Merge branch 'main' into feature/VDYP-400-grow-qmd+lh

# Conflicts: # vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/io/write/VriAdjustInputWriter.java # vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/model/BaseVdypLayer.java # vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/model/VdypLayer.java # vdyp-lib/vdyp-fip/src/main/java/ca/bc/gov/nrs/vdyp/fip/FipStart.java # vdyp-lib/vdyp-vri/src/main/java/ca/bc/gov/nrs/vdyp/vri/VriStart.java # vdyp-lib/vdyp-vri/src/test/java/ca/bc/gov/nrs/vdyp/vri/VriStartTest.java
bcgov · Sep 10, 2024 · 210d841 · 210d841
2 parents c60977f + 34c530e
commit 210d841
Show file tree

Hide file tree

Showing 15 changed files with 376 additions and 49 deletions.
diff --git a/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/io/write/VriAdjustInputWriter.java b/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/io/write/VriAdjustInputWriter.java
@@ -6,6 +6,16 @@
 
 import ca.bc.gov.nrs.vdyp.common.ControlKey;
 import ca.bc.gov.nrs.vdyp.io.FileResolver;
+import ca.bc.gov.nrs.vdyp.model.BaseVdypSpecies;
+import ca.bc.gov.nrs.vdyp.model.LayerType;
+import ca.bc.gov.nrs.vdyp.model.PolygonMode;
+import ca.bc.gov.nrs.vdyp.model.Sp64Distribution;
+import ca.bc.gov.nrs.vdyp.model.UtilizationClass;
+import ca.bc.gov.nrs.vdyp.model.VdypLayer;
+import ca.bc.gov.nrs.vdyp.model.VdypPolygon;
+import ca.bc.gov.nrs.vdyp.model.VdypSite;
+import ca.bc.gov.nrs.vdyp.model.VdypSpecies;
+import ca.bc.gov.nrs.vdyp.model.VdypUtilizationHolder;
 
