Merge pull request #55 from bcgov/feature/VdypPolygon-class-set-changes

Feature/vdyp polygon class set changes
bcgov · Aug 15, 2024 · 60006f6 · 60006f6
2 parents 2015855 + f822b2e
commit 60006f6
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Showing 128 changed files with 3,843 additions and 3,450 deletions.
diff --git a/.../vdyp/forward/GenusDefinitionMapTest.java → ...b/vdyp-common/GenusDefinitionMapTest.java b/.../vdyp/forward/GenusDefinitionMapTest.java → ...b/vdyp-common/GenusDefinitionMapTest.java
@@ -2,25 +2,21 @@
 
 import static ca.bc.gov.nrs.vdyp.test.VdypMatchers.controlMapHasEntry;
 import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.allOf;
-import static org.hamcrest.Matchers.hasItem;
 import static org.hamcrest.Matchers.hasProperty;
-import static org.hamcrest.Matchers.instanceOf;
 import static org.hamcrest.Matchers.is;
 
 import java.io.IOException;
-import java.util.List;
 import java.util.Map;
 
 import org.hamcrest.Matcher;
+import org.hamcrest.Matchers;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
 import ca.bc.gov.nrs.vdyp.common.ControlKey;
 import ca.bc.gov.nrs.vdyp.common.GenusDefinitionMap;
 import ca.bc.gov.nrs.vdyp.forward.test.VdypForwardTestUtils;
 import ca.bc.gov.nrs.vdyp.io.parse.common.ResourceParseException;
-import ca.bc.gov.nrs.vdyp.model.GenusDefinition;
 
 class GenusDefinitionMapTest {
 
@@ -35,22 +31,18 @@ void before() throws IOException, ResourceParseException {
 		controlMap = VdypForwardTestUtils.parse(parser, "VDYP.CTR");
 		assertThat(
 				controlMap,
-				(Matcher) controlMapHasEntry(
-						ControlKey.SP0_DEF, allOf(instanceOf(List.class), hasItem(instanceOf(GenusDefinition.class)))
-				)
+				(Matcher) controlMapHasEntry(ControlKey.SP0_DEF, Matchers.instanceOf(GenusDefinitionMap.class))
 		);
-
 	}
 
 	@Test
 	void test() {
-		@SuppressWarnings("unchecked")
-		var gdMap = new GenusDefinitionMap((List<GenusDefinition>) controlMap.get(ControlKey.SP0_DEF.name()));
+		var gdMap = (GenusDefinitionMap) controlMap.get(ControlKey.SP0_DEF.name());
 
 		assertThat(gdMap.contains("AC"), is(true));
-		assertThat(gdMap.get("AC"), hasProperty("alias", is("AC")));
+		assertThat(gdMap.getByAlias("AC"), hasProperty("alias", is("AC")));
 		assertThat(gdMap.getByIndex(3), hasProperty("alias", is("B")));
-		assertThat(gdMap.getIndex("B"), is(3));
-		assertThat(gdMap.getNSpecies(), is(16));
+		assertThat(gdMap.getIndexByAlias("B"), is(3));
+		assertThat(gdMap.getNGenera(), is(16));
 	}
 }
diff --git a/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/application/LowValueException.java b/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/application/LowValueException.java
@@ -13,7 +13,7 @@ public class LowValueException extends StandProcessingException {
 	final private float threshold;
 
 	public LowValueException(String message, float value, float threshold) {
-		super(String.format("%s %f was lass than %f", message, value, threshold));
+		super(String.format("%s %f was less than %f", message, value, threshold));
 		this.value = value;
 		this.threshold = threshold;
 	}

diff --git a/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/application/VdypStartApplication.java b/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/application/VdypStartApplication.java
@@ -271,8 +271,8 @@ protected Coefficients getCoeForSpecies(BaseVdypSpecies<?> species, ControlKey c
 	protected L requireLayer(P polygon, LayerType type) throws ProcessingException {
 		if (!polygon.getLayers().containsKey(type)) {
 			throw validationError(
-					"Polygon \"%s\" has no %s layer, or that layer has non-positive height or crown closure.",
-					polygon.getPolygonIdentifier(), type
+					"Polygon \"%s\" has no %s layer, or that layer has non-positive height or crown closure.", polygon
+							.getPolygonIdentifier(), type
 			);
 		}
 
