marked all _v2 classes as deprecated

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/FileType.java

@@ -1,5 +1,9 @@
 package org.janelia.colormipsearch.api_v2;
 
+/**
+ * @see org.janelia.colormipsearch.model.FileType
+ */
+@Deprecated
 public enum FileType {
     SignalMip("_1_raw.png"),
     SignalMipMasked("_2_masked_raw.png"),

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/Results.java

@@ -3,6 +3,7 @@
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
+@Deprecated
 public class Results<T> {
     @JsonProperty
     public final T results;

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/Utils.java

@@ -11,6 +11,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@Deprecated
 public class Utils {
     private static final Logger LOG = LoggerFactory.getLogger(Utils.class);
 

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdmips/AbstractMetadata.java

@@ -19,6 +19,7 @@
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 
+@Deprecated
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public abstract class AbstractMetadata implements Serializable {
     private String id;

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdmips/MIPIdentifier.java

@@ -3,6 +3,7 @@
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 
+@Deprecated
 public class MIPIdentifier {
     private final String id;
     private final String publishedName;

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdmips/MIPImage.java

@@ -5,6 +5,10 @@
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.janelia.colormipsearch.imageprocessing.ImageArray;
 
+/**
+ * @see org.janelia.colormipsearch.mips.NeuronMIP
+ */
+@Deprecated
 public class MIPImage implements Serializable {
     private final MIPMetadata mipInfo;
     private final ImageArray<?> imageArray;

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdmips/MIPMetadata.java

@@ -1,5 +1,6 @@
 package org.janelia.colormipsearch.api_v2.cdmips;
 
+@Deprecated
 public class MIPMetadata extends AbstractMetadata {
 
     public MIPMetadata variantAsMIP(String variant) {

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdmips/MIPsUtils.java

@@ -33,6 +33,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+/**
+ * @see org.janelia.colormipsearch.mips.NeuronMIPUtils
+ */
+@Deprecated
 public class MIPsUtils {
 
     private static final Logger LOG = LoggerFactory.getLogger(MIPsUtils.class);

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/AbstractColorDepthSearchAlgorithm.java

@@ -6,11 +6,14 @@
 import java.util.function.BiPredicate;
 
 import org.janelia.colormipsearch.imageprocessing.ImageArray;
+import org.janelia.colormipsearch.imageprocessing.ImageRegionDefinition;
 
 /**
  * Common methods that can be used by various ColorDepthQuerySearchAlgorithm implementations.
+ * @see org.janelia.colormipsearch.cds.AbstractColorDepthSearchAlgorithm
  * @param <S> score type
  */
+@Deprecated
 public abstract class AbstractColorDepthSearchAlgorithm<S extends ColorDepthMatchScore> implements ColorDepthSearchAlgorithm<S> {
 
     private static class PixelPositions implements Serializable {
@@ -41,14 +44,14 @@ int size() {
     final ImageArray<?> negQueryImage;
     final PixelPositions queryPositions;
     final PixelPositions negQueryPositions;
-    final ImageRegionGenerator ignoredRegionsProvider;
+    final ImageRegionDefinition ignoredRegionsProvider;
     final int targetThreshold;
     final double zTolerance;
 
     protected AbstractColorDepthSearchAlgorithm(ImageArray<?> queryImage, int queryThreshold,
                                                 ImageArray<?> negQueryImage, int negQueryThreshold,
                                                 int targetThreshold, double zTolerance,
-                                                ImageRegionGenerator ignoredRegionsProvider) {
+                                                ImageRegionDefinition ignoredRegionsProvider) {
         this.queryImage = queryImage;
         this.negQueryImage = negQueryImage;
         this.targetThreshold = targetThreshold;

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/CDSMatches.java

@@ -13,6 +13,7 @@
 import org.janelia.colormipsearch.api_v2.Results;
 import org.janelia.colormipsearch.api_v2.cdmips.MIPIdentifier;
 
+@Deprecated
 public class CDSMatches extends Results<List<ColorMIPSearchMatchMetadata>> {
 
     public static CDSMatches EMPTY = new CDSMatches(

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/ColorDepthMatchScore.java

@@ -2,6 +2,10 @@
 
 import java.io.Serializable;
 
