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Param vector updates #418

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Param vector updates #418

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5e73ddc
Made SpatialBoundingBox a BoundingBox.
CloneDeath Jun 17, 2020
6061516
Fixed compilation issues from change of SpatialBoundingBox and Initia…
CloneDeath Jun 19, 2020
3697050
Changed P.BoundingBox to be a Geometry::BoundingBox, and updated usages.
CloneDeath Jun 22, 2020
e27c374
Replaced infectee_x/y with infectee_position. Fixed usages.
CloneDeath Jun 22, 2020
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44 changes: 22 additions & 22 deletions src/CovidSim.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,8 @@
#include <strings.h>
#endif

using namespace Geometry;

void ReadParams(char*, char*);
void ReadInterventions(char*);
int GetXMLNode(FILE*, const char*, const char*, char*, int);
Expand Down Expand Up @@ -953,7 +955,7 @@ void ReadParams(char* ParamFile, char* PreParamFile)
P.NumSeedLocations = MAX_NUM_SEED_LOCATIONS;
}
GetInputParameter(PreParamFile_dat, AdminFile_dat, "Initial number of infecteds", "%i", (void*)P.NumInitialInfections, P.NumSeedLocations, 1, 0);
if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Location of initial infecteds", "%lf", (void*)&(P.LocationInitialInfection[0][0]), P.NumSeedLocations * 2, 1, 0)) P.LocationInitialInfection[0][0] = P.LocationInitialInfection[0][1] = 0.0;
if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Location of initial infecteds", "%lf", (void*)&(P.LocationInitialInfection[0].x), P.NumSeedLocations * 2, 1, 0)) P.LocationInitialInfection[0] = Vector2<double>(0, 0);
if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Minimum population in microcell of initial infection", "%i", (void*) & (P.MinPopDensForInitialInfection), 1, 1, 0)) P.MinPopDensForInitialInfection = 0;
if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Maximum population in microcell of initial infection", "%i", (void*)&(P.MaxPopDensForInitialInfection), 1, 1, 0)) P.MaxPopDensForInitialInfection = 10000000;
if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Randomise initial infection location", "%i", (void*) & (P.DoRandomInitialInfectionLoc), 1, 1, 0)) P.DoRandomInitialInfectionLoc=1;
Expand Down Expand Up @@ -1215,15 +1217,15 @@ void ReadParams(char* ParamFile, char* PreParamFile)
P.CFR_ILI_ByAge[i] = 0.00;
}

