private Set<Long> parseMechanisms(String keyword) throws IOException {
checkDup(keyword);
Set<Long> mechs = new HashSet<Long>();
parseEquals();
parseOpenBraces();
while (true) {
int token = nextToken();
if (isCloseBraces(token)) {
break;
}
if (token == TT_EOL) {
continue;
}
if (token != TT_WORD) {
throw excToken("Expected mechanism, read");
}
long mech = parseMechanism(st.sval);
mechs.add(Long.valueOf(mech));
}
if (DEBUG) {
System.out.print("mechanisms: [");
for (Long mech : mechs) {
System.out.print(Functions.getMechanismName(mech));
System.out.print(", ");
}
System.out.println("]");
}
return mechs;
}
private long parseObjectClass() throws IOException {
String name = parseWord();
try {
return Functions.getObjectClassId(name);
} catch (IllegalArgumentException e) {
throw excLine("Unknown object class " + name);
}
}
private long decodeAttributeName(String name) throws IOException {
if (isNumber(name)) {
return decodeNumber(name);
} else {
try {
return Functions.getAttributeId(name);
} catch (IllegalArgumentException e) {
throw excLine("Unknown attribute name " + name);
}
}
}
private long parseMechanism(String mech) throws IOException {
if (isNumber(mech)) {
return decodeNumber(mech);
} else {
try {
return Functions.getMechanismId(mech);
} catch (IllegalArgumentException e) {
throw excLine("Unknown mechanism: " + mech);
}
}
}
private long parseKeyAlgorithm() throws IOException {
String name = parseWord();
if (isNumber(name)) {
return decodeNumber(name);
} else {
try {
return Functions.getKeyId(name);
} catch (IllegalArgumentException e) {
throw excLine("Unknown key algorithm " + name);
}
}
}
/**
* Save a generated biomass dataset to an HDF5 file in the output directory given by the outputDir
* attribute.
*
* @param biomass The generated biomass as a (num_timesteps) x (num_nodes) array
* @param nodeIDs The node IDs. The order must correspond to the columns of the biomass array
* @param matchingTimesteps The matching timesteps returned by getMatchingTimesteps()
* @param nodeConfig The node configuration string used to generate the data
* @param numTimesteps The number of time steps of biomass data to save
*/
private void saveHDF5OutputFile(
double[][] biomass,
int[] nodeIDs,
int[] matchingTimesteps,
String nodeConfig,
int numTimesteps) {
// Determine the filename
File file = Functions.getNewOutputFile(new File(outputDir), "ATN", ".h5");
System.out.println("Writing output to " + file.toString());
// Write the data to the output file
IHDF5Writer writer = HDF5Factory.configure(file).writer();
if (Constants.ROUND_BIOMASS) {
// Scale biomass for consistency with CSV output.
// Round and cast to 32-bit integers to facilitate deflate compression.
// Note: there is technically a risk of integer overflow,
// but it won't happen unless scaled biomass exceeds 2 billion.
int[][] scaledBiomass = new int[numTimesteps][nodeIDs.length];
for (int t = 0; t < numTimesteps; t++) {
for (int i = 0; i < nodeIDs.length; i++) {
scaledBiomass[t][i] = (int) Math.round((biomass[t][i] * Constants.BIOMASS_SCALE));
}
}
writer.int32().writeMatrix("biomass", scaledBiomass, HDF5IntStorageFeatures.INT_DEFLATE);
} else {
// Scale biomass for consistency with CSV output, but do not round.
