/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/egs_brachy.cpp

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/*
################################################################################
#
#  egs_brachy egs_brachy.cpp
#  Copyright (C) 2016 Rowan Thomson, Dave Rogers, Randle Taylor, and Marc
#  Chamberland
#
#  This file is part of egs_brachy
#
#  egs_brachy is free software: you can redistribute it and/or modify it
#  under the terms of the GNU Affero General Public License as published
#  by the Free Software Foundation, either version 3 of the License, or
#  (at your option) any later version.
#
#  egs_brachy is distributed in the hope that it will be useful, but
#  WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
#  Affero General Public License for more details:
#  <http://www.gnu.org/licenses/>.
#
################################################################################
#
#  When egs_brachy is used for publications, please cite our paper:
#  M. J. P. Chamberland, R. E. P. Taylor, D. W. O. Rogers, and R. M. Thomson,
#  egs brachy: a versatile and fast Monte Carlo code for brachytherapy,
#  Phys. Med. Biol. 61, 8214-8231 (2016).
#
################################################################################
#
#  Author:        Randle Taylor, 2016
#
#  Contributors:  Marc Chamberland
#                 Dave Rogers
#                 Rowan Thomson
#
################################################################################
*/
 
#include <algorithm>
#include <fstream>
#include <string>
#include <iomanip>
#include <assert.h>
#include <sys/stat.h>
#include "gzstream.h"
#include "zlib.h"
 
#include "egs_brachy.h"
#include "egs_ausgab_object.h"
#include "egs_rndm.h"
#include "egs_run_control.h"
 
 
using namespace std;
 
/* taken from egs_advance_application.cpp for outputData functions */
#define egsGetRNGPointers F77_OBJ_(egs_get_rng_pointers,EGS_GET_RNG_POINTERS)
extern __extc__ void egsGetRNGPointers(EGS_I32 *, EGS_I32 *);
#define egsGetRNGArray F77_OBJ_(egs_get_rng_array,EGS_GET_RNG_ARRAY)
extern __extc__ void egsGetRNGArray(EGS_Float *);
#define egsSetRNGState F77_OBJ_(egs_set_rng_state,EGS_SET_RNG_STATE)
extern __extc__ void egsSetRNGState(const EGS_I32 *, const EGS_Float *);
#define egsGetSteps F77_OBJ_(egs_get_steps,EGS_GET_STEPS)
extern __extc__ void egsGetSteps(double *, double *);
#define egsSetSteps F77_OBJ_(egs_set_steps,EGS_SET_STEPS)
extern __extc__ void egsSetSteps(const double *, const double *);
#define egsOpenUnits F77_OBJ_(egs_open_units,EGS_OPEN_UNITS)
extern __extc__ void egsOpenUnits(const EGS_I32 *);
#define egsGetElectronData F77_OBJ_(egs_get_electron_data,EGS_GET_ELECTRON_DATA)
extern __extc__ void egsGetElectronData(void (*func)(EGS_I32 *,EGS_Float *,
                                        EGS_Float *,EGS_Float *,EGS_Float *),const EGS_I32 *,const EGS_I32 *);
#define egsGetPhotonData F77_OBJ_(egs_get_photon_data,EGS_GET_PHOTON_DATA)
extern __extc__ void egsGetPhotonData(void (*func)(EGS_I32 *,EGS_Float *,
                                      EGS_Float *,EGS_Float *,EGS_Float *),const EGS_I32 *,const EGS_I32 *);
/* end taken from egs_advance_application.cpp for outputData functions */
 
extern "C" void F77_OBJ_(egs_scale_xcc,EGS_SCALE_XCC)(const int *,const EGS_Float *);
extern "C" void F77_OBJ_(egs_scale_bc,EGS_SCALE_BC)(const int *,const EGS_Float *);
extern "C" void F77_OBJ_(egs_bcse,EGS_BCSE)(const int *,const EGS_Float *);
extern "C" void F77_OBJ_(egs_uniform_photons,EGS_UNIFORM_PHOTONS)(const int *,const EGS_Float *);
 
void printParticleWithSpherical(EGS_Particle p) {
    EGS_Float x,y,z, r, R, theta, phi;
 
    x = p.x.x;
    y = p.x.y;
    z = p.x.z;
 
    r = sqrt(x*x + y*y);
    R = sqrt(x*x + y*y + z*z);
    theta = acos(z/R)*180/M_PI;
    phi = atan2(y, x)*180/M_PI;
 
    PRINT_PARTICLE_WITH_DIR(p);
    cout << " R           = " << R << "\n";
    cout << " r           = " << r << "\n";
    cout << " z           = " << z << "\n";
    cout << " theta (deg) = " << theta << "\n";
    cout << " phi (deg)   = " << phi << "\n";
 
}
 
 
string EB_Application::revision = "$Revision: 0.9.1 $";
 
const EGS_Float EB_Application::DEFAULT_BCSE_FACTOR = 100;
 
 
void EB_Application::describeUserCode() const {
    egsInformation(
        "\n               ***************************************************"
        "\n               *                                                 *"
        "\n               *                  egs_brachy                     *"
        "\n               *                                                 *"
        "\n               ***************************************************"
        "\n\n");
    egsInformation("This is EB_Application %s based on\n"
                   "      EGS_AdvancedApplication %s\n\n",
                   egsSimplifyCVSKey(revision).c_str(),
                   egsSimplifyCVSKey(base_revision).c_str());
}
 
void EB_Application::describeSimulation() {
 
    if (!geometry && !source) {
        return;
    }
 
    egsInformation("\n\negs_brachy Run Mode Information\n%s\n\n",string(80,'=').c_str());
    egsInformation("Run mode                                   =  %s\n", run_mode_name.c_str());
    egsInformation("Single generator  (may be overriden later) =  %s\n", single_generator ? "yes" :"no");
    if (gcr_phantom) {
        egsInformation(
            "getCurrentResult phantom/reg               =  %s %d",
            gcr_phantom->geometry->getName().c_str(),
            gcr_phantom_reg
        );
    }
 
    egsInformation("\n\negs_brachy Geometry Information\n%s\n\n", string(80,'=').c_str());
 
    ginfo.printInfo();
 
    egsInformation("\n\negs_brachy Phantom Details\n%s\n\n", string(80,'=').c_str());
    egsInformation("                              |                      |           |              |  Sph (Rmin, Rmax)    |                      |   \n");
    egsInformation("                              |                      |           |  Avg Vox Vol |   RZ (Rmin, Rmax)    |   RZ (Zmin, Zmax)    |   \n");
    egsInformation("Name                          |      Type            |   Nreg    |    / cm^3    |  XYZ (Xmin, Xmax)    |  XYZ (Ymin, Ymax)    | XYZ (Zmin, Zmax)\n");
    egsInformation("%s\n", string(145, '-').c_str());
 
    for (size_t p=0; p < phantom_geoms.size(); p++) {
 
        EB_Phantom *phant = phantom_geoms[p];
        EGS_BaseGeometry *geom = phant->geometry;
 
        string type = geom->getType();
 
        if (type == "EGS_XYZGeometry") {
            int nx, ny, nz;
            nx = geom->getNRegDir(EB_Phantom::XDIR);
            ny = geom->getNRegDir(EB_Phantom::YDIR);
            nz = geom->getNRegDir(EB_Phantom::ZDIR);
 
            EGS_Float xmin, xmax, ymin, ymax, zmin, zmax;
            xmin = geom->getBound(EB_Phantom::XDIR, 0);
            xmax = geom->getBound(EB_Phantom::XDIR, nx);
            ymin = geom->getBound(EB_Phantom::YDIR, 0);
            ymax = geom->getBound(EB_Phantom::YDIR, ny);
            zmin = geom->getBound(EB_Phantom::ZDIR, 0);
            zmax = geom->getBound(EB_Phantom::ZDIR, nz);
 
            egsInformation(
                "%-30s| %20s | %9d | %12.5G | (%8.3F, %8.3F) | (%8.3F, %8.3F) | (%8.3F, %8.3F)\n",
                geom->getName().c_str(), type.c_str(), geom->regions(), phant->avgVoxelVol(),
                xmin, xmax, ymin, ymax, zmin, zmax
            );
 
        } else if (type == "EGS_RZ") {
            int nr, nz;
            nr = geom->getNRegDir(EGS_RZGeometry::RDIR);
            nz = geom->getNRegDir(EGS_RZGeometry::ZDIR);
 
            EGS_Float rmin, rmax, zmin, zmax;
            rmin = geom->getBound(EGS_RZGeometry::RDIR, 0);
            rmax = geom->getBound(EGS_RZGeometry::RDIR, nr-1);
            zmin = geom->getBound(EGS_RZGeometry::ZDIR, 0);
            zmax = geom->getBound(EGS_RZGeometry::ZDIR, nz-1);
 
            egsInformation(
                "%-30s| %20s | %9d | %12.5G | (%8.3F, %8.3F) | (%8.3F, %8.3F) |\n",
                geom->getName().c_str(), type.c_str(), geom->regions(), phant->avgVoxelVol(),
                rmin, rmax, zmin, zmax
            );
        } else if (type == "EGS_cSphericalShell" || type == "EGS_cSpheres") {
            type = (type == "EGS_cSphericalShell" ? "SphSh" : "Sph");
 
            int nr = geom->getNRegDir(0);
 
            EGS_Float rmin, rmax;
            rmin = geom->getBound(EGS_cSpheres::RDIR, 0);
            rmax = geom->getBound(EGS_cSpheres::RDIR, nr);
 
            egsInformation(
                "%-30s| %20s | %9d | %12.5G | (%8.3F, %8.3F) |                      | \n",
                geom->getName().c_str(), type.c_str(), geom->regions(), phant->avgVoxelVol(),
                rmin, rmax
            );
        } else {
            egsInformation(
                "%-30s| %20s | %9d | %12.5G |                      |                      | \n",
                geom->getName().c_str(), type.c_str(), geom->regions(), phant->avgVoxelVol(),
                -1, -1
            );
        }
 
    if (type == "EGS_XYZGeometryT") {
            egsWarning("\n***WARNING***\nPhantom of type transformed XYZ geometry used. The number of voxels in each direction and their bounds in the egslog, 3ddose, and egsphant files will be incorrect due to current limitations of the egs++ geometry library.\n***WARNING***\n");
        }
 