@@ -293,8 +293,8 @@ protected float getPercentTotal(L layer) throws StandProcessingException {
 				.sum();
 		if (Math.abs(percentTotal - 100f) > 0.01f) {
 			throw validationError(
-					"Polygon \"%s\" has %s layer where species entries have a percentage total that does not sum to 100%%.",
-					layer.getPolygonIdentifier(), LayerType.PRIMARY
+					"Polygon \"%s\" has %s layer where species entries have a percentage total that does not sum to 100%%.", layer
+							.getPolygonIdentifier(), LayerType.PRIMARY
 			);
 		}
 		return percentTotal;
@@ -533,8 +533,8 @@ protected float estimatePrimaryBaseArea(
 
 		var decayBecAlias = bec.getDecayBec().getAlias();
 		Coefficients coe = weightedCoefficientSum(
-				List.of(0, 1, 2, 3, 4, 5), 9, 0, layer.getSpecies().values(), BaseVdypSpecies::getFractionGenus,
-				s -> coeMap.get(decayBecAlias, s.getGenus())
+				List.of(0, 1, 2, 3, 4, 5), 9, 0, layer.getSpecies()
+						.values(), BaseVdypSpecies::getFractionGenus, s -> coeMap.get(decayBecAlias, s.getGenus())
 		);
 
 		float ageToUse = clamp(breastHeightAge, 5f, 350f);
@@ -649,10 +649,6 @@ protected Optional<L> getVeteranLayer(P poly) throws StandProcessingException {
 		return Utils.optSafe(poly.getLayers().get(LayerType.VETERAN));
 	}
 
-	protected BecDefinition getBec(P poly) throws ProcessingException {
-		return Utils.getBec(poly.getBiogeoclimaticZone(), controlMap);
-	}
-
 	protected static <E extends Throwable> void throwIfPresent(Optional<E> opt) throws E {
 		if (opt.isPresent()) {
 			throw opt.get();
@@ -768,7 +764,7 @@ public float estimatePercentForestLand(P polygon, Optional<L> vetLayer, L primar
 
 		float yieldFactor = getYieldFactor(polygon);
 
-		var bec = Utils.getBec(polygon.getBiogeoclimaticZone(), controlMap);
+		var bec = polygon.getBiogeoclimaticZone();
 
 		breastHeightAge = max(5.0f, breastHeightAge);
 		// EMP040
@@ -851,8 +847,8 @@ protected float estimatePrimaryQuadMeanDiameter(
 
 		var decayBecAlias = bec.getDecayBec().getAlias();
 		Coefficients coe = weightedCoefficientSum(
-				List.of(0, 1, 2, 3, 4), 8, 0, layer.getSpecies().values(), BaseVdypSpecies::getFractionGenus,
-				s -> coeMap.get(decayBecAlias, s.getGenus())
+				List.of(0, 1, 2, 3, 4), 8, 0, layer.getSpecies()
+						.values(), BaseVdypSpecies::getFractionGenus, s -> coeMap.get(decayBecAlias, s.getGenus())
 		);
 
 		var trAge = log(clamp(breastHeightAge, 5f, 350f));
@@ -909,7 +905,7 @@ protected void applyGroups(BaseVdypPolygon<?, ?, ?, ?> fipPolygon, Collection<Vd
 			throws ProcessingException {
 		// Lookup volume group, Decay Group, and Breakage group for each species.
 
