src/test/java/org/apache/sysds/test/applications/BivariateCategoricalCategoricallTest.java

/*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 * 
 *   http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied.  See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */

package org.apache.sysds.test.applications;

import java.util.HashMap;

import org.junit.Test;
import org.apache.sysds.runtime.matrix.data.MatrixValue.CellIndex;
import org.apache.sysds.test.AutomatedTestBase;
import org.apache.sysds.test.TestConfiguration;
import org.apache.sysds.test.TestUtils;


public class BivariateCategoricalCategoricallTest extends AutomatedTestBase 
{
	
	private final static String TEST_DIR = "applications/descriptivestats/";
	private final static String TEST_CLASS_DIR = TEST_DIR + BivariateCategoricalCategoricallTest.class.getSimpleName() + "/";
	private final static String TEST_NOMINAL_NOMINAL = "CategoricalCategorical";
	private final static String TEST_NOMINAL_NOMINAL_WEIGHTS = "CategoricalCategoricalWithWeightsTest";
	private final static String TEST_ODDS_RATIO = "OddsRatio";

	private final static double eps = 1e-9;
	private int rows = 10000;  // # of rows in each vector
	private int ncatA = 100;   // # of categories in A
	private int ncatB = 150;   // # of categories in B
	private int maxW = 100;    // maximum weight
	
	@Override
	public void setUp() {
		addTestConfiguration(TEST_NOMINAL_NOMINAL, 
			new TestConfiguration(TEST_CLASS_DIR, TEST_NOMINAL_NOMINAL, 
				new String[] { "PValue"+".scalar", "CramersV"+".scalar" }));
		addTestConfiguration(TEST_NOMINAL_NOMINAL_WEIGHTS, 
			new TestConfiguration(TEST_CLASS_DIR, TEST_NOMINAL_NOMINAL_WEIGHTS, 
				new String[] { "PValue"+".scalar", "CramersV"+".scalar" }));
		addTestConfiguration(TEST_ODDS_RATIO, 
			new TestConfiguration(TEST_CLASS_DIR, TEST_ODDS_RATIO, 
				new String[] { 	
					"oddsRatio"+".scalar", 
					"sigma"+".scalar", 
					"leftConf"+".scalar", 
					"rightConf"+".scalar", 
					"sigmasAway"+".scalar" 
					//"chiSquared"+".scalar", 
					//"degFreedom"+".scalar", 
					//"pValue"+".scalar", 
					//"cramersV"+".scalar"
					}));
	}

	@Test
	public void testCategoricalCategorical() {
		TestConfiguration config = getTestConfiguration(TEST_NOMINAL_NOMINAL);
		config.addVariable("rows", rows);
		loadTestConfiguration(config);

		/* This is for running the junit test the new way, i.e., construct the arguments directly */
		String CC_HOME = SCRIPT_DIR + TEST_DIR;
		fullDMLScriptName = CC_HOME + TEST_NOMINAL_NOMINAL + ".dml";
		programArgs = new String[]{"-args", input("A"), Integer.toString(rows), input("B"), 
			output("PValue"), output("CramersV")};
		
		fullRScriptName = CC_HOME + TEST_NOMINAL_NOMINAL + ".R";
		rCmd = "Rscript" + " " + fullRScriptName + " " + inputDir() + " " + expectedDir();

		double[][] A = getRandomMatrix(rows, 1, 1, ncatA, 1, 3);
		double[][] B = getRandomMatrix(rows, 1, 1, ncatB, 1, 7);
		TestUtils.round(A);
		TestUtils.round(B);

		writeInputMatrix("A", A, true);
		writeInputMatrix("B", B, true);

		/*
		 * Expected number of jobs:
		 * Reblock - 1 job 
		 * While loop iteration - 7 jobs
		 * Final output write - 1 job
		 */
		//boolean exceptionExpected = false;
		//int expectedNumberOfJobs = 5;
		runTest(true, false, null, -1);
		
		runRScript(true);
		
		for(String file: config.getOutputFiles())
		{
			/* NOte that some files do not contain matrix, but just a single scalar value inside */
			HashMap<CellIndex, Double> dmlfile;
			HashMap<CellIndex, Double> rfile;
			if (file.endsWith(".scalar")) {
				file = file.replace(".scalar", "");
				dmlfile = readDMLScalarFromOutputDir(file);
				rfile = readRScalarFromExpectedDir(file);
			}
			else {
				dmlfile = readDMLMatrixFromOutputDir(file);
				rfile = readRMatrixFromExpectedDir(file);
			}
			TestUtils.compareMatrices(dmlfile, rfile, eps, file+"-DML", file+"-R");
		}
		
