Feature/vdyp 400 grow qmd+lh

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

@@ -0,0 +1,10 @@
+package ca.bc.gov.nrs.vdyp.application;
+
+public class InitializationIncompleteException extends RuntimeException {
+
+	private static final long serialVersionUID = -4549468703592060502L;
+
+	public InitializationIncompleteException(String reason) {
+		super(reason);
+	}
+}

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

@@ -41,13 +41,14 @@
 import ca.bc.gov.nrs.vdyp.common.Utils;
 import ca.bc.gov.nrs.vdyp.common.ValueOrMarker;
 import ca.bc.gov.nrs.vdyp.common_calculators.BaseAreaTreeDensityDiameter;
+import ca.bc.gov.nrs.vdyp.controlmap.ResolvedControlMapImpl;
 import ca.bc.gov.nrs.vdyp.io.FileSystemFileResolver;
 import ca.bc.gov.nrs.vdyp.io.parse.coe.UpperCoefficientParser;
 import ca.bc.gov.nrs.vdyp.io.parse.common.ResourceParseException;
 import ca.bc.gov.nrs.vdyp.io.parse.control.BaseControlParser;
 import ca.bc.gov.nrs.vdyp.io.parse.streaming.StreamingParser;
 import ca.bc.gov.nrs.vdyp.io.parse.streaming.StreamingParserFactory;
-import ca.bc.gov.nrs.vdyp.io.write.VriAdjustInputWriter;
+import ca.bc.gov.nrs.vdyp.io.write.VdypOutputWriter;
 import ca.bc.gov.nrs.vdyp.math.FloatMath;
 import ca.bc.gov.nrs.vdyp.model.BaseVdypLayer;
 import ca.bc.gov.nrs.vdyp.model.BaseVdypPolygon;
@@ -164,7 +165,7 @@ protected static void doMain(VdypStartApplication<?, ?, ?, ?> app, final String.
 				.filter(x -> !x.getName().contains("Volume")).toList();
 	}
 
-	protected VriAdjustInputWriter vriWriter;
+	protected VdypOutputWriter vriWriter;
 
 	protected Map<String, Object> controlMap = new HashMap<>();
 
@@ -226,7 +227,7 @@ public void init(FileSystemFileResolver resolver, Map<String, Object> controlMap
 
 		setControlMap(controlMap);
 		closeVriWriter();
-		vriWriter = new VriAdjustInputWriter(controlMap, resolver);
+		vriWriter = new VdypOutputWriter(controlMap, resolver);
 	}
 
 	protected abstract BaseControlParser getControlFileParser();
@@ -240,7 +241,7 @@ void closeVriWriter() throws IOException {
 
 	protected void setControlMap(Map<String, Object> controlMap) {
 		this.controlMap = controlMap;
-		this.estimationMethods = new EstimationMethods(controlMap);
+		this.estimationMethods = new EstimationMethods(new ResolvedControlMapImpl(controlMap));
 	}
 
 	protected <T> StreamingParser<T> getStreamingParser(ControlKey key) throws ProcessingException {
@@ -271,8 +272,8 @@ 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 +294,8 @@ 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;
@@ -323,7 +324,7 @@ protected List<S> findPrimarySpecies(Collection<S> allSpecies) {
 				continue;
 			}
 			var groupPrimary = copySpecies(
-					// groupSpecies.size() is at least 2 so findFirest will not be empty
+					// groupSpecies.size() is at least 2 so findFirst will not be empty
 					groupSpecies.stream().sorted(PERCENT_GENUS_DESCENDING).findFirst().orElseThrow(), builder -> {
 						var total = (float) groupSpecies.stream().mapToDouble(BaseVdypSpecies::getPercentGenus).sum();
 						builder.percentGenus(total);
@@ -507,7 +508,7 @@ public int findEmpiricalRelationshipParameterIndex(String specAlias, BecDefiniti
 		return group;
 	}
 
-	protected VriAdjustInputWriter getVriWriter() {
+	protected VdypOutputWriter getVriWriter() {
 		return vriWriter;
 	}
 
@@ -533,8 +534,8 @@ 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);
@@ -847,8 +848,8 @@ 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));
@@ -1192,7 +1193,8 @@ 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))
 				);
 			}
@@ -1210,7 +1212,8 @@ 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))
 				);
 			}
@@ -1227,9 +1230,8 @@ 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) {
@@ -1244,28 +1246,28 @@ 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
 					);
 				}
 			}
@@ -1316,12 +1318,12 @@ 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()
 			);
 		}
 		{
@@ -1354,14 +1356,14 @@ 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();
 			hlVector.scalarInPlace((float x, UtilizationClass uc) -> ba.get(uc) > 0 ? x / ba.get(uc) : x);
 
