catsim-test 0.0.5__cp313-cp313-manylinux_2_31_x86_64.whl

gecatsim/clib_build/src/phantom.y

@@ -0,0 +1,624 @@
+// Copyright 2024, GE Precision HealthCare. All rights reserved. See https://github.com/xcist/main/tree/master/license
+
+#include <stdio.h>
+#include <string.h>
+#include <math.h>
+#include <stdlib.h>
+#include <algorithm>
+#include "TreePhantom.h"
+#include "BaseObject.h"
+#include "Cube.h"
+#include "Sphere.h"
+#include "Cylinder.h"
+  
+  extern "C" {
+    int phantomlex(void);
+    extern int linecount;
+  }
+
+  extern int phantomparse(void);
+  extern int phantomdebug;
+  
+  // This contains the final stack of objects
+  LinearPhantom ostack;
+  BaseObject *top;
+  int objectCount;
+  MaterialTable localtab;
+  
+  // These are the state variables modified by the
+  // assignments
+  double lengthx, lengthy, lengthz;
+  double radius1, radius2;
+  double axis_x, axis_y, axis_z;
+  double rho;
+  double ax_x, ax_y, ax_z;
+  double ay_x, ay_y, ay_z;
+  double az_x, az_y, az_z;
+  bool ax_given, ay_given, az_given, axis_given; 
+  double x, y, z;
+  double length, radius;
+  double scale_factor; 
+  int clip_count;
+  double bb_radius; 
+  double clipcoefs[50][4];
+  std::string material;
+  
+  void phantomerror(const char *str)  {
+    fprintf(stderr,"error: %s on line %d\n",str,linecount);
+    exit(1);
+  }
+  
+  int mapMaterialNameToOrdinal(std::string materialname) {
+    MaterialTable::iterator result = std::find(localtab.begin(),
+					       localtab.end(),
+					       materialname);
+    if (result == localtab.end()) {
+      localtab.push_back(materialname);
+      return localtab.size();
+    }
+    return result - localtab.begin() + 1;
+  }
+
+  void printMaterialTable(FILE *fp) {
+    std::string myString;
+    const char *ch;
+    for(MaterialTable::iterator result = localtab.begin();result != localtab.end();result++)
+      {
+	myString = *result;
+	ch = myString.data();
+	fprintf(fp,"%s\n",ch);
+      }
+  }
+
+  void resetParameters() {
+    lengthx = lengthy = lengthz = 1;
+    radius1 = radius2 = 1;
+    axis_x = axis_y = axis_z = 0;
+    rho = 1.0;
+    ax_x = ax_y = ax_z = 0;
+    ay_x = ay_y = ay_z = 0;
+    az_x = az_y = az_z = 0;
+    axis_given = false;
+    ax_given = ay_given = az_given = false;
+    x = y = z = 0;
+    length = 1;
+    radius = 1;
+    top = NULL;
+    clip_count = 0;
+    bb_radius = 0;
+    material = "water";
+  }
+  
+  LinearPhantom parsePhantomDefFile(double scaleFactor, MaterialTable &dmtab) {
+    ostack.clear();
+    objectCount = 0;
+    scale_factor = scaleFactor;
+    resetParameters();
+    localtab.clear();
+    phantomparse();
+    dmtab = localtab;
+    return ostack;
+  }
+
+  void cross(double a1, double a2, double a3,
+	     double b1, double b2, double b3,
+	     double&c1, double&c2, double&c3) {
+    c1 = a2*b3-a3*b2;
+    c2 = a3*b1-a1*b3;
+    c3 = a1*b2-a2*b1;
+  }
+  
+  int sign(double x) {
+    if (x >=0 ) return 1;
+    if (x <=0 ) return -1;
+    return 0;
+  }
+  
+  void yyexpect(char *str) {
+    fprintf(stderr,"Error - while parsing the phantom file, expected %s on line %d\n",str,linecount);
+    exit(1);
+  }
+  
+  %}
+
+%union {