double[][] scaledBiomass = new double[numTimesteps][nodeIDs.length];
for (int t = 0; t < numTimesteps; t++) {
for (int i = 0; i < nodeIDs.length; i++) {
scaledBiomass[t][i] = (biomass[t][i] * Constants.BIOMASS_SCALE);
}
}
writer.float64().writeMatrix("biomass", scaledBiomass);
}
writer.writeIntArray("node_ids", nodeIDs);
if (matchingTimesteps != null) writer.writeIntArray("matching_timesteps", matchingTimesteps);
writer.string().setAttr("/", "node_config", nodeConfig);
writer.close();
}
@Override
public String getHelpFile() {
return Functions.getResourcePath() + "/plugin/android-device/help-buildConfig.html";
}
private void initOutputStreams() {
System.out.println("Ecosystem output will be written to:");
System.out.println("Network output will be written to:");
// psATN = Functions.getPrintStream("ATN", userInput.destDir);
psATN = Functions.getPrintStream("ATN", outputDir);
}
// loop through current job/results, assembling dataset
private HashMap<Integer, SpeciesZoneType> genSpeciesDataset(
SimJob job,
EcosystemTimesteps ecosysTimesteps,
Map<Integer, NodeRelationships> ecosysRelationships) {
// calc information relevant to entire ecosystem
int speciesCnt = ecosysTimesteps.getNodeList().size(); // Number of species
int timesteps = ecosysTimesteps.getTimesteps(); // Maximum number of timesteps to run simulation
int timestepsToSave = 0; // Number of timesteps of data to save to output file
int[] matchingTimesteps =
null; // Array of matching timesteps returned by findMatchingTimesteps()
// read in link parameters; this was explicitly configured to allow
// manipulation of link parameter values, but no manipulation is
// performed in this version
LinkParams lPs = new LinkParams(propertiesConfig);
// loop through node values and assemble summary data
int[] speciesID = new int[speciesCnt];
SimJobSZT[] sztArray = new SimJobSZT[speciesCnt];
int spNum = 0;
for (NodeTimesteps nodeTimesteps : ecosysTimesteps.getTimestepMapValues()) {
SimJobSZT sjSzt = job.getSpeciesZoneByNodeId(nodeTimesteps.getNodeId());
sztArray[spNum] = sjSzt;
speciesID[spNum] = sjSzt.getNodeIndex();
spNum++;
}
// define objects to track species' contributions
double[][][] contribs = new double[timesteps][speciesCnt][speciesCnt];
double[][] calcBiomass = new double[timesteps][speciesCnt];
double[][] contribsT; // current timestep
// note: WebServices ATN Model uses B0 with default = 0.5. This presumes
// that biomasses are small, i.e. < 1.0. Division by biomassScale
// here is consistent with usage in WoB_Server.SimulationEngine to
// normalize biomasses.
// need to store bm as it varies over time through integration;
// start with initial bm for each species
double[] currBiomass = new double[speciesCnt];
for (int i = 0; i < speciesCnt; i++) {
NodeTimesteps nodeTimeSteps = ecosysTimesteps.getTimestepMap().get(speciesID[i]);
// manually set biomass vals for excluded initial timesteps; this
// includes the first value to be used as input
currBiomass[i] = nodeTimeSteps.getBiomass(initTimeIdx) / biomassScale;
calcBiomass[0][i] = currBiomass[i];
}
if (Constants.useCommonsMathIntegrator) {
// Use Apache Commons Math GraggBulirschStoerIntegrator
FirstOrderIntegrator integrator =
new GraggBulirschStoerIntegrator(
1.0e-8, // minimal step
100.0, // maximal step
ATNEquations.EXTINCT, // allowed absolute error
1.0e-10); // allowed relative error
// Set up the ATN equations based on the current food web and parameters
ATNEquations ode = new ATNEquations(sztArray, ecosysRelationships, lPs);
ATNEventHandler eventHandler = new ATNEventHandler(ode);
// FIXME: Choose best parameter values
integrator.addEventHandler(
new EventFilter(eventHandler, FilterType.TRIGGER_ONLY_DECREASING_EVENTS),
1, // maximal time interval between switching function checks (this interval prevents
// missing sign changes in case the integration steps becomes very large)
0.0001, // convergence threshold in the event time search
1000, // upper limit of the iteration count in the event time search
new BisectionSolver());
// Set up the StepHandler, which is triggered at each time step by the integrator,
// and copies the current biomass of each species into calcBiomass[timestep].
// See the "Continuous Output" section of
// https://commons.apache.org/proper/commons-math/userguide/ode.html
FixedStepHandler fixedStepHandler =
new FixedStepHandler() {
public void init(double t0, double[] y0, double t) {}
private int timestep = 0;
public void handleStep(double t, double[] y, double[] yDot, boolean isLast) {
// Ensure we don't go past the last time step due to rounding error
if (timestep < calcBiomass.length) {
System.arraycopy(y, 0, calcBiomass[timestep], 0, speciesCnt);
}
timestep++;
}
};
StepHandler stepHandler = new StepNormalizer(timeIntvl, fixedStepHandler);
integrator.addStepHandler(stepHandler);
// Run the integrator to compute the biomass time series
integrator.integrate(ode, 0.0, currBiomass, timeIntvl * timesteps, currBiomass);
if (eventHandler.integrationWasStopped()) {
timestepsToSave = (int) (eventHandler.getTimeStopped() / timeIntvl);
} else {
// Check for an oscillating steady state,
// and only save the data through the first period of the oscillation
matchingTimesteps = findMatchingTimesteps(calcBiomass, timesteps - 1);
System.err.println("\nmatchingTimesteps = " + Arrays.toString(matchingTimesteps));
// Save timesteps up through the second matching timestep,
// or all timesteps if there was no second matching timestep.