+/**
+ * @see org.janelia.colormipsearch.cds.ColorDepthMatchScore
+ */
+@Deprecated
 public interface ColorDepthMatchScore extends Serializable {
     /**
      * Return the score value

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/ColorDepthSearchAlgorithm.java

@@ -12,7 +12,9 @@
 /**
  * ColorMIPMaskCompare encapsulates a query image and it provides a method to search
  * the enclosed query in other target images.
+ * @see org.janelia.colormipsearch.cds.ColorDepthSearchAlgorithm
  */
+@Deprecated
 public interface ColorDepthSearchAlgorithm<S extends ColorDepthMatchScore> extends Serializable {
 
     /**

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/ColorDepthSearchAlgorithmProvider.java

@@ -6,9 +6,11 @@
 
 /**
  * Creator of a ColorMIPQuerySearch for a given mask that generates a certain score type.
+ * @see org.janelia.colormipsearch.cds.ColorDepthSearchAlgorithmProvider
  *
  * @param <S> color depth match score type
  */
+@Deprecated
 public interface ColorDepthSearchAlgorithmProvider<S extends ColorDepthMatchScore> extends Serializable {
     /**
      * @return default color depth search parameters.

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/ColorDepthSearchAlgorithmProviderFactory.java

@@ -3,6 +3,7 @@
 import org.janelia.colormipsearch.imageprocessing.ColorTransformation;
 import org.janelia.colormipsearch.imageprocessing.ImageArray;
 import org.janelia.colormipsearch.imageprocessing.ImageProcessing;
+import org.janelia.colormipsearch.imageprocessing.ImageRegionDefinition;
 import org.janelia.colormipsearch.imageprocessing.ImageTransformation;
 import org.janelia.colormipsearch.imageprocessing.LImage;
 import org.janelia.colormipsearch.imageprocessing.LImageUtils;
@@ -11,7 +12,9 @@
 
 /**
  * Factory for a color depth search comparator.
+ * @see org.janelia.colormipsearch.cds.ColorDepthSearchAlgorithmProviderFactory
  */
+@Deprecated
 public class ColorDepthSearchAlgorithmProviderFactory {
 
     private static final Logger LOG = LoggerFactory.getLogger(ColorDepthSearchAlgorithmProviderFactory.class);
@@ -30,7 +33,7 @@ public static ColorDepthSearchAlgorithmProvider<ColorMIPMatchScore> createPixMat
             int targetThreshold,
             double pixColorFluctuation,
             int xyShift,
-            ImageRegionGenerator ignoredRegionsProvider) {
+            ImageRegionDefinition ignoredRegionsProvider) {
         LOG.info("Create mask comparator with mirrorQuery={}, dataThreshold={}, pixColorFluctuation={}, xyShift={}",
                 mirrorMask, targetThreshold, pixColorFluctuation, xyShift);
         return new ColorDepthSearchAlgorithmProvider<ColorMIPMatchScore>() {
@@ -71,7 +74,7 @@ public static ColorDepthSearchAlgorithmProvider<NegativeColorDepthMatchScore> cr
             int negativeRadius,
             int borderSize,
             ImageArray<?> roiMaskImageArray,
-            ImageRegionGenerator ignoredRegionsProvider) {
+            ImageRegionDefinition ignoredRegionsProvider) {
         if (negativeRadius <= 0) {
             throw new IllegalArgumentException("The value for negative radius must be a positive integer - current value is " + negativeRadius);
         }
@@ -135,7 +138,7 @@ public static ColorDepthSearchAlgorithmProvider<ColorMIPMatchScore> createPixMat
             int xyShift,
             int negativeRadius,
             ImageArray<?> roiMaskImageArray,
-            ImageRegionGenerator ignoredRegionsProvider) {
+            ImageRegionDefinition ignoredRegionsProvider) {
         if (negativeRadius <= 0) {
             throw new IllegalArgumentException("The value for negative radius must be a positive integer - current value is " + negativeRadius);
         }

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/ColorDepthSearchParams.java

@@ -6,6 +6,10 @@
 
 import org.apache.commons.lang3.StringUtils;
 
+/**
+ * @see org.janelia.colormipsearch.cds.ColorDepthSearchParams
+ */
+@Deprecated
 public class ColorDepthSearchParams implements Serializable {
     private final Map<String, Object> params = new LinkedHashMap<>();
 