    }
 
    egsInformation("\n\negs_brachy Volume correction details\n%s\n", string(80, '-').c_str());
 
    egsInformation("\nSource specific volume correction details\n%s\n", string(80, '-').c_str());
    source_vc_results.outputResults("Source");
 
    egsInformation("\nExtra volume correction details\n%s\n", string(80, '-').c_str());
    gen_vc_results.outputResults("Extra");
 
    egsInformation("\nFile volume correction details\n%s\n", string(80, '-').c_str());
    file_vc_results.outputResults();
 
    egsInformation("\n\n");
    if (geometry) {
        geometry->printInfo();
    }
 
    if (source) {
        egsInformation("\n\negs_brachy Source Information\n%s\n", string(80,'=').c_str());
        egsInformation("%s\n\n", source->getSourceDescription());
        egsInformation("Number of source locations = %d\n", source_transforms.size());
        egsInformation("Single source generator    = %s\n", (single_generator ? "yes" : "no"));
        egsInformation("Source | Location (x cm, y cm, z cm)  | Rotated | Weight\n%s\n", string(80,'-').c_str());
        for (size_t tt =0; tt < source_transforms.size(); tt++) {
            EGS_Vector trans = source_transforms[tt]->getTranslation();
            egsInformation(
                "%6d | ( % 7.3F, % 7.3F, % 7.3F) |  %5s  | % 7.2G\n",
                tt+1, trans.x, trans.y, trans.z,
                source_transforms[tt]->hasRotation() ? "true":"false",
                source_weights[tt]
            );
        }
    }
 
    if (rndm) {
        egsInformation("\n\n");
        rndm->describeRNG();
    }
 
    if (a_objects_list.size() > 0) {
        egsInformation("The following ausgab objects are included in the simulation\n");
        egsInformation("===========================================================\n\n");
        for (size_t j=0; j<a_objects_list.size(); ++j) {
            egsInformation("%s",a_objects_list[j]->getObjectDescription());
        }
        egsInformation("\n\n");
    }
 
    printIncludedFiles();
 
    if (final_job) {
        helpInit(0,false);
    }
}
 
bool containsInclude(string str) {
    string::iterator end_pos = std::remove(str.begin(), str.end(), ' ');
    str.erase(end_pos, str.end());
    size_t found = str.find("includefile");
    return found != string::npos;
}
 
void EB_Application::printIncludedFiles() {
 
 
    string fname = constructIOFileName(".egsinp", false);
    egsInformation("\n\nIncluded Files\n%s\n", string(80,'=').c_str());
    egsInformation("Input file:\n\t%s\n", fname.c_str());
    egsInformation("The following files were included in this simulation:\n");
    ifstream inf(fname.c_str());
 
    string line;
    while (inf) {
        getline(inf, line);
        if (containsInclude(line)) {
            egsInformation("\t%s\n", muen::trim(line).c_str());
        }
    };
 
}
 
 
int EB_Application::initGeometry() {
    // override default initGeometry so we can manually create our own geometry
    // which will allow us to track region numbers for each geometry object individually
 
    timing_blocks.addTimer("egs_brachy::initGeometry");
 
    EGS_Input *ginput = input->getInputItem("geometry definition");
 
    if (!ginput) {
        egsWarning("EB_Application::createGeometry: no geometry specification in this input\n");
        egsFatal("Simulation stopped\n");
    }
 
    int err = ginfo.initializeFromInput(ginput);
    if (err) {
        egsWarning("EB_Application::createGeometry: incomplete or incorrect geometry specification\n");
        delete ginput;
        egsFatal("Simulation stopped\n");
    }
 
    err = EGS_AdvancedApplication::initGeometry();
 
    if (err) {
        egsWarning("Failed to create a geometry from input file\n");
        delete ginput;
        egsFatal("Simulation stopped\n");
    }
    
    geometry->ref();
 
    ginfo.setGeometryIndexes(geometry);
 
 
 
    if (run_mode == RM_SUPERPOSITION) {
        if (ginfo.source_envelope_name == "") {
            egsFatal("Missing 'source envelope geometry' input required for superposition mode\n");
        }
 
        source_envelope_geom = EGS_BaseGeometry::getGeometry(ginfo.source_envelope_name);
        if (!source_envelope_geom) {
            egsFatal("source envelope geometry '%s' can not be found\n", ginfo.source_envelope_name.c_str());
        }
 
        if (source_envelope_geom->getType() != "EGS_ASwitchedEnvelope") {
            egsFatal("You must use an %s source envelope geometry type for superposition mode\n", "EGS_ASwitchedEnvelope");
        }
        superpos_geom = static_cast<EGS_ASwitchedEnvelope *>(source_envelope_geom);
    }else{
        for (int gg=0; gg < ginfo.ngeom; gg++) {
            GeomRegionInfo gr = ginfo.ordered_geom_data[gg];
            if (gr.type == "EGS_ASwitchedEnvelope"){
                egsFatal("EGS_ASwitchedEnvelope should not be used when not using 'run mode = superposition\n");
            }
        }
    }
 
 
    err = initSourceTransforms();
    if (err) {
        egsFatal("Failed to initiate source locations\n");
    }
 
    delete ginput;
 
    err = createPhantoms();
    if (err) {
        egsWarning("Failed to create phantom objects\n");
        egsFatal("Simulation stopped\n");
    }
 
    err = correctVolumes();
 
    timing_blocks.stopTimer();
    return 0;
 
}
 
vector<EGS_AffineTransform *> EB_Application::createTransforms(EGS_Input *input) {
 
    vector<EGS_AffineTransform *> transforms;
    if (input) {
        EGS_Input *trans_inp;
 
        while ((trans_inp = input->takeInputItem("transformation"))) {
            EGS_AffineTransform *transform = EGS_AffineTransform::getTransformation(trans_inp);
            if (!transform) {
                egsWarning("Invalid transform input given\n");
 
            }
            transforms.push_back(transform);
            delete trans_inp;
 
        }
    }
 
    return transforms;
 
}
 
int EB_Application::initSourceTransforms() {
 
    if (!input) {
        return -1;
    }
 
    EGS_Input *source_inp = input->getInputItem("source definition");
 
    if (!source_inp) {
        return -1;
    }
 
 
    EGS_Input *source_loc_inp = source_inp->takeInputItem("transformations");
 
    if (source_loc_inp) {
        source_transforms = createTransforms(source_loc_inp);
        delete source_loc_inp;
    }
 
    if (source_transforms.size() == 0) {
        EGS_AffineTransform *unity_trans = new EGS_AffineTransform();
        source_transforms.push_back(unity_trans);
        egsWarning("EB_Application:: missing or invalid source `transformations` input item. Assuming single source at origin\n");
    }
    nsources = (int)source_transforms.size();
    base_transform = source_transforms[0];
    base_transform_inv = new EGS_AffineTransform(base_transform->inverse());
 
    EGS_Input *source_overlap_inp = source_inp->takeInputItem("source overlap check");
    if (source_overlap_inp){
        int err = checkSourceOverlaps(source_overlap_inp);
        if (err){
            egsFatal("EB_Application:: checkSourceOverlaps detected an error.");
        }
    }
 
    return 0;
 
}
 
int EB_Application::checkSourceOverlaps(EGS_Input *inp) {
 
    timing_blocks.addTimer("egs_brachy::checkSourceOverlaps");
 
    vector<string> yn_choices;
    yn_choices.push_back("no");
    yn_choices.push_back("yes");
    bool check_source_overlap = (bool)inp->getInput("check source overlaps", yn_choices, 0);
 
    if (!check_source_overlap || source_transforms.size() <= 1){
        /* not requested or only 1 source so no need to check for overlap */
        timing_blocks.stopTimer();
        return 0;
    }
 
    vector<string> mode_choices;
    mode_choices.push_back("warning");
    mode_choices.push_back("fatal");
 
    bool fatal = (bool)inp->getInput("warning mode", mode_choices, 1);
 
    EGS_Input *shape_inp = inp->takeInputItem("shape");
 
    EGS_BaseShape *bounds = EGS_BaseShape::createShape(shape_inp);
 
    if (!shape_inp) {
        egsWarning("egs_brachy::checkSourceOverlaps - no `shape` input found.\n");
        return 1;
    }
 
    EGS_Float bounds_volume = ebvolcor::getShapeVolume(shape_inp);
    if (bounds_volume < 0){
        egsWarning("egs_brachy::checkSourceOverlaps - Unable to get shape volume.");
        return 1;
    }
 
    vector<string> excluded;
    inp->getInput("excluded geometries", excluded);
 
    EGS_Float density;
    int err = inp->getInput("density of random points (cm^-3)", density);
    if (err) {
        egsWarning("egs_brachy::checkSourceOverlaps - The volume correction 'density of random points (cm^-3)' input was not found. Using 1E6/cm^3\n");
        density = 1E6;
    }
    EGS_I64 npoints = (EGS_I64)floor(max(1., density*bounds_volume));
 
 
    EGS_RandomGenerator *rng = EGS_RandomGenerator::defaultRNG();
    EGS_Vector point;
 
    /* find first source geometry defined */
    EGS_BaseGeometry *base_source = 0;
    string base_source_name;
    for (int gg=0; gg < ginfo.ngeom; gg++) {
        GeomRegionInfo gr = ginfo.ordered_geom_data[gg];
        if (find(ginfo.source_names.begin(), ginfo.source_names.end(), gr.name) != ginfo.source_names.end()){
            base_source = EGS_BaseGeometry::getGeometry(gr.name);
            base_source_name = gr.name;
            break;
        }
    }
    if (!base_source){
        egsFatal("egs_brachy::checkSourceOverlaps - did not find base source geometry");
    }
 
    /* now lets see if our base source is in an autoenvelope */
    EGS_AffineTransform base_transform;
    EGS_AffineTransform inv_base_transform;
    for (int gg=0; gg < ginfo.ngeom; gg++) {
        GeomRegionInfo gr = ginfo.ordered_geom_data[gg];
        if (find(gr.children.begin(), gr.children.end(), base_source_name) != gr.children.end()){
            /* base source is child of this geometry */
            if (gr.type != "EGS_AEnvelope" && gr.type != "EGS_ASwitchedEnvelope"){
                base_transform = *source_transforms[0];
                inv_base_transform = base_transform.inverse();
            }
            break;
        }
    }
 
    vector<int> overlaps;
 
    for (EGS_I64 i=0; i < npoints; i++) {
 
        /* Generate a point and check if its contained within base source. If
         * it's not actually in a source, go back and generate a new point.  */
        point = bounds->getRandomPoint(rng);
        base_transform.transform(point);
        if (base_source->isWhere(point) < 0) {
            continue;
        }
        inv_base_transform.transform(point);
 
        for (size_t sa_idx = 0; sa_idx < source_transforms.size(); sa_idx++){
 
            overlaps.clear();
 
            EGS_Vector transformed(point);
 
            // transform from point relative to origin to point
            // relative to source A we are checking against other sources (B)
            source_transforms[sa_idx]->transform(transformed);
 
            for (size_t sb_idx = sa_idx + 1; sb_idx < source_transforms.size(); sb_idx++){
 
                EGS_Vector inner_transformed(transformed);
 
                // use current source we are checking transform to back relative to origin
                source_transforms[sb_idx]->inverse().transform(inner_transformed);
                base_transform.transform(inner_transformed);
                if (base_source->isWhere(inner_transformed) >= 0) {
                    /* point falls within Source A & B so they must be overlapping */
                    overlaps.push_back(sa_idx);
                    overlaps.push_back(sb_idx);
                    goto overlap_found;
                }
            }
        }
    }
 
overlap_found:
 
    if (rng){
        delete rng;
    }
    if (shape_inp){
        delete shape_inp;
    }
    timing_blocks.stopTimer();
 
    if (overlaps.size() > 1){
        string msg = "Possible overlap of sources: ";
        for (int i=0; i < overlaps.size(); i++){
            msg += to_string(overlaps[i]);
            if (i != overlaps.size() -1 ){
                msg += ", ";
            }
        }
        egsInformation((msg+"\n").c_str());
    }
 
    if (overlaps.size() > 1){
        return fatal ? 1 : 0;
    }
 
    return 0;
}
 
int EB_Application::correctVolumes() {
 
 
    timing_blocks.addTimer("egs_brachy::correctVolumes");
    EGS_Input *vol_cor_inp = input->takeInputItem("volume correction");
    if (!vol_cor_inp) {
        egsWarning("Input item `volume correction` was not found\n");
        return 1;
    }
 
    if (run_mode == RM_SUPERPOSITION) {
        for (int i=0; i < nsources; i++) {
            superpos_geom->activateByIndex(i);
        }
    }
    ebvolcor::VolumeCorrector vc(vol_cor_inp, phantom_geoms, geometry, &ginfo, source_transforms);
 
    source_vc_results = vc.runSourceCorrection(timing_blocks);
 
    gen_vc_results = vc.runGeneralCorrection(timing_blocks);
 
    file_vc_results = vc.runFileCorrection(timing_blocks);
 