if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Bounding box for bitmap", "%lf", (void*) & (P.BoundingBox[0]), 4, 1, 0))
if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Bounding box for bitmap", "%lf", (void*) & (P.BoundingBox.start.x), 4, 1, 0))
{
P.BoundingBox[0] = P.BoundingBox[1] = 0.0;
P.BoundingBox[2] = P.BoundingBox[3] = 1.0;
P.BoundingBox.start = Vector2<double>(0, 0);
P.BoundingBox.end = Vector2<double>(1, 1);
}
if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Spatial domain for simulation", "%lf", (void*) & (P.SpatialBoundingBox[0]), 4, 1, 0))
if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Spatial domain for simulation", "%lf", (void*) & (P.SpatialBoundingBox.start.x), 4, 1, 0))
{
P.SpatialBoundingBox[0] = P.SpatialBoundingBox[1] = 0.0;
P.SpatialBoundingBox[2] = P.SpatialBoundingBox[3] = 1.0;
P.SpatialBoundingBox.start = Vector2<double>(0, 0);
P.SpatialBoundingBox.end = Vector2<double>(1, 1);
}
if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Grid size", "%lf", (void*) & (P.in_cells_.width), 1, 1, 0)) P.in_cells_.width = 1.0 / 120.0;
if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Use long/lat coord system", "%i", (void*) & (P.DoUTM_coords), 1, 1, 0)) P.DoUTM_coords = 1;
Expand Down Expand Up @@ -2324,16 +2326,16 @@ void ReadAirTravel(char* AirTravelFile)
ERR_CRITICAL("fscanf failed in void ReadAirTravel\n");
}
traf *= (P.AirportTrafficScale * sc);
if ((Airports[i].loc.x < P.SpatialBoundingBox[0]) || (Airports[i].loc.x >= P.SpatialBoundingBox[2])
|| (Airports[i].loc.y < P.SpatialBoundingBox[1]) || (Airports[i].loc.y >= P.SpatialBoundingBox[3]))
if ((Airports[i].loc.x < P.SpatialBoundingBox.start.x) || (Airports[i].loc.x >= P.SpatialBoundingBox.end.x)
|| (Airports[i].loc.y < P.SpatialBoundingBox.start.y) || (Airports[i].loc.y >= P.SpatialBoundingBox.end.y))
{
Airports[i].loc.x = Airports[i].loc.y = -1;
Airports[i].total_traffic = 0;
}
else
{
Airports[i].loc.x -= (float)P.SpatialBoundingBox[0];
Airports[i].loc.y -= (float)P.SpatialBoundingBox[1];
Airports[i].loc.x -= (float)P.SpatialBoundingBox.start.x;
Airports[i].loc.y -= (float)P.SpatialBoundingBox.start.y;
Airports[i].total_traffic = (float)traf;
}
t = 0;
Expand Down Expand Up @@ -2778,7 +2780,8 @@ void InitModel(int run) // passing run number so we can save run number in the i
nEvents = 0;
for (int i = 0; i < P.MaxInfEvents; i++)
{
InfEventLog[i].t = InfEventLog[i].infectee_x = InfEventLog[i].infectee_y = InfEventLog[i].t_infector = 0.0;
InfEventLog[i].infectee_position = Vector2<double>(0, 0);
InfEventLog[i].t = InfEventLog[i].t_infector = 0.0;
InfEventLog[i].infectee_ind = InfEventLog[i].infector_ind = 0;
InfEventLog[i].infectee_adunit = InfEventLog[i].listpos = InfEventLog[i].infectee_cell = InfEventLog[i].infector_cell = InfEventLog[i].thread = 0;
}
Expand Down Expand Up @@ -2827,8 +2830,8 @@ void SeedInfection(double t, int* NumSeedingInfections_byLocation, int rf, int r
{
if ((!P.DoRandomInitialInfectionLoc) || ((P.DoAllInitialInfectioninSameLoc) && (rf))) //// either non-random locations, doing all initial infections in same location, and not initializing.
{
k = (int)(P.LocationInitialInfection[i][0] / P.in_microcells_.width);
l = (int)(P.LocationInitialInfection[i][1] / P.in_microcells_.height);
k = (int)(P.LocationInitialInfection[i].x / P.in_microcells_.width);
l = (int)(P.LocationInitialInfection[i].y / P.in_microcells_.height);
j = k * P.get_number_of_micro_cells_high() + l;
m = 0;
for (k = 0; (k < NumSeedingInfections_byLocation[i]) && (m < 10000); k++)
Expand All @@ -2841,8 +2844,7 @@ void SeedInfection(double t, int* NumSeedingInfections_byLocation, int rf, int r
