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Dev merge: connectivity and defaults for eggTemp, mortSal #6

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merged 4 commits into from
Feb 5, 2025
Merged

Dev merge: connectivity and defaults for eggTemp, mortSal #6

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2669666
continuous tally of connectivity via arrivals rather than once per ho…
Sz-Tim Jan 31, 2025
8d329eb
only calculate connectivity if needed; connect depth 2 bug fix
Sz-Tim Feb 3, 2025
0ac1cfd
modified logistic mortality defaults
Sz-Tim Feb 3, 2025
5a85b3e
updated defaults for eggTemp to reflect estimated Adult Females, not …
Sz-Tim Feb 4, 2025
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32 changes: 19 additions & 13 deletions biotracker/Arrival.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,28 +16,34 @@
* @author sa01ta
*/
public class Arrival {
private final int sourceLocation;
private final int arrivalLocation;
private final double arrivalTime;
private final String sourceSiteID;
private final String arrivalSiteID;
private final int arrivalStatus;
private final double arrivalDepth;
private final double arrivalDensity;

public Arrival(int sourceLocation, int arrivalLocation, double arrivalTime, double arrivalDensity) {
this.sourceLocation = sourceLocation;
this.arrivalLocation = arrivalLocation;
this.arrivalTime = arrivalTime;
public Arrival(String sourceSiteID, String arrivalSiteID, int arrivalStatus, double arrivalDepth, double arrivalDensity) {
this.sourceSiteID = sourceSiteID;
this.arrivalSiteID = arrivalSiteID;
this.arrivalStatus = arrivalStatus;
this.arrivalDepth = arrivalDepth;
this.arrivalDensity = arrivalDensity;
}

public int getSourceLocation() {
return this.sourceLocation;
public String getSourceSiteID() {
return this.sourceSiteID;
}

public int getArrivalLocation() {
return this.arrivalLocation;
public String getArrivalSiteID() {
return this.arrivalSiteID;
}

public double getArrivalTime() {
return this.arrivalTime;
public int getArrivalStatus() {
return this.arrivalStatus;
}

public double getArrivalDepth() {
return this.arrivalDepth;
}

public double getArrivalDensity() {
Expand Down
25 changes: 0 additions & 25 deletions biotracker/IOUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -994,31 +994,6 @@ public static void particleLocsToNetcdfFile() {
}


public static void arrivalToFile(Particle p, ISO_datestr currentDate, double currentTime, String filename, boolean append) {
try {
// Create file
FileWriter fstream = new FileWriter(filename, append);
PrintWriter out = new PrintWriter(fstream);
out.printf("%d,%s,%.2f,%s,%s,%.2f,%s,%f,%f\n",
p.getID(),
p.getStartDate().getDateStr(),
p.getStartTime(),
p.getStartID(),
currentDate.getDateStr(),
currentTime,
p.getLastArrival(),
p.getAge(),
p.getDensity()
);

//Close the output stream
out.close();
} catch (Exception e) {//Catch exception if any
System.err.println("Error: " + e.getMessage());
}
}


/**
* Print (append) single particle location to file
*/
Expand Down
29 changes: 9 additions & 20 deletions biotracker/ParallelParticleMover.java
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Original file line number Diff line number Diff line change
Expand Up @@ -109,20 +109,11 @@ public static void move(Particle part, double elapsedHours, int hour, int step,

// Get local salinity, temperature
if (!rp.readHydroVelocityOnly) {
if (rp.fixDepth) {
if (rp.needS) {
localSalinity = hf.getAvgFromTrinodes(m, part.getLocation(), part.getDepthLayer(), part.getElem(), hour, "salinity", rp);
}
if (rp.needT) {
localTemperature = hf.getAvgFromTrinodes(m, part.getLocation(), part.getDepthLayer(), part.getElem(), hour, "temp", rp);
}
} else {
if (rp.needS) {
localSalinity = hf.getValueAtDepth(m, part, part.getLocation(), part.getDepth(), hour, "salinity", rp, nearestLayers);
}
if (rp.needT) {
localTemperature = hf.getValueAtDepth(m, part, part.getLocation(), part.getDepth(), hour, "temp", rp, nearestLayers);
}
if (rp.needS) {
localSalinity = hf.getValueAtDepth(m, part, part.getLocation(), part.getDepth(), hour, "salinity", rp, nearestLayers);
}
if (rp.needT) {
localTemperature = hf.getValueAtDepth(m, part, part.getLocation(), part.getDepth(), hour, "temp", rp, nearestLayers);
}
}

Expand Down Expand Up @@ -267,18 +258,16 @@ public static void move(Particle part, double elapsedHours, int hour, int step,
}

