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refactoring post processing input, unit test for primary statistics
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137 changes: 137 additions & 0 deletions
137
vcell-core/src/test/java/cbit/vcell/simdata/LangevinPostProcessorTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,137 @@ | ||
| package cbit.vcell.simdata; | ||
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| import cbit.vcell.math.ODESolverResultSetColumnDescription; | ||
| import cbit.vcell.solver.ode.ODESolverResultSet; | ||
| import com.google.common.io.Files; | ||
| import com.google.common.io.Resources; | ||
| import org.junit.jupiter.api.AfterAll; | ||
| import org.junit.jupiter.api.BeforeAll; | ||
| import org.junit.jupiter.api.Tag; | ||
| import org.junit.jupiter.api.Test; | ||
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| import java.io.*; | ||
| import java.util.LinkedHashMap; | ||
| import java.util.Map; | ||
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| import static org.junit.jupiter.api.Assertions.assertFalse; | ||
| import static org.junit.jupiter.api.Assertions.assertTrue; | ||
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| @Tag("Fast") | ||
| public class LangevinPostProcessorTest { | ||
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| // the .IDA files are in vcell-core/src/test/java /cbit/vcell/simdata | ||
| static File ida_0_File; | ||
| static File ida_1_File; | ||
| static File ida_2_File; | ||
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| @BeforeAll | ||
| public static void setUp() throws IOException { | ||
| ida_0_File = File.createTempFile("SimID_284673710_0_", ".ida"); | ||
| Resources.asByteSource(Resources.getResource("cbit/vcell/simdata/SimID_284673710_0_.ida")) | ||
| .copyTo(Files.asByteSink(ida_0_File)); | ||
| ida_1_File = File.createTempFile("SimID_284673710_1_", ".ida"); | ||
| Resources.asByteSource(Resources.getResource("cbit/vcell/simdata/SimID_284673710_1_.ida")) | ||
| .copyTo(Files.asByteSink(ida_1_File)); | ||
| ida_2_File = File.createTempFile("SimID_284673710_2_", ".ida"); | ||
| Resources.asByteSource(Resources.getResource("cbit/vcell/simdata/SimID_284673710_2_.ida")) | ||
| .copyTo(Files.asByteSink(ida_2_File)); | ||
| } | ||
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| @AfterAll | ||
| public static void tearDown() { | ||
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| ida_0_File.delete(); | ||
| ida_1_File.delete(); | ||
| ida_2_File.delete(); | ||
| // if (inputStream != null) { | ||
| // inputStream.close(); | ||
| } | ||
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| @Test | ||
| public void testRead() throws IOException { | ||
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| // read the input data (3 .IDA files) | ||
| ODESolverResultSet osrs_0 = getOdeSolverResultSet(ida_0_File); | ||
| ODESolverResultSet osrs_1 = getOdeSolverResultSet(ida_1_File); | ||
| ODESolverResultSet osrs_2 = getOdeSolverResultSet(ida_2_File); | ||
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| Map<Integer, ODESolverResultSet> odeSolverResultSetMap = new LinkedHashMap<>(); | ||
| odeSolverResultSetMap.put(0, osrs_0); | ||
| odeSolverResultSetMap.put(1, osrs_1); | ||
| odeSolverResultSetMap.put(2, osrs_2); | ||
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| LangevinPostProcessorInput lppInput = new LangevinPostProcessorInput(null, null); | ||
| lppInput.setFailed(false); | ||
| lppInput.setOdeSolverResultSetMap(odeSolverResultSetMap); | ||
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| // compute primary statistics | ||
| LangevinPostProcessor lpp = new LangevinPostProcessor(); | ||
| LangevinPostProcessorOutput lppOutput = lpp.postProcessLangevinResults(lppInput); | ||
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| assertFalse(lppOutput.isFailed(), "expected to not fail"); | ||
| assertTrue(lppOutput.isMultiTrial(), "expected to be multi-trial"); | ||
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| // get some timepoint for some variable | ||
| String name = osrs_0.getColumnDescriptions()[7].getName(); | ||
| double anAverage = lppOutput.getAveragesResultSet().getRow(10)[7]; // TOTAL_MT0__Site1__state0 | ||
| double aStd = lppOutput.getStdResultSet().getRow(10)[7]; | ||
| double aMin = lppOutput.getMinResultSet().getRow(10)[7]; | ||
| double aMax = lppOutput.getMaxResultSet().getRow(10)[7]; | ||
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| // compare to what's expected | ||
| assertTrue("TOTAL_MT0__Site1__state0".contentEquals(name), "expecting column name 'TOTAL_MT0__Site1__state0', found: '" + name + "'"); | ||
| assertTrue(anAverage == 21.0 ? true : false, "expecting 21.0, found " + anAverage); | ||
| assertTrue(aStd == 0.816496580927726 ? true : false, "expecting 0.816496580927726, found " + aStd); | ||
| assertTrue(aMin == 20.0 ? true : false, "expecting 20.0, found " + aMin); | ||
| assertTrue(aMax == 22.0 ? true : false, "expecting 22.0, found " + aMax); | ||
| } | ||
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| // | ||
| // ------- IDA file parsing / initializing ODESolverResultSet ----------------------------------------------------- | ||
| // | ||
| private static ODESolverResultSet getOdeSolverResultSet(File idaFile) throws IOException { | ||
| ODESolverResultSet odeSolverResultSet = new ODESolverResultSet(); | ||
| FileInputStream inputStream = null; | ||
| inputStream = new FileInputStream(idaFile); | ||
| if(readIDA(odeSolverResultSet, inputStream) == null) { | ||
| return null; | ||
| } | ||
| return (odeSolverResultSet); | ||
| } | ||
| private static ODESolverResultSet readIDA(ODESolverResultSet odeSolverResultSet, FileInputStream inputStream) throws IOException { | ||
| InputStreamReader inputStreamReader = new InputStreamReader(inