Checkpoint

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/application/VdypComponent.java

@@ -8,7 +8,6 @@
 import java.time.LocalTime;
 import java.util.Properties;
 
-@SuppressWarnings({ "java:S100", "java:S116" })
 public class VdypComponent {
  private static final String COPYRIGHT_HOLDER = "Government of British Columbia";
 

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/application/VdypStartApplication.java

@@ -383,13 +383,6 @@ protected List<S> findPrimarySpecies(Collection<S> allSpecies) {
  * @return
  * @throws ProcessingException
  */
- @SuppressWarnings(
- { //
- "java:S1301", // Using switch instead of if for consistency
- "java:S3776" // Inherently a lot of branching in a consistent manner, breaking into more
- // functions would make it less comprehensible
- }
- )
  protected int findItg(List<S> primarySecondary) throws StandProcessingException {
  var primary = primarySecondary.get(0);
 
@@ -747,7 +740,6 @@ public static <T> Coefficients weightedCoefficientSum(
  }
 
  // FIPLAND
- @SuppressWarnings("java:S3655")
  public float estimatePercentForestLand(P polygon, Optional<L> vetLayer, L primaryLayer) throws ProcessingException {
  if (polygon.getPercentAvailable().isPresent()) {
  return polygon.getPercentAvailable().get();

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/common/ComputationMethods.java

@@ -76,12 +76,12 @@ public ComputationMethods(EstimationMethods estimationMethods, VdypApplicationId
  }
 
  /**
- * YUC1 - compute Utilization components (quad-mean-diameter, basal area and trees-per-hectare) and,
- * optionally, volumes for a polygon's primary layer.
- * 
- * @param bec Bec zone
- * @param vdypLayer (primary) layer in question
- * @param volumeComputeMode the {@link VolumeComputeMode} under which this method is to operate
+ * YUC1 - compute Utilization components (quad-mean-diameter, basal area and trees-per-hectare) and, optionally,
+ * volumes for a polygon's primary layer.
+ *
+ * @param bec  Bec zone
+ * @param vdypLayer  (primary) layer in question
+ * @param volumeComputeMode  the {@link VolumeComputeMode} under which this method is to operate
  * @param compatibilityVariableMode the {@link CompatibilityVariableMode} under which this method is to operate.
  * @throws ProcessingException
  */

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/common/EstimationMethods.java

@@ -889,15 +889,18 @@ public float estimateBaseAreaYield(
  * @throws StandProcessingException in the event of a processing error
  */
  public float estimateQuadMeanDiameterYield(
- Coefficients coefficients, int controlVariable2Setting, float dominantHeight, float breastHeightAge,
+ Coefficients coefficients, int debugVariable2Value, float dominantHeight, float breastHeightAge,
  Optional<Float> veteranBaseArea, float upperBoundQuadMeanDiameter
  ) throws StandProcessingException {
 
  if (dominantHeight <= 5) {
  return 7.6f;
  }
 
- final float ageUse = breastHeightAge;
+ float ageUse = breastHeightAge;
+ if (debugVariable2Value > 0) {
+ ageUse = Math.min(ageUse, debugVariable2Value * 100.0f);
+ }
 
  if (ageUse <= 0f) {
  throw new StandProcessingException("Primary breast height age must be positive but was " + ageUse);
@@ -909,8 +912,8 @@ public float estimateQuadMeanDiameterYield(
  final float c1 = Math.max(coefficients.getCoe(1) + coefficients.getCoe(2) * trAge, 0f);
  final float c2 = Math.max(coefficients.getCoe(3) + coefficients.getCoe(4) * trAge, 0f);
 
- float dq = c0 + c1 * FloatMath.pow(dominantHeight - 5f, c2);
-
+ float dq = c0 + c1 * FloatMath.pow(dominantHeight - 5f, c2)
+ * FloatMath.exp(veteranBaseArea.orElse(0.0f) * coefficients.getCoe(5));
  return FloatMath.clamp(dq, 7.6f, upperBoundQuadMeanDiameter);
  }
 

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/common/ReconcilationMethods.java

@@ -80,7 +80,6 @@ public static void reconcileComponents(
  }
  }
 
- @SuppressWarnings("java:S3655")
  public static void reconcileComponentsMode1(
  UtilizationVector baseAreaUtil, UtilizationVector treesPerHectareUtil,
  UtilizationVector quadMeanDiameterUtil, float tphSumHigh
@@ -250,7 +249,6 @@ public static void reconcileComponentsMode2(
  }
  }
 
- @SuppressWarnings("java:S3655")
  public static void reconcileComponentsMode3(
  UtilizationVector baseAreaUtil, UtilizationVector treesPerHectareUtil,
  UtilizationVector quadMeanDiameterUtil