-		BecDefinition bec = Utils.getBec(fipPolygon.getBiogeoclimaticZone(), controlMap);
+		BecDefinition bec = fipPolygon.getBiogeoclimaticZone();
 		var volumeGroupMap = getGroupMap(ControlKey.VOLUME_EQN_GROUPS);
 		var decayGroupMap = getGroupMap(ControlKey.DECAY_GROUPS);
 		var breakageGroupMap = getGroupMap(ControlKey.BREAKAGE_GROUPS);
@@ -976,7 +972,7 @@ public void estimateSmallComponents(P fPoly, VdypLayer layer) throws ProcessingE
 		float treesPerHectareSum = 0f;
 		float volumeSum = 0f;
 
-		Region region = Utils.getBec(fPoly.getBiogeoclimaticZone(), controlMap).getRegion();
+		Region region = fPoly.getBiogeoclimaticZone().getRegion();
 
 		for (VdypSpecies spec : layer.getSpecies().values()) {
 			@SuppressWarnings("unused")
@@ -1196,8 +1192,7 @@ public void computeUtilizationComponentsPrimary(
 			// Calculate tree density components
 			for (var uc : VdypStartApplication.UTIL_CLASSES) {
 				treesPerHectareUtil.set(
-						uc,
-						BaseAreaTreeDensityDiameter
+						uc, BaseAreaTreeDensityDiameter
 								.treesPerHectare(baseAreaUtil.getCoe(uc.index), quadMeanDiameterUtil.get(uc))
 				);
 			}
@@ -1215,8 +1210,7 @@ public void computeUtilizationComponentsPrimary(
 
 			for (var uc : VdypStartApplication.UTIL_CLASSES) {
 				treesPerHectareUtil.setCoe(
-						uc.index,
-						BaseAreaTreeDensityDiameter
+						uc.index, BaseAreaTreeDensityDiameter
 								.treesPerHectare(baseAreaUtil.getCoe(uc.index), quadMeanDiameterUtil.getCoe(uc.index))
 				);
 			}
@@ -1233,8 +1227,9 @@ public void computeUtilizationComponentsPrimary(
 
 				// EMP091
 				estimationMethods.estimateWholeStemVolume(
-						UtilizationClass.ALL, adjustCloseUtil.getCoe(4), spec.getVolumeGroup(), loreyHeightSpec,
-						quadMeanDiameterUtil, baseAreaUtil, wholeStemVolumeUtil
+						UtilizationClass.ALL, adjustCloseUtil.getCoe(
+								4
+						), spec.getVolumeGroup(), loreyHeightSpec, quadMeanDiameterUtil, baseAreaUtil, wholeStemVolumeUtil
 				);
 
 				if (compatibilityVariableMode == CompatibilityVariableMode.ALL) {
@@ -1249,28 +1244,28 @@ public void computeUtilizationComponentsPrimary(
 
 				// EMP092
 				estimationMethods.estimateCloseUtilizationVolume(
-						UtilizationClass.ALL, adjustCloseUtil, spec.getVolumeGroup(), loreyHeightSpec,
-						quadMeanDiameterUtil, wholeStemVolumeUtil, closeVolumeUtil
+						UtilizationClass.ALL, adjustCloseUtil, spec
+								.getVolumeGroup(), loreyHeightSpec, quadMeanDiameterUtil, wholeStemVolumeUtil, closeVolumeUtil
 				);
 
 				// EMP093
 				estimationMethods.estimateNetDecayVolume(
-						spec.getGenus(), bec.getRegion(), UtilizationClass.ALL, adjustCloseUtil, spec.getDecayGroup(),
-						vdypLayer.getBreastHeightAge().orElse(0f), quadMeanDiameterUtil, closeVolumeUtil,
-						closeVolumeNetDecayUtil
+						spec.getGenus(), bec.getRegion(), UtilizationClass.ALL, adjustCloseUtil, spec
+								.getDecayGroup(), vdypLayer.getBreastHeightAge()
+										.orElse(0f), quadMeanDiameterUtil, closeVolumeUtil, closeVolumeNetDecayUtil
 				);
 
