improve unconnected cross MFOV logging

saalfeldlab · Mar 26, 2024 · b6b5ae8 · b6b5ae8
1 parent 0350acc
commit b6b5ae8
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Showing 3 changed files with 18 additions and 9 deletions.
diff --git a/render-app/src/main/java/org/janelia/alignment/multisem/UnconnectedMFOVPairsForStack.java b/render-app/src/main/java/org/janelia/alignment/multisem/UnconnectedMFOVPairsForStack.java
@@ -89,6 +89,15 @@ public void addUnconnectedPair(final OrderedMFOVPair unconnectedPair) {
         unconnectedMFOVPairs.add(unconnectedPair);
     }
 
+    @Override
+    public String toString() {
+        return "{'renderStackId': '" + renderStackId.toDevString() +
+               "', 'mFOVMontageStackName': '" + mFOVMontageStackName +
+               "', 'matchCollectionId': '" + matchCollectionId.toDevString() +
+               "', 'unconnectedMFOVPairs': [" + unconnectedMFOVPairs +
+               "]}";
+    }
+
     public static List<UnconnectedMFOVPairsForStack> load(final String dataFile)
             throws IOException, IllegalArgumentException {
 

diff --git a/...a-client/src/main/java/org/janelia/render/client/multisem/UnconnectedCrossMFOVClient.java b/...a-client/src/main/java/org/janelia/render/client/multisem/UnconnectedCrossMFOVClient.java
@@ -1,7 +1,6 @@
 package org.janelia.render.client.multisem;
 
 import com.beust.jcommander.ParametersDelegate;
-import com.fasterxml.jackson.core.JsonProcessingException;
 
 import java.io.IOException;
 import java.nio.file.Path;
@@ -14,7 +13,6 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
-import org.janelia.alignment.json.JsonUtils;
 import org.janelia.alignment.match.CanvasMatches;
 import org.janelia.alignment.match.MatchCollectionId;
 import org.janelia.alignment.multisem.LayerMFOV;
@@ -146,10 +144,10 @@ public void logOrStoreUnconnectedMFOVPairs(final List<UnconnectedMFOVPairsForSta
         }
     }
 
-    public static void logUnconnectedMFOVPairs(final List<UnconnectedMFOVPairsForStack> unconnectedMFOVsForAllStacks)
-            throws JsonProcessingException {
-        LOG.info("findUnconnectedMFOVs: unconnected MFOV pairs for all stacks are: \n{}",
-                 JsonUtils.FAST_MAPPER.writeValueAsString(unconnectedMFOVsForAllStacks));
+    public static void logUnconnectedMFOVPairs(final List<UnconnectedMFOVPairsForStack> unconnectedMFOVsForAllStacks) {
+        for (final UnconnectedMFOVPairsForStack unconnectedMFOVPairs : unconnectedMFOVsForAllStacks) {
+            LOG.info("found unconnected MFOV pairs {}", unconnectedMFOVPairs);
+        }
     }
 
     public static void storeUnconnectedMFOVPairs(final List<UnconnectedMFOVPairsForStack> unconnectedMFOVsForAllStacks,

diff --git a/...nt/src/main/java/org/janelia/render/client/spark/multisem/UnconnectedCrossMFOVClient.java b/...nt/src/main/java/org/janelia/render/client/spark/multisem/UnconnectedCrossMFOVClient.java
@@ -26,6 +26,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import static org.janelia.render.client.multisem.UnconnectedCrossMFOVClient.logUnconnectedMFOVPairs;
+
 /**
  * Spark client for patching matches missing from adjacent SFOV tile pairs within the same MFOV and z layer.
  * Core logic is implemented in {@link org.janelia.render.client.multisem.MFOVMontageMatchPatchClient}.
@@ -103,9 +105,9 @@ public void runPipelineStep(final JavaSparkContext sparkContext,
                 findUnconnectedMFOVs(sparkContext, clientParameters);
 
         if (! unconnectedMFOVsForAllStacks.isEmpty()) {
-            final String errorMessage =
-                    "found " + unconnectedMFOVsForAllStacks.size() + " stacks with unconnected MFOVs";
-            LOG.error("runPipelineStep: {}: {}", errorMessage, unconnectedMFOVsForAllStacks);
+            final String errorMessage = "found " + unconnectedMFOVsForAllStacks.size() + " stacks with unconnected MFOVs";
+            LOG.error("runPipelineStep: {}", errorMessage);
+            logUnconnectedMFOVPairs(unconnectedMFOVsForAllStacks);
             throw new IOException(errorMessage);
         } else {
             LOG.info("runPipelineStep: all MFOVs in all stacks are connected");