 
    // automatic volumes now done, now get any manually specified volumes
    EGS_Input *ij;
    vector<string> user_vols;
 
    while ((ij = vol_cor_inp->takeInputItem("phantom region volumes")) != 0) {
 
        string phant_name;
        ij->getInput("phantom name", phant_name);
        EB_Phantom *phant = getPhantomByName(phant_name);
        if (!phant) {
            egsFatal("`phanton region volume` specified for phantom `%s` which does not exist.", phant_name.c_str());
        }else{
            user_vols.push_back(phant_name);
        }
 
        vector<int> phantom_regs;
        ij->getInput("region numbers", phantom_regs);
 
        vector<EGS_Float> phantom_vols;
        ij->getInput("region volumes", phantom_vols);
 
        if (phantom_regs.size() != phantom_vols.size()){
            egsFatal(
                "Mismatched number of inputs for `region numbers` and `region volumes` for phantom `%s`",
                phant_name.c_str()
            );
        }else if (phantom_regs.size() == 0){
            egsFatal(
                "Missing `region numbers` or `region volumes` input for `phantom region volumes` block for phantom `%s`",
                phant_name.c_str()
            );
        }
 
        for (size_t r = 0; r < phantom_regs.size(); r++){
            phant->setCorrectedVolume(phantom_regs[r], phantom_vols[r]);
        }
 
 
        delete ij;
    }
 
    /* now we check to ensure that user has specified volumes for any phantoms
     * which require it */
    for (size_t p=0; p < phantom_geoms.size(); p++){
        EB_Phantom *phant = phantom_geoms[p];
        string name = phant->geometry->getName();
        string type = phant->geometry->getType();
        if (phant->needs_user_geoms && find(user_vols.begin(), user_vols.end(), name) == user_vols.end()){
            egsFatal(
                "Missing `phantom region volume` block for phantom `%s`."
                "Phantoms of type `%s` can not calculate volumes automatically.",
                name.c_str(),
                type.c_str()
            );
        }
    }
 
    delete vol_cor_inp;
 
    timing_blocks.stopTimer();
 
    return 0;
 
}
 
 
// set up Phantom objects for any geometries that user has requested scoring for
int EB_Application::createPhantoms() {
 
    for (size_t idx=0; idx < ginfo.phantom_names.size(); idx++) {
        string name = ginfo.phantom_names[idx];
 
        EGS_BaseGeometry *phant_geom = EGS_BaseGeometry::getGeometry(name);
        if (!phant_geom) {
            egsInformation("\n\nUnable to find phantom geometry `%s`.\n\n    This is a fatal error\n\n", name.c_str());
            return 1;
        }
 
 
        set<int> global_regions;
 
        for (int reg=0; reg < ginfo.nreg_total; reg++) {
            if (ginfo.phantomFromRegion(reg) == (int)idx) {
                global_regions.insert(reg);
            }
        }
 
        if (global_regions.size()==0) {
            egsFatal(
                "EB_Application::createPhantoms - No phantom regions detected for geometry '%s'.\n"
                "Are you sure your phantom was included in the final simulation geometry?\n",
                (phant_geom->getName()).c_str()
            );
        }
        EB_Phantom *phantom = new EB_Phantom(this, phant_geom, global_regions, nsources, &pevent_pub);
        phantom_geoms.push_back(phantom);
 
    }
 
    return 0;
 
}
 
 
int EB_Application::initSource() {
 
 
    EGS_Input *source_inp = input->getInputItem("source definition");
 
    if (!source_inp) {
        return -1;
    }
 
 
    /* check if user has defined source weighting */
    source_inp->getInput("source weights", source_weights);
 
    // fill up source_weights so it always has length==nsources
    while ((int)source_weights.size() < nsources) {
        source_weights.push_back(1);
    }
 
    // normalize weights
    double max_wt = *max_element(source_weights.begin(), source_weights.end());
    vector<EGS_Float>::iterator it =source_weights.begin();
    for (; it != source_weights.end(); ++it) {
        *it /= max_wt;
    }
 
    int err = EGS_AdvancedApplication::initSource();
    if (err) {
        egsFatal("Failed to initialize source\n");
    }
 
    string stype = source->getObjectType();
    is_phsp_source = stype == "EGS_PhspSource" || stype == "EB_IAEAPHSPSource";
 
    if (is_phsp_source && !single_generator) {
        single_generator = true;
        egsInformation("Phase space being used. Overriding requested 'single generator = no' parameter. Setting to 'yes'\n");
    }
 
 
    return err;
 
}
 
int EB_Application::initSimulation() {
 
    timing_blocks.addTimer("egs_brachy::initSimulation");
    initRunMode();
 
    int res = EGS_AdvancedApplication::initSimulation();
 
    if (run_mode == RM_VC_ONLY) {
        output_3ddose_files = false;
        describeSimulation();
        finishSimulation();
        timing_blocks.stopTimer();
        return 1;
    }
 
    timing_blocks.stopTimer();
    return res;
 
}
 
int EB_Application::initRunControl() {
 
    vector<string> format_choices;
    format_choices.push_back("text");
    format_choices.push_back("gzip");
    EGS_Input *run_control = input->getInputItem("run control");
    int format = run_control->getInput("egsdat file format", format_choices, 0);
    output_egsdat_format = format == 0 ? "text" : "gzip";
 
    if (run) {
        delete run;
    }
    if (simple_run) {
        run = new EGS_RunControl(this);
    }
    else if (uniform_run) {
        run = new EB_UniformRunControl(this, output_egsdat_format);
    }
    else {
        run = EGS_RunControl::getRunControlObject(this);
    }
    if (!run) {
        return 1;
    }
    return 0;
}
 
int EB_Application::initRunMode() {
    timing_blocks.addTimer("egs_brachy::initRunMode");
 
    string run_mode_inp;
    EGS_Input *rm = input->takeInputItem("run mode");
    if (!rm) {
        timing_blocks.stopTimer();
        return 1;
    }
 
    vector<string> choices;
    choices.push_back("normal"); // RM_NORMAL
    choices.push_back("superposition"); //RM_SUPERPOSITION
    choices.push_back("volume correction only"); //RM_VC_ONLY
 
    run_mode = (RunMode)rm->getInput("run mode", choices, (int)RM_NORMAL);
    run_mode_name = choices[run_mode];
 
 
    vector<string> yn_choices;
    yn_choices.push_back("no");
    yn_choices.push_back("yes");
 
    single_generator = (bool)rm->getInput("single generator", yn_choices, 1);
 
    delete rm;
 
    timing_blocks.stopTimer();
 
    return 0;
 
}
 
int EB_Application::initCrossSections() {
    timing_blocks.addTimer("egs_brachy::initCrossSections");
    EGS_Input *transportp = input->getInputItem("MC transport parameter");
    if (!transportp) {
        transportp = input->getInputItem("transport parameter");
    }
 
    if (!transportp) {
        egsFatal("Missing `MC transport parameter` input item\n");
        return 1;
    }
 
    int err = transportp->getInput("fluorescent photon cutoff", flu_cutoff);
    if (err) {
        flu_cutoff = 0.001;
    }
 
    int ret = EGS_AdvancedApplication::initCrossSections();
 
    global_ecut = the_bounds->ecut;
    global_pcut = the_bounds->pcut;
 
    err = transportp->getInput("source ecut", source_ecut);
    if (err) {
        source_ecut = global_ecut;
    }
 
    err = transportp->getInput("source pcut", source_pcut);
    if (err) {
        source_pcut = global_pcut;
    }
 
    egsInformation("\negs_brachy transport parameter options:\n%s\n",string(80,'-').c_str());
    egsInformation("Fluorescent photon cutoff                         %.3G\n", flu_cutoff);
    egsInformation("Source PCUT                                       %.3G\n", source_pcut);
    egsInformation("Source ECUT                                       %.3G\n", source_ecut);
 
    timing_blocks.stopTimer();
    return ret;
}
 
 
int EB_Application::initScoring() {
 
    timing_blocks.addTimer("egs_brachy::initScoring");
 
    EGS_Input *options = input->takeInputItem("scoring options");
 
    if (options) {
 
        initGCRScoring(options);
        initAusgabCalls();
        initTrackLengthScoring(options);
        initEDepScoring(options);
        initScatScoring(options);
        initXCCScaling(options);
        initDoseScaling(options);
        initSpectrumScoring(options);
 
        escoring = new EnergyScoringStats(&pevent_pub);
 
        initPHSPScoring(options);
        initOutputFiles(options);
 
 
        delete options;
    } else {
        egsFatal("\n\nMissing input section 'scoring options'\n\n");
    }
 
    initVarianceReduction();
 
    timing_blocks.stopTimer();
    return 0;
}
 
void EB_Application::initGCRScoring(EGS_Input *inp) {
 
    gcr_phantom = 0;
    gcr_phantom_reg = 0;
 
    vector<string> gcr_inp;
    int err = inp->getInput("current result phantom region", gcr_inp);
    if (err || gcr_inp.size()==0) {
        gcr_phantom = phantom_geoms[0];
        gcr_phantom_reg = 0;
        return;
    }
 
 
    // user requested a phantom, find it
    if (gcr_inp.size() >= 1) {
        for (size_t idx=0; idx < ginfo.phantom_names.size(); idx++) {
            if (ginfo.phantom_names[idx] == gcr_inp[0]) {
                gcr_phantom = phantom_geoms[idx];
            }
        }
    }
 
    // couldn't find requested phantom
    if (!gcr_phantom) {
        egsWarning(
            "Did not find '%s' phantom for getCurrentResult. Using phantom %s\n",
            gcr_inp[0].c_str(), ginfo.phantom_names[0].c_str()
        );
        gcr_phantom = phantom_geoms[0];
        gcr_phantom_reg = 0;
        return;
    }
 
    // user has also requested a region
    if (gcr_inp.size() > 1) {
        int ireg = atol(gcr_inp[1].c_str());
        if (ireg > 0 && ireg < gcr_phantom->geometry->regions()) {
            gcr_phantom_reg = ireg;
        }
    }
 
}
 
EB_Phantom* EB_Application::getPhantomByName(string name){
    for (size_t idx=0; idx < ginfo.phantom_names.size(); idx++) {
        if (ginfo.phantom_names[idx] == name) {
            return phantom_geoms[idx];
        }
    }
 
    return 0;
}
 
 
void EB_Application::initOutputFiles(EGS_Input *inp) {
 
    vector<string> yn_choices;
    yn_choices.push_back("no");
    yn_choices.push_back("yes");
    output_egsphant = (bool)inp->getInput("output egsphant files", yn_choices, 0);
    output_voxinfo = (bool)inp->getInput("output voxel info files", yn_choices, 0);
    inp->getInput("output volume correction files for phantoms", output_volcor_phantoms);
 
    vector<string> format_choices;
    format_choices.push_back("text");
    format_choices.push_back("gzip");
 
    int format = inp->getInput("dose file format", format_choices, 0);
    output_dose_format = format == 0 ? "text" : "gzip";
 
    format = inp->getInput("egsphant file format", format_choices, 0);
    output_egsphant_format = format == 0 ? "text" : "gzip";
 
    format = inp->getInput("voxel info file format", format_choices, 0);
    output_voxinfo_format = format == 0 ? "text" : "gzip";
 
    format = inp->getInput("volume correction file format", format_choices, 0);
    output_volcor_format = format == 0 ? "text" : "gzip";
 
    inp->getInput("record initial particle positions", record_n_init);
 
