From a35504ff1337f3202581bf672c7646112a21bcc8 Mon Sep 17 00:00:00 2001 From: martin-boettcher Date: Tue, 31 Jan 2023 22:50:39 +0100 Subject: [PATCH 01/12] draft implementation of MSI cloud post-processing with a single-pass algorithm --- .../S2IdepixCloudPostProcess2Op.java | 361 ++++++++++++++++++ .../org.esa.snap.core.gpf.OperatorSpi | 1 + pom.xml | 2 +- 3 files changed, 363 insertions(+), 1 deletion(-) create mode 100644 idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java diff --git a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java new file mode 100644 index 00000000..700c55c3 --- /dev/null +++ b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java @@ -0,0 +1,361 @@ +package org.esa.snap.idepix.s2msi.operators; + +import com.bc.ceres.core.ProgressMonitor; +import org.esa.snap.core.datamodel.Band; +import org.esa.snap.core.datamodel.Product; +import org.esa.snap.core.gpf.Operator; +import org.esa.snap.core.gpf.OperatorException; +import org.esa.snap.core.gpf.OperatorSpi; +import org.esa.snap.core.gpf.Tile; +import org.esa.snap.core.gpf.annotations.OperatorMetadata; +import org.esa.snap.core.gpf.annotations.Parameter; +import org.esa.snap.core.gpf.annotations.SourceProduct; +import org.esa.snap.core.util.ProductUtils; +import org.esa.snap.core.util.RectangleExtender; +import org.esa.snap.idepix.s2msi.util.S2IdepixUtils; + +import java.awt.Rectangle; + +import static org.esa.snap.idepix.s2msi.util.S2IdepixConstants.*; + +/** + * Adds a cloud buffer to cloudy pixels and does a cloud discrimination on urban areas. + */ +@OperatorMetadata(alias = "Idepix.S2CloudPostProcess2", + version = "3.0", + internal = true, + authors = "Olaf Danne, Martin Boettcher", + copyright = "(c) 2016-2023 by Brockmann Consult", + description = "Performs post processing of cloudy pixels and adds optional cloud buffer.") +public class S2IdepixCloudPostProcess2Op extends Operator { + + private static final int IDEPIX_CLOUD_AMBIGUOUS_BIT = 1 << IDEPIX_CLOUD_AMBIGUOUS; + private static final int IDEPIX_CLOUD_SURE_BIT = 1 << IDEPIX_CLOUD_SURE; + private static final int IDEPIX_CLOUD_BIT = 1 << IDEPIX_CLOUD; + private static final int IDEPIX_CIRRUS_AMBIGUOUS_BIT = 1 << IDEPIX_CIRRUS_AMBIGUOUS; + private static final int IDEPIX_CIRRUS_SURE_BIT = 1 << IDEPIX_CIRRUS_SURE; + private static final int IDEPIX_WATER_BIT = 1 << IDEPIX_WATER; + + @SourceProduct(alias = "classifiedProduct") + private Product classifiedProduct; + + @Parameter(defaultValue = "true", label = "Compute cloud buffer for cloud ambiguous pixels too.") + private boolean computeCloudBufferForCloudAmbiguous; + + @Parameter(defaultValue = "2", label = "Width of cloud buffer (# of pixels)") + private int cloudBufferWidth; + + private int landWaterContextSize; + private int urbanContextSize = 11; + private int cdiStddevContextSize = 7; + private int contextSize; + private int cloudBufferSize; + + private int landWaterContextRadius; + private int urbanContextRadius = urbanContextSize / 2; + private int cdiStddevContextRadius = cdiStddevContextSize / 2; + private int contextRadius; + + private static final float COAST_BUFFER_SIZE = 1000f; + private Band origClassifFlagBand; + private Band b2Band; + private Band b7Band; + private Band b8Band; + private Band b8aBand; + private Band b11Band; + private RectangleExtender pixelStateRectCalculator; + private RectangleExtender urbanRectCalculator; + private RectangleExtender cdiRectCalculator; + private RectangleExtender contextRectCalculator; + private RectangleExtender cloudBufferRectCalculator; + + private static final double CDI_THRESHOLD = -0.5; + + @Override + public void initialize() throws OperatorException { + + final int resolution = S2IdepixUtils.determineResolution(classifiedProduct); + landWaterContextSize = (int) Math.floor((2 * COAST_BUFFER_SIZE) / resolution); // TODO is a +1 required here? + landWaterContextRadius = landWaterContextSize / 2; + contextSize = Math.max(landWaterContextSize, Math.max(urbanContextSize, cdiStddevContextSize)); + contextRadius = contextSize / 2; + cloudBufferSize = 2 * cloudBufferWidth + 1; + + pixelStateRectCalculator = createRectCalculator(contextSize/2); + urbanRectCalculator = createRectCalculator(urbanContextSize/2); + cdiRectCalculator = createRectCalculator(cdiStddevContextSize/2); + contextRectCalculator = createRectCalculator(contextSize/2); + cloudBufferRectCalculator = createRectCalculator(cloudBufferWidth); + + Product cloudBufferProduct = createTargetProduct(classifiedProduct, + classifiedProduct.getName(), + classifiedProduct.getProductType()); + origClassifFlagBand = classifiedProduct.getBand(IDEPIX_CLASSIF_FLAGS); + ProductUtils.copyBand(IDEPIX_CLASSIF_FLAGS, classifiedProduct, cloudBufferProduct, false); + b2Band = classifiedProduct.getBand("B2"); + b7Band = classifiedProduct.getBand("B7"); + b8Band = classifiedProduct.getBand("B8"); + b8aBand = classifiedProduct.getBand("B8A"); + b11Band = classifiedProduct.getBand("B11"); + + setTargetProduct(cloudBufferProduct); + } + + @Override + public void computeTile(Band targetBand, Tile targetTile, ProgressMonitor pm) throws OperatorException { + + Rectangle targetRectangle = targetTile.getRectangle(); + final Rectangle pixelStateRectangle = pixelStateRectCalculator.extend(targetRectangle); + final Rectangle urbanRectangle = urbanRectCalculator.extend(targetRectangle); + final Rectangle cdiRectangle = cdiRectCalculator.extend(targetRectangle); + final Rectangle contextRectangle = contextRectCalculator.extend(targetRectangle); + final Rectangle cloudBufferRectangle = cloudBufferRectCalculator.extend(targetRectangle); + + final Tile sourceFlagTile = getSourceTile(origClassifFlagBand, pixelStateRectangle); + final Tile b7Tile = getSourceTile(b7Band, cdiRectangle); + final Tile b8Tile = getSourceTile(b8Band, cdiRectangle); + final Tile b8aTile = getSourceTile(b8aBand, cdiRectangle); + final Tile b2Tile = getSourceTile(b2Band, targetRectangle); + final Tile b11Tile = getSourceTile(b11Band, targetRectangle); + + correctCoastalAndUrbanClouds(contextRectangle, pixelStateRectangle, urbanRectangle, cdiRectangle, targetRectangle, + b7Tile, b2Tile, b8Tile, b8aTile, b11Tile, sourceFlagTile, targetTile); + + // cloud buffer is based on the corrected clouds + addCloudBuffer(targetRectangle, cloudBufferRectangle, sourceFlagTile, targetTile); + } + + private void correctCoastalAndUrbanClouds(Rectangle contextRectangle, Rectangle pixelStateRectangle, Rectangle urbanRectangle, Rectangle cdiRectangle, Rectangle targetRectangle, Tile b7Tile, Tile b2Tile, Tile b8Tile, Tile b8aTile, Tile b11Tile, Tile sourceFlagTile, Tile targetTile) { + // allocate and initialise some lines of full width to collect pixel contributions + // The lines will be re-used for later image lines in a rolling manner. + final boolean[][] landAccu = new boolean[contextSize][targetRectangle.width]; + final boolean[][] waterAccu = new boolean[contextSize][targetRectangle.width]; + final boolean[][] urbanSomeClearAccu = new boolean[contextSize][targetRectangle.width]; + final double m7[][] = new double[contextSize][targetRectangle.width]; + final double c7[][] = new double[contextSize][targetRectangle.width]; + final double m8[][] = new double[contextSize][targetRectangle.width]; + final double c8[][] = new double[contextSize][targetRectangle.width]; + final short n78[][] = new short[contextSize][targetRectangle.width]; + + // loop over extended source tile + for (int y = contextRectangle.y; y < contextRectangle.y + contextRectangle.height; y++) { + checkForCancellation(); + for (int x = contextRectangle.x; x < contextRectangle.x + contextRectangle.width; x++) { + + // write dilated land and water patch into accu, required for coastal cloud distinction + if (pixelStateRectangle.contains(x, y)) { + if (isLand(sourceFlagTile, y, x)) { + fillPatchInAccu(y, x, targetRectangle, landWaterContextRadius, contextSize, true, landAccu); + } + if (isWater(sourceFlagTile, y, x)) { + fillPatchInAccu(y, x, targetRectangle, landWaterContextRadius, contextSize, true, waterAccu); + } + } + + // write 11x11 "filtered" non-cloud patch into accu, required for urban cloud distinction + if (urbanRectangle.contains(x, y)) { + if (!isCloud(sourceFlagTile, y, x)) { + fillPatchInAccu(y, x, targetRectangle, urbanContextRadius, contextSize, true, urbanSomeClearAccu); + } + } + + // add stddev contributions to accu of sums, squares, counts, required for urban cloud distinction + if (cdiRectangle.contains(x, y)) { + final float b7 = b7Tile.getSampleFloat(x, y); + final float b8 = b8Tile.getSampleFloat(x, y); + final float b8a = b8aTile.getSampleFloat(x, y); + if (!Float.isNaN(b7) && !Float.isNaN(b8) && b8a != 0.0f) { + final float b7b8a = b7 / b8a; + final float b8b8a = b8 / b8a; + final float b7b8a2 = b7b8a * b7b8a; + final float b8b8a2 = b8b8a * b8b8a; + addStddevPatchInAccu(y, x, targetRectangle, cdiStddevContextRadius, b8b8a, b7b8a2, b8b8a2, b7b8a, m7, c7, m8, c8, n78); + } + } + + // evaluate accu if we have enough context + // target pixel yt/xt + final int yt = y - contextRadius; + final int xt = x - contextRadius; + // accu position jt/it + final int jt = (yt - targetRectangle.y) % contextSize; + final int it = xt - targetRectangle.x; + if (targetRectangle.contains(xt, yt)) { + // read pixel classif flags from source, apply corrections, write it to target + int pixelClassifFlags = sourceFlagTile.getSampleInt(xt, yt); + pixelClassifFlags = coastalCloudDistinction(yt, xt, jt, it, landAccu, waterAccu, sourceFlagTile, b2Tile, b8Tile, b11Tile, pixelClassifFlags); + pixelClassifFlags = urbanCloudDistinction(jt, it, urbanSomeClearAccu, m7, m8, c7, c8, n78, pixelClassifFlags); + targetTile.setSample(xt, yt, pixelClassifFlags); + } + } + } + } + + private void fillPatchInAccu(int y, int x, Rectangle targetRectangle, int halfWidth, int contextSize, boolean value, boolean[][] accu) { + // reduce patch to part overlapping with target image + final int jMin = Math.max(y - targetRectangle.y - halfWidth, 0); + final int jMax = Math.min(y - targetRectangle.y + 1 + halfWidth, targetRectangle.height); + final int iMin = Math.max(x - targetRectangle.x - halfWidth, 0); + final int iMax = Math.min(x - targetRectangle.x + 1 + halfWidth, targetRectangle.width); + // fill patch with value + for (int j = jMin; j < jMax; ++j) { + final int jj = j % contextSize; + for (int i = iMin; i < iMax; ++i) { + accu[jj][i] = value; + } + } + } + + private void addStddevPatchInAccu(int y, int x, Rectangle targetRectangle, int halfWidth, + float b8b8a, float b7b8a2, float b8b8a2, float b7b8a, + double[][] m7, double[][] c7, double[][] m8, double[][] c8, short[][] n78) { + // reduce patch to part overlapping with target image + final int jMin = Math.max(y - targetRectangle.y - halfWidth, 0); + final int jMax = Math.min(y - targetRectangle.y + 1 + halfWidth, targetRectangle.height); + final int iMin = Math.max(x - targetRectangle.x - halfWidth, 0); + final int iMax = Math.min(x - targetRectangle.x + 1 + halfWidth, targetRectangle.width); + // add to mean and to sum of squares within patch + for (int j = jMin; j < jMax; ++j) { + final int jj = j % contextSize; + for (int i = iMin; i < iMax; ++i) { + m7[jj][i] += b7b8a; + c7[jj][i] += b7b8a2; + m8[jj][i] += b8b8a; + c8[jj][i] += b8b8a2; + n78[jj][i] += 1; + } + } + } + + private static int coastalCloudDistinction(int yt, int xt, int jt, int it, + boolean[][] landAccu, boolean[][] waterAccu, + Tile sourceFlagTile, Tile b2Tile, Tile b8Tile, Tile b11Tile, + int pixelClassifFlags) { + // not land but there is some land nearby, or not water and some water nearby + final boolean isCoastal = + (!isLand(sourceFlagTile, yt, xt) && landAccu[jt][it]) || + (!isWater(sourceFlagTile, yt, xt) && waterAccu[jt][it]); + if (isCoastal) { + // another cloud test + final float b2 = b2Tile.getSampleFloat(xt, yt); + final float b8 = b8Tile.getSampleFloat(xt, yt); + final float b11 = b11Tile.getSampleFloat(xt, yt); + final float idx1 = b2 / b11; + final float idx2 = b8 / b11; + final boolean notCoastalCloud = idx1 > 0.7f || (idx1 > 0.6f && idx2 > 0.9f); + if (notCoastalCloud) { + // clear cloud flags if cloud test fails + pixelClassifFlags = removeBit(pixelClassifFlags, IDEPIX_CLOUD_AMBIGUOUS); + pixelClassifFlags = removeBit(pixelClassifFlags, IDEPIX_CLOUD_SURE); + pixelClassifFlags = removeBit(pixelClassifFlags, IDEPIX_CLOUD); + } else if ((pixelClassifFlags & ((1 << IDEPIX_CLOUD_AMBIGUOUS) | (1 << IDEPIX_CLOUD_SURE))) == 0) { + // align cloud flag with combination of ambiguous and sure if none of them is set + pixelClassifFlags = removeBit(pixelClassifFlags, IDEPIX_CLOUD); + } else { + // align cloud flag with combination of ambiguous and sure if one of them is set + pixelClassifFlags |= IDEPIX_CLOUD_BIT; + } + } + // reset accu for re-use + landAccu[jt][it] = false; + waterAccu[jt][it] = false; + return pixelClassifFlags; + } + + private static int urbanCloudDistinction(int jt, int it, boolean[][] urbanSomeClearAccu, double[][] m7, double[][] m8, double[][] c7, double[][] c8, short[][] n78, int pixelClassifFlags) { + // some clear pixels nearby, and not cirrus or water + final boolean notInTheMiddleOfACloud = urbanSomeClearAccu[jt][it]; + if (notInTheMiddleOfACloud + && (pixelClassifFlags & (IDEPIX_CIRRUS_AMBIGUOUS_BIT | IDEPIX_CIRRUS_SURE_BIT | IDEPIX_WATER_BIT)) == 0 + && (pixelClassifFlags & (IDEPIX_CLOUD_AMBIGUOUS_BIT | IDEPIX_CLOUD_SURE_BIT | IDEPIX_CLOUD_BIT)) != 0) { + // another non-cloud test + final double variance7 = variance_of(c7[jt][it], m7[jt][it], n78[jt][it]); + final double variance8 = variance_of(c8[jt][it], m8[jt][it], n78[jt][it]); + final double cdiValue = (variance7 - variance8) / (variance7 + variance8); + if (cdiValue >= CDI_THRESHOLD) { + // clear cloud flags if CDI test succeeds + pixelClassifFlags = removeBit(pixelClassifFlags, IDEPIX_CLOUD_AMBIGUOUS); + pixelClassifFlags = removeBit(pixelClassifFlags, IDEPIX_CLOUD_SURE); + pixelClassifFlags = removeBit(pixelClassifFlags, IDEPIX_CLOUD); + } + } + // clear accu for re-use + urbanSomeClearAccu[jt][it] = false; + return pixelClassifFlags; + } + + private void addCloudBuffer(Rectangle targetRectangle, Rectangle cloudBufferRectangle, Tile sourceFlagTile, Tile targetTile) { + final boolean[][] cloudBufferAccu = new boolean[cloudBufferSize][targetRectangle.width]; + for (int y = cloudBufferRectangle.y; y < cloudBufferRectangle.y + cloudBufferRectangle.height; y++) { + checkForCancellation(); + for (int x = cloudBufferRectangle.x; x < cloudBufferRectangle.x + cloudBufferRectangle.width; x++) { + if (isCloudForBuffer(targetRectangle.contains(x, y) ? targetTile : sourceFlagTile, x, y)) { + fillPatchInAccu(y, x, targetRectangle, cloudBufferWidth, cloudBufferSize, true, cloudBufferAccu); + } + // target pixel yt/xt + final int yt = y - cloudBufferWidth; + final int xt = x - cloudBufferWidth; + // accu position jt/it + final int jt = (yt - targetRectangle.y) % cloudBufferSize; + final int it = xt - targetRectangle.x; + // evaluate accu if we have enough context + // set cloud buffer flag if it is not cloud but there is a cloud nearby + if (targetRectangle.contains(xt, yt) + && cloudBufferAccu[jt][it] + && (targetTile.getSampleInt(xt, yt) & ((1 << IDEPIX_CLOUD_AMBIGUOUS) | (1 << IDEPIX_CLOUD_SURE) | (1 << IDEPIX_CLOUD))) == 0) { + targetTile.setSample(xt, yt, IDEPIX_CLOUD_BUFFER, true); + } + } + } + } + + + private RectangleExtender createRectCalculator(int width) { + return new RectangleExtender(new Rectangle(classifiedProduct.getSceneRasterWidth(), + classifiedProduct.getSceneRasterHeight()), + width, width); + } + + private static Product createTargetProduct(Product sourceProduct, String name, String type) { + final int sceneWidth = sourceProduct.getSceneRasterWidth(); + final int sceneHeight = sourceProduct.getSceneRasterHeight(); + Product targetProduct = new Product(name, type, sceneWidth, sceneHeight); + ProductUtils.copyGeoCoding(sourceProduct, targetProduct); + targetProduct.setStartTime(sourceProduct.getStartTime()); + targetProduct.setEndTime(sourceProduct.getEndTime()); + return targetProduct; + } + + private static int removeBit(int x, int i) { + final int mask = -1 << i; + return ((x ^ (x >>> 1)) & mask) ^ x; + } + + private static boolean isLand(Tile tile, int y, int x) { + return tile.getSampleBit(x, y, IDEPIX_LAND); + } + + private static boolean isWater(Tile tile, int y, int x) { + return tile.getSampleBit(x, y, IDEPIX_WATER); + } + + private static boolean isCloud(Tile tile, int y, int x) { + return (tile.getSampleInt(x, y) & ((1 << IDEPIX_CLOUD_AMBIGUOUS) | (1 << IDEPIX_CLOUD_SURE) | (1 << IDEPIX_CLOUD))) != 0; + } + + private static double variance_of(double c, double m, int n) { + return n == 0 ? Double.NaN : n == 1 ? 0.0 : (c - m * m / n) / (n - 1); + } + + private boolean isCloudForBuffer(Tile targetTile, int x, int y) { + return targetTile.getSampleBit(x, y, IDEPIX_CLOUD_SURE) || + (computeCloudBufferForCloudAmbiguous && targetTile.getSampleBit(x, y, IDEPIX_CLOUD_AMBIGUOUS)); + } + + + public static class Spi extends OperatorSpi { + public Spi() { + super(S2IdepixCloudPostProcess2Op.class); + } + } +} diff --git a/idepix-s2msi/src/main/resources/META-INF/services/org.esa.snap.core.gpf.OperatorSpi b/idepix-s2msi/src/main/resources/META-INF/services/org.esa.snap.core.gpf.OperatorSpi index 2231f4aa..c21861e5 100644 --- a/idepix-s2msi/src/main/resources/META-INF/services/org.esa.snap.core.gpf.OperatorSpi +++ b/idepix-s2msi/src/main/resources/META-INF/services/org.esa.snap.core.gpf.OperatorSpi @@ -2,6 +2,7 @@ org.esa.snap.idepix.s2msi.S2IdepixOp$Spi org.esa.snap.idepix.s2msi.S2IdepixPostProcessOp$Spi org.esa.snap.idepix.s2msi.S2IdepixClassificationOp$Spi org.esa.snap.idepix.s2msi.operators.S2IdepixCloudPostProcessOp$Spi +org.esa.snap.idepix.s2msi.operators.S2IdepixCloudPostProcess2Op$Spi org.esa.snap.idepix.s2msi.operators.mountainshadow.SlopeAspectOrientationOp$Spi org.esa.snap.idepix.s2msi.operators.mountainshadow.S2IdepixMountainShadowOp$Spi org.esa.snap.idepix.s2msi.operators.cloudshadow.S2IdepixCloudShadowOp$Spi diff --git a/pom.xml b/pom.xml index 30f98c36..49185f57 100644 --- a/pom.xml +++ b/pom.xml @@ -29,7 +29,7 @@ UTF-8 - 9.0.2 + 9.0.5-SNAPSHOT RELEASE82 2.0.05 From 91b575ca6909cccbaa305fe78838878474679719 Mon Sep 17 00:00:00 2001 From: martin-boettcher Date: Fri, 3 Feb 2023 12:53:21 +0100 Subject: [PATCH 02/12] implementation of MSI cloud post-processing with a single-pass algorithm --- idepix-s2msi/pom.xml | 2 +- .../org/esa/snap/idepix/s2msi/S2IdepixOp.java | 8 +- .../S2IdepixCloudPostProcess2Op.java | 199 ++++++++++++------ 3 files changed, 137 insertions(+), 72 deletions(-) diff --git a/idepix-s2msi/pom.xml b/idepix-s2msi/pom.xml index 26b700cb..e7a696e4 100644 --- a/idepix-s2msi/pom.xml +++ b/idepix-s2msi/pom.xml @@ -26,7 +26,7 @@ idepix-s2msi - 9.0.2-SNAPSHOT + 9.0.3-SNAPSHOT nbm diff --git a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixOp.java b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixOp.java index 91381d97..c36908b1 100644 --- a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixOp.java +++ b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixOp.java @@ -11,6 +11,7 @@ import org.esa.snap.core.gpf.annotations.SourceProduct; import org.esa.snap.core.gpf.annotations.TargetProduct; import org.esa.snap.dem.gpf.AddElevationOp; +import org.esa.snap.idepix.s2msi.operators.S2IdepixCloudPostProcess2Op; import org.esa.snap.idepix.s2msi.operators.S2IdepixCloudPostProcessOp; import org.esa.snap.idepix.s2msi.util.AlgorithmSelector; import org.esa.snap.idepix.s2msi.util.S2IdepixConstants; @@ -108,6 +109,9 @@ private void processSentinel2() { int cacheSize = Integer.parseInt(System.getProperty(S2IdepixUtils.TILECACHE_PROPERTY, "1600")); s2ClassifProduct = S2IdepixUtils.computeTileCacheProduct(s2ClassifProduct, cacheSize); + targetProduct = s2ClassifProduct; + if (true) return; + // Post Cloud Classification: cloud shadow, cloud buffer, mountain shadow Product postProcessingProduct = computePostProcessProduct(sourceProduct, s2ClassifProduct); @@ -146,7 +150,9 @@ private Product computePostProcessProduct(Product l1cProduct, Product classifica Map paramsBuffer = new HashMap<>(); paramsBuffer.put("cloudBufferWidth", cloudBufferWidth); paramsBuffer.put("computeCloudBufferForCloudAmbiguous", computeCloudBufferForCloudAmbiguous); - Product cloudBufferProduct = GPF.createProduct(OperatorSpi.getOperatorAlias(S2IdepixCloudPostProcessOp.class), + //Product cloudBufferProduct = GPF.createProduct(OperatorSpi.getOperatorAlias(S2IdepixCloudPostProcessOp.class), + // paramsBuffer, input); + Product cloudBufferProduct = GPF.createProduct(OperatorSpi.getOperatorAlias(S2IdepixCloudPostProcess2Op.class), paramsBuffer, input); int cacheSize = Integer.parseInt(System.getProperty(S2IdepixUtils.TILECACHE_PROPERTY, "1600")) / 5; diff --git a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java index 700c55c3..1a77bced 100644 --- a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java +++ b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java @@ -10,6 +10,7 @@ import org.esa.snap.core.gpf.annotations.OperatorMetadata; import org.esa.snap.core.gpf.annotations.Parameter; import org.esa.snap.core.gpf.annotations.SourceProduct; +import org.esa.snap.core.util.BitSetter; import org.esa.snap.core.util.ProductUtils; import org.esa.snap.core.util.RectangleExtender; import org.esa.snap.idepix.s2msi.util.S2IdepixUtils; @@ -36,6 +37,8 @@ public class S2IdepixCloudPostProcess2Op extends Operator { private static final int IDEPIX_CIRRUS_SURE_BIT = 1 << IDEPIX_CIRRUS_SURE; private static final int IDEPIX_WATER_BIT = 1 << IDEPIX_WATER; + private static final boolean BORDER_COPY = true; + @SourceProduct(alias = "classifiedProduct") private Product classifiedProduct; @@ -81,10 +84,10 @@ public void initialize() throws OperatorException { contextRadius = contextSize / 2; cloudBufferSize = 2 * cloudBufferWidth + 1; - pixelStateRectCalculator = createRectCalculator(contextSize/2); - urbanRectCalculator = createRectCalculator(urbanContextSize/2); - cdiRectCalculator = createRectCalculator(cdiStddevContextSize/2); - contextRectCalculator = createRectCalculator(contextSize/2); + pixelStateRectCalculator = createRectCalculator(contextRadius); + urbanRectCalculator = createRectCalculator(urbanContextRadius); + cdiRectCalculator = createRectCalculator(cdiStddevContextRadius); + contextRectCalculator = createRectCalculator(contextRadius); cloudBufferRectCalculator = createRectCalculator(cloudBufferWidth); Product cloudBufferProduct = createTargetProduct(classifiedProduct, @@ -98,6 +101,9 @@ public void initialize() throws OperatorException { b8aBand = classifiedProduct.getBand("B8A"); b11Band = classifiedProduct.getBand("B11"); + ProductUtils.copyBand("pixel_classif_flags", classifiedProduct, + "flags_before_postprocessing", cloudBufferProduct, true); + setTargetProduct(cloudBufferProduct); } @@ -108,8 +114,13 @@ public void computeTile(Band targetBand, Tile targetTile, ProgressMonitor pm) th final Rectangle pixelStateRectangle = pixelStateRectCalculator.extend(targetRectangle); final Rectangle urbanRectangle = urbanRectCalculator.extend(targetRectangle); final Rectangle cdiRectangle = cdiRectCalculator.extend(targetRectangle); - final Rectangle contextRectangle = contextRectCalculator.extend(targetRectangle); + final Rectangle cdiExtendedRectangle = new Rectangle(targetRectangle); + cdiExtendedRectangle.grow(cdiStddevContextRadius, cdiStddevContextRadius); + final Rectangle contextRectangle = new Rectangle(targetRectangle); + contextRectangle.grow(contextRadius, contextRadius); //contextRectCalculator.extend(targetRectangle); final Rectangle cloudBufferRectangle = cloudBufferRectCalculator.extend(targetRectangle); + final Rectangle cloudBufferExtendedRectangle = new Rectangle(targetRectangle); + cloudBufferExtendedRectangle.grow(cloudBufferWidth, cloudBufferWidth); final Tile sourceFlagTile = getSourceTile(origClassifFlagBand, pixelStateRectangle); final Tile b7Tile = getSourceTile(b7Band, cdiRectangle); @@ -118,24 +129,31 @@ public void computeTile(Band targetBand, Tile targetTile, ProgressMonitor pm) th final Tile b2Tile = getSourceTile(b2Band, targetRectangle); final Tile b11Tile = getSourceTile(b11Band, targetRectangle); - correctCoastalAndUrbanClouds(contextRectangle, pixelStateRectangle, urbanRectangle, cdiRectangle, targetRectangle, - b7Tile, b2Tile, b8Tile, b8aTile, b11Tile, sourceFlagTile, targetTile); + correctCoastalAndUrbanClouds(contextRectangle, + pixelStateRectangle, urbanRectangle, cdiRectangle, cdiExtendedRectangle, + targetRectangle, + b2Tile, b7Tile, b8Tile, b8aTile, b11Tile, sourceFlagTile, targetTile); // cloud buffer is based on the corrected clouds - addCloudBuffer(targetRectangle, cloudBufferRectangle, sourceFlagTile, targetTile); + addCloudBuffer(cloudBufferExtendedRectangle, cloudBufferRectangle, targetRectangle, sourceFlagTile, targetTile); } - private void correctCoastalAndUrbanClouds(Rectangle contextRectangle, Rectangle pixelStateRectangle, Rectangle urbanRectangle, Rectangle cdiRectangle, Rectangle targetRectangle, Tile b7Tile, Tile b2Tile, Tile b8Tile, Tile b8aTile, Tile b11Tile, Tile sourceFlagTile, Tile targetTile) { + private void correctCoastalAndUrbanClouds(Rectangle contextRectangle, + Rectangle pixelStateRectangle, Rectangle urbanRectangle, + Rectangle cdiRectangle, Rectangle cdiExtendedRectangle, + Rectangle targetRectangle, + Tile b2Tile, Tile b7Tile, Tile b8Tile, Tile b8aTile, Tile b11Tile, + Tile sourceFlagTile, Tile targetTile) { // allocate and initialise some lines of full width to collect pixel contributions // The lines will be re-used for later image lines in a rolling manner. final boolean[][] landAccu = new boolean[contextSize][targetRectangle.width]; final boolean[][] waterAccu = new boolean[contextSize][targetRectangle.width]; final boolean[][] urbanSomeClearAccu = new boolean[contextSize][targetRectangle.width]; - final double m7[][] = new double[contextSize][targetRectangle.width]; - final double c7[][] = new double[contextSize][targetRectangle.width]; - final double m8[][] = new double[contextSize][targetRectangle.width]; - final double c8[][] = new double[contextSize][targetRectangle.width]; - final short n78[][] = new short[contextSize][targetRectangle.width]; + final double[][] m7 = new double[contextSize][targetRectangle.width]; + final double[][] c7 = new double[contextSize][targetRectangle.width]; + final double[][] m8 = new double[contextSize][targetRectangle.width]; + final double[][] c8 = new double[contextSize][targetRectangle.width]; + final short[][] n78 = new short[contextSize][targetRectangle.width]; // loop over extended source tile for (int y = contextRectangle.y; y < contextRectangle.y + contextRectangle.height; y++) { @@ -145,31 +163,55 @@ private void correctCoastalAndUrbanClouds(Rectangle contextRectangle, Rectangle // write dilated land and water patch into accu, required for coastal cloud distinction if (pixelStateRectangle.contains(x, y)) { if (isLand(sourceFlagTile, y, x)) { - fillPatchInAccu(y, x, targetRectangle, landWaterContextRadius, contextSize, true, landAccu); + fillPatchInAccu(y, x, targetRectangle, landWaterContextRadius, contextSize, + true, landAccu); } if (isWater(sourceFlagTile, y, x)) { - fillPatchInAccu(y, x, targetRectangle, landWaterContextRadius, contextSize, true, waterAccu); + fillPatchInAccu(y, x, targetRectangle, landWaterContextRadius, contextSize, + true, waterAccu); } } // write 11x11 "filtered" non-cloud patch into accu, required for urban cloud distinction if (urbanRectangle.contains(x, y)) { if (!isCloud(sourceFlagTile, y, x)) { - fillPatchInAccu(y, x, targetRectangle, urbanContextRadius, contextSize, true, urbanSomeClearAccu); + fillPatchInAccu(y, x, targetRectangle, urbanContextRadius, contextSize, + true, urbanSomeClearAccu); } } // add stddev contributions to accu of sums, squares, counts, required for urban cloud distinction - if (cdiRectangle.contains(x, y)) { - final