///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below.       //
// Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006,       //
// 2007, 2008, 2009, 2010, 2014, 2015, 2022 by Peter Spirtes, Richard        //
// Scheines, Joseph Ramsey, and Clark Glymour.                               //
//                                                                           //
// This program is free software; you can redistribute it and/or modify      //
// it under the terms of the GNU General Public License as published by      //
// the Free Software Foundation; either version 2 of the License, or         //
// (at your option) any later version.                                       //
//                                                                           //
// This program is distributed in the hope that it will be useful,           //
// but WITHOUT ANY WARRANTY; without even the implied warranty of            //
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the             //
// GNU General Public License for more details.                              //
//                                                                           //
// You should have received a copy of the GNU General Public License         //
// along with this program; if not, write to the Free Software               //
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA //
///////////////////////////////////////////////////////////////////////////////

package edu.cmu.tetrad.test;

import edu.cmu.tetrad.algcomparison.Comparison;
import edu.cmu.tetrad.algcomparison.algorithm.Algorithms;
import edu.cmu.tetrad.algcomparison.algorithm.multi.Fask;
import edu.cmu.tetrad.algcomparison.algorithm.multi.FaskConcatenated;
import edu.cmu.tetrad.algcomparison.simulation.Simulations;
import edu.cmu.tetrad.algcomparison.statistic.*;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.Params;

/**
 * Pulling this test out for Madelyn.
 *
 * @author josephramsey
 */
public class TestSimulatedFmri3 {

    public void TestCycles_Data_fMRI_FASK() {
        Parameters parameters = new Parameters();

        parameters.set(Params.PENALTY_DISCOUNT, 4);
        parameters.set(Params.DEPTH, -1);
        parameters.set(Params.TWO_CYCLE_ALPHA, .001);
        parameters.set("thresholdForReversing", 1);

        parameters.set(Params.NUM_RUNS, 60);
//        parameters.set("randomSelectionSize", 10);

//        parameters.set("penaltyDiscount", 6);
//        parameters.set("depth", -1);
//        parameters.set("twoCycleAlpha", 1e-15);
//
//        parameters.set("numRuns", 10);

        // For automatically generated concatenations if you're doing them.
//        parameters.set("randomSelectionSize", 5);

        parameters.set("Structure", "Placeholder");

        Statistics statistics = new Statistics();

        statistics.add(new ParameterColumn("Structure"));
        statistics.add(new AdjacencyPrecision());
        statistics.add(new AdjacencyRecall());
        statistics.add(new ArrowheadPrecision());
        statistics.add(new ArrowheadRecall());
        statistics.add(new TwoCyclePrecision());
        statistics.add(new TwoCycleRecall());
        statistics.add(new TwoCycleFalsePositive());
        statistics.add(new TwoCycleFalseNegative());
        statistics.add(new TwoCycleTruePositive());
        statistics.add(new ElapsedCpuTime());

        statistics.setWeight("AP", 1.0);
        statistics.setWeight("AR", 1.0);
        statistics.setWeight("AHP", 1.0);
        statistics.setWeight("AHR", 1.0);
        statistics.setWeight("2CP", 1.0);
        statistics.setWeight("2CR", 1.0);
        statistics.setWeight("2CFP", 1.0);

        Simulations simulations = new Simulations();

//        String dir =  "/Users/user/Downloads/Cycles_Data_fMRI_Training/";
        final String dir = "/Users/user/Downloads/CyclesTestingData/";
        final String subdir = "data_fslfilter_concat";
//        String subdir = "data_fslfilter";

        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network1_amp", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network2_amp", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network3_amp", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network4_amp", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network5_amp", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network5_cont", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network5_cont_p3n7", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network5_cont_p7n3", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network6_amp", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network6_cont", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network7_amp", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network7_cont", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network8_amp_amp", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network8_amp_cont", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network8_cont_amp", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network9_amp_amp", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network9_amp_cont", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Network9_cont_amp", subdir));
        simulations.add(new LoadContinuousDataAndSingleGraph(
                dir + "Diamond", subdir));

        Algorithms algorithms = new Algorithms();

        algorithms.add(new Fask());