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/common/Utils.java

@@ -27,6 +27,7 @@
 import ca.bc.gov.nrs.vdyp.model.GenusDefinitionMap;
 import ca.bc.gov.nrs.vdyp.model.UtilizationClass;
 import ca.bc.gov.nrs.vdyp.model.UtilizationVector;
+import ca.bc.gov.nrs.vdyp.model.VdypEntity;
 import ca.bc.gov.nrs.vdyp.model.VdypLayer;
 import ca.bc.gov.nrs.vdyp.model.VdypSpecies;
 import ca.bc.gov.nrs.vdyp.model.VdypUtilizationHolder;
@@ -382,6 +383,37 @@ public static <T> String optPretty(Optional<T> value, Function<T, String> string
  return (String) optNa(value.map(stringify));
  }
 
+ /**
+ * If <code>f</code> is <code>null</code> or <code>f.isNan()</code> is true, this method returns
+ * <code>Optional.empty()</code> otherwise, <code>Optional.of(f)</code> is returned.
+ *
+ * @param f the Float to be made into an Optional
+ * @return as described.
+ */
+ public static Optional<Float> optFloat(Float f) {
+ assert VdypEntity.MISSING_FLOAT_VALUE.isNaN();
+ if (f == null || f.isNaN()) {
+ return Optional.empty();
+ } else {
+ return Optional.of(f);
+ }
+ }
+
+ /**
+ * If <code>f</code> is <code>null</code> or <code>f.isNan()</code> is true, this method returns
+ * <code>Optional.empty()</code> otherwise, <code>Optional.of(f)</code> is returned.
+ *
+ * @param i the Float to be made into an Optional
+ * @return as described.
+ */
+ public static Optional<Integer> optInt(Integer i) {
+ if (i == null || i == VdypEntity.MISSING_INTEGER_VALUE) {
+ return Optional.empty();
+ } else {
+ return Optional.of(i);
+ }
+ }
+
  /**
  * Iterates over all but the last entry, passing them to the first consumer then passes the last entry to the second
  * consumer

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/common/ValueOrMarker.java

@@ -12,7 +12,6 @@
  * @param <Value>
  * @param <Marker>
  */
-@SuppressWarnings("java:S119")
 public class ValueOrMarker<Value, Marker> {
  private final boolean isMarker;
  private final Object obj;

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/common_calculators/AgeToAge.java

@@ -16,7 +16,6 @@
  */
 public class AgeToAge {
 
- @SuppressWarnings("java:S3776, java:S6541, java:S1479")
  public static double ageToAge(
  SiteIndexEquation cuIndex, double sourceAge, SiteIndexAgeType sourceAgeType, SiteIndexAgeType targetAgeType,
  double years2BreastHeight

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/common_calculators/Height2SiteIndex.java

@@ -22,14 +22,12 @@
  * Height2SiteIndex.java - given age and height, computes site index. - if age is total, site index and years to breast
  * height are iterated until stable.
  */
-@SuppressWarnings("java:S1479")
 public class Height2SiteIndex {
  // Taken from sindex.h
 
  /* error codes */
  private static final int SI_ERR_NO_ANS = -4;
 
- @SuppressWarnings("java:S3776, java:S6541")
  public static double heightToIndex(
  SiteIndexEquation cuIndex, double age, SiteIndexAgeType ageType, double height,
  SiteIndexEstimationType siEstType
@@ -91,7 +89,6 @@ public static double heightToIndex(
  return index;
  }
 
- @SuppressWarnings("java:S3776, java:S6541")
  public static double
  baHeightToIndex(SiteIndexEquation cuIndex, double bhage, double height, SiteIndexEstimationType siEstType)
  throws CommonCalculatorException {
@@ -3756,7 +3753,6 @@ public static double siteIterate(SiteIndexEquation cuIndex, double age, SiteInde
 
  }
 
- @SuppressWarnings("java:S3776, java:S6541")
  public static double huGarciaQ(double siteIndex, double breastHeightAge) {
  double h, q, step, diff, lastdiff;
 

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/common_calculators/SiteIndex2Height.java

@@ -20,7 +20,6 @@
 /**
  * SiteIndex2Height.java - given site index and age, computes site height.
  */
-@SuppressWarnings("java:S1479")
 public class SiteIndex2Height {
 
  /**
@@ -2083,7 +2082,7 @@ private static double wiley(
  }
 
  height = Utils.computeInFeet(siteIndex, siteIndexFt -> {
- double x1 = 2500 / (siteIndex - 4.5);
+ double x1 = 2500 / (siteIndexFt - 4.5);
 
  double x2 = -1.7307 + 0.1394 * x1;
  double x3 = -0.0616 + 0.0137 * x1;

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/coe/HLNonprimaryCoefficientParser.java