float b7 = b7Tile.getSampleFloat(x, y); - final float b8 = b8Tile.getSampleFloat(x, y); - final float b8a = b8aTile.getSampleFloat(x, y); - if (!Float.isNaN(b7) && !Float.isNaN(b8) && b8a != 0.0f) { - final float b7b8a = b7 / b8a; - final float b8b8a = b8 / b8a; - final float b7b8a2 = b7b8a * b7b8a; - final float b8b8a2 = b8b8a * b8b8a; - addStddevPatchInAccu(y, x, targetRectangle, cdiStddevContextRadius, b8b8a, b7b8a2, b8b8a2, b7b8a, m7, c7, m8, c8, n78); + if (BORDER_COPY) { + if (cdiExtendedRectangle.contains(x, y)) { + final int xt = + x < cdiRectangle.x ? cdiRectangle.x + : x >= cdiRectangle.x + cdiRectangle.width ? cdiRectangle.x + cdiRectangle.width - 1 + : x; + final int yt = + y < cdiRectangle.y ? cdiRectangle.y + : y >= cdiRectangle.y + cdiRectangle.height ? cdiRectangle.y + cdiRectangle.height - 1 + : y; + final float b7 = b7Tile.getSampleFloat(xt, yt); + final float b8 = b8Tile.getSampleFloat(xt, yt); + final float b8a = b8aTile.getSampleFloat(xt, yt); + if (!Float.isNaN(b7) && !Float.isNaN(b8) && b8a != 0.0f) { + final float b7b8a = b7 / b8a; + final float b8b8a = b8 / b8a; + addStddevPatchInAccu(y, x, targetRectangle, cdiStddevContextRadius, b7b8a, b8b8a, + m7, c7, m8, c8, n78); + } + } + } else { + if (cdiRectangle.contains(x, y)) { + final float b7 = b7Tile.getSampleFloat(x, y); + final float b8 = b8Tile.getSampleFloat(x, y); + final float b8a = b8aTile.getSampleFloat(x, y); + if (!Float.isNaN(b7) && !Float.isNaN(b8) && b8a != 0.0f) { + final float b7b8a = b7 / b8a; + final float b8b8a = b8 / b8a; + addStddevPatchInAccu(y, x, targetRectangle, cdiStddevContextRadius, b7b8a, b8b8a, + m7, c7, m8, c8, n78); + } } } @@ -177,21 +219,26 @@ private void correctCoastalAndUrbanClouds(Rectangle contextRectangle, Rectangle // target pixel yt/xt final int yt = y - contextRadius; final int xt = x - contextRadius; - // accu position jt/it - final int jt = (yt - targetRectangle.y) % contextSize; + // tile relative pixel, already mapped to accu position + final int jjt = (yt - targetRectangle.y) % contextSize; final int it = xt - targetRectangle.x; if (targetRectangle.contains(xt, yt)) { // read pixel classif flags from source, apply corrections, write it to target int pixelClassifFlags = sourceFlagTile.getSampleInt(xt, yt); - pixelClassifFlags = coastalCloudDistinction(yt, xt, jt, it, landAccu, waterAccu, sourceFlagTile, b2Tile, b8Tile, b11Tile, pixelClassifFlags); - pixelClassifFlags = urbanCloudDistinction(jt, it, urbanSomeClearAccu, m7, m8, c7, c8, n78, pixelClassifFlags); + pixelClassifFlags = coastalCloudDistinction(yt, xt, jjt, it, landAccu, waterAccu, + sourceFlagTile, b2Tile, b8Tile, b11Tile, + pixelClassifFlags); + pixelClassifFlags = urbanCloudDistinction(jjt, it, urbanSomeClearAccu, + m7, m8, c7, c8, n78, + pixelClassifFlags); targetTile.setSample(xt, yt, pixelClassifFlags); } } } } - private void fillPatchInAccu(int y, int x, Rectangle targetRectangle, int halfWidth, int contextSize, boolean value, boolean[][] accu) { + private void fillPatchInAccu(int y, int x, Rectangle targetRectangle, int halfWidth, int contextSize, + boolean value, boolean[][] accu) { // reduce patch to part overlapping with target image final int jMin = Math.max(y - targetRectangle.y - halfWidth, 0); final int jMax = Math.min(y - targetRectangle.y + 1 + halfWidth, targetRectangle.height); @@ -207,7 +254,7 @@ private void fillPatchInAccu(int y, int x, Rectangle targetRectangle, int halfWi } private void addStddevPatchInAccu(int y, int x, Rectangle targetRectangle, int halfWidth, - float b8b8a, float b7b8a2, float b8b8a2, float b7b8a, + float b7b8a, float b8b8a, double[][] m7, double[][] c7, double[][] m8, double[][] c8, short[][] n78) { // reduce patch to part overlapping with target image final int jMin = Math.max(y - targetRectangle.y - halfWidth, 0); @@ -215,7 +262,9 @@ private void addStddevPatchInAccu(int y, int x, Rectangle targetRectangle, int h final int iMin = Math.max(x - targetRectangle.x - halfWidth, 0); final int iMax = Math.min(x - targetRectangle.x + 1 + halfWidth, targetRectangle.width); // add to mean and to sum of squares within patch - for (int j = jMin; j < jMax; ++j) { + final float b7b8a2 = b7b8a * b7b8a; + final float b8b8a2 = b8b8a * b8b8a; + for (int j = jMin; j < jMax; ++j) { final int jj = j % contextSize; for (int i = iMin; i < iMax; ++i) { m7[jj][i] += b7b8a; @@ -227,14 +276,14 @@ private void addStddevPatchInAccu(int y, int x, Rectangle targetRectangle, int h } } - private static int coastalCloudDistinction(int yt, int xt, int jt, int it, + private static int coastalCloudDistinction(int yt, int xt, int jjt, int it, boolean[][] landAccu, boolean[][] waterAccu, Tile sourceFlagTile, Tile b2Tile, Tile b8Tile, Tile b11Tile, int pixelClassifFlags) { // not land but there is some land nearby, or not water and some water nearby final boolean isCoastal = - (!isLand(sourceFlagTile, yt, xt) && landAccu[jt][it]) || - (!isWater(sourceFlagTile, yt, xt) && waterAccu[jt][it]); + (!isLand(sourceFlagTile, yt, xt) && landAccu[jjt][it]) || + (!isWater(sourceFlagTile, yt, xt) && waterAccu[jjt][it]); if (isCoastal) { // another cloud test final float b2 = b2Tile.getSampleFloat(xt, yt); @@ -245,65 +294,79 @@ private static int coastalCloudDistinction(int yt, int xt, int jt, int it, final boolean notCoastalCloud = idx1 > 0.7f || (idx1 > 0.6f && idx2 > 0.9f); if (notCoastalCloud) { // clear cloud flags if cloud test fails - pixelClassifFlags = removeBit(pixelClassifFlags, IDEPIX_CLOUD_AMBIGUOUS); - pixelClassifFlags = removeBit(pixelClassifFlags, IDEPIX_CLOUD_SURE); - pixelClassifFlags = removeBit(pixelClassifFlags, IDEPIX_CLOUD); + pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD_AMBIGUOUS, false); + pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD_SURE, false); + pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD, false); } else if ((pixelClassifFlags & ((1 << IDEPIX_CLOUD_AMBIGUOUS) | (1 << IDEPIX_CLOUD_SURE))) == 0) { // align cloud flag with combination of ambiguous and sure if none of them is set - pixelClassifFlags = removeBit(pixelClassifFlags, IDEPIX_CLOUD); + pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD, false); } else { // align cloud flag with combination of ambiguous and sure if one of them is set pixelClassifFlags |= IDEPIX_CLOUD_BIT; } } // reset accu for re-use - landAccu[jt][it] = false; - waterAccu[jt][it] = false; + landAccu[jjt][it] = false; + waterAccu[jjt][it] = false; return pixelClassifFlags; } - private static int urbanCloudDistinction(int jt, int it, boolean[][] urbanSomeClearAccu, double[][] m7, double[][] m8, double[][] c7, double[][] c8, short[][] n78, int pixelClassifFlags) { + private static int urbanCloudDistinction(int jjt, int it, + boolean[][] urbanSomeClearAccu, + double[][] m7, double[][] m8, double[][] c7, double[][] c8, short[][] n78, + int pixelClassifFlags) { // some clear pixels nearby, and not cirrus or water - final boolean notInTheMiddleOfACloud = urbanSomeClearAccu[jt][it]; + final boolean notInTheMiddleOfACloud = urbanSomeClearAccu[jjt][it]; if (notInTheMiddleOfACloud && (pixelClassifFlags & (IDEPIX_CIRRUS_AMBIGUOUS_BIT | IDEPIX_CIRRUS_SURE_BIT | IDEPIX_WATER_BIT)) == 0 && (pixelClassifFlags & (IDEPIX_CLOUD_AMBIGUOUS_BIT | IDEPIX_CLOUD_SURE_BIT | IDEPIX_CLOUD_BIT)) != 0) { // another non-cloud test - final double variance7 = variance_of(c7[jt][it], m7[jt][it], n78[jt][it]); - final double variance8 = variance_of(c8[jt][it], m8[jt][it], n78[jt][it]); + final double variance7 = variance_of(c7[jjt][it], m7[jjt][it], n78[jjt][it]); + final double variance8 = variance_of(c8[jjt][it], m8[jjt][it], n78[jjt][it]); final double cdiValue = (variance7 - variance8) / (variance7 + variance8); if (cdiValue >= CDI_THRESHOLD) { // clear cloud flags if CDI test succeeds - pixelClassifFlags = removeBit(pixelClassifFlags, IDEPIX_CLOUD_AMBIGUOUS); - pixelClassifFlags = removeBit(pixelClassifFlags, IDEPIX_CLOUD_SURE); - pixelClassifFlags = removeBit(pixelClassifFlags, IDEPIX_CLOUD); + pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD_AMBIGUOUS, false); + pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD_SURE, false); + pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD, false); } } // clear accu for re-use - urbanSomeClearAccu[jt][it] = false; + urbanSomeClearAccu[jjt][it] = false; + c7[jjt][it] = 0.0; + m7[jjt][it] = 0.0; + c8[jjt][it] = 0.0; + m8[jjt][it] = 0.0; + n78[jjt][it] = 0; return pixelClassifFlags; } - private void addCloudBuffer(Rectangle targetRectangle, Rectangle cloudBufferRectangle, Tile sourceFlagTile, Tile targetTile) { + private void addCloudBuffer(Rectangle cloudBufferExtendedRectangle, Rectangle cloudBufferRectangle, + Rectangle targetRectangle, Tile sourceFlagTile, Tile targetTile) { final boolean[][] cloudBufferAccu = new boolean[cloudBufferSize][targetRectangle.width]; - for (int y = cloudBufferRectangle.y; y < cloudBufferRectangle.y + cloudBufferRectangle.height; y++) { + for (int y = cloudBufferExtendedRectangle.y; y < cloudBufferExtendedRectangle.y + cloudBufferExtendedRectangle.height; y++) { checkForCancellation(); - for (int x = cloudBufferRectangle.x; x < cloudBufferRectangle.x + cloudBufferRectangle.width; x++) { - if (isCloudForBuffer(targetRectangle.contains(x, y) ? targetTile : sourceFlagTile, x, y)) { - fillPatchInAccu(y, x, targetRectangle, cloudBufferWidth, cloudBufferSize, true, cloudBufferAccu); + for (int x = cloudBufferExtendedRectangle.x; x < cloudBufferExtendedRectangle.x + cloudBufferExtendedRectangle.width; x++) { + if (cloudBufferRectangle.contains(x, y)) { + if (isCloudForBuffer(targetRectangle.contains(x, y) ? targetTile : sourceFlagTile, x, y)) { + fillPatchInAccu(y, x, targetRectangle, cloudBufferWidth, cloudBufferSize, true, cloudBufferAccu); + } } // target pixel yt/xt final int yt = y - cloudBufferWidth; final int xt = x - cloudBufferWidth; - // accu position jt/it - final int jt = (yt - targetRectangle.y) % cloudBufferSize; + // accu position jjt/it + final int jjt = (yt - targetRectangle.y) % cloudBufferSize; final int it = xt - targetRectangle.x; // evaluate accu if we have enough context // set cloud buffer flag if it is not cloud but there is a cloud nearby - if (targetRectangle.contains(xt, yt) - && cloudBufferAccu[jt][it] + if (targetRectangle.contains(xt, yt)) { + if (cloudBufferAccu[jjt][it] && (targetTile.getSampleInt(xt, yt) & ((1 << IDEPIX_CLOUD_AMBIGUOUS) | (1 << IDEPIX_CLOUD_SURE) | (1 << IDEPIX_CLOUD))) == 0) { - targetTile.setSample(xt, yt, IDEPIX_CLOUD_BUFFER, true); + targetTile.setSample(xt, yt, IDEPIX_CLOUD_BUFFER, true); + } + // clear accu for re-use + cloudBufferAccu[jjt][it] = false; } } } @@ -326,11 +389,6 @@ private static Product createTargetProduct(Product sourceProduct, String name, S return targetProduct; } - private static int removeBit(int x, int i) { - final int mask = -1 << i; - return ((x ^ (x >>> 1)) & mask) ^ x; - } - private static boolean isLand(Tile tile, int y, int x) { return tile.getSampleBit(x, y, IDEPIX_LAND); } @@ -343,15 +401,16 @@ private static boolean isCloud(Tile tile, int y, int x) { return (tile.getSampleInt(x, y) & ((1 << IDEPIX_CLOUD_AMBIGUOUS) | (1 << IDEPIX_CLOUD_SURE) | (1 << IDEPIX_CLOUD))) != 0; } - private static double variance_of(double c, double m, int n) { - return n == 0 ? Double.NaN : n == 1 ? 0.0 : (c - m * m / n) / (n - 1); - } - private boolean isCloudForBuffer(Tile targetTile, int x, int y) { return targetTile.getSampleBit(x, y, IDEPIX_CLOUD_SURE) || (computeCloudBufferForCloudAmbiguous && targetTile.getSampleBit(x, y, IDEPIX_CLOUD_AMBIGUOUS)); } + private static double variance_of(double c, double m, int n) { + //return n == 0 ? Double.NaN : n == 1 ? 0.0 : (c - m * m / n) / (n - 1); + return n == 0 ? Double.NaN : n == 1 ? 0.0 : (c - m * m / n) / n; + } + public static class Spi extends OperatorSpi { public Spi() { From cdf9b57275992eee0d1bfc2360c6a62f6860fd88 Mon Sep 17 00:00:00 2001 From: martin-boettcher Date: Mon, 6 Feb 2023 22:21:52 +0100 Subject: [PATCH 03/12] implementation of OLCI CTP with a single call into Tensorflow as recommended by Ralf --- .../java/org/esa/snap/idepix/olci/CtpOp.java | 38 ++++++++++----- .../idepix/olci/TensorflowNNCalculator.java | 46 +++++++++++++++++-- 2 files changed, 69 insertions(+), 15 deletions(-) diff --git a/idepix-olci/src/main/java/org/esa/snap/idepix/olci/CtpOp.java b/idepix-olci/src/main/java/org/esa/snap/idepix/olci/CtpOp.java index 7c874d35..f60baf86 100644 --- a/idepix-olci/src/main/java/org/esa/snap/idepix/olci/CtpOp.java +++ b/idepix-olci/src/main/java/org/esa/snap/idepix/olci/CtpOp.java @@ -139,8 +139,11 @@ public void doExecute(ProgressMonitor pm) throws OperatorException { @Override public void computeTile(Band targetBand, Tile targetTile, ProgressMonitor pm) throws OperatorException { + if (!"ctp".equals(targetBand.getName())) { + throw new OperatorException("Unexpected target band name: '" + targetBand.getName() + "' - exiting."); + } + final Rectangle targetRectangle = targetTile.getRectangle(); - final String targetBandName = targetBand.getName(); final Tile szaTile = getSourceTile(szaBand, targetRectangle); final Tile ozaTile = getSourceTile(ozaBand, targetRectangle); @@ -154,6 +157,8 @@ public void computeTile(Band targetBand, Tile targetTile, ProgressMonitor pm) th final Tile l1FlagsTile = getSourceTile(sourceProduct.getRasterDataNode("quality_flags"), targetRectangle); + float[][] nnInputs = new float[targetRectangle.height * targetRectangle.width][]; + float[] dummyNnInput = new float[7]; for (int y = targetRectangle.y; y < targetRectangle.y + targetRectangle.height; y++) { checkForCancellation(); for (int x = targetRectangle.x; x < targetRectangle.x + targetRectangle.width; x++) { @@ -180,22 +185,33 @@ public void computeTile(Band targetBand, Tile targetTile, ProgressMonitor pm) th final float tra15 = tra15Tile.getSampleFloat(x, y); final float mLogTra15 = (float) -Math.log(tra15); - float[] nnInput = new float[]{cosSza, cosOza, aziDiff, refl12, mLogTra13, mLogTra14, mLogTra15}; - final float[][] nnResult = nnCalculator.calculate(nnInput); - final float ctp = TensorflowNNCalculator.convertNNResultToCtp(nnResult[0][0]); + float[] nnInput = new float[] {cosSza, cosOza, aziDiff, refl12, mLogTra13, mLogTra14, mLogTra15}; + //final float[][] nnResult = nnCalculator.calculate(nnInput); + //final float ctp = TensorflowNNCalculator.convertNNResultToCtp(nnResult[0][0]); + //targetTile.setSample(x, y, ctp); + nnInputs[(y-targetRectangle.y) * targetRectangle.width + (x-targetRectangle.x)] = nnInput; + } else { + //targetTile.setSample(x, y, Float.NaN); + nnInputs[(y-targetRectangle.y) * targetRectangle.width + (x-targetRectangle.x)] = dummyNnInput; + } + } + } + + // call tensorflow once with the complete tile stack + final float[][] nnResult = nnCalculator.calculate1(nnInputs); - if (targetBandName.equals("ctp")) { - targetTile.setSample(x, y, ctp); - } else { - throw new OperatorException("Unexpected target band name: '" + - targetBandName + "' - exiting."); - } + // convert output of tf into ctp and set value into target tile + for (int y = targetRectangle.y; y < targetRectangle.y + targetRectangle.height; y++) { + checkForCancellation(); + for (int x = targetRectangle.x; x < targetRectangle.x + targetRectangle.width; x++) { + final boolean pixelIsValid = !l1FlagsTile.getSampleBit(x, y, IdepixOlciConstants.L1_F_INVALID); + if (pixelIsValid) { + targetTile.setSample(x, y, TensorflowNNCalculator.convertNNResultToCtp(nnResult[(y-targetRectangle.y) * targetRectangle.width + (x-targetRectangle.x)][0])); } else { targetTile.setSample(x, y, Float.NaN); } } } - } private void preProcess() { diff --git a/idepix-olci/src/main/java/org/esa/snap/idepix/olci/TensorflowNNCalculator.java b/idepix-olci/src/main/java/org/esa/snap/idepix/olci/TensorflowNNCalculator.java index e2a87f4e..94f74bbc 100644 --- a/idepix-olci/src/main/java/org/esa/snap/idepix/olci/TensorflowNNCalculator.java +++ b/idepix-olci/src/main/java/org/esa/snap/idepix/olci/TensorflowNNCalculator.java @@ -40,9 +40,11 @@ class TensorflowNNCalculator { try { TensorFlow.version(); // triggers init of TensorFlow } catch (LinkageError e) { - throw new IllegalStateException("TensorFlow could not be initialised. " + - "Make sure that your CPU supports 64Bit and AVX instruction set " + - "(Are you using a VM?) and that you have installed the Microsoft Visual C++ 2015 Redistributable when you are on windows.", e); + throw new IllegalStateException( + "TensorFlow could not be initialised. " + + "Make sure that your CPU supports 64Bit and AVX instruction set " + + "(Are you using a VM?) and that you have installed the Microsoft Visual C++ 2015 " + + "Redistributable when you are on windows.", e); } this.transformMethod = transformMethod; @@ -181,7 +183,6 @@ private void loadModel() throws Exception { * Requires that loadModel() is run once before. * * @param nnInput - input vector for neural net - * * @return float[][] - the converted result array */ float[][] calculate(float[] nnInput) { @@ -210,5 +211,42 @@ float[][] calculate(float[] nnInput) { } } + /** + * Applies NN to vector of pixel band stacks and returns converted array. + * Functional implementation of setNnTensorInput(.) plus getNNResult(). + * Makes sure the Tensors are closed after use. + * Requires that loadModel() is run once before. + * + * @param nnInput - image vector of band vectors, band vectors are input for neural net + * @return float[][] - image vector of output band vector (length 1) + */ + float[][] calculate1(float[][] nnInput) { + if (transformMethod.equals("sqrt")) { + for (int i = 0; i < nnInput.length; i++) { + for (int j = 0; j < nnInput[i].length; j++) { + nnInput[i][j] = (float) Math.sqrt(nnInput[i][j]); + } + } + } else if (transformMethod.equals("log")) { + for (int i = 0; i < nnInput.length; i++) { + for (int j = 0; j < nnInput[i].length; j++) { + nnInput[i][j] = (float) Math.log10(nnInput[i][j]); + } + } + } + final Session.Runner runner = model.session().runner(); + try ( + Tensor inputTensor = Tensor.create(nnInput); + Tensor outputTensor = runner.feed(firstNodeName, inputTensor).fetch(lastNodeName).run().get(0) + ) { + long[] ts = outputTensor.shape(); + int numPixels = (int) ts[0]; + int numOutputVars = (int) ts[1]; + float[][] m = new float[numPixels][numOutputVars]; + outputTensor.copyTo(m); + return m; + } + } + } From 3391b645dc4f407641d7866407ac9f1ed2c54c87 Mon Sep 17 00:00:00 2001 From: martin-boettcher Date: Tue, 7 Feb 2023 09:17:13 +0100 Subject: [PATCH 04/12] implementation of OLCI CTP with a single call to Tensorflow, increased version --- idepix-olci/pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/idepix-olci/pom.xml b/idepix-olci/pom.xml index 0768c0ff..ffb50a0c 100644 --- a/idepix-olci/pom.xml +++ b/idepix-olci/pom.xml @@ -26,7 +26,7 @@ idepix-olci - 9.0.2-SNAPSHOT + 9.0.3-SNAPSHOT nbm From 8f0c624edc42c2d396618440e3f834e6531a63a4 Mon Sep 17 00:00:00 2001 From: martin-boettcher Date: Fri, 10 Feb 2023 09:44:50 +0100 Subject: [PATCH 05/12] make coastal and urban cloud correction robust against invalid and NaN in spatial neighbourhood --- .../operators/S2IdepixCloudPostProcess2Op.java | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java index 1a77bced..acde77ef 100644 --- a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java +++ b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java @@ -174,7 +174,7 @@ private void correctCoastalAndUrbanClouds(Rectangle contextRectangle, // write 11x11 "filtered" non-cloud patch into accu, required for urban cloud distinction if (urbanRectangle.contains(x, y)) { - if (!isCloud(sourceFlagTile, y, x)) { + if (!mayBeCloud(sourceFlagTile, y, x)) { fillPatchInAccu(y, x, targetRectangle, urbanContextRadius, contextSize, true, urbanSomeClearAccu); } @@ -284,15 +284,17 @@ private static int coastalCloudDistinction(int yt, int xt, int jjt, int it, final boolean isCoastal = (!isLand(sourceFlagTile, yt, xt) && landAccu[jjt][it]) || (!isWater(sourceFlagTile, yt, xt) && waterAccu[jjt][it]); - if (isCoastal) { + if (isCoastal && (pixelClassifFlags & (1 << IDEPIX_INVALID)) == 0) { // another cloud test final float b2 = b2Tile.getSampleFloat(xt, yt); final float b8 = b8Tile.getSampleFloat(xt, yt); final float b11 = b11Tile.getSampleFloat(xt, yt); final float idx1 = b2 / b11; final float idx2 = b8 / b11; - final boolean notCoastalCloud = idx1 > 0.7f || (idx1 > 0.6f && idx2 > 0.9f); - if (notCoastalCloud) { + //final boolean notCoastal = idx1 > 0.7f || (idx1 > 0.6f && idx2 > 0.9f); + // handles NaN as non-coastal + final boolean isCoastal2 = idx1 <= 0.6f || (idx1 <= 0.7f && idx2 <= 0.9f); + if (isCoastal2) { // clear cloud flags if cloud test fails pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD_AMBIGUOUS, false); pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD_SURE, false); @@ -302,7 +304,7 @@ private static int coastalCloudDistinction(int yt, int xt, int jjt, int it, pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD, false); } else { // align cloud flag with combination of ambiguous and sure if one of them is set - pixelClassifFlags |= IDEPIX_CLOUD_BIT; + pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD, true);; } } // reset accu for re-use @@ -362,7 +364,7 @@ private void addCloudBuffer(Rectangle cloudBufferExtendedRectangle, Rectangle cl // set cloud buffer flag if it is not cloud but there is a cloud nearby if (targetRectangle.contains(xt, yt)) { if (cloudBufferAccu[jjt][it] - && (targetTile.getSampleInt(xt, yt) & ((1 << IDEPIX_CLOUD_AMBIGUOUS) | (1 << IDEPIX_CLOUD_SURE) | (1 << IDEPIX_CLOUD))) == 0) { + && (targetTile.getSampleInt(xt, yt) & ((1 << IDEPIX_CLOUD_AMBIGUOUS) | (1 << IDEPIX_CLOUD_SURE) | (1 << IDEPIX_CLOUD) | (1 << IDEPIX_INVALID))) == 0) { targetTile.setSample(xt, yt, IDEPIX_CLOUD_BUFFER, true); } // clear accu for re-use @@ -397,8 +399,8 @@ private static boolean isWater(Tile tile, int y, int x) { return tile.getSampleBit(x, y, IDEPIX_WATER); } - private static boolean isCloud(Tile tile, int y, int x) { - return (tile.getSampleInt(x, y) & ((1 << IDEPIX_CLOUD_AMBIGUOUS) | (1 << IDEPIX_CLOUD_SURE) | (1 << IDEPIX_CLOUD))) != 0; + private static boolean mayBeCloud(Tile tile, int y, int x) { + return (tile.getSampleInt(x, y) & ((1 << IDEPIX_CLOUD_AMBIGUOUS) | (1 << IDEPIX_CLOUD_SURE) | (1 << IDEPIX_CLOUD) | 1 << IDEPIX_INVALID)) != 0; } private boolean isCloudForBuffer(Tile targetTile, int x, int y) { From b3d058180028397701d972cbe091593c6faaad1a Mon Sep 17 00:00:00 2001 From: martin-boettcher Date: Fri, 10 Feb 2023 09:45:38 +0100 Subject: [PATCH 06/12] correct option for debug output of CDI band, but comment out for operational use --- .../snap/idepix/s2msi/UrbanCloudDistinction.java | 12 ++++++++---- .../operators/S2IdepixCloudPostProcessOp.java | 14 ++++++++++++++ 2 files changed, 22 insertions(+), 4 deletions(-) diff --git a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/UrbanCloudDistinction.java b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/UrbanCloudDistinction.java index a1f687ec..07b14ee2 100644 --- a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/UrbanCloudDistinction.java +++ b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/UrbanCloudDistinction.java @@ -163,17 +163,21 @@ public void correctCloudFlag(int x, int y, Tile classifFlagTile, Tile targetFlag } + public float getCdiValue(int x, int y) { + return cdiBand.getSampleFloat(x, y); + } + /** * Adds debug band to the target product. */ - public void addDebugBandsToTargetProduct() { - ucd_oldCloud_debug = s2ClassifProduct.addBand("__ucd_oldCloud__", ProductData.TYPE_INT8); + public void addDebugBandsToTargetProduct(Product targetProduct) { + ucd_oldCloud_debug = targetProduct.addBand("__ucd_oldCloud__", ProductData.TYPE_INT8); ucd_oldCloud_debug.ensureRasterData(); - ucd_cdi_debug = s2ClassifProduct.addBand("__ucd_cdi__", ProductData.TYPE_FLOAT32); + ucd_cdi_debug = targetProduct.addBand("__ucd_cdi__", ProductData.TYPE_FLOAT32); ucd_cdi_debug.setNoDataValue(Float.NaN); ucd_cdi_debug.ensureRasterData(); - ucd_cloudMean11_debug = s2ClassifProduct.addBand("__ucd_cloudMean11__", ProductData.TYPE_FLOAT32); + ucd_cloudMean11_debug = targetProduct.addBand("__ucd_cloudMean11__", ProductData.TYPE_FLOAT32); ucd_cloudMean11_debug.setNoDataValue(Float.NaN); ucd_cloudMean11_debug.ensureRasterData(); debugBandsEnabled = true; diff --git a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcessOp.java b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcessOp.java index fdca4f7b..c02085ab 100644 --- a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcessOp.java +++ b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcessOp.java @@ -67,6 +67,7 @@ public void initialize() throws OperatorException { coastalCloudDistinction = new CoastalCloudDistinction(classifiedProduct); urbanCloudDistinction = new UrbanCloudDistinction(classifiedProduct); + //urbanCloudDistinction.addDebugBandsToTargetProduct(cloudBufferProduct); setTargetProduct(cloudBufferProduct); } @@ -89,6 +90,19 @@ public void computeTile(Band targetBand, Tile targetTile, ProgressMonitor pm) th Rectangle targetRectangle = targetTile.getRectangle(); final Rectangle srcRectangle = rectCalculator.extend(targetRectangle); +// if (! "pixel_classif_flags".equals(targetBand.getName())) { +// if ("__ucd_cdi__".equals(targetBand.getName())) { +// for (int y = srcRectangle.y; y < srcRectangle.y + srcRectangle.height; y++) { +// for (int x = srcRectangle.x; x < srcRectangle.x + srcRectangle.width; x++) { +// if (targetRectangle.contains(x, y)) { +// targetTile.setSample(x, y, urbanCloudDistinction.getCdiValue(x, y)); +// } +// } +// } +// } +// return; +// } + final Tile sourceFlagTile = getSourceTile(origClassifFlagBand, srcRectangle); for (int y = srcRectangle.y; y < srcRectangle.y + srcRectangle.height; y++) { From 37ab8e0bc40bc03fea1df3da0eb97f17162d339b Mon Sep 17 00:00:00 2001 From: martin-boettcher Date: Fri, 10 Feb 2023 23:01:09 +0100 Subject: [PATCH 07/12] integration of cloud buffer into single-pass computation of cloud post-processing --- .../org/esa/snap/idepix/s2msi/S2IdepixOp.java | 4 +- .../S2IdepixCloudPostProcess2Op.java | 539 +++++++++++------- 2 files changed, 319 insertions(+), 224 deletions(-) diff --git a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixOp.java b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixOp.java index c36908b1..42868aff 100644 --- a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixOp.java +++ b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixOp.java @@ -109,9 +109,6 @@ private void processSentinel2() { int cacheSize = Integer.parseInt(System.getProperty(S2IdepixUtils.TILECACHE_PROPERTY, "1600")); s2ClassifProduct = S2IdepixUtils.computeTileCacheProduct(s2ClassifProduct, cacheSize); - targetProduct = s2ClassifProduct; - if (true) return; - // Post Cloud Classification: cloud shadow, cloud buffer, mountain shadow Product postProcessingProduct = computePostProcessProduct(sourceProduct, s2ClassifProduct); @@ -152,6 +149,7 @@ private Product computePostProcessProduct(Product l1cProduct, Product classifica paramsBuffer.put("computeCloudBufferForCloudAmbiguous", computeCloudBufferForCloudAmbiguous); //Product cloudBufferProduct = GPF.createProduct(OperatorSpi.getOperatorAlias(S2IdepixCloudPostProcessOp.class), // paramsBuffer, input); + paramsBuffer.put("computeCloudBuffer", computeCloudBuffer); Product cloudBufferProduct = GPF.createProduct(OperatorSpi.getOperatorAlias(S2IdepixCloudPostProcess2Op.class), paramsBuffer, input); diff --git a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java index acde77ef..103f3f3d 100644 --- a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java +++ b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java @@ -20,7 +20,7 @@ import static org.esa.snap.idepix.s2msi.util.S2IdepixConstants.*; /** - * Adds a cloud buffer to cloudy pixels and does a cloud discrimination on urban areas. + * Adds a cloud buffer to cloudy pixels and does a cloud discrimination on coastal areas and urban areas. */ @OperatorMetadata(alias = "Idepix.S2CloudPostProcess2", version = "3.0", @@ -30,24 +30,26 @@ description = "Performs post processing of cloudy pixels and adds optional cloud buffer.") public class S2IdepixCloudPostProcess2Op extends Operator { - private static final int IDEPIX_CLOUD_AMBIGUOUS_BIT = 1 << IDEPIX_CLOUD_AMBIGUOUS; - private static final int IDEPIX_CLOUD_SURE_BIT = 1 << IDEPIX_CLOUD_SURE; - private static final int IDEPIX_CLOUD_BIT = 1 << IDEPIX_CLOUD; - private static final int IDEPIX_CIRRUS_AMBIGUOUS_BIT = 1 << IDEPIX_CIRRUS_AMBIGUOUS; - private static final int IDEPIX_CIRRUS_SURE_BIT = 1 << IDEPIX_CIRRUS_SURE; - private static final int IDEPIX_WATER_BIT = 1 << IDEPIX_WATER; - - private static final boolean BORDER_COPY = true; - @SourceProduct(alias = "classifiedProduct") private Product classifiedProduct; + @Parameter(defaultValue = "true", label = "Compute a cloud buffer") + private boolean computeCloudBuffer; + @Parameter(defaultValue = "true", label = "Compute cloud buffer for cloud ambiguous pixels too.") private boolean computeCloudBufferForCloudAmbiguous; @Parameter(defaultValue = "2", label = "Width of cloud buffer (# of pixels)") private int cloudBufferWidth; + // variables set in initialize and used in computeTile + private Band origClassifFlagBand; + private Band b2Band; + private Band b7Band; + private Band b8Band; + private Band b8aBand; + private Band b11Band; + private int landWaterContextSize; private int urbanContextSize = 11; private int cdiStddevContextSize = 7; @@ -59,232 +61,237 @@ public class S2IdepixCloudPostProcess2Op extends Operator { private int cdiStddevContextRadius = cdiStddevContextSize / 2; private int contextRadius; - private static final float COAST_BUFFER_SIZE = 1000f; - private Band origClassifFlagBand; - private Band b2Band; - private Band b7Band; - private Band b8Band; - private Band b8aBand; - private Band b11Band; private RectangleExtender pixelStateRectCalculator; private RectangleExtender urbanRectCalculator; private RectangleExtender cdiRectCalculator; - private RectangleExtender contextRectCalculator; private RectangleExtender cloudBufferRectCalculator; + private static final float COAST_BUFFER_SIZE = 1000f; // [m] private static final double CDI_THRESHOLD = -0.5; + /** + * Creates the output product with a pixel_classif_flags band, gets bands of the input product, and + * determines sizes for buffers. It prepares rectangle calculators that limit the rectangle + * to the image at the border even if source tile is extended. + * + * @throws OperatorException + */ @Override public void initialize() throws OperatorException { - final int resolution = S2IdepixUtils.determineResolution(classifiedProduct); - landWaterContextSize = (int) Math.floor((2 * COAST_BUFFER_SIZE) / resolution); // TODO is a +1 required here? - landWaterContextRadius = landWaterContextSize / 2; - contextSize = Math.max(landWaterContextSize, Math.max(urbanContextSize, cdiStddevContextSize)); - contextRadius = contextSize / 2; - cloudBufferSize = 2 * cloudBufferWidth + 1; - - pixelStateRectCalculator = createRectCalculator(contextRadius); - urbanRectCalculator = createRectCalculator(urbanContextRadius); - cdiRectCalculator = createRectCalculator(cdiStddevContextRadius); - contextRectCalculator = createRectCalculator(contextRadius); - cloudBufferRectCalculator = createRectCalculator(cloudBufferWidth); - Product cloudBufferProduct = createTargetProduct(classifiedProduct, classifiedProduct.getName(), classifiedProduct.getProductType()); - origClassifFlagBand = classifiedProduct.getBand(IDEPIX_CLASSIF_FLAGS); ProductUtils.copyBand(IDEPIX_CLASSIF_FLAGS, classifiedProduct, cloudBufferProduct, false); + setTargetProduct(cloudBufferProduct); + + origClassifFlagBand = classifiedProduct.getBand(IDEPIX_CLASSIF_FLAGS); b2Band = classifiedProduct.getBand("B2"); b7Band = classifiedProduct.getBand("B7"); b8Band = classifiedProduct.getBand("B8"); b8aBand = classifiedProduct.getBand("B8A"); b11Band = classifiedProduct.getBand("B11"); - ProductUtils.copyBand("pixel_classif_flags", classifiedProduct, - "flags_before_postprocessing", cloudBufferProduct, true); + // add previous state for debugging, comment out in operational version + //ProductUtils.copyBand("pixel_classif_flags", classifiedProduct, + // "flags_before_postprocessing", cloudBufferProduct, true); - setTargetProduct(cloudBufferProduct); + if (!computeCloudBuffer) { + cloudBufferWidth = 0; + } + + final int resolution = S2IdepixUtils.determineResolution(classifiedProduct); + landWaterContextSize = (int) Math.floor((2 * COAST_BUFFER_SIZE) / resolution); // TODO shall this be odd? + landWaterContextRadius = landWaterContextSize / 2; + contextSize = Math.max(landWaterContextSize, Math.max(urbanContextSize, cdiStddevContextSize)); + contextRadius = contextSize / 2; + cloudBufferSize = 2 * cloudBufferWidth + 1; + + pixelStateRectCalculator = createRectCalculator(contextRadius + cloudBufferWidth); + urbanRectCalculator = createRectCalculator(urbanContextRadius + cloudBufferWidth); + cdiRectCalculator = createRectCalculator(cdiStddevContextRadius + cloudBufferWidth); + cloudBufferRectCalculator = createRectCalculator(cloudBufferWidth); } + /** + * Corrects pixel classification and eliminates false cloud flags in coastal and in + * urban regions, adds cloud buffer. Cloud flags in mixed land-water areas are tested + * with a test based on B2, B8, B11. Cloud flags in regions with clear pixels nearby + * are tested with a test based on the spatial variance of a cloud displacement index + * using B7, B8, and B8A. + * + * This single-pass implementation uses several accumulators of the full tile width + * and a few lines to memorise and pre-compute various filtered values. Example: + * To determine whether there is a clear pixel in a 11x11 box around a pixel we use an + * accu with 11 lines. The accu is initialised with "false". A "clear" contribution + * writes a patch of 11x11 values "true" into the accu. This value will be used 5 lines + * and 5 rows later to determine whether there are clear pixels nearby. This is the last + * time the pixel may have got a clear contribution by some pixel passed in the + * single-pass. (Later pixels are more than 5 pixels away.) + * The accu lines are used in a rolling manner (with modulo for line selection). The + * values used are cleared for re-use. + * + * There are accumulators for + * * landNearby 33x33 (60m), 100x100 (20m), 200x200 (10m) + * * waterNearby 33x33 (60m), 100x100 (20m), 200x200 (10m) + * * clearNearby 11x11 + * * sum, square sum, and count of two band ratio expressions for the CDI + * * cloudBuffer 5x5 (cloudBufferWidth=2) + * For simplicity all the accus except cloudBuffer use the maximum number of lines that + * occurs (contextSize). This does not change the logic, just the buffer line used. + * + * Cloud buffer shall be determined based on the corrected cloud flags. It memorises + * the flag value to be written into the target image and delays its writing by cloud + * buffer width lines and columns. The flag may get updated by cloud pixels showing up + * one or two lines later. + * + * @param targetBand The target band, pixel_classif_flags. + * @param targetTile The current tile associated with the target band to be computed. + * @param pm A progress monitor which should be used to determine computation cancellation requests. + * @throws OperatorException + */ @Override public void computeTile(Band targetBand, Tile targetTile, ProgressMonitor pm) throws OperatorException { - Rectangle targetRectangle = targetTile.getRectangle(); + final Rectangle targetRectangle = targetTile.getRectangle(); final Rectangle pixelStateRectangle = pixelStateRectCalculator.extend(targetRectangle); final Rectangle urbanRectangle = urbanRectCalculator.extend(targetRectangle); final Rectangle cdiRectangle = cdiRectCalculator.extend(targetRectangle); final Rectangle cdiExtendedRectangle = new Rectangle(targetRectangle); - cdiExtendedRectangle.grow(cdiStddevContextRadius, cdiStddevContextRadius); - final Rectangle contextRectangle = new Rectangle(targetRectangle); - contextRectangle.grow(contextRadius, contextRadius); //contextRectCalculator.extend(targetRectangle); + cdiExtendedRectangle.grow(cdiStddevContextRadius + cloudBufferWidth, cdiStddevContextRadius + cloudBufferWidth); + final Rectangle contextExtendedRectangle = new Rectangle(targetRectangle); + contextExtendedRectangle.grow(contextRadius + cloudBufferWidth, contextRadius + cloudBufferWidth); final Rectangle cloudBufferRectangle = cloudBufferRectCalculator.extend(targetRectangle); - final Rectangle cloudBufferExtendedRectangle = new Rectangle(targetRectangle); - cloudBufferExtendedRectangle.grow(cloudBufferWidth, cloudBufferWidth); + // get source tiles with different extents final Tile sourceFlagTile = getSourceTile(origClassifFlagBand, pixelStateRectangle); final Tile b7Tile = getSourceTile(b7Band, cdiRectangle); final Tile b8Tile = getSourceTile(b8Band, cdiRectangle); final Tile b8aTile = getSourceTile(b8aBand, cdiRectangle); - final Tile b2Tile = getSourceTile(b2Band, targetRectangle); - final Tile b11Tile = getSourceTile(b11Band, targetRectangle); + final Tile b2Tile = getSourceTile(b2Band, cloudBufferRectangle); + final Tile b11Tile = getSourceTile(b11Band, cloudBufferRectangle); - correctCoastalAndUrbanClouds(contextRectangle, - pixelStateRectangle, urbanRectangle, cdiRectangle, cdiExtendedRectangle, - targetRectangle, - b2Tile, b7Tile, b8Tile, b8aTile, b11Tile, sourceFlagTile, targetTile); - - // cloud buffer is based on the corrected clouds - addCloudBuffer(cloudBufferExtendedRectangle, cloudBufferRectangle, targetRectangle, sourceFlagTile, targetTile); - } - - private void correctCoastalAndUrbanClouds(Rectangle contextRectangle, - Rectangle pixelStateRectangle, Rectangle urbanRectangle, - Rectangle cdiRectangle, Rectangle cdiExtendedRectangle, - Rectangle targetRectangle, - Tile b2Tile, Tile b7Tile, Tile b8Tile, Tile b8aTile, Tile b11Tile, - Tile sourceFlagTile, Tile targetTile) { - // allocate and initialise some lines of full width to collect pixel contributions + // allocate and initialise some lines of full width plus cloud buffer to collect pixel contributions // The lines will be re-used for later image lines in a rolling manner. - final boolean[][] landAccu = new boolean[contextSize][targetRectangle.width]; - final boolean[][] waterAccu = new boolean[contextSize][targetRectangle.width]; - final boolean[][] urbanSomeClearAccu = new boolean[contextSize][targetRectangle.width]; - final double[][] m7 = new double[contextSize][targetRectangle.width]; - final double[][] c7 = new double[contextSize][targetRectangle.width]; - final double[][] m8 = new double[contextSize][targetRectangle.width]; - final double[][] c8 = new double[contextSize][targetRectangle.width]; - final short[][] n78 = new short[contextSize][targetRectangle.width]; + final boolean[][] landNearbyAccu = new boolean[contextSize][cloudBufferRectangle.width]; + final boolean[][] waterNearbyAccu = new boolean[contextSize][cloudBufferRectangle.width]; + final boolean[][] clearNearbyAccu = new boolean[contextSize][cloudBufferRectangle.width]; + final double[][] m7 = new double[contextSize][cloudBufferRectangle.width]; + final double[][] c7 = new double[contextSize][cloudBufferRectangle.width]; + final double[][] m8 = new double[contextSize][cloudBufferRectangle.width]; + final double[][] c8 = new double[contextSize][cloudBufferRectangle.width]; + final short[][] n78 = new short[contextSize][cloudBufferRectangle.width]; + // the accu for pixelClassifFlags can be smaller because we only read it within the target tile + final int[][] cloudBufferAccu = new int[cloudBufferSize][targetRectangle.width]; // loop over extended source tile - for (int y = contextRectangle.y; y < contextRectangle.y + contextRectangle.height; y++) { + // y/x run from target tile y/x - context radius - cloud buffer width to ... + for (int y = contextExtendedRectangle.y; y < contextExtendedRectangle.y + contextExtendedRectangle.height; y++) { checkForCancellation(); - for (int x = contextRectangle.x; x < contextRectangle.x + contextRectangle.width; x++) { + for (int x = contextExtendedRectangle.x; x < contextExtendedRectangle.x + contextExtendedRectangle.width; x++) { // write dilated land and water patch into accu, required for coastal cloud distinction - if (pixelStateRectangle.contains(x, y)) { - if (isLand(sourceFlagTile, y, x)) { - fillPatchInAccu(y, x, targetRectangle, landWaterContextRadius, contextSize, - true, landAccu); - } - if (isWater(sourceFlagTile, y, x)) { - fillPatchInAccu(y, x, targetRectangle, landWaterContextRadius, contextSize, - true, waterAccu); - } + if (pixelStateRectangle.contains(x, y)) { + collectLand(y, x, sourceFlagTile, cloudBufferRectangle, landNearbyAccu); + collectWater(y, x, sourceFlagTile, cloudBufferRectangle, waterNearbyAccu); } // write 11x11 "filtered" non-cloud patch into accu, required for urban cloud distinction if (urbanRectangle.contains(x, y)) { - if (!mayBeCloud(sourceFlagTile, y, x)) { - fillPatchInAccu(y, x, targetRectangle, urbanContextRadius, contextSize, - true, urbanSomeClearAccu); - } + collectClear(y, x, sourceFlagTile, cloudBufferRectangle, clearNearbyAccu); } // add stddev contributions to accu of sums, squares, counts, required for urban cloud distinction - if (BORDER_COPY) { - if (cdiExtendedRectangle.contains(x, y)) { - final int xt = - x < cdiRectangle.x ? cdiRectangle.x - : x >= cdiRectangle.x + cdiRectangle.width ? cdiRectangle.x + cdiRectangle.width - 1 - : x; - final int yt = - y < cdiRectangle.y ? cdiRectangle.y - : y >= cdiRectangle.y + cdiRectangle.height ? cdiRectangle.y + cdiRectangle.height - 1 - : y; - final float b7 = b7Tile.getSampleFloat(xt, yt); - final float b8 = b8Tile.getSampleFloat(xt, yt); - final float b8a = b8aTile.getSampleFloat(xt, yt); - if (!Float.isNaN(b7) && !Float.isNaN(b8) && b8a != 0.0f) { - final float b7b8a = b7 / b8a; - final float b8b8a = b8 / b8a; - addStddevPatchInAccu(y, x, targetRectangle, cdiStddevContextRadius, b7b8a, b8b8a, - m7, c7, m8, c8, n78); - } - } - } else { - if (cdiRectangle.contains(x, y)) { - final float b7 = b7Tile.getSampleFloat(x, y); - final float b8 = b8Tile.getSampleFloat(x, y); - final float b8a = b8aTile.getSampleFloat(x, y); - if (!Float.isNaN(b7) && !Float.isNaN(b8) && b8a != 0.0f) { - final float b7b8a = b7 / b8a; - final float b8b8a = b8 / b8a; - addStddevPatchInAccu(y, x, targetRectangle, cdiStddevContextRadius, b7b8a, b8b8a, - m7, c7, m8, c8, n78); - } - } + if (cdiExtendedRectangle.contains(x, y)) { + collectCdiSumsAndSquares(y, x, b7Tile, b8Tile, b8aTile, cdiRectangle, cloudBufferRectangle, + m7, c7, m8, c8, n78); } - // evaluate accu if we have enough context - // target pixel yt/xt + // yt/xt is the target pixel where we have just seen the last pixel of its context final int yt = y - contextRadius; final int xt = x - contextRadius; - // tile relative pixel, already mapped to accu position - final int jjt = (yt - targetRectangle.y) % contextSize; - final int it = xt - targetRectangle.x; - if (targetRectangle.contains(xt, yt)) { - // read pixel classif flags from source, apply corrections, write it to target - int pixelClassifFlags = sourceFlagTile.getSampleInt(xt, yt); - pixelClassifFlags = coastalCloudDistinction(yt, xt, jjt, it, landAccu, waterAccu, - sourceFlagTile, b2Tile, b8Tile, b11Tile, - pixelClassifFlags); - pixelClassifFlags = urbanCloudDistinction(jjt, it, urbanSomeClearAccu, - m7, m8, c7, c8, n78, - pixelClassifFlags); - targetTile.setSample(xt, yt, pixelClassifFlags); + if (cloudBufferRectangle.contains(xt, yt)) { + correctFlagsOfPixel(yt, xt, + landNearbyAccu, waterNearbyAccu, clearNearbyAccu, + m7, c7, m8, c8, n78, + sourceFlagTile, b2Tile, b8Tile, b11Tile, + targetRectangle, cloudBufferRectangle, + cloudBufferAccu); + } + // yb/xb is the target pixel where we have seen just the last pixel of some possible cloud buffer + final int yb = yt - cloudBufferWidth; + final int xb = xt - cloudBufferWidth; + if (targetRectangle.contains(xb, yb)) { + writeFlagsOfPixel(yb, xb, cloudBufferAccu, targetRectangle, targetTile); } } } } - private void fillPatchInAccu(int y, int x, Rectangle targetRectangle, int halfWidth, int contextSize, - boolean value, boolean[][] accu) { - // reduce patch to part overlapping with target image - final int jMin = Math.max(y - targetRectangle.y - halfWidth, 0); - final int jMax = Math.min(y - targetRectangle.y + 1 + halfWidth, targetRectangle.height); - final int iMin = Math.max(x - targetRectangle.x - halfWidth, 0); - final int iMax = Math.min(x - targetRectangle.x + 1 + halfWidth, targetRectangle.width); - // fill patch with value - for (int j = jMin; j < jMax; ++j) { - final int jj = j % contextSize; - for (int i = iMin; i < iMax; ++i) { - accu[jj][i] = value; + private void correctFlagsOfPixel(int yt, int xt, + boolean[][] landAccu, boolean[][] waterAccu, boolean[][] clearNearbyAccu, + double[][] m7, double[][] c7, double[][] m8, double[][] c8, short[][] n78, + Tile sourceFlagTile, Tile b2Tile, Tile b8Tile, Tile b11Tile, + Rectangle targetRectangle, Rectangle cloudBufferRectangle, + int[][] cloudBufferAccu) { + // land/water/urban accu pixel position + final int jt = (yt - cloudBufferRectangle.y) % contextSize; + final int it = xt - cloudBufferRectangle.x; + // read pixel classif flags from source, apply corrections + int pixelClassifFlags = sourceFlagTile.getSampleInt(xt, yt); + if (isValid(pixelClassifFlags)) { + pixelClassifFlags = coastalCloudDistinction(yt, xt, jt, it, landAccu, waterAccu, + sourceFlagTile, b2Tile, b8Tile, b11Tile, + pixelClassifFlags); + pixelClassifFlags = urbanCloudDistinction(jt, it, clearNearbyAccu, + m7, m8, c7, c8, n78, + pixelClassifFlags); + // patch cloud buffer into accu + if (computeCloudBuffer && isCloudForBuffer(pixelClassifFlags)) { + addCloudBufferInAccu(yt, xt, targetRectangle, cloudBufferWidth, cloudBufferAccu); } } - } - - private void addStddevPatchInAccu(int y, int x, Rectangle targetRectangle, int halfWidth, - float b7b8a, float b8b8a, - double[][] m7, double[][] c7, double[][] m8, double[][] c8, short[][] n78) { - // reduce patch to part overlapping with target image - final int jMin = Math.max(y - targetRectangle.y - halfWidth, 0); - final int jMax = Math.min(y - targetRectangle.y + 1 + halfWidth, targetRectangle.height); - final int iMin = Math.max(x - targetRectangle.x - halfWidth, 0); - final int iMax = Math.min(x - targetRectangle.x + 1 + halfWidth, targetRectangle.width); - // add to mean and to sum of squares within patch - final float b7b8a2 = b7b8a * b7b8a; - final float b8b8a2 = b8b8a * b8b8a; - for (int j = jMin; j < jMax; ++j) { - final int jj = j % contextSize; - for (int i = iMin; i < iMax; ++i) { - m7[jj][i] += b7b8a; - c7[jj][i] += b7b8a2; - m8[jj][i] += b8b8a; - c8[jj][i] += b8b8a2; - n78[jj][i] += 1; + // add cloud buffer flag from accu to pixelClassifFlags + // memorize p.c.f. in accu for later updates of cloud buffer flag and final writing + if (targetRectangle.contains(xt, yt)) { + final int jb = (yt - targetRectangle.y) % cloudBufferSize; + final int ib = xt - targetRectangle.x; + // read cloud buffer from accu (for clouds in upper left direction seen before) + if (isCloudBuffer(cloudBufferAccu[jb][ib]) && isClear(pixelClassifFlags)) { + pixelClassifFlags |= (1 << IDEPIX_CLOUD_BUFFER); } + // write corrected pixel classif flags to accu + cloudBufferAccu[jb][ib] = pixelClassifFlags; } + // reset accu for re-use + landAccu[jt][it] = false; + waterAccu[jt][it] = false; + clearNearbyAccu[jt][it] = false; + c7[jt][it] = 0.0; + m7[jt][it] = 0.0; + c8[jt][it] = 0.0; + m8[jt][it] = 0.0; + n78[jt][it] = 0; } - private static int coastalCloudDistinction(int yt, int xt, int jjt, int it, + private void writeFlagsOfPixel(int yb, int xb, int[][] cloudBufferAccu, Rectangle targetRectangle, Tile targetTile) { + // transfer accu to target + final int jb = (yb - targetRectangle.y) % cloudBufferSize; + final int ib = xb - targetRectangle.x; + targetTile.setSample(xb, yb, cloudBufferAccu[jb][ib]); + // clear accu for re-use + cloudBufferAccu[jb][ib] = 0; + } + + private static int coastalCloudDistinction(int yt, int xt, int jt, int it, boolean[][] landAccu, boolean[][] waterAccu, Tile sourceFlagTile, Tile b2Tile, Tile b8Tile, Tile b11Tile, int pixelClassifFlags) { // not land but there is some land nearby, or not water and some water nearby final boolean isCoastal = - (!isLand(sourceFlagTile, yt, xt) && landAccu[jjt][it]) || - (!isWater(sourceFlagTile, yt, xt) && waterAccu[jjt][it]); - if (isCoastal && (pixelClassifFlags & (1 << IDEPIX_INVALID)) == 0) { + (!isLand(sourceFlagTile, yt, xt) && landAccu[jt][it]) || + (!isWater(sourceFlagTile, yt, xt) && waterAccu[jt][it]); + if (isCoastal && isValid(pixelClassifFlags)) { // another cloud test final float b2 = b2Tile.getSampleFloat(xt, yt); final float b8 = b8Tile.getSampleFloat(xt, yt); @@ -299,32 +306,23 @@ private static int coastalCloudDistinction(int yt, int xt, int jjt, int it, pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD_AMBIGUOUS, false); pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD_SURE, false); pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD, false); - } else if ((pixelClassifFlags & ((1 << IDEPIX_CLOUD_AMBIGUOUS) | (1 << IDEPIX_CLOUD_SURE))) == 0) { - // align cloud flag with combination of ambiguous and sure if none of them is set - pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD, false); } else { - // align cloud flag with combination of ambiguous and sure if one of them is set - pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD, true);; + // align cloud flag with combination of ambiguous and sure + pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD, isAmbigousOrSure(pixelClassifFlags)); } } - // reset accu for re-use - landAccu[jjt][it] = false; - waterAccu[jjt][it] = false; return pixelClassifFlags; } - private static int urbanCloudDistinction(int jjt, int it, - boolean[][] urbanSomeClearAccu, + private static int urbanCloudDistinction(int jt, int it, + boolean[][] clearNearbyAccu, double[][] m7, double[][] m8, double[][] c7, double[][] c8, short[][] n78, int pixelClassifFlags) { // some clear pixels nearby, and not cirrus or water - final boolean notInTheMiddleOfACloud = urbanSomeClearAccu[jjt][it]; - if (notInTheMiddleOfACloud - && (pixelClassifFlags & (IDEPIX_CIRRUS_AMBIGUOUS_BIT | IDEPIX_CIRRUS_SURE_BIT | IDEPIX_WATER_BIT)) == 0 - && (pixelClassifFlags & (IDEPIX_CLOUD_AMBIGUOUS_BIT | IDEPIX_CLOUD_SURE_BIT | IDEPIX_CLOUD_BIT)) != 0) { + if (isCloud(pixelClassifFlags) && isNotCirrusNotWater(pixelClassifFlags) && clearNearbyAccu[jt][it]) { // another non-cloud test - final double variance7 = variance_of(c7[jjt][it], m7[jjt][it], n78[jjt][it]); - final double variance8 = variance_of(c8[jjt][it], m8[jjt][it], n78[jjt][it]); + final double variance7 = variance_of(c7[jt][it], m7[jt][it], n78[jt][it]); + final double variance8 = variance_of(c8[jt][it], m8[jt][it], n78[jt][it]); final double cdiValue = (variance7 - variance8) / (variance7 + variance8); if (cdiValue >= CDI_THRESHOLD) { // clear cloud flags if CDI test succeeds @@ -333,42 +331,112 @@ private static int urbanCloudDistinction(int jjt, int it, pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD, false); } } - // clear accu for re-use - urbanSomeClearAccu[jjt][it] = false; - c7[jjt][it] = 0.0; - m7[jjt][it] = 0.0; - c8[jjt][it] = 0.0; - m8[jjt][it] = 0.0; - n78[jjt][it] = 0; return pixelClassifFlags; } - private void addCloudBuffer(Rectangle cloudBufferExtendedRectangle, Rectangle cloudBufferRectangle, - Rectangle targetRectangle, Tile sourceFlagTile, Tile targetTile) { - final boolean[][] cloudBufferAccu = new boolean[cloudBufferSize][targetRectangle.width]; - for (int y = cloudBufferExtendedRectangle.y; y < cloudBufferExtendedRectangle.y + cloudBufferExtendedRectangle.height; y++) { - checkForCancellation(); - for (int x = cloudBufferExtendedRectangle.x; x < cloudBufferExtendedRectangle.x + cloudBufferExtendedRectangle.width; x++) { - if (cloudBufferRectangle.contains(x, y)) { - if (isCloudForBuffer(targetRectangle.contains(x, y) ? targetTile : sourceFlagTile, x, y)) { - fillPatchInAccu(y, x, targetRectangle, cloudBufferWidth, cloudBufferSize, true, cloudBufferAccu); - } - } - // target pixel yt/xt - final int yt = y - cloudBufferWidth; - final int xt = x - cloudBufferWidth; - // accu position jjt/it - final int jjt = (yt - targetRectangle.y) % cloudBufferSize; - final int it = xt - targetRectangle.x; - // evaluate accu if we have enough context - // set cloud buffer flag if it is not cloud but there is a cloud nearby - if (targetRectangle.contains(xt, yt)) { - if (cloudBufferAccu[jjt][it] - && (targetTile.getSampleInt(xt, yt) & ((1 << IDEPIX_CLOUD_AMBIGUOUS) | (1 << IDEPIX_CLOUD_SURE) | (1 << IDEPIX_CLOUD) | (1 << IDEPIX_INVALID))) == 0) { - targetTile.setSample(xt, yt, IDEPIX_CLOUD_BUFFER, true); - } - // clear accu for re-use - cloudBufferAccu[jjt][it] = false; + private void collectLand(int y, int x, + Tile sourceFlagTile, + Rectangle cloudBufferRectangle, + boolean[][] landAccu) { + if (isLand(sourceFlagTile, y, x)) { + fillPatchInAccu(y, x, cloudBufferRectangle, landWaterContextRadius, landAccu); + } + } + + private void collectWater(int y, int x, + Tile sourceFlagTile, + Rectangle cloudBufferRectangle, + boolean[][] waterAccu) { + if (isWater(sourceFlagTile, y, x)) { + fillPatchInAccu(y, x, cloudBufferRectangle, landWaterContextRadius, waterAccu); + } + } + + private void collectClear(int y, int x, + Tile sourceFlagTile, + Rectangle cloudBufferRectangle, + boolean[][] clearNearbyAccu) { + if (isClear(sourceFlagTile, y, x)) { + fillPatchInAccu(y, x, cloudBufferRectangle, urbanContextRadius, clearNearbyAccu); + } + } + + private void collectCdiSumsAndSquares(int y, int x, + Tile b7Tile, Tile b8Tile, Tile b8aTile, + Rectangle cdiRectangle, Rectangle cloudBufferRectangle, + double[][] m7, double[][] c7, double[][] m8, double[][] c8, short[][] n78) { + // determine nearest position inside complete image, COPY-extend image + final int xt = + x < cdiRectangle.x ? cdiRectangle.x + : x >= cdiRectangle.x + cdiRectangle.width ? cdiRectangle.x + cdiRectangle.width - 1 + : x; + final int yt = + y < cdiRectangle.y ? cdiRectangle.y + : y >= cdiRectangle.y + cdiRectangle.height ? cdiRectangle.y + cdiRectangle.height - 1 + : y; + // determine values + final float b7 = b7Tile.getSampleFloat(xt, yt); + final float b8 = b8Tile.getSampleFloat(xt, yt); + final float b8a = b8aTile.getSampleFloat(xt, yt); + if (!Float.isNaN(b7) && !Float.isNaN(b8) && b8a != 0.0f) { + final float b7b8a = b7 / b8a; + final float b8b8a = b8 / b8a; + addStddevPatchInAccu(y, x, cloudBufferRectangle, cdiStddevContextRadius, + b7b8a, b8b8a, + m7, c7, m8, c8, n78); + } + } + + private void fillPatchInAccu(int y, int x, Rectangle cloudBufferRectangle, int halfWidth, boolean[][] accu) { + // reduce patch to part overlapping with target image + final int jMin = Math.max(y - cloudBufferRectangle.y - halfWidth, 0); + final int jMax = Math.min(y - cloudBufferRectangle.y + 1 + halfWidth, cloudBufferRectangle.height); + final int iMin = Math.max(x - cloudBufferRectangle.x - halfWidth, 0); + final int iMax = Math.min(x - cloudBufferRectangle.x + 1 + halfWidth, cloudBufferRectangle.width); + // fill patch with value + for (int j = jMin; j < jMax; ++j) { + final int jj = j % contextSize; + for (int i = iMin; i < iMax; ++i) { + accu[jj][i] = true; + } + } + } + + private void addStddevPatchInAccu(int y, int x, Rectangle cloudBufferRectangle, int halfWidth, + float b7b8a, float b8b8a, + double[][] m7, double[][] c7, double[][] m8, double[][] c8, short[][] n78) { + // reduce patch to part overlapping with target image + final int jMin = Math.max(y - cloudBufferRectangle.y - halfWidth, 0); + final int jMax = Math.min(y - cloudBufferRectangle.y + 1 + halfWidth, cloudBufferRectangle.height); + final int iMin = Math.max(x - cloudBufferRectangle.x - halfWidth, 0); + final int iMax = Math.min(x - cloudBufferRectangle.x + 1 + halfWidth, cloudBufferRectangle.width); + // add to mean and to sum of squares within patch + final float b7b8a2 = b7b8a * b7b8a; + final float b8b8a2 = b8b8a * b8b8a; + for (int j = jMin; j < jMax; ++j) { + final int jj = j % contextSize; + for (int i = iMin; i < iMax; ++i) { + m7[jj][i] += b7b8a; + c7[jj][i] += b7b8a2; + m8[jj][i] += b8b8a; + c8[jj][i] += b8b8a2; + n78[jj][i] += 1; + } + } + } + + private void addCloudBufferInAccu(int y, int x, Rectangle targetRectangle, int halfWidth, + int[][] cloudBufferAccu) { + // reduce patch to part overlapping with target image + final int jMin = Math.max(y - targetRectangle.y - halfWidth, 0); + final int jMax = Math.min(y - targetRectangle.y + 1 + halfWidth, targetRectangle.height); + final int iMin = Math.max(x - targetRectangle.x - halfWidth, 0); + final int iMax = Math.min(x - targetRectangle.x + 1 + halfWidth, targetRectangle.width); + for (int j = jMin; j < jMax; ++j) { + final int jj = j % cloudBufferSize; + for (int i = iMin; i < iMax; ++i) { + if (isClear(cloudBufferAccu[jj][i])) { + cloudBufferAccu[jj][i] |= (1 << IDEPIX_CLOUD_BUFFER); } } } @@ -398,18 +466,47 @@ private static boolean isLand(Tile tile, int y, int x) { private static boolean isWater(Tile tile, int y, int x) { return tile.getSampleBit(x, y, IDEPIX_WATER); } + + private static boolean isValid(int pixelClassifFlags) { + return (pixelClassifFlags & 1 << IDEPIX_INVALID) == 0; + } - private static boolean mayBeCloud(Tile tile, int y, int x) { - return (tile.getSampleInt(x, y) & ((1 << IDEPIX_CLOUD_AMBIGUOUS) | (1 << IDEPIX_CLOUD_SURE) | (1 << IDEPIX_CLOUD) | 1 << IDEPIX_INVALID)) != 0; + private static boolean isAmbigousOrSure(int pixelClassifFlags) { + return (pixelClassifFlags & (1 << IDEPIX_CLOUD_AMBIGUOUS | 1 << IDEPIX_CLOUD_SURE)) != 0; } - private boolean isCloudForBuffer(Tile targetTile, int x, int y) { - return targetTile.getSampleBit(x, y, IDEPIX_CLOUD_SURE) || - (computeCloudBufferForCloudAmbiguous && targetTile.getSampleBit(x, y, IDEPIX_CLOUD_AMBIGUOUS)); + private static boolean isCloudBuffer(int pixelClassifFlags) { + return (pixelClassifFlags & 1 << IDEPIX_CLOUD_BUFFER) != 0; + } + + private static boolean isClear(int pixelClassifFlags) { + return (pixelClassifFlags + & (1 << IDEPIX_CLOUD_AMBIGUOUS | 1 << IDEPIX_CLOUD_SURE + | 1 << IDEPIX_CLOUD | 1 << IDEPIX_INVALID)) == 0; + } + + private static boolean isCloud(int pixelClassifFlags) { + return (pixelClassifFlags & (1 << IDEPIX_CLOUD_AMBIGUOUS | 1 << IDEPIX_CLOUD_SURE | 1 << IDEPIX_CLOUD)) != 0; + } + + private static boolean isNotCirrusNotWater(int pixelClassifFlags) { + return (pixelClassifFlags & (1 << IDEPIX_CIRRUS_AMBIGUOUS | 1 << IDEPIX_CIRRUS_SURE | 1 << IDEPIX_WATER)) == 0; + } + + private static boolean isClear(Tile tile, int y, int x) { + return (tile.getSampleInt(x, y) + & (1 << IDEPIX_CLOUD_AMBIGUOUS | 1 << IDEPIX_CLOUD_SURE + | 1 << IDEPIX_CLOUD | 1 << IDEPIX_INVALID)) == 0; + } + + private boolean isCloudForBuffer(int pixelClassifFlags) { + return + (pixelClassifFlags & 1 << IDEPIX_CLOUD_SURE) != 0 || + (computeCloudBufferForCloudAmbiguous && (pixelClassifFlags & 1 << IDEPIX_CLOUD_AMBIGUOUS) != 0); } private static double variance_of(double c, double m, int n) { - //return n == 0 ? Double.NaN : n == 1 ? 0.0 : (c - m * m / n) / (n - 1); + //return n == 0 ? Double.NaN : n == 1 ? 0.0 : (c - m * m / n) / (n - 1); // seems JNI uses different formula return n == 0 ? Double.NaN : n == 1 ? 0.0 : (c - m * m / n) / n; } From 2749b95c776a542c479570c40571e1e12a0d5e66 Mon Sep 17 00:00:00 2001 From: martin-boettcher Date: Sat, 11 Feb 2023 22:32:06 +0100 Subject: [PATCH 08/12] small modifications to reproduce exactly the former result: asymmetric kernel with even number of pixels, comparison of float and double --- .../org/esa/snap/idepix/s2msi/S2IdepixOp.java | 4 ++ .../S2IdepixCloudPostProcess2Op.java | 59 ++++++------------- 2 files changed, 21 insertions(+), 42 deletions(-) diff --git a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixOp.java b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixOp.java index 42868aff..f2fe4624 100644 --- a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixOp.java +++ b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixOp.java @@ -109,6 +109,10 @@ private void processSentinel2() { int cacheSize = Integer.parseInt(System.getProperty(S2IdepixUtils.TILECACHE_PROPERTY, "1600")); s2ClassifProduct = S2IdepixUtils.computeTileCacheProduct(s2ClassifProduct, cacheSize); + // breakpoint output to generate input for cloud post-processing + //targetProduct = s2ClassifProduct; + //if (true) return; + // Post Cloud Classification: cloud shadow, cloud buffer, mountain shadow Product postProcessingProduct = computePostProcessProduct(sourceProduct, s2ClassifProduct); diff --git a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java index 103f3f3d..8defa29a 100644 --- a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java +++ b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/operators/S2IdepixCloudPostProcess2Op.java @@ -191,14 +191,16 @@ public void computeTile(Band targetBand, Tile targetTile, ProgressMonitor pm) th for (int x = contextExtendedRectangle.x; x < contextExtendedRectangle.x + contextExtendedRectangle.width; x++) { // write dilated land and water patch into accu, required for coastal cloud distinction - if (pixelStateRectangle.contains(x, y)) { - collectLand(y, x, sourceFlagTile, cloudBufferRectangle, landNearbyAccu); - collectWater(y, x, sourceFlagTile, cloudBufferRectangle, waterNearbyAccu); + if (pixelStateRectangle.contains(x, y) && isLand(sourceFlagTile, y, x)) { + fillPatchInAccu(y, x, cloudBufferRectangle, landWaterContextSize, landNearbyAccu); + } + if (pixelStateRectangle.contains(x, y) && isWater(sourceFlagTile, y, x)) { + fillPatchInAccu(y, x, cloudBufferRectangle, landWaterContextSize, waterNearbyAccu); } // write 11x11 "filtered" non-cloud patch into accu, required for urban cloud distinction - if (urbanRectangle.contains(x, y)) { - collectClear(y, x, sourceFlagTile, cloudBufferRectangle, clearNearbyAccu); + if (urbanRectangle.contains(x, y) && isClear(sourceFlagTile, y, x)) { + fillPatchInAccu(y, x, cloudBufferRectangle, urbanContextSize, clearNearbyAccu); } // add stddev contributions to accu of sums, squares, counts, required for urban cloud distinction @@ -215,7 +217,7 @@ public void computeTile(Band targetBand, Tile targetTile, ProgressMonitor pm) th landNearbyAccu, waterNearbyAccu, clearNearbyAccu, m7, c7, m8, c8, n78, sourceFlagTile, b2Tile, b8Tile, b11Tile, - targetRectangle, cloudBufferRectangle, + cloudBufferRectangle, targetRectangle, cloudBufferAccu); } // yb/xb is the target pixel where we have seen just the last pixel of some possible cloud buffer @@ -232,7 +234,7 @@ private void correctFlagsOfPixel(int yt, int xt, boolean[][] landAccu, boolean[][] waterAccu, boolean[][] clearNearbyAccu, double[][] m7, double[][] c7, double[][] m8, double[][] c8, short[][] n78, Tile sourceFlagTile, Tile b2Tile, Tile b8Tile, Tile b11Tile, - Rectangle targetRectangle, Rectangle cloudBufferRectangle, + Rectangle cloudBufferRectangle, Rectangle targetRectangle, int[][] cloudBufferAccu) { // land/water/urban accu pixel position final int jt = (yt - cloudBufferRectangle.y) % contextSize; @@ -298,9 +300,9 @@ private static int coastalCloudDistinction(int yt, int xt, int jt, int it, final float b11 = b11Tile.getSampleFloat(xt, yt); final float idx1 = b2 / b11; final float idx2 = b8 / b11; - //final boolean notCoastal = idx1 > 0.7f || (idx1 > 0.6f && idx2 > 0.9f); - // handles NaN as non-coastal - final boolean isCoastal2 = idx1 <= 0.6f || (idx1 <= 0.7f && idx2 <= 0.9f); + //final boolean notCoast = idx1 > 0.7 || (idx1 < 1 && idx1 > 0.6 && idx2 > 0.9); + // inverted condition handles NaN as non-coastal, using double for constants preserves former results + final boolean isCoastal2 = idx1 <= 0.6 || (idx1 <= 0.7 && idx2 <= 0.9); if (isCoastal2) { // clear cloud flags if cloud test fails pixelClassifFlags = BitSetter.setFlag(pixelClassifFlags, IDEPIX_CLOUD_AMBIGUOUS, false); @@ -334,33 +336,6 @@ private static int urbanCloudDistinction(int jt, int it, return pixelClassifFlags; } - private void collectLand(int y, int x, - Tile sourceFlagTile, - Rectangle cloudBufferRectangle, - boolean[][] landAccu) { - if (isLand(sourceFlagTile, y, x)) { - fillPatchInAccu(y, x, cloudBufferRectangle, landWaterContextRadius, landAccu); - } - } - - private void collectWater(int y, int x, - Tile sourceFlagTile, - Rectangle cloudBufferRectangle, - boolean[][] waterAccu) { - if (isWater(sourceFlagTile, y, x)) { - fillPatchInAccu(y, x, cloudBufferRectangle, landWaterContextRadius, waterAccu); - } - } - - private void collectClear(int y, int x, - Tile sourceFlagTile, - Rectangle cloudBufferRectangle, - boolean[][] clearNearbyAccu) { - if (isClear(sourceFlagTile, y, x)) { - fillPatchInAccu(y, x, cloudBufferRectangle, urbanContextRadius, clearNearbyAccu); - } - } - private void collectCdiSumsAndSquares(int y, int x, Tile b7Tile, Tile b8Tile, Tile b8aTile, Rectangle cdiRectangle, Rectangle cloudBufferRectangle, @@ -387,12 +362,12 @@ private void collectCdiSumsAndSquares(int y, int x, } } - private void fillPatchInAccu(int y, int x, Rectangle cloudBufferRectangle, int halfWidth, boolean[][] accu) { + private void fillPatchInAccu(int y, int x, Rectangle cloudBufferRectangle, int width, boolean[][] accu) { // reduce patch to part overlapping with target image - final int jMin = Math.max(y - cloudBufferRectangle.y - halfWidth, 0); - final int jMax = Math.min(y - cloudBufferRectangle.y + 1 + halfWidth, cloudBufferRectangle.height); - final int iMin = Math.max(x - cloudBufferRectangle.x - halfWidth, 0); - final int iMax = Math.min(x - cloudBufferRectangle.x + 1 + halfWidth, cloudBufferRectangle.width); + final int jMin = Math.max(y - cloudBufferRectangle.y - width / 2, 0); + final int jMax = Math.min(y - cloudBufferRectangle.y - width / 2 + width, cloudBufferRectangle.height); + final int iMin = Math.max(x - cloudBufferRectangle.x - width / 2, 0); + final int iMax = Math.min(x - cloudBufferRectangle.x - width / 2 + width, cloudBufferRectangle.width); // fill patch with value for (int j = jMin; j < jMax; ++j) { final int jj = j % contextSize; From 2229dc975f79c65555968113f6a4df8ec4a7490d Mon Sep 17 00:00:00 2001 From: martin-boettcher Date: Thu, 15 Dec 2022 11:38:18 +0100 Subject: [PATCH 09/12] support SecondaryMetadata.anyelement from standard CollocationOp as alternative to SLSTRmetadata global attribute --- .../c3solcislstr/rad2refl/SlstrRadReflConverter.java | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/idepix-c3solcislstr/src/main/java/org/esa/snap/idepix/c3solcislstr/rad2refl/SlstrRadReflConverter.java b/idepix-c3solcislstr/src/main/java/org/esa/snap/idepix/c3solcislstr/rad2refl/SlstrRadReflConverter.java index 7d6702ab..0b925da0 100644 --- a/idepix-c3solcislstr/src/main/java/org/esa/snap/idepix/c3solcislstr/rad2refl/SlstrRadReflConverter.java +++ b/idepix-c3solcislstr/src/main/java/org/esa/snap/idepix/c3solcislstr/rad2refl/SlstrRadReflConverter.java @@ -74,8 +74,12 @@ static Map getSolarFluxMapFromC3SSYNMetadata(Product sourceProduc final int spectralIndex = Integer.parseInt(bandName.substring(1, 2)) - 1; final String bandNameChannel = bandName.substring(0, 2); final String stringToReplace = radToReflMode ? "radiance" : "reflectance"; - final MetadataElement qualityElement = sourceProduct.getMetadataRoot().getElement("SLSTRmetadata"); - + final MetadataElement qualityElement = + sourceProduct.getMetadataRoot().containsElement("SLSTRmetadata") ? + sourceProduct.getMetadataRoot().getElement("SLSTRmetadata") : + sourceProduct.getMetadataRoot().containsElement("SecondaryMetadata") ? + sourceProduct.getMetadataRoot().getElement("SecondaryMetadata").getElementAt(0) : + null; if (qualityElement != null) { final MetadataElement variableAttributesElement = qualityElement.getElement(bandNameChannel); if (variableAttributesElement != null) { From 461c34e253d8560dc7f24641531eecf385f9ae50 Mon Sep 17 00:00:00 2001 From: Olaf Danne Date: Mon, 20 Mar 2023 18:21:56 +0100 Subject: [PATCH 10/12] Idepix OLCI: introduced user option to use an alternative NN for pixel classification; minor cleanup of log messages. --- .../C3SOlciSlstrClassificationOp.java | 2 +- .../IdepixMerisLandClassificationOp.java | 2 +- .../olci/IdepixOlciClassificationOp.java | 42 +++++++++++++++--- .../esa/snap/idepix/olci/IdepixOlciOp.java | 7 +++ .../olci/docs/images/OlciParameters.png | Bin 95858 -> 22784 bytes .../docs/olci/OlciProcessorDescription.html | 6 +++ .../olcislstr/OlciSlstrClassificationOp.java | 2 +- .../s2msi/S2IdepixClassificationOp.java | 2 +- .../idepix/spotvgt/VgtClassificationOp.java | 2 +- 9 files changed, 53 insertions(+), 12 deletions(-) diff --git a/idepix-c3solcislstr/src/main/java/org/esa/snap/idepix/c3solcislstr/C3SOlciSlstrClassificationOp.java b/idepix-c3solcislstr/src/main/java/org/esa/snap/idepix/c3solcislstr/C3SOlciSlstrClassificationOp.java index d975f471..062cbdf9 100644 --- a/idepix-c3solcislstr/src/main/java/org/esa/snap/idepix/c3solcislstr/C3SOlciSlstrClassificationOp.java +++ b/idepix-c3solcislstr/src/main/java/org/esa/snap/idepix/c3solcislstr/C3SOlciSlstrClassificationOp.java @@ -303,7 +303,7 @@ public void computeTileStack(Map targetTiles, Rectangle rectangle, P } } } catch (Exception e) { - throw new OperatorException("Failed to provide GA cloud screening:\n" + e.getMessage(), e); + throw new OperatorException("Failed to provide cloud screening:\n" + e.getMessage(), e); } } diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisLandClassificationOp.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisLandClassificationOp.java index a75bdf79..0e6d2699 100644 --- a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisLandClassificationOp.java +++ b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisLandClassificationOp.java @@ -207,7 +207,7 @@ public void computeTileStack(Map targetTiles, Rectangle rectangle, P } } } catch (Exception e) { - throw new OperatorException("Failed to provide GA cloud screening:\n" + e.getMessage(), e); + throw new OperatorException("Failed to provide cloud screening:\n" + e.getMessage(), e); } } diff --git a/idepix-olci/src/main/java/org/esa/snap/idepix/olci/IdepixOlciClassificationOp.java b/idepix-olci/src/main/java/org/esa/snap/idepix/olci/IdepixOlciClassificationOp.java index 107a2da0..b6fc636c 100644 --- a/idepix-olci/src/main/java/org/esa/snap/idepix/olci/IdepixOlciClassificationOp.java +++ b/idepix-olci/src/main/java/org/esa/snap/idepix/olci/IdepixOlciClassificationOp.java @@ -24,8 +24,8 @@ import org.locationtech.jts.geom.Polygon; import java.awt.Rectangle; -import java.io.IOException; -import java.io.InputStream; +import java.io.*; +import java.nio.file.Files; import java.util.Calendar; import java.util.Map; @@ -63,6 +63,11 @@ public class IdepixOlciClassificationOp extends Operator { description = " If applied, write Schiller NN value to the target product ") private boolean outputSchillerNNValue; + @Parameter(description = "Alternative NN file. " + + "If set, it MUST follow format and input/output as used in default '11x10x4x3x2_207.9.net. ", + label = " Alternative NN file") + private File alternativeNNFile; + @Parameter(defaultValue = "false", description = "Check for sea/lake ice also outside Sea Ice Climatology area.", label = "Check for sea/lake ice also outside Sea Ice Climatology area" @@ -144,8 +149,21 @@ public void initialize() throws OperatorException { } private void readSchillerNeuralNets() { - InputStream olciAllIS = getClass().getResourceAsStream(OLCI_ALL_NET_NAME); - olciAllNeuralNet = SchillerNeuralNetWrapper.create(olciAllIS); + InputStream olciAllInputStream; + try { + olciAllInputStream = getNNInputStream(); + } catch (IOException e) { + throw new OperatorException("Cannot read specified alternative Neural Net - please check!", e); + } + olciAllNeuralNet = SchillerNeuralNetWrapper.create(olciAllInputStream); + } + + private InputStream getNNInputStream() throws IOException { + if (alternativeNNFile != null) { + return Files.newInputStream(alternativeNNFile.toPath()); + } else { + return getClass().getResourceAsStream(OLCI_ALL_NET_NAME); + } } private void initSeaIceClassifier() { @@ -243,7 +261,7 @@ public void computeTileStack(Map targetTiles, Rectangle rectangle, P } } } catch (Exception e) { - throw new OperatorException("Failed to provide GA cloud screening:\n" + e.getMessage(), e); + throw new OperatorException("Failed to provide cloud screening:\n" + e.getMessage(), e); } } @@ -300,7 +318,12 @@ private void classifyOverLand(Tile[] olciReflectanceTiles, } final float olciReflectance21 = olciReflectances[Rad2ReflConstants.OLCI_REFL_BAND_NAMES.length - 1]; - SchillerNeuralNetWrapper nnWrapper = olciAllNeuralNet.get(); + SchillerNeuralNetWrapper nnWrapper; + try { + nnWrapper = olciAllNeuralNet.get(); + } catch (Exception e) { + throw new OperatorException("Cannot get values from Neural Net file - check format!" + e.getMessage()); + } double[] inputVector = nnWrapper.getInputVector(); for (int i = 0; i < inputVector.length; i++) { inputVector[i] = Math.sqrt(olciReflectances[i]); @@ -392,7 +415,12 @@ private boolean isOlciInlandWaterPixel(int x, int y, Tile olciL1bFlagTile) { } private double[] getOlciNNOutput(int x, int y, Tile[] rhoToaTiles) { - SchillerNeuralNetWrapper nnWrapper = olciAllNeuralNet.get(); + SchillerNeuralNetWrapper nnWrapper; + try { + nnWrapper = olciAllNeuralNet.get(); + } catch (Exception e) { + throw new OperatorException("Cannot get values from Neural Net file - check format! " + e.getMessage()); + } double[] nnInput = nnWrapper.getInputVector(); for (int i = 0; i < nnInput.length; i++) { nnInput[i] = Math.sqrt(rhoToaTiles[i].getSampleFloat(x, y)); diff --git a/idepix-olci/src/main/java/org/esa/snap/idepix/olci/IdepixOlciOp.java b/idepix-olci/src/main/java/org/esa/snap/idepix/olci/IdepixOlciOp.java index d94b5bc3..3800bbe1 100644 --- a/idepix-olci/src/main/java/org/esa/snap/idepix/olci/IdepixOlciOp.java +++ b/idepix-olci/src/main/java/org/esa/snap/idepix/olci/IdepixOlciOp.java @@ -16,6 +16,7 @@ import org.locationtech.jts.geom.Geometry; import org.locationtech.jts.geom.Polygon; +import java.io.File; import java.util.HashMap; import java.util.Map; @@ -79,6 +80,11 @@ public class IdepixOlciOp extends BasisOp { description = " If applied, write NN value to the target product ") private boolean outputSchillerNNValue; + @Parameter(description = "Alternative NN file. " + + "If set, it MUST follow format and input/output as used in default '11x10x4x3x2_207.9.net. 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zUErez#T;8Vo}%-;@|PH^A@gMCOS=0fL8OPod@w7q{NqYcK*;S3Q41*+7;5xe&`h3O z?=`)a5<%mmuQ@v_yQG6GbqBO*N_7aaJv71m0YtAh-7K})w;MaxQ6Pll{VuojM;g22Y(`tGJ=zJG0UCor;Q|^7}h}x?9b!YS?RZ+s-*%(JQCa zbfPgN+qbs15e2+Vazv=2x9jV5R`>rGhvY-LmBujXuc~b=)19iTDCj-LS8ZBrC~VD< zlrhvu--lRx8uupf)msq8`5y}hzxQE?(euCXNUsyLf_hE5Z^UGx#pR6PhdpMIk(CLM~cP<9)NCDHG`hNf@8A;;+ diff --git a/idepix-olci/src/main/javahelp/org/esa/snap/idepix/olci/docs/olci/OlciProcessorDescription.html b/idepix-olci/src/main/javahelp/org/esa/snap/idepix/olci/docs/olci/OlciProcessorDescription.html index cb6c9ab6..9bd89f99 100644 --- a/idepix-olci/src/main/javahelp/org/esa/snap/idepix/olci/docs/olci/OlciProcessorDescription.html +++ b/idepix-olci/src/main/javahelp/org/esa/snap/idepix/olci/docs/olci/OlciProcessorDescription.html @@ -107,6 +107,12 @@

The Processing Parameters

(floating point number on the interval [0.0, 5.0]) is written to the target product. The default is 'false'.

+

+ Alternative NN file:
+ Alternative NN file. If selected, this file MUST follow format and input/output as used in + default '11x10x4x3x2_207.9.net'. +

+

Compute mountain shadow:
If set, a mountain shadow is computed and added to the pixel classification. The default value is 'true'. diff --git a/idepix-olcislstr/src/main/java/org/esa/snap/idepix/olcislstr/OlciSlstrClassificationOp.java b/idepix-olcislstr/src/main/java/org/esa/snap/idepix/olcislstr/OlciSlstrClassificationOp.java index 62d84c4c..9cb5f701 100644 --- a/idepix-olcislstr/src/main/java/org/esa/snap/idepix/olcislstr/OlciSlstrClassificationOp.java +++ b/idepix-olcislstr/src/main/java/org/esa/snap/idepix/olcislstr/OlciSlstrClassificationOp.java @@ -207,7 +207,7 @@ public void computeTileStack(Map targetTiles, Rectangle rectangle, P } } } catch (Exception e) { - throw new OperatorException("Failed to provide GA cloud screening:\n" + e.getMessage(), e); + throw new OperatorException("Failed to provide cloud screening:\n" + e.getMessage(), e); } } diff --git a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixClassificationOp.java b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixClassificationOp.java index 01e92625..987bf7a1 100644 --- a/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixClassificationOp.java +++ b/idepix-s2msi/src/main/java/org/esa/snap/idepix/s2msi/S2IdepixClassificationOp.java @@ -218,7 +218,7 @@ public void computeTileStack(Map targetTiles, Rectangle rectangle, P } } catch (Exception e) { - throw new OperatorException("Failed to provide GA cloud screening:\n" + e.getMessage(), e); + throw new OperatorException("Failed to provide cloud screening:\n" + e.getMessage(), e); } } diff --git a/idepix-spotvgt/src/main/java/org/esa/snap/idepix/spotvgt/VgtClassificationOp.java b/idepix-spotvgt/src/main/java/org/esa/snap/idepix/spotvgt/VgtClassificationOp.java index e9a2d205..df7c724a 100644 --- a/idepix-spotvgt/src/main/java/org/esa/snap/idepix/spotvgt/VgtClassificationOp.java +++ b/idepix-spotvgt/src/main/java/org/esa/snap/idepix/spotvgt/VgtClassificationOp.java @@ -211,7 +211,7 @@ public void computeTileStack(Map targetTiles, Rectangle rectangle, P } } } catch (Exception e) { - throw new OperatorException("Failed to provide GA cloud screening:\n" + e.getMessage(), e); + throw new OperatorException("Failed to provide cloud screening:\n" + e.getMessage(), e); } } From 7ba4f63d519bbef23e682bd379057f001dc1c732 Mon Sep 17 00:00:00 2001 From: Olaf Danne Date: Wed, 29 Mar 2023 22:14:07 +0200 Subject: [PATCH 11/12] Idepix Meris: added mountain shadow detection (same algo as for OLCI); some cleanup (removed code duplication) --- .../util/SlopeAspectOrientationUtils.java | 183 ++++++++ .../idepix/meris/IdepixMerisConstants.java | 35 +- .../meris/IdepixMerisMountainShadowOp.java | 140 ++++++ .../esa/snap/idepix/meris/IdepixMerisOp.java | 18 +- .../meris/IdepixMerisPostProcessOp.java | 74 +++- .../IdepixMerisSlopeAspectOrientationOp.java | 202 +++++++++ .../snap/idepix/meris/IdepixMerisUtils.java | 81 +++- .../IdepixMerisViewAngleInterpolationOp.java | 189 ++++++++ .../Meris3rd4thReprocessingAdapter.java | 406 ------------------ .../Meris3rd4thReprocessingMetadata.java | 101 ----- .../reprocessing/ReprocessingAdapter.java | 27 -- .../meris/docs/images/MerisParameters.png | Bin 28161 -> 32494 bytes .../docs/meris/MerisProcessorDescription.html | 11 + .../org.esa.snap.core.gpf.OperatorSpi | 4 +- .../Meris3rd4thReprocessingAdapterTest.java | 270 ------------ .../Meris3rd4thReprocessingMetadataTest.java | 95 ---- .../IdepixOlciSlopeAspectOrientationOp.java | 184 +------- ...depixOlciSlopeAspectOrientationOpTest.java | 87 ---- 18 files changed, 928 insertions(+), 1179 deletions(-) create mode 100644 idepix-core/src/main/java/org/esa/snap/idepix/core/util/SlopeAspectOrientationUtils.java create mode 100644 idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisMountainShadowOp.java create mode 100644 idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisSlopeAspectOrientationOp.java create mode 100644 idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisViewAngleInterpolationOp.java delete mode 100644 idepix-meris/src/main/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingAdapter.java delete mode 100644 idepix-meris/src/main/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingMetadata.java delete mode 100644 idepix-meris/src/main/java/org/esa/snap/idepix/meris/reprocessing/ReprocessingAdapter.java delete mode 100644 idepix-meris/src/test/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingAdapterTest.java delete mode 100644 idepix-meris/src/test/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingMetadataTest.java delete mode 100644 idepix-olci/src/test/java/org/esa/snap/idepix/olci/IdepixOlciSlopeAspectOrientationOpTest.java diff --git a/idepix-core/src/main/java/org/esa/snap/idepix/core/util/SlopeAspectOrientationUtils.java b/idepix-core/src/main/java/org/esa/snap/idepix/core/util/SlopeAspectOrientationUtils.java new file mode 100644 index 00000000..786a7f84 --- /dev/null +++ b/idepix-core/src/main/java/org/esa/snap/idepix/core/util/SlopeAspectOrientationUtils.java @@ -0,0 +1,183 @@ +package org.esa.snap.idepix.core.util; + +import org.esa.snap.core.datamodel.GeoCoding; +import org.esa.snap.core.datamodel.GeoPos; +import org.esa.snap.core.datamodel.PixelPos; +import org.esa.snap.core.datamodel.Product; +import org.esa.snap.core.gpf.Tile; +import org.esa.snap.core.util.math.MathUtils; + +public class SlopeAspectOrientationUtils { + + private final static float EARTH_MIN_ELEVATION = -428.0f; // at shoreline of Dead Sea + private final static float EARTH_MAX_ELEVATION = 8848.0f; // Mt. Everest + + /** + * Provides data from a 3x3 macropixel of a float source tile + * + * @param sourceTile - + * @param y - + * @param x - + * @return float[9] + */ + public static float[] get3x3MacropixelData(Tile sourceTile, int y, int x) { + float[] macropixelData = new float[9]; + macropixelData[0] = sourceTile.getSampleFloat(x - 1, y - 1); + macropixelData[1] = sourceTile.getSampleFloat(x, y - 1); + macropixelData[2] = sourceTile.getSampleFloat(x + 1, y - 1); + macropixelData[3] = sourceTile.getSampleFloat(x - 1, y); + macropixelData[4] = sourceTile.getSampleFloat(x, y); + macropixelData[5] = sourceTile.getSampleFloat(x + 1, y); + macropixelData[6] = sourceTile.getSampleFloat(x - 1, y + 1); + macropixelData[7] = sourceTile.getSampleFloat(x, y + 1); + macropixelData[8] = sourceTile.getSampleFloat(x + 1, y + 1); + + return macropixelData; + } + + /** + * Checks if 3x3 box of elevations around reference pixel is valid + * (i.e. not NaN and all values inside real values possible on Earth) + * + * @param elevationData - 3x3 box of elevations + * @return boolean + */ + public static boolean is3x3ElevationDataValid(float[] elevationData) { + for (final float elev : elevationData) { + if (elev == 0.0f || Float.isNaN(elev) || elev < EARTH_MIN_ELEVATION || elev > EARTH_MAX_ELEVATION) { + return false; + } + } + return true; + } + + /** + * Computes slope and aspect for a 3x3 altitude array + * + * @param elev - 3x3 elevation array + * @param orientation - orientation angle of box + * @param vza - view zenith angle + * @param vaa - view azimuth angle + * @param saa - sun azimuth angle + * @param spatialResolution - spatial resolution in m + * @return float[]{slope, aspect} + */ + public static float[] computeSlopeAspect3x3(float[] elev, float orientation, float vza, float vaa, float saa, + double spatialResolution) { + //DM: geometric correction of resolution necessary for observations not in nadir view. + // generates steeper slopes. Needs vza, vaa, angle between y-pixel axis and north direction (orientation). + //DM: orientation in rad! + float b = (elev[2] + 2 * elev[5] + elev[8] - elev[0] - 2 * elev[3] - elev[6]) / 8f; //direction x + float c = (elev[0] + 2 * elev[1] + elev[2] - elev[6] - 2 * elev[7] - elev[8]) / 8f; //direction y + double vaa_orientation = (360.0 - (vaa + orientation / MathUtils.DTOR)) * MathUtils.DTOR; + double spatialRes = spatialResolution / Math.cos(vza * MathUtils.DTOR); + float slope = (float) Math.atan(Math.sqrt(Math.pow(b / (spatialRes * Math.sin(vaa_orientation)), 2) + + Math.pow(c / (spatialRes * Math.cos(vaa_orientation)), 2))); + float aspect = (float) Math.atan2(-b, -c); + if (saa > 270. || saa < 90) { //Sun from North (mostly southern hemisphere) + aspect -= Math.PI; + } + if (aspect < 0.0f) { + // map from [-180, 180] into [0, 360], see e.g. https://www.e-education.psu.edu/geog480/node/490 + aspect += 2.0 * Math.PI; + } + if (slope <= 0.0) { + aspect = Float.NaN; + } + + return new float[]{slope, aspect}; + } + + /** + * Computes the orientation of a 3x3 lat/lon box, i.e. uses 3rd and 5th point. + * + * @param latData - 3x3 lat values + * @param lonData - 3x3 lon values + * @return float + */ + public static float computeOrientation3x3Box(float[] latData, float[] lonData) { + final float lat1 = latData[3]; + final float lat2 = latData[5]; + final float lon1 = lonData[3]; + final float lon2 = lonData[5]; + + return computeOrientation(lat1, lat2, lon1, lon2); + } + + /** + * Provides orientation ('bearing') between two points. + * See theory e.g. at + * ... + * + * @param lat1 - first latitude + * @param lat2 - second latitude + * @param lon1 - first longitude + * @param lon2 - second longitude + * @return float + */ + public static float computeOrientation(float lat1, float lat2, float lon1, float lon2) { +// final float lat1Rad = lat1 * MathUtils.DTOR_F; +// final float deltaLon = lon2 - lon1; + // we use this formula, as in S2-MSI: +// return (float) Math.atan2(-(lat2 - lat1), deltaLon * Math.cos(lat1Rad)); + + // DM: formulas from theory, see above + double X = Math.cos(lat2 * MathUtils.DTOR) * Math.sin((lon2 - lon1) * MathUtils.DTOR); + double Y = Math.cos(lat1 * MathUtils.DTOR) * Math.sin(lat2 * MathUtils.DTOR) - Math.sin(lat1 * MathUtils.DTOR) * X; + return (float) (Math.atan2(X, Y)); + + } + + /** + * Computes product spatial resolution from great circle distances at the product edges. + * To be used as fallback if we have no CRS geocoding. + * + * @param l1bProduct - the source product + * @param sourceGeoCoding - the source scene geocoding + * @return spatial resolution in metres + */ + public static double computeSpatialResolution(Product l1bProduct, GeoCoding sourceGeoCoding) { + final double width = l1bProduct.getSceneRasterWidth(); + final double height = l1bProduct.getSceneRasterHeight(); + + final GeoPos leftPos = sourceGeoCoding.getGeoPos(new PixelPos(0, height / 2), null); + final GeoPos rightPos = sourceGeoCoding.getGeoPos(new PixelPos(width - 1, height / 2), null); + final double distance1 = + computeDistance(leftPos.getLat(), leftPos.getLon(), rightPos.getLat(), rightPos.getLon()); + final double xRes = 1000.0 * distance1 / (width - 1); + + final GeoPos upperPos = sourceGeoCoding.getGeoPos(new PixelPos(width / 2, 0), null); + final GeoPos lowerPos = sourceGeoCoding.getGeoPos(new PixelPos(width / 2, height - 1), null); + final double distance2 = + computeDistance(upperPos.getLat(), upperPos.getLon(), lowerPos.getLat(), lowerPos.getLon()); + final double yRes = 1000.0 * distance2 / (height - 1); + + return 0.5 * (xRes + yRes); + } + + /** + * Calculate the great-circle distance between two points on Earth using Haversine formula. + * See e.g. ... + * + * @param lat1 - first point latitude + * @param lon1 - first point longitude + * @param lat2 - second point latitude + * @param lon2 - second point longitude + * @return distance in km + */ + public static double computeDistance(double lat1, double lon1, double lat2, double lon2) { + final double deltaLatR = (lat1 - lat2) * MathUtils.DTOR; + final double deltaLonR = (lon1 - lon2) * MathUtils.DTOR; + + final double a = Math.sin(deltaLatR / 2.0) * Math.sin(deltaLatR / 2.0) + + Math.cos(lat1 * MathUtils.DTOR) * Math.cos(lat2 * MathUtils.DTOR) * + Math.sin(deltaLonR / 2.0) * Math.sin(deltaLonR / 2.0); + + final double c = 2.0 * Math.atan2(Math.sqrt(a), Math.sqrt(1 - a)); + + final double R = 6371.0; // Earth radius in km + + return R * c; + } + +} diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisConstants.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisConstants.java index 0b4bb7e5..12a17427 100644 --- a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisConstants.java +++ b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisConstants.java @@ -9,11 +9,44 @@ */ public class IdepixMerisConstants { - public static final int IDEPIX_GLINT_RISK = IdepixConstants.NUM_DEFAULT_FLAGS + 1; + public static final int IDEPIX_MOUNTAIN_SHADOW = IdepixConstants.NUM_DEFAULT_FLAGS; // first non-default flag + static final String IDEPIX_MOUNTAIN_SHADOW_DESCR_TEXT = "Pixel is affected by a mountain/hill shadow"; + public static final int IDEPIX_GLINT_RISK = IdepixConstants.NUM_DEFAULT_FLAGS + 1; static final String IDEPIX_GLINT_RISK_DESCR_TEXT = "Glint risk pixel"; /* Level 1 Flags Positions */ static final int L1_F_LAND = 4; static final int L1_F_INVALID = 7; + + + public static final String MERIS_LATITUDE_BAND_NAME = "latitude"; + public static final String MERIS_LONGITUDE_BAND_NAME = "longitude"; + + public static final String MERIS_ALTITUDE_BAND_NAME = "dem_alt"; + public static final String MERIS_SUN_ZENITH_BAND_NAME = "sun_zenith"; + public static final String MERIS_SUN_AZIMUTH_BAND_NAME = "sun_azimuth"; + public static final String MERIS_VIEW_ZENITH_BAND_NAME = "view_zenith"; + public static final String MERIS_VIEW_AZIMUTH_BAND_NAME = "view_azimuth"; + + public static final String MERIS_4RP_ALTITUDE_BAND_NAME = "altitude"; + public static final String MERIS_4RP_SUN_ZENITH_BAND_NAME = "SZA"; + public static final String MERIS_4RP_SUN_AZIMUTH_BAND_NAME = "SAA"; + public static final String MERIS_4RP_VIEW_ZENITH_BAND_NAME = "OZA"; + public static final String MERIS_4RP_VIEW_AZIMUTH_BAND_NAME = "OAA"; + + public static final String MERIS_VIEW_ZENITH_INTERPOLATED_BAND_NAME = "OZA_interp"; + public static final String MERIS_VIEW_AZIMUTH_INTERPOLATED_BAND_NAME = "OAA_interp"; + + public static final double[] POLYNOM_FIT_INITIAL = new double[]{0., 0., 0.}; + + // view angle interpolation at discontinuities: + static final int MERIS_FR_FULL_PRODUCT_WIDTH = 4481; + static final int MERIS_RR_FULL_PRODUCT_WIDTH = 1121; + static final int MERIS_FR_DEFAULT_NX_CHANGE = 2241; + static final int MERIS_RR_DEFAULT_NX_CHANGE = 561; + static final int[] MERIS_DEFAULT_FR_NX_VZA = new int[]{2100, 2180, 2302, 2382}; + static final int[] MERIS_DEFAULT_RR_NX_VZA = new int[]{525, 545, 576, 596}; + static final int[] MERIS_DEFAULT_FR_NX_VAA = new int[]{1000, 2000, 2500, MERIS_FR_FULL_PRODUCT_WIDTH}; + static final int[] MERIS_DEFAULT_RR_NX_VAA = new int[]{250, 500, 625, MERIS_RR_FULL_PRODUCT_WIDTH}; } diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisMountainShadowOp.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisMountainShadowOp.java new file mode 100644 index 00000000..394b55a6 --- /dev/null +++ b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisMountainShadowOp.java @@ -0,0 +1,140 @@ +package org.esa.snap.idepix.meris; + +import org.esa.snap.core.datamodel.GeoPos; +import org.esa.snap.core.datamodel.PixelPos; +import org.esa.snap.core.datamodel.Product; +import org.esa.snap.core.datamodel.ProductData; +import org.esa.snap.core.gpf.GPF; +import org.esa.snap.core.gpf.OperatorException; +import org.esa.snap.core.gpf.OperatorSpi; +import org.esa.snap.core.gpf.annotations.OperatorMetadata; +import org.esa.snap.core.gpf.annotations.Parameter; +import org.esa.snap.core.gpf.annotations.SourceProduct; +import org.esa.snap.core.gpf.pointop.*; +import org.esa.snap.core.util.math.MathUtils; + +import java.util.HashMap; + +/** + * Computes mountain/hill shadow for a Sentinel-3 MERIS product using slope, aspect and orientation. + * See theory e.g. at + * ..., or + * ... + * + * @author Tonio Fincke, Olaf Danne + */ +@OperatorMetadata(alias = "Idepix.Meris.MountainShadow", + version = "2.0", + internal = true, + authors = "Tonio Fincke, Olaf Danne", + copyright = "(c) 2018-2021 by Brockmann Consult", + description = "Computes mountain/hill shadow for a Sentinel-3 OLCI product using slope, aspect and orientation.") +public class IdepixMerisMountainShadowOp extends PixelOperator { + + @SourceProduct(alias = "l1b") + private Product l1bProduct; + + @Parameter(label = " Extent of mountain shadow", defaultValue = "0.9", interval = "[0,1]", + description = "Extent of mountain shadow detection") + private double mntShadowExtent; + + private final static int SZA_INDEX = 0; + private final static int SAA_INDEX = 1; + private final static int OZA_INDEX = 2; + private final static int OAA_INDEX = 3; + private final static int SLOPE_INDEX = 4; + private final static int ASPECT_INDEX = 5; + private final static int ORIENTATION_INDEX = 6; + + + private final static int MOUNTAIN_SHADOW_FLAG_BAND_INDEX = 0; + + public final static String MOUNTAIN_SHADOW_FLAG_BAND_NAME = "mountainShadowFlag"; + + private Product saoProduct; + + @Override + protected void prepareInputs() throws OperatorException { + super.prepareInputs(); + HashMap input = new HashMap<>(); + input.put("l1b", l1bProduct); + saoProduct = GPF.createProduct(OperatorSpi.getOperatorAlias(IdepixMerisSlopeAspectOrientationOp.class), + GPF.NO_PARAMS, input); + } + + @Override + protected void configureTargetProduct(ProductConfigurer productConfigurer) { + super.configureTargetProduct(productConfigurer); + productConfigurer.addBand(MOUNTAIN_SHADOW_FLAG_BAND_NAME, ProductData.TYPE_INT8); + } + + @Override + protected void configureSourceSamples(SourceSampleConfigurer sampleConfigurer) throws OperatorException { + sampleConfigurer.defineSample(SZA_INDEX, IdepixMerisConstants.MERIS_SUN_ZENITH_BAND_NAME, l1bProduct); + sampleConfigurer.defineSample(SAA_INDEX, IdepixMerisConstants.MERIS_SUN_AZIMUTH_BAND_NAME, l1bProduct); + sampleConfigurer.defineSample(OZA_INDEX, IdepixMerisConstants.MERIS_VIEW_ZENITH_INTERPOLATED_BAND_NAME, + saoProduct); + sampleConfigurer.defineSample(OAA_INDEX, IdepixMerisConstants.MERIS_VIEW_AZIMUTH_INTERPOLATED_BAND_NAME, + saoProduct); + sampleConfigurer.defineSample(SLOPE_INDEX, IdepixMerisSlopeAspectOrientationOp.SLOPE_BAND_NAME, saoProduct); + sampleConfigurer.defineSample(ASPECT_INDEX, IdepixMerisSlopeAspectOrientationOp.ASPECT_BAND_NAME, saoProduct); + sampleConfigurer.defineSample(ORIENTATION_INDEX, IdepixMerisSlopeAspectOrientationOp.ORIENTATION_BAND_NAME, + saoProduct); + } + + @Override + protected void configureTargetSamples(TargetSampleConfigurer sampleConfigurer) throws OperatorException { + sampleConfigurer.defineSample(MOUNTAIN_SHADOW_FLAG_BAND_INDEX, MOUNTAIN_SHADOW_FLAG_BAND_NAME); + } + + @Override + protected void computePixel(int x, int y, Sample[] sourceSamples, WritableSample[] targetSamples) { + final float slope = sourceSamples[SLOPE_INDEX].getFloat(); + final float aspect = sourceSamples[ASPECT_INDEX].getFloat(); + if (!Float.isNaN(slope) && + !Float.isNaN(aspect)) { + final float sza = sourceSamples[SZA_INDEX].getFloat(); + final float saa = sourceSamples[SAA_INDEX].getFloat(); + final float oza = sourceSamples[OZA_INDEX].getFloat(); + final float oaa = sourceSamples[OAA_INDEX].getFloat(); + final float orientation = sourceSamples[ORIENTATION_INDEX].getFloat(); + + final PixelPos pixelPos = new PixelPos(x + 0.5f, y + 0.5f); + final GeoPos geoPos = l1bProduct.getSceneGeoCoding().getGeoPos(pixelPos, null); + final double saaApparent = IdepixMerisUtils.computeApparentSaa(sza, saa, oza, oaa, geoPos.getLat()); + + if (x == 2783 && y == 642) { + System.out.println("x, y = " + x + ", " + y); // small subset, shadow + } + if (x == 2783 && y == 2181) { + System.out.println("x, y = " + x + ", " + y); // large subset, no shadow + } + final boolean isMountainShadow = + isMountainShadow(sza, (float) saaApparent, slope, aspect, orientation, mntShadowExtent); + + if (isMountainShadow) { + System.out.println("x, y, slope, aspect, orientation = " + + x + ", " + y + ", " + slope + ", " + aspect + ", " + orientation); + } + targetSamples[MOUNTAIN_SHADOW_FLAG_BAND_INDEX].set(isMountainShadow); + } + } + + /* package local for testing */ + static boolean isMountainShadow(float sza, float saa, float slope, float aspect, float orientation, double mntShadowExtent) { + final double cosBeta = computeCosBeta(sza, saa, slope, aspect, orientation); + return cosBeta < (-1 * (1 - mntShadowExtent)); + } + + /* package local for testing */ + static double computeCosBeta(float sza, float saa, float slope, float aspect, float orientation) { + return Math.cos(sza * MathUtils.DTOR) * Math.cos(slope) + Math.sin(sza * MathUtils.DTOR) * Math.sin(slope) * + Math.cos(saa * MathUtils.DTOR - (aspect + orientation)); + } + + public static class Spi extends OperatorSpi { + public Spi() { + super(IdepixMerisMountainShadowOp.class); + } + } +} diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisOp.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisOp.java index a87a4645..6df00007 100644 --- a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisOp.java +++ b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisOp.java @@ -102,6 +102,13 @@ public class IdepixMerisOp extends BasisOp { description = " NN cloud ambiguous cloud sure/snow separation value") double schillerLandNNCloudSureSnowSeparationValue; + @Parameter(defaultValue = "true", label = " Compute mountain shadow") + private boolean computeMountainShadow; + + @Parameter(label = " Extent of mountain shadow", defaultValue = "0.9", interval = "[0,1]", + description = "Extent of mountain shadow detection") + private double mntShadowExtent; + @Parameter(defaultValue = "true", label = " Compute cloud shadow", description = " Compute cloud shadow with the algorithm from 'Fronts' project") @@ -137,10 +144,18 @@ public void initialize() throws OperatorException { throw new OperatorException(IdepixConstants.INPUT_INCONSISTENCY_ERROR_MESSAGE); } - if (IdepixIO.isMeris4thReprocessingL1bProduct(sourceProduct.getProductType())) { + final boolean isMeris4thReprocessingProduct = + IdepixIO.isMeris4thReprocessingL1bProduct(sourceProduct.getProductType()); + computeMountainShadow = computeMountainShadow && isMeris4thReprocessingProduct; + if (isMeris4thReprocessingProduct) { // adapt to 3rd reprocessing... Meris3rd4thReprocessingAdapter reprocessingAdapter = new Meris3rd4thReprocessingAdapter(); inputProductToProcess = reprocessingAdapter.convertToLowerVersion(sourceProduct); + if (computeMountainShadow) { + // altitude TPG is too coarse in this case! + ProductUtils.copyBand(IdepixMerisConstants.MERIS_4RP_ALTITUDE_BAND_NAME, sourceProduct, + inputProductToProcess, true); + } } else { inputProductToProcess = sourceProduct; } @@ -240,6 +255,7 @@ private void postProcess() { Map params = new HashMap<>(); params.put("computeCloudShadow", computeCloudShadow); + params.put("computeMountainShadow", computeMountainShadow); params.put("refineClassificationNearCoastlines", true); // always an improvement final Product classifiedProduct = GPF.createProduct(OperatorSpi.getOperatorAlias(IdepixMerisPostProcessOp.class), diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisPostProcessOp.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisPostProcessOp.java index b87021ba..bf05478e 100644 --- a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisPostProcessOp.java +++ b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisPostProcessOp.java @@ -2,23 +2,21 @@ import com.bc.ceres.core.ProgressMonitor; import org.esa.snap.core.datamodel.*; -import org.esa.snap.core.gpf.Operator; -import org.esa.snap.core.gpf.OperatorException; -import org.esa.snap.core.gpf.OperatorSpi; -import org.esa.snap.core.gpf.Tile; +import org.esa.snap.core.gpf.*; import org.esa.snap.core.gpf.annotations.OperatorMetadata; import org.esa.snap.core.gpf.annotations.Parameter; import org.esa.snap.core.gpf.annotations.SourceProduct; import org.esa.snap.core.util.ProductUtils; import org.esa.snap.core.util.RectangleExtender; import org.esa.snap.dataio.envisat.EnvisatConstants; - import org.esa.snap.idepix.core.CloudShadowFronts; import org.esa.snap.idepix.core.IdepixConstants; import org.esa.snap.idepix.core.util.IdepixIO; import org.esa.snap.idepix.core.util.IdepixUtils; import java.awt.*; +import java.util.HashMap; +import java.util.Map; /** * Operator used to consolidate IdePix classification flag for MERIS: @@ -35,6 +33,13 @@ description = "Refines the MERIS pixel classification over both land and water.") public class IdepixMerisPostProcessOp extends Operator { + @Parameter(defaultValue = "true", label = " Compute mountain shadow") + private boolean computeMountainShadow; + + @Parameter(label = " Extent of mountain shadow", defaultValue = "0.9", interval = "[0,1]", + description = "Extent of mountain shadow detection") + private double mntShadowExtent; + @Parameter(defaultValue = "true", label = " Compute cloud shadow", description = " Compute cloud shadow with latest 'fronts' algorithm") @@ -58,10 +63,11 @@ public class IdepixMerisPostProcessOp extends Operator { private Band waterFractionBand; private Band origCloudFlagBand; private Band ctpBand; - private TiePointGrid szaTPG; - private TiePointGrid saaTPG; - private TiePointGrid altTPG; + private TiePointGrid szaTpg; + private TiePointGrid saaTpg; + private TiePointGrid altTpg; private GeoCoding geoCoding; + private Band mountainShadowFlagBand; private RectangleExtender rectCalculator; @@ -77,9 +83,13 @@ public void initialize() throws OperatorException { geoCoding = l1bProduct.getSceneGeoCoding(); origCloudFlagBand = merisCloudProduct.getBand(IdepixConstants.CLASSIF_BAND_NAME); - szaTPG = l1bProduct.getTiePointGrid(EnvisatConstants.MERIS_SUN_ZENITH_DS_NAME); - saaTPG = l1bProduct.getTiePointGrid(EnvisatConstants.MERIS_SUN_AZIMUTH_DS_NAME); - altTPG = l1bProduct.getTiePointGrid(EnvisatConstants.MERIS_DEM_ALTITUDE_DS_NAME); + szaTpg = l1bProduct.getTiePointGrid(EnvisatConstants.MERIS_SUN_ZENITH_DS_NAME); + saaTpg = l1bProduct.getTiePointGrid(EnvisatConstants.MERIS_SUN_AZIMUTH_DS_NAME); + altTpg = l1bProduct.getTiePointGrid(EnvisatConstants.MERIS_DEM_ALTITUDE_DS_NAME); + + final TiePointGrid latTpg = l1bProduct.getTiePointGrid(IdepixMerisConstants.MERIS_LATITUDE_BAND_NAME); + final TiePointGrid lonTpg = l1bProduct.getTiePointGrid(IdepixMerisConstants.MERIS_LONGITUDE_BAND_NAME); + if (ctpProduct != null) { ctpBand = ctpProduct.getBand("cloud_top_press"); } @@ -99,25 +109,45 @@ public void initialize() throws OperatorException { extendedWidth, extendedHeight ); + if (computeMountainShadow) { + ensureBandsAreCopied(l1bProduct, merisCloudProduct, latTpg.getName(), lonTpg.getName(), altTpg.getName()); + Map mntShadowParams = new HashMap<>(); + mntShadowParams.put("mntShadowStrength", mntShadowExtent); + + HashMap input = new HashMap<>(); + input.put("l1b", l1bProduct); + final Product mountainShadowProduct = GPF.createProduct( + OperatorSpi.getOperatorAlias(IdepixMerisMountainShadowOp.class), mntShadowParams, input); + mountainShadowFlagBand = mountainShadowProduct.getBand( + IdepixMerisMountainShadowOp.MOUNTAIN_SHADOW_FLAG_BAND_NAME); + } ProductUtils.copyBand(IdepixConstants.CLASSIF_BAND_NAME, merisCloudProduct, postProcessedCloudProduct, false); setTargetProduct(postProcessedCloudProduct); } + private void ensureBandsAreCopied(Product source, Product target, String... bandNames) { + for (String bandName : bandNames) { + if (!target.containsBand(bandName)) { + ProductUtils.copyBand(bandName, source, target, true); + } + } + } + @Override public void computeTile(Band targetBand, final Tile targetTile, ProgressMonitor pm) throws OperatorException { Rectangle targetRectangle = targetTile.getRectangle(); final Rectangle srcRectangle = rectCalculator.extend(targetRectangle); final Tile sourceFlagTile = getSourceTile(origCloudFlagBand, srcRectangle); - Tile szaTile = getSourceTile(szaTPG, srcRectangle); - Tile saaTile = getSourceTile(saaTPG, srcRectangle); + Tile szaTile = getSourceTile(szaTpg, srcRectangle); + Tile saaTile = getSourceTile(saaTpg, srcRectangle); Tile ctpTile = null; if (ctpBand != null) { ctpTile = getSourceTile(ctpBand, srcRectangle); } - Tile altTile = getSourceTile(altTPG, targetRectangle); + Tile altTile = getSourceTile(altTpg, targetRectangle); final Tile waterFractionTile = getSourceTile(waterFractionBand, srcRectangle); for (int y = srcRectangle.y; y < srcRectangle.y + srcRectangle.height; y++) { @@ -161,10 +191,7 @@ protected boolean isCloudForShadow(int x, int y) { is_cloud_current = targetTile.getSampleBit(x, y, IdepixConstants.IDEPIX_CLOUD); } if (is_cloud_current) { - final boolean isNearCoastline = isNearCoastline(x, y, waterFractionTile, srcRectangle); - if (!isNearCoastline) { - return true; - } + return !isNearCoastline(x, y, waterFractionTile, srcRectangle); } return false; } @@ -186,6 +213,17 @@ protected void setCloudShadow(int x, int y) { }; cloudShadowFronts.computeCloudShadow(); } + + if (computeMountainShadow) { + final Tile mountainShadowFlagTile = getSourceTile(mountainShadowFlagBand, targetRectangle); + for (int y = targetRectangle.y; y < targetRectangle.y + targetRectangle.height; y++) { + checkForCancellation(); + for (int x = targetRectangle.x; x < targetRectangle.x + targetRectangle.width; x++) { + final boolean mountainShadow = mountainShadowFlagTile.getSampleInt(x, y) > 0; + targetTile.setSample(x, y, IdepixMerisConstants.IDEPIX_MOUNTAIN_SHADOW, mountainShadow); + } + } + } } private void combineFlags(int x, int y, Tile sourceFlagTile, Tile targetTile) { diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisSlopeAspectOrientationOp.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisSlopeAspectOrientationOp.java new file mode 100644 index 00000000..d6974fd1 --- /dev/null +++ b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisSlopeAspectOrientationOp.java @@ -0,0 +1,202 @@ +package org.esa.snap.idepix.meris; + +import com.bc.ceres.core.ProgressMonitor; +import org.esa.snap.core.datamodel.*; +import org.esa.snap.core.gpf.Operator; +import org.esa.snap.core.gpf.OperatorException; +import org.esa.snap.core.gpf.OperatorSpi; +import org.esa.snap.core.gpf.Tile; +import org.esa.snap.core.gpf.annotations.OperatorMetadata; +import org.esa.snap.core.gpf.annotations.SourceProduct; +import org.esa.snap.core.util.ProductUtils; +import org.esa.snap.idepix.core.util.SlopeAspectOrientationUtils; + +import javax.media.jai.BorderExtender; +import java.awt.*; +import java.util.Map; + +/** + * Computes Slope, Aspect and Orientation for a MERIS L1b product. + * Only 4RP, as this contains altitude band with original resolution. In 3RP we have only TPG. + * See theory e.g. at + * ..., or + * ... + * + * @author Tonio Fincke, Olaf Danne, Dagmar Mueller + */ +@OperatorMetadata(alias = "Idepix.Meris.SlopeAspect", + version = "2.0", + internal = true, + authors = "Tonio Fincke, Olaf Danne, Dagmar Mueller", + copyright = "(c) 2018-2021 by Brockmann Consult", + description = "Computes Slope, Aspect and Orientation for a Sentinel-3 OLCI product. " + + "See theory e.g. at https://www.e-education.psu.edu/geog480/node/490, or " + + "https://desktop.arcgis.com/en/arcmap/10.3/tools/spatial-analyst-toolbox/how-hillshade-works.htm") +public class IdepixMerisSlopeAspectOrientationOp extends Operator { + + @SourceProduct(alias = "l1b") + private Product l1bProduct; + + private static final String ELEVATION_BAND_NAME = IdepixMerisConstants.MERIS_4RP_ALTITUDE_BAND_NAME; + + private double spatialResolution; + + private TiePointGrid latitudeTpg; + private TiePointGrid longitudeTpg; + private TiePointGrid sunAzimuthTpg; + private TiePointGrid viewZenithTpg; + private TiePointGrid viewAzimuthTpg; + private Band elevationBand; + private Band viewZenithBand; + private Band viewAzimuthBand; + private Band slopeBand; + private Band aspectBand; + private Band orientationBand; + private final static String TARGET_PRODUCT_NAME = "Slope-Aspect-Orientation"; + private final static String TARGET_PRODUCT_TYPE = "slope-aspect-orientation"; + final static String SLOPE_BAND_NAME = "slope"; + final static String ASPECT_BAND_NAME = "aspect"; + final static String ORIENTATION_BAND_NAME = "orientation"; + private final static String SLOPE_BAND_DESCRIPTION = "Slope of each pixel as angle"; + private final static String ASPECT_BAND_DESCRIPTION = + "Aspect of each pixel as angle between raster -Y direction and steepest slope, clockwise"; + private final static String ORIENTATION_BAND_DESCRIPTION = + "Orientation of each pixel as angle between east and raster X direction, clockwise"; + private final static String SLOPE_BAND_UNIT = "rad [0..pi/2]"; + private final static String ASPECT_BAND_UNIT = "rad [-pi..pi]"; + private final static String ORIENTATION_BAND_UNIT = "rad [-pi..pi]"; + + @Override + public void initialize() throws OperatorException { + + if (!(l1bProduct.containsBand(IdepixMerisConstants.MERIS_4RP_ALTITUDE_BAND_NAME))) { + throw new OperatorException("Slope/Aspect/Orientation requires altitude band at original resolution. " + + "Use MERIS 4RP input product"); + } + + ensureSingleRasterSize(l1bProduct); + GeoCoding sourceGeoCoding = l1bProduct.getSceneGeoCoding(); + if (sourceGeoCoding == null) { + throw new OperatorException("Source product has no geo-coding"); + } + + spatialResolution = SlopeAspectOrientationUtils.computeSpatialResolution(l1bProduct, sourceGeoCoding); + + elevationBand = l1bProduct.getBand(ELEVATION_BAND_NAME); + if (elevationBand == null) { + throw new OperatorException("Elevation band required to compute slope or aspect"); + } + latitudeTpg = l1bProduct.getTiePointGrid(IdepixMerisConstants.MERIS_LATITUDE_BAND_NAME); + longitudeTpg = l1bProduct.getTiePointGrid(IdepixMerisConstants.MERIS_LONGITUDE_BAND_NAME); + + Product targetProduct = createTargetProduct(); + + if (IdepixMerisUtils.isFullResolution(l1bProduct) || IdepixMerisUtils.isReducedResolution(l1bProduct)) { + IdepixMerisViewAngleInterpolationOp viewAngleInterpolationOp = new IdepixMerisViewAngleInterpolationOp(); + viewAngleInterpolationOp.setParameterDefaultValues(); + viewAngleInterpolationOp.setSourceProduct(l1bProduct); + Product viewAngleInterpolationProduct = viewAngleInterpolationOp.getTargetProduct(); + + viewZenithBand = viewAngleInterpolationProduct.getBand(IdepixMerisConstants.MERIS_VIEW_ZENITH_INTERPOLATED_BAND_NAME); + viewAzimuthBand = viewAngleInterpolationProduct.getBand(IdepixMerisConstants.MERIS_VIEW_AZIMUTH_INTERPOLATED_BAND_NAME); + ProductUtils.copyBand(IdepixMerisConstants.MERIS_VIEW_ZENITH_INTERPOLATED_BAND_NAME, + viewAngleInterpolationProduct, targetProduct, true); + ProductUtils.copyBand(IdepixMerisConstants.MERIS_VIEW_AZIMUTH_INTERPOLATED_BAND_NAME, + viewAngleInterpolationProduct, targetProduct, true); + } else { + viewZenithTpg = l1bProduct.getTiePointGrid(IdepixMerisConstants.MERIS_VIEW_ZENITH_BAND_NAME); + viewAzimuthTpg = l1bProduct.getTiePointGrid(IdepixMerisConstants.MERIS_VIEW_AZIMUTH_BAND_NAME); + } + + sunAzimuthTpg = l1bProduct.getTiePointGrid(IdepixMerisConstants.MERIS_SUN_AZIMUTH_BAND_NAME); + + setTargetProduct(targetProduct); + } + + private Band createBand(Product targetProduct, String bandName, String description, String unit) { + Band band = targetProduct.addBand(bandName, ProductData.TYPE_FLOAT32); + band.setDescription(description); + band.setUnit(unit); + band.setNoDataValue(-9999.); + band.setNoDataValueUsed(true); + return band; + } + + @Override + public void computeTileStack(Map targetTiles, Rectangle targetRectangle, ProgressMonitor pm) + throws OperatorException { + final Rectangle sourceRectangle = getSourceRectangle(targetRectangle); + final BorderExtender borderExtender = BorderExtender.createInstance(BorderExtender.BORDER_COPY); + final Tile latitudeTile = getSourceTile(latitudeTpg, sourceRectangle, borderExtender); + final Tile longitudeTile = getSourceTile(longitudeTpg, sourceRectangle, borderExtender); + final Tile elevationTile = getSourceTile(elevationBand, sourceRectangle, borderExtender); + Tile viewZenithAngleTile; + Tile viewAzimuthAngleTile; + if (IdepixMerisUtils.isFullResolution(l1bProduct) || IdepixMerisUtils.isReducedResolution(l1bProduct)) { + viewZenithAngleTile = getSourceTile(viewZenithBand, sourceRectangle, borderExtender); + viewAzimuthAngleTile = getSourceTile(viewAzimuthBand, sourceRectangle, borderExtender); + } else { + viewZenithAngleTile = getSourceTile(viewZenithTpg, sourceRectangle, borderExtender); + viewAzimuthAngleTile = getSourceTile(viewAzimuthTpg, sourceRectangle, borderExtender); + } + final Tile sunAzimuthAngleTile = getSourceTile(sunAzimuthTpg, sourceRectangle, borderExtender); + + final Tile slopeTile = targetTiles.get(slopeBand); + final Tile aspectTile = targetTiles.get(aspectBand); + final Tile orientationTile = targetTiles.get(orientationBand); + for (int y = targetRectangle.y; y < targetRectangle.y + targetRectangle.height; y++) { + for (int x = targetRectangle.x; x < targetRectangle.x + targetRectangle.width; x++) { + slopeTile.setSample(x, y, Float.NaN); + aspectTile.setSample(x, y, Float.NaN); + orientationTile.setSample(x, y, Float.NaN); + final float[] elevationDataMacropixel = SlopeAspectOrientationUtils.get3x3MacropixelData(elevationTile, y, x); + if (SlopeAspectOrientationUtils.is3x3ElevationDataValid(elevationDataMacropixel)) { + final float vza = viewZenithAngleTile.getSampleFloat(x, y); + final float vaa = viewAzimuthAngleTile.getSampleFloat(x, y); + final float saa = sunAzimuthAngleTile.getSampleFloat(x, y); + if (x == 2783 && y == 642) { + System.out.println("x, y = " + x + ", " + y); // small subset, shadow + } + final float[] latitudeDataMacropixel = + SlopeAspectOrientationUtils.get3x3MacropixelData(latitudeTile, y, x); + final float[] longitudeDataMacropixel = + SlopeAspectOrientationUtils.get3x3MacropixelData(longitudeTile, y, x); + final float orientation = SlopeAspectOrientationUtils.computeOrientation3x3Box(latitudeDataMacropixel, + longitudeDataMacropixel); + orientationTile.setSample(x, y, orientation); + final float[] slopeAspect = SlopeAspectOrientationUtils.computeSlopeAspect3x3(elevationDataMacropixel, + orientation, vza, vaa, saa, spatialResolution); + slopeTile.setSample(x, y, slopeAspect[0]); + aspectTile.setSample(x, y, slopeAspect[1]); + } + } + } + } + + private static Rectangle getSourceRectangle(Rectangle targetRectangle) { + return new Rectangle(targetRectangle.x - 1, targetRectangle.y - 1, + targetRectangle.width + 2, targetRectangle.height + 2); + } + + private Product createTargetProduct() { + final int sceneWidth = l1bProduct.getSceneRasterWidth(); + final int sceneHeight = l1bProduct.getSceneRasterHeight(); + Product targetProduct = new Product(TARGET_PRODUCT_NAME, TARGET_PRODUCT_TYPE, sceneWidth, sceneHeight); + ProductUtils.copyGeoCoding(l1bProduct, targetProduct); + targetProduct.setStartTime(l1bProduct.getStartTime()); + targetProduct.setEndTime(l1bProduct.getEndTime()); + + slopeBand = createBand(targetProduct, SLOPE_BAND_NAME, SLOPE_BAND_DESCRIPTION, SLOPE_BAND_UNIT); + aspectBand = createBand(targetProduct, ASPECT_BAND_NAME, ASPECT_BAND_DESCRIPTION, ASPECT_BAND_UNIT); + orientationBand = createBand(targetProduct, ORIENTATION_BAND_NAME, ORIENTATION_BAND_DESCRIPTION, ORIENTATION_BAND_UNIT); + + return targetProduct; + } + + + public static class Spi extends OperatorSpi { + public Spi() { + super(IdepixMerisSlopeAspectOrientationOp.class); + } + } +} diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisUtils.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisUtils.java index cf95b947..23241192 100644 --- a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisUtils.java +++ b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisUtils.java @@ -1,5 +1,6 @@ package org.esa.snap.idepix.meris; +import org.apache.commons.math3.fitting.PolynomialFitter; import org.esa.s3tbx.processor.rad2refl.Rad2ReflConstants; import org.esa.s3tbx.processor.rad2refl.Rad2ReflOp; import org.esa.s3tbx.processor.rad2refl.Sensor; @@ -11,6 +12,7 @@ import org.esa.snap.core.util.BitSetter; import org.esa.snap.core.util.ProductUtils; +import org.esa.snap.core.util.math.MathUtils; import org.esa.snap.idepix.core.IdepixConstants; import org.esa.snap.idepix.core.IdepixFlagCoding; @@ -33,8 +35,13 @@ class IdepixMerisUtils { static FlagCoding createMerisFlagCoding() { FlagCoding flagCoding = IdepixFlagCoding.createDefaultFlagCoding(IdepixConstants.CLASSIF_BAND_NAME); - flagCoding.addFlag("IDEPIX_GLINT_RISK", BitSetter.setFlag(0, IdepixMerisConstants.IDEPIX_GLINT_RISK), - IdepixMerisConstants.IDEPIX_GLINT_RISK_DESCR_TEXT); + flagCoding.addFlag("IDEPIX_MOUNTAIN_SHADOW", BitSetter.setFlag(0, + IdepixMerisConstants.IDEPIX_MOUNTAIN_SHADOW), + IdepixMerisConstants.IDEPIX_MOUNTAIN_SHADOW_DESCR_TEXT); + + flagCoding.addFlag("IDEPIX_GLINT_RISK", BitSetter.setFlag(0, + IdepixMerisConstants.IDEPIX_GLINT_RISK), + IdepixMerisConstants.IDEPIX_GLINT_RISK_DESCR_TEXT); return flagCoding; } @@ -52,9 +59,14 @@ static void setupMerisClassifBitmask(Product classifProduct) { Mask mask; Random r = new Random(1234567); + mask = Mask.BandMathsType.create("IDEPIX_MOUNTAIN_SHADOW", IdepixMerisConstants.IDEPIX_MOUNTAIN_SHADOW_DESCR_TEXT, w, h, + "pixel_classif_flags.IDEPIX_MOUNTAIN_SHADOW", + IdepixFlagCoding.getRandomColour(r), 0.5f); + classifProduct.getMaskGroup().add(index++, mask); + mask = Mask.BandMathsType.create("IDEPIX_GLINT_RISK", IdepixMerisConstants.IDEPIX_GLINT_RISK_DESCR_TEXT, w, h, - "pixel_classif_flags.IDEPIX_GLINT_RISK", - IdepixFlagCoding.getRandomColour(r), 0.5f); + "pixel_classif_flags.IDEPIX_GLINT_RISK", + IdepixFlagCoding.getRandomColour(r), 0.5f); classifProduct.getMaskGroup().add(index, mask); } @@ -84,4 +96,65 @@ static Product computeCloudTopPressureProduct(Product sourceProduct) { return GPF.createProduct("Meris.CloudTopPressureOp", GPF.NO_PARAMS, sourceProduct); } + static double computeApparentSaa(double sza, double saa, double oza, double oaa, double lat) { + final double szaRad = sza * MathUtils.DTOR; + final double ozaRad = oza * MathUtils.DTOR; + + double deltaPhi; + if (oaa < 0.0) { + deltaPhi = 360.0 - Math.abs(oaa) - saa; + } else { + deltaPhi = saa - oaa; + } + final double deltaPhiRad = deltaPhi * MathUtils.DTOR; + final double numerator = Math.tan(szaRad) - Math.tan(ozaRad) * Math.cos(deltaPhiRad); + final double denominator = Math.sqrt(Math.tan(ozaRad) * Math.tan(ozaRad) + Math.tan(szaRad) * Math.tan(szaRad) - + 2.0 * Math.tan(szaRad) * Math.tan(ozaRad) * Math.cos(deltaPhiRad)); + + double delta = Math.acos(numerator / denominator); +// Sun in the North (Southern hemisphere), change sign! + if (saa > 270. || saa < 90){ + delta = -1.0 * delta; + } + if (oaa < 0.0) { + return saa - delta * MathUtils.RTOD; + } else { + return saa + delta * MathUtils.RTOD; + } + } + + static boolean isFullResolution(Product sourceProduct) { + // less strict to allow subsets: + return sourceProduct.getProductType().contains("_FR"); + } + + static boolean isReducedResolution(Product sourceProduct) { + // less strict to allow subsets: + return sourceProduct.getProductType().contains("_RR"); + } + static float[] interpolateViewAngles(PolynomialFitter curveFitter1, PolynomialFitter curveFitter2, + float[] viewAngleOrig, int[] nx, int nxChange) { + float[] viewAngleInterpol = viewAngleOrig.clone(); + + curveFitter1.clearObservations(); + for (int x = nx[0]; x < nx[1]; x++) { + curveFitter1.addObservedPoint(x * 1.0f, viewAngleOrig[x]); + } + final double[] fit1 = curveFitter1.fit(IdepixMerisConstants.POLYNOM_FIT_INITIAL); + + curveFitter2.clearObservations(); + for (int x = nx[2]; x < nx[3]; x++) { + curveFitter2.addObservedPoint(x * 1.0f, viewAngleOrig[x]); + } + final double[] fit2 = curveFitter2.fit(IdepixMerisConstants.POLYNOM_FIT_INITIAL); + + for (int x = nx[1]; x < nxChange; x++) { + viewAngleInterpol[x] = (float) (fit1[0] + fit1[1] * x + fit1[2] * x * x); + } + for (int x = nxChange; x < nx[2]; x++) { + viewAngleInterpol[x] = (float) (fit2[0] + fit2[1] * x + fit2[2] * x * x); + } + + return viewAngleInterpol; + } } diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisViewAngleInterpolationOp.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisViewAngleInterpolationOp.java new file mode 100644 index 00000000..15bb5954 --- /dev/null +++ b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisViewAngleInterpolationOp.java @@ -0,0 +1,189 @@ +package org.esa.snap.idepix.meris; + +import com.bc.ceres.core.ProgressMonitor; +import org.apache.commons.math3.fitting.PolynomialFitter; +import org.apache.commons.math3.optim.nonlinear.vector.jacobian.LevenbergMarquardtOptimizer; +import org.esa.snap.core.datamodel.Band; +import org.esa.snap.core.datamodel.Product; +import org.esa.snap.core.datamodel.ProductData; +import org.esa.snap.core.datamodel.TiePointGrid; +import org.esa.snap.core.gpf.Operator; +import org.esa.snap.core.gpf.OperatorException; +import org.esa.snap.core.gpf.OperatorSpi; +import org.esa.snap.core.gpf.Tile; +import org.esa.snap.core.gpf.annotations.OperatorMetadata; +import org.esa.snap.core.gpf.annotations.SourceProduct; +import org.esa.snap.core.util.ProductUtils; +import org.esa.snap.idepix.core.AlgorithmSelector; +import org.esa.snap.idepix.core.IdepixConstants; +import org.esa.snap.idepix.core.util.IdepixIO; + +import java.awt.*; +import java.util.Map; + +/** + * Performs interpolation at view zenith and azimuth discontinuities for MERIS L1b input products. + * + * @author olafd + */ +@OperatorMetadata(alias = "MerisViewAngleInterpolation", version = "0.6", + authors = "Olaf Danne, Dagmar Müller (Brockmann Consult)", + internal = true, + category = "Optical/Preprocessing/Masking/IdePix (Clouds, Land, Water, ...)", + copyright = "Copyright (C) 2023 by Brockmann Consult", + description = "Performs interpolation at view zenith and azimuth discontinuities for MERIS L1b input products.") +public class IdepixMerisViewAngleInterpolationOp extends Operator { + + @SourceProduct(description = "Input product", + label = "MERIS L1b product") + private Product sourceProduct; + + private int nxChange = -1; + private int[] nx_vza; + private int[] nx_vaa; + + private Band vzaInterpolBand; + private Band vaaInterpolBand; + + + @Override + public void initialize() throws OperatorException { + + final boolean inputProductIsValid = IdepixIO.validateInputProduct(sourceProduct, AlgorithmSelector.MERIS); + if (!inputProductIsValid) { + throw new OperatorException(IdepixConstants.INPUT_INCONSISTENCY_ERROR_MESSAGE); + } + + setInterpolationIntervals(); + + Product targetProduct = createTargetProduct(); + + setTargetProduct(targetProduct); + } + + @Override + public void computeTileStack(Map targetTiles, Rectangle targetRectangle, ProgressMonitor pm) throws OperatorException { + + try { + final Tile vzaTile = + getSourceTile(sourceProduct.getTiePointGrid(IdepixMerisConstants.MERIS_VIEW_ZENITH_BAND_NAME), + targetRectangle); + final Tile vaaTile = + getSourceTile(sourceProduct.getTiePointGrid(IdepixMerisConstants.MERIS_VIEW_AZIMUTH_BAND_NAME), + targetRectangle); + + final Tile vzaInterpolTile = targetTiles.get(vzaInterpolBand); + final Tile vaaInterpolTile = targetTiles.get(vaaInterpolBand); + + float[] vzaOrigLine = new float[targetRectangle.width]; + float[] vaaOrigLine = new float[targetRectangle.width]; + + PolynomialFitter curveFitter1 = new PolynomialFitter(new LevenbergMarquardtOptimizer()); + PolynomialFitter curveFitter2 = new PolynomialFitter(new LevenbergMarquardtOptimizer()); + + for (int y = targetRectangle.y; y < targetRectangle.y + targetRectangle.height; y++) { + checkForCancellation(); + + for (int x = 0; x < targetRectangle.width; x++) { + vzaOrigLine[x] = vzaTile.getSampleFloat(x, y); + vaaOrigLine[x] = vaaTile.getSampleFloat(x, y); + } + + if (nxChange != -1 && nx_vza[1] > 0 && nx_vza[2] < targetRectangle.width && + nx_vaa[1] > 0 && nx_vaa[2] < targetRectangle.width) { + // we need a sufficient product width to do interpolation... + float[] vzaInterpolLine = IdepixMerisUtils.interpolateViewAngles(curveFitter1, curveFitter2, + vzaOrigLine, nx_vza, nxChange); + float[] vaaInterpolLine = IdepixMerisUtils.interpolateViewAngles(curveFitter1, curveFitter2, + vaaOrigLine, nx_vaa, nxChange); + for (int x = 0; x < targetRectangle.width; x++) { + vzaInterpolTile.setSample(x, y, vzaInterpolLine[x]); + vaaInterpolTile.setSample(x, y, vaaInterpolLine[x]); + } + } else { + for (int x = 0; x < targetRectangle.width; x++) { + vzaInterpolTile.setSample(x, y, vzaOrigLine[x]); + vaaInterpolTile.setSample(x, y, vaaOrigLine[x]); + } + } + } + } catch (Exception e) { + throw new OperatorException(e); + } + } + + private Product createTargetProduct() { + final int w = sourceProduct.getSceneRasterWidth(); + final int h = sourceProduct.getSceneRasterHeight(); + Product targetProduct = new Product(sourceProduct.getName(), sourceProduct.getProductType(), w, h); + targetProduct.setPreferredTileSize(w, 16); // we need tiles over whole source width + + ProductUtils.copyMetadata(sourceProduct, targetProduct); + ProductUtils.copyGeoCoding(sourceProduct, targetProduct); + targetProduct.setStartTime(sourceProduct.getStartTime()); + targetProduct.setEndTime(sourceProduct.getEndTime()); + + vzaInterpolBand = createInterpolatedBand(targetProduct, IdepixMerisConstants.MERIS_VIEW_ZENITH_INTERPOLATED_BAND_NAME, + "Interpolated OZA"); + vaaInterpolBand = createInterpolatedBand(targetProduct, IdepixMerisConstants.MERIS_VIEW_AZIMUTH_INTERPOLATED_BAND_NAME, + "Interpolated OAA"); + + return targetProduct; + } + + private Band createInterpolatedBand(Product targetProduct, String bandName, String description) { + Band band = targetProduct.addBand(bandName, ProductData.TYPE_FLOAT32); + band.setDescription(description); + band.setUnit("deg"); + band.setNoDataValue(-9999.); + band.setNoDataValueUsed(true); + return band; + } + + private void setInterpolationIntervals() { + final int productWidth = sourceProduct.getSceneRasterWidth(); + final boolean isFullResolution = IdepixMerisUtils.isFullResolution(sourceProduct); + if (isFullResolution && productWidth == IdepixMerisConstants.MERIS_FR_FULL_PRODUCT_WIDTH) { + // full width, full resolution + nxChange = IdepixMerisConstants.MERIS_FR_DEFAULT_NX_CHANGE; + nx_vza = IdepixMerisConstants.MERIS_DEFAULT_FR_NX_VZA; + nx_vaa = IdepixMerisConstants.MERIS_DEFAULT_FR_NX_VAA; + } else if (!isFullResolution && productWidth == IdepixMerisConstants.MERIS_RR_FULL_PRODUCT_WIDTH) { + // full width, reduced resolution + nxChange = IdepixMerisConstants.MERIS_RR_DEFAULT_NX_CHANGE; + nx_vza = IdepixMerisConstants.MERIS_DEFAULT_RR_NX_VZA; + nx_vaa = IdepixMerisConstants.MERIS_DEFAULT_RR_NX_VAA; + } else { + // subset: find discontinuity + final TiePointGrid vaaTpg = sourceProduct.getTiePointGrid(IdepixMerisConstants.MERIS_VIEW_AZIMUTH_BAND_NAME); + final float[] vaaProfile = (float[]) vaaTpg.getRasterData().getElems(); + for (int i = 0; i < productWidth -2; i++) { + if (vaaProfile[i+1] < 0.0 && vaaProfile[i] > 0.0) { + nxChange = i+2; + break; + } + } + + if (nxChange != -1) { + nx_vza = new int[4]; + nx_vaa = new int[4]; + nx_vza[0] = (int) (0.97*nxChange); + nx_vza[1] = (int) (0.99*nxChange); + nx_vza[2] = Math.min(productWidth, (int) (1.01*nxChange)); + nx_vza[3] = Math.min(productWidth, (int) (1.03*nxChange)); + nx_vaa[0] = (int) (0.55*nxChange); + nx_vaa[1] = (int) (0.94*nxChange); + nx_vaa[2] = Math.min(productWidth, (int) (1.08*nxChange)); + nx_vaa[3] = productWidth; + } + + } + } + + public static class Spi extends OperatorSpi { + + public Spi() { + super(IdepixMerisViewAngleInterpolationOp.class); + } + } +} \ No newline at end of file diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingAdapter.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingAdapter.java deleted file mode 100644 index 410a050c..00000000 --- a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingAdapter.java +++ /dev/null @@ -1,406 +0,0 @@ -package org.esa.snap.idepix.meris.reprocessing; - -import com.bc.ceres.core.ProgressMonitor; -import com.bc.ceres.glevel.MultiLevelImage; -import org.esa.snap.core.datamodel.*; -import org.esa.snap.core.util.BitSetter; -import org.esa.snap.core.util.ProductUtils; -import org.esa.snap.dataio.envisat.EnvisatConstants; - -import javax.media.jai.RenderedOp; -import javax.media.jai.operator.MeanDescriptor; -import java.awt.*; -import java.awt.image.renderable.ParameterBlock; -import java.io.IOException; -import java.util.HashMap; -import java.util.Map; - -/** - * Class providing the adaptation of a MERIS L1b product from fourth to third reprocessing version. - * - * @author olafd - */ -public class Meris3rd4thReprocessingAdapter implements ReprocessingAdapter { - - private final Map qualityToL1FlagMap = new HashMap<>(); - - public Meris3rd4thReprocessingAdapter() { - setupQualityToL1FlagMap(); - } - - @Override - public Product convertToLowerVersion(Product inputProduct) { - Product thirdReproProduct = new Product(inputProduct.getName(), - inputProduct.getProductType(), - inputProduct.getSceneRasterWidth(), - inputProduct.getSceneRasterHeight()); - - ProductUtils.copyGeoCoding(inputProduct, thirdReproProduct); - adaptProductInformationToThirdRepro(inputProduct, thirdReproProduct); - - // adapt band names: - // ## M%02d_radiance --> radiance_%d - // ## detector_index --> detector_index - adaptBandNamesToThirdRepro(inputProduct, thirdReproProduct); - - // adapt tie point grids: - // TP_latitude --> latitude - // TP_longitude --> longitude - // TP_altitude --> dem_alt // todo: clarify this! - // n.a. --> dem_rough // todo: clarify this! - // n.a. --> lat_corr // todo: clarify this! - // n.a. --> lon_corr // todo: clarify this! - // SZA --> sun_zenith - // OZA --> view_zenith - // SAA --> sun_azimuth - // OAA --> view_azimuth - // horiz_wind_vector_1 --> zonal_wind - // horiz_wind_vector_2 --> merid_wind - // sea_level_pressure --> atm_press - // total_ozone --> ozone , convert units - // humidity_pressure_level_14 --> rel_hum // relative humidity at 850 hPa - adaptTiePointGridsToThirdRepro(inputProduct, thirdReproProduct); - - // adapt flag band and coding: - // quality_flags --> l1_flags - // ## cosmetic (2^24) --> COSMETIC (1) - // ## duplicated (2^23) --> DUPLICATED (2) - // ## sun_glint_risk (2^22) --> GLINT_RISK (4) - // ## dubious (2^21) --> SUSPECT (8) - // ## land (2^31) --> LAND_OCEAN (16) - // ## bright (2^27) --> BRIGHT (32) - // ## coastline (2^30) --> COASTLINE (64) - // ## invalid (2^2^25) --> INVALID (128) - try { - adaptFlagBandToThirdRepro(inputProduct, thirdReproProduct); - } catch (IOException e) { - e.printStackTrace(); - } - - // adapt metadata: - // Idepix MERIS does not use any product metadata - // --> for the moment, copy just a few elements from element metadataSection: - Meris3rd4thReprocessingMetadata.fillMetadataInThirdRepro(inputProduct, thirdReproProduct); - - return thirdReproProduct; - } - - @Override - public Product convertToHigherVersion(Product inputProduct) { - // todo: implement - return null; - } - - /* package local for testing */ - int convertQualityToL1FlagValue(long qualityFlagValue) { - int l1FlagValue = 0; - for (int i = 0; i < Integer.SIZE; i++) { - if (qualityToL1FlagMap.containsKey(i) && BitSetter.isFlagSet(qualityFlagValue, i)) { - l1FlagValue += qualityToL1FlagMap.get(i); - } - } - return l1FlagValue; - } - - /* package local for testing */ - static float getMeanSolarFluxFrom4thReprocessing(Band solarFluxBand) { - final MultiLevelImage sourceImage = solarFluxBand.getSourceImage(); - ParameterBlock pb = new ParameterBlock(); - pb.addSource(sourceImage);// The source image - pb.add(null); // null ROI means whole image - pb.add(1); // check every pixel horizontally - pb.add(1); // check every pixel vertically - - // Perform the mean operation on the source image. - final RenderedOp meanImage = MeanDescriptor.create(sourceImage, null, 1, 1, null); - double[] mean = (double[]) meanImage.getProperty("mean"); - - return (float) mean[0]; - } - - private void adaptProductInformationToThirdRepro(Product inputProduct, Product thirdReproProduct) { - // we often need the start/stop times for downstream processors... - thirdReproProduct.setStartTime(inputProduct.getStartTime()); - thirdReproProduct.setEndTime(inputProduct.getEndTime()); - // todo: discuss what else we want to set back to 3RP here - thirdReproProduct.setPreferredTileSize(inputProduct.getPreferredTileSize()); - - if (isMerisRR(inputProduct)) { - // we often need the 3RP product type for downstream processors (e.g. for loading MER Auxdata) - thirdReproProduct.setProductType("MER_RR__1P"); - } else if (isMerisFR(inputProduct)) { - thirdReproProduct.setProductType("MER_FRG_1P"); - } - } - - private boolean isMerisRR(Product inputProduct) { - return inputProduct.getProductType().startsWith("ME_1_R"); - } - - private boolean isMerisFR(Product inputProduct) { - return inputProduct.getProductType().startsWith("ME_1_F"); - } - - private void adaptFlagBandToThirdRepro(Product inputProduct, Product thirdReproProduct) throws IOException { - - Band l1FlagBand = createL1bFlagBand(thirdReproProduct); - setupL1FlagsBitmask(thirdReproProduct); - - final Band qualityFlagBand = inputProduct.getBand("quality_flags"); - final int width = inputProduct.getSceneRasterWidth(); - final int height = inputProduct.getSceneRasterHeight(); - int[] qualityFlagData = new int[width * height]; - int[] l1FlagData = new int[width * height]; - qualityFlagBand.readPixels(0, 0, width, height, qualityFlagData, ProgressMonitor.NULL); - for (int i = 0; i < width * height; i++) { - l1FlagData[i] = convertQualityToL1FlagValue(qualityFlagData[i]); - } - - l1FlagBand.ensureRasterData(); - l1FlagBand.setPixels(0, 0, width, height, l1FlagData); - l1FlagBand.setSourceImage(l1FlagBand.getSourceImage()); - thirdReproProduct.addBand(l1FlagBand); - } - - private void adaptTiePointGridsToThirdRepro(Product inputProduct, Product thirdReproProduct) { - // adapt tie point grids: - // TP_latitude --> latitude - // TP_longitude --> longitude - // TP_altitude --> dem_alt // todo: clarify this! - // n.a. --> dem_rough // todo: clarify this! - // n.a. --> lat_corr // todo: clarify this! - // n.a. --> lon_corr // todo: clarify this! - // SZA --> sun_zenith - // OZA --> view_zenith - // SAA --> sun_azimuth - // OAA --> view_azimuth - // horizontal_wind_vector_1 --> zonal_wind - // horizontal_wind_vector_2 --> merid_wind - // sea_level_pressure --> atm_press - // total_ozone --> ozone // todo: check units! - // humidity_pressure_level_14 --> rel_hum // relative humidity at 850 hPa - - if (!thirdReproProduct.containsTiePointGrid("TP_latitude")) { - ProductUtils.copyTiePointGrid("TP_latitude", inputProduct, thirdReproProduct); - } - final TiePointGrid latitudeTargetTPG = thirdReproProduct.getTiePointGrid("TP_latitude"); - latitudeTargetTPG.setName("latitude"); - latitudeTargetTPG.setDescription("Latitude of the tie points (WGS-84), positive N"); - latitudeTargetTPG.setUnit("deg"); - - if (!thirdReproProduct.containsTiePointGrid("TP_longitude")) { - ProductUtils.copyTiePointGrid("TP_longitude", inputProduct, thirdReproProduct); - } - final TiePointGrid longitudeTargetTPG = thirdReproProduct.getTiePointGrid("TP_longitude"); - longitudeTargetTPG.setName("longitude"); - longitudeTargetTPG.setDescription("Longitude of the tie points (WGS-84), Greenwich origin, positive E"); - longitudeTargetTPG.setUnit("deg"); - - final TiePointGrid altitudeTargetTPG = - ProductUtils.copyTiePointGrid("TP_altitude", inputProduct, thirdReproProduct); - altitudeTargetTPG.setName("dem_alt"); - altitudeTargetTPG.setDescription("Digital elevation model altitude"); - - final TiePointGrid szaTargetTPG = - ProductUtils.copyTiePointGrid("SZA", inputProduct, thirdReproProduct); - szaTargetTPG.setName("sun_zenith"); - szaTargetTPG.setDescription("Viewing zenith angles"); - szaTargetTPG.setUnit("deg"); - - final TiePointGrid saaTargetTPG = - ProductUtils.copyTiePointGrid("SAA", inputProduct, thirdReproProduct); - saaTargetTPG.setName("sun_azimuth"); - saaTargetTPG.setDescription("Sun azimuth angles"); - saaTargetTPG.setUnit("deg"); - // SAA: 4th --> 3rd: if (saa <= 0.0) then saa += 360.0 - final float[] saaTiePoints = saaTargetTPG.getTiePoints(); - for (int i = 0; i < saaTiePoints.length; i++) { - if (saaTiePoints[i] <= 0.0) { - saaTiePoints[i] += 360.0; - } - } - - final TiePointGrid vzaTargetTPG = - ProductUtils.copyTiePointGrid("OZA", inputProduct, thirdReproProduct); - vzaTargetTPG.setName("view_zenith"); - - final TiePointGrid vaaTargetTPG = - ProductUtils.copyTiePointGrid("OAA", inputProduct, thirdReproProduct); - vaaTargetTPG.setName("view_azimuth"); - vaaTargetTPG.setDescription("Viewing azimuth angles"); - vaaTargetTPG.setUnit("deg"); - // OAA: 4th --> 3rd: if (oaa <= 0.0) then oaa += 360.0 - final float[] vaaTiePoints = vaaTargetTPG.getTiePoints(); - for (int i = 0; i < vaaTiePoints.length; i++) { - if (vaaTiePoints[i] <= 0.0) { - vaaTiePoints[i] += 360.0; - } - } - - final TiePointGrid zonalWindTPG = - ProductUtils.copyTiePointGrid("horizontal_wind_vector_1", inputProduct, thirdReproProduct); - zonalWindTPG.setName("zonal_wind"); - zonalWindTPG.setDescription("Zonal wind"); - - final TiePointGrid meridionalWindTPG = - ProductUtils.copyTiePointGrid("horizontal_wind_vector_2", inputProduct, thirdReproProduct); - meridionalWindTPG.setName("merid_wind"); - meridionalWindTPG.setDescription("Meridional wind"); - - final TiePointGrid atmPressTPG = - ProductUtils.copyTiePointGrid("sea_level_pressure", inputProduct, thirdReproProduct); - atmPressTPG.setName("atm_press"); - - final TiePointGrid ozoneTPG = - ProductUtils.copyTiePointGrid("total_ozone", inputProduct, thirdReproProduct); - ozoneTPG.setName("ozone"); - ozoneTPG.setDescription("Total ozone"); - ozoneTPG.setUnit("DU"); - double conversionFactor = 1.0 / 2.1415e-5; // convert from kg/m2 to DU, https://sacs.aeronomie.be/info/dobson.php - final float[] ozoneTiePoints = ozoneTPG.getTiePoints(); - for (int i = 0; i < ozoneTiePoints.length; i++) { - ozoneTiePoints[i] *= conversionFactor; - } - - // relative humidity: take humidity_pressure_level_14 which - // corresponds to rel_hum in 3RP, which is at 850hPa according to MERIS Product Handbook v2.1, page 52, - // https://earth.esa.int/pub/ESA_DOC/ENVISAT/MERIS/meris.ProductHandbook.2_1.pdf) - final TiePointGrid relHumTPG = - ProductUtils.copyTiePointGrid("humidity_pressure_level_14", inputProduct, thirdReproProduct); - relHumTPG.setName("rel_hum"); - relHumTPG.setDescription("Relative humidity"); - } - - private void adaptBandNamesToThirdRepro(Product inputProduct, Product thirdReproProduct) { - // ## detector_index --> detector_index - // ## M%02d_radiance --> radiance_%d - Band detectorIndexTargetBand = - ProductUtils.copyBand(EnvisatConstants.MERIS_DETECTOR_INDEX_DS_NAME, - inputProduct, thirdReproProduct, true); - final Band detectorIndexSourceBand = inputProduct.getBand(EnvisatConstants.MERIS_DETECTOR_INDEX_DS_NAME); - detectorIndexTargetBand.setDescription(detectorIndexSourceBand.getDescription()); - detectorIndexTargetBand.setNoDataValueUsed(false); - detectorIndexTargetBand.setNoDataValue(0.0); - detectorIndexTargetBand.setValidPixelExpression(null); - - for (int i = 0; i < EnvisatConstants.MERIS_L1B_NUM_SPECTRAL_BANDS; i++) { - final String inputBandName = "M" + String.format("%02d", i + 1) + "_radiance"; - final String thirdReproBandName = EnvisatConstants.MERIS_L1B_SPECTRAL_BAND_NAMES[i]; - final Band inputRadianceBand = inputProduct.getBand(inputBandName); - final Band targetRadianceBand = ProductUtils.copyBand(inputBandName, inputProduct, - thirdReproBandName, thirdReproProduct, true); - copyGeneralBandProperties(inputRadianceBand, targetRadianceBand); - copySpectralBandProperties(inputRadianceBand, targetRadianceBand); - - // set solar flux: - final Band solarFluxBand = inputProduct.getBand("solar_flux_band_" + (i + 1)); - // todo: solar flux is not needed for Idepix, but later for general adapter. Discuss how to set. - // For the moment, compute the mean of the corresponding solar flux band image. - // Later, implement GK suggestion - targetRadianceBand.setSolarFlux(getMeanSolarFluxFrom4thReprocessing(solarFluxBand)); - - // set valid pixel expression: - targetRadianceBand.setValidPixelExpression("!l1_flags.INVALID"); - } - } - - private static void copyGeneralBandProperties(Band sourceBand, Band targetBand) { - targetBand.setUnit(sourceBand.getUnit()); - } - - private static void copySpectralBandProperties(Band sourceBand, Band targetBand) { - targetBand.setDescription("TOA radiance band " + sourceBand.getSpectralBandIndex()); - targetBand.setSpectralBandIndex(sourceBand.getSpectralBandIndex()); - targetBand.setSpectralWavelength(sourceBand.getSpectralWavelength()); - targetBand.setSpectralBandwidth(sourceBand.getSpectralBandwidth()); - targetBand.setNoDataValueUsed(false); - targetBand.setNoDataValue(0.0); - } - - private static Band createL1bFlagBand(Product thirdReproProduct) { - - Band l1FlagBand = new Band("l1_flags", ProductData.TYPE_INT32, - thirdReproProduct.getSceneRasterWidth(), thirdReproProduct.getSceneRasterHeight()); - l1FlagBand.setDescription("Level 1b classification and quality flags"); - - FlagCoding l1FlagCoding = new FlagCoding("l1_flags"); - l1FlagCoding.addFlag("COSMETIC", BitSetter.setFlag(0, 0), "Pixel is cosmetic"); - l1FlagCoding.addFlag("DUPLICATED", BitSetter.setFlag(0, 1), "Pixel has been duplicated (filled in)"); - l1FlagCoding.addFlag("GLINT_RISK", BitSetter.setFlag(0, 2), "Pixel has glint risk"); - l1FlagCoding.addFlag("SUSPECT", BitSetter.setFlag(0, 3), "Pixel is suspect"); - l1FlagCoding.addFlag("LAND_OCEAN", BitSetter.setFlag(0, 4), "Pixel is over land, not ocean"); - l1FlagCoding.addFlag("BRIGHT", BitSetter.setFlag(0, 5), "Pixel is bright"); - l1FlagCoding.addFlag("COASTLINE", BitSetter.setFlag(0, 6), "Pixel is part of a coastline"); - l1FlagCoding.addFlag("INVALID", BitSetter.setFlag(0, 7), "Pixel is invalid"); - - l1FlagBand.setSampleCoding(l1FlagCoding); - thirdReproProduct.getFlagCodingGroup().add(l1FlagCoding); - - return l1FlagBand; - } - - private void setupQualityToL1FlagMap() { - // quality_flags --> l1_flags - // ## cosmetic (2^24) --> COSMETIC (1) - // ## duplicated (2^23) --> DUPLICATED (2) - // ## sun_glint_risk (2^22) --> GLINT_RISK (4) - // ## dubious (2^21) --> SUSPECT (8) - // ## land (2^31) --> LAND_OCEAN (16) - // ## bright (2^27) --> BRIGHT (32) - // ## coastline (2^30) --> COASTLINE (64) - // ## invalid (2^25) --> INVALID (128) - qualityToL1FlagMap.put(24, 1); - qualityToL1FlagMap.put(23, 2); - qualityToL1FlagMap.put(22, 4); - qualityToL1FlagMap.put(21, 8); - qualityToL1FlagMap.put(31, 16); - qualityToL1FlagMap.put(27, 32); - qualityToL1FlagMap.put(30, 64); - qualityToL1FlagMap.put(25, 128); - } - - private static void setupL1FlagsBitmask(Product thirdReproProduct) { - - int index = 0; - int w = thirdReproProduct.getSceneRasterWidth(); - int h = thirdReproProduct.getSceneRasterHeight(); - Mask mask; - - mask = Mask.BandMathsType.create("cosmetic", "Pixel is cosmetic", w, h, - "l1_flags.COSMETIC", new Color(204, 153, 255), 0.5f); - thirdReproProduct.getMaskGroup().add(index++, mask); - - mask = Mask.BandMathsType.create("duplicated", "Pixel has been duplicated (filled in)", w, h, - "l1_flags.DUPLICATED", new Color(255, 200, 0), 0.5f); - thirdReproProduct.getMaskGroup().add(index++, mask); - - mask = Mask.BandMathsType.create("glint_risk", "Pixel has glint risk", w, h, - "l1_flags.GLINT_RISK", new Color(255, 0, 255), 0.5f); - thirdReproProduct.getMaskGroup().add(index++, mask); - - mask = Mask.BandMathsType.create("suspect", "Pixel is suspect", w, h, - "l1_flags.SUSPECT", new Color(204, 102, 255), 0.5f); - thirdReproProduct.getMaskGroup().add(index++, mask); - - mask = Mask.BandMathsType.create("land", "Pixel is over land, not ocean", w, h, - "l1_flags.LAND_OCEAN", new Color(51, 153, 0), 0.5f); - thirdReproProduct.getMaskGroup().add(index++, mask); - - mask = Mask.BandMathsType.create("water", "Pixel is over ocean, not land", w, h, - "not l1_flags.LAND_OCEAN", new Color(153, 153, 255), 0.5f); - thirdReproProduct.getMaskGroup().add(index++, mask); - - mask = Mask.BandMathsType.create("bright", "Pixel is bright", w, h, - "l1_flags.BRIGHT", new Color(255, 255, 0), 0.5f); - thirdReproProduct.getMaskGroup().add(index++, mask); - - mask = Mask.BandMathsType.create("coastline", "Pixel is part of a coastline", w, h, - "l1_flags.COASTLINE", Color.GREEN, 0.5f); - thirdReproProduct.getMaskGroup().add(index++, mask); - - mask = Mask.BandMathsType.create("invalid", "Pixel is invaid", w, h, - "l1_flags.INVALID", Color.RED, 0.5f); - thirdReproProduct.getMaskGroup().add(index, mask); - } - -} diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingMetadata.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingMetadata.java deleted file mode 100644 index 24c6f4f2..00000000 --- a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingMetadata.java +++ /dev/null @@ -1,101 +0,0 @@ -package org.esa.snap.idepix.meris.reprocessing; - -import org.esa.snap.core.datamodel.MetadataAttribute; -import org.esa.snap.core.datamodel.MetadataElement; -import org.esa.snap.core.datamodel.Product; - -/** - * Class providing methods for metadata extraction/conversion between 3RP and 4RP. - * - * @author olafd - */ -public class Meris3rd4thReprocessingMetadata { - - /** - * Transfers selected metadata from 4RP into 3RP product. - * - * @param fourthReproProduct - MERIS L1b 4RP product - * @param thirdReproProduct - MERIS L1b 3RP product - */ - public static void fillMetadataInThirdRepro(Product fourthReproProduct, Product thirdReproProduct) { - final MetadataElement inputProductMetadataRoot = fourthReproProduct.getMetadataRoot(); - final MetadataElement thirdReproProductMetadataRoot = thirdReproProduct.getMetadataRoot(); - if (thirdReproProductMetadataRoot != null && inputProductMetadataRoot != null) { - final MetadataElement mphElement = new MetadataElement("MPH"); - thirdReproProductMetadataRoot.addElement(mphElement); - final MetadataElement manifestElement = inputProductMetadataRoot.getElement("Manifest"); - if (manifestElement != null) { - final MetadataElement metadataSectionMetadataElement = manifestElement.getElement("metadataSection"); - if (metadataSectionMetadataElement != null) { - // MPH --> PRODUCT - // Manifest --> metadataSection --> generalProductInformation --> productName - final MetadataElement generalProductInformationMetadataElement = - metadataSectionMetadataElement.getElement("generalProductInformation"); - if (generalProductInformationMetadataElement != null) { - final MetadataAttribute productNameAttr = - generalProductInformationMetadataElement.getAttribute("productName"); - if (productNameAttr != null) { - mphElement.addAttribute(new MetadataAttribute("PRODUCT", productNameAttr.getData(), true)); - } - } - - // MPH --> SENSING_START - // Manifest --> metadataSection --> acquisitionPeriod --> startTime - // MPH --> SENSING_STOP - // Manifest --> metadataSection --> acquisitionPeriod --> stopTime - final MetadataElement acquisitionPeriodMetadataElement = - metadataSectionMetadataElement.getElement("acquisitionPeriod"); - if (acquisitionPeriodMetadataElement != null) { - final MetadataAttribute startTimeAttr = - acquisitionPeriodMetadataElement.getAttribute("startTime"); - if (startTimeAttr != null) { - mphElement.addAttribute(new MetadataAttribute("SENSING_START", startTimeAttr.getData(), true)); - } - final MetadataAttribute stopTimeAttr = - acquisitionPeriodMetadataElement.getAttribute("stopTime"); - if (stopTimeAttr != null) { - mphElement.addAttribute(new MetadataAttribute("SENSING_STOP", stopTimeAttr.getData(), true)); - } - } - - // MPH --> CYCLE - // Manifest --> metadataSection --> orbitReference --> cycleNumber - // MPH --> REL_ORBIT - // Manifest --> metadataSection --> orbitReference --> relativeOrbitNumber --> relativeOrbitNumber - // MPH --> ABS_ORBIT - // Manifest --> metadataSection --> orbitReference --> orbitNumber --> orbitNumber - final MetadataElement orbitReferenceMetadataElement = - metadataSectionMetadataElement.getElement("orbitReference"); - if (orbitReferenceMetadataElement != null) { - final MetadataAttribute cycleNumberAttr = - orbitReferenceMetadataElement.getAttribute("cycleNumber"); - if (cycleNumberAttr != null) { - mphElement.addAttribute(new MetadataAttribute("CYCLE", cycleNumberAttr.getData(), true)); - } - - final MetadataElement relativeOrbitNumberMetadataElement = - orbitReferenceMetadataElement.getElement("relativeOrbitNumber"); - if (relativeOrbitNumberMetadataElement != null) { - final MetadataAttribute relativeOrbitNumberAttr = - relativeOrbitNumberMetadataElement.getAttribute("relativeOrbitNumber"); - if (relativeOrbitNumberAttr != null) { - mphElement.addAttribute(new MetadataAttribute("REL_ORBIT", relativeOrbitNumberAttr.getData(), true)); - } - } - - final MetadataElement orbitNumberMetadataElement = - orbitReferenceMetadataElement.getElement("orbitNumber"); - if (orbitNumberMetadataElement != null) { - final MetadataAttribute orbitNumberAttr = - orbitNumberMetadataElement.getAttribute("orbitNumber"); - if (orbitNumberAttr != null) { - mphElement.addAttribute(new MetadataAttribute("ABS_ORBIT", orbitNumberAttr.getData(), true)); - } - } - } - } - // todo: discuss what else is needed? - } - } - } -} diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/reprocessing/ReprocessingAdapter.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/reprocessing/ReprocessingAdapter.java deleted file mode 100644 index 83134f7d..00000000 --- a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/reprocessing/ReprocessingAdapter.java +++ /dev/null @@ -1,27 +0,0 @@ -package org.esa.snap.idepix.meris.reprocessing; - -import org.esa.snap.core.datamodel.Product; - -/** - * Interface for adaptation of reprocessed L1 source data (here i.e. MERIS 3rd <--> 4th reprocessing) - * todo: move this to a more general place in SNAP - * - */ -public interface ReprocessingAdapter { - - /** - * Provides the conversion to lower version product for given higher version input product - * - * @param inputProduct - the higher version input product - * @return Product lowerVersionProduct - */ - Product convertToLowerVersion(Product inputProduct); - - /** - * Provides the conversion to higher version product for given lower version input product - * - * @param inputProduct - the lower version input product - * @return Product higherVersionProduct - */ - Product convertToHigherVersion(Product inputProduct); -} diff --git 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zFQM}9s_pMY|F7Bme>pM2ORzD%1oa^*l41GDKq3sHFI)xm9wp_J6G$O$!-;L_$VkMD z8%<8e#w!5QAmLklY5>mtQ%3#2UQ=4HZ!nVK(5#&hiR**REf{!5ON9y2KX;#F3}xa3bO0BcMn|5%)!KK=C&zOeDd=mJ&#!Iz|{Gzg+X zONaPV6*jIo795UkL;PLNXy+ar)80=n=7T&JDcIf?%{H1l`)F=ApJM4l9j=K0+eGv5 z)8Dmice7u}wJ9VV0H~fYY?-#2QwoT3AHlWVsnA1u`zY$+S0^ zxmd4nQHPrQwb%PC6xgU(2jz6z6C+1c@*E*z77q+ke6BO4Zm$;wAqFWz5}-;(BI&`oI`B0#F`XaJEr~6XQ2i}#0D>m<8N0oI z4;V7=2j6jXqAfn7@BkThe Processing Parameters under certain conditions. The default value is 4.6.

+

+ Compute mountain shadow:
+ If set, a mountain shadow is computed and added to the pixel classification. The default value is 'true'. +

+ +

+ Extent of mountain shadow:
+ A value between zero and 1 defining how extensive the cloud shadow is flagged. A higher value means more shadow is flagged. + The best value is dependent on the current scene. As default 0.9 is set. +

+

Compute cloud shadow:
If set, a cloud shadow is computed and added to the pixel classification. The default value is 'true'. diff --git a/idepix-meris/src/main/resources/META-INF/services/org.esa.snap.core.gpf.OperatorSpi b/idepix-meris/src/main/resources/META-INF/services/org.esa.snap.core.gpf.OperatorSpi index 0924dcd5..7941b126 100644 --- a/idepix-meris/src/main/resources/META-INF/services/org.esa.snap.core.gpf.OperatorSpi +++ b/idepix-meris/src/main/resources/META-INF/services/org.esa.snap.core.gpf.OperatorSpi @@ -2,4 +2,6 @@ org.esa.snap.idepix.meris.IdepixMerisOp$Spi org.esa.snap.idepix.meris.IdepixMerisLandClassificationOp$Spi org.esa.snap.idepix.meris.IdepixMerisWaterClassificationOp$Spi org.esa.snap.idepix.meris.IdepixMerisMergeLandWaterOp$Spi -org.esa.snap.idepix.meris.IdepixMerisPostProcessOp$Spi \ No newline at end of file +org.esa.snap.idepix.meris.IdepixMerisPostProcessOp$Spi +org.esa.snap.idepix.meris.IdepixMerisMountainShadowOp$Spi +org.esa.snap.idepix.meris.IdepixMerisSlopeAspectOrientationOp$Spi \ No newline at end of file diff --git a/idepix-meris/src/test/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingAdapterTest.java b/idepix-meris/src/test/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingAdapterTest.java deleted file mode 100644 index fc9e4835..00000000 --- a/idepix-meris/src/test/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingAdapterTest.java +++ /dev/null @@ -1,270 +0,0 @@ -package org.esa.snap.idepix.meris.reprocessing; - -import com.bc.ceres.core.ProgressMonitor; -import org.esa.snap.core.datamodel.*; -import org.esa.snap.dataio.envisat.EnvisatConstants; -import org.junit.Before; -import org.junit.Test; - -import java.io.IOException; - -import static org.junit.Assert.*; - -public class Meris3rd4thReprocessingAdapterTest { - - private Product fourthReproTestProduct; - private Meris3rd4thReprocessingAdapter adapter; - private Product thirdReproProduct; - - @Before - public void setUp() { - createFourthReproTestProduct(); - adapter = new Meris3rd4thReprocessingAdapter(); - thirdReproProduct = adapter.convertToLowerVersion(fourthReproTestProduct); - } - - @Test - public void testConvertQualityToL1FlagValue() { - // mapping quality_flags --> l1_flags: - // ## cosmetic (2^24) --> COSMETIC (1) - // ## duplicated (2^23) --> DUPLICATED (2) - // ## sun_glint_risk (2^22) --> GLINT_RISK (4) - // ## dubious (2^21) --> SUSPECT (8) - // ## land (2^31) --> LAND_OCEAN (16) - // ## bright (2^27) --> BRIGHT (32) - // ## coastline (2^30) --> COASTLINE (64) - // ## invalid (2^25) --> INVALID (128) - - // quality flag: pixel is cosmetic, dubious, coastline - // NOTE: quality_flag is uint32 in the 4RP product, we treat it as a long here - long qualityFlagValue = (long) (Math.pow(2.0, 24) + Math.pow(2.0, 21) + Math.pow(2.0, 30)); - int expectedL1FlagValue = 1 + 8 + 64; - int l1FlagValue = adapter.convertQualityToL1FlagValue(qualityFlagValue); - assertEquals(expectedL1FlagValue, l1FlagValue); - - // quality flag: pixel is duplicated, sun glint risk, land, bright - qualityFlagValue = (long) (Math.pow(2.0, 23) + Math.pow(2.0, 22) + Math.pow(2.0, 31) + Math.pow(2.0, 27)); - expectedL1FlagValue = 2 + 4 + 16 + 32; - l1FlagValue = adapter.convertQualityToL1FlagValue(qualityFlagValue); - assertEquals(expectedL1FlagValue, l1FlagValue); - - // quality flag: pixel is invalid - qualityFlagValue = (long) (Math.pow(2.0, 25)); - expectedL1FlagValue = 128; - l1FlagValue = adapter.convertQualityToL1FlagValue(qualityFlagValue); - assertEquals(expectedL1FlagValue, l1FlagValue); - } - - @Test - public void testConvertToLowerVersion_spectralBands() throws IOException { - for (int i = 0; i < EnvisatConstants.MERIS_L1B_NUM_SPECTRAL_BANDS; i++) { - // spectral bands - final String fourthReproSpectralBandName = "M" + String.format("%02d", i + 1) + "_radiance"; - final String thirdReproSpectralBandName = EnvisatConstants.MERIS_L1B_SPECTRAL_BAND_NAMES[i]; - final Band fourthReproSpectralBand = fourthReproTestProduct.getBand(fourthReproSpectralBandName); - final Band thirdReproSpectralBand = thirdReproProduct.getBand(thirdReproSpectralBandName); - assertNotNull(thirdReproSpectralBand); - float[] fourthReproSpectralData = new float[3 * 2]; - float[] thirdReproSpectralData = new float[3 * 2]; - fourthReproSpectralBand.readPixels(0, 0, 3, 2, fourthReproSpectralData, ProgressMonitor.NULL); - thirdReproSpectralBand.readPixels(0, 0, 3, 2, thirdReproSpectralData, ProgressMonitor.NULL); - assertArrayEquals(fourthReproSpectralData, thirdReproSpectralData, 0.0f); - - // solar fluxes - final String fourthReproSolarFluxBandName = "solar_flux_band_" + (i + 1); - final Band fourthReproSolarFluxSpectralBand = fourthReproTestProduct.getBand(fourthReproSolarFluxBandName); - assertNotNull(fourthReproSolarFluxSpectralBand); - float[] fourthReproSolarFluxData = new float[3 * 2]; - fourthReproSolarFluxSpectralBand.readPixels(0, 0, 3, 2, fourthReproSolarFluxData, ProgressMonitor.NULL); - float expectedMeanSolarFlux = (fourthReproSolarFluxData[0] + fourthReproSolarFluxData[1] + - fourthReproSolarFluxData[2] + fourthReproSolarFluxData[3] + - fourthReproSolarFluxData[4] + fourthReproSolarFluxData[5]) / 6.0f; - float computedMeanSolarFlux = - Meris3rd4thReprocessingAdapter.getMeanSolarFluxFrom4thReprocessing(fourthReproSolarFluxSpectralBand); - assertEquals(expectedMeanSolarFlux, computedMeanSolarFlux, 1.E-6f); - assertEquals(expectedMeanSolarFlux, thirdReproSpectralBand.getSolarFlux(), 1.E-6f); - } - } - - @Test - public void testConvertToLowerVersion_detectorIndex() throws IOException { - // detector index - final Band fourthReproDetectorIndexBand = fourthReproTestProduct.getBand("detector_index"); - final Band thirdReproDetectorIndexBand = thirdReproProduct.getBand("detector_index"); - assertNotNull(thirdReproDetectorIndexBand); - int[] fourthReproDetectorIndexData = new int[3 * 2]; - int[] thirdReproDetectorIndexData = new int[3 * 2]; - fourthReproDetectorIndexBand.readPixels(0, 0, 3, 2, fourthReproDetectorIndexData, ProgressMonitor.NULL); - thirdReproDetectorIndexBand.readPixels(0, 0, 3, 2, thirdReproDetectorIndexData, ProgressMonitor.NULL); - assertArrayEquals(fourthReproDetectorIndexData, thirdReproDetectorIndexData); - } - - @Test - public void testConvertToLowerVersion_flagBands() throws IOException { - // l1b flag - final Band fourthReproQualityFlagBand = fourthReproTestProduct.getBand("quality_flags"); - final Band thirdReproL1bFlagBand = thirdReproProduct.getBand("l1_flags"); - assertNotNull(thirdReproL1bFlagBand); - int[] fourthReproQualityFlagData = new int[3 * 2]; - int[] thirdReproL1bFlagData = new int[3 * 2]; - fourthReproQualityFlagBand.readPixels(0, 0, 3, 2, fourthReproQualityFlagData, ProgressMonitor.NULL); - thirdReproL1bFlagBand.readPixels(0, 0, 3, 2, thirdReproL1bFlagData, ProgressMonitor.NULL); - assertNotNull(thirdReproL1bFlagData); - - int[] expectedFourthReproQualityFlagData = new int[]{ - (int) (Math.pow(2.0, 24) + Math.pow(2.0, 21) + Math.pow(2.0, 30)), - (int) (Math.pow(2.0, 22) + Math.pow(2.0, 23) + Math.pow(2.0, 27)), - (int) (Math.pow(2.0, 22) + Math.pow(2.0, 23) + Math.pow(2.0, 24)), - (int) (Math.pow(2.0, 24) + Math.pow(2.0, 30)), - (int) (Math.pow(2.0, 24) + Math.pow(2.0, 27) + Math.pow(2.0, 30)), - (int) (Math.pow(2.0, 25)), - }; - assertArrayEquals(expectedFourthReproQualityFlagData, fourthReproQualityFlagData); - int[] expectedThirdReproL1bFlagData = new int[]{ - 1+8+64, - 2+4+32, - 1+2+4, - 1+64, - 1+32+64, - 128, - }; - assertArrayEquals(expectedThirdReproL1bFlagData, thirdReproL1bFlagData); - } - - private void createFourthReproTestProduct() { - fourthReproTestProduct = new Product("ME_1_RRG_4RP_test", "ME_1_RRG", 3, 2); - - // add bands - for (int i = 0; i < EnvisatConstants.MERIS_L1B_NUM_SPECTRAL_BANDS; i++) { - final String fourthReproSpectralBandName = "M" + String.format("%02d", i + 1) + "_radiance"; - Band fourthReproSpectralBand = new Band(fourthReproSpectralBandName, ProductData.TYPE_FLOAT32, 3, 2); - fourthReproSpectralBand.ensureRasterData(); - float[] testFloat32s = new float[]{(i + 1) * 1.f, (i + 1) * 2.f, (i + 1) * 3.f, - (i + 1) * 4.f, (i + 1) * 5.f, (i + 1) * 6.f}; - fourthReproSpectralBand.setPixels(0, 0, 3, 2, testFloat32s); - fourthReproSpectralBand.setSourceImage(fourthReproSpectralBand.getSourceImage()); - fourthReproTestProduct.addBand(fourthReproSpectralBand); - - Band solarFluxBand = new Band("solar_flux_band_" + (i + 1), ProductData.TYPE_FLOAT32, 3, 2); - solarFluxBand.ensureRasterData(); - float[] testFloat32sSolarFlux = new float[]{1400 + (i + 1) * 1.f, 1400 + (i + 1) * 2.f, 1400 + (i + 1) * 3.f, - 1400 + (i + 1) * 4.f, 1400 + (i + 1) * 5.f, 1400 + (i + 1) * 6.f}; - solarFluxBand.setPixels(0, 0, 3, 2, testFloat32sSolarFlux); - solarFluxBand.setSourceImage(solarFluxBand.getSourceImage()); - fourthReproTestProduct.addBand(solarFluxBand); - } - - Band detectorIndexBand = new Band("detector_index", ProductData.TYPE_INT16, 3, 2); - detectorIndexBand.ensureRasterData(); - int[] testInt16sDetectorIndex = new int[]{111, 222, 333, 444, 555, 666}; - detectorIndexBand.setPixels(0, 0, 3, 2, testInt16sDetectorIndex); - detectorIndexBand.setSourceImage(detectorIndexBand.getSourceImage()); - fourthReproTestProduct.addBand(detectorIndexBand); - - Band qualityFlagBand = new Band("quality_flags", ProductData.TYPE_UINT32, 3, 2); - qualityFlagBand.ensureRasterData(); - int[] testInt16sQualityFlag = new int[]{ - (int) (Math.pow(2.0, 24) + Math.pow(2.0, 21) + Math.pow(2.0, 30)), - (int) (Math.pow(2.0, 22) + Math.pow(2.0, 23) + Math.pow(2.0, 27)), - (int) (Math.pow(2.0, 22) + Math.pow(2.0, 23) + Math.pow(2.0, 24)), - (int) (Math.pow(2.0, 24) + Math.pow(2.0, 30)), - (int) (Math.pow(2.0, 24) + Math.pow(2.0, 27) + Math.pow(2.0, 30)), - (int) (Math.pow(2.0, 25)), - }; - qualityFlagBand.setPixels(0, 0, 3, 2, testInt16sQualityFlag); - qualityFlagBand.setSourceImage(qualityFlagBand.getSourceImage()); - fourthReproTestProduct.addBand(qualityFlagBand); - - // add tie point grids: - // TP_latitude --> latitude - // TP_longitude --> longitude - // TP_altitude --> dem_alt - // SZA --> sun_zenith - // OZA --> view_zenith - // SAA --> sun_azimuth - // OAA --> view_azimuth - // horizontal_wind_vector_1 --> zonal_wind - // horizontal_wind_vector_2 --> merid_wind - // sea_level_pressure --> atm_press - // total_ozone --> ozone - // humidity_pressure_level_14 --> rel_hum // relative humidity at 850 hPa - - float[] tpLatTestData = new float[]{31.f, 32.f, 33.f, 27.f, 28.f, 29.f}; - TiePointGrid tpLatTpg = new TiePointGrid("TP_latitude", 3, 2, 0, 0, 1, 1, tpLatTestData); - fourthReproTestProduct.addTiePointGrid(tpLatTpg); - - float[] tpLonTestData = new float[]{51.f, 52.f, 33.f, 51.f, 52.f, 53.f}; - TiePointGrid tpLonTpg = new TiePointGrid("TP_longitude", 3, 2, 0, 0, 1, 1, tpLonTestData); - fourthReproTestProduct.addTiePointGrid(tpLonTpg); - - float[] tpAltTestData = new float[]{234.f, 567.f, 789.f, 1133.f, 1244.f, 1355.f}; - TiePointGrid tpAltTpg = new TiePointGrid("TP_altitude", 3, 2, 0, 0, 1, 1, tpAltTestData); - fourthReproTestProduct.addTiePointGrid(tpAltTpg); - - float[] szaTestData = new float[]{41.f, 42.f, 43.f, 47.f, 48.f, 49.f}; - TiePointGrid szaTpg = new TiePointGrid("SZA", 3, 2, 0, 0, 1, 1, szaTestData); - fourthReproTestProduct.addTiePointGrid(szaTpg); - - float[] saaTestData = new float[]{-14.f, -24.f, -34.f, 74.f, 84.f, 89.f}; - TiePointGrid saaTpg = new TiePointGrid("SAA", 3, 2, 0, 0, 1, 1, saaTestData); - fourthReproTestProduct.addTiePointGrid(saaTpg); - - float[] ozaTestData = new float[]{11.f, 22.f, 33.f, 12.f, 23.f, 34.f}; - TiePointGrid ozaTpg = new TiePointGrid("OZA", 3, 2, 0, 0, 1, 1, ozaTestData); - fourthReproTestProduct.addTiePointGrid(ozaTpg); - - float[] oaaTestData = new float[]{-55.f, -56.f, -57.f, 58.f, 59.f, 60.f}; - TiePointGrid oaaTpg = new TiePointGrid("OAA", 3, 2, 0, 0, 1, 1, oaaTestData); - fourthReproTestProduct.addTiePointGrid(oaaTpg); - - float[] zonalWindTestData = new float[]{10.f, 11.f, 12.f, 16.f, 17.f, 18.f}; - TiePointGrid zonalWindTpg = new TiePointGrid("horizontal_wind_vector_1", 3, 2, 0, 0, 1, 1, zonalWindTestData); - fourthReproTestProduct.addTiePointGrid(zonalWindTpg); - - float[] meridionalWindTestData = new float[]{5.f, 6.f, 7.f, 2.f, 3.f, 4.f}; - TiePointGrid meridionalWindTpg = new TiePointGrid("horizontal_wind_vector_2", 3, 2, 0, 0, 1, 1, meridionalWindTestData); - fourthReproTestProduct.addTiePointGrid(meridionalWindTpg); - - float[] slpTestData = new float[]{1005.f, 1006.f, 1008.f, 1002.f, 1003.f, 1004.f}; - TiePointGrid slpTpg = new TiePointGrid("sea_level_pressure", 3, 2, 0, 0, 1, 1, slpTestData); - fourthReproTestProduct.addTiePointGrid(slpTpg); - - float[] ozoneTestData = new float[]{0.005f, 0.0055f, 0.006f, 0.0065f, 0.007f, 0.0075f}; - TiePointGrid ozoneTpg = new TiePointGrid("total_ozone", 3, 2, 0, 0, 1, 1, ozoneTestData); - fourthReproTestProduct.addTiePointGrid(ozoneTpg); - - float[] relHumTestData = new float[]{2.34f, 13.7f, 11.5f, 33.4f, 35.8f, 39.2f}; - TiePointGrid relHumTpg = new TiePointGrid("humidity_pressure_level_14", 3, 2, 0, 0, 1, 1, relHumTestData); - fourthReproTestProduct.addTiePointGrid(relHumTpg); - - fourthReproTestProduct.setAutoGrouping("M*_radiance:solar_flux"); - - // metadata - final MetadataElement manifestElement = new MetadataElement("Manifest"); - fourthReproTestProduct.getMetadataRoot().addElement(manifestElement); - final MetadataElement metadataSectionElement = new MetadataElement("metadataSection"); - manifestElement.addElement(metadataSectionElement); - final MetadataElement generalProductInformationElement = new MetadataElement("generalProductInformation"); - metadataSectionElement.addElement(generalProductInformationElement); - generalProductInformationElement.addAttribute(new MetadataAttribute("productName", - ProductData.createInstance(fourthReproTestProduct.getName()), true)); - final MetadataElement acquisitionPeriodElement = new MetadataElement("acquisitionPeriod"); - metadataSectionElement.addElement(acquisitionPeriodElement); - acquisitionPeriodElement.addAttribute(new MetadataAttribute("startTime", - ProductData.createInstance("2011-07-02T14:08:01.955726Z"), true)); - acquisitionPeriodElement.addAttribute(new MetadataAttribute("stopTime", - ProductData.createInstance("2011-07-02T14:51:57.552001Z"), true)); - final MetadataElement orbitReferenceElement = new MetadataElement("orbitReference"); - orbitReferenceElement.addAttribute(new MetadataAttribute("cycleNumber", - ProductData.createInstance(new int[]{104}), true)); - final MetadataElement orbitNumberElement = new MetadataElement("orbitNumber"); - orbitNumberElement.addAttribute(new MetadataAttribute("orbitNumber", - ProductData.createInstance(new int[]{48832}), true)); - orbitReferenceElement.addElement(orbitNumberElement); - final MetadataElement relativeOrbitNumberElement = new MetadataElement("relativeOrbitNumber"); - relativeOrbitNumberElement.addAttribute(new MetadataAttribute("relativeOrbitNumber", - ProductData.createInstance(new int[]{111}), true)); - orbitReferenceElement.addElement(relativeOrbitNumberElement); - metadataSectionElement.addElement(orbitReferenceElement); - } -} diff --git a/idepix-meris/src/test/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingMetadataTest.java b/idepix-meris/src/test/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingMetadataTest.java deleted file mode 100644 index 28d4539b..00000000 --- a/idepix-meris/src/test/java/org/esa/snap/idepix/meris/reprocessing/Meris3rd4thReprocessingMetadataTest.java +++ /dev/null @@ -1,95 +0,0 @@ -package org.esa.snap.idepix.meris.reprocessing; - -import org.esa.snap.core.datamodel.MetadataAttribute; -import org.esa.snap.core.datamodel.MetadataElement; -import org.esa.snap.core.datamodel.Product; -import org.esa.snap.core.datamodel.ProductData; -import org.junit.Before; -import org.junit.Test; - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; - -public class Meris3rd4thReprocessingMetadataTest { - - private Product fourthReproTestProduct; - - @Before - public void setUp() { - createFourthReproTestProduct_metadataOnly(); - } - - @Test - public void testFillMetadataInThirdRepro() { - final Product thirdReproProduct = new Product("ME_1_RRG_3RP_test", "ME_1_RRG", 3, 2); - Meris3rd4thReprocessingMetadata.fillMetadataInThirdRepro(fourthReproTestProduct, thirdReproProduct); - - final MetadataElement thirdReproProductMetadataRoot = thirdReproProduct.getMetadataRoot(); - assertNotNull(thirdReproProductMetadataRoot); - - final MetadataElement mphElement = thirdReproProductMetadataRoot.getElement("MPH"); - assertNotNull(mphElement); - - final MetadataAttribute productAttr = mphElement.getAttribute("PRODUCT"); - assertNotNull(productAttr); - assertNotNull(productAttr.getData()); - assertEquals(fourthReproTestProduct.getName(), productAttr.getData().getElemString()); - - final MetadataAttribute sensingStartAttr = mphElement.getAttribute("SENSING_START"); - assertNotNull(sensingStartAttr); - assertNotNull(sensingStartAttr.getData()); - assertEquals("2011-07-02T14:08:01.955726Z", sensingStartAttr.getData().getElemString()); - - final MetadataAttribute sensingStopAttr = mphElement.getAttribute("SENSING_STOP"); - assertNotNull(sensingStopAttr); - assertNotNull(sensingStopAttr.getData()); - assertEquals("2011-07-02T14:51:57.552001Z", sensingStopAttr.getData().getElemString()); - - final MetadataAttribute cycleAttr = mphElement.getAttribute("CYCLE"); - assertNotNull(cycleAttr); - assertNotNull(cycleAttr.getData()); - assertEquals(104, cycleAttr.getData().getElemInt()); - - final MetadataAttribute relOrbitAttr = mphElement.getAttribute("REL_ORBIT"); - assertNotNull(relOrbitAttr); - assertNotNull(relOrbitAttr.getData()); - assertEquals(111, relOrbitAttr.getData().getElemInt()); - - final MetadataAttribute absOrbitAttr = mphElement.getAttribute("ABS_ORBIT"); - assertNotNull(absOrbitAttr); - assertNotNull(absOrbitAttr.getData()); - assertEquals(48832, absOrbitAttr.getData().getElemInt()); - } - - private void createFourthReproTestProduct_metadataOnly() { - fourthReproTestProduct = new Product("ME_1_RRG_4RP_test", "ME_1_RRG", 3, 2); - - // add metadata - final MetadataElement manifestElement = new MetadataElement("Manifest"); - fourthReproTestProduct.getMetadataRoot().addElement(manifestElement); - final MetadataElement metadataSectionElement = new MetadataElement("metadataSection"); - manifestElement.addElement(metadataSectionElement); - final MetadataElement generalProductInformationElement = new MetadataElement("generalProductInformation"); - metadataSectionElement.addElement(generalProductInformationElement); - generalProductInformationElement.addAttribute(new MetadataAttribute("productName", - ProductData.createInstance(fourthReproTestProduct.getName()), true)); - final MetadataElement acquisitionPeriodElement = new MetadataElement("acquisitionPeriod"); - metadataSectionElement.addElement(acquisitionPeriodElement); - acquisitionPeriodElement.addAttribute(new MetadataAttribute("startTime", - ProductData.createInstance("2011-07-02T14:08:01.955726Z"), true)); - acquisitionPeriodElement.addAttribute(new MetadataAttribute("stopTime", - ProductData.createInstance("2011-07-02T14:51:57.552001Z"), true)); - final MetadataElement orbitReferenceElement = new MetadataElement("orbitReference"); - orbitReferenceElement.addAttribute(new MetadataAttribute("cycleNumber", - ProductData.createInstance(new int[]{104}), true)); - final MetadataElement orbitNumberElement = new MetadataElement("orbitNumber"); - orbitNumberElement.addAttribute(new MetadataAttribute("orbitNumber", - ProductData.createInstance(new int[]{48832}), true)); - orbitReferenceElement.addElement(orbitNumberElement); - final MetadataElement relativeOrbitNumberElement = new MetadataElement("relativeOrbitNumber"); - relativeOrbitNumberElement.addAttribute(new MetadataAttribute("relativeOrbitNumber", - ProductData.createInstance(new int[]{111}), true)); - orbitReferenceElement.addElement(relativeOrbitNumberElement); - metadataSectionElement.addElement(orbitReferenceElement); - } -} diff --git a/idepix-olci/src/main/java/org/esa/snap/idepix/olci/IdepixOlciSlopeAspectOrientationOp.java b/idepix-olci/src/main/java/org/esa/snap/idepix/olci/IdepixOlciSlopeAspectOrientationOp.java index 5df76810..981e1622 100644 --- a/idepix-olci/src/main/java/org/esa/snap/idepix/olci/IdepixOlciSlopeAspectOrientationOp.java +++ b/idepix-olci/src/main/java/org/esa/snap/idepix/olci/IdepixOlciSlopeAspectOrientationOp.java @@ -9,19 +9,17 @@ import org.esa.snap.core.gpf.annotations.OperatorMetadata; import org.esa.snap.core.gpf.annotations.SourceProduct; import org.esa.snap.core.util.ProductUtils; -import org.esa.snap.core.util.math.MathUtils; -import org.opengis.referencing.operation.MathTransform; +import org.esa.snap.idepix.core.util.SlopeAspectOrientationUtils; import javax.media.jai.BorderExtender; import java.awt.