 				// EMP094
 				estimationMethods.estimateNetDecayAndWasteVolume(
-						bec.getRegion(), UtilizationClass.ALL, adjustCloseUtil, spec.getGenus(), loreyHeightSpec,
-						quadMeanDiameterUtil, closeVolumeUtil, closeVolumeNetDecayUtil, closeVolumeNetDecayWasteUtil
+						bec.getRegion(), UtilizationClass.ALL, adjustCloseUtil, spec
+								.getGenus(), loreyHeightSpec, quadMeanDiameterUtil, closeVolumeUtil, closeVolumeNetDecayUtil, closeVolumeNetDecayWasteUtil
 				);
 
 				if (this.getId().isStart()) {
 					// EMP095
 					estimationMethods.estimateNetDecayWasteAndBreakageVolume(
-							UtilizationClass.ALL, spec.getBreakageGroup(), quadMeanDiameterUtil, closeVolumeUtil,
-							closeVolumeNetDecayWasteUtil, closeVolumeNetDecayWasteBreakUtil
+							UtilizationClass.ALL, spec
+									.getBreakageGroup(), quadMeanDiameterUtil, closeVolumeUtil, closeVolumeNetDecayWasteUtil, closeVolumeNetDecayWasteBreakUtil
 					);
 				}
 			}
@@ -1321,12 +1316,12 @@ public void computeUtilizationComponentsPrimary(
 							"For species {}, Species LH (7.5cm+): {}, Species BA (7.5cm+): {}, Weighted LH (7.5cm+): {}"
 					).log();
 			vdypLayer.getLoreyHeightByUtilization().scalarInPlace(
-					UtilizationClass.SMALL,
-					x -> x + spec.getLoreyHeightByUtilization().getSmall() * spec.getBaseAreaByUtilization().getSmall()
+					UtilizationClass.SMALL, x -> x
+							+ spec.getLoreyHeightByUtilization().getSmall() * spec.getBaseAreaByUtilization().getSmall()
 			);
 			vdypLayer.getLoreyHeightByUtilization().scalarInPlace(
-					UtilizationClass.ALL,
-					x -> x + spec.getLoreyHeightByUtilization().getAll() * spec.getBaseAreaByUtilization().getAll()
+					UtilizationClass.ALL, x -> x
+							+ spec.getLoreyHeightByUtilization().getAll() * spec.getBaseAreaByUtilization().getAll()
 			);
 		}
 		{
@@ -1359,8 +1354,8 @@ protected void computeLayerUtilizationComponentsFromSpecies(VdypLayer vdypLayer)
 			vdypLayer.getSpecies().values().stream().forEach(spec -> {
 				var ba = spec.getBaseAreaByUtilization();
 				hlVector.pairwiseInPlace(
-						spec.getLoreyHeightByUtilization(),
-						(float x, float y, UtilizationClass uc) -> x + y * ba.get(uc)
+						spec.getLoreyHeightByUtilization(), (float x, float y, UtilizationClass uc) -> x
+								+ y * ba.get(uc)
 				);
 			});
 			var ba = vdypLayer.getBaseAreaByUtilization();

diff --git a/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/common/EstimationMethods.java b/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/common/EstimationMethods.java
@@ -198,8 +198,8 @@ public float estimateNonPrimaryLoreyHeight(
 		var coe = coeMap.get(vspec, vspecPrime, bec.getRegion()).orElseThrow(
 				() -> new ProcessingException(
 						String.format(
-								"Could not find Lorey Height Nonprimary Coefficients for %s %s %s", vspec, vspecPrime,
-								bec.getRegion()
+								"Could not find Lorey Height Nonprimary Coefficients for %s %s %s", vspec, vspecPrime, bec
+										.getRegion()
 						)
 				)
 		);
@@ -324,8 +324,7 @@ public float estimateQuadMeanDiameterForSpecies(
 		var limits = getLimitsForHeightAndDiameter(species, region);
 
 		quadMeanDiameter1 = estimateQuadMeanDiameterClampResult(
-				limits, standTreesPerHectare, minQuadMeanDiameter, loreyHeightSpec, baseArea1, baseArea2,
-				quadMeanDiameter1, treesPerHectare2, quadMeanDiameter2
+				limits, standTreesPerHectare, minQuadMeanDiameter, loreyHeightSpec, baseArea1, baseArea2, quadMeanDiameter1, treesPerHectare2, quadMeanDiameter2
 		);
 		return quadMeanDiameter1;
 	}
@@ -681,8 +680,7 @@ public void estimateWholeStemVolume(
 	) throws ProcessingException {
 
 		estimateWholeStemVolume(
-				controlMap, utilizationClass, adjustCloseUtil, volumeGroup, hlSp, quadMeanDiameterUtil, baseAreaUtil,
-				wholeStemVolumeUtil
+				controlMap, utilizationClass, adjustCloseUtil, volumeGroup, hlSp, quadMeanDiameterUtil, baseAreaUtil, wholeStemVolumeUtil
 		);
 	}
 
