Made clustering distance configurable.

assemble-tools.sh

@@ -12,7 +12,7 @@ cd $BASE_DIR/build/oceandsl-tools
 mkdir bin
 mkdir lib
 
-for I in allen-upper-limit cmi dar delta fxca maa mktable mop mvis sar relabel restructuring ; do
+for I in allen-upper-limit cmi dar delta fxca maa mktable mop mt mvis sar relabel restructuring ; do
 	unzip $BASE_DIR/tools/$I/build/distributions/$I-$VERSION.zip
 	mv $I-$VERSION/lib/* lib/
 	mv $I-$VERSION/bin/* bin/

tools/mt/build.gradle

@@ -25,11 +25,9 @@ dependencies {
 	implementation 'com.sun.xml.bind:jaxb-impl:2.3.3'
 	implementation 'org.apache.commons:commons-compress:1.20'
 	implementation 'org.apache.commons:commons-lang3:3.12.0'
-    
-    // https://mvnrepository.com/artifact/org.apache.commons/commons-text
-    implementation 'org.apache.commons:commons-text:1.10.0'
-    // https://mvnrepository.com/artifact/com.edwardraff/JSAT
-    implementation 'com.edwardraff:JSAT:0.0.9'
+
+	// https://mvnrepository.com/artifact/org.apache.commons/commons-text
+	implementation 'org.apache.commons:commons-text:1.10.0'
 
 	implementation 'org.csveed:csveed:0.7.4'
 }

tools/mt/src/main/java/org/oceandsl/tools/mt/Settings.java

@@ -40,6 +40,12 @@ public class Settings { // NOPMD data class
             "--sort" }, required = true, converter = SortDescriptorConverter.class, description = "Sort description")
     private SortDescriptor sortDescription;
 
+    @Parameter(names = { "-p", "--min-ptr" }, required = false, description = "Min ptr value for clustering")
+    private Integer minPtr;
+
+    @Parameter(names = { "-d", "--cluster-distance" }, required = true, description = "Min cluster distance")
+    private double clusteringDistance;
+
     public Path getInputTable() {
         return this.inputTable;
     }
@@ -52,4 +58,16 @@ public class Settings { // NOPMD data class
         return this.sortDescription;
     }
 
+    public int getMinPtr() {
+        if (this.minPtr == null) {
+            return 1;
+        } else {
+            return this.minPtr;
+        }
+    }
+
+    public double getClusteringDistance() {
+        return this.clusteringDistance;
+    }
+
 }

tools/mt/src/main/java/org/oceandsl/tools/mt/TeetimeConfiguration.java

@@ -48,10 +48,6 @@ public class TeetimeConfiguration extends Configuration {
 
     public TeetimeConfiguration(final Settings settings) throws IOException {
 
-        final double clusteringDistance = 0.11;
-
-        final int minPtr = 1;
-
         final String inputFileName = settings.getInputTable().getFileName().toString();
 
         final CsvTableReaderProducerStage<String, MoveOperationEntry> csvTableReaderStage = new CsvTableReaderProducerStage<>(
@@ -80,26 +76,25 @@ public class TeetimeConfiguration extends Configuration {
         final MTreeGeneratorStage<OpticsData<MoveOperationEntry>> mTreeGeneratorStage = new MTreeGeneratorStage<>(
                 distanceFunction);
 
-        final OpticsStage<MoveOperationEntry> opticsStage = new OpticsStage<>(clusteringDistance, minPtr);
+        final OpticsStage<MoveOperationEntry> opticsStage = new OpticsStage<>(settings.getClusteringDistance(),
+                settings.getMinPtr());
 
         final ExtractDBScanClustersStage<MoveOperationEntry> clustering = new ExtractDBScanClustersStage<>(
-                clusteringDistance);
+                settings.getClusteringDistance());
 
         final ConstructTableStage constructTableStage = new ConstructTableStage(inputFileName);
 
         final SingleFileTableCsvSink<String, MoveOperationEntry> tableSink = new SingleFileTableCsvSink<>(
                 settings.getOutputTable(), MoveOperationEntry.class, true, TableCsvSink.LF);
 
-        this.connectPorts(csvTableReaderStage.getOutputPort(), sortModelStage.getInputPort());
-        this.connectPorts(sortModelStage.getOutputPort(), converterStage.getInputPort());
+        this.connectPorts(csvTableReaderStage.getOutputPort(), converterStage.getInputPort());
         this.connectPorts(converterStage.getOutputPort(), distributor.getInputPort());
         this.connectPorts(distributor.getNewOutputPort(), mTreeGeneratorStage.getInputPort());
         this.connectPorts(mTreeGeneratorStage.getOutputPort(), opticsStage.getMTreeInputPort());
         this.connectPorts(distributor.getNewOutputPort(), opticsStage.getModelsInputPort());
         this.connectPorts(opticsStage.getOutputPort(), clustering.getInputPort());
         this.connectPorts(clustering.getOutputPort(), constructTableStage.getInputPort());
-        this.connectPorts(constructTableStage.getOutputPort(), tableSink.getInputPort());
-
-        // tableSink.getInputPort());
+        this.connectPorts(constructTableStage.getOutputPort(), sortModelStage.getInputPort());
+        this.connectPorts(sortModelStage.getOutputPort(), tableSink.getInputPort());
     }
 }