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reserve.hpp
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reserve.hpp
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#pragma once
// Stores information relating to the reserve configuration.
#include <limits>
#include <cmath>
#include <random>
#include <utility>
#include <array>
#include "common.hpp"
#include "pu.hpp"
#include "zones.hpp"
namespace marzone
{
using namespace std;
// Tracks all computed changes on each move so they can be applied without recalculation.
// Changes stored in pairs, usually first term = index of spec or zonespec, and second term is the value of change.
typedef struct schange : scost
{
vector<pair<int,double>> specListChangeTarget; // list of spindex,target pairs.
vector<int> specListChangeOcc; // index corresponds with above target vector.
vector<pair<int, double>> zoneTargetChange;
vector<int> zoneOccChange; // ind corresponds to zoneTargetChange.first
vector<pair<int, double>> speciesClumpChange;
}
schange;
class Reserve
{
public:
Reserve() // Empty constructor.
{
InitializeObjective();
}
Reserve(Species &spec, int zoneCount, int clumptype, int id = 0) : clumptype(clumptype), id(id)
{
InitializeZoneSpec(spec.spno, zoneCount);
speciesAmounts.resize(spec.spno, {}); // init amounts struct
if (spec.aggexist)
speciesClump.resize(spec.spno);
InitializeObjective();
}
// Clone existing reserve.
Reserve(const Reserve& r) {
solution = r.solution;
zoneSpec = r.zoneSpec;
speciesAmounts = r.speciesAmounts;
speciesClump = r.speciesClump;
objective = r.objective;
id = r.id;
clumptype = r.clumptype;
}
// Replace existing reserve with given reserve.
void Assign(const Reserve& r) {
solution = r.solution;
zoneSpec = r.zoneSpec;
speciesAmounts = r.speciesAmounts;
speciesClump = r.speciesClump;
objective = r.objective;
id = r.id;
clumptype = r.clumptype;
}
// Initializes a change structure to re-use for change calculations
schange InitializeChange(Species& spec, Zones& zones) {
schange change = {}; // init and pre-allocate
change.specListChangeTarget.reserve(spec.spno);
change.specListChangeOcc.reserve(spec.spno);
if (zones.zoneTarget.size())
{
change.zoneTargetChange.reserve(spec.spno * zones.zoneCount);
change.zoneOccChange.reserve(spec.spno * zones.zoneCount);
}
if (spec.aggexist)
change.speciesClumpChange.reserve(spec.spno);
return change;
}
void InitializeSolution(uint64_t puno)
{
solution.assign(puno, 0);
}
void RandomiseSolution(Pu &pu, mt19937 &rngEngine, int zoneCount)
{
uniform_int_distribution<int> random_dist(0, numeric_limits<int>::max());
for (int i = 0; i < pu.puno; i++)
{
spustuff &puTerm = pu.puList[i];
if (puTerm.fPULock == 1)
{
solution[i] = puTerm.iPULock;
continue; // pu lock takes precedence above all.
}
solution[i] = 0; // default setting is 0
if (puTerm.status > 0) // starting pu state detected
solution[i] = puTerm.status;
if (puTerm.numZones > 0)
{ // enforce puzone
int zoneInd = random_dist(rngEngine) % puTerm.numZones;
solution[i] = pu.puZone[i][zoneInd]; // solution array stores the zero-indexed zone.
}
else if (puTerm.numZones == 0)
{
// set to any random zone
solution[i] = random_dist(rngEngine) % zoneCount;
}
}
}
// Recomputes and updates all speciesAmounts and zoneSpec, including clumps, from scratch.
void ComputeSpeciesAmounts(Pu &pu, Species &spec, Zones &zones)
{
int isp, ism, iZoneSpecIndex;
double rContribAmount;
// Set species amounts to 0 and set target2 species.
for (int isp = 0; isp < speciesAmounts.size(); isp++)
{
speciesAmounts[isp].amount = 0;
speciesAmounts[isp].occurrence = 0;
// Clear map clumps for this species
if (spec.specList[isp].target2)
ClearClumps(isp); // for target2 species, clear existing pu.
// Reset zone species if specified
int zoneBase = isp * zones.zoneCount;
for (int i = 0; i < zones.zoneCount; i++) {
iZoneSpecIndex = zoneBase + i;
zoneSpec[iZoneSpecIndex].amount = 0;
zoneSpec[iZoneSpecIndex].occurrence = 0;
}
}
for (int ipu = 0; ipu < solution.size(); ipu++)
{
if (pu.puList[ipu].richness)
{
if (solution[ipu] >= 0)
{
for (int i = 0; i < pu.puList[ipu].richness; i++)
{
ism = pu.puList[ipu].offset + i;
isp = pu.puvspr[ism].spindex;
rContribAmount = pu.puvspr[ism].amount*zones.GetZoneContrib(ipu, pu.puno, isp, solution[ipu]);
if (spec.specList[isp].target2 == 0)
{
if (pu.puvspr[ism].amount)
{
iZoneSpecIndex = (isp * zones.zoneCount) + solution[ipu];
zoneSpec[iZoneSpecIndex].amount += pu.puvspr[ism].amount;
zoneSpec[iZoneSpecIndex].occurrence += (pu.puvspr[ism].amount > 0);
}
if (rContribAmount)
{
speciesAmounts[isp].amount += rContribAmount;
speciesAmounts[isp].occurrence += (rContribAmount > 0);
}
}
else {
// Add amount to species clumping.
if (rContribAmount)
AddNewPuToClump(ipu, isp, rContribAmount);
}
}
}
}
}
//Compute species amounts for target2 species.
for (int isp = 0; isp < speciesAmounts.size(); isp++)
{
if (spec.specList[isp].target2)
SpeciesAmounts4(isp, spec.specList[isp].target2); // for target2 species, recompute
}
}
// Counts missing species and proportion of lowest species
int CountMissing(Species& spec, Zones& zones, double misslevel, double& rMinimumProportionMet) {
double rProportionMet;
int specCount = 0, iArrayIndex;
rMinimumProportionMet = 1;
for (int i = 0; i < spec.spno; i++)
{
rProportionMet = 1;
if (spec.specList[i].target > 0)
{
if (speciesAmounts[i].amount < spec.specList[i].target)
{
rProportionMet = speciesAmounts[i].amount / spec.specList[i].target;
if (rProportionMet < rMinimumProportionMet)
rMinimumProportionMet = rProportionMet;
}
if (rProportionMet < misslevel)
{
specCount++;
continue;
}
}
if (spec.specList[i].targetocc > 0)
{
if (speciesAmounts[i].occurrence < spec.specList[i].targetocc)
{
rProportionMet = (double)speciesAmounts[i].occurrence / (double)spec.specList[i].targetocc;
if (rProportionMet < rMinimumProportionMet)
rMinimumProportionMet = rProportionMet;
}
if (rProportionMet < misslevel)
{
specCount++;
continue;
}
}
// only necessary if zoneTarget is set
if (zones.zoneTarget.size())
for (int j = 0; j < zones.zoneCount; j++)
{
iArrayIndex = (i * zones.zoneCount) + j;
if (zones.zoneTarget[i][j].target > 0)
{
if (zoneSpec[iArrayIndex].amount < zones.zoneTarget[i][j].target)
{
rProportionMet = zoneSpec[iArrayIndex].amount / zones.zoneTarget[i][j].target;
if (rProportionMet < rMinimumProportionMet)
rMinimumProportionMet = rProportionMet;
if (rProportionMet < misslevel)
{
specCount++;
}
}
}
if (zones.zoneTarget[i][j].occurrence > 0)
{
if (zoneSpec[iArrayIndex].occurrence < zones.zoneTarget[i][j].occurrence)
{
rProportionMet = zoneSpec[iArrayIndex].occurrence / zones.zoneTarget[i][j].occurrence;
if (rProportionMet < rMinimumProportionMet)
rMinimumProportionMet = rProportionMet;
if (rProportionMet < misslevel)
{
specCount++;
}
}
}
}
}
return specCount;
}
// returns a formatted string based on zone distribution of the current solution
string CountPuZones(Zones& zones) {
vector<int> zoneDist(zones.zoneCount, 0);
stringstream sLine;
for (int i=0; i < solution.size(); i++) {
zoneDist[solution[i]] += 1;
}
for (int i=0;i<zones.zoneCount;i++)
{
sLine << " " << zones.zoneNames[i].name << " " << zoneDist[i];
}
return sLine.str();
}
/* * * * * Set Penalties for a given Type 4 Species ***/
/* Returns 1 if the species is a 'bad species' and -1 if it is a 'good species' */
// Used for initial penalty calculation. and updates spec with the penalty.
// NOTE: currently does no support sepnum/sepdistance feature.
int ComputePenaltyType4(sspecies& spec, vector<penaltyTerm>& costTerms, int isp, double target, double target2, int targetocc) {
int sepCount;
/* Check first to see if I've already satisfied targets for this species with the current clump setup*/
SpeciesAmounts4(isp, target2); // recompute amounts for this species.
if ((speciesAmounts[isp].amount >= target)
&& (speciesAmounts[isp].occurrence >= targetocc)) {
// Targets met for this spec can exit
return -1;
}
// Go down costTerms until an amount is less than target2, or target is met
bool targetMet = false;
for (penaltyTerm &p : costTerms)
{
if (p.amount > target2)
{
speciesAmounts[isp].amount += p.amount;
speciesAmounts[isp].occurrence++;
spec.penalty += p.cost;
}
// Check if targets met
if (speciesAmounts[isp].amount >= target && speciesAmounts[isp].occurrence >= targetocc)
{
targetMet = true;
break;
}
}
if (targetMet)
return -1;
else
{
double scaleFactor = 1;
// scale up the penalty
if (speciesAmounts[isp].amount == 0)
speciesAmounts[isp].amount = numeric_limits<double>::epsilon();
if (speciesAmounts[isp].amount < target)
scaleFactor = target/speciesAmounts[isp].amount;
if (speciesAmounts[isp].occurrence && speciesAmounts[isp].occurrence < targetocc)
scaleFactor += (double) targetocc/ (double) speciesAmounts[isp].occurrence;
spec.penalty *= scaleFactor;
return 1;
}
}
// * * * * **** Change in penalty for moving single PU between zones ******
// we need to know the penalty with ipu in its existing zone and the penalty with ipu in its proposed zone.
// change in penalty = penalty in proposed configuration - penalty in existing configuration
double ComputeChangePenalty(Pu& pu, Zones& zones, Species& spec, schange& change, int ipu, int iPreZone, int iPostZone) {
int ism, isp, iArrayIndex, iNewOccurrence, iCurrentShortfall, iNewShortfall;
double rShortFraction, rNewShortFraction, rOldShortfall, rNewShortfall, rNewAmount, rSumDeltaPenalty = 0, rDeltaPenalty,
rCurrentContribAmount, rNewContribAmount, t_diff, o_diff;
change.shortfall = 0;
array<int, 2> zonesToTarget{iPreZone, iPostZone};
// clean up the vectors in the change object.
change.specListChangeTarget.clear();
change.specListChangeOcc.clear();
change.speciesClumpChange.clear();
change.zoneOccChange.clear();
change.zoneTargetChange.clear();
if (pu.puList[ipu].richness)
{
for (int i = 0; i < pu.puList[ipu].richness; i++)
{
ism = pu.puList[ipu].offset + i;
isp = pu.puvspr[ism].spindex;
if (pu.puvspr[ism].amount)
{
rOldShortfall = 0, rShortFraction = 0, iCurrentShortfall = 0;
// init variables tracking shortfall in proposed zone
rNewShortfall = 0, rNewShortFraction = 0, iNewShortfall = 0;
// shortfall with respect to overall targets
rCurrentContribAmount = pu.puvspr[ism].amount*zones.GetZoneContrib(ipu, pu.puno, isp, iPreZone);
rNewContribAmount = pu.puvspr[ism].amount*zones.GetZoneContrib(ipu, pu.puno, isp, iPostZone);
// Apply any target2 requirements on these contrib amounts.
if (spec.specList[isp].target2) {
change.speciesClumpChange.push_back(pair<int,double>(isp, rNewContribAmount));
rCurrentContribAmount = rCurrentContribAmount > spec.specList[isp].target2 ? rCurrentContribAmount : PartialPen4(spec.specList[isp].target2, rCurrentContribAmount);
rNewContribAmount = rNewContribAmount > spec.specList[isp].target2 ? rNewContribAmount : PartialPen4(spec.specList[isp].target2, rNewContribAmount);
}
// Set change vectors
t_diff = rNewContribAmount - rCurrentContribAmount;
o_diff = (rNewContribAmount > 0) - (rCurrentContribAmount > 0);
if (t_diff != 0) // only need to execute below if there is change.