-			// Update percent based on updated areas 
+			// Update percent based on updated areas
 			vdypLayer.getSpecies().values().stream().forEach(spec -> {
 				spec.setPercentGenus(100 * spec.getBaseAreaByUtilization().getAll() / ba.getAll());
 			});
@@ -1456,44 +1458,38 @@ protected void computeUtilizationComponentsVeteran(VdypLayer vdypLayer, BecDefin
 				var adjust = new Coefficients(new float[] { 0f, 0f, 0f, 0f }, 1);
 
 				// EMP091
-				EstimationMethods.estimateWholeStemVolume(
-						controlMap, utilizationClass, volumeAdjustCoe.getCoe(1), vdypSpecies.getVolumeGroup(), hlSp,
+				estimationMethods.estimateWholeStemVolume(
+						utilizationClass, volumeAdjustCoe.getCoe(1), vdypSpecies.getVolumeGroup(), hlSp,
 						quadMeanDiameterUtil, baseAreaUtil, wholeStemVolumeUtil
 				);
 
 				adjust.setCoe(4, volumeAdjustCoe.getCoe(2));
 				// EMP092
-				EstimationMethods.estimateCloseUtilizationVolume(
-						controlMap, utilizationClass, adjust, vdypSpecies.getVolumeGroup(), hlSp, quadMeanDiameterUtil,
+				estimationMethods.estimateCloseUtilizationVolume(
+						utilizationClass, adjust, vdypSpecies.getVolumeGroup(), hlSp, quadMeanDiameterUtil,
 						wholeStemVolumeUtil, closeUtilizationVolumeUtil
 				);
 
 				adjust.setCoe(4, volumeAdjustCoe.getCoe(3));
 				// EMP093
-				EstimationMethods.estimateNetDecayVolume(
-						controlMap, vdypSpecies.getGenus(), bec.getRegion(), utilizationClass, adjust,
-						vdypSpecies.getDecayGroup(), vdypLayer.getBreastHeightAge().orElse(0f), quadMeanDiameterUtil,
-						closeUtilizationVolumeUtil, closeUtilizationNetOfDecayUtil
+				estimationMethods.estimateNetDecayVolume(
+						vdypSpecies.getGenus(), bec.getRegion(), utilizationClass, adjust, vdypSpecies.getDecayGroup(),
+						vdypLayer.getBreastHeightAge().orElse(0f), quadMeanDiameterUtil, closeUtilizationVolumeUtil,
+						closeUtilizationNetOfDecayUtil
 				);
 
 				adjust.setCoe(4, volumeAdjustCoe.getCoe(4));
 				// EMP094
-				final var netDecayCoeMap = Utils.<Map<String, Coefficients>>expectParsedControl(
-						controlMap, ControlKey.VOLUME_NET_DECAY_WASTE, java.util.Map.class
-				);
-				final var wasteModifierMap = Utils.<MatrixMap2<String, Region, Float>>expectParsedControl(
-						controlMap, ControlKey.WASTE_MODIFIERS, ca.bc.gov.nrs.vdyp.model.MatrixMap2.class
-				);
-				EstimationMethods.estimateNetDecayAndWasteVolume(
-						bec.getRegion(), utilizationClass, adjust, vdypSpecies.getGenus(), hlSp, netDecayCoeMap,
-						wasteModifierMap, quadMeanDiameterUtil, closeUtilizationVolumeUtil,
-						closeUtilizationNetOfDecayUtil, closeUtilizationNetOfDecayAndWasteUtil
+				estimationMethods.estimateNetDecayAndWasteVolume(
+						bec.getRegion(), utilizationClass, adjust, vdypSpecies.getGenus(), hlSp, quadMeanDiameterUtil,
+						closeUtilizationVolumeUtil, closeUtilizationNetOfDecayUtil,
+						closeUtilizationNetOfDecayAndWasteUtil
 				);
 
 				if (getId().isStart()) {
 					// EMP095
-					EstimationMethods.estimateNetDecayWasteAndBreakageVolume(
-							controlMap, utilizationClass, vdypSpecies.getBreakageGroup(), quadMeanDiameterUtil,
+					estimationMethods.estimateNetDecayWasteAndBreakageVolume(
+							utilizationClass, vdypSpecies.getBreakageGroup(), quadMeanDiameterUtil,
 							closeUtilizationVolumeUtil, closeUtilizationNetOfDecayAndWasteUtil,
 							closeUtilizationNetOfDecayWasteAndBreakageUtil
 					);