmpLine, &range) < 0) return -35;
                                 this->checkpoint();

cpp/frams/genetics/f4/f4_conv.h

@@ -83 +83 @@
 private:
         f4_Cells *cells;
-        int        buildModelRec(f4_Cell *ndad);
+        int        buildModelRecur(f4_Cell *ndad);
         /**
          * Get a cell which is a stick, by traversing dadlinks.

cpp/frams/genetics/f4/f4_general.cpp

@@ -12 +12 @@
 #include <frams/model/model.h> // for min and max attributes
 #include <common/nonstd_math.h>
+#include <algorithm> // std::min, std::max
 
 #ifdef DMALLOC
@@ -46 +47 @@
         anglepos = nangle;
         commacount = 0;
-        childcount = 0;
+        stickchildcount = 0;
         P = newP;
         rolling = 0;
@@ -65 +66 @@
                         //firstend = ndad->lastend;
                         //OM = ndad->OM;
-                        ndad->childcount++;
+                        ndad->stickchildcount++;
                 }
                 if (ndad->type == CELL_NEURON)
@@ -76 +77 @@
         // adjust lastend
         //lastend = firstend + ((Orient)OM * (Pt3D(1,0,0) * P.len));
-        mz = 1;
+        P.muscle_bend_range = 1;
 }
 
@@ -96 +97 @@
         anglepos = nangle;
         commacount = 0;
-        childcount = 0;
+        stickchildcount = 0;
         P = newP;
         rolling = 0;
@@ -115 +116 @@
                         //firstend = ndad->lastend;
                         //OM = ndad->OM;
-                        ndad->childcount++;
+                        ndad->stickchildcount++;
                 }
                 if (ndad->type == CELL_NEURON)
@@ -126 +127 @@
         // adjust lastend
         //lastend = firstend + ((Orient)OM * (Pt3D(1,0,0) * P.len));
-        mz = 1;
+        P.muscle_bend_range = 1;
 }
 
@@ -548 +549 @@
 
 
-void f4_Cell::adjustRec()
-{
-        //f4_OrientMat rot;
-        int i;
-
-        if (recProcessedFlag)
+void f4_Cell::adjustRecur()
+{
+        if (recurProcessedFlag)
                 // already processed
                 return;
 
         // mark it processed
-        recProcessedFlag = 1;
+        recurProcessedFlag = true;
 
         // make sure its parent is processed first
         if (dadlink != NULL)
-                dadlink->adjustRec();
+                dadlink->adjustRecur();
 
         // count children
-        childcount = 0;
-        for (i = 0; i < org->cell_count; i++)
+        stickchildcount = 0;
+        for (int i = 0; i < org->cell_count; i++)
         {
                 if (org->C[i]->dadlink == this)
                         if (org->C[i]->type == CELL_STICK)
-                                childcount++;
-        }
+                                stickchildcount++;
+        }
+
+        if (dadlink == NULL)
+                P.muscle_bend_range = 1.0;
+        else
+                P.muscle_bend_range = 1.0 / std::max(1, dadlink->stickchildcount); //bend range in f1: 0, 1 (line XX[|]) -> 100%, 2 (Y-shape X(X[|],X)) -> 50%, 3 (cross X(X[|],X,X)) -> 33%
+        //MacKo 2023-05: but shouldn't this formula ^^ also take commacount into consideration, like in f1?
 
         if (type == CELL_STICK)
@@ -580 +584 @@
                         // rotation due to rolling
                         xrot = rolling;
-                        mz = 1;
                 }
                 else
@@ -589 +592 @@
                         Padj.propagateAlong(false);
 
-                        //rot = Orient_1;
+                        //f4_OrientMat rot = Orient_1;
 
                         // rotation due to rolling
@@ -612 +615 @@
                         // rotation in world coordinates
                         //OM =  ((f4_OrientMat)dadlink->OM) * OM;
-                        mz = dadlink->mz / dadlink->childcount;
                 }
                 //Pt3D lastoffset = (Orient)OM * (Pt3D(1,0,0)*P.len);
@@ -737 +739 @@
         // reset recursive traverse flags
         for (int i = 0; i < cell_count; i++)
-                C[i]->recProcessedFlag = 0;
+                C[i]->recurProcessedFlag = false;
         // process every cell
         for (int i = 0; i < cell_count; i++)
-                C[i]->adjustRec();
+                C[i]->adjustRecur();
 
         //DB( printf("Cell simulation done, %d cells. \n", nc); )
 
         if (PRINT_CELLS_DEVELOPMENT) print_cells("Final");
+        if (PRINT_CELLS_DEVELOPMENT)
+                for (int i = 0; i < cell_count; i++)
+                        printf("%d,%d,dad=%d\tstick_children=%d\tcommas=%d\t|:range=%g\n", i, C[i]->nr, C[i]->dadlink ? C[i]->dadlink->nr : -1, C[i]->stickchildcount, C[i]->commacount, C[i]->P.muscle_bend_range);
 
         return errorcode;

cpp/frams/genetics/f4/f4_general.h

@@ -181 +181 @@
          * Adjusts properties of stick objects.
          */
-        void  adjustRec();
-
-        int        nr;                 ///<number of cell (seems to be used only in old f1 converter for neuron connections)
+        void  adjustRecur();
+
+        int        nr;                 ///<number of cell (seems to be used only in the approximate f1 converter for neuron connections)
         int        type;               ///<type
         f4_Cell *dadlink;              ///<pointer to cell parent
@@ -192 +192 @@
         f4_Node *old_gcur;             ///<used externally by f4_Cells::oneStep() to track changes of gcur, i.e., to detect progress in cell development
         repeat_stack repeat;           ///<stack holding repetition nodes and counters
-        int recProcessedFlag;          ///<used during recursive traverse
+        bool recurProcessedFlag;       ///<used during recursive traverse
         MultiRange genoRange;          ///<remember the genotype codes affecting this cell so far
 
         GeneProps    P;                ///<properties
         int          anglepos;         ///<number of position within dad's children (,)
-        int          childcount;       ///<number of children
+        int          stickchildcount;  ///<number of children (sticks only)
         int          commacount;       ///<number of postitions at lastend (>=childcount)
         double       rolling;          ///<rolling angle ('R') (around x)
@@ -203 +203 @@
         double       zrot;             ///<horizontal rotation angle due to branching (around z)
 
-        double       mz;               ///<freedom in z
         int          p2_refno;         ///<the number of the last end part object, used in f0
         int          joint_refno;      ///<the number of the joint object, used in f0
         int          neuro_refno;      ///<the number of the neuro object, used in f0
 
-        double       inertia;          ///<inertia of neuron
-        double       force;            ///<force of neuron
-        double       sigmo;            ///<sigmoid of neuron
+        double       inertia;          ///<inertia of neuron N
+        double       force;            ///<force of neuron N
+        double       sigmo;            ///<sigmoid of neuron N
         f4_CellConn *conns[F4_MAX_CELL_INPUTS]; ///<array of neuron connections
         int          conns_count;      ///<number of connections

cpp/frams/genetics/geneprops.h

@@ -98 +98 @@
 
 /**
- * Contains physical, biological and other properties of
- * stick, except for rotation. The constructor initializes properties of sticks with
- * default values. In order to change a property of a stick, the executeModifier() method
+ * Contains physical, biological and other properties of a Part and a Joint (as handled
+ * by the f1 and f4 encodings), except for rotation. The constructor initializes properties with
+ * default values. In order to change a property, the executeModifier() method
  * should be called. Modification of length, curvedness and twist properties
  * usually affects further sticks, so new sticks should have properties of