{
change.specListChangeTarget.push_back(pair<int,double>(isp, t_diff));
change.specListChangeOcc.push_back(o_diff);
rNewAmount = speciesAmounts[isp].amount + t_diff;
iNewOccurrence = speciesAmounts[isp].occurrence + o_diff;
if (spec.specList[isp].target > 0)
{
if (spec.specList[isp].target > speciesAmounts[isp].amount)
{
rOldShortfall = spec.specList[isp].target - speciesAmounts[isp].amount;
rShortFraction += rOldShortfall / spec.specList[isp].target;
iCurrentShortfall++;
}
if (spec.specList[isp].target > rNewAmount)
{
rNewShortfall = spec.specList[isp].target - rNewAmount;
rNewShortFraction += rNewShortfall / spec.specList[isp].target;
iNewShortfall++;
}
/*
#ifdef DEBUG_PEW_CHANGE_PEN
sprintf(debugline, "%i,%i,%i,%i,%i,%i,%i,%g,%g,%g,%g,%g,%g,%g,%g,%i,%i,0\n", iIteration, ipu, isp, pu[ipu].id, spec[isp].name, R[ipu], iZone, spec[isp].target, SM[ism].amount, spec[isp].amount, rNewAmount, change.shortfall, rNewShortfall, rShortFraction, rNewShortFraction, iCurrentShortfall, iNewShortfall);
AppendDebugFile("debug_MarZone_PewChangePen.csv", debugline, fnames);
AppendDebugTraceFile("iteration,ipu,isp,puid,spid,Zone,newZone,Target,PUAmount,Amount,newAmount,Shortfall,newShortfall,rSF,rNSF,iCSF,iNSF,zone\n");
AppendDebugTraceFile(debugline);
#endif
*/
}
if (spec.specList[isp].targetocc > 0)
{
if (spec.specList[isp].targetocc > speciesAmounts[isp].occurrence)
{
rOldShortfall += spec.specList[isp].targetocc - speciesAmounts[isp].occurrence;
rShortFraction += (spec.specList[isp].targetocc - speciesAmounts[isp].occurrence) / spec.specList[isp].targetocc;
iCurrentShortfall++;
}
if (spec.specList[isp].targetocc > iNewOccurrence)
{
rNewShortfall += spec.specList[isp].targetocc - iNewOccurrence;
rNewShortFraction += (spec.specList[isp].targetocc - iNewOccurrence) / spec.specList[isp].targetocc;
iNewShortfall++;
}
}
}
// compute existing & proposed shortfall for this feature across any relevant zone targets
// only necessary if zoneTarget is set
if (zones.zoneTarget.size())
for (int k: zonesToTarget)
{
iArrayIndex = (isp * zones.zoneCount) + k;
double currZoneAmount = zoneSpec[iArrayIndex].amount;
double currZoneOcc = zoneSpec[iArrayIndex].occurrence;
// compute amount of feature if change is made
if (k == iPreZone) // zone is existing zone, reduce zone amount by amount at site
{
change.zoneTargetChange.push_back(pair<int, double>(iArrayIndex, -pu.puvspr[ism].amount));
change.zoneOccChange.push_back(-1); // reduce occ by 1
rNewAmount = currZoneAmount - pu.puvspr[ism].amount;
iNewOccurrence = currZoneOcc - 1;
}
else // zone is proposed zone, increase zone amount by amount at site
{
change.zoneTargetChange.push_back(pair<int, double>(iArrayIndex, pu.puvspr[ism].amount));
change.zoneOccChange.push_back(1); // add occ by one.
rNewAmount = currZoneAmount + pu.puvspr[ism].amount;
iNewOccurrence = currZoneOcc + 1;
}
// do we have areal zone target?
double currZoneTarget = zones.zoneTarget[isp][k].target;
if (currZoneTarget > 0)
{
// compute existing shortfall
if (currZoneTarget > currZoneAmount)
{
rOldShortfall += currZoneTarget - currZoneAmount;
rShortFraction += (currZoneTarget - currZoneAmount) / currZoneTarget;
iCurrentShortfall++;
}
// compute proposed shortfall
if (currZoneTarget > rNewAmount)
{
rNewShortfall += currZoneTarget - rNewAmount;
rNewShortFraction += (currZoneTarget - rNewAmount) / currZoneTarget;
iNewShortfall++;
}
/*
#ifdef DEBUG_PEW_CHANGE_PEN
sprintf(debugline, "%i,%i,%i,%i,%i,%i,%i,%g,%g,%g,%g,%g,%g,%g,%g,%i,%i,1\n", iIteration, ipu, isp, pu[ipu].id, spec[isp].name, R[ipu], iZone, zones.zoneTarget[i][j].target, SM[ism].amount, ZoneSpec[iArrayIndex].amount, rNewAmount, change.shortfall, rNewShortfall, rShortFraction, rNewShortFraction, iCurrentShortfall, iNewShortfall);
AppendDebugFile("debug_MarZone_PewChangePen.csv", debugline, fnames);
AppendDebugTraceFile("iteration,ipu,isp,puid,spid,Zone,newZone,ZoneTarget,PUAmount,Amount,newAmount,Shortfall,newShortfall,rSF,rNSF,iCSF,iNSF,zone\n");
AppendDebugTraceFile(debugline);
#endif
*/
}
// do we have occurrence zone target?