}
 
void EB_Application::initPHSPScoring(EGS_Input *inp) {
 
    EGS_Input *phsp_inp = inp->takeInputItem("phsp scoring");
 
    if (phsp_inp) {
        phsp = new PHSPControl(phsp_inp, base_transform_inv, this, &pevent_pub);
    }
 
}
 
 
int EB_Application::initVarianceReduction() {
 
    timing_blocks.addTimer("egs_brachy::initVarianceReduction");
 
    egsInformation("\n\negs_brachy Variance Reduction Information\n%s\n\n",string(80,'=').c_str());
 
    EGS_Input *vr = input->takeInputItem("variance reduction");
 
    /* Range rejection on by default in non source objects
     * and off in any source objects */
    global_i_do_rr = true;
    global_e_max_rr = 2.511;
 
    source_i_do_rr = false;
    source_e_max_rr = 0.512;
 
    the_egsvr->i_do_rr = (int)source_i_do_rr;
    the_egsvr->e_max_rr = source_e_max_rr;
 
    if (!vr) {
        egsInformation("Global Range Rejection                           = %s\n",  global_i_do_rr ? "Yes" : "No");
        egsInformation("Global Range Rejection Maximum Energy            = %.3G MeV\n",  global_e_max_rr);
        egsInformation("Source Range Rejection                           = %s\n",  source_i_do_rr ? "Yes" : "No");
        egsInformation("Source Range Rejection Maximum Energy            = %.3G MeV\n",  source_e_max_rr);
        timing_blocks.stopTimer();
        return 1;
    }
 
 
    EGS_Input *ri = vr->takeInputItem("particle recycling");
    if (ri) {
        if (score_scat) {
            egsFatal("Primary-scatter dose scoring is not available with recycling. Please turn off recycling or disable scatter dose scoring.\n");
        }
        egsInformation("Particle Recycling\n");
        recycle_opts = new RecycleOpts(ri);
        recycle_opts->printInfo();
        if (!single_generator) {
            single_generator = true;
            egsInformation("    Overriding requested 'single generator = no' parameter. Setting to 'yes'\n");
        }
        egsInformation("\n");
 
        delete ri;
    }
    
    /* Range rejection */
    vector<string> yn_choices;
    yn_choices.push_back("no");
    yn_choices.push_back("yes");
 
    string old_rr_setting;
    int err = vr->getInput("range rejection", old_rr_setting);
    if (!err) {
        egsFatal(
            "'range rejection' is not a valid setting for egs_brachy.\n"
            "Please use 'global range rejection' and 'source range rejection' settings instead.\n"
        );
    }
 
    EGS_Float old_rr_max_e;
    err = vr->getInput("range rejection max energy", old_rr_max_e);
    if (!err) {
        egsFatal(
            "'range rejection max energy' is not a valid setting for egs_brachy.\n"
            "Please use 'global range rejection max energy' and 'source range rejection max energy' settings instead.\n"
        );
    }
 
 
    global_i_do_rr = vr->getInput("global range rejection", yn_choices, 1);
    egsInformation("Global Range Rejection                           = %s\n",  global_i_do_rr ? "Yes" : "No");
    if (global_i_do_rr) {
        int err = vr->getInput("global range rejection max energy", global_e_max_rr);
        if (err) {
            global_e_max_rr = 2.511;
        }
        if (global_e_max_rr < 0.512) {
            egsFatal("Global Range Rejection max energy must be at least 0.512MeV\n");
        } else {
            egsInformation("Global Range Rejection Maximum Energy            = %.3G MeV\n",  global_e_max_rr);
        }
    }
 
    source_i_do_rr = vr->getInput("source range rejection", yn_choices, 0);
    egsInformation("Source Range Rejection                           = %s\n",  source_i_do_rr ? "Yes" : "No");
    if (source_i_do_rr) {
        int err = vr->getInput("source range rejection max energy", source_e_max_rr);
        if (err) {
            source_e_max_rr = 2.511;
        }
        if (source_e_max_rr < 0.512) {
            egsFatal("Source Range Rejection max energy must be at least 0.512MeV\n");
        } else {
            egsInformation("Source Range Rejection Maximum Energy            = %.3G MeV\n",  source_e_max_rr);
        }
    }
 
    the_egsvr->i_do_rr = source_i_do_rr;
    the_egsvr->e_max_rr = source_e_max_rr;
 
 
    /* Brem Cross Section Enhancement*/
    err = initBCSE(vr);
    egsInformation("BCSE                                      = %s\n",  do_bcse ? "Yes" : "No");
    if (!err) {
        egsInformation(
            "    Brem Cross Section Enhancement medium = %s (%d)\n",
            EGS_BaseGeometry::getMediumName(bcse_med_num), bcse_med_num
        );
        egsInformation("    Brem Cross Section Enhancement factor = %.3G\n", bcse_factor);
    }
 
 
    /* Brem Splitting */
    err = vr->getInput("split brem photons", nbr_split);
    egsInformation("Brem Splitting                            = %s\n",  nbr_split > 1? "Yes" : "No");
    if (!err && nbr_split > 1) {
        do_brem_split = true;
        egsInformation("    Splitting brem photons N times        = %d\n", nbr_split);
        the_egsvr->nbr_split = nbr_split;
    }
 
 
    /* Charged Particle Russian Roulette*/
    err =  initRussianRoulette(vr);
    egsInformation("Charged Particle Russian Roulette         = %s\n", the_egsvr->i_play_RR ? "Yes" : "No");
    if (!err || the_egsvr->i_play_RR) {
 
        if (bcse_factor > 1) {
            the_egsvr->prob_RR = 1./(nbr_split*bcse_factor);
            egsInformation(
                "    Survival probability (1/nbrsplt*bcse) = 1/(%d*%.3G) (%.3G%%)\n",
                nbr_split, bcse_factor,  the_egsvr->prob_RR*100
            );
        } else {
            the_egsvr->prob_RR = 1./nbr_split;
            egsInformation(
                "    Survival probability  (1/nbrsplt)     = 1/%d (%.3G%%)\n",
                nbr_split, the_egsvr->prob_RR*100
            );
        }
    }
 
 
    delete vr;
    timing_blocks.stopTimer();
    return 0;
 
}
 
int EB_Application::initRussianRoulette(EGS_Input *scoring_options) {
 
    vector<string> yn_choices;
    yn_choices.push_back("no");
    yn_choices.push_back("yes");
 
    int play_rr = scoring_options->getInput("russian roulette", yn_choices, 0);
    if (play_rr == 0) {
        return 1;
    }
 
    the_egsvr->i_play_RR = 1;
 
    AusgabCall rr_calls[] = {
        BeforeBrems, AfterBrems,
        BeforeAnnihFlight, AfterAnnihFlight,
        BeforeAnnihRest, AfterAnnihRest,
        FluorescentEvent
    };
 
    int ncalls = sizeof(rr_calls)/sizeof(rr_calls[0]);
    enableAusgabCalls(ncalls, rr_calls);
 
    return 0;
}
 
int EB_Application::initBCSE(EGS_Input *inp) {
 
    vector<string> bcse_inp;
    int err = inp->getInput("bcse medium", bcse_inp);
    if (err || bcse_inp.size()==0) {
        return 1;
    }
 
    bcse_med_num = EGS_BaseGeometry::getMediumIndex(bcse_inp[0]);
    if (bcse_med_num < 0) {
        egsWarning("Requested an unknown medium `%s` for BCSE\n",bcse_inp[0].c_str());
        return 1;
    }
 
 
    if (bcse_inp.size() == 1) {
        bcse_factor = DEFAULT_BCSE_FACTOR;
    } else {
        bcse_factor = atof(bcse_inp[1].c_str());
    }
 
    do_bcse = bcse_factor > 1;
    if (!do_bcse) {
        return 1;
    }
 
    the_egsvr->i_play_RR = 1;
 
    AusgabCall bcse_calls[] = {BeforeBrems, AfterBrems, FluorescentEvent};
    enableAusgabCalls(3, bcse_calls);
 
    int egs_med_num = bcse_med_num+1;
    F77_OBJ_(egs_bcse, EGS_BCSE)(&egs_med_num, &bcse_factor);
 
    return 0;
}
 
void EB_Application::initSpectrumScoring(EGS_Input *scoring_input) {
 
    bool header_printed = false;
 
    while (EGS_Input *spec_inp=scoring_input->takeInputItem("spectrum scoring")) {
 
        if (!header_printed) {
            egsInformation("\n\negs_brachy Spectrum Scoring Information\n%s\n\n",string(80,'=').c_str());
            header_printed = true;
        }
 
        BaseSpectrumScorer *scorer = BaseSpectrumScorer::getSpectrumScorer(spec_inp, source, &ginfo, &pevent_pub);
 
        if (scorer) {
            spectrum_scorers.push_back(scorer);
            egsInformation("Added scorer with title: %s\n", scorer->getInfo().c_str());
        }
        delete spec_inp;
    }
}
 
void EB_Application::clearAusgabCalls() {
    for (size_t call=BeforeTransport; call <= UnknownCall; call++) {
        setAusgabCall((AusgabCall)call, false);
    }
 
}
 
void EB_Application::initAusgabCalls() {
 
 
    clearAusgabCalls();
 
    AusgabCall always_call[] = {BeforeTransport, AfterTransport, FluorescentEvent};
    enableAusgabCalls(3, always_call);
 
}
 
 
 
void EB_Application::initTrackLengthScoring(EGS_Input *scoring_options) {
 
    vector<string> choices;
    choices.push_back("no");
    choices.push_back("yes");
 
    score_tlen = scoring_options->getInput("score tracklength dose", choices, 1);
 
    if (score_tlen) {
        for (size_t p=0; p < phantom_geoms.size(); p++) {
            phantom_geoms[p]->enableTLenScoring();
        }
        initMuenData(scoring_options);
    }
 
}
 
map<string, string> getMuenForMedia(EGS_Input *scoring_options) {
 
    map<string, string> muen_for_med;
 
    vector<string> muen_meds;
    scoring_options->getInput("muen for media", muen_meds);
 
    for (size_t i=0; i < muen_meds.size(); i++) {
        string med_name = muen_meds[i];
        muen_for_med[med_name] = med_name;
    };
 
    EGS_Input *muen_inp;
    while ((muen_inp = scoring_options->takeInputItem("muen for medium"))) {
        string scoring, transport;
        int err = muen_inp->getInput("transport medium", transport);
        if (err) {
            egsFatal("Missing 'transport medium' key in 'muen for medium' block\n");
            delete muen_inp;
        }
        err = muen_inp->getInput("scoring medium", scoring);
        if (err) {
            egsFatal("Missing 'scoring medium' key in 'muen for medium' block\n");
            delete muen_inp;
        }
 
        muen_for_med[transport] = scoring;
 
        delete muen_inp;
    }
 
    return muen_for_med;
 
}
 
void EB_Application::initMuenData(EGS_Input *scoring_options) {
 
    egsInformation("\n\negs_brachy Muen Data Information\n%s\n\n",string(80,'=').c_str());
 
    string muen_file;
    bool missing_muen = scoring_options->getInput("muen file", muen_file) != 0;
    if (missing_muen) {
        egsFatal("\n\nMissing input scoring options: muen file\n\n    This is a fatal error\n\n");
    }
 
    // transport med name -> scoring med name
    media_muen_names = getMuenForMedia(scoring_options);
 
    if (media_muen_names.size()==0) {
        egsWarning(
            "EB_Application:: missing or invalid 'muen for media' input item or 'muen substitution' block(s).\n"
            "   No muen data has been read.\n"
        );
    }
 
