Merge branch 'development' of https://github.com/cmu-phil/tetrad into…

… remove_other_boss_specs
cmu-phil · Feb 14, 2023 · 28a8b65 · 28a8b65
2 parents cf1b419 + fd96cea
commit 28a8b65
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Showing 7 changed files with 55 additions and 61 deletions.
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/FgesRunner.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/FgesRunner.java
@@ -200,7 +200,7 @@ public void execute() {
             }
         }
 
-        this.fges.setExternalGraph(this.externalGraph);
+        this.fges.setBoundGraph(this.externalGraph);
         this.fges.setKnowledge((Knowledge) getParams().get("knowledge", new Knowledge()));
         this.fges.setVerbose(true);
         Graph graph = this.fges.search();

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/multi/FgesConcatenated.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/multi/FgesConcatenated.java
@@ -75,7 +75,7 @@ public Graph search(List<DataModel> dataModels, Parameters parameters) {
             }
 
             if (initial != null) {
-                search.setExternalGraph(initial);
+                search.setBoundGraph(initial);
             }
 
             return search.search();

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/Fges.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/Fges.java
@@ -3,6 +3,7 @@
 import edu.cmu.tetrad.algcomparison.algorithm.Algorithm;
 import edu.cmu.tetrad.algcomparison.score.ScoreWrapper;
 import edu.cmu.tetrad.algcomparison.utils.HasKnowledge;
+import edu.cmu.tetrad.algcomparison.utils.TakesExternalGraph;
 import edu.cmu.tetrad.algcomparison.utils.UsesScoreWrapper;
 import edu.cmu.tetrad.annotation.AlgType;
 import edu.cmu.tetrad.annotation.Bootstrapping;
@@ -33,14 +34,15 @@
         algoType = AlgType.forbid_latent_common_causes
 )
 @Bootstrapping
-public class Fges implements Algorithm, HasKnowledge, UsesScoreWrapper {
+public class Fges implements Algorithm, HasKnowledge, UsesScoreWrapper, TakesExternalGraph {
 
     static final long serialVersionUID = 23L;
 
     private ScoreWrapper score;
     private Knowledge knowledge = new Knowledge();
 
-    private Graph wxternalGraph = null;
+    private Graph externalGraph = null;
+    private Algorithm algorithm = null;
 
     public Fges() {
 
@@ -63,12 +65,21 @@ public Graph search(DataModel dataModel, Parameters parameters) {
                 knowledge = timeSeries.getKnowledge();
             }
 
+            if (this.algorithm != null) {
+                Graph _graph = this.algorithm.search(dataModel, parameters);
+
+                if (_graph != null) {
+                    this.externalGraph = _graph;
+                }
+            }
+
             Score score = this.score.getScore(dataModel, parameters);
             Graph graph;
 
             edu.cmu.tetrad.search.Fges search
                     = new edu.cmu.tetrad.search.Fges(score);
-            search.setExternalGraph(wxternalGraph);
+//            search.setInitialGraph(externalGraph);
+            search.setBoundGraph(externalGraph);
             search.setKnowledge(this.knowledge);
             search.setVerbose(parameters.getBoolean(Params.VERBOSE));
             search.setMeekVerbose(parameters.getBoolean(Params.MEEK_VERBOSE));
@@ -87,6 +98,9 @@ public Graph search(DataModel dataModel, Parameters parameters) {
             return graph;
         } else {
             Fges fges = new Fges(this.score);
+            if (this.externalGraph != null) {
+                fges.setExternalGraph(this.externalGraph);
+            }
 
             DataSet data = (DataSet) dataModel;
             GeneralResamplingTest search = new GeneralResamplingTest(
@@ -137,7 +151,7 @@ public Knowledge getKnowledge() {
 
     @Override
     public void setKnowledge(Knowledge knowledge) {
-        this.knowledge = new Knowledge((Knowledge) knowledge);
+        this.knowledge = new Knowledge(knowledge);
     }
 
     @Override
@@ -150,7 +164,24 @@ public void setScoreWrapper(ScoreWrapper score) {
         this.score = score;
     }
 
+
+    @Override
+    public Graph getExternalGraph() {
+        return this.externalGraph;
+    }
+
+    @Override
     public void setExternalGraph(Graph externalGraph) {
-        this.wxternalGraph = externalGraph;
+        this.externalGraph = externalGraph;
+    }
+
+    @Override
+    public void setExternalGraph(Algorithm algorithm) {
+        if (algorithm == null) {
+            throw new IllegalArgumentException("This EB algorithm needs both data and a graph source as inputs; it \n"
+                    + "will orient the edges in the input graph using the data.");
+        }
+
+        this.algorithm = algorithm;
     }
 }
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Bridges2.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Bridges2.java
@@ -138,7 +138,7 @@ public Graph search() {
                     g.removeEdge(edge);
                     g.addEdge(reversed);
 