*; -import java.awt.geom.AffineTransform; import java.util.Map; /** * Computes Slope, Aspect and Orientation for a Sentinel-3 OLCI product. * See theory e.g. at - * https://www.e-education.psu.edu/geog480/node/490, or - * https://desktop.arcgis.com/en/arcmap/10.3/tools/spatial-analyst-toolbox/how-hillshade-works.htm + * ..., or + * ... * * @author Tonio Fincke, Olaf Danne, Dagmar Mueller */ @@ -38,9 +36,6 @@ public class IdepixOlciSlopeAspectOrientationOp extends Operator { @SourceProduct(alias = "l1b") private Product l1bProduct; - private final static float EARTH_MIN_ELEVATION = -428.0f; // at shoreline of Dead Sea - private final static float EARTH_MAX_ELEVATION = 8848.0f; // Mt. Everest - private static final String ELEVATION_BAND_NAME = IdepixOlciConstants.OLCI_ALTITUDE_BAND_NAME; private double spatialResolution; @@ -77,16 +72,9 @@ public void initialize() throws OperatorException { if (sourceGeoCoding == null) { throw new OperatorException("Source product has no geo-coding"); } - if (sourceGeoCoding instanceof CrsGeoCoding) { - final MathTransform i2m = sourceGeoCoding.getImageToMapTransform(); - if (i2m instanceof AffineTransform) { - spatialResolution = ((AffineTransform) i2m).getScaleX(); - } else { - spatialResolution = computeSpatialResolution(l1bProduct, sourceGeoCoding); - } - } else { - spatialResolution = computeSpatialResolution(l1bProduct, sourceGeoCoding); - } + + spatialResolution = SlopeAspectOrientationUtils.computeSpatialResolution(l1bProduct, sourceGeoCoding); + elevationBand = l1bProduct.getBand(ELEVATION_BAND_NAME); if (elevationBand == null) { throw new OperatorException("Elevation band required to compute slope or aspect"); @@ -154,16 +142,20 @@ public void computeTileStack(Map targetTiles, Rectangle targetRectan slopeTile.setSample(x, y, Float.NaN); aspectTile.setSample(x, y, Float.NaN); orientationTile.setSample(x, y, Float.NaN); - final float[] elevationDataMacropixel = get3x3MacropixelData(elevationTile, y, x); - if (is3x3ElevationDataValid(elevationDataMacropixel)) { + final float[] elevationDataMacropixel = SlopeAspectOrientationUtils.get3x3MacropixelData(elevationTile, y, x); + if (SlopeAspectOrientationUtils.is3x3ElevationDataValid(elevationDataMacropixel)) { final float vza = viewZenithAngleTile.getSampleFloat(x, y); final float vaa = viewAzimuthAngleTile.getSampleFloat(x, y); final float saa = sunAzimuthAngleTile.getSampleFloat(x, y); - final float[] latitudeDataMacropixel = get3x3MacropixelData(latitudeTile, y, x); - final float[] longitudeDataMacropixel = get3x3MacropixelData(longitudeTile, y, x); - final float orientation = computeOrientation(latitudeDataMacropixel, longitudeDataMacropixel); + final float[] latitudeDataMacropixel = + SlopeAspectOrientationUtils.get3x3MacropixelData(latitudeTile, y, x); + final float[] longitudeDataMacropixel = + SlopeAspectOrientationUtils.get3x3MacropixelData(longitudeTile, y, x); + final float orientation = SlopeAspectOrientationUtils.computeOrientation3x3Box(latitudeDataMacropixel, + longitudeDataMacropixel); orientationTile.setSample(x, y, orientation); - final float[] slopeAspect = computeSlopeAspect(elevationDataMacropixel, orientation, vza, vaa, saa, + final float[] slopeAspect = SlopeAspectOrientationUtils.computeSlopeAspect3x3(elevationDataMacropixel, + orientation, vza, vaa, saa, spatialResolution); slopeTile.setSample(x, y, slopeAspect[0]); aspectTile.setSample(x, y, slopeAspect[1]); @@ -172,150 +164,6 @@ public void computeTileStack(Map targetTiles, Rectangle targetRectan } } - private float[] get3x3MacropixelData(Tile sourceTile, int y, int x) { - float[] macropixelData = new float[9]; - macropixelData[0] = sourceTile.getSampleFloat(x - 1, y - 1); - macropixelData[1] = sourceTile.getSampleFloat(x, y - 1); - macropixelData[2] = sourceTile.getSampleFloat(x + 1, y - 1); - macropixelData[3] = sourceTile.getSampleFloat(x - 1, y); - macropixelData[4] = sourceTile.getSampleFloat(x, y); - macropixelData[5] = sourceTile.getSampleFloat(x + 1, y); - macropixelData[6] = sourceTile.getSampleFloat(x - 1, y + 1); - macropixelData[7] = sourceTile.getSampleFloat(x, y + 1); - macropixelData[8] = sourceTile.getSampleFloat(x + 1, y + 1); - - return macropixelData; - } - - /** - * Checks if 3x3 box of elevations around reference pixel is valid - * (i.e. not NaN and all values inside real values possible on Earth) - * - * @param elevationData - 3x3 box of elevations - * @return boolean - */ - static boolean is3x3ElevationDataValid(float[] elevationData) { - for (final float elev : elevationData) { - if (elev == 0.0f || Float.isNaN(elev) || elev < EARTH_MIN_ELEVATION || elev > EARTH_MAX_ELEVATION) { - return false; - } - } - return true; - } - - /* package local for testing */ - static float[] computeSlopeAspect(float[] elev, float orientation, float vza, float vaa, float saa, double spatialResolution) { - //DM: geometric correction of resolution necessary for observations not in nadir view. - // generates steeper slopes. Needs vza, vaa, angle between y-pixel axis and north direction (orientation). - //DM: orientation in rad! - float b = (elev[2] + 2 * elev[5] + elev[8] - elev[0] - 2 * elev[3] - elev[6]) / 8f; //direction x - float c = (elev[0] + 2 * elev[1] + elev[2] - elev[6] - 2 * elev[7] - elev[8]) / 8f; //direction y - double vaa_orientation = (360.0 - (vaa + orientation / MathUtils.DTOR)) * MathUtils.DTOR; - double spatialRes = spatialResolution / Math.cos(vza * MathUtils.DTOR); - float slope = (float) Math.atan(Math.sqrt(Math.pow(b / (spatialRes * Math.sin(vaa_orientation)), 2) + - Math.pow(c / (spatialRes * Math.cos(vaa_orientation)), 2))); - float aspect = (float) Math.atan2(-b, -c); - if (saa > 270. || saa < 90) { //Sun from North (mostly southern hemisphere) - aspect -= Math.PI; - } - if (aspect < 0.0f) { - // map from [-180, 180] into [0, 360], see e.g. https://www.e-education.psu.edu/geog480/node/490 - aspect += 2.0 * Math.PI; - } - if (slope <= 0.0) { - aspect = Float.NaN; - } - - return new float[]{slope, aspect}; - } - - /* package local for testing */ - static float computeOrientation(float[] latData, float[] lonData) { - final float lat1 = latData[3]; - final float lat2 = latData[5]; - final float lon1 = lonData[3]; - final float lon2 = lonData[5]; - - return computeOrientation(lat1, lat2, lon1, lon2); - } - - /** - * Provides orientation ('bearing') between two points. - * See theory e.g. at - * https://www.igismap.com/formula-to-find-bearing-or-heading-angle-between-two-points-latitude-longitude/ - * - * @param lat1 - first latitude - * @param lat2 - second latitude - * @param lon1 - first longitude - * @param lon2 - second longitude - * - * @return float - */ - static float computeOrientation(float lat1, float lat2, float lon1, float lon2) { -// final float lat1Rad = lat1 * MathUtils.DTOR_F; -// final float deltaLon = lon2 - lon1; - // we use this formula, as in S2-MSI: -// return (float) Math.atan2(-(lat2 - lat1), deltaLon * Math.cos(lat1Rad)); - - // DM: formulas from theory, see above - double X = Math.cos(lat2 * MathUtils.DTOR) * Math.sin((lon2 - lon1) * MathUtils.DTOR); - double Y = Math.cos(lat1 * MathUtils.DTOR) * Math.sin(lat2 * MathUtils.DTOR) - Math.sin(lat1 * MathUtils.DTOR) * X; - return (float) (Math.atan2(X, Y)); - - } - - /** - * Computes product spatial resolution from great circle distances at the product edges. - * To be used as fallback if we have no CRS geocoding. - * - * @param l1bProduct - the source product - * @param sourceGeoCoding - the source scene geocoding - * @return spatial resolution in metres - */ - static double computeSpatialResolution(Product l1bProduct, GeoCoding sourceGeoCoding) { - final double width = l1bProduct.getSceneRasterWidth(); - final double height = l1bProduct.getSceneRasterHeight(); - - final GeoPos leftPos = sourceGeoCoding.getGeoPos(new PixelPos(0, height / 2), null); - final GeoPos rightPos = sourceGeoCoding.getGeoPos(new PixelPos(width - 1, height / 2), null); - final double distance1 = - computeDistance(leftPos.getLat(), leftPos.getLon(), rightPos.getLat(), rightPos.getLon()); - - final GeoPos upperPos = sourceGeoCoding.getGeoPos(new PixelPos(width / 2, 0), null); - final GeoPos lowerPos = sourceGeoCoding.getGeoPos(new PixelPos(width / 2, height - 1), null); - final double distance2 = - computeDistance(upperPos.getLat(), upperPos.getLon(), lowerPos.getLat(), lowerPos.getLon()); - - final double distance = 0.5 * (distance1 + distance2); - - return 1000.0 * distance / (width - 1); - } - - /** - * Calculate the great-circle distance between two points on Earth using Haversine formula. - * See e.g. https://www.movable-type.co.uk/scripts/latlong.html - * - * @param lat1 - first point latitude - * @param lon1 - first point longitude - * @param lat2 - second point latitude - * @param lon2 - second point longitude - * @return distance in km - */ - static double computeDistance(double lat1, double lon1, double lat2, double lon2) { - final double deltaLatR = (lat1 - lat2) * MathUtils.DTOR; - final double deltaLonR = (lon1 - lon2) * MathUtils.DTOR; - - final double a = Math.sin(deltaLatR / 2.0) * Math.sin(deltaLatR / 2.0) + - Math.cos(lat1 * MathUtils.DTOR) * Math.cos(lat2 * MathUtils.DTOR) * - Math.sin(deltaLonR / 2.0) * Math.sin(deltaLonR / 2.0); - - final double c = 2.0 * Math.atan2(Math.sqrt(a), Math.sqrt(1 - a)); - - final double R = 6371.0; // Earth radius in km - - return R * c; - } - private static Rectangle getSourceRectangle(Rectangle targetRectangle) { return new Rectangle(targetRectangle.x - 1, targetRectangle.y - 1, targetRectangle.width + 2, targetRectangle.height + 2); diff --git a/idepix-olci/src/test/java/org/esa/snap/idepix/olci/IdepixOlciSlopeAspectOrientationOpTest.java b/idepix-olci/src/test/java/org/esa/snap/idepix/olci/IdepixOlciSlopeAspectOrientationOpTest.java deleted file mode 100644 index 0411b8f5..00000000 --- a/idepix-olci/src/test/java/org/esa/snap/idepix/olci/IdepixOlciSlopeAspectOrientationOpTest.java +++ /dev/null @@ -1,87 +0,0 @@ -package org.esa.snap.idepix.olci; - -import org.junit.Ignore; -import org.junit.Test; - -import static org.junit.Assert.assertEquals; - -/** - * @author Tonio Fincke - */ -public class IdepixOlciSlopeAspectOrientationOpTest { - -// @Test -// public void computeSlopeAndAspect() { -// // flat plane over 3x3 box -// float[] altitude = new float[]{ -// 0.0f, 0.0f, 0.0f, -// 0.0f, 0.0f, 0.0f, -// 0.0f, 0.0f, 0.0f}; -// float[] slopeAndAspect = IdepixOlciSlopeAspectOrientationOp.computeSlopeAspect(altitude, 300); -// assertEquals(slopeAndAspect[0], 0.0f, 1e-7); -// assertEquals(slopeAndAspect[1], Float.NaN, 1e-8); -// -// // ratio 1:1 (45deg) inclined plane over 3x3 box, ascending to the north -// altitude = new float[]{ -// 600.0f, 600.0f, 600.0f, -// 300.0f, 300.0f, 300.0f, -// 0.0f, 0.0f, 0.0f}; -// slopeAndAspect = IdepixOlciSlopeAspectOrientationOp.computeSlopeAspect(altitude, 300); -// assertEquals(slopeAndAspect[0], Math.PI / 4, 1e-7); -// assertEquals(slopeAndAspect[1], Math.PI, 1e-6); -// -// // ratio 1:1 (45deg) inclined plane over 3x3 box, ascending to the west -// altitude = new float[]{ -// 600.0f, 300.0f, 0.0f, -// 600.0f, 300.0f, 0.0f, -// 600.0f, 300.0f, 0.0f}; -// slopeAndAspect = IdepixOlciSlopeAspectOrientationOp.computeSlopeAspect(altitude, 300); -// assertEquals(slopeAndAspect[0], Math.PI / 4, 1e-7); -// assertEquals(slopeAndAspect[1], Math.PI / 2, 1e-6); -// -// // ratio 1:2 inclined plane over 3x3 box, ascending to the east -// altitude = new float[]{ -// 0.0f, 300.0f, 600.0f, -// 0.0f, 300.0f, 600.0f, -// 0.0f, 300.0f, 600.0f}; -// slopeAndAspect = IdepixOlciSlopeAspectOrientationOp.computeSlopeAspect(altitude, 600); -// assertEquals(slopeAndAspect[0], Math.atan(0.5), 1e-7); -// assertEquals(slopeAndAspect[1], Math.PI * 3.0 / 2.0, 1e-6); -// } - - @Test - @Ignore - public void testComputeOrientation() { - - // todo: does not work after DM's latest changes, check why - // east-west 3x3 box, orientaton is 0 deg - float[] latitudes = new float[]{50.0f, 50.0f, 50.0f, - 50.1f, 50.1f, 50.1f, - 50.2f, 50.2f, 50.2f}; - float[] longitudes = new float[]{10.0f, 10.1f, 10.2f, - 10.0f, 10.1f, 10.2f, - 10.0f, 10.1f, 10.2f}; - float orientation = IdepixOlciSlopeAspectOrientationOp.computeOrientation(latitudes, longitudes); - assertEquals(0.0f, orientation, 1e-8); - - // 3x3 box tilted 90deg clockwise --> orientation is -90 deg - latitudes = new float[]{50.0f, 50.1f, 50.2f, - 50.0f, 50.1f, 50.2f, - 50.0f, 50.1f, 50.2f}; - longitudes = new float[]{10.2f, 10.2f, 10.2f, - 10.1f, 10.1f, 10.1f, - 10.0f, 10.0f, 10.0f}; - orientation = IdepixOlciSlopeAspectOrientationOp.computeOrientation(latitudes, longitudes); - assertEquals(-Math.PI / 2.0f, orientation, 1e-6); - - // 3x3 box tilted 45deg counterclockwise --> orientation is 45 deg - latitudes = new float[]{-0.1f, -0.05f, 0.0f, - -0.05f, 0.0f, 0.05f, - 0.0f, 0.05f, 0.1f}; - longitudes = new float[]{10.0f, 10.05f, 10.1f, - 10.05f, 10.1f, 10.15f, - 10.1f, 10.15f, 10.2f}; - orientation = IdepixOlciSlopeAspectOrientationOp.computeOrientation(latitudes, longitudes); - assertEquals(-Math.PI / 4.0f, orientation, 1e-3); - } -} \ No newline at end of file From 18b7c83d111561c56a736ff2e240f81ad7a7bda8 Mon Sep 17 00:00:00 2001 From: martin-boettcher Date: Wed, 5 Apr 2023 22:04:35 +0200 Subject: [PATCH 12/12] Idepix MERIS optimised use of trigonometric functions --- .../snap/idepix/core/util/IdepixUtils.java | 9 +++ .../meris/IdepixMerisMountainShadowOp.java | 20 +++--- .../IdepixMerisSlopeAspectOrientationOp.java | 6 +- .../snap/idepix/meris/IdepixMerisUtils.java | 31 +++++---- .../IdepixMerisWaterClassificationOp.java | 25 +++++++- .../IdepixMerisWaterClassificationOpTest.java | 63 +++++++++++++++++++ pom.xml | 2 +- 7 files changed, 124 insertions(+), 32 deletions(-) create mode 100644 idepix-meris/src/test/java/org/esa/snap/idepix/meris/IdepixMerisWaterClassificationOpTest.java diff --git a/idepix-core/src/main/java/org/esa/snap/idepix/core/util/IdepixUtils.java b/idepix-core/src/main/java/org/esa/snap/idepix/core/util/IdepixUtils.java index 5246628e..2b3a31f9 100644 --- a/idepix-core/src/main/java/org/esa/snap/idepix/core/util/IdepixUtils.java +++ b/idepix-core/src/main/java/org/esa/snap/idepix/core/util/IdepixUtils.java @@ -147,6 +147,15 @@ public static GeoPos getGeoPos(GeoCoding geoCoding, int x, int y) { * @return the azimuth difference [degree] */ public static double computeAzimuthDifference(final double vaa, final double saa) { + final double delta = (720.0 + vaa - saa) % 360.0; + if (delta > 180.0) { + return 360.0 - delta; + } else { + return delta; + } + } + + public static double computeAzimuthDifference1(final double vaa, final double saa) { return MathUtils.RTOD * Math.acos(Math.cos(MathUtils.DTOR * (vaa - saa))); } } diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisMountainShadowOp.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisMountainShadowOp.java index 394b55a6..42758eeb 100644 --- a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisMountainShadowOp.java +++ b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisMountainShadowOp.java @@ -103,19 +103,19 @@ protected void computePixel(int x, int y, Sample[] sourceSamples, WritableSample final GeoPos geoPos = l1bProduct.getSceneGeoCoding().getGeoPos(pixelPos, null); final double saaApparent = IdepixMerisUtils.computeApparentSaa(sza, saa, oza, oaa, geoPos.getLat()); - if (x == 2783 && y == 642) { - System.out.println("x, y = " + x + ", " + y); // small subset, shadow - } - if (x == 2783 && y == 2181) { - System.out.println("x, y = " + x + ", " + y); // large subset, no shadow - } +// if (x == 2783 && y == 642) { +// System.out.println("x, y = " + x + ", " + y); // small subset, shadow +// } +// if (x == 2783 && y == 2181) { +// System.out.println("x, y = " + x + ", " + y); // large subset, no shadow +// } final boolean isMountainShadow = isMountainShadow(sza, (float) saaApparent, slope, aspect, orientation, mntShadowExtent); - if (isMountainShadow) { - System.out.println("x, y, slope, aspect, orientation = " + - x + ", " + y + ", " + slope + ", " + aspect + ", " + orientation); - } +// if (isMountainShadow) { +// System.out.println("x, y, slope, aspect, orientation = " + +// x + ", " + y + ", " + slope + ", " + aspect + ", " + orientation); +// } targetSamples[MOUNTAIN_SHADOW_FLAG_BAND_INDEX].set(isMountainShadow); } } diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisSlopeAspectOrientationOp.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisSlopeAspectOrientationOp.java index d6974fd1..59d8ddb9 100644 --- a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisSlopeAspectOrientationOp.java +++ b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisSlopeAspectOrientationOp.java @@ -154,9 +154,9 @@ public void computeTileStack(Map targetTiles, Rectangle targetRectan final float vza = viewZenithAngleTile.getSampleFloat(x, y); final float vaa = viewAzimuthAngleTile.getSampleFloat(x, y); final float saa = sunAzimuthAngleTile.getSampleFloat(x, y); - if (x == 2783 && y == 642) { - System.out.println("x, y = " + x + ", " + y); // small subset, shadow - } +// if (x == 2783 && y == 642) { +// System.out.println("x, y = " + x + ", " + y); // small subset, shadow +// } final float[] latitudeDataMacropixel = SlopeAspectOrientationUtils.get3x3MacropixelData(latitudeTile, y, x); final float[] longitudeDataMacropixel = diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisUtils.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisUtils.java index 23241192..f578ada0 100644 --- a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisUtils.java +++ b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisUtils.java @@ -97,24 +97,23 @@ static Product computeCloudTopPressureProduct(Product sourceProduct) { } static double computeApparentSaa(double sza, double saa, double oza, double oaa, double lat) { - final double szaRad = sza * MathUtils.DTOR; - final double ozaRad = oza * MathUtils.DTOR; - - double deltaPhi; - if (oaa < 0.0) { - deltaPhi = 360.0 - Math.abs(oaa) - saa; - } else { - deltaPhi = saa - oaa; - } - final double deltaPhiRad = deltaPhi * MathUtils.DTOR; - final double numerator = Math.tan(szaRad) - Math.tan(ozaRad) * Math.cos(deltaPhiRad); - final double denominator = Math.sqrt(Math.tan(ozaRad) * Math.tan(ozaRad) + Math.tan(szaRad) * Math.tan(szaRad) - - 2.0 * Math.tan(szaRad) * Math.tan(ozaRad) * Math.cos(deltaPhiRad)); - +// final double deltaPhi; +// if (oaa < 0.0) { +// deltaPhi = 360.0 - Math.abs(oaa) - saa; +// } else { +// deltaPhi = saa - oaa; +// } +// final double cosDeltaPhi = Math.cos(deltaPhi * MathUtils.DTOR); + final double tanSza = Math.tan(sza * MathUtils.DTOR); + final double tanOza = Math.tan(oza * MathUtils.DTOR); + final double cosDeltaPhi = Math.cos((saa - oaa) * MathUtils.DTOR); + final double numerator = tanSza - tanOza * cosDeltaPhi; + final double denominator = Math.sqrt(tanOza * tanOza + tanSza * tanSza - + 2.0 * tanSza * tanOza * cosDeltaPhi); double delta = Math.acos(numerator / denominator); -// Sun in the North (Southern hemisphere), change sign! + // Sun in the North (Southern hemisphere), change sign! if (saa > 270. || saa < 90){ - delta = -1.0 * delta; + delta = -delta; } if (oaa < 0.0) { return saa - delta * MathUtils.RTOD; diff --git a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisWaterClassificationOp.java b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisWaterClassificationOp.java index 94aaa25c..8c82ba0a 100644 --- a/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisWaterClassificationOp.java +++ b/idepix-meris/src/main/java/org/esa/snap/idepix/meris/IdepixMerisWaterClassificationOp.java @@ -333,9 +333,27 @@ private double computeChiW(int x, int y, Tile winduTile, Tile windvTile, Tile sa return MathUtils.RTOD * (Math.acos(Math.cos(arg))); } + static double computeChiW1(double windU, double windV, double saa) { + final double phiw = azimuth(windU, windV); + /* and "scattering" angle */ + final double arg = MathUtils.DTOR * (saa - phiw); + return MathUtils.RTOD * (Math.acos(Math.cos(arg))); + } + + static double computeChiW2(double windU, double windV, double saa) { + final double phiw = MathUtils.RTOD * Math.atan2(windU, windV); + final double delta = (720.0 + saa - phiw) % 360.0; + if (delta > 180.0) { + return 360.0 - delta; + } else { + return delta; + } + } + private double computeRhoGlint(int x, int y, Tile winduTile, Tile windvTile, Tile szaTile, Tile vzaTile, Tile saaTile, Tile vaaTile) { - final double chiw = computeChiW(x, y, winduTile, windvTile, saaTile); + //final double chiw = computeChiW(x, y, winduTile, windvTile, saaTile); + final double chiw = computeChiW2(winduTile.getSampleFloat(x, y), windvTile.getSampleFloat(x, y), saaTile.getSampleFloat(x, y)); final float vaa = vaaTile.getSampleFloat(x, y); final float saa = saaTile.getSampleFloat(x, y); final double deltaAzimuth = (float) IdepixUtils.computeAzimuthDifference(vaa, saa); @@ -390,7 +408,7 @@ private GeoPos getGeoPos(int x, int y) { return geoPos; } - private double azimuth(double x, double y) { + static double azimuth1(double x, double y) { if (y > 0.0) { // DPM #2.6.5.1.1-1 return (MathUtils.RTOD * Math.atan(x / y)); @@ -402,6 +420,9 @@ private double azimuth(double x, double y) { return (x >= 0.0 ? 90.0 : 270.0); } } + static double azimuth(double y, double x) { + return MathUtils.RTOD * Math.atan2(y, x); + } public static class Spi extends OperatorSpi { public Spi() { diff --git a/idepix-meris/src/test/java/org/esa/snap/idepix/meris/IdepixMerisWaterClassificationOpTest.java b/idepix-meris/src/test/java/org/esa/snap/idepix/meris/IdepixMerisWaterClassificationOpTest.java new file mode 100644 index 00000000..dc141db8 --- /dev/null +++ b/idepix-meris/src/test/java/org/esa/snap/idepix/meris/IdepixMerisWaterClassificationOpTest.java @@ -0,0 +1,63 @@ +package org.esa.snap.idepix.meris; + +import junit.framework.TestCase; +import org.esa.snap.core.util.math.MathUtils; +import org.esa.snap.idepix.core.util.IdepixUtils; + +/** + * TODO add API doc + * + * @author Martin Boettcher + */ +public class IdepixMerisWaterClassificationOpTest extends TestCase { + public void testAtan() { + double ator = Math.PI / 180.0; + for (double y = -10.0; y <= 10.0; y += 1.0) { + for (double x = -10.0; y <= 10.0; y += 1.0) { + double v1 = IdepixMerisWaterClassificationOp.azimuth1(x * ator, y * ator); + double v2 = IdepixMerisWaterClassificationOp.azimuth(x * ator, y * ator); + assertEquals(x+","+y, v1, v2, 1.0e-5); + } + } + } + + public void testChiw() { + double ator = Math.PI / 180.0; + for (double u = -180.0; u <= 180.0; u += 45.0) { + for (double v = -180.0; v <= 180.0; v += 45.0) { + for (double s = -180.0; s <= 180.0; s += 15.0) { + double w1 = IdepixMerisWaterClassificationOp.computeChiW1(u * ator, v * ator, s); + double w2 = IdepixMerisWaterClassificationOp.computeChiW2(u * ator, v * ator, s); + assertEquals(u + "," + v + "," + s, w1, w2, 1.0e-5); + } + } + } + } + + public void testCos() { + for (double oaa = -180.0; oaa <= 360.0; oaa += 45.0) { + for (double saa = -180.0; saa <= 360.0; saa += 45.0) { + final double deltaPhi; + if (oaa < 0.0) { + deltaPhi = 360.0 - Math.abs(oaa) - saa; + } else { + deltaPhi = saa - oaa; + } + double v1 = Math.cos(MathUtils.DTOR * deltaPhi); + double v2 = Math.cos(MathUtils.DTOR * (saa - oaa)); + assertEquals(oaa + "," + saa, v1, v2, 1e-5); + } + } + } + + public void testAzimuthDifference() { + for (double oaa = -180.0; oaa <= 360.0; oaa += 45.0) { + for (double saa = -180.0; saa <= 360.0; saa += 45.0) { + double v1 = IdepixUtils.computeAzimuthDifference1(oaa, saa); + double v2 = IdepixUtils.computeAzimuthDifference(oaa, saa); + assertEquals(oaa + "," + saa, v1, v2, 1e-5); + } + } + } + +} \ No newline at end of file diff --git a/pom.xml b/pom.xml index 49185f57..9513df00 100644 --- a/pom.xml +++ b/pom.xml @@ -29,7 +29,7 @@ UTF-8 - 9.0.5-SNAPSHOT + 9.0.6-SNAPSHOT RELEASE82 2.0.05