Merge pull request #146

Add region labels to egs_chamber and egs_dose_scoring.

HEN_HOUSE/egs++/ausgab_objects/egs_dose_scoring/egs_dose_scoring.cpp

@@ -114,6 +114,12 @@ void EGS_DoseScoring::setApplication(EGS_Application *App) {
  if (!app) {
  return;
  }
+
+ if(d_regionString.length() > 0 && d_region.size() < 1) {
+ getNumberRegions(d_regionString, d_region);
+ getLabelRegions(d_regionString, d_region);
+ }
+
  // Get the number of regions in the geometry.
  nreg = app->getnRegions();
  // Get the number of media in the input file
@@ -234,6 +240,14 @@ void EGS_DoseScoring::setApplication(EGS_Application *App) {
  }
 }
 
+void EGS_DoseScoring::getNumberRegions(const string &str, vector<int> &regs) {
+ app->getNumberRegions(str, regs);
+}
+
+void EGS_DoseScoring::getLabelRegions(const string &str, vector<int> &regs) {
+ app->getLabelRegions(str, regs);
+}
+
 void EGS_DoseScoring::reportResults() {
  egsInformation("\n======================================================\n");
  egsInformation("Dose Scoring Object(%s)\n",name.c_str());
@@ -438,10 +452,11 @@ extern "C" {
  int d_in_region = input->getInput("region dose",allowed_mode,1);
 
  /* get dose regions */
+ string d_regionsString;
  vector <int> d_regions;
  bool using_all_regions=true;
  vector <int> d_start, d_stop;
- if (!input->getInput("dose regions",d_regions)&& d_regions.size()>0) {
+ if (!input->getInput("dose regions",d_regionsString)&& d_regionsString.length()>0) {
  using_all_regions = false; // individual regions
  }
  else {
@@ -498,7 +513,11 @@ extern "C" {
  result->setVol(1.0); // default value if no entry
  }
  if (!using_all_regions) {
- result->setDoseRegions(d_regions);
+ if(d_regions.size() > 0) {
+ result->setDoseRegions(d_regions);
+ } else {
+ result->setDoseRegions(d_regionsString);
+ }
  }
  if (d_in_medium) {
  result->setMediumScoring(true);

HEN_HOUSE/egs++/ausgab_objects/egs_dose_scoring/egs_dose_scoring.h

@@ -205,6 +205,10 @@ class EGS_DOSE_SCORING_EXPORT EGS_DoseScoring : public EGS_AusgabObject {
  };
 
  void setApplication(EGS_Application *App);
+
+ void getNumberRegions(const string &str, vector<int> &regs);
+
+ void getLabelRegions(const string &str, vector<int> &regs);
 
  void reportResults();
 
@@ -236,6 +240,9 @@ class EGS_DOSE_SCORING_EXPORT EGS_DoseScoring : public EGS_AusgabObject {
  void setDoseRegions(const vector <int> d_reg) {
  d_region=d_reg;
  };
+ void setDoseRegions(const string d_reg) {
+ d_regionString=d_reg;
+ };
  void setMediumScoring(bool flag) {
  score_medium_dose=flag;
  };
@@ -258,6 +265,7 @@ class EGS_DOSE_SCORING_EXPORT EGS_DoseScoring : public EGS_AusgabObject {
  EGS_ScoringArray *doseM; //!< Scoring dose in each medium
  vector <EGS_Float> vol_list; // Input list of region volumes
  vector <int> d_region; // Input list of dose scoring regions d_reg[i] = ir
+ string d_regionString;
  vector <int> d_reg_index; // list index for dose scoring regions d_reg_index[ir]= 0..d_reg.size()-1
  vector <EGS_Float> vol; // geometrical region volumes
  EGS_Float norm_u;

HEN_HOUSE/egs++/egs_application.h

@@ -637,6 +637,37 @@ class EGS_EXPORT EGS_Application {
  int isWhere(EGS_Vector &r) {
  return geometry->isWhere(r);
  }
+
+ /*! \brief Gets numbers out of \a str and pushes them onto \a regs
+ 
+ Finds integer numbers in \a str and pushes them onto the vector \a regs.
+ For an input string containing a mixture of labels and region numbers,
+ this extracts the region numbers.
+ 
+ Usually you will do something like:
+ \verbatim
+ string regionString;
+ vector<int> regionVector;
+ int err1 = input->getInput("cavity regions",regionString);
+ geom->getNumberRegions(regionString, regionVector);
+ geom->getLabelRegions(regionString, regionVector);
+ \endverbatim
+ */
+ void getNumberRegions(const string &str, vector<int> &regs) {
+ geometry->getNumberRegions(str, regs);
+ }
+
+ /*! \brief Gets the regions for the labels in \a str and pushes onto \a regs
+ 
+ This function is used after \a getNumberRegions. It looks for labels
+ in \a str, finds the corresponding local region numbers, and pushes those
+ region numbers onto the region number vector \a regs.
+ 
+ The \a regs vector is sorted by this function, and duplicates are removed!
+ */
+ void getLabelRegions(const string &str, vector<int> &regs) {
+ geometry->getLabelRegions(str, regs);
+ }
 