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/ColorMIPMatchScore.java

@@ -4,7 +4,9 @@
 
 /**
  * ColorMIPCompareOutput represents the color depth match summary result.
+ * @see org.janelia.colormipsearch.cds.PixelMatchScore
  */
+@Deprecated
 public class ColorMIPMatchScore implements ColorDepthMatchScore {
     public static ColorMIPMatchScore NO_MATCH = new ColorMIPMatchScore(0, 0, false, null);
 

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/ColorMIPSearch.java

@@ -8,7 +8,9 @@
 
 /**
  * Creates a color depth search for a given mask.
+ * @see org.janelia.colormipsearch.cds.ColorMIPSearch
  */
+@Deprecated
 public class ColorMIPSearch implements Serializable {
 
     private final ColorDepthSearchAlgorithmProvider<ColorMIPMatchScore> cdsAlgorithmProvider;

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/ColorMIPSearchMatchMetadata.java

@@ -12,6 +12,7 @@
 import org.janelia.colormipsearch.api_v2.cdmips.AbstractMetadata;
 import org.janelia.colormipsearch.api_v2.cdmips.MIPMetadata;
 
+@Deprecated
 @JsonClassDescription("Color Depth Search Match")
 public class ColorMIPSearchMatchMetadata extends AbstractMetadata {
 

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/ColorMIPSearchResult.java

@@ -12,6 +12,7 @@
  *
  * @author <a href="mailto:[email protected]">Konrad Rokicki</a>
  */
+@Deprecated
 public class ColorMIPSearchResult implements Serializable {
 
     private final MIPMetadata maskMIP;

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/ColorMIPSearchResultUtils.java

@@ -28,6 +28,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@Deprecated
 public class ColorMIPSearchResultUtils {
     private static final Logger LOG = LoggerFactory.getLogger(ColorMIPSearchResultUtils.class);
 

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/GradientAreaGapUtils.java

@@ -2,7 +2,10 @@
 
 /**
  * Utils for calculating gradient area gap scores.
+ * This utility is only used in the commonad line tools so this clqss
+ * has been moved actually in the colormipsearch-tools module.
  */
+@Deprecated
 public class GradientAreaGapUtils {
 
     public static final int HIGH_EXPRESSION_FACTOR = 2;

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/GradientBasedNegativeScoreColorDepthSearchAlgorithm.java

@@ -20,7 +20,9 @@
 
 /**
  * This calculates the gradient area gap between an encapsulated EM mask and an LM (segmented) image.
+ * @see org.janelia.colormipsearch.cds.ShapeMatchColorDepthSearchAlgorithm
  */
+@Deprecated
 public class GradientBasedNegativeScoreColorDepthSearchAlgorithm implements ColorDepthSearchAlgorithm<NegativeColorDepthMatchScore> {
 
     private static final Logger LOG = LoggerFactory.getLogger(GradientBasedNegativeScoreColorDepthSearchAlgorithm.class);

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/NegativeColorDepthMatchScore.java

@@ -2,6 +2,10 @@
 
 import org.apache.commons.lang3.builder.ToStringBuilder;
 
+/**
+ * @see org.janelia.colormipsearch.cds.ShapeMatchScore
+ */
+@Deprecated
 public class NegativeColorDepthMatchScore implements ColorDepthMatchScore {
     private final long gradientAreaGap;
     private final long highExpressionArea;

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/PixelMatchColorDepthSearchAlgorithm.java

@@ -8,13 +8,16 @@
 import javax.annotation.Nonnull;
 
 import org.janelia.colormipsearch.imageprocessing.ImageArray;
+import org.janelia.colormipsearch.imageprocessing.ImageRegionDefinition;
 