@@ -82,9 +82,7 @@ public boolean isIgnoredLine(String line) {
  speciesIndicies, speciesIndicies, regionIndicies, MatrixMap3Impl.emptyDefault()
  );
  lineParser.parse(is, result, (value, r, line) -> {
- @SuppressWarnings("java:S117")
  var sp0_1 = (String) value.get(NON_PRIMARY_SPECIES_KEY);
- @SuppressWarnings("java:S117")
  var sp0_2 = (String) value.get(PRIMARY_SPECIES_KEY);
  var ieqn = (Integer) value.get(EQUATION_KEY);
  var region = (Region) value.get(REGION_KEY);

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/io/parse/common/ParseEntryHandler.java

@@ -13,7 +13,6 @@
  * @param <Result>
  */
 @FunctionalInterface
-@SuppressWarnings("java:S119")
 public interface ParseEntryHandler<Entry, Result> {
 
  /**

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/io/write/VdypOutputWriter.java

@@ -127,7 +127,7 @@ public void setPolygonYear(int currentYear) {
  * Write the given polygon record for the given year to the polygon file.
  *
  * @param polygon the polygon to be written
- * @param year the year of the polygon
+ * @param year  the year of the polygon
  * @throws IOException
  */
  public void writePolygonWithSpeciesAndUtilizationForYear(VdypPolygon polygon, int year) throws IOException {
@@ -143,9 +143,13 @@ public void writePolygonWithSpeciesAndUtilizationForYear(VdypPolygon polygon, in
  */
  // VDYP_OUT when JPROGRAM = 1 (FIPSTART) or 3 (VRISTART)
  public void writePolygonWithSpeciesAndUtilization(VdypPolygon polygon) throws IOException {
- 
+
  writePolygon(polygon);
- for (var layer : polygon.getLayers().values()) {
+
+ // Primary then Veteran (if present)
+ var sortedLayers = polygon.getLayers().values().stream()
+ .sorted((l1, l2) -> l1.getLayerType().getIndex() - l2.getLayerType().getIndex()).toList();
+ for (var layer : sortedLayers) {
  writeUtilization(polygon, layer, layer);
  List<VdypSpecies> specs = new ArrayList<>(layer.getSpecies().size());
  specs.addAll(layer.getSpecies().values());

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/math/FloatMath.java

@@ -41,7 +41,6 @@ public static float ceil(float f) {
  return (float) Math.ceil(f);
  }
 
- @SuppressWarnings("squid:S4274")
  public static float clamp(float x, float min, float max) {
  assert max >= min : "Maximum " + max + " was less than minimum " + min;
  if (x < min)

lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/model/GenusDefinition.java

@@ -6,7 +6,6 @@ public class GenusDefinition extends AliasedEntity implements Comparable<GenusDe
 
  private final int index;
 
- @SuppressWarnings("java:S2789")
  public GenusDefinition(String alias, int index, String name) {
  super(alias, name);
 

lib/vdyp-common/src/test/java/ca/bc/gov/nrs/vdyp/test/VdypMatchers.java

@@ -53,9 +53,9 @@
 public class VdypMatchers {
 
  static final float EPSILON = 0.001f;
- 
+
  private static float currentEpsilon = EPSILON;
- 
+
  public static void setEpsilon(float newValue) {
  currentEpsilon = newValue;
  }

lib/vdyp-forward/src/main/java/ca/bc/gov/nrs/vdyp/forward/Bank.java

@@ -12,6 +12,7 @@
 import org.slf4j.LoggerFactory;
 
 import ca.bc.gov.nrs.vdyp.application.ProcessingException;
+import ca.bc.gov.nrs.vdyp.common.Utils;
 import ca.bc.gov.nrs.vdyp.common_calculators.BaseAreaTreeDensityDiameter;
 import ca.bc.gov.nrs.vdyp.model.BecDefinition;
 import ca.bc.gov.nrs.vdyp.model.Sp64DistributionSet;
@@ -65,8 +66,7 @@ class Bank {
  public final float[/* nSpecies + 1, including 0 */][/* all ucs */] treesPerHectare; // BANK1 TPHB
  public final float[/* nSpecies + 1, including 0 */][/* all ucs */] wholeStemVolumes; // BANK1 VOLWSB
 
- public Bank(VdypLayer layer, BecDefinition becZone, Predicate<VdypSpecies> retainCriteria)
- throws ProcessingException {
+ public Bank(VdypLayer layer, BecDefinition becZone, Predicate<VdypSpecies> retainCriteria) {
 
  this.layer = layer;
  this.becZone = becZone;
@@ -185,7 +185,7 @@ void refreshBank(VdypLayer layer) throws ProcessingException {
  }
  }
 
- private void transferSpeciesIntoBank(int index, VdypSpecies species) throws ProcessingException {
+ private void transferSpeciesIntoBank(int index, VdypSpecies species) {
 
  speciesNames[index] = species.getGenus();
  sp64Distributions[index] = species.getSp64DistributionSet();
@@ -235,13 +235,12 @@ private void transferUtilizationSetIntoBank(int index, VdypUtilizationHolder uh)
  }
 