double currZoneTargetOcc = zones.zoneTarget[isp][k].occurrence;
if (currZoneTargetOcc > 0)
{
// compute existing shortfall
if (currZoneTargetOcc > currZoneOcc)
{
rOldShortfall += currZoneTargetOcc - currZoneOcc;
rShortFraction += (currZoneTargetOcc - currZoneOcc) / currZoneTargetOcc;
iCurrentShortfall++;
}
// compute proposed shortfall
if (currZoneTargetOcc > iNewOccurrence)
{
rNewShortfall += currZoneTargetOcc - iNewOccurrence;
rNewShortFraction += (currZoneTargetOcc - iNewOccurrence) / currZoneTargetOcc;
iNewShortfall++;
}
}
}
if (rNewShortFraction - rShortFraction != 0)
{
rDeltaPenalty = spec.specList[isp].penalty * spec.specList[isp].spf * (rNewShortFraction - rShortFraction);
/* renable if needed
#ifdef DEBUG_PEW_CHANGE_PEN
// rDeltaPenalty,spec[isp].penalty,spec[isp].spf,rNewShortFraction,rShortFraction
AppendDebugTraceFile("rDeltaPenalty,spec.penalty,spec.spf,rNewShortFraction,rShortFraction\n");
sprintf(debugline, "%g,%g,%g,%g,%g\n", rDeltaPenalty, spec[isp].penalty, spec[isp].spf, rNewShortFraction, rShortFraction);
AppendDebugTraceFile(debugline);
#endif
*/
rSumDeltaPenalty += rDeltaPenalty;
change.shortfall += rNewShortfall - rOldShortfall;
}
} // Only worry about PUs where species occurs
/* renable if needed
#ifdef DEBUG_PEW_CHANGE_PEN
sprintf(debugline, "rSumDeltaPenalty %g\n", rSumDeltaPenalty);
AppendDebugTraceFile(debugline);
#endif
#ifdef DEBUG_CHANGE_PEN
sprintf(debugline, "%i,%g,%g,%g,%g,%g,%g\n",
spec[isp].name, spec[isp].target, _ZoneTarget[(isp * iZoneCount) + R[ipu] - 1].target,
_ZoneTarget[(isp * iZoneCount) + iZone - 1].target, rOldShortfall, rNewShortfall, rDeltaPenalty);
AppendDebugTraceFile(debugline);
#endif
*/
}
}
/* renable if needed
#ifdef DEBUG_CHANGE_PEN
sprintf(debugline,"ChangePen end rSumDeltaPenalty %g\n",rSumDeltaPenalty);
AppendDebugTraceFile(debugline);
#endif
*/
return rSumDeltaPenalty;
}
// Computes the change in value of a pu from preZone to postZone
void CheckChangeValue(schange& change, int puindex, int iPreZone, int iPostZone, Pu& pu, Zones& zones, Species& spec,
double costthresh, double blm, double tpf1 = 0, double tpf2 = 0, double timeprop = 1) {
int imode = 1;
double threshpen = 0;
// Change cost only if there's zone cost adjustment
if (zones.availableZoneCost)
{
auto& puCostArray = pu.puList[puindex].costBreakdown;
change.cost = zones.AggregateTotalCostByPuAndZone(iPostZone, puCostArray) - zones.AggregateTotalCostByPuAndZone(iPreZone, puCostArray);
}
// Connection cost
if (pu.connectionsEntered)
change.connection = zones.ConnectionCost2(pu, puindex, imode, solution, iPostZone, blm)
- zones.ConnectionCost2(pu, puindex, imode, solution, iPreZone, blm);
change.penalty = ComputeChangePenalty(pu, zones, spec, change, puindex, iPreZone, iPostZone);
if (costthresh)
{ // Threshold Penalty for costs
if (objective.cost + objective.connection <= costthresh)
{
if (change.cost + change.connection + objective.cost + objective.connection <= costthresh)
threshpen = 0;
else
threshpen = (change.cost + change.connection +
objective.cost + objective.connection - costthresh) *
ThresholdPenalty(tpf1, tpf2, timeprop);
}
else
{
if (change.cost + change.connection + objective.cost + objective.connection <= costthresh)
threshpen = (objective.cost + objective.connection - costthresh) * ThresholdPenalty(tpf1, tpf2, timeprop);
else
threshpen = (change.cost + change.connection) * ThresholdPenalty(tpf1, tpf2, timeprop);
}
}
change.threshpen = threshpen;
change.total = change.cost + change.connection + change.penalty + change.threshpen;
/*
#ifdef DEBUGCHECKCHANGE
if (iDebugMode)
{
sprintf(debugline,"%i,%i,%i,%g,%g,%g,%g,%g\n",ipu,pu[ipu].id,R[ipu],change->total,change->cost,change->connection,change->penalty,change->threshpen);
AppendDebugFile("debug_MarZone_CheckChange.csv",debugline,fnames);
}
#endif
#ifdef DEBUGCHECKCHANGE
if (iDebugMode)
AppendDebugTraceFile("CheckChange end\n");
#endif
*/
//return change;
}
// Applies changes described. Switches puindex to zone, and applies scost change.
