add excludePairsWithTileIdPattern parameter to match copy clients

saalfeldlab · Apr 30, 2024 · be048a7 · be048a7
1 parent 50571c9
commit be048a7
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Showing 2 changed files with 28 additions and 4 deletions.
diff --git a/render-ws-java-client/src/main/java/org/janelia/render/client/CopyMatchClient.java b/render-ws-java-client/src/main/java/org/janelia/render/client/CopyMatchClient.java
@@ -4,6 +4,7 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.regex.Pattern;
 
 import org.janelia.alignment.match.CanvasMatches;
 import org.janelia.alignment.match.MatchAggregator;
@@ -57,7 +58,7 @@ private void copyMatches(final Parameters parameters)
         final RenderDataClient sourceMatchClient = parameters.matchClient.getDataClient();
         final RenderDataClient targetMatchClient = parameters.matchCopy.buildTargetMatchClient(sourceMatchClient);
         final List<String> pGroupIds;
-        if ((parameters.matchCopy.pGroupIds == null) || (parameters.matchCopy.pGroupIds.size() == 0)) {
+        if ((parameters.matchCopy.pGroupIds == null) || parameters.matchCopy.pGroupIds.isEmpty()) {
             pGroupIds = sourceMatchClient.getMatchPGroupIds();
         } else {
             pGroupIds = parameters.matchCopy.pGroupIds;
@@ -73,15 +74,31 @@ public static void copyMatches(final RenderDataClient sourceMatchClient,
                                    final String pGroupId,
                                    final MatchCopyParameters matchCopy) throws Exception {
 
-        final List<CanvasMatches> groupMatches =
-                sourceMatchClient.getMatchesWithPGroupId(pGroupId, false);
+        List<CanvasMatches> groupMatches = sourceMatchClient.getMatchesWithPGroupId(pGroupId, false);
 
-        if (groupMatches.size() > 0) {
+        if (! groupMatches.isEmpty()) {
 
             if (matchCopy.removeExisting) {
                 targetMatchClient.deleteMatchesWithPGroupId(pGroupId);
             }
 
+            if (matchCopy.excludePairsWithTileIdPattern != null) {
+                final Pattern excludePattern = Pattern.compile(matchCopy.excludePairsWithTileIdPattern);
+                final List<CanvasMatches> matchesToKeep = new ArrayList<>(groupMatches.size());
+                final long originalPairCount = groupMatches.size();
+                for (final CanvasMatches match : groupMatches) {
+                    final String pTileId = match.getpId();
+                    final String qTileId = match.getqId();
+                    if (! excludePattern.matcher(pTileId).matches() && ! excludePattern.matcher(qTileId).matches()) {
+                        matchesToKeep.add(match);
+                    }
+                }
+                groupMatches = matchesToKeep;
+
+                LOG.info("copyMatches: reduced {} to {} pairs that do not include a tileId with the pattern {}",
+                         originalPairCount, groupMatches.size(), matchCopy.excludePairsWithTileIdPattern);
+            }
+
             if (matchCopy.isAggregationRequested()) {
                 final long originalMatchCount = countMatches(groupMatches);
                 aggregateMatches(groupMatches, matchCopy);

diff --git a/...ws-java-client/src/main/java/org/janelia/render/client/parameter/MatchCopyParameters.java b/...ws-java-client/src/main/java/org/janelia/render/client/parameter/MatchCopyParameters.java
@@ -68,6 +68,13 @@ public class MatchCopyParameters
             description = "Pixel radius for cross layer match filtering")
     public Double matchAggregationRadiusCross;
 
+    @Parameter(
+            names = "--excludePairsWithTileIdPattern",
+            description = "Do not copy match pairs that include at least one tile with an ID matching this pattern, " +
+                          "e.g. .*_0000(01|02|03|04|07|08|12|13|16|17|18|19)_.*",
+            variableArity = true)
+    public String excludePairsWithTileIdPattern;
+
     public MatchCopyParameters() {
     }