  /**
- * For each species, set uc All to the sum of the UC values, UC 7.5 and above only, 
- * for the summable values, and calculate quad-mean-diameter from these values.
+ * For each species, set uc All to the sum of the UC values, UC 7.5 and above only, for the summable values, and
+ * calculate quad-mean-diameter from these values.
  * <p>
- * For the layer, set uc All values (for summable types) to the sum of those of the
- * individual species and set the other uc values to the sum of those of the
- * individual species. Calculate the uc All value for quad-mean-diameter, and the
- * uc All and Small value for lorey-height.
+ * For the layer, set uc All values (for summable types) to the sum of those of the individual species and set the
+ * other uc values to the sum of those of the individual species. Calculate the uc All value for quad-mean-diameter,
+ * and the uc All and Small value for lorey-height.
  */
  private void setCalculateUtilizationClassAllValues() {
 
@@ -250,7 +249,7 @@ private void setCalculateUtilizationClassAllValues() {
  int ucSmallIndex = UtilizationClass.SMALL.ordinal();
 
  // Each species
- 
+
  for (int sp0Index : indices) {
 
  basalAreas[sp0Index][ucAllIndex] = sumUtilizationClassValues(
@@ -277,7 +276,7 @@ private void setCalculateUtilizationClassAllValues() {
  .quadMeanDiameter(basalAreas[sp0Index][ucAllIndex], treesPerHectare[sp0Index][ucAllIndex]);
  }
  }
- 
+
  // Layer
 
  basalAreas[layerIndex][ucAllIndex] = sumSpeciesUtilizationClassValues(basalAreas, UtilizationClass.ALL);
@@ -366,7 +365,7 @@ private float sumSpeciesUtilizationClassValues(float[][] ucValues, UtilizationCl
  *
  * @return as described
  */
- VdypLayer getLayer() {
+ VdypLayer buildLayerFromBank() {
 
  transferUtilizationsFromBank(0, layer);
 
@@ -375,7 +374,7 @@ VdypLayer getLayer() {
  newSpecies.add(transferSpeciesFromBank(i, layer.getSpecies().get(speciesNames[i])));
  }
  layer.setSpecies(newSpecies);
- 
+
  return layer;
  }
 
@@ -384,15 +383,28 @@ private VdypSpecies transferSpeciesFromBank(int index, VdypSpecies species) {
  VdypSpecies newSpecies = VdypSpecies.build(speciesBuilder -> {
  speciesBuilder.copy(species);
  speciesBuilder.percentGenus(this.percentagesOfForestedLand[index]);
- species.getSite().ifPresent(site -> speciesBuilder.addSite(VdypSite.build(siteBuilder -> {
+ species.getSite().ifPresentOrElse(site -> speciesBuilder.addSite(VdypSite.build(siteBuilder -> {
  siteBuilder.copy(site);
- siteBuilder.ageTotal(this.ageTotals[index]);
- siteBuilder.height(this.dominantHeights[index]);
- siteBuilder.siteCurveNumber(this.siteCurveNumbers[index]);
  siteBuilder.siteGenus(this.speciesNames[index]);
- siteBuilder.siteIndex(this.siteIndices[index]);
- siteBuilder.yearsToBreastHeight(this.yearsToBreastHeight[index]);
- })));
+ siteBuilder.ageTotal(Utils.optFloat(ageTotals[index]));
+ siteBuilder.height(Utils.optFloat(this.dominantHeights[index]));
+ siteBuilder.siteCurveNumber(Utils.optInt(this.siteCurveNumbers[index]));
+ siteBuilder.siteIndex(Utils.optFloat(this.siteIndices[index]));
+ siteBuilder.yearsToBreastHeight(Utils.optFloat(this.yearsToBreastHeight[index]));
+ })), () -> {
+ VdypSite site = VdypSite.build(siteBuilder -> {
+ siteBuilder.polygonIdentifier(species.getPolygonIdentifier());
+ siteBuilder.layerType(species.getLayerType());
+ siteBuilder.siteGenus(this.speciesNames[index]);
+ siteBuilder.ageTotal(Utils.optFloat(this.ageTotals[index]));
+ siteBuilder.height(Utils.optFloat(this.dominantHeights[index]));
+ siteBuilder.siteCurveNumber(Utils.optInt(this.siteCurveNumbers[index]));
+ siteBuilder.siteIndex(Utils.optFloat(this.siteIndices[index]));
+ siteBuilder.yearsToBreastHeight(Utils.optFloat(this.yearsToBreastHeight[index]));
+ });
+
+ speciesBuilder.addSite(site);
+ });
  });
 
  transferUtilizationsFromBank(index, newSpecies);