void ApplyChange(int ipu, int iZone, schange& change, Pu& pu, Zones& zones, Species& spec) {
int i,ism,isp, iPreviousZone, iArrayIndexDestination;
double rAmount, rCurrentContribAmount, rNewContribAmount;
objective.cost += change.cost;
objective.connection += change.connection;
objective.penalty += change.penalty;
objective.shortfall += change.shortfall;
// iterate over amount/target changes and any clumping
for (int i = 0; i < change.specListChangeTarget.size(); i++) {
isp = change.specListChangeTarget[i].first; // contains spindex
if (change.specListChangeTarget[i].second != 0) { //only need to worry if there's an actual change
// Apply amounts as usual
speciesAmounts[isp].amount += change.specListChangeTarget[i].second;
speciesAmounts[isp].occurrence += change.specListChangeOcc[i];
}
/* feature does not work - disable for now.
if (spec[isp].sepnum > 0) // Count separation but only if it is possible that it has changed
if ((imode == 1 && spec[isp].separation < spec[isp].sepnum) || (imode == -1 && spec[isp].separation > 1))
spec[isp].separation = CountSeparation2(isp, 0, NULL, puno, R, pu, SM, spec, 0);
*/
}
// Iterate through clump changes (if any)
for (int i = 0; i < change.speciesClumpChange.size(); i++) {
isp = change.specListChangeTarget[i].first; // contains spindex
if (change.specListChangeTarget[i].second) {
// add or modify existing pu clump
AddNewPuToClump(ipu, isp, change.specListChangeTarget[i].second);
}
else {
// Contrib is now 0, remove
RemovePuFromClump(ipu, isp);
}
}
// Iterate through zone changes
int ind;
for (int i = 0; i < change.zoneTargetChange.size(); i++) {
ind = change.zoneTargetChange[i].first;
zoneSpec[ind].amount += change.zoneTargetChange[i].second;
zoneSpec[ind].occurrence += change.zoneOccChange[i];
}
solution[ipu] = iZone; // change the zone set in solution
objective.total = objective.cost + objective.connection + objective.penalty;
}
// Writes the current solution to a file.
void WriteSolution(string filename, Pu &pu, Zones& zones, int imode)
{
ofstream myfile;
myfile.open(filename);
if (imode > 1)
myfile << "planning_unit,zone\n";
for (int i = 0; i < pu.puno; i++)
{
if (imode > 1)
myfile << pu.puList[i].id << "," << zones.IndexToId(solution[i]) << "\n";
}
myfile.close();
}
void WriteZoneConnectivitySum(string filename, Pu &pu, Zones &zones, int imode)
{
vector<vector<double>> ZCS = zones.InitializeZoneMatrix();
//string delim = imode > 1 ? "," : " ";
ComputeZoneConnectivitySum(pu, ZCS); // populate ZCS
ofstream myfile;
myfile.open(filename);
if (imode > 1)
myfile << "\"Zone_Connectivity_Sum\"";
for (int i = 0; i < zones.zoneCount; i++)
myfile << ",\"" << zones.IndexToName(i) << "\"";
myfile << "\n";
// write a data row for each zone
for (int i = 0; i < zones.zoneCount; i++)
{
myfile << "\"" << zones.IndexToName(i) << "\"";
for (int j = 0; j < zones.zoneCount; j++)
myfile << "," << ZCS[i][j];
myfile << "\n";
}
myfile.close();
}
// Given zones and pu, and using current solution.
void ComputeZoneConnectivitySum(Pu &pu, vector<vector<double>> &ZCS)
{
if (pu.connectionsEntered) // only applies if pu has connections
{
for (int i = 0; i < pu.puno; i++)
{
// fixed cost for ipu is between this zone and itself
ZCS[solution[i]][solution[i]] += pu.connections[i].fixedcost;
// traverse connections for this ipu
for (sneighbour &p : pu.connections[i].first)
{
if (p.nbr > i) // avoid double counting connnections
{
if (solution[i] != solution[p.nbr]) // ignore internal connections within a zone
{
// connections are symmetric
ZCS[solution[i]][solution[p.nbr]] += p.cost;
ZCS[solution[p.nbr]][solution[i]] += p.cost;
}
}
}
}
}
}
/* * * * * Greedy Species Penalty * * * * * * * * * * * */
double GreedyPen(int ipu, Pu& pu, Species& spec)
{
double famount = 0.0, fold, newamount, newpen;
// Get all spec contribs for the given ipu
vector<double> specValuesForPu = pu.RtnAmountAllSpecAtPu(ipu, spec.spno);
for (int i = 0; i < spec.spno; i++)
{
fold = (spec.specList[i].target - speciesAmounts[i].amount);
if (fold > 0)
{
if (spec.specList[i].target2)
{
// Convert contribution down to tagret4 penalty version.