    // read muen data file and set media_muen for all media requested
    muen::MuenDataParser dp;
    int err = dp.setMuenFile(muen_file);
    if (err) {
        egsFatal("Failed to read muen data from %s\n",muen_file.c_str());
    }
 
    egsInformation("Read muen data from %s\n", muen_file.c_str());
 
    map<string, string>::iterator mit = media_muen_names.begin();
    for (; mit != media_muen_names.end(); mit++) {
 
        string transport_med = mit->first;
        string scoring_med = mit->second;
        EGS_Interpolator *tmp_muen = dp.getMuenInterpolator(scoring_med);
        if (!tmp_muen) {
            egsFatal("EB_Application::Failed to get muen interpolator for %s\n", scoring_med.c_str());
        }
 
        int med_idx = EGS_BaseGeometry::getMediumIndex(transport_med);
        if (med_idx < 0) {
            egsFatal(
                "EB_Application:: You requested scoring medium %s for transport medium %s but %s"
                " is not present in the geometry\n", scoring_med.c_str(), transport_med.c_str(), transport_med.c_str()
            );
        }
 
        media_muen[med_idx] = tmp_muen;
        egsInformation(
            "Set medium %d (%s) to use muen data: %s\n",
            med_idx, transport_med.c_str(), scoring_med.c_str()
        );
    }
 
 
}
 
void EB_Application::enableAusgabCalls(int ncalls, AusgabCall calls[]) {
    for (int i= 0; i <  ncalls; i++) {
        setAusgabCall(calls[i], true);
    }
 
}
 
void EB_Application::initEDepScoring(EGS_Input *scoring_options) {
    // Set up energy deposition scoring if requested by user
 
    vector<string> choices;
    choices.push_back("no");
    choices.push_back("yes");
 
    score_edep = scoring_options->getInput("score energy deposition", choices, 0);
 
    if (score_edep) {
        for (size_t p=0; p < phantom_geoms.size(); p++) {
            phantom_geoms[p]->enableInteractionScoring();
        }
 
        AusgabCall edep_calls[] = {ExtraEnergy, UserDiscard, PegsCut, EgsCut};
        enableAusgabCalls(4, edep_calls);
    }
}
 
void EB_Application::initScatScoring(EGS_Input *scoring_options) {
    // Set up energy deposition scoring if requested by user
 
    vector<string> choices;
    choices.push_back("no");
    choices.push_back("yes");
 
    score_scat = scoring_options->getInput("score scatter dose", choices, 0);
    if (score_scat && !score_tlen) {
        egsFatal("\nPrimary-scatter dose scoring requires tracklength scoring. Please enable tracklength scoring or disable scatter dose scoring.\n");
    }
 
    if (score_scat && (source_transforms.size() > 1)) {
        egsFatal("\nPrimary-scatter dose scoring is only available in simulations with a single source. Please simulate a single source or disable scatter dose scoring.\n");
    }
 
    if (score_scat && is_phsp_source) {
        egsFatal("\nPrimary-scatter dose scoring is not available with phase-space sources. Please do not use a phase-space source or disable scatter dose scoring.\n");
    }
 
    if (score_scat) {
 
        for (size_t p=0; p < phantom_geoms.size(); p++) {
            phantom_geoms[p]->enableScatterScoring();
        }
 
        AusgabCall photon_scat_calls[] = {
            AfterAnnihFlight, AfterAnnihRest,
            AfterPair, AfterCompton, AfterPhoto, AfterRayleigh,
            FluorescentEvent
        };
 
        int ncalls = sizeof(photon_scat_calls)/sizeof(photon_scat_calls[0]);
        enableAusgabCalls(ncalls, photon_scat_calls);
    }
}
 
void EB_Application::initDoseScaling(EGS_Input *scoring_options) {
 
    EGS_Float scale = 1.;
 
    int err = scoring_options->getInput("dose scaling factor", scale);
 
    if (!err && scale > 0) {
        for (size_t p=0; p < phantom_geoms.size(); p++) {
            phantom_geoms[p]->setDoseScale(scale);
        }
    }
}
 
void EB_Application::initXCCScaling(EGS_Input *scoring_options) {
 
    EGS_Input *scale;
 
    while ((scale = scoring_options->takeInputItem("scale xcc"))) {
        vector<string> tmp;
        int err = scale->getInput("scale xcc",tmp);
        //egsInformation("Found 'scale xcc', err=%d tmp.size()=%d\n",err,tmp.size());
        if (!err && tmp.size() == 2) {
            int imed = EGS_BaseGeometry::getMediumIndex(tmp[0]) + 1;
            if (imed > 0) {
                EGS_Float fac = atof(tmp[1].c_str());
                egsInformation("\n ***** Scaling xcc of medium %d with %G\n",imed,fac);
                F77_OBJ_(egs_scale_xcc,EGS_SCALE_XCC)(&imed,&fac);
            }
        }
        delete scale;
    }
 
    while ((scale = scoring_options->takeInputItem("scale bc"))) {
        vector<string> tmp;
        int err = scale->getInput("scale bc",tmp);
        //egsInformation("Found 'scale xcc', err=%d tmp.size()=%d\n",err,tmp.size());
        if (!err && tmp.size() == 2) {
            int imed = EGS_BaseGeometry::getMediumIndex(tmp[0]) + 1;
            if (imed > 0) {
                EGS_Float fac = atof(tmp[1].c_str());
                egsInformation("\n ***** Scaling bc of medium %d with %G\n",imed,fac);
                F77_OBJ_(egs_scale_bc,EGS_SCALE_BC)(&imed,&fac);
            }
        }
        delete scale;
    }
}
 
 
void EB_Application::copyParticleToSourceLoc(EGS_Particle *p, int source, bool kill_orig, bool rotate,
        EGS_Float new_wt) {
 
    // copy current location of particle
    EGS_Vector new_loc(p->x);
    EGS_Vector new_dir(p->u);
 
    // first move back to non transformed location
    base_transform_inv->transform(new_loc);
    base_transform_inv->rotate(new_dir);
 
    if (rotate) {
        double angle = 2*M_PI*rndm->getUniform();
        EGS_RotationMatrix rot = EGS_RotationMatrix::rotZ(angle);
        new_loc *= rot;
        new_dir *= rot;
    }
 
    // now transform particle to position of requested source
    source_transforms[source]->transform(new_loc);
    source_transforms[source]->rotate(new_dir);
 
    // where is new particle
    int new_reg = geometry->isWhere(new_loc);
    int new_med = geometry->medium(new_reg);
 
    // add a new particle to top of stack
 
    int cur_np = the_stack->np;
    int new_np = the_stack->np+1;
    int np_idx = new_np-1;
 
    the_stack->ir[np_idx] = new_reg + 2;
    the_stack->latch[np_idx] = p->latch;
    the_stack->E[np_idx] = p->E;
    the_stack->wt[np_idx] = new_wt;;
    the_stack->iq[np_idx] = p->q;
    the_stack->x[np_idx] = new_loc.x;
    the_stack->y[np_idx] = new_loc.y;
    the_stack->z[np_idx] = new_loc.z;
    the_stack->u[np_idx] = new_dir.x;
    the_stack->v[np_idx] = new_dir.y;
    the_stack->w[np_idx] = new_dir.z;
    the_stack->dnear[np_idx] = 0; // set to 0 because this move happens at boundary
 
    the_stack->np += 1;
    the_stack->npold = cur_np;
 
    the_epcont->irnew = new_reg+2;
    the_useful->medium_new = new_med+1;
 
    enterNewRegion();
 
    if (kill_orig) {
        the_stack->wt[np_idx-1] = 0;
        p->wt = 0;
    }
}
 
void EB_Application::startNewParticle() {
 
    EGS_AdvancedApplication::startNewParticle();
 
    int ireg = the_stack->ir[the_stack->np-1] - 2;
    if (ginfo.isSource(ireg)) {
        the_bounds->ecut = source_ecut;
        the_bounds->pcut = source_pcut;
    } else {
        the_bounds->ecut = global_ecut;
        the_bounds->pcut = global_pcut;
    }
 
}
 
void EB_Application::enterNewRegion() {
 
    EGS_AdvancedApplication::enterNewRegion();
 
    int ireg = the_epcont->irnew-2;
    if (ginfo.isSource(ireg)) {
        the_bounds->ecut_new = source_ecut;
        the_bounds->pcut_new = source_pcut;
        the_egsvr->i_do_rr = source_i_do_rr;
        the_egsvr->e_max_rr = source_e_max_rr;
    } else {
        the_bounds->ecut_new = global_ecut;
        the_bounds->pcut_new = global_pcut;
        the_egsvr->i_do_rr = global_i_do_rr;
        the_egsvr->e_max_rr = global_e_max_rr;
    }
 
}
 
void EB_Application::discardTopParticle(int idisc) {
 
    top_p.wt = 0;
    the_stack->wt[the_stack->np-1] = 0;
    the_epcont->idisc = idisc;
 
}
 
void EB_Application::addRecycledParticlesToStack(EGS_Particle *p, bool new_hist) {
 
    if (!recycle_opts) {
        return;
    }
 
    EGS_Float wt = p->wt/source_weights[active_source];
 
    for (int recycle_idx=0; recycle_idx < recycle_opts->nrecycle; recycle_idx++) {
 
        int start_loc, stop_loc;
 
        if (run_mode == RM_SUPERPOSITION) {
            start_loc = active_source;
            stop_loc = start_loc + 1;
        } else {
            start_loc = 0;
            stop_loc = nsources;
        }
 
        for (int source_loc = start_loc; source_loc < stop_loc; source_loc++) {
            // we only want to kill the original particle if this is not
            // new history from phsp
            bool kill =  source_loc == start_loc && recycle_idx == 0 && !new_hist;
            EGS_Float new_wt = wt*source_weights[source_loc];
            copyParticleToSourceLoc(p, source_loc, kill, recycle_opts->rotate, new_wt);
        }
    }
 
 
}
 
bool EB_Application::isStuck() {
 
    /* if particle number has changed, reset the stuck particle counter so that
     * particles generated from splitting don't trigger same position error */
    bool same_particle = the_stack->npold == the_stack->np;
    if (!same_particle){
        steps_at_same_loc = 0;
        return false;
    }
 
    cur_R = top_p.x.length2();
    bool in_same_pos = fabs(cur_R - last_R) < SAME_POSITION_TOLERANCE;
    if (in_same_pos) {
        steps_at_same_loc++;
    }
    last_R = cur_R;
 
    if (steps_at_same_loc > NUM_STUCK_STEPS) {
        //PRINT_PARTICLE(top_p);
        egsWarning("Particle hasn't moved in %d steps. Discarding particle\n", NUM_STUCK_STEPS);
        printParticleWithSpherical(top_p);
        n_stuck++;
        discardTopParticle();
 
        return true;
    }
    return false;
 
}
 
int EB_Application::ausgab(int iarg) {
 
    bool is_photon = top_p.q == 0;
    bool is_before_transport = iarg == BeforeTransport;
    bool is_after_transport = iarg == AfterTransport;
 
    if (is_after_transport && isStuck()) {
        the_stack->latch[the_stack->np - 1] = top_p.latch;
        return 1;
    }
 
    int global_ir = top_p.ir;
    int irnew = the_epcont->irnew-2;
    int irold = the_epcont->irold-2;
 
    bool in_phantom = ginfo.isPhantom(global_ir);
    bool in_source = ginfo.isSource(global_ir);
 
    bool is_extra_scoring_reg = false;
    string local_geom_name = "";
    int local_geom_ir = -1;
    int extra_reg_dose_index = -1;
 
    if (extra_scoring_reg.size() > 0 && global_ir >= 0){
 
        // local geom object info
        GeomRegT local = ginfo.globalToLocal(global_ir);
        local_geom_ir = local.second;
        local_geom_name = local.first->getName();
 