	}
	
	@Test
	public void testCategoricalCategoricalWithWeights() {
		TestConfiguration config = getTestConfiguration(TEST_NOMINAL_NOMINAL_WEIGHTS);
		config.addVariable("rows", rows);
		loadTestConfiguration(config);

		/* This is for running the junit test the new way, i.e., construct the arguments directly */
		String CC_HOME = SCRIPT_DIR + TEST_DIR;
		fullDMLScriptName = CC_HOME + TEST_NOMINAL_NOMINAL_WEIGHTS + ".dml";
		programArgs = new String[]{"-args", input("A"), Integer.toString(rows),
			input("B"), input("WM"), output("PValue"), output("CramersV") };
		
		fullRScriptName = CC_HOME + TEST_NOMINAL_NOMINAL_WEIGHTS + ".R";
		rCmd = "Rscript" + " " + fullRScriptName + " " + inputDir() + " " + expectedDir();

		double[][] A = getRandomMatrix(rows, 1, 1, ncatA, 1, System.currentTimeMillis());
		double[][] B = getRandomMatrix(rows, 1, 1, ncatB, 1, System.currentTimeMillis()+1);
		double[][] WM = getRandomMatrix(rows, 1, 1, maxW, 1, System.currentTimeMillis()+2);
		TestUtils.round(A);
		TestUtils.round(B);
		TestUtils.round(WM);

		writeInputMatrix("A", A, true);
		writeInputMatrix("B", B, true);
		writeInputMatrix("WM", WM, true);
		createHelperMatrix();
		
		/*
		 * Expected number of jobs:
		 * Mean etc - 2 jobs (reblock & gmr)
		 * Cov etc - 2 jobs
		 * Final output write - 1 job
		 */
		//boolean exceptionExpected = false;
		//int expectedNumberOfJobs = 5;
		//runTest(exceptionExpected, null, expectedNumberOfJobs);
		
        runTest(true, false, null, -1);
		runRScript(true);
		
		for(String file: config.getOutputFiles())
		{
			HashMap<CellIndex, Double> dmlfile;
			HashMap<CellIndex, Double> rfile;
			if (file.endsWith(".scalar")) {
				file = file.replace(".scalar", "");
				dmlfile = readDMLScalarFromOutputDir(file);
				rfile = readRScalarFromExpectedDir(file);
			}
			else {
				dmlfile = readDMLMatrixFromOutputDir(file);
				rfile = readRMatrixFromExpectedDir(file);
			}
			TestUtils.compareMatrices(dmlfile, rfile, eps, file+"-DML", file+"-R");
		}
		
	}
	
	@Test
	public void testOddsRatio() {
		TestConfiguration config = getTestConfiguration(TEST_ODDS_RATIO);
		config.addVariable("rows", rows);
		loadTestConfiguration(config);

		/* This is for running the junit test the new way, i.e., construct the arguments directly */
		String CC_HOME = SCRIPT_DIR + TEST_DIR;
		fullDMLScriptName = CC_HOME + TEST_ODDS_RATIO + ".dml";
		programArgs = new String[]{"-args",  input("A"), Integer.toString(rows), input("B"), 
			output("oddsRatio"), 
			output("sigma"), 
			output("leftConf"), 
			output("rightConf"), 
			output("sigmasAway")
			//output("chiSquared"), 
			//output(degFreedom"), 
			//output("pValue"), 
			//output("cramersV")
			};
		
		fullRScriptName = CC_HOME + TEST_ODDS_RATIO + ".R";
		rCmd = "Rscript" + " " + fullRScriptName + " " + inputDir() + " " + expectedDir();

		// current test works only for 2x2 contingency tables => #categories must be 2
		int numCat = 2;
		double[][] A = getRandomMatrix(rows, 1, 1, numCat, 1, System.currentTimeMillis());
		double[][] B = getRandomMatrix(rows, 1, 1, numCat, 1, System.currentTimeMillis()+1);
		TestUtils.round(A);
		TestUtils.round(B);

		writeInputMatrix("A", A, true);
		writeInputMatrix("B", B, true);

		runTest(true, false, null, -1);
		
		runRScript(true);
		
		for(String file: config.getOutputFiles())
		{
			/* NOte that some files do not contain matrix, but just a single scalar value inside */
			HashMap<CellIndex, Double> dmlfile;
			HashMap<CellIndex, Double> rfile;
			if (file.endsWith(".scalar")) {
				file = file.replace(".scalar", "");
				dmlfile = readDMLScalarFromOutputDir(file);
				rfile = readRScalarFromExpectedDir(file);
			}
			else {
				dmlfile = readDMLMatrixFromOutputDir(file);
				rfile = readRMatrixFromExpectedDir(file);
			}
			TestUtils.compareMatrices(dmlfile, rfile, eps, file+"-DML", file+"-R");
		}
		
	}
	
}