some changes in the gradscore calculation

Author: cgoina

colormipsearch-api/src/main/java/org/janelia/colormipsearch/cds/ColorDepthSearchAlgorithmProviderFactory.java

@@ -113,15 +113,15 @@ public ColorDepthSearchAlgorithm<ShapeMatchScore> createColorDepthSearchAlgorith
                         queryImage.mapi(ImageTransformation.unsafeMaxFilter(60)),
                         queryImage.mapi(ImageTransformation.unsafeMaxFilter(20)),
                         (p1, p2) -> {
-                            return (p2 & 0xFFFFFF) != 0 ? 0xFF000000 : p1;
+                            return (p2 & 0xFFFFFF) != 0 ? 0xFF000000 : ((p1 & 0xFFFFFF) == 0 ? 0 : 1);
                         } // mask pixels from the 60x image if they are present in the 20x image
                 );
                 ShapeMatchColorDepthSearchAlgorithm maskNegativeScoresCalculator = new ShapeMatchColorDepthSearchAlgorithm(
                         queryImage,
                         queryImage.map(ColorTransformation.toGray16WithNoGammaCorrection()).map(ColorTransformation.gray8Or16ToSignal(2)).reduce(),
                         maskForRegionsWithTooMuchExpression.map(ColorTransformation.toGray16WithNoGammaCorrection()).map(ColorTransformation.gray8Or16ToSignal(0)).reduce(),
                         roiMaskImage,
-                        cdsParams.getIntParam("queryThreshold", queryThreshold),
+                        queryThreshold,
                         cdsParams.getBoolParam("mirrorMask", mirrorMask),
                         clearIgnoredRegions
                 );

colormipsearch-api/src/main/java/org/janelia/colormipsearch/cds/GradientAreaGapUtils.java

@@ -228,13 +228,14 @@ public static double calculateNormalizedScore(int pixelMatchScore,
         if (pixelMatchScore == 0 || maxPixelMatch == 0 || shapeScore < 0 || maxShapeScore <= 0) {
             return pixelMatchScore;
         } else {
+            double normalizedPixelScore = (double) pixelMatchScore / maxPixelMatch;
             double normalizedShapeScore = (double)shapeScore / maxShapeScore;
             double boundedShapeScore = Math.min(
                     Math.max(normalizedShapeScore * 2.5, LOW_NORMALIZED_NEGATIVE_SCORE),
                     HIGH_NORMALIZED_NEGATIVE_SCORE
             );
 
-            return (double)pixelMatchScore / (double)maxPixelMatch / boundedShapeScore * 100;
+            return normalizedPixelScore / boundedShapeScore * 100;
         }
     }
 

colormipsearch-api/src/main/java/org/janelia/colormipsearch/imageprocessing/ColorTransformation.java

@@ -150,16 +150,6 @@ static ColorTransformation toBinary8(int threshold) {
         return ColorTransformation.toGray8WithNoGammaCorrection().thenApplyColorTransformation(pv -> ColorTransformation.grayToBinary8(pv, threshold));
     }
 
-    public static ColorTransformation rgbToSignal(int threshold) {
-        return new ColorTransformation(pt -> pt) {
-            @Override
-            public Integer apply(ImageType pt, Integer pv) {
-                int grayPixelValue = ColorTransformation.rgbToGrayNoGammaCorrection(pv, 255);
-                return grayPixelValue > threshold ? 1 : 0;
-            }
-        };
-    }
-
     public static ColorTransformation gray8Or16ToSignal(int threshold) {
         return new ColorTransformation(pt -> pt) {
             @Override

colormipsearch-api/src/main/java/org/janelia/colormipsearch/model/CDMatchEntity.java

@@ -84,7 +84,7 @@ public boolean hasGradScore() {
     }
 
     private boolean has2DShapeScore() {
-        return gradientAreaGap != null && gradientAreaGap >= 0 && highExpressionArea != null && highExpressionArea > 0;
+        return gradientAreaGap != null && gradientAreaGap >= 0 && highExpressionArea != null && highExpressionArea >= 0;
     }
 
     private boolean has3DBidirectionalShapeScore() {

colormipsearch-tools/src/main/java/org/janelia/colormipsearch/cmd/CalculateGradientScoresCmd.java