 /**
  * PixelMatchColorDepthQuerySearchAlgorithm - implements the color depth mip comparison
  * using internal arrays containg the positions from the mask that are above the mask threshold
  * and the positions after applying the specified x-y shift and mirroring transformations.
  * The mask pixels are compared against the target pixels tht
+ * @see org.janelia.colormipsearch.cds.PixelMatchColorDepthSearchAlgorithm
  */
+@Deprecated
 public class PixelMatchColorDepthSearchAlgorithm extends AbstractColorDepthSearchAlgorithm<ColorMIPMatchScore> {
 
     private final int[][] targetMasksList;
@@ -28,7 +31,7 @@ public PixelMatchColorDepthSearchAlgorithm(ImageArray<?> queryImage, int queryTh
                                                ImageArray<?> negQueryImage, int negQueryThreshold,
                                                boolean mirrorNegQuery, int targetThreshold,
                                                double zTolerance, int xyshift,
-                                               ImageRegionGenerator ignoredRegionsProvider) {
+                                               ImageRegionDefinition ignoredRegionsProvider) {
         super(queryImage, queryThreshold, negQueryImage, negQueryThreshold, targetThreshold, zTolerance, ignoredRegionsProvider);
         // shifting
         targetMasksList = generateShiftedMasks(queryPixelPositions(), xyshift, queryImage.getWidth(), queryImage.getHeight());

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/cdsearch/PixelMatchWithNegativeScoreColorDepthSearchAlgorithm.java

@@ -9,6 +9,7 @@
 
 import org.janelia.colormipsearch.imageprocessing.ImageArray;
 
+@Deprecated
 public class PixelMatchWithNegativeScoreColorDepthSearchAlgorithm implements ColorDepthSearchAlgorithm<ColorMIPMatchScore> {
 
     private final Set<String> requiredVariantTypes = new LinkedHashSet<>();

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/pppsearch/AbstractPPPMatch.java

@@ -20,6 +20,7 @@
  * These are the source PPP matches as they are imported from the original matches.
  * This object contains all fields currently read from the original result file.
  */
+@Deprecated
 @JsonInclude(JsonInclude.Include.NON_NULL)
 @JsonAutoDetect(
         fieldVisibility = JsonAutoDetect.Visibility.NONE,

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/pppsearch/EmPPPMatch.java

@@ -9,6 +9,7 @@
  * These are the source PPP matches as they are imported from the original matches.
  * This object contains all fields currently read from the original result file.
  */
+@Deprecated
 @JsonClassDescription("Patch per Pixel Match")
 @JsonInclude(JsonInclude.Include.NON_NULL)
 @JsonPropertyOrder({

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/pppsearch/EmPPPMatches.java

@@ -15,6 +15,7 @@
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.janelia.colormipsearch.api_v2.Results;
 
+@Deprecated
 @JsonInclude(JsonInclude.Include.NON_NULL)
 @JsonPropertyOrder({"maskId", "maskPublishedName", "maskLibraryName", "neuronType", "neuronInstance", "sourceMaskName", "results"})
 public class EmPPPMatches extends Results<List<EmPPPMatch>> {

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/pppsearch/PPPScreenshotType.java

@@ -2,6 +2,7 @@
 
 import org.janelia.colormipsearch.api_v2.FileType;
 
+@Deprecated
 public enum PPPScreenshotType {
     RAW(FileType.SignalMip),
     MASKED_RAW(FileType.SignalMipMasked),

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/pppsearch/PPPUtils.java

@@ -8,6 +8,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@Deprecated
 public class PPPUtils {
     private static final Logger LOG = LoggerFactory.getLogger(PPPUtils.class);
 

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/pppsearch/PublishedEmPPPMatch.java

@@ -8,6 +8,7 @@
  * This is the published PPP match. It is very similar with the source PPP match
  * but without internal fields that we do not to want to expose.
  */
+@Deprecated
 @JsonInclude(JsonInclude.Include.NON_NULL)
 @JsonPropertyOrder({
         "id", "publishedName", "libraryName",

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/pppsearch/RawPPPMatchesReader.java

@@ -21,6 +21,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@Deprecated
 public class RawPPPMatchesReader {
     private static final Logger LOG = LoggerFactory.getLogger(RawPPPMatchesReader.class);
 

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/pppsearch/RawSkeletonMatches.java

@@ -4,6 +4,7 @@
 
 import org.apache.commons.lang3.builder.ToStringBuilder;
 
+@Deprecated
 class RawSkeletonMatches {
     @JsonProperty("skel_ids")
     private String bestSkeletonIds;

colormipsearch-api/src/main/java/org/janelia/colormipsearch/api_v2/pppsearch/SourceSkeletonMatch.java

@@ -7,6 +7,7 @@
 
 import org.apache.commons.lang3.builder.ToStringBuilder;
 
+@Deprecated
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public class SourceSkeletonMatch {
     private String id;