@@ -711,8 +709,7 @@ public static void estimateWholeStemVolume(
 				);
 
 		estimateWholeStemVolume(
-				utilizationClass, adjustCloseUtil, volumeGroup, hlSp, wholeStemUtilizationComponentMap,
-				quadMeanDiameterUtil, baseAreaUtil, wholeStemVolumeUtil
+				utilizationClass, adjustCloseUtil, volumeGroup, hlSp, wholeStemUtilizationComponentMap, quadMeanDiameterUtil, baseAreaUtil, wholeStemVolumeUtil
 		);
 	}
 
@@ -786,8 +783,7 @@ public void estimateCloseUtilizationVolume(
 			UtilizationVector closeUtilizationVolumeUtil
 	) throws ProcessingException {
 		estimateCloseUtilizationVolume(
-				controlMap, utilizationClass, aAdjust, volumeGroup, hlSp, quadMeanDiameterUtil, wholeStemVolumeUtil,
-				closeUtilizationVolumeUtil
+				controlMap, utilizationClass, aAdjust, volumeGroup, hlSp, quadMeanDiameterUtil, wholeStemVolumeUtil, closeUtilizationVolumeUtil
 		);
 	}
 
@@ -814,8 +810,7 @@ public static void estimateCloseUtilizationVolume(
 						controlMap, ControlKey.CLOSE_UTIL_VOLUME, MatrixMap2.class
 				);
 		estimateCloseUtilizationVolume(
-				utilizationClass, aAdjust, volumeGroup, hlSp, closeUtilizationCoeMap, quadMeanDiameterUtil,
-				wholeStemVolumeUtil, closeUtilizationVolumeUtil
+				utilizationClass, aAdjust, volumeGroup, hlSp, closeUtilizationCoeMap, quadMeanDiameterUtil, wholeStemVolumeUtil, closeUtilizationVolumeUtil
 		);
 	}
 
@@ -881,8 +876,7 @@ public void estimateNetDecayVolume(
 	) throws ProcessingException {
 
 		estimateNetDecayVolume(
-				controlMap, genus, region, utilizationClass, aAdjust, decayGroup, ageBreastHeight, quadMeanDiameterUtil,
-				closeUtilizationUtil, closeUtilizationNetOfDecayUtil
+				controlMap, genus, region, utilizationClass, aAdjust, decayGroup, ageBreastHeight, quadMeanDiameterUtil, closeUtilizationUtil, closeUtilizationNetOfDecayUtil
 		);
 	}
 
@@ -913,8 +907,7 @@ public static void estimateNetDecayVolume(
 				controlMap, ModifierParser.CONTROL_KEY_MOD301_DECAY, MatrixMap2.class
 		);
 		estimateNetDecayVolume(
-				genus, region, utilizationClass, aAdjust, decayGroup, ageBreastHeight, netDecayCoeMap, decayModifierMap,
-				quadMeanDiameterUtil, closeUtilizationUtil, closeUtilizationNetOfDecayUtil
+				genus, region, utilizationClass, aAdjust, decayGroup, ageBreastHeight, netDecayCoeMap, decayModifierMap, quadMeanDiameterUtil, closeUtilizationUtil, closeUtilizationNetOfDecayUtil
 		);
 	}
 