//only reset the initial location if rf==0, i.e. when initial seeds are being set, not when imported cases are being set
if (rf == 0)
{
P.LocationInitialInfection[i][0] = Households[Hosts[l].hh].loc.x;
P.LocationInitialInfection[i][1] = Households[Hosts[l].hh].loc.y;
P.LocationInitialInfection[i] = Vector2<double>(Households[Hosts[l].hh].loc);
}
Hosts[l].infector = -2;
Hosts[l].infect_type = INFECT_TYPE_MASK - 1;
Expand Down Expand Up @@ -2874,8 +2876,7 @@ void SeedInfection(double t, int* NumSeedingInfections_byLocation, int rf, int r
{
if (CalcPersonSusc(l, 0, 0, 0) > 0)
{
P.LocationInitialInfection[i][0] = Households[Hosts[l].hh].loc.x;
P.LocationInitialInfection[i][1] = Households[Hosts[l].hh].loc.y;
P.LocationInitialInfection[i] = Vector2<double>(Households[Hosts[l].hh].loc);
Hosts[l].infector = -2; Hosts[l].infect_type = INFECT_TYPE_MASK - 1;
DoInfect(l, t, 0, run);
m = 0;
Expand Down Expand Up @@ -2910,8 +2911,7 @@ void SeedInfection(double t, int* NumSeedingInfections_byLocation, int rf, int r
{
if (CalcPersonSusc(l, 0, 0, 0) > 0)
{
P.LocationInitialInfection[i][0] = Households[Hosts[l].hh].loc.x;
P.LocationInitialInfection[i][1] = Households[Hosts[l].hh].loc.y;
P.LocationInitialInfection[i] = Vector2<double>(Households[Hosts[l].hh].loc);
Hosts[l].infector = -2; Hosts[l].infect_type = INFECT_TYPE_MASK - 1;
DoInfect(l, t, 0, run);
m = 0;
Expand Down Expand Up @@ -3409,7 +3409,7 @@ void SaveResults(void)
sprintf(outname, "%s.ge" DIRECTORY_SEPARATOR "%s.%i.png", OutFile, OutFile, i + 1);
fprintf(dat, "<Icon>\n<href>%s</href>\n</Icon>\n", outname);
fprintf(dat, "<LatLonBox>\n<north>%.10f</north>\n<south>%.10f</south>\n<east>%.10f</east>\n<west>%.10f</west>\n</LatLonBox>\n",
P.SpatialBoundingBox[3], P.SpatialBoundingBox[1], P.SpatialBoundingBox[2], P.SpatialBoundingBox[0]);
P.SpatialBoundingBox.end.y, P.SpatialBoundingBox.start.y, P.SpatialBoundingBox.end.x, P.SpatialBoundingBox.start.x);
fprintf(dat, "</GroundOverlay>\n");
}
fprintf(dat, "</Document>\n</kml>\n");
Expand Down Expand Up @@ -4261,7 +4261,7 @@ void SaveEvents(void)
for (i = 0; i < nEvents; i++)
{
fprintf(dat, "%i\t%.10f\t%i\t%i\t%i\t%i\t%i\t%.10f\t%.10f\t%.10f\t%i\t%i\n",
InfEventLog[i].type, InfEventLog[i].t, InfEventLog[i].thread, InfEventLog[i].infectee_ind, InfEventLog[i].infectee_cell, InfEventLog[i].listpos, InfEventLog[i].infectee_adunit, InfEventLog[i].infectee_x, InfEventLog[i].infectee_y, InfEventLog[i].t_infector, InfEventLog[i].infector_ind, InfEventLog[i].infector_cell);
InfEventLog[i].type, InfEventLog[i].t, InfEventLog[i].thread, InfEventLog[i].infectee_ind, InfEventLog[i].infectee_cell, InfEventLog[i].listpos, InfEventLog[i].infectee_adunit, InfEventLog[i].infectee_position.x, InfEventLog[i].infectee_position.y, InfEventLog[i].t_infector, InfEventLog[i].infector_ind, InfEventLog[i].infector_cell);
}
fclose(dat);
}
Expand Down
4 changes: 2 additions & 2 deletions src/Dist.cpp
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Expand Up @@ -34,11 +34,11 @@ double dist2UTM(double x1, double y1, double x2, double y2)
y -= yi;
x = (1 - x) * sinx[(int)xi] + x * sinx[((int)xi) + 1];
y = (1 - y) * sinx[(int)yi] + y * sinx[((int)yi) + 1];
yt = fabs(y1 + P.SpatialBoundingBox[1]);
yt = fabs(y1 + P.SpatialBoundingBox.start.y);
yi = floor(yt);
cy1 = yt - yi;
cy1 = (1 - cy1) * cosx[((int)yi)] + cy1 * cosx[((int)yi) + 1];
yt = fabs(y2 + P.SpatialBoundingBox[1]);
yt = fabs(y2 + P.SpatialBoundingBox.start.y);
yi = floor(yt);
cy2 = yt - yi;
cy2 = (1 - cy2) * cosx[((int)yi)] + cy2 * cosx[((int)yi) + 1];
Expand Down
6 changes: 6 additions & 0 deletions src/Geometry/Vector2.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,12 @@