if (matchingTimesteps[1] != -1) {
timestepsToSave = matchingTimesteps[1] + 1;
} else {
timestepsToSave = timesteps;
}
}
} else {
// Use BulirschStoerIntegration
// create integration object
boolean isTest = false;
BulirschStoerIntegration bsi =
new BulirschStoerIntegration(
timeIntvl, speciesID, sztArray, ecosysRelationships, lPs, maxBSIErr, equationSet);
// calculate delta-biomass and biomass "contributions" from each related
// species
for (int t = initTimeIdx + 1; t < timesteps; t++) {
boolean success = bsi.performIntegration(time(initTime, t), currBiomass);
if (!success) {
System.out.printf("Integration failed to converge, t = %d\n", t);
System.out.print(bsi.extrapArrayToString(biomassScale));
break;
}
currBiomass = bsi.getYNew();
System.arraycopy(currBiomass, 0, calcBiomass[t], 0, speciesCnt);
contribsT = bsi.getContribs();
for (int i = 0; i < speciesCnt; i++) {
System.arraycopy(contribsT[i], 0, contribs[t - 1][i], 0, speciesCnt);
}
} // timestep loop
}
if (useHDF5) {
saveHDF5OutputFile(
calcBiomass, speciesID, matchingTimesteps, job.getNode_Config(), timestepsToSave);
return null;
}
double[][] webServicesData = new double[speciesCnt][timesteps];
if (Constants.useSimEngine) { // We need the webServicesData only for marginOfErrorCalculation
// extract timestep data from CSV
Functions.extractCSVDataRelns(job.getCsv(), ecosysTimesteps, ecosysRelationships);
spNum = 0;
for (NodeTimesteps nodeTimesteps : ecosysTimesteps.getTimestepMapValues()) {
// copy nodetimestep data to local array for easier access
System.arraycopy(nodeTimesteps.getBiomassArray(), 0, webServicesData[spNum], 0, timesteps);
spNum++;
}
}
// output data
// A. print header
psATN.printf("timesteps");
for (int i = 0; i < timesteps; i++) {
psATN.printf(",%d", i);
}
psATN.println();
/* Convert to CSV String */
String biomassCSV = "";
biomassCSV = "Manipulation_id: " + job.getATNManipulationId() + "\n\n";
int maxTimestep = job.getTimesteps();
// Create Timestep Labels
for (int j = 1; j <= maxTimestep; j++) {
biomassCSV += "," + j;
}
HashMap<Integer, SpeciesZoneType> mSpecies = new HashMap<Integer, SpeciesZoneType>();
// loop through each species
for (int i = 0; i < speciesCnt; i++) {
if (Constants.useSimEngine) {
psATN.printf("i.%d.sim", speciesID[i]);
// B. print WebServices simulation data for species
for (int t = 0; t < timesteps; t++) {
psATN.printf(",%9.0f", webServicesData[i][t]);
}
psATN.println();
}
// B. print combined biomass contributions (i.e. locally calculated biomass)
// for current species.
psATN.printf("i.%d.calc", speciesID[i]);
for (int t = 0; t < timesteps; t++) {
psATN.printf(",%9.0f", calcBiomass[t][i] * biomassScale);
}
psATN.println();
// //C. print individual biomass contributions from other species
// for (int j = 0; j < speciesCnt; j++) {
// psATN.printf("i.%d.j.%d.", speciesID[i], speciesID[j]);
// for (int t = 0; t < timesteps; t++) {
// psATN.printf(",%9.0f", contribs[t][i][j] * biomassScale);
// }
// psATN.println();
// }
float extinction = 1.E-15f;
SimJobSZT sjSzt = job.getSpeciesZoneByNodeId(speciesID[i]);
// add nodes to list in the order that they are received from infos
String name = sjSzt.getName().replaceAll(",", " ") + " [" + sjSzt.getNodeIndex() + "]";
String tempStr = name;
for (int t = 0; t < maxTimestep; t++) {
tempStr += ",";
double biomass = calcBiomass[t][i] * biomassScale;
if (biomass > 0) {
tempStr += biomass > extinction ? Math.ceil(biomass) : 0;
}
if (t == maxTimestep - 1) {
SpeciesZoneType szt = null;
if (!mSpecies.containsKey(sjSzt.getNodeIndex())) {
szt = new SpeciesZoneType(sjSzt.getName(), sjSzt.getNodeIndex(), 0, 0, biomass, null);
mSpecies.put(sjSzt.getNodeIndex(), szt);
} else { // update existing species current biomass
szt = mSpecies.get(sjSzt.getNodeIndex());
szt.setCurrentBiomass(biomass);
}
}
}
biomassCSV += "\n" + tempStr;
}
// Append node config to the ATN CSV
psATN.println();
psATN.println("\"node-config: " + job.getNode_Config() + "\"");
biomassCSV += "\n\n";
biomassCSV += job.getConsumeMap().toString() + "\n\n";
biomassCSV += job.getPathTable().toString();
job.setBiomassCsv(biomassCSV);
// System.out.println(biomassCSV);
return mSpecies;
}