 /**
  * Write files to be input into VRI Adjust.
@@ -44,4 +54,186 @@ public VriAdjustInputWriter(Map<String, Object> controlMap, FileResolver resolve
 				controlMap
 		);
 	}
+
+	static OutputStream getOutputStream(Map<String, Object> controlMap, FileResolver resolver, String key)
+			throws IOException {
+		String fileName = Utils.expectParsedControl(controlMap, key, String.class);
+		return resolver.resolveForOutput(fileName);
+	}
+
+	// V7W_AIP
+	/**
+	 * Write a polygon record to the polygon file
+	 *
+	 * @param polygon
+	 * @throws IOException
+	 */
+	void writePolygon(VdypPolygon polygon) throws IOException {
+		writeFormat(
+				polygonFile, //
+				POLY_FORMAT, //
+
+				polygon.getPolygonIdentifier(), //
+				polygon.getBiogeoclimaticZone().getAlias(), //
+				polygon.getForestInventoryZone(), //
+
+				polygon.getPercentAvailable().intValue(), //
+				polygon.getLayers().get(LayerType.PRIMARY).getInventoryTypeGroup().orElse(EMPTY_INT), //
+				polygon.getLayers().get(LayerType.PRIMARY).getEmpiricalRelationshipParameterIndex().orElse(EMPTY_INT), //
+				polygon.getMode().orElse(PolygonMode.START).getCode()
+		);
+	}
+
+	/**
+	 * Write a species record to the species file
+	 *
+	 * @param layer
+	 * @param spec
+	 * @throws IOException
+	 */
+	void writeSpecies(VdypLayer layer, VdypSpecies spec) throws IOException {
+
+		// Ensure we have a list of 4 distribution entries
+		var specDistributionEntries = Stream.concat(
+				spec.getSp64DistributionSet().getSp64DistributionList().stream(), Stream
+						.generate(() -> new Sp64Distribution(0, "", 0f))
+		).limit(4).toList();
+		// 082E004 615 1988 P 9 L LW 100.0 0.0 0.0 0.0 -9.00 -9.00 -9.0 -9.0 -9.0 0 -9
+		writeFormat(
+				speciesFile, //
+				SPEC_FORMAT, //
+
+				spec.getPolygonIdentifier(), //
+				spec.getLayerType().getAlias(), //
+
+				spec.getGenusIndex(), //
+				spec.getGenus(), //
+
+				specDistributionEntries.get(0).getGenusAlias(), //
+				specDistributionEntries.get(0).getPercentage(), //
+				specDistributionEntries.get(1).getGenusAlias(), //
+				specDistributionEntries.get(1).getPercentage(), //
+				specDistributionEntries.get(2).getGenusAlias(), //
+				specDistributionEntries.get(2).getPercentage(), //
+				specDistributionEntries.get(3).getGenusAlias(), //
+				specDistributionEntries.get(3).getPercentage(), //
+
+				spec.getSite().flatMap(VdypSite::getSiteIndex).orElse(EMPTY_FLOAT),
+				spec.getSite().flatMap(VdypSite::getHeight).orElse(EMPTY_FLOAT),
+				spec.getSite().flatMap(VdypSite::getAgeTotal).orElse(EMPTY_FLOAT),
+				spec.getSite().flatMap(VdypSite::getYearsAtBreastHeight).orElse(EMPTY_FLOAT),
+				spec.getSite().flatMap(VdypSite::getYearsToBreastHeight).orElse(EMPTY_FLOAT),
+				layer.getPrimaryGenus().map(spec.getGenus()::equals).orElse(false) ? 1 : 0,
+				spec.getSite().flatMap(VdypSite::getSiteCurveNumber).orElse(EMPTY_INT)
+
+		);
+
+	}
+
+	/**
+	 * Write the utilization records for a layer or species to the utilization file.
+	 *
+	 * @param layer
+	 * @param utils
+	 * @throws IOException
+	 */
+	// V7W_AIU Internalized loop over utilization classes
+	void writeUtilization(VdypLayer layer, VdypUtilizationHolder utils) throws IOException {
+		Optional<String> specId = Optional.empty();
+		Optional<Integer> specIndex = Optional.empty();
+		if (utils instanceof VdypSpecies spec) {
+			specId = Optional.of(spec.getGenus());
+			specIndex = Optional.of(spec.getGenusIndex());
+		}
+
+		for (var uc : UtilizationClass.values()) {
+			Optional<Float> height = Optional.empty();
+			if (uc.index < 1) {
+				height = Optional.of(utils.getLoreyHeightByUtilization().getCoe(uc.index)).filter(x -> x > 0f);
+			}
+			Optional<Float> quadMeanDiameter = Optional.empty();
+			if (utils.getBaseAreaByUtilization().getCoe(uc.index) > 0) {
+				quadMeanDiameter = Optional.of(
+						BaseAreaTreeDensityDiameter.quadMeanDiameter(
+								utils.getBaseAreaByUtilization().getCoe(uc.index), utils
+										.getTreesPerHectareByUtilization().getCoe(uc.index)
+						)
+				);
+			}
+
+			writeFormat(
+					utilizationFile, //
+					UTIL_FORMAT, //
+
+					layer.getPolygonIdentifier(), //
+					layer.getLayerType().getAlias(), //
+
+					specIndex.orElse(0), //
+					specId.orElse("  "), //
+
+					uc.index,
+
+					utils.getBaseAreaByUtilization().getCoe(uc.index), //
+					utils.getTreesPerHectareByUtilization().getCoe(uc.index), //
+					height.orElse(EMPTY_FLOAT), //
+
+					utils.getWholeStemVolumeByUtilization().getCoe(uc.index), //
+					utils.getCloseUtilizationVolumeByUtilization().getCoe(uc.index), //
+					utils.getCloseUtilizationVolumeNetOfDecayByUtilization().getCoe(uc.index), //
+					utils.getCloseUtilizationVolumeNetOfDecayAndWasteByUtilization().getCoe(uc.index), //
+					utils.getCloseUtilizationVolumeNetOfDecayWasteAndBreakageByUtilization().getCoe(uc.index), //
+
+					quadMeanDiameter.orElse(layer.getLayerType() == LayerType.PRIMARY ? //
+							EMPTY_FLOAT : 0f
+					) // FIXME: VDYP7 is being inconsistent. Should consider using -9 for both.
+			);
+		}
+	}
+
+	/**
+	 * Output a polygon and its children.
+	 *
+	 * @param polygon
+	 * @throws IOException
+	 */
+	// VDYP_OUT when JPROGRAM = 1 (FIPSTART) or 3 (VRISTART)
+	public void writePolygonWithSpeciesAndUtilization(VdypPolygon polygon) throws IOException {
+
+		writePolygon(polygon);
+		for (var layer : polygon.getLayers().values()) {
+			writeUtilization(layer, layer);
+			List<VdypSpecies> specs = new ArrayList<>(layer.getSpecies().size());
+			specs.addAll(layer.getSpecies().values());
+			specs.sort(Utils.compareUsing(BaseVdypSpecies::getGenus));
+			for (var species : specs) {
+				writeSpecies(layer, species);
+				writeUtilization(layer, species);
+			}
+		}
+		writeSpeciesEndRecord(polygon);
+		writeUtilizationEndRecord(polygon);
+	}
+
+	private void writeEndRecord(OutputStream os, VdypPolygon polygon) throws IOException {
+		writeFormat(os, END_RECORD_FORMAT, polygon.getPolygonIdentifier());
+	}
+
+	private void writeUtilizationEndRecord(VdypPolygon polygon) throws IOException {
+		writeEndRecord(utilizationFile, polygon);
+	}
+
+	private void writeSpeciesEndRecord(VdypPolygon polygon) throws IOException {
+		writeEndRecord(speciesFile, polygon);
+	}
+
+	void writeFormat(OutputStream os, String format, Object... params) throws IOException {
+		os.write(String.format(format, params).getBytes());
+	}
+
+	@Override
+	public void close() throws IOException {
+		polygonFile.close();
+		speciesFile.close();
+		utilizationFile.close();
+	}
 }
diff --git a/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/model/BaseVdypLayer.java b/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/model/BaseVdypLayer.java
@@ -13,6 +13,8 @@
 import java.util.function.Consumer;
 import java.util.stream.Collectors;
 