using namespace Geometry;

Vector2<double> Geometry::operator+(const Vector2<double> &left, const Vector2<float> &right){
return left + Vector2<double>(right);
}
Vector2<double> Geometry::operator+(const Vector2<float> &left, const Vector2<double> &right){
return Vector2<double>(left) + right;
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Suggested change
return Vector2<double>(left) + right;
return right + Vector2<double>(left);

Uses associativity of addition here. In that case, if you change something in one of the two, you don't have to change the other one.

}
Vector2<double> Geometry::operator*(const Vector2<double> &left, const Vector2<float> &right){
return left * Vector2<double>(right);
}
Expand Down
2 changes: 2 additions & 0 deletions src/Geometry/Vector2.h
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Expand Up @@ -149,6 +149,8 @@ namespace Geometry {
return Vector2<U>((U)this->x, (U)this->y);
}

Vector2<double> operator+(const Vector2<double> &left, const Vector2<float> &right);
Vector2<double> operator+(const Vector2<float> &left, const Vector2<double> &right);
Vector2<double> operator*(const Vector2<double> &left, const Vector2<float> &right);
Vector2<double> operator*(const Vector2<float> &left, const Vector2<double> &right);

Expand Down
4 changes: 3 additions & 1 deletion src/Model.h
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Expand Up @@ -185,7 +185,9 @@ const std::size_t ResultsDoubleOffsetStart = offsetof(Results, S) / sizeof(doubl
*/
struct Events
{
double infectee_x, infectee_y, t, t_infector;
Geometry::Vector2<double> infectee_position;

double t, t_infector;
int run, infectee_ind, infector_ind, type, infectee_adunit, listpos, infectee_cell, infector_cell, thread;
};

Expand Down
13 changes: 11 additions & 2 deletions src/Param.h
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Expand Up @@ -8,6 +8,7 @@
#include "MicroCellPosition.hpp"

#include "Geometry/Size.h"
#include "Geometry/BoundingBox.h"

/** @brief Enumeration of bitmap formats. */
enum struct BitmapFormats
Expand Down Expand Up @@ -80,7 +81,11 @@ struct Param
int ResetSeeds,KeepSameSeeds, ResetSeedsPostIntervention, ResetSeedsFlag, TimeToResetSeeds;
int OutputBitmap; // Whether to output a bitmap
double LongitudeCutLine; // Longitude to image earth is cut at to produce a flat map. Default -360 degrees (effectively -180). Use to ensure countries have a contiguous boundary
double SpatialBoundingBox[4], LocationInitialInfection[MAX_NUM_SEED_LOCATIONS][2], InitialInfectionsAdminUnitWeight[MAX_NUM_SEED_LOCATIONS], TimeStepsPerDay;

Geometry::BoundingBox<double> SpatialBoundingBox;
Geometry::Vector2<double> LocationInitialInfection[MAX_NUM_SEED_LOCATIONS];

double InitialInfectionsAdminUnitWeight[MAX_NUM_SEED_LOCATIONS], TimeStepsPerDay;
double FalsePositiveRate, FalsePositivePerCapitaIncidence, FalsePositiveAgeRate[NUM_AGE_GROUPS];
double latent_icdf[CDF_RES + 1], infectious_icdf[CDF_RES + 1], infectious_prof[INFPROF_RES + 1], infectiousness[MAX_INFECTIOUS_STEPS];

Expand Down Expand Up @@ -152,7 +157,11 @@ struct Param
double PlaceCloseCasePropThresh, PlaceCloseAdunitPropThresh, PlaceCloseFracIncTrig;
int DoHolidays, NumHolidays;
double HolidayEffect[NUM_PLACE_TYPES], HolidayStartTime[DAYS_PER_YEAR], HolidayDuration[DAYS_PER_YEAR];
double ColourPeriod, BoundingBox[4], BitmapScale;
double ColourPeriod;

Geometry::BoundingBox<double> BoundingBox;

double BitmapScale;
double TreatSuscDrop, TreatInfDrop, TreatDeathDrop, TreatSympDrop, TreatDelayMean, TreatTimeStart, TreatPlaceGeogDuration;
double TreatProphCourseLength, TreatCaseCourseLength, TreatPropRadial, TreatRadius, TreatRadius2, TreatCellIncThresh;
double CaseIsolation_CellIncThresh, HHQuar_CellIncThresh, DigitalContactTracing_CellIncThresh;
Expand Down
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