double newSpecValue = PartialPen4(spec.specList[i].target2, specValuesForPu[i]);
newpen = spec.specList[i].target - speciesAmounts[i].amount - newSpecValue;
}
else
{
newpen = spec.specList[i].target - speciesAmounts[i].amount - specValuesForPu[i];
}
newamount = (newpen < 0) ? 0 : newpen;
famount += (newamount - fold) * spec.specList[i].spf;
} /* Add new penalty if species isn't already in the system */
}
return (famount); /* Negative means decrease in amount missing */
} /** Greedy Species Penalty **/
/**** Partial Penalty for type 4 species ***/
double PartialPen4(double target2, double amount)
{
if (amount >= target2)
return (amount); /* I'm not a partial penalty */
else
switch (clumptype)
{
case 0:
return (0.0); /* default step function */
case 1:
return (amount / 2.0); /* nicer step function */
case 2:
if (target2)
return (amount / target2 * amount);
default:
return (0.0);
}
} /* Partial Penalty for type 4 species */
// * * * * ****** Value of a Zonation System * * * *
// Note! This call is expensive as it does a full recompute of the reserve value, based on the current solution.
void EvaluateObjectiveValue(Pu &pu, Species &spec, Zones &zones, double blm)
{
// Evaluate the existing solution and update the scost values
objective.cost = 0, objective.penalty = 0, objective.connection = 0, objective.shortfall = 0;
double rShortfall, iShortfall, rShortFraction, rTotalShortfall = 0;
int specZoneIndex, iMissingFeatures = 0;
ComputeSpeciesAmounts(pu, spec, zones);
for (int i = 0; i < spec.spno; i++) {
rShortfall = 0;
iShortfall = 0;
rShortFraction = 0;
// shortfall with respect to overall targets
if (spec.specList[i].target > 0)
{
if (spec.specList[i].target > speciesAmounts[i].amount)
{
rShortfall += spec.specList[i].target - speciesAmounts[i].amount;
rShortFraction += (spec.specList[i].target - speciesAmounts[i].amount) / spec.specList[i].target;
iShortfall++;
objective.shortfall += spec.specList[i].target - speciesAmounts[i].amount;
}
}
if (spec.specList[i].targetocc > 0)
{
if (spec.specList[i].targetocc > speciesAmounts[i].occurrence)
{
rShortfall += spec.specList[i].targetocc - speciesAmounts[i].occurrence;
rShortFraction += (spec.specList[i].targetocc - speciesAmounts[i].occurrence) / spec.specList[i].targetocc;
iShortfall++;
objective.shortfall += spec.specList[i].targetocc - speciesAmounts[i].occurrence;
}
}
// shortfall with respect to zone targets (removing pu from existing zone)
// loop through all zones to compute target achievement (only necessary if zoneTarget set)
if (zones.zoneTarget.size())
for (int k = 0; k < zones.zoneCount; k++)
{
specZoneIndex = (i * zones.zoneCount) + k;
if (zones.zoneTarget[i][k].target > 0)
if (zones.zoneTarget[i][k].target > zoneSpec[specZoneIndex].amount)
{
rShortfall += zones.zoneTarget[i][k].target - zoneSpec[specZoneIndex].amount;
rShortFraction += (zones.zoneTarget[i][k].target - zoneSpec[specZoneIndex].amount) / zones.zoneTarget[i][k].target;
iShortfall++;
objective.shortfall += zones.zoneTarget[i][k].target - zoneSpec[specZoneIndex].amount;
}
if (zones.zoneTarget[i][k].occurrence > 0)
if (zones.zoneTarget[i][k].occurrence > zoneSpec[specZoneIndex].occurrence)
{
rShortfall += zones.zoneTarget[i][k].occurrence - zoneSpec[specZoneIndex].occurrence;
rShortFraction += (zones.zoneTarget[i][k].occurrence - zoneSpec[specZoneIndex].occurrence) / zones.zoneTarget[i][k].occurrence;
iShortfall++;
objective.shortfall += zones.zoneTarget[i][k].occurrence - zoneSpec[specZoneIndex].occurrence;
}
}
rTotalShortfall += rShortfall;
iMissingFeatures += iShortfall;
objective.penalty += rShortFraction * spec.specList[i].penalty * spec.specList[i].spf;
/*
if (fDebugPenaltyNegative)
{
fprintf(DebugFile,"%i,%i,%g,%g,%g,%g\n",i,spec[i].name,rCurrentShortfall,spec[i].penalty,spec[i].spf,reserve->penalty);
//"i,SPID,shortfall,spec_penalty,spf,reserve_penalty"
}
#ifdef DEBUG_ZONATION_COST
sprintf(debugbuffer,"ZonationCost spid %i targ %g reserved %g Shortfall %g rShort %g missing features %i spec.pen %g spec.spf %g\n"
,spec[i].name,spec[i].target,spec[i].amount,rShortfall,rCurrentShortfall,iShortfall,spec[i].penalty,spec[i].spf);
AppendDebugTraceFile(debugbuffer);
#endif
*/
}
for (int j = 0; j < pu.puno; j++)
{
objective.cost += zones.AggregateTotalCostByPuAndZone(solution[j], pu.puList[j].costBreakdown);
if (pu.connectionsEntered)
{
objective.connection += zones.ConnectionCost2Linear(pu, j, 1, solution, blm); // confirm imode 1
}
}
objective.total = objective.cost + objective.connection + objective.penalty;
}
// Writes amounts related to species amounts in this particular reserve to a file.
