/*
  Test run for integration using problem with known solution:
  equationSet 1:
  y' = (-y sin x + 2 tan x) y
  y(pi/6) = 2 / sqrt(3)
  exact solution: y(x) = 1 / cos x

  equationSet 2:
  y' = -200x * y^2
  y(0) = 1
  y(x) = 1 / (1 + 100x^2)

  */
  private void genODETestDataset() {
    int timesteps = 20;
    // setup values depending on ODE selected
    switch (equationSet) {
      case 1:
        initTime = Math.PI / 6.0;
        initVal = 2.0 / Math.sqrt(3.0);
        timeIntvl = 0.2;
        break;
      case 2:
        initTime = 0.0;
        initVal = 1.0;
        timeIntvl = 0.02;
        break;
      default:
        break;
    }

    double[][] bsiSoln = new double[timesteps][1];
    bsiSoln[0][0] = initVal;

    initTimeIdx = 0;
    maxBSIErr = 1.0E-3;

    initOutputStreams();

    // create integration object
    BulirschStoerIntegration bsi =
        new BulirschStoerIntegration(
            timeIntvl,
            new int[1], // needed to calc number of elements
            null,
            null,
            null,
            maxBSIErr,
            equationSet);

    // calculate integration solution
    double[] currVal = new double[1];
    currVal[0] = bsiSoln[0][0];
    for (int t = initTimeIdx + 1; t < timesteps; t++) {
      boolean success = bsi.performIntegration(time(initTime, t - 1), currVal);
      if (!success) {
        // System.out.printf("Integration failed to converge, t = %d\n", t);
        // System.out.print(bsi.extrapArrayToString(1));
        break;
      }
      currVal[0] = bsi.getYNew()[0];
      bsiSoln[t][0] = currVal[0];
    } // timestep loop

    // output data
    // A. print header
    psATN.printf("timesteps");
    for (int t = 0; t < timesteps; t++) {
      psATN.printf(",% 9.2f", time(initTime, t));
    }
    psATN.println();

    // B. print true solution: y(x) = 1 / cos x
    for (int t = 0; t < timesteps; t++) {
      // psATN.printf(",%9.2f", 1.0 / Math.cos (time(initTime, t))); //needs t++
      psATN.printf(",% 9.2f", 1.0 / (1.0 + 100.0 * Math.pow(time(initTime, t), 2.0)));
    }
    psATN.println();

    // C. print bsi solution
    for (int t = 0; t < timesteps; t++) {
      psATN.printf(",% 9.2f", bsiSoln[t][0]);
    }
    psATN.println();
  }
  // 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;
  }