// **************** if able to settle, is it close to a possible settlement location? ******************************
if (part.isInfectious() || rp.connectImmature) {
if (rp.recordConnectivity && (part.isInfectious() || rp.connectImmature)) {
for (HabitatSite site : habitatEnd) {
double dist = Particle.distanceEuclid2(part.getLocation()[0], part.getLocation()[1],
site.getLocation()[0], site.getLocation()[1], rp.coordOS);
if (dist < rp.connectivityThresh && !part.hasSettledThisHour()) { // TODO: I think this doesn't make sense? Necessary for part.setLastArrival(site.getID()) for connectivity though.
if (rp.endOnArrival && part.isInfectious()) {
if (dist < rp.connectivityThresh) {
part.addArrival(new Arrival(part.getStartID(), site.getID(), part.getStatus(), part.getDepth(), part.getDensity() * subStepDt / rp.dt));
if (rp.endOnArrival) {
part.setArrived(true);
part.setStatus(3);
}
part.setSettledThisHour(true);
part.setLastArrival(site.getID());
break;
}
}
}
Expand Down
35 changes: 9 additions & 26 deletions biotracker/Particle.java
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Original file line number Diff line number Diff line change
Expand Up @@ -52,22 +52,18 @@ public class Particle {
private boolean arrived = false;
private boolean viable = false;
private boolean free = false;
private boolean settledThisHour = false;
private boolean boundaryExit = false;

private String species = "sealice";

private String lastArrival = "0";

private double xTotal = 0;
private double yTotal = 0;
private double xyTotal = 0;
private double zTotal = 0;

// A list to store data on the arrivals made by each particle.
// If rp.endOnArrival=true, this will contain a maximum of one element.
// --- Not presently used ---
private List<Arrival> arrivals;
private ArrayList<Arrival> arrivals = new ArrayList<>();

public Particle(double xstart, double ystart, double startDepth, String startSiteID, int startIndex, int id, double mortalityRate,
ISO_datestr startDate, double startTime, boolean coordOS, String species) {
Expand Down Expand Up @@ -129,13 +125,16 @@ public String toString() {
return this.getID() + " " + Arrays.toString(this.xy);
}

// Not presently used
public void reportArrival(int sourceLocation, int arrivalLocation, double arrivalTime, double arrivalDensity) {
arrivals.add(new Arrival(sourceLocation, arrivalLocation, arrivalTime, arrivalDensity));
public ArrayList<Arrival> getArrivals() {
return this.arrivals;
}

public List<Arrival> getArrivals() {
return this.arrivals;
public void addArrival(Arrival arrival) {
this.arrivals.add(arrival);
}

public void clearArrivals() {
this.arrivals.clear();
}

public void setReleaseTime(double releaseTime) {
Expand Down Expand Up @@ -370,18 +369,6 @@ public void setArrived(boolean arrived) {
this.arrived = arrived;
}

public void setLastArrival(String loc) {
this.lastArrival = loc;
}

public String getLastArrival() {
return this.lastArrival;
}

public void setSettledThisHour(boolean settled) {
this.settledThisHour = settled;
}

public void setFree(boolean free) {
this.free = free;
}
Expand All @@ -398,10 +385,6 @@ public boolean hasArrived() {
return this.arrived;
}

public boolean hasSettledThisHour() {
return this.settledThisHour;
}

public boolean isFree() {
return this.free;
}
Expand Down
74 changes: 29 additions & 45 deletions biotracker/Particle_track.java
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Expand Up @@ -358,45 +358,38 @@ public static void main(String[] args) throws Exception {
IOUtils.particlesToRestartFile(particles, currentHour, "locations_" + today + ".csv", true, rp, 1); // rp.nparts * rp.numberOfDays * 10
}