@@ -99,6 +99,7 @@ static class CalculateGradientScoresArgs extends AbstractGradientScoresArgs {
     /**
      * Generator State is used by Reactor flux to generate new items.
      * Initially I thought I would use it to set up more context but now the only context that we keep is the start time.
+     *
      * @param <E>
      */
     static class GeneratorState<E> {
@@ -235,6 +236,10 @@ private void calculateAllGradientScores() {
     @Nonnull
     private <M extends AbstractNeuronEntity, T extends AbstractNeuronEntity>
     List<CDMatchEntity<M, T>> startAllGradientScores() {
+        LOG.info("Calculate gradient scores using: top {} / {} / {} best lines / best samples per line / best matches per sample, " +
+                        "percentPositivePixels > {}%, negative radius = {}, mask threshold = {}, mirror mask = {}",
+                args.numberOfBestLines, args.numberOfBestSamplesPerLine, args.numberOfBestMatchesPerSample,
+                args.pctPositivePixels, args.negativeRadius, args.maskThreshold, args.mirrorMask);
         ImageRegionDefinition excludedRegions = args.getRegionGeneratorForTextLabels();
         NeuronMatchesReader<CDMatchEntity<M, T>> cdMatchesReader = getCDMatchesReader();
         Collection<String> maskIdsToProcess = cdMatchesReader.listMatchesLocations(
@@ -583,7 +588,7 @@ private <M extends AbstractNeuronEntity, T extends AbstractNeuronEntity> void no
                             (s1, s2) -> new CombinedMatchScore(
                                     Math.max(s1.getPixelMatches(), s2.getPixelMatches()),
                                     Math.max(s1.getGradScore(), s2.getGradScore())));
-            LOG.info("Max scores for {} matches is {}", matchesByMask.getKey(), maxScores);
+            LOG.info("Max scores for {} matches with {} targets is {}", matchesByMask.getKey(), matchesByMask.getItemsCount(), maxScores);
             // update normalized scores for all matches for this mask
             matchesByMask.getItems().forEach(m -> {
                 double normalizedScore = GradientAreaGapUtils.calculateNormalizedScore(

colormipsearch-tools/src/main/java/org/janelia/colormipsearch/cmd/jacsdata/ColorDepthMIP.java

@@ -10,6 +10,7 @@
 
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.janelia.colormipsearch.dto.AbstractNeuronMetadata;
 import org.janelia.colormipsearch.dto.EMNeuronMetadata;
@@ -175,6 +176,7 @@ public String emAnatomicalArea() {
                 ? emBody.emDataSet.anatomicalArea
                 : anatomicalArea;
     }
+
     public String em3DFilename(String prefix, String em3DFile, String ext) {
         if (StringUtils.isBlank(em3DFile)) {
             return null;
@@ -252,7 +254,14 @@ public void updateEMNeuron(EMNeuronMetadata emNeuron, NeuronPublishedURLs neuron
 
         emNeuron.setPublishedName(emBodyId());
         emNeuron.setFullPublishedName(emPublishedName());
-        emNeuron.setAnatomicalArea(emAnatomicalArea());
+        // this is to handle cases where anatomical area is not set as expected
+        // this happens for CNS for example where the anatomical area is set to CNS
+        String anatomicalArea = emAnatomicalArea();
+        if (Strings.CI.equals("brain", anatomicalArea) || Strings.CI.equals("vnc", anatomicalArea)) {
+            emNeuron.setAnatomicalArea(anatomicalArea);
+        } else {
+            emNeuron.setAnatomicalArea(getAnatomicalAreaFromAlignmentSpace(emNeuron.getAlignmentSpace()));
+        }
         emNeuron.setNeuronInstance(neuronInstance);
         emNeuron.setNeuronType(neuronType);
         emNeuron.setGender(Gender.fromVal(emGender()));
@@ -269,6 +278,14 @@ public void updateEMNeuron(EMNeuronMetadata emNeuron, NeuronPublishedURLs neuron
         }
     }
 
+    private String getAnatomicalAreaFromAlignmentSpace(String alignmentSpace) {
+        switch (alignmentSpace) {
+            case "JRC2018_Unisex_20x_HR": return "Brain";
+            case "JRC2018_VNC_Unisex_40x_DS": return "VNC";
+            default: throw new IllegalArgumentException("Invalid alignmentSpace " + alignmentSpace);
+        }
+    }
+
     private String getNeuronURL(NeuronPublishedURLs neuronURLs, String fileType) {
         if (neuronURLs == null) {
             return null;