+import ca.bc.gov.nrs.vdyp.common.Computed;
+
 public abstract class BaseVdypLayer<S extends BaseVdypSpecies<I>, I extends BaseVdypSite> {
 
 	private final PolygonIdentifier polygonIdentifier;
@@ -81,6 +83,17 @@ public void setInventoryTypeGroup(Optional<Integer> inventoryTypeGroup) {
 		this.inventoryTypeGroup = inventoryTypeGroup;
 	}
 
+	public abstract Optional<String> getPrimaryGenus();
+
+	@Computed
+	public Optional<S> getPrimarySpeciesRecord() {
+		return getPrimaryGenus().map(this.getSpecies()::get);
+	}
+
+	@Computed
+	public Optional<I> getPrimarySite() {
+		return getPrimaryGenus().map(this.getSites()::get);
+
 	@Override
 	public String toString() {
 		return polygonIdentifier.toStringCompact() + "-" + layerType;

diff --git a/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/model/InputLayer.java b/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/model/InputLayer.java
@@ -1,5 +1,6 @@
 package ca.bc.gov.nrs.vdyp.model;
 
+
 public interface InputLayer {
 
 	public float getCrownClosure();

diff --git a/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/model/SingleSiteLayer.java b/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/model/SingleSiteLayer.java
@@ -55,4 +55,9 @@ public LinkedHashMap<String, I> getSites() {
 		return result;
 	}
 
+	@Override
+	public Optional<String> getPrimaryGenus() {
+		return getSiteGenus();
+	}
+
 }
diff --git a/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/model/VdypLayer.java b/vdyp-lib/vdyp-common/src/main/java/ca/bc/gov/nrs/vdyp/model/VdypLayer.java
@@ -1,12 +1,13 @@
 package ca.bc.gov.nrs.vdyp.model;
 
 import java.util.Optional;
+import java.util.function.BiConsumer;
 import java.util.function.Consumer;
 
 import ca.bc.gov.nrs.vdyp.common.Computed;
 import ca.bc.gov.nrs.vdyp.common.Utils;
 
-public class VdypLayer extends SingleSiteLayer<VdypSpecies, VdypSite> implements VdypUtilizationHolder {
+public class VdypLayer extends BaseVdypLayer<VdypSpecies, VdypSite> implements VdypUtilizationHolder {
 
 	private UtilizationVector baseAreaByUtilization = //
 			VdypUtilizationHolder.emptyUtilization(); // LVCOM/BA species 0
@@ -28,21 +29,38 @@ public class VdypLayer extends SingleSiteLayer<VdypSpecies, VdypSite> implements
 	private UtilizationVector closeUtilizationVolumeNetOfDecayWasteAndBreakageByUtilization = //
 			VdypUtilizationHolder.emptyUtilization(); // LVCOM/VOL_DWB species 0
 
