import 3d segmentation variant - there may still be problems here bec…

…ause the names may not have the same template
JaneliaSciComp · May 28, 2024 · f5bbbe4 · f5bbbe4
1 parent f51a84e
commit f5bbbe4
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Showing 5 changed files with 15 additions and 13 deletions.
diff --git a/colormipsearch-api/src/main/java/org/janelia/colormipsearch/dto/AbstractNeuronMetadata.java b/colormipsearch-api/src/main/java/org/janelia/colormipsearch/dto/AbstractNeuronMetadata.java
@@ -5,7 +5,6 @@
 import java.util.Map;
 import java.util.Set;
 import java.util.function.BiFunction;
-import java.util.function.Function;
 
 import javax.validation.GroupSequence;
 import javax.validation.constraints.NotBlank;
@@ -48,7 +47,7 @@ public abstract class AbstractNeuronMetadata {
     private String alignmentSpace;
     private String anatomicalArea;
     private Gender gender;
-    private List<String> terms;
+    private List<String> annotations;
     private boolean unpublished;
     // neuronFiles holds S3 files used by the NeuronBridge app
     private final Map<FileType, String> neuronFiles = new HashMap<>();
@@ -156,12 +155,12 @@ public void setGender(Gender gender) {
         this.gender = gender;
     }
 
-    public List<String> getTerms() {
-        return terms;
+    public List<String> getAnnotations() {
+        return annotations;
     }
 
-    public void setTerms(List<String> terms) {
-        this.terms = terms;
+    public void setAnnotations(List<String> annotations) {
+        this.annotations = annotations;
     }
 
     @JsonIgnore

diff --git a/colormipsearch-api/src/main/java/org/janelia/colormipsearch/model/ComputeFileType.java b/colormipsearch-api/src/main/java/org/janelia/colormipsearch/model/ComputeFileType.java
@@ -11,6 +11,7 @@ public enum ComputeFileType {
     GradientImage,
     // RGB 20px Z-gap images
     ZGapImage,
+    Vol3DSegmentation,
     SkeletonSWC,
     SkeletonOBJ;
 

diff --git a/colormipsearch-api/src/main/java/org/janelia/colormipsearch/model/EMNeuronEntity.java b/colormipsearch-api/src/main/java/org/janelia/colormipsearch/model/EMNeuronEntity.java
@@ -1,9 +1,7 @@
 package org.janelia.colormipsearch.model;
 
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 import org.janelia.colormipsearch.dto.EMNeuronMetadata;
 
@@ -62,7 +60,7 @@ public EMNeuronMetadata metadata() {
         n.setPublishedName(getPublishedName());
         n.setNeuronType(getNeuronType());
         n.setNeuronInstance(getNeuronInstance());
-        n.setTerms(getNeuronTerms());
+        n.setAnnotations(getNeuronTerms());
         getComputeFiles().forEach((ft, fd) -> n.setNeuronComputeFile(ft, fd.getFileName()));
         getProcessedTags().forEach(n::putProcessedTags);
         return n;

diff --git a/colormipsearch-api/src/main/java/org/janelia/colormipsearch/model/LMNeuronEntity.java b/colormipsearch-api/src/main/java/org/janelia/colormipsearch/model/LMNeuronEntity.java
@@ -1,9 +1,7 @@
 package org.janelia.colormipsearch.model;
 
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
 
@@ -137,7 +135,7 @@ public LMNeuronMetadata metadata() {
         n.setAnatomicalArea(anatomicalArea);
         n.setGender(gender);
         n.setObjective(objective);
-        n.setTerms(getNeuronTerms());
+        n.setAnnotations(getNeuronTerms());
         getComputeFiles().forEach((ft, fd) -> n.setNeuronComputeFile(ft, fd.getFileName()));
         getProcessedTags().forEach(n::putProcessedTags);
         return n;

diff --git a/colormipsearch-tools/src/main/java/org/janelia/colormipsearch/cmd/CreateCDSDataInputCmd.java b/colormipsearch-tools/src/main/java/org/janelia/colormipsearch/cmd/CreateCDSDataInputCmd.java
@@ -112,6 +112,8 @@ static class CreateColorDepthSearchDataInputArgs extends AbstractCmdArgs {
             put("searchable", ComputeFileType.InputColorDepthImage.name());
             put("searchable_neurons", ComputeFileType.InputColorDepthImage.name());
             put("segmentation", ComputeFileType.InputColorDepthImage.name());
+            put("3d-segmentation", ComputeFileType.Vol3DSegmentation.name());
+            put("vol-segmentation", ComputeFileType.Vol3DSegmentation.name());
             put("fl", ComputeFileType.InputColorDepthImage.name());
             put("grad", ComputeFileType.GradientImage.name());
             put("gradient", ComputeFileType.GradientImage.name());
@@ -363,7 +365,11 @@ private void createColorDepthSearchInputData(Pair<FileData.FileDataType, Map<Str
                     )
                     .peek(cdmip -> populateOtherComputeFilesFromInput(
                             cdmip.getNeuronMetadata(),
-                            EnumSet.of(ComputeFileType.GradientImage, ComputeFileType.ZGapImage),
+                            EnumSet.of(
+                                    ComputeFileType.GradientImage,
+                                    ComputeFileType.ZGapImage,
+                                    ComputeFileType.Vol3DSegmentation
+                            ),
                             libraryVariants,
                             searchableLibraryVariant.variantTypeSuffix))
                     .peek(cdmip -> this.updateTag(cdmip.getNeuronMetadata()))