+  double val;
+  double vec[3];
+  char str[128];
+}
+
+%token SPHERE BOX CYLX CYLY CYLZ CYL ELLIP ELLIPFREE
+%token ELLIPCYL ECYLX ECYLY ECYLZ CONE CONEX CONEY CONEZ
+%token RHO SIN COS SQRT
+%token MATERIAL
+
+%right '='
+%left '-' '+'
+%left '*' '/'
+%left NEG
+
+%token <val> LENGTHX LENGTHY LENGTHZ RADIUS1 NUMBER RADIUS2 
+%token <vec> AXIS AX AY AZ 
+%type  <vec> vectorExpression
+%type  <val> expression
+%token <str> STRING
+
+%%
+objectdefs:
+| objectdefs objectdef
+;
+
+objectdef: 
+'{' labeldef volumedef dmspec '}' 
+{
+  if (top != NULL) {
+    top->Transform().Translate(Vec3(scale_factor*x,scale_factor*y,scale_factor*z));
+    top->Density(rho);
+    top->Priority(++objectCount);
+    top->Material(mapMaterialNameToOrdinal(material));
+    for (int m=0;m<clip_count;m++) 
+      top->AddClipPlane(ClipPlane(Vec3(clipcoefs[m][0],clipcoefs[m][1],clipcoefs[m][2]),clipcoefs[m][3]));
+    top->UpdateBoundingSphere();
+    top->ID(ostack.size()+1);
+    ostack.push_back(top);
+  }
+  resetParameters();
+}
+;
+
+
+dmspec:
+materialdef | densitydef | densitydef materialdef | materialdef densitydef
+;
+
+materialdef:
+MATERIAL '=' STRING {material = std::string(strdup($3))} 
+;
+
+densitydef:
+RHO '=' expression { rho = $3 }
+;
+
+labeldef:
+| quotedstring
+;
+
+quotedstring:
+'"' NUMBER '"'
+;
+
+volumedef: sphereDef
+| boxDef
+| cylinderXDef
+| cylinderYDef
+| cylinderZDef
+| cylinderDef
+| ellipsoidDef
+| freeEllipsoidDef
+| ellipticalCylDef
+| eCylinderXDef
+| eCylinderYDef
+| eCylinderZDef
+| coneDef
+| coneXDef
+| coneYDef
+| coneZDef
+;
+
+commonAssignments: 
+positionAssignment 
+| clipPlanes;
+
+sphereDef:
+'[' SPHERE ':' sphereAssignmentBlock ']' {
+  top = new Sphere;
+  top->Transform().Scale(Vec3(scale_factor*radius,scale_factor*radius,scale_factor*radius));
+}
+;
+
+sphereAssignmentBlock:
+| sphereAssignmentBlock radiusAssignment
+| sphereAssignmentBlock commonAssignments
+;
+
+boxDef:
+'[' BOX ':' boxAssignmentBlock ']' {
+  top = new Cube;
+  top->Transform().Scale(Vec3(scale_factor*lengthx,scale_factor*lengthy,scale_factor*lengthz));
+  if (!ax_given)
+    cross(ay_x,ay_y,ay_z,az_x,az_y,az_z,ax_x,ax_y,ax_z);
+  if (!ay_given)
+    cross(az_x,az_y,az_z,ax_x,ax_y,ax_z,ay_x,ay_y,ay_z);
+  if (!az_given)
+    cross(ax_x,ax_y,ax_z,ay_x,ay_y,ay_z,az_x,az_y,az_z);
+  double a1 = sqrt(ax_x*ax_x + ax_y*ax_y);
+  double a2 = (az_x*ax_x + az_y*ax_y);
+  double a3 = (az_y*ax_x - az_x*ax_y);
+  double a4 = sqrt(a2*a2+az_z*az_z);
+  double rotangle = 0;
+  if (a3 != 0) {
+    if (a4 == 0) {
+      rotangle = 90.0*sign(a3);
+    } else {
+      rotangle = atan2(a3,a4*a1)*180.0/M_PI;
+    }
+  }
+  top->Transform().RotateX(rotangle);
+  rotangle = 0;
+  if (ax_z != 0) {
+    if (a1 == 0) {
+      rotangle = 90*sign(ax_z);
+    } else {
+      rotangle = atan2(ax_z,a1)*180.0/M_PI;
+    }
+  }
+  top->Transform().RotateY(rotangle);
+  rotangle = 0;
+  if (ax_y != 0) {
+    if (ax_x == 0) {
+      rotangle = 90*sign(ax_y);
+    } else {
+      rotangle = atan2(ax_y,ax_x)*180.0/M_PI;
+    }
+  }
+  top->Transform().RotateZ(rotangle);
+}
+;
+
+boxAssignmentBlock:
+| boxAssignmentBlock lengthsAssignment
+| boxAssignmentBlock axesAssignment
