| /* |
| * 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 = readDMLScalarFromHDFS(file); |
| rfile = readRScalarFromFS(file); |
| } |
| else { |
| dmlfile = readDMLMatrixFromHDFS(file); |
| rfile = readRMatrixFromFS(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 = readDMLScalarFromHDFS(file); |
| rfile = readRScalarFromFS(file); |
| } |
| else { |
| dmlfile = readDMLMatrixFromHDFS(file); |
| rfile = readRMatrixFromFS(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 = readDMLScalarFromHDFS(file); |
| rfile = readRScalarFromFS(file); |
| } |
| else { |
| dmlfile = readDMLMatrixFromHDFS(file); |
| rfile = readRMatrixFromFS(file); |
| } |
| TestUtils.compareMatrices(dmlfile, rfile, eps, file+"-DML", file+"-R"); |
| } |
| |
| } |
| |
| } |