double elapsedHourRemainder = Math.round((elapsedHours % 1) * 100.0) / 100.0;
if (elapsedHourRemainder == 1 || elapsedHourRemainder == 0) {
// It's the end of an hour, so if particles are allowed to infect more than once, reactivate them
for (Particle part : particles) {
if (part.hasSettledThisHour()) {
if (part.isInfectious()) { // copepodids
// Save arrival
if (rp.recordArrivals) {
IOUtils.arrivalToFile(part, currentIsoDate, currentHour, "arrivals_" + today + ".csv", true);
}
// Add arrival to connectivity file
int destIndex = siteEndNames.indexOf(part.getLastArrival());
double pDepth = part.getDepth();
if (pDepth >= rp.connectDepth1_min && pDepth <= rp.connectDepth1_max) {
connectivity[part.getStartIndex()][destIndex] += (float) part.getDensity();
}
if (rp.recordConnectivityDepth2 && pDepth >= rp.connectDepth2_min && pDepth <= rp.connectDepth2_max) {
connectivityDepth2[part.getStartIndex()][destIndex] += (float) part.getDensity();
}
} else if (rp.connectImmature & part.getStatus()==1) { // nauplii
// Add arrival to connectivity file
int destIndex = siteEndNames.indexOf(part.getLastArrival());
double pDepth = part.getDepth();
if (pDepth >= rp.connectDepth1_min && pDepth <= rp.connectDepth1_max) {
connectivityImmature[part.getStartIndex()][destIndex] += (float) part.getDensity();
}
if (rp.recordConnectivityDepth2 && pDepth >= rp.connectDepth2_min && pDepth <= rp.connectDepth2_max) {
connectivityImmatureDepth2[part.getStartIndex()][destIndex] += (float) part.getDensity();
// update connectivity
if (rp.recordConnectivity) {
for (Particle particle : particles) {
if (particle.getArrivals() != null) {
for (Arrival arrival : particle.getArrivals()) {
int destIndex = siteEndNames.indexOf(arrival.getArrivalSiteID());
if (arrival.getArrivalStatus() == 2) { // copepodids
if (arrival.getArrivalDepth() >= rp.connectDepth1_min &&
arrival.getArrivalDepth() <= rp.connectDepth1_max) {
connectivity[particle.getStartIndex()][destIndex] += (float) arrival.getArrivalDensity();
}
if (rp.recordConnectivityDepth2 &&
arrival.getArrivalDepth() >= rp.connectDepth2_min &&
arrival.getArrivalDepth() <= rp.connectDepth2_max) {
connectivityDepth2[particle.getStartIndex()][destIndex] += (float) arrival.getArrivalDensity();
}
} else if (rp.connectImmature && arrival.getArrivalStatus() == 1) {
if (arrival.getArrivalDepth() >= rp.connectDepth1_min &&
arrival.getArrivalDepth() <= rp.connectDepth1_max) {
connectivityImmature[particle.getStartIndex()][destIndex] += (float) arrival.getArrivalDensity();
}
if (rp.recordConnectivityDepth2 &&
arrival.getArrivalDepth() >= rp.connectDepth2_min &&
arrival.getArrivalDepth() <= rp.connectDepth2_max) {
connectivityImmatureDepth2[particle.getStartIndex()][destIndex] += (float) arrival.getArrivalDensity();
}
}
}

// Reset ability to settle
part.setSettledThisHour(false);
}
}
}


// Hourly updates to pstep arrays
if (rp.recordPsteps) {
IOUtils.pstepsUpdater(particles, rp, pstepsMature, pstepsImmature, rp.dt);
Expand Down Expand Up @@ -431,6 +424,9 @@ public static void main(String[] args) throws Exception {
connectivityImmatureDepth2 = new float[habitat.size()][habitatEnd.size()];
}
}
for (Particle particle : particles) {
particle.clearArrivals();
}
}

if (rp.recordVertDistr) {
Expand Down Expand Up @@ -916,18 +912,6 @@ public static int[] particleCountStatus(List<Particle> parts, int[] previousStat
}


// calculate a connectivity matrix detailing the
public static double[][] connectFromParticleArrivals(List<Particle> particles, int nStartLocs, int nEndLocs, int npartsPerSite) {
double[][] connectMatrix = new double[nStartLocs][nEndLocs];
for (Particle part : particles) {
for (Arrival arrival : part.getArrivals()) {
connectMatrix[arrival.getSourceLocation()][arrival.getArrivalLocation()] += arrival.getArrivalDensity() / npartsPerSite;
}
}
return connectMatrix;
}


public static int[] nonZeroVals(int[] A) {
int count = 0;
for (int j : A) {
Expand Down
8 changes: 4 additions & 4 deletions biotracker/RunProperties.java
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Original file line number Diff line number Diff line change
Expand Up @@ -211,13 +211,13 @@ public RunProperties(String filename) {
case "constant" -> "28.2";
// Linear model comes from data in Kragesteen 2023 Table 1
// eggs_d = b[0] + b[1]*temperature
case "linear" -> "9.835,4.579";
case "linear" -> "8.27,3.79";
// Norwegian model uses Stien et al 2005
// eggs_d = b[0] * (temperature + b[1])^2
case "quadratic" -> "0.17,4.28";
case "quadratic" -> "0.109,8.54";
// Logistic model comes from data in Kragesteen 2023 Table 1
// eggs_d = b[0]/(1 + exp(-b[1] * (temperature - b[2]))) + b[3]
case "logistic" -> "85.94,0.4696,8.193,7.649";
case "logistic" -> "65.5,0.550,8.49,10.51";
default -> "28.2";
};
String eggTemp_b_Str = properties.getProperty("eggTemp_b", eggTemp_defaults);
Expand All @@ -233,7 +233,7 @@ public RunProperties(String filename) {
case "quadratic" -> "0.0011,1.1239,-0.07";
// estimated logistic fit to Bricknell et al. 2006 Table 1
// mort_h = b[0]/(1 + exp(-b[1] * (salinity - b[2]))) + b[3]
case "logistic" -> "0.9087,-0.6457,13.31,0.05071";
case "logistic" -> "0.941,-0.594,13.5,0.0205";
default -> "0.01";
};
String mortSal_b_Str = properties.getProperty("mortSal_b", mortSal_defaults);
Expand Down