        // check if the current geometry has extra scoring regions
        map<string, vector<int> >::iterator i = extra_scoring_reg.find(local_geom_name);
        if (i != extra_scoring_reg.end()){
            vector<int>::iterator it = find(i->second.begin(), i->second.end(), local_geom_ir);
            if (it != i->second.end()){
                is_extra_scoring_reg = true;
                extra_reg_dose_index = distance(i->second.begin(), it);
            }
        }
    }
 
    /* track number of steps */
    if (is_before_transport) {
        if (in_source) {
            steps_in_sources[top_p.q]++;
        } else if (in_phantom) {
            steps_in_phantoms[top_p.q]++;
        } else {
            steps_in_other[top_p.q]++;
        }
    }
 
    /* Fluorescent photon cutoff */
    bool discard_fluorescent = iarg == FluorescentEvent && top_p.E <= flu_cutoff;
    if (discard_fluorescent) {
        discardTopParticle();
        the_stack->latch[the_stack->np - 1] = top_p.latch;
        return 0;
    }
 
    /* track scattering with latch bits if required */
    if (score_scat && (iarg > AfterTransport) && !in_source) {
        latch_control.addScatter(&top_p);
        for (int ip=the_stack->npold-1; ip < the_stack->np; ip++) {
            latch_control.addScatter(the_stack->latch[ip]);
        }
    }
 
    bool next_is_source = ginfo.isSource(irnew);
    bool last_was_source = ginfo.isSource(irold);
 
    /* note a particle leaving source could be a particle that has re-entered a
     * source. escaping_source will only be true on first time leaving source*/
    bool leaving_source = is_before_transport && in_source && !next_is_source;
    bool escaping_source = leaving_source && !latch_control.hasEscaped(&top_p);
 
    /* same as leaving/escaping but for after transport rather than before*/
    bool left_source = is_after_transport && !in_source && last_was_source;
    bool escaped_source = left_source && !latch_control.hasEscaped(&top_p);
 
    bool escaping_geom = is_before_transport && irnew  < 0;
    bool escaped_geom = global_ir < 0;
 
 
    /* these notifications may be used by subscribers like spectrum
     * scoring objects, latch control etc */
    EBSendMessage send_messages[] = {
        EBSendMessage(is_before_transport, PARTICLE_TAKING_STEP),
        EBSendMessage(is_after_transport, PARTICLE_TOOK_STEP),
        EBSendMessage(escaping_source, PARTICLE_ESCAPING_SOURCE),
        EBSendMessage(escaped_source, PARTICLE_ESCAPED_SOURCE),
        EBSendMessage(escaping_geom, PARTICLE_ESCAPING_GEOM),
        EBSendMessage(escaped_geom, PARTICLE_ESCAPED_GEOM)
    };
    int nmesg = sizeof(send_messages)/sizeof(send_messages[0]);
    for (int m=0; m < nmesg; m++) {
        if (send_messages[m].first) {
            pevent_pub.notify(send_messages[m].second, &top_p);
        }
    }
 
    /* copy the top_p.latch bit to the stack before returning from ausgab.
     * Since top_p.latch gets reset every step */
    the_stack->latch[the_stack->np - 1] = top_p.latch;
 
    if (escaped_geom) {
        return 0;
    }
 
    /* move particles to new locations if single generator or recycling */
    if (escaped_source && is_after_transport) {
 
        EGS_Float wt = top_p.wt;
 
        if (run_mode == RM_SUPERPOSITION) {
            superpos_geom->setActiveByIndex(active_source);
        }
 
        if (recycle_opts) {
            addRecycledParticlesToStack(&top_p);
        } else if (single_generator && active_source > 0) {
            copyParticleToSourceLoc(&top_p, active_source, true, false, wt);
        }
 
        return 0;
 
    }
 
    /* handle bcse and splitting */
    doPhotonSplitting(iarg);
 
 
    /* And finally below here we handle dose scoring */
    bool in_vaccuum = the_useful->medium <= 0;
    bool score_tracklength = score_tlen && is_photon && is_before_transport;
    bool score_interaction = score_edep && iarg <= ExtraEnergy;
    bool dose_scoring_not_needed = !is_extra_scoring_reg && (!in_phantom || in_vaccuum || !(score_tracklength || score_interaction));
 
    if (dose_scoring_not_needed) {
        return 0;
    }
 
 
    // which phantom/region are we in
    int phant_idx = ginfo.phantomFromRegion(global_ir);
    int phant_ir = ginfo.globalToLocalReg(global_ir);
 
    EB_Phantom *phant = phantom_geoms[phant_idx];
 
    bool needs_vol_cor = run_mode == RM_SUPERPOSITION && superpos_geom->hasInactiveGeom(global_ir);
 
 
    if (score_tracklength) {
 
        EGS_Interpolator *interp = media_muen[the_useful->medium-1];
        EGS_Float muen_val = interp ? interp->interpolateFast(the_epcont->gle) : 0;
        EGS_Float tracklength_edep = the_epcont->tvstep*top_p.E*muen_val*top_p.wt;
 
        EGS_Float vol;
 
        if (in_phantom){
            if (needs_vol_cor) {
                vol = phant->getUncorrectedVolume(phant_ir);
            } else {
                vol = phant->getCorrectedVolume(phant_ir);
            }
 
            if (vol > 0) {
                phant->scoreTlen(phant_ir, tracklength_edep / vol, &top_p);
            }
        }
 
        if (is_extra_scoring_reg){
            vol = extra_scoring_vols[local_geom_name][extra_reg_dose_index];
            extra_scoring_doses[local_geom_name]->score(extra_reg_dose_index, tracklength_edep / vol);
        }
    }
 
    if (score_interaction) {
 
        EGS_Float mass;
 
        EGS_Float edep = getEdep()*top_p.wt;
 
        if (in_phantom){
 
            if(needs_vol_cor) {
                mass = phant->getUncorrectedMass(phant_ir);
            } else {
                mass = phant->getRealMass(phant_ir);
            }
 
            if (mass > 0) {
                phant->scoreEdep(phant_ir, edep / mass);
            }
        }
 
        if (is_extra_scoring_reg){
            mass = extra_scoring_mass[local_geom_name][extra_reg_dose_index];
            extra_scoring_doses[local_geom_name]->score(extra_reg_dose_index, edep / mass);
        }
    }
 
    return 0;
}
 
void EB_Application::doPhotonSplitting(int iarg) {
 
    bool is_phat = fabs(top_p.wt - 1.) < EB_EPSILON;
 
    if (do_bcse) {
 
        bool in_bcse_med = the_useful->medium - 1 == bcse_med_num;
 
        if (iarg == BeforeBrems) {
            the_egsvr->nbr_split = do_brem_split ? nbr_split : 1;
            if (!in_bcse_med) {
                /* standard UBS for brem photons OUTSIDE MED_BCSE */
                the_egsvr->nbr_split *= (int)bcse_factor;
            }
        } else if (iarg == AfterBrems) {
            if (in_bcse_med) {
                /* Just came back from a brem event in MED_BCSE, reduce photon weight
                and play Russian Roulette to whether or not reduce electron energy */
                for (int ip=the_stack->npold; ip < the_stack->np; ip++) {
                    the_stack->wt[ip] /= bcse_factor;
                }
                EGS_Float rnd = rndm->getUniform();
                if (rnd > 1./bcse_factor) {
                    the_stack->E[the_stack->npold-1] += top_p.E;
                }
            } else {
                /* Turn off UBS after splitting that one fat brem photons outside MED_BCSE */
                the_egsvr->nbr_split = 1;
            }
 
        } else if (iarg == FluorescentEvent && is_phat) {
 
            /* Uniformly splits fat relaxation photons that are descendents of either:
                1. eii in MED_BCSE (usually MED_BCSE is the target) or, 2.
                back-scattered fat electrons that escaped target and interacted
                elsewhere (eii and photo) This is done using UNIFORM_PHOTONS  */
 
            int nsplit = do_brem_split ? (int)(bcse_factor*nbr_split) : (int)(bcse_factor);
            the_stack->npold = the_stack->np;
            F77_OBJ_(egs_uniform_photons, EGS_UNIFORM_PHOTONS)(&nsplit, &top_p.E);
 
        }
 
    } else if (do_brem_split && iarg == FluorescentEvent && is_phat) {
 
        /* a fluorescent photon has just been put on the stack - split it */
        the_stack->npold = the_stack->np;
        F77_OBJ_(egs_uniform_photons, EGS_UNIFORM_PHOTONS)(&nbr_split, &top_p.E);
    }
 
}
 
void EB_Application::calcEffectiveHistories() {
 
    if (is_phsp_source) {
        effective_histories = source->getFluence();
    } else {
        effective_histories = last_case;
    }
 
    if (recycle_opts) {
        if (run_mode == RM_SUPERPOSITION) {
            // only recycle at 1 source location in superposition mode
            effective_histories *= recycle_opts->nrecycle;
        } else {
            effective_histories *= recycle_opts->nrecycle*nsources;
        }
    }
}
 
 
void EB_Application::outputResults() {
    timing_blocks.addTimer("egs_brachy::outputResults");
 
    calcEffectiveHistories();
 
    string sep(80, '=');
    egsInformation(
        "\n\nResults for egs_brachy run\n%s\n",
        string(80, '-').c_str()
    );
 
 
    egsInformation("\n\nHistory Information\n%s\n",sep.c_str());
    egsInformation("Last case            = %llu\n", last_case);
    egsInformation("current case         = %llu\n", current_case);
    egsInformation("run->getNcase()      = %llu\n", run->getNcase());
    egsInformation("source->getFluence() = %f\n", source->getFluence());
    if (recycle_opts) {
        egsInformation("Particles recycled  = %d\n", recycle_opts->nrecycle);
    }
    egsInformation("Effective histories  = %.5G\n", effective_histories);
 
 
    egsInformation("\n\nGeometry Errors\n%s\n", sep.c_str());
    egsInformation("Number of geometry errors (/max allowed) = %d / %d\n", run->geomErrorCount, run->geomErrorMax);
    egsInformation("Number of 'stuck' particles discarded    = %llu\n", n_stuck);
 