-                    fges.setExternalGraph(g);
+                    fges.setInitialGraph(g);
                     Graph g1 = fges.search();
                     double s1 = fges.getModelScore();
 

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/BridgesOld.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/BridgesOld.java
@@ -66,7 +66,7 @@ public Graph search() {
 
                     meeks.orientImplied(g);
 
-                    ges.setExternalGraph(g);
+                    ges.setInitialGraph(g);
                     Graph g1 = ges.search();
                     double s1 = ges.getModelScore();
 

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Fges.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Fges.java
@@ -89,7 +89,7 @@ public final class Fges implements GraphSearch, GraphScorer {
     /**
      * An initial graph to start from.
      */
-    private Graph externalGraph;
+    private Graph initialGraph;
     /**
      * If non-null, edges not adjacent in this graph will not be added.
      */
@@ -192,8 +192,8 @@ public Graph search() {
             boundGraph = GraphUtils.replaceNodes(boundGraph, getVariables());
         }
 
-        if (externalGraph != null) {
-            graph = new EdgeListGraph(externalGraph);
+        if (initialGraph != null) {
+            graph = new EdgeListGraph(initialGraph);
             graph = GraphUtils.replaceNodes(graph, getVariables());
         }
 
@@ -268,24 +268,24 @@ public LinkedList<ScoredGraph> getTopGraphs() {
     /**
      * Sets the initial graph.
      */
-    public void setExternalGraph(Graph externalGraph) {
-        if (externalGraph == null) {
-            this.externalGraph = null;
+    public void setInitialGraph(Graph initialGraph) {
+        if (initialGraph == null) {
+            this.initialGraph = initialGraph;
             return;
         }
 
-        externalGraph = GraphUtils.replaceNodes(externalGraph, variables);
+        initialGraph = GraphUtils.replaceNodes(initialGraph, variables);
 
         if (verbose) {
-            out.println("External graph variables: " + externalGraph.getNodes());
+            out.println("External graph variables: " + initialGraph.getNodes());
             out.println("Data set variables: " + variables);
         }
 
-        if (!new HashSet<>(externalGraph.getNodes()).equals(new HashSet<>(variables))) {
+        if (!new HashSet<>(initialGraph.getNodes()).equals(new HashSet<>(variables))) {
             throw new IllegalArgumentException("Variables aren't the same.");
         }
 
-        this.externalGraph = externalGraph;
+        this.initialGraph = initialGraph;
     }
 
     /**
@@ -322,7 +322,11 @@ public void setOut(PrintStream out) {
      * If non-null, edges not adjacent in this graph will not be added.
      */
     public void setBoundGraph(Graph boundGraph) {
-        this.boundGraph = GraphUtils.replaceNodes(boundGraph, getVariables());
+        if (boundGraph == null) {
+            this.boundGraph = null;
+        } else {
+            this.boundGraph = GraphUtils.replaceNodes(boundGraph, getVariables());
+        }
     }
 
     /**

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/SearchGraphUtils.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/SearchGraphUtils.java
@@ -1964,47 +1964,6 @@ public static int[][] graphComparison(Graph trueCpdag, Graph estCpdag, PrintStre
         return counts;
     }
 
-    public static Graph reorient(Graph graph, DataModel dataModel, Knowledge knowledge) {
-        if (dataModel instanceof DataModelList) {
-            DataModelList list = (DataModelList) dataModel;
-            List<DataModel> dataSets = new ArrayList<>(list);
-            Fges images = new Fges(new SemBicScoreImages(dataSets));
-
-            images.setBoundGraph(graph);
-            images.setKnowledge(knowledge);
-            return images.search();
-        } else if (dataModel instanceof DataSet) {
-            DataSet dataSet = (DataSet) dataModel;
-
-            Score score;
-
-            if (dataModel.isContinuous()) {
-                score = new SemBicScore(new CovarianceMatrix(dataSet));
-            } else if (dataSet.isDiscrete()) {
-                score = new BDeuScore(dataSet);
-            } else {
-                throw new NullPointerException();
-            }
-
-            Fges ges = new Fges(score);
-
-            ges.setBoundGraph(graph);
-            ges.setKnowledge(knowledge);
-            return ges.search();
-        } else if (dataModel instanceof CovarianceMatrix) {
-            ICovarianceMatrix cov = (CovarianceMatrix) dataModel;
-            Score score = new SemBicScore(cov);
-
-            Fges ges = new Fges(score);
-
-            ges.setBoundGraph(graph);
-            ges.setKnowledge(knowledge);
-            return ges.search();
-        }
-
-        throw new IllegalStateException("Can do that that reorientation.");
-    }
-
     @NotNull
     public static Graph dagToPag(Graph trueGraph) {
         return new DagToPag(trueGraph).convert();