+| boxAssignmentBlock commonAssignments
+;
+
+cylinderXDef:
+'[' CYLX ':' acylinderAssignmentBlock ']' {
+  top = new Cylinder;
+  top->Transform().Scale(Vec3(scale_factor*radius,scale_factor*radius,scale_factor*length));
+  top->Transform().RotateY(90);
+}
+;
+
+cylinderYDef:
+'[' CYLY ':' acylinderAssignmentBlock ']' {
+  top = new Cylinder;
+  top->Transform().Scale(Vec3(scale_factor*radius,scale_factor*radius,scale_factor*length));
+  top->Transform().RotateX(90);
+}
+;
+
+cylinderZDef:
+'[' CYLZ ':' acylinderAssignmentBlock ']' {
+  top = new Cylinder;
+  top->Transform().Scale(Vec3(scale_factor*radius,scale_factor*radius,scale_factor*length));
+  top->Transform().RotateZ(90);
+}
+;
+
+acylinderAssignmentBlock:
+| acylinderAssignmentBlock radiusAssignment 
+| acylinderAssignmentBlock lengthAssignment
+| acylinderAssignmentBlock commonAssignments
+;
+
+cylinderDef:
+'[' CYL ':' cylinderAssignmentBlock ']' {
+  top = new Cylinder;
+  top->Transform().Scale(Vec3(scale_factor*radius,scale_factor*radius,scale_factor*length));
+   double rotang;
+  rotang = -atan2(sqrt(axis_x*axis_x+axis_y*axis_y),axis_z)*180.0/M_PI;
+  top->Transform().RotateX(rotang);
+  rotang = -atan2(axis_x,axis_y)*180.0/M_PI;
+  top->Transform().RotateZ(rotang);
+}
+;
+
+cylinderAssignmentBlock:
+| cylinderAssignmentBlock radiusAssignment 
+| cylinderAssignmentBlock lengthAssignment
+| cylinderAssignmentBlock axisAssignment
+| cylinderAssignmentBlock commonAssignments
+;
+
+ellipsoidDef:
+'[' ELLIP ':' ellipsoidAssignmentBlock ']' {
+  top = new Sphere;
+  top->Transform().Scale(Vec3(scale_factor*lengthx,scale_factor*lengthy,scale_factor*lengthz));
+}
+;
+
+ellipsoidAssignmentBlock:
+| ellipsoidAssignmentBlock ellipsoidAssignmentStatement;
+
+ellipsoidAssignmentStatement:
+lengthsAssignment 
+| commonAssignments
+;
+
+freeEllipsoidDef:
+'[' ELLIPFREE ':' freeEllipsoidAssignmentBlock ']' { 
+  top = new Sphere;
+  top->Transform().Scale(Vec3(scale_factor*lengthx,scale_factor*lengthy,scale_factor*lengthz));
+  if (!ax_given)
+    cross(ay_x,ay_y,ay_z,az_x,az_y,az_z,ax_x,ax_y,ax_z);
+  if (!ay_given)
+    cross(az_x,az_y,az_z,ax_x,ax_y,ax_z,ay_x,ay_y,ay_z);
+  if (!az_given)
+    cross(ax_x,ax_y,ax_z,ay_x,ay_y,ay_z,az_x,az_y,az_z);
+  double a1 = sqrt(ax_x*ax_x + ax_y*ax_y);
+  double a2 = (az_x*ax_x + az_y*ax_y);
+  double a3 = (az_y*ax_x - az_x*ax_y);
+  double a4 = sqrt(a2*a2+az_z*az_z);
+  double rotangle = 0;
+  if (a3 != 0) {
+    if (a4 == 0) {
+      rotangle = 90.0*sign(a3);
+    } else {
+      rotangle = atan2(a3,a4*a1)*180.0/M_PI;
+    }
+  }
+  top->Transform().RotateX(rotangle);
+  rotangle = 0;
+  if (ax_z != 0) {
+    if (a1 == 0) {
+      rotangle = 90*sign(ax_z);
+    } else {
+      rotangle = atan2(ax_z,a1)*180.0/M_PI;
+    }
+  }
+  top->Transform().RotateY(rotangle);
+  rotangle = 0;
+  if (ax_y != 0) {
+    if (ax_x == 0) {
+      rotangle = 90*sign(ax_y);
+    } else {
+      rotangle = atan2(ax_y,ax_x)*180.0/M_PI;
+    }
+  }
+  top->Transform().RotateZ(rotangle);
+};
+
+freeEllipsoidAssignmentBlock:
+| freeEllipsoidAssignmentBlock lengthsAssignment
+| freeEllipsoidAssignmentBlock axesAssignment
+| freeEllipsoidAssignmentBlock commonAssignments