  /*! \brief User scoring function for accumulation of results and VRT implementation
 

HEN_HOUSE/egs++/egs_base_geometry.cpp

@@ -891,16 +891,58 @@ void EGS_BaseGeometry::addBooleanProperty(int bit, int start, int end,
  }
 }
 
-void EGS_BaseGeometry::getLabelRegions(const string &str, vector<int> &regs) {
+// Gets region numbers from a string
+// Pushes the regions onto the array regs
+void EGS_BaseGeometry::getNumberRegions(const string &str, vector<int> &regs) {
+
+ if(!str.empty()) {
+
+ // Tokenize the input string
+ vector<string> tokens;
+ const char *ptr = str.c_str();
+ do {
+ const char *begin = ptr;
+ while (*ptr != ' ' && *ptr) {
+ ptr++;
+ }
+ tokens.push_back(string(begin, ptr));
+ }
+ while (*ptr++ != '\0');
 
- // get all regions lists for this named label
- for (int i=0; i<labels.size(); i++) {
- if (labels[i].name.compare(str) == 0) {
- regs.insert(regs.end(), labels[i].regions.begin(), labels[i].regions.end());
+ for (int i=0; i<tokens.size(); i++) {
+ // Search for tokens that are numbers, not strings
+ // Push the region numbers onto the regions array
+ if(tokens[i].find_first_not_of(" -0123456789") == std::string::npos) {
+ regs.push_back(atoi(tokens[i].c_str()));
+ }
  }
  }
+}
 
- // sort region list and remove duplicates
+void EGS_BaseGeometry::getLabelRegions(const string &str, vector<int> &regs) {
+
+ // Tokenize the input string - this allows for multiple labels
+ vector<string> tokens;
+ const char *ptr = str.c_str();
+ do {
+ const char *begin = ptr;
+ while (*ptr != ' ' && *ptr) {
+ ptr++;
+ }
+ tokens.push_back(string(begin, ptr));
+ }
+ while (*ptr++ != '\0');
+
+ // Get all regions lists for this named label
+ for (int j=0; j<tokens.size(); j++) {
+ for (int i=0; i<labels.size(); i++) {
+ if (labels[i].name.compare(tokens[j]) == 0) {
+ regs.insert(regs.end(), labels[i].regions.begin(), labels[i].regions.end());
+ }
+ }
+ }
+
+ // Sort region list and remove duplicates
  sort(regs.begin(), regs.end());
  regs.erase(unique(regs.begin(), regs.end()), regs.end());
 }

HEN_HOUSE/egs++/egs_base_geometry.h

@@ -636,6 +636,9 @@ class EGS_EXPORT EGS_BaseGeometry {
  EGS_Float getBoundaryTolerance() {
  return boundaryTolerance;
  };
+
+ /*! \brief Get a list of all the regions labeled with a number */
+ virtual void getNumberRegions(const string &str, vector<int> &regs);
 
  /*! \brief Get the list of all regions labeled with \a str */
  virtual void getLabelRegions(const string &str, vector<int> &regs);

HEN_HOUSE/user_codes/egs_chamber/egs_chamber.cpp

@@ -1117,12 +1117,15 @@ int EGS_ChamberApplication::initScoring() {
  while( (aux = options->takeInputItem("calculation geometry")) ) {
  string gname;
  int err = aux->getInput("geometry name",gname);
+
+ string cavString;
  vector<int> cav;
- int err1 = aux->getInput("cavity regions",cav);
-
+ int err1 = aux->getInput("cavity regions",cavString);
+
+ string ecut_rString;
  vector<int> ecut_r;
  EGS_Float ecut_v;
- int err5 = aux->getInput("ECUT regions",ecut_r); // jwu
+ int err5 = aux->getInput("ECUT regions",ecut_rString); // jwu
  int err6 = aux->getInput("ECUT",ecut_v);
 
  string cav_gname;
@@ -1133,30 +1136,15 @@ int EGS_ChamberApplication::initScoring() {
  do_mcav = false;
  }
  int err11, err12;
+ string cs_regString;
  vector<int> cs_reg;
  vector<int> cs_fac;
  if( do_cse ) {
- err11 = aux->getInput("enhance regions",cs_reg);
+ err11 = aux->getInput("enhance regions",cs_regString);
  err12 = aux->getInput("enhancement",cs_fac);
  }
  else{ err11 = 1; err12 = 1; }
 