 
    // tell scoring objects how many histories were actually run
    // (needed for parallel run normalization)
    EGS_I64 hist_norm = run->getNdone();
    pevent_pub.notify(NEW_HISTORY, &hist_norm);
 
    if (!single_generator) {
        egsInformation(
            "Warning: Stats about energy escaping source may not be accurate when "
            "not using a single source generator\n"
        );
    }
 
    if (phsp) {
        phsp->finish(current_case);
        phsp->outputResults();
        phsp->destroySource();
    }
 
    if (escoring) {
        escoring->outputResults();
    }
 
    if (spectrum_scorers.size() > 0) {
        egsInformation("\nSpectrum scoring results\n%s\n",sep.c_str());
        string root = constructIOFileName("", true);
        vector<BaseSpectrumScorer *>::iterator it = spectrum_scorers.begin();
        for (; it != spectrum_scorers.end(); it++) {
            (*it)->setEffectiveHistories(effective_histories);
            (*it)->outputResults(root);
        }
    }
 
    if (record_n_init > 0) {
 
        string fname = constructIOFileName("", true)+".pinit";
        ofstream out;
        out.open(fname.c_str());
        out << std::fixed << std::showpoint << std::setprecision(6);
        for (vector<EGS_Vector>::iterator it = p_init_locs.begin(); it != p_init_locs.end(); ++it) {
            out << (*it).x << "\t" << (*it).y << "\t" << (*it).z << "\n";
        }
        out.close();
        egsInformation("\nInitial Particle Positions\n%s\n",sep.c_str());
        egsInformation("%d Initial particle positions written to .pinit file\n", p_init_locs.size());
    }
 
    timing_blocks.addTimer("egs_brachy::outputPhantomResults");
    for (vector<EB_Phantom *>::iterator p = phantom_geoms.begin(); p != phantom_geoms.end(); p++) {
        (*p)->setEffectiveHistories(effective_histories);
        bool output_vc = find(output_volcor_phantoms.begin(), output_volcor_phantoms.end(),
                              (*p)->geometry->getName()) != output_volcor_phantoms.end();
        string dd_format = output_3ddose_files ? output_dose_format : "";
        string vc_format = output_vc ? output_volcor_format : "";
        string ep_format = output_egsphant ? output_egsphant_format : "";
        string vi_format = output_voxinfo ? output_voxinfo_format : "";
        (*p)->outputResults(20, dd_format, ep_format, vi_format, vc_format);
    }
 
    timing_blocks.stopTimer();
 
    egsInformation("\nStep Counts\n%s\n", sep.c_str());
    EGS_Float total_steps = 0;
 
    for (int i=-1; i < 2; i++) {
        total_steps += steps_in_sources[i];
        total_steps += steps_in_phantoms[i];
        total_steps += steps_in_other[i];
    }
 
    egsInformation("Total particle steps               : %20llu\n", (EGS_I64)total_steps);
    for (int i=-1; i < 2; i++) {
        if (steps_in_sources[i]  > 0) {
            egsInformation("q=%2d Steps taken in sources        : %20llu (%.2f%%)\n", i, steps_in_sources[i],
                           100*steps_in_sources[i]/total_steps);
        }
        if (steps_in_phantoms[i]  > 0) {
            egsInformation("q=%2d Steps taken in phantoms       : %20llu (%.2f%%)\n", i, steps_in_phantoms[i],
                           100*steps_in_phantoms[i]/total_steps);
        }
        if (steps_in_other[i]  > 0) {
            egsInformation("q=%2d Steps taken in other objects  : %20llu (%.2f%%)\n", i, steps_in_other[i],
                           100*steps_in_other[i]/total_steps);
        }
    }
 
    timing_blocks.stopTimer();
    timing_blocks.outputInfo();
 
 
}
 
 
void EB_Application::getCurrentResult(double &sum, double &sum2, double &norm, double &count) {
 
    count = current_case;
    calcEffectiveHistories();
    gcr_phantom->setEffectiveHistories(effective_histories);
    gcr_phantom->getCurrentScore(gcr_phantom_reg, sum, sum2);
    norm=gcr_phantom->getTlenNorm(gcr_phantom_reg);
 
}
 
int EB_Application::runSimulation() {
    timing_blocks.addTimer("egs_brachy::runSimulation");
    int result = EGS_Application::runSimulation();
    timing_blocks.stopTimer();
    return result;
}
 
/* \brief initialize a particle from source and then transform to next source */
int EB_Application::simulateSingleShower() {
 
    last_case = current_case;
 
    current_case = source->getNextParticle(rndm, p.q, p.latch, p.E, p.wt, p.x, p.u);
 
    int initial_source;
    if ((is_phsp_source && !recycle_opts) || !single_generator) {
        initial_source = active_source;
    } else {
        initial_source = 0;
    }
 
    p.wt *= source_weights[active_source];
 
    if (run_mode == RM_SUPERPOSITION) {
        superpos_geom->setActiveByIndex(initial_source);
    }
 
    // transform particle to position of next source
    source_transforms[initial_source]->transform(p.x);
    source_transforms[initial_source]->rotate(p.u);
 
    p.ir = geometry->isWhere(p.x);
 
    if (p.ir < 0) {
        egsWarning("EB_Application::simulateSingleShower() - particle initiated at (x, y, z) = (%.2g, %.2g, %.2g)\n", p.x.x, p.x.y, p.x.z);
        egsFatal("EB_Application::simulateSingleShower() - Particle initiated outside "
                 "the geometry! Please check your source locations.\n");
    }
 
    if (is_phsp_source) {
        // we assume phase space particles are outside the source
        pevent_pub.notify(PARTICLE_ESCAPED_SOURCE, &p);
 
        // set up stack with particles if recyling and phsp source
        if (recycle_opts) {
            addRecycledParticlesToStack(&p, true);
        }
    } else if (!ginfo.isSource(p.ir)) {
 
        GeomRegT r = ginfo.globalToLocal(p.ir);
 
        printParticleWithSpherical(p);
        egsFatal(
            "Particle started in region %d (%s reg %d) which is outside a source geometry. Please check your geometry\n",
            p.ir,
            r.first->getName().c_str(),
            r.second
        );
 
    }
 
    if (record_n_init > 0 && (int)p_init_locs.size() < record_n_init) {
        p_init_locs.push_back(p.x);
    }
 
    cur_R = p.x.length2();
    last_R = cur_R;
    steps_at_same_loc = 0;
 
    int err = startNewShower();
    if (err) {
        return err;
    }
 
    // shower() just resets the stack before calling egsShower() but when using
    // a phsp source with recycling, we've already set up stack so go straight
    // to egsShower() in that case;
    if (is_phsp_source && recycle_opts) {
        err = 0;
        egsShower();
    } else {
        err = shower();
    }
 
    active_source++;
    if (active_source == nsources) {
        active_source =0;
    }
 
    return err || finishShower();
}
 
 
int EB_Application::startNewShower() {
 
 
    // notify subscribers a valid particle has been initialized
    pevent_pub.notify(PARTICLE_INITIALIZED, &p);
 
    //  sets current case in ausgab objects
    int err = EGS_Application::startNewShower();
 
    if (err) {
        return err;
    }
 
    // now set current case in all phantom objects
    if (current_case != last_case) {
 
        pevent_pub.notify(NEW_HISTORY, &current_case);
 
        last_case = current_case;
    }
 
    return 0;
}
 
 
/* start of stop/restart functionality  ****************************************/
int EB_Application::egsApplicationOutputData(ostream *out) {
    /* adapted from egs_application.cpp::outputData */
    if (!run->storeState(*out)) {
        return 2;
    }
    if (!egsStoreI64(*out,current_case)) {
        return 3;
    }
    (*out) << "\n";
    if (!rndm->storeState(*out)) {
        return 4;
    }
    if (!source->storeState(*out)) {
        return 5;
    }
    for (size_t j=0; j<a_objects_list.size(); ++j) {
        if (!a_objects_list[j]->storeState(*out)) {
            return 6;
        }
    }
 
    return 0;
}
 
int EB_Application::egsAdvApplicationOutputData(ostream *out) {
    /* adapted from egs_advanced_application.cpp::outputData */
    EGS_I32 np, ip;
    egsGetRNGPointers(&np,&ip);
    if (np < 1) {
        return 11;
    }
    if (np > 10000000) {
        egsWarning("EGS_AdvancedApplication::outputData(): egsGetRNGPointers"
                   " returns a huge number? (%d)\n",np);
        return 12;
    }
    EGS_Float *array = new EGS_Float [np];
    egsGetRNGArray(array);
    (*out) << "  " << np << "  " << ip << "\n";
    for (int j=0; j<np; j++) {
        (*out) << array[j] << " ";
    }
    (*out) << "\n";
    double ch_steps, all_steps;
    egsGetSteps(&ch_steps,&all_steps);
    (*out) << ch_steps << "  " << all_steps << "\n";
    delete [] array;
    return out->good() ? 0 : 13;
 
}
 
int EB_Application::egsBrachyOutputData(ostream *out) {
 
    int err;
 
    (*out) << std::setprecision(9);
 
    for (int i=-1; i < 2; i++) {
        (*out) << steps_in_sources[i] << " ";
        (*out) << steps_in_phantoms[i] << " ";
        (*out) << steps_in_other[i] << "\n";
    }
 
    if (escoring) {
        err= escoring->outputData(out);
        if (err) {
            return err;
        }
    }
 
    vector<BaseSpectrumScorer *>::iterator spec_it = spectrum_scorers.begin();
    for (; spec_it != spectrum_scorers.end(); ++spec_it) {
        err = (*spec_it)->outputData(out);
        if (err) {
            return err;
        }
    }
 
    vector<EB_Phantom *>::iterator phant_it = phantom_geoms.begin();
    for (; phant_it != phantom_geoms.end(); phant_it++) {
        err = (*phant_it)->outputData(out);
        if (err) {
            return err;
        }
    }
 
    return 0;
 
}
 
int EB_Application::outputDataHelper(ostream *out) {
 
    int err = egsApplicationOutputData(out);
    if (err) {
        return err;
    }
    err = egsAdvApplicationOutputData(out);
    if (err) {
        return err;
    }
 
    return egsBrachyOutputData(out);
}
 
int EB_Application::outputData() {
 
    timing_blocks.addTimer("egs_brachy::outputData");
 
    bool use_gz = output_egsdat_format == "gzip";
    string extension(".egsdat");
    extension += (use_gz ? ".gz" : "");
    string ofile = constructIOFileName(extension.c_str(), true);
 
    int err;
    if (use_gz) {
        if (gz_data_out) {
            delete gz_data_out;
        }
        gz_data_out = new ogzstream(ofile.c_str());
 
        if (!(gz_data_out)) {
            egsWarning("EGS_Application::outputData: failed to open %s for writing\n",ofile.c_str());
            timing_blocks.stopTimer();
            return 1;
        }
        err = outputDataHelper(gz_data_out);
        gz_data_out->close();
    } else {
 
        if (data_out) {
            delete data_out;
        }
        data_out = new ofstream(ofile.c_str());
        if (!(*data_out)) {
            egsWarning("EGS_Application::outputData: failed to open %s for writing\n",ofile.c_str());
            timing_blocks.stopTimer();
            return 1;
        }
        err = outputDataHelper(data_out);
    }
 
    timing_blocks.stopTimer();
    return err;
 
}
 
int EB_Application::egsApplicationReadData(istream *in) {
    /* adapted from egs_application.cpp::readData */
    if (!run->setState(*in)) {
        return 2;
    }
    if (!egsGetI64(*in,current_case)) {
        return 3;
    }
    last_case = current_case;
    if (!rndm->setState(*in)) {
        return 4;
    }
    if (!source->setState(*in)) {
        return 5;
    }
    for (int j=0; j<a_objects_list.size(); ++j) {
        if (!a_objects_list[j]->setState(*in)) {
            return 6;
        }
    }
    return 0;
}
 
int EB_Application::egsAdvApplicationReadData(istream *in) {
    /* adapted from egs_advanced_application.cpp::readData */
    int np, ip;
    (*in) >> np >> ip;
    if (np < 1) {
        return 11;
    }
    if (np > 10000000) {
        egsWarning("EB_Application::egsAdvApplicationReadData(): got huge size "
                   "for the mortran random array? (%d)\n",np);
        return 12;
    }
    EGS_Float *array = new EGS_Float [np];
    for (int j=0; j<np; j++) {
        (*in) >> array[j];
    }
    if (!in->good()) {
        return 13;
    }
    egsSetRNGState(&ip,array);
    delete [] array;
    double ch_steps, all_steps;
    (*in) >> ch_steps >> all_steps;
    egsSetSteps(&ch_steps,&all_steps);
    return in->good() ? 0 : 13;
 