+;
+
+
+ellipticalCylDef:
+'[' ELLIPCYL ':' eCylinderAssignmentBlock ']' {
+  top = new Cylinder;
+  top->Transform().Scale(Vec3(scale_factor*lengthx,scale_factor*lengthy,scale_factor*length));
+  if (axis_given) {
+    az_x = axis_x;
+    az_y = axis_y;
+    az_z = axis_z;
+  }
+  if (!ax_given)
+    cross(ay_x,ay_y,ay_z,az_x,az_y,az_z,ax_x,ax_y,ax_z);
+  if (!ay_given)
+    cross(az_x,az_y,az_z,ax_x,ax_y,ax_z,ay_x,ay_y,ay_z);
+  if (!az_given)
+    cross(ax_x,ax_y,ax_z,ay_x,ay_y,ay_z,az_x,az_y,az_z);
+  double a1 = sqrt(ax_x*ax_x + ax_y*ax_y);
+  double a2 = (az_x*ax_x + az_y*ax_y);
+  double a3 = (az_y*ax_x - az_x*ax_y);
+  double a4 = sqrt(a2*a2+az_z*az_z);
+  double rotangle = 0;
+  if (a3 != 0) {
+    if (a4 == 0) {
+      rotangle = 90.0*sign(a3);
+    } else {
+      rotangle = atan2(a3,a4*a1)*180.0/M_PI;
+    }
+  }
+  top->Transform().RotateX(rotangle);
+  rotangle = 0;
+  if (ax_z != 0) {
+    if (a1 == 0) {
+      rotangle = 90*sign(ax_z);
+    } else {
+      rotangle = atan2(ax_z,a1)*180.0/M_PI;
+    }
+  }
+  top->Transform().RotateY(rotangle);
+  rotangle = 0;
+  if (ax_y != 0) {
+    if (ax_x == 0) {
+      rotangle = 90*sign(ax_y);
+    } else {
+      rotangle = atan2(ax_y,ax_x)*180.0/M_PI;
+    }
+  }
+  top->Transform().RotateZ(rotangle);
+};
+
+eCylinderAssignmentBlock:
+| eCylinderAssignmentBlock axisAssignment
+| eCylinderAssignmentBlock axesAssignment
+| eCylinderAssignmentBlock lengthsAssignment
+| eCylinderAssignmentBlock lengthAssignment
+| eCylinderAssignmentBlock commonAssignments
+;
+
+eCylinderXDef:
+'[' ECYLX ':' aECylAssignmentBlock ']' {
+  top = new Cylinder();
+  top->Transform().Scale(Vec3(scale_factor*lengthz,scale_factor*lengthy,scale_factor*length));
+  top->Transform().RotateY(90);
+}
+;
+
+eCylinderYDef:
+'[' ECYLY ':' aECylAssignmentBlock ']'  {
+  top = new Cylinder();
+  top->Transform().Scale(Vec3(scale_factor*lengthx,scale_factor*lengthz,scale_factor*length));
+  top->Transform().RotateX(90);
+}
+;
+
+eCylinderZDef:
+'[' ECYLZ ':' aECylAssignmentBlock ']'  {
+  top = new Cylinder();
+  top->Transform().Scale(Vec3(scale_factor*lengthx,scale_factor*lengthy,scale_factor*length));
+}
+;
+
+aECylAssignmentBlock:
+| aECylAssignmentBlock lengthAssignment
+| aECylAssignmentBlock lengthsAssignment
+| aECylAssignmentBlock commonAssignments
+;
+
+coneDef:
+'[' CONE ':' coneAssignmentBlock ']'
+;
+
+coneAssignmentBlock:
+| coneAssignmentBlock axisAssignment
+| coneAssignmentBlock lengthAssignment
+| coneAssignmentBlock radiiAssignment
+| coneAssignmentBlock commonAssignments
+;
+
+coneXDef:
+'[' CONEX ':' aConeAssignmentBlock ']'
+;
+
+coneYDef:
+'[' CONEY ':' aConeAssignmentBlock ']'
+;
+
+coneZDef:
+'[' CONEZ ':' aConeAssignmentBlock ']'
+;
+
+aConeAssignmentBlock:
+| coneAssignmentBlock lengthAssignment
+| coneAssignmentBlock radiiAssignment
+| coneAssignmentBlock commonAssignments
+;
+
+
+// Position the center of the object
+positionAssignment:
+'x' '=' expression   { x = $3 }
+| 'y' '=' expression { y = $3 }
+| 'z' '=' expression { z = $3 }
+;
+
+// Set the radius of the object
+radiusAssignment:
+'r' '=' expression { radius = $3 }
+;
+
+// Set the lengths of an object along the x, y & z axes