// See zones.WriteZoneTargetHeaders for header structure.
void WriteSpeciesAmounts(string filename, Species &spec, Zones &zones, int imode, double misslevel)
{
ofstream myfile;
myfile.open(filename, ofstream::app); // append mode
double rMPM, rTestMPM, rTarget, rAmountHeld;
int rOccurrenceTarget, rOccurrencesHeld;
string temp, d = imode > 1 ? "," : "\t";
for (int isp = 0; isp < spec.spno; isp++)
{
rMPM = 1;
// Write species status
myfile << spec.specList[isp].name << d << spec.specList[isp].sname << d << spec.specList[isp].target;
if (imode > 1)
myfile << d << spec.specList[isp].totalarea;
else
myfile << d << speciesAmounts[isp].amount;
myfile << d << speciesAmounts[isp].amount << d << spec.specList[isp].targetocc << d << speciesAmounts[isp].occurrence;
temp = ReturnStringIfTargetMet(spec.specList[isp].target, speciesAmounts[isp].amount,
spec.specList[isp].targetocc, speciesAmounts[isp].occurrence, rMPM, misslevel);
myfile << d << temp;
int iZoneArrayIndex;
if (zones.zoneTarget.size())
for (int i = 0; i < zones.zoneCount; i++)
{
iZoneArrayIndex = (isp * zones.zoneCount) + i;
rTarget = zones.zoneTarget[isp][i].target;
rAmountHeld = zoneSpec[iZoneArrayIndex].amount;
rOccurrenceTarget = zones.zoneTarget[isp][i].occurrence;
rOccurrencesHeld = zoneSpec[iZoneArrayIndex].occurrence;
myfile << d << rTarget << d << rAmountHeld << d << zones.zoneContribValues[iZoneArrayIndex]*rAmountHeld << d << rOccurrenceTarget << d << rOccurrencesHeld;
temp = ReturnStringIfTargetMet(rTarget, rAmountHeld, rOccurrenceTarget, rOccurrencesHeld, rMPM, misslevel);
myfile << d << temp;
}
myfile << d << rMPM << "\n";
}
myfile.close();
}
// Not threadsafe.
void AppendSolutionsMatrix(string filename, int zoneCount, int delimType, int iIncludeHeaders) {
stringstream text;
string sDelimiter = delimType == 3 ? "," : " ";
for (int i = 1; i <= zoneCount; i++)
{
if (iIncludeHeaders == 1)
{
text << "Z" << i << "S" << id << sDelimiter;
}
for (int j = 0; j < solution.size(); j++)
{
if (j > 0)
text << sDelimiter;
if (solution[j] == i-1)
text << "1";
else
text << "0";
}
text << "\n";
}
// open file for as little time as possible.
ofstream myfile;
myfile.open(filename, ofstream::app);
myfile << text.str();
myfile.close();
}
// Not threadsafe.
void AppendSolutionsMatrixZone(string filename, int iZone, int delimType, int iIncludeHeaders)
{
stringstream text;
string sDelimiter = delimType == 3 ? "," : " ";
if (iIncludeHeaders == 1)
{
text << "S" << id << sDelimiter;
}
for (int j = 0; j < solution.size(); j++)
{
if (j > 0)
text << sDelimiter;
if (solution[j] == iZone)
text << "1";