        Comparison comparison = new Comparison();

        comparison.setShowAlgorithmIndices(true);
        comparison.setShowSimulationIndices(true);
        comparison.setSortByUtility(false);
        comparison.setShowUtilities(false);
        comparison.setSaveGraphs(false);
        comparison.setTabDelimitedTables(false);

        comparison.compareFromSimulations("comparison", simulations, algorithms, statistics, parameters);
    }

    public void TestMadelynDAta() {
        Parameters parameters = new Parameters();

        parameters.set(Params.PENALTY_DISCOUNT, 10);
        parameters.set(Params.DEPTH, -1);
        parameters.set(Params.TWO_CYCLE_ALPHA, 1e-12);
        parameters.set("thresholdForReversing", 1);

        parameters.set(Params.NUM_RUNS, 10);
        parameters.set(Params.RANDOM_SELECTION_SIZE, 10);

//        parameters.set("penaltyDiscount", 6);
//        parameters.set("depth", -1);
//        parameters.set("twoCycleAlpha", 1e-15);
//
//        parameters.set("numRuns", 10);

        // For automatically generated concatenations if you're doing them.
//        parameters.set("randomSelectionSize", 5);

        parameters.set("Structure", "Placeholder");

        Statistics statistics = new Statistics();

        statistics.add(new AdjacencyPrecision());
        statistics.add(new AdjacencyRecall());
        statistics.add(new ArrowheadPrecision());
        statistics.add(new ArrowheadRecall());
        statistics.add(new TwoCyclePrecision());
        statistics.add(new TwoCycleRecall());
        statistics.add(new TwoCycleFalsePositive());
        statistics.add(new TwoCycleFalseNegative());
        statistics.add(new TwoCycleTruePositive());
        statistics.add(new ElapsedCpuTime());

        statistics.setWeight("AP", 1.0);
        statistics.setWeight("AR", 1.0);
        statistics.setWeight("AHP", 1.0);
        statistics.setWeight("AHR", 1.0);
        statistics.setWeight("2CP", 1.0);
        statistics.setWeight("2CR", 1.0);
        statistics.setWeight("2CFP", 1.0);


        final String dir = "/Users/user/Downloads/SimulatedData_2/";

        String[] dirs = {"AllNegative", "AllPositive", "TwoCycleNegative", "XYNegative", "XYPositive",
                "XZNegative", "XZPositive", "YZNegative", "YZPositive"};
        String[] suffixes = {"allneg", "allpos", "twocycleneg", "XYneg", "XYpos", "XZneg", "XZpos",
                "YZneg", "YZpos"};

        for (int i = 0; i < dirs.length; i++) {
            System.out.println("Directory " + dirs[i]);
            Simulations simulations = new Simulations();

            simulations.add(new LoadMadelynData(
                    dir + dirs[i], suffixes[i], 1));
            simulations.add(new LoadMadelynData(
                    dir + dirs[i], suffixes[i], 2));
            simulations.add(new LoadMadelynData(
                    dir + dirs[i], suffixes[i], 3));
            simulations.add(new LoadMadelynData(
                    dir + dirs[i], suffixes[i], 4));
            simulations.add(new LoadMadelynData(
                    dir + dirs[i], suffixes[i], 5));
            simulations.add(new LoadMadelynData(
                    dir + dirs[i], suffixes[i], 6));
            simulations.add(new LoadMadelynData(
                    dir + dirs[i], suffixes[i], 7));

            Algorithms algorithms = new Algorithms();

            algorithms.add(new FaskConcatenated());

            Comparison comparison = new Comparison();

            comparison.setShowAlgorithmIndices(true);
            comparison.setShowSimulationIndices(true);
            comparison.setSortByUtility(false);
            comparison.setShowUtilities(false);
//            comparison.setParallelized(false);
            comparison.setSaveGraphs(false);
            comparison.setTabDelimitedTables(false);
            comparison.setComparisonGraph(Comparison.ComparisonGraph.true_DAG);

            comparison.compareFromSimulations("comparison_" + dirs[i], simulations, algorithms, statistics, parameters);
        }
    }

    public static void main(String... args) {
        new TestSimulatedFmri3().TestCycles_Data_fMRI_FASK();
    }
}