+lengthsAssignment:
+LENGTHX '=' expression   { lengthx = $3 }
+| LENGTHY '=' expression { lengthy = $3 }
+| LENGTHZ '=' expression { lengthz = $3 }
+;
+
+// Set a single length
+lengthAssignment:
+'l' '=' expression     { length = $3 }  
+;
+
+// Set multiple radii
+radiiAssignment:
+RADIUS1 '=' expression   { radius1 = $3 }
+| RADIUS2 '=' expression { radius2 = $3 }
+;
+
+axisAssignment:
+AXIS vectorExpression  { axis_x = $2[0]; axis_y = $2[1]; axis_z = $2[2]; axis_given = true; }
+;
+
+axesAssignment:
+AX vectorExpression  { ax_x = $2[0]; ax_y = $2[1]; ax_z = $2[2]; ax_given = true; }
+| AY vectorExpression  { ay_x = $2[0]; ay_y = $2[1]; ay_z = $2[2]; ay_given = true;}
+| AZ vectorExpression  { az_x = $2[0]; az_y = $2[1]; az_z = $2[2]; az_given = true;}
+;
+
+vectorExpression:
+'(' expression ',' expression ',' expression ')'
+{ $$[0] = $2; $$[1] = $4; $$[2] = $6; }
+;
+
+clipPlanes:
+//	  clipPlanes clipPlane
+//	  ;
+//
+//clipPlane:
+'x' '<' expression {
+  clipcoefs[clip_count][0] = -1.0;
+  clipcoefs[clip_count][1] = 0.0;
+  clipcoefs[clip_count][2] = 0.0;
+  clipcoefs[clip_count][3] = -scale_factor*$3;
+  clip_count++;
+}
+| 'x' '>' expression {
+  clipcoefs[clip_count][0] = 1.0;
+  clipcoefs[clip_count][1] = 0.0;
+  clipcoefs[clip_count][2] = 0.0;
+  clipcoefs[clip_count][3] = scale_factor*$3;
+  clip_count++;
+}
+| 'y' '<' expression {
+  clipcoefs[clip_count][0] = 0.0;
+  clipcoefs[clip_count][1] = -1.0;
+  clipcoefs[clip_count][2] = 0.0;
+  clipcoefs[clip_count][3] = -scale_factor*$3;
+  clip_count++;
+}
+| 'y' '>' expression {
+  clipcoefs[clip_count][0] = 0.0;
+  clipcoefs[clip_count][1] = 1.0;
+  clipcoefs[clip_count][2] = 0.0;
+  clipcoefs[clip_count][3] = scale_factor*$3;
+  clip_count++;
+}
+| 'z' '<' expression {
+  clipcoefs[clip_count][0] = 0.0;
+  clipcoefs[clip_count][1] = 0.0;
+  clipcoefs[clip_count][2] = -1.0;
+  clipcoefs[clip_count][3] = -scale_factor*$3;
+  clip_count++;
+}
+| 'z' '>' expression {
+  clipcoefs[clip_count][0] = 0.0;
+  clipcoefs[clip_count][1] = 0.0;
+  clipcoefs[clip_count][2] = 1.0;
+  clipcoefs[clip_count][3] = scale_factor*$3;
+  clip_count++;
+}
+| 'r' vectorExpression '<' expression {
+  double norm = sqrt($2[0]*$2[0] + $2[1]*$2[1] + $2[2]*$2[2]);
+  clipcoefs[clip_count][0] = -$2[0]/norm;
+  clipcoefs[clip_count][1] = -$2[1]/norm;
+  clipcoefs[clip_count][2] = -$2[2]/norm;
+  clipcoefs[clip_count][3] = -scale_factor*$4;
+  clip_count++;
+}
+| 'r' vectorExpression '>' expression {
+  double norm = sqrt($2[0]*$2[0] + $2[1]*$2[1] + $2[2]*$2[2]);
+  clipcoefs[clip_count][0] = $2[0]/norm;
+  clipcoefs[clip_count][1] = $2[1]/norm;
+  clipcoefs[clip_count][2] = $2[2]/norm;
+  clipcoefs[clip_count][3] = scale_factor*$4;
+  clip_count++;
+}
+;
+
+expression:
+NUMBER
+| SIN '(' expression ')' { $$ = sin($3*M_PI/180.0) }
+| COS '(' expression ')' { $$ = cos($3*M_PI/180.0) }
+| SQRT '(' expression ')' { $$ = sqrt($3) }
+| expression '+' expression { $$ = $1 + $3 }
+| expression '-' expression { $$ = $1 - $3 }
+| expression '*' expression { $$ = $1 * $3 }
+| expression '/' expression { $$ = $1 / $3 }
+| '-' expression %prec NEG  { $$ = -$2 }
+| '(' expression ')'        { $$ = $2 }
+;