update MFOV tools so that they work with wafer 60/61 tile IDs

render-ws-java-client/src/main/java/org/janelia/render/client/multisem/MFOVPositionPair.java

@@ -14,9 +14,9 @@
  *
  *     identifies tile pairs:
  *       ...
- *       groupId "1247.0", p "001_000006_019_20220407_115555.1247.0" and q "001_000006_037_20220407_115555.1247.0"
- *       groupId "1248.0", p "001_000006_019_20220407_172027.1248.0" and q "001_000006_037_20220407_172027.1248.0"
- *       groupId "1249.0", p "001_000006_019_20220407_224819.1249.0" and q "001_000006_037_20220407_224819.1249.0"
+ *       groupId "1.0", p "w60_magc0399_scan004_m0013_s001" and q "w60_magc0399_scan004_m0013_s002"
+ *       groupId "2.0", p "w60_magc0399_scan005_m0013_s001" and q "w60_magc0399_scan005_m0013_s002"
+ *       groupId "3.0", p "w60_magc0399_scan006_m0013_s001" and q "w60_magc0399_scan006_m0013_s002"
  *       ...
  * </pre>
  *
@@ -33,13 +33,13 @@ public MFOVPositionPair(final OrderedCanvasIdPair pair)
 
     /**
      * Converts canvasId based upon section and tile to multi-field-of-view position id based upon slab and mfov_sfov
-     * (e.g. "1247.0", "001_000006_019_20220407_115555.1247.0" to "001", "000006_019").
+     * (e.g. "2.0", "w60_magc0399_scan005_m0013_s001" to "magc0399", "m0013_s001").
      *
      * @return multi-field-of-view position id derived from specified canvasId.
      */
     public static CanvasId toPositionCanvasId(final CanvasId canvasId) {
-        return new CanvasId(canvasId.getId().substring(0, 3),   // slab id
-                            canvasId.getId().substring(5, 14)); // <mfov>_<sfov>
+        return new CanvasId(canvasId.getId().substring(4, 12),  // slab id: magc0399
+                            canvasId.getId().substring(21));  // <mfov>_<sfov>: m0013_s001
     }
 
 }

render-ws-java-client/src/main/java/org/janelia/render/client/multisem/Utilities.java

@@ -36,33 +36,40 @@
 public class Utilities {
 
     /**
-     * @return 001_000006 for 001_000006_019_20220407_115555.1247.0
+     * @return 0399_m0013 for w60_magc0399_scan005_m0013_s001
      */
     public static String getMFOVForTileId(final String tileId) throws IllegalArgumentException {
-        if (tileId.length() < 10) {
+        final int magcIndex = tileId.indexOf("magc");
+        if ((magcIndex < 0) || (tileId.length() < (magcIndex + 18))) {
             throw new IllegalArgumentException("MFOV identifier cannot be derived from tileId " + tileId);
         }
-        return tileId.substring(0, 10);
+        final String magcName = tileId.substring((magcIndex + 4), (magcIndex + 8)); // 0399
+        final String mfovName = tileId.substring((magcIndex + 16), (magcIndex + 22)); // _m0013
+        return magcName + mfovName;
     }
 
     /**
-     * @return 001_000006_019 for 001_000006_019_20220407_115555.1247.0
+     * @return 0399_m0013_s001 for w60_magc0399_scan005_m0013_s001
      */
     public static String getSFOVForTileId(final String tileId) throws IllegalArgumentException {
-        if (tileId.length() < 14) {
+        final int magcIndex = tileId.indexOf("magc");
+        if ((magcIndex < 0) || (tileId.length() < (magcIndex + 27))) {
             throw new IllegalArgumentException("SFOV identifier cannot be derived from tileId " + tileId);
         }
-        return tileId.substring(0, 14);
+        final String magcName = tileId.substring((magcIndex + 4), (magcIndex + 8)); // 0399
+        final String mfovSfovName = tileId.substring((magcIndex + 16), (magcIndex + 27)); // _m0013_s001
+        return magcName + mfovSfovName;
     }
 
     /**
-     * @return 019 for 001_000006_019_20220407_115555.1247.0
+     * @return 001 for w60_magc0399_scan005_m0013_s001
      */
     public static String getSFOVIndexForTileId(final String tileId) throws IllegalArgumentException {
-        if (tileId.length() < 14) {
+        final int scanIndex = tileId.indexOf("scan");
+        if ((scanIndex < 0) || (tileId.length() < (scanIndex + 18))) {
             throw new IllegalArgumentException("SFOV index cannot be derived from tileId " + tileId);
         }
-        return tileId.substring(11, 14);
+        return tileId.substring(scanIndex + 15);
     }
 
     /**

render-ws-java-client/src/main/java/org/janelia/render/client/parameter/MFOVMontageMatchPatchParameters.java

