adjusted SWC export to be compliant with new specification

JaneliaSciComp · Nov 14, 2024 · 93c1f15 · 93c1f15
1 parent 6f2d8b2
commit 93c1f15
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Showing 4 changed files with 24 additions and 17 deletions.
diff --git a/...ommonGUI/src/main/resources/org/janelia/workstation/common/release_notes/curr_release.txt b/...ommonGUI/src/main/resources/org/janelia/workstation/common/release_notes/curr_release.txt
@@ -1,6 +1,4 @@
-// 9.20.1
+// 9.21
 
 Horta
-* Added "deeplink" functionality, that allows the creation of a positional cross-sample bookmark in Horta3D
-* Added protections for Null Zarr Actors in Horta3D
-* Removed stable branch to simplify deployment
+* Adjusted SWC export to be compliant with new specification
diff --git a/...mmonGUI/src/main/resources/org/janelia/workstation/common/release_notes/prev_releases.txt b/...mmonGUI/src/main/resources/org/janelia/workstation/common/release_notes/prev_releases.txt
@@ -1,3 +1,10 @@
+// 9.20.1
+
+Horta
+* Added "deeplink" functionality, that allows the creation of a positional cross-sample bookmark in Horta3D
+* Added protections for Null Zarr Actors in Horta3D
+* Removed stable branch to simplify deployment
+
 // 9.19.1
 
 Horta

diff --git a/modules/Viewer3D/src/main/java/org/janelia/workstation/swc/SWCDataConverter.java b/modules/Viewer3D/src/main/java/org/janelia/workstation/swc/SWCDataConverter.java
@@ -367,17 +367,12 @@ private List<SWCNode> nodesFromSubtrees(TmNeuronMetadata neuron, double xcenter,
     }
 
     private static SWCNode.SegmentType getSegmentType(TmGeoAnnotation ann) {
-        SWCNode.SegmentType segmentType;
-        // only marking "fork" and "end, as that's
-        //  all we can surmise from geometry
-        if (ann.getChildIds().size() == 0) {
-            segmentType = SWCNode.SegmentType.end_point;
-        } else if (ann.getChildIds().size() > 1) {
-            segmentType = SWCNode.SegmentType.fork_point;
-        } else {
-            segmentType = SWCNode.SegmentType.undefined;
-        }
-        return segmentType;
+        // historical note: before the spec linked at top existed, we marked
+        //  branches and endpoints as type 5 and 6; we currently
+        //  do not classify nodes at all, but I'm leaving this method here in
+        //  case we decide to add that capability back in the future
+
+        return SWCNode.SegmentType.undefined;
     }
 
     private double[] calcDefaultCenterOfMass(double[] rtnVal) {

diff --git a/modules/Viewer3D/src/main/java/org/janelia/workstation/swc/SWCNode.java b/modules/Viewer3D/src/main/java/org/janelia/workstation/swc/SWCNode.java
@@ -6,14 +6,21 @@
 /**
  * used by the SWCData class to hold each point in the neuron
  *
- * see http://research.mssm.edu/cnic/swc.html; node holds info
+ * see https://swc-specification.readthedocs.io/en/latest/; node holds info
  * from one line in SWC file
  */
 public class SWCNode {
 
     private static final Map<Integer,SegmentType> decodeToSegment = new HashMap<>();
     public static enum SegmentType {
-        undefined(0), soma(1), axon(2), dendrite(3), apical_dendrite(4), fork_point(5), end_point(6), custom(7);
+        undefined(0),
+        soma(1),
+        axon(2),
+        basal_dendrite(3),
+        apical_dendrite(4),
+        custom(5),
+        unspecified_neurite(6),
+        glia_process(7);
 
         private int decodeNum;
         public static SegmentType getSegmentType( String typeName ) {