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package edu.cmu.tetrad.algcomparison.examples;

import edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fas;
import edu.cmu.tetrad.algcomparison.independence.SemBicTest;
import edu.cmu.tetrad.data.BoxDataSet;
import edu.cmu.tetrad.data.ContinuousVariable;
import edu.cmu.tetrad.data.DoubleDataBox;
import edu.cmu.tetrad.data.Knowledge;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.Parameters;
import edu.pitt.dbmi.data.reader.DataColumn;
import edu.pitt.dbmi.data.reader.Delimiter;
import edu.pitt.dbmi.data.reader.tabular.ContinuousTabularData;
import edu.pitt.dbmi.data.reader.tabular.ContinuousTabularDatasetFileReader;

import java.io.IOException;
import java.io.PrintWriter;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;

/**
 * RunKemmeren class.
 *
 * @author josephramsey
 * @version $Id: $Id
 */
public class RunKemmeren {

    /**
     * Constructor for RunKemmeren.
     */
    public RunKemmeren() {

    }

    /**
     * main.
     *
     * @param args a {@link java.lang.String} object
     */
    public static void main(String... args) {

//        Path path = Paths.get("/home/bandrews/Desktop/Kemmeren/data_kemmeren_centered.txt");
        Path path = Paths.get("/home/bandrews/Desktop/Kemmeren/obs_data.txt");

        System.out.println("Loading Data");

        ContinuousTabularDatasetFileReader reader = new ContinuousTabularDatasetFileReader(path, Delimiter.TAB);

        try {
            ContinuousTabularData data = ((ContinuousTabularData) reader.readInData());
            List variables = new ArrayList<>();
            for (DataColumn column : data.getDataColumns()) {
                Node node = new ContinuousVariable(column.getName());
                variables.add(node);
            }

            BoxDataSet dataSet = new BoxDataSet(new DoubleDataBox(data.getData()), variables);

            System.out.println("Generating Background Knowledge");

            Knowledge knowledge = new Knowledge(dataSet.getVariableNames());

            System.out.println("Running Search");

            Parameters parameters = new Parameters();
            parameters.set("penaltyDiscount", 2);
            parameters.set("structurePrior", 1);
            parameters.set("faithfulnessAssumed", true);
            parameters.set("symmetricFirstStep", false);
            parameters.set("maxDegree", -1);
            parameters.set("depth", 1);
            parameters.set("sepsetsReturnEmptyIfNotFixed", true);
            parameters.set("verbose", true);

            SemBicTest test = new SemBicTest();

//            Fges search = new Fges(score);
            Fas search = new Fas(test);
//            Gfci search = new Gfci(test, score);
            search.setKnowledge(knowledge);
            Graph graph = search.search(dataSet, parameters);

            System.out.println("Writing Output");

            PrintWriter out = new PrintWriter("/home/bandrews/Desktop/out.txt");
            out.println(graph.toString());
            out.close();

        } catch (IOException e) {
            e.printStackTrace();
        }


    }
}