@@ -199,7 +199,7 @@ private void validateAndSetupDerivedValues()
             qTileIdPrefixForRun = getTileIdPrefixForRun(qTileId);
             pTileIdPrefixForRun = multiFieldOfViewId;
         } else if ((multiFieldOfViewId == null) || (multiFieldOfViewId.length() != 10)) {
-            throw new IllegalArgumentException("--mfov should be a 10 character value (e.g. 001_000006)");
+            throw new IllegalArgumentException("--mfov should be a 10 character value (e.g. 0399_m0013)");
         } else {
             pTileIdPrefixForRun = multiFieldOfViewId;
             qTileIdPrefixForRun = multiFieldOfViewId;

render-ws-java-client/src/test/java/org/janelia/render/client/multisem/MFOVMontageMatchPatchClientTest.java

@@ -18,18 +18,18 @@ public void testParameterParsing() throws Exception {
     public static void main(final String[] args) {
 
         final String[] effectiveArgs = (args != null) && (args.length > 0) ? args : new String[] {
-                "--baseDataUrl", "http://renderer-dev.int.janelia.org:8080/render-ws/v1",
-                "--owner", "hess_wafer_53",
-                "--project", "cut_000_to_009",
-                "--stack", "c001_s145_v01",
+                "--baseDataUrl", "http://10.40.3.113:8080/render-ws/v1",
+                "--owner", "trautmane",
+                "--project", "w60_serial_290_to_299",
+                "--stack", "w60_s296_r00_d00",
                 "--xyNeighborFactor", "0.6", // for tiles completely within mFov
                 "--sameLayerDerivedMatchWeight", "0.15",
                 "--crossLayerDerivedMatchWeight", "0.1",
 //                "--pTileId", "145_000010_001_20220618_040953.80.0",
 //                "--qTileId", "145_000010_002_20220618_040953.80.0",
 
-                "--matchCollection", "c001_s145_v01_match",
-                "--matchStorageCollection", "c001_s145_v01_match_try3",
+                "--matchCollection", "w60_s296_r00_d00_match",
+                "--matchStorageCollection", "w60_s296_r00_d00_match_test",
 
 
         //"--mfov", "001_000003",

render-ws-java-client/src/test/java/org/janelia/render/client/multisem/MFOVPositionPairTest.java

@@ -0,0 +1,25 @@
+package org.janelia.render.client.multisem;
+
+import org.janelia.alignment.match.CanvasId;
+import org.janelia.alignment.match.MontageRelativePosition;
+import org.junit.Assert;
+import org.junit.Test;
+
+/**
+ * Tests the {@link MFOVPositionPair} class.
+ *
+ * @author Eric Trautman
+ */
+public class MFOVPositionPairTest {
+
+    @Test
+    public void testToPositionCanvasId() {
+        final CanvasId tilePairId = new CanvasId("1.0",
+                                                 "w60_magc0399_scan004_m0013_s001",
+                                                 MontageRelativePosition.LEFT);
+        final CanvasId positionPairId = MFOVPositionPair.toPositionCanvasId(tilePairId);
+        Assert.assertEquals("invalid canvas group id", "magc0399", positionPairId.getGroupId());
+        Assert.assertEquals("invalid canvas id", "m0013_s001", positionPairId.getId());
+    }
+
+}

render-ws-java-client/src/test/java/org/janelia/render/client/multisem/UnconnectedCrossMFOVClientTest.java

@@ -18,12 +18,12 @@ public void testParameterParsing() throws Exception {
     public static void main(final String[] args) {
 
         final String[] effectiveArgs = (args != null) && (args.length > 0) ? args : new String[] {
-                "--baseDataUrl", "http://renderer-dev.int.janelia.org:8080/render-ws/v1",
-                "--owner", "hess_wafer_53",
-                "--project", "cut_000_to_009",
-                "--stack", "c001_s145_v01",
-                "--minPairsForConnection", "6",
-                "--unconnectedMFOVPairsDirectory", "/Users/trautmane/Desktop/mfov",
+                "--baseDataUrl", "http://10.40.3.113:8080/render-ws/v1",
+                "--owner", "trautmane",
+                "--project", "w60_serial_290_to_299",
+                "--stack", "w60_s296_r00_d00",
+                "--minPairsForConnection", "2",
+                "--unconnectedMFOVPairsDirectory", "/Users/trautmane/Desktop/mfov_2",
                 "--montageStackSuffix", "_mfov_montage"
         };
 

render-ws-java-client/src/test/java/org/janelia/render/client/multisem/UtilitiesTest.java

@@ -0,0 +1,24 @@
+package org.janelia.render.client.multisem;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+/**
+ * Tests the {@link Utilities} class.
+ *
+ * @author Eric Trautman
+ */
+public class UtilitiesTest {
+
+    @Test
+    public void testTileIdParsers() {
+        final String tileId = "w60_magc0399_scan005_m0013_s001";
+        Assert.assertEquals("invalid MFOVForTileId",
+                            "0399_m0013", Utilities.getMFOVForTileId(tileId));
+        Assert.assertEquals("invalid SFOVForTileId",
+                            "0399_m0013_s001", Utilities.getSFOVForTileId(tileId));
+        Assert.assertEquals("invalid SFOVIndexForTileId",
+                            "001", Utilities.getSFOVIndexForTileId(tileId));
+    }
+
+}