}
 
int EB_Application::egsBrachyReadData(istream *in) {
    int err;
 
    for (int i=-1; i < 2; i++) {
        (*in) >> steps_in_sources[i];
        (*in) >> steps_in_phantoms[i];
        (*in) >> steps_in_other[i];
    }
 
    if (escoring) {
        err= escoring->readData(in);
        if (err) {
            return err;
        }
    }
 
    vector<BaseSpectrumScorer *>::iterator spec_it = spectrum_scorers.begin();
    for (; spec_it != spectrum_scorers.end(); ++spec_it) {
        err = (*spec_it)->readData(in);
        if (err) {
            return err;
        }
    }
 
    vector<EB_Phantom *>::iterator phant_it = phantom_geoms.begin();
    for (; phant_it != phantom_geoms.end(); phant_it++) {
        err = (*phant_it)->readData(in);
        if (err) {
            return err;
        }
    }
    return 0;
 
}
 
int EB_Application::readDataHelper(istream *in) {
 
    int err = egsApplicationReadData(in);
    if (err) {
        return err;
    }
    err = egsAdvApplicationReadData(in);
    if (err) {
        return err;
    }
 
    return egsBrachyReadData(in);
}
 
/* start of stop/restart functionality  ****************************************/
int EB_Application::readData() {
 
    timing_blocks.addTimer("egs_brachy::readData");
 
    bool use_gz = output_egsdat_format == "gzip";
    string extension(".egsdat");
    extension += (use_gz ? ".gz" : "");
    string ifile = constructIOFileName(extension.c_str(), false);
 
    int err;
    if (use_gz) {
        if (gz_data_in) {
            delete gz_data_in;
        }
        gz_data_in = new igzstream(ifile.c_str());
 
        if (!(gz_data_in)) {
            egsWarning("EGS_Application::readData: failed to open %s for reading\n", ifile.c_str());
            timing_blocks.stopTimer();
            return 1;
        }
        err = readDataHelper(gz_data_in);
    } else {
 
        if (data_in) {
            delete data_in;
        }
        data_in = new ifstream(ifile.c_str());
        if (!(*data_in)) {
            egsWarning("EGS_Application::readData: failed to open %s for writing\n",ifile.c_str());
            timing_blocks.stopTimer();
            return 1;
        }
        err = readDataHelper(data_in);
    }
 
    timing_blocks.stopTimer();
    return err;
 
}
 
 
int EB_Application::combineResults() {
    /* Adapted from egs_application.cpp::combineResults */
    egsInformation(
        "\n                      Suming the following .egsdat files:\n"
        "=======================================================================\n");
    char buf[512];
    resetCounter();
    EGS_Float last_cpu = 0;
    EGS_I64 last_ncase = 0;
    int ndat = 0;
    bool ok = true;
    for (int j=1; j<500; j++) {
 
        bool use_gz = output_egsdat_format == "gzip";
        string name("%s_w%d.egsdat");
        name += (use_gz ? ".gz" : "");
 
        sprintf(buf, name.c_str(), output_file.c_str(), j);
        string dfile = egsJoinPath(app_dir,buf);
        istream *data;
        ifstream in;
        igzstream gzin;
        bool opened = false;
        if (use_gz) {
            gzin.open(dfile.c_str());
            opened = gzin.rdbuf()->is_open();
            data = &gzin;
        } else {
            in.open(dfile.c_str());
            opened = in.is_open();
            data = &in;
        }
 
        if (opened) {
            int err = addState(*data);
            ++ndat;
            if (!err) {
                EGS_I64 ncase = run->getNdone();
                EGS_Float cpu = run->getCPUTime();
                egsInformation("%2d %-30s ncase=%-14lld cpu=%-11.2f\n",
                               ndat,buf,ncase-last_ncase,cpu-last_cpu);
                last_ncase = ncase;
                last_cpu = cpu;
            } else {
                ok = false;
                egsWarning("%2d %-30s error %d\n",ndat,buf,err);
            }
        }
    }
    if (ndat > 0) {
        egsInformation(
            "=======================================================================\n");
        egsInformation("%40s%-14lld cpu=%-11.2f\n\n","Total ncase=",last_ncase,
                       last_cpu);
    }
    if (ndat > 0) {
        return ok ? 0 : -1;
    } else {
        return 1;
    }
}
 
void EB_Application::resetCounter() {
    // Reset everything in the base class
    EGS_AdvancedApplication::resetCounter();
    // Reset our own data to zero.
 
    for (int i=-1; i < 2; i++) {
        steps_in_sources[i] = 0;
        steps_in_phantoms[i] = 0;
        steps_in_other[i] = 0;
    }
 
    if (escoring) {
        escoring->resetCounter();
    }
 
    vector<BaseSpectrumScorer *>::iterator spec_it = spectrum_scorers.begin();
    for (; spec_it != spectrum_scorers.end(); ++spec_it) {
        (*spec_it)->resetCounter();
    }
 
    vector<EB_Phantom *>::iterator phant_it = phantom_geoms.begin();
    for (; phant_it != phantom_geoms.end(); phant_it++) {
        (*phant_it)->resetCounter();
    }
 
}
 
int EB_Application::addState(istream &data) {
    // Call first the base class addState() function to read and add
    // all data related to source, RNG, CPU time, etc.
    int err = EGS_AdvancedApplication::addState(data);
    if (err) {
        return err;
    }
 
    for (int i=-1; i < 2; i++) {
        EGS_I64 steps_in_sources_tmp;
        EGS_I64 steps_in_phantoms_tmp;
        EGS_I64 steps_in_other_tmp;
 
        data >> steps_in_sources_tmp;
        data >> steps_in_phantoms_tmp;
        data >> steps_in_other_tmp;
 
        steps_in_sources[i] += steps_in_sources_tmp;
        steps_in_phantoms[i] += steps_in_phantoms_tmp;
        steps_in_other[i] += steps_in_other_tmp;
    }
 
    if (escoring) {
        err = escoring->addState(data);
        if (err) {
            return err;
        }
    }
 
    vector<BaseSpectrumScorer *>::iterator spec_it = spectrum_scorers.begin();
    for (; spec_it != spectrum_scorers.end(); ++spec_it) {
        err = (*spec_it)->addState(data);
        if (err) {
            return err;
        }
    }
 
    vector<EB_Phantom *>::iterator phant_it = phantom_geoms.begin();
    for (; phant_it != phantom_geoms.end(); phant_it++) {
        err = (*phant_it)->addState(data);
        if (err) {
            return err;
        }
    }
 
    return 0;
 
}
/* end of stop/restart functionality  ****************************************/
 
bool fileExists(const string &name) {
    struct stat buffer;
    return (stat(name.c_str(), &buffer) == 0);
}
 
int EB_Application::howManyJobsDone() {
 
    char buf[512];
    int  n_of_egsdat = 0;
 
    bool use_gz = output_egsdat_format == "gzip";
    string name("%s_w%d.egsdat");
    name += (use_gz ? ".gz" : "");
 
    for (int i = first_parallel; i < first_parallel + n_parallel; i++) {
        sprintf(buf,name.c_str(),final_output_file.c_str(),i);
        string dfile = egsJoinPath(app_dir,buf);
        if (fileExists(dfile)) {
            n_of_egsdat++;
        }
    }
 
    return n_of_egsdat;
}
 
EB_UniformRunControl::EB_UniformRunControl(EB_Application *a, string egsdat_format) :
    EGS_RunControl(a), app(a), output_egsdat_format(egsdat_format), milliseconds(1000), check_intervals(5),
    njob(0), npar(app->getNparallel()), ipar(app->getIparallel()), ifirst(app->getFirstParallel()),
    check_egsdat(true), watcher_job(false) {
 
    rco_type = uniform;
 
    if (input) {
 
        /*Change waiting time to check for parallel run completion*/
        int dummy;
        int err = input->getInput("interval wait time", dummy);
        if (!err) {
            milliseconds = dummy;
        }
 
        /*Change how many times to check for parallel run completion*/
        err = input->getInput("number of intervals", dummy);
        if (!err) {
            check_intervals = dummy;
        }
 
        /* Define watcher jobs to check for parallel run completion*/
        vector<int> w_jobs;
        err = input->getInput("watcher jobs", w_jobs);
        if (!err) {
            for (int i = 0; i < w_jobs.size(); i++) {
                if (ipar == w_jobs[i]) {
                    watcher_job = true;
                    break;
                }
            }
        }
        else { // use defaults
            /* last job is watcher job */
            if (ipar == ifirst + npar - 1) {
                watcher_job = true;
            }
            else {
                watcher_job = false;
            }
        }
 
        /* Request checking parallel run completion */
        vector<string> check_options;
        check_options.push_back("yes");
        check_options.push_back("no");
        int ichk = input->getInput("check jobs completed",check_options,0);
        if (ichk != 0) {
            check_egsdat = false;    // true by default
        }
 
    }
    else { // use defaults if no RCO input found
        /* last job is watcher job */
        if (ipar == ifirst + npar - 1) {
            watcher_job = true;
        }
    }
}
 
int EB_UniformRunControl::startSimulation() {
 
 
    /* Check run completion based on *egsdat files requires erasing
       existing files from previous runs.
     */
    bool use_gz = output_egsdat_format == "gzip";
    string name("%s_w%d.egsdat");
    name += (use_gz ? ".gz" : "");
 
    if (check_egsdat) {
        char buf[512];
        sprintf(buf,name.c_str(),app->getFinalOutputFile().c_str(), ipar);
        string datFile = egsJoinPath(app->getAppDir(),buf);
        if (remove(datFile.c_str()) == 0) {
            egsWarning("EB_UniformRunControl: %s deleted\n",
                       datFile.c_str());
        }
    }
 
    return EGS_RunControl::startSimulation();
}
 
void EB_UniformRunControl::describeRCO() {
 
    EGS_RunControl::describeRCO();
 
    if (watcher_job) {
        if (check_egsdat) {
            egsInformation(
                "   Watcher job: remains running after completion checking\n"
                "                for other jobs finishing every %d s for %d s!\n",
                milliseconds/1000, check_intervals*milliseconds/1000);
        }
        else {
            egsInformation(
                "   Option to check for finishing jobs is OFF!\n\n");
        }
    }
 
}
 
void rco_sleep(const int &mscnds) {
#ifdef WIN32
    Sleep(mscnds);
#else
    usleep(mscnds * 1000);
#endif
}
 
int EB_UniformRunControl::finishSimulation() {
    int err = EGS_RunControl::finishSimulation();
    if (err < 0) {
        return err;
    }
    /* Check and wait for all jobs to finish */
    if (watcher_job) {
        int interval = 0, njobs_done = 0, njobs_done_old= 0;
        while (interval < check_intervals) {
            rco_sleep(milliseconds);
            if (check_egsdat) {
                njobs_done = app->howManyJobsDone();
                //egsInformation("\n-> Finished %d jobs...\n",njobs_done);
                if (njobs_done == npar - 1) {
                    watcher_job=false;//don't enter this after all jobs done!
                    break;
                }
                // Only combine if new jobs finished
                if (njobs_done_old < njobs_done) {
                    egsInformation("=> Combining %d jobs ...\n",njobs_done);
                    app->combinePartialResults();
                }
                njobs_done_old = njobs_done;
            }
            interval++;
        }
        return 1;
    }
    /*I am not a watcher job, do not combine results yet!*/
    return 0;
}
 
#ifdef BUILD_APP_LIB
APP_LIB(EB_Application);
#else
APP_MAIN(EB_Application);
#endif