@@ -993,8 +986,7 @@ public void estimateNetDecayAndWasteVolume(
 	) throws ProcessingException {
 
 		estimateNetDecayAndWasteVolume(
-				controlMap, region, utilizationClass, aAdjust, genus, loreyHeight, quadMeanDiameterUtil,
-				closeUtilizationUtil, closeUtilizationNetOfDecayUtil, closeUtilizationNetOfDecayAndWasteUtil
+				controlMap, region, utilizationClass, aAdjust, genus, loreyHeight, quadMeanDiameterUtil, closeUtilizationUtil, closeUtilizationNetOfDecayUtil, closeUtilizationNetOfDecayAndWasteUtil
 		);
 	}
 
@@ -1027,9 +1019,7 @@ public static void estimateNetDecayAndWasteVolume(
 		);
 
 		estimateNetDecayAndWasteVolume(
-				region, utilizationClass, aAdjust, genus, loreyHeight, netDecayWasteCoeMap, wasteModifierMap,
-				quadMeanDiameterUtil, closeUtilizationUtil, closeUtilizationNetOfDecayUtil,
-				closeUtilizationNetOfDecayAndWasteUtil
+				region, utilizationClass, aAdjust, genus, loreyHeight, netDecayWasteCoeMap, wasteModifierMap, quadMeanDiameterUtil, closeUtilizationUtil, closeUtilizationNetOfDecayUtil, closeUtilizationNetOfDecayAndWasteUtil
 		);
 	}
 
@@ -1056,8 +1046,9 @@ public static void estimateNetDecayAndWasteVolume(
 			UtilizationVector closeUtilizationNetOfDecayUtil, UtilizationVector closeUtilizationNetOfDecayAndWasteUtil
 	) throws ProcessingException {
 		estimateUtilization(
-				closeUtilizationNetOfDecayUtil, closeUtilizationNetOfDecayAndWasteUtil, utilizationClass,
-				(i, netDecay) -> {
+				closeUtilizationNetOfDecayUtil, closeUtilizationNetOfDecayAndWasteUtil, utilizationClass, (
+						i, netDecay
+				) -> {
 					if (Float.isNaN(netDecay) || netDecay <= 0f) {
 						return 0f;
 					}
@@ -1132,8 +1123,7 @@ public void estimateNetDecayWasteAndBreakageVolume(
 	) throws ProcessingException {
 
 		estimateNetDecayWasteAndBreakageVolume(
-				controlMap, utilizationClass, breakageGroup, quadMeanDiameterUtil, closeUtilizationUtil,
-				closeUtilizationNetOfDecayAndWasteUtil, closeUtilizationNetOfDecayWasteAndBreakageUtil
+				controlMap, utilizationClass, breakageGroup, quadMeanDiameterUtil, closeUtilizationUtil, closeUtilizationNetOfDecayAndWasteUtil, closeUtilizationNetOfDecayWasteAndBreakageUtil
 		);
 	}
 
@@ -1159,8 +1149,7 @@ public static void estimateNetDecayWasteAndBreakageVolume(
 				.<Map<Integer, Coefficients>>expectParsedControl(controlMap, ControlKey.BREAKAGE, Map.class);
 
 		estimateNetDecayWasteAndBreakageVolume(
-				utilizationClass, breakageGroup, netBreakageCoeMap, quadMeanDiameterUtil, closeUtilizationUtil,
-				closeUtilizationNetOfDecayAndWasteUtil, closeUtilizationNetOfDecayWasteAndBreakageUtil
+				utilizationClass, breakageGroup, netBreakageCoeMap, quadMeanDiameterUtil, closeUtilizationUtil, closeUtilizationNetOfDecayAndWasteUtil, closeUtilizationNetOfDecayWasteAndBreakageUtil
 		);
 	}
 
@@ -1193,8 +1182,9 @@ public static void estimateNetDecayWasteAndBreakageVolume(
 		final var a4 = coefficients.getCoe(4);
 
 		estimateUtilization(
-				closeUtilizationNetOfDecayAndWasteUtil, closeUtilizationNetOfDecayWasteAndBreakageUtil,
-				utilizationClass, (uc, netWaste) -> {
+				closeUtilizationNetOfDecayAndWasteUtil, closeUtilizationNetOfDecayWasteAndBreakageUtil, utilizationClass, (
+						uc, netWaste
+				) -> {
 
 					if (netWaste <= 0f) {
 						return 0f;