-	private Optional<Integer> empiricalRelationshipParameterIndex = Optional.empty(); // INXL1/GRPBA1
+	private Optional<Integer> empericalRelationshipParameterIndex = Optional.empty(); // INXL1/GRPBA1
+	private Optional<String> primarySp0;
 
 	public VdypLayer(
 			PolygonIdentifier polygonIdentifier, LayerType layer, Optional<Integer> inventoryTypeGroup,
-			Optional<Integer> empiricalRelationshipParameterIndex
+			Optional<Integer> empericalRelationshipParameterIndex, Optional<String> primarySp0
 	) {
 		super(polygonIdentifier, layer, inventoryTypeGroup);
-		this.empiricalRelationshipParameterIndex = empiricalRelationshipParameterIndex;
+		this.empericalRelationshipParameterIndex = empericalRelationshipParameterIndex;
+		this.primarySp0 = primarySp0;
 	}
 
 	@Computed
 	public Optional<Float> getBreastHeightAge() {
 		return this.getAgeTotal().flatMap(at -> this.getYearsToBreastHeight().map(bha -> at - bha));
 	}
 
+	@Computed
+	public Optional<Float> getAgeTotal() {
+		return this.getPrimarySite().flatMap(BaseVdypSite::getAgeTotal);
+	}
+
+	@Computed
+	public Optional<Float> getYearsToBreastHeight() {
+		return this.getPrimarySite().flatMap(BaseVdypSite::getYearsToBreastHeight);
+	}
+
+	@Computed
+	public Optional<Float> getHeight() {
+		return this.getPrimarySite().flatMap(BaseVdypSite::getHeight);
+	}
+
 	@Override
 	public UtilizationVector getBaseAreaByUtilization() {
 		return baseAreaByUtilization;
@@ -147,6 +165,11 @@ public void setEmpericalRelationshipParameterIndex(Optional<Integer> empericalRe
 		this.empiricalRelationshipParameterIndex = empericalRelationshipParameterIndex;
 	}
 
+	@Override
+	public Optional<String> getPrimaryGenus() {
+		return primarySp0;
+	}
+
 	/**
 	 * Accepts a configuration function that accepts a builder to configure.
 	 *
@@ -199,7 +222,18 @@ public void empiricalRelationshipParameterIndex(int empiricalRelationshipParamet
 			this.empiricalRelationshipParameterIndex(Optional.of(empiricalRelationshipParameterIndex));
 		}
 
-		UtilizationVector loreyHeightByUtilization = VdypUtilizationHolder.emptyLoreyHeightUtilization();
+		protected Optional<String> primarySp0 = Optional.empty();
+
+		public VdypLayer.Builder primaryGenus(Optional<String> primarySp0) {
+			this.primarySp0 = primarySp0;
+			return this;
+		}
+
+		public VdypLayer.Builder primaryGenus(String primarySp0) {
+			return primaryGenus(Optional.of(primarySp0));
+		}
+
+		UtilizationVector loreyHeight = VdypUtilizationHolder.emptyLoreyHeightUtilization();
 
 		public void loreyHeightByUtilization(float height) {
 			this.loreyHeightByUtilization = Utils.heightVector(0, height);
@@ -348,7 +382,8 @@ protected VdypLayer doBuild() {
 					polygonIdentifier.get(), //
 					layerType.get(), //
 					inventoryTypeGroup, //
-					empiricalRelationshipParameterIndex
+					empericalRelationshipParameterIndex, //
+					primarySp0
 			);
 		}
 
@@ -360,5 +395,30 @@ protected VdypSpecies buildSpecies(Consumer<VdypSpecies.Builder> config) {
 				builder.layerType(this.layerType.get());
 			});
 		}
+
+		public void baseAreaByUtilization(UtilizationVector utilizationVector) {
+			// TODO Auto-generated method stub
+
+		}
+
+		@Override
+		public <S2 extends BaseVdypSpecies<I2>, I2 extends BaseVdypSite>
+				BaseVdypLayer.Builder<VdypLayer, VdypSpecies, VdypSite, VdypSpecies.Builder, VdypSite.Builder>
+				adaptSpecies(
+						BaseVdypLayer<S2, ?> toCopy, BiConsumer<VdypSpecies.Builder, S2> config
+				) {
+			this.primaryGenus(toCopy.getPrimaryGenus());
+			return super.adaptSpecies(toCopy, config);
+		}
+
+		@Override
+		public BaseVdypLayer.Builder<VdypLayer, VdypSpecies, VdypSite, VdypSpecies.Builder, VdypSite.Builder>
+				copySpecies(
+						VdypLayer toCopy, BiConsumer<VdypSpecies.Builder, VdypSpecies> config
+				) {
+			this.primaryGenus(toCopy.getPrimaryGenus());
+			return super.copySpecies(toCopy, config);
+		}
+
 	}
 }