- if (do_cse && cs_reg[0]<0 && cs_reg[1]<0 && cs_reg.size()==2) {
- int start = -cs_reg[0];
- int end = -cs_reg[1];
- cs_reg.clear();
- for (int i=start; i<=end; i++) {
- cs_reg.push_back(i);
- }
- }
- if (do_cse && cs_fac[0]<0 && cs_fac.size()==1) {
- int tmp = -cs_fac[0];
- cs_fac.clear();
- for (int i=0; i<cs_reg.size(); i++) {
- cs_fac.push_back(tmp);
- }
- }
-
  EGS_Float cmass;
  int err2 = aux->getInput("cavity mass",cmass);
  if( err ) egsWarning("initScoring: missing/wrong 'geometry name' "
@@ -1172,10 +1160,7 @@ int EGS_ChamberApplication::initScoring() {
  if( err12 ) egsWarning("initScoring: missing/wrong 'enhancement' "
  "input\n");
  int err13 = 0;
- if( !err11 && !err12 && (cs_reg.size() != cs_fac.size() )){
- egsWarning("initScoring: number of 'enhance regions' must match 'enhancement'\n");
- err13 = 1;
- }
+
  if( err || err1 ) egsWarning(" --> input ignored\n");
  else {
  EGS_BaseGeometry::setActiveGeometryList(app_index);
@@ -1186,12 +1171,42 @@ int EGS_ChamberApplication::initScoring() {
  " input ignored\n",cav_gname.c_str());
  cg = 0;
  }
-
+ 
  EGS_BaseGeometry *g = EGS_BaseGeometry::getGeometry(gname);
- if( !g ) egsWarning("initScoring: no geometry named %s -->"
+ if( !g ) {
+ egsWarning("initScoring: no geometry named %s -->"
  " input ignored\n",gname.c_str());
+ } else {
+ g->getNumberRegions(cavString, cav);
+ g->getLabelRegions(cavString, cav);
+ g->getNumberRegions(cs_regString, cs_reg);
+ g->getLabelRegions(cs_regString, cs_reg);
+ g->getNumberRegions(ecut_rString, ecut_r);
+ g->getLabelRegions(ecut_rString, ecut_r);
+ }
+
+ if (do_cse && cs_reg[0]<0 && cs_reg[1]<0 && cs_reg.size()==2) {
+ int start = -cs_reg[0];
+ int end = -cs_reg[1];
+ cs_reg.clear();
+ for (int i=start; i<=end; i++) {
+ cs_reg.push_back(i);
+ }
+ }
+ if (do_cse && cs_fac[0]<0 && cs_fac.size()==1) {
+ int tmp = -cs_fac[0];
+ cs_fac.clear();
+ for (int i=0; i<cs_reg.size(); i++) {
+ cs_fac.push_back(tmp);
+ }
+ }
+ if( !err11 && !err12 && (cs_reg.size() != cs_fac.size() )){
+ egsWarning("initScoring: number of 'enhance regions' must match 'enhancement'\n");
+ err13 = 1;
+ }
 
- else {
+ if( g ) {
+
  int nreg = g->regions();
  int *regs = new int [cav.size()];
  int ncav = 0;
@@ -1277,8 +1292,11 @@ int EGS_ChamberApplication::initScoring() {
  if ( do_TmpPhsp ){
  vector<string> subgeom_name;
  int err777 = aux->getInput("sub geometries",subgeom_name);
+ string subgeom_regsString;
  vector<int> subgeom_regs;
- int err888 = aux->getInput("subgeom regions",subgeom_regs);
+ int err888 = aux->getInput("subgeom regions",subgeom_regsString);
+ cg->getNumberRegions(subgeom_regsString, subgeom_regs);
+ cg->getLabelRegions(subgeom_regsString, subgeom_regs);
  if( err777 ){
  egsWarning("initScoring: missing/wrong 'sub geometries' "
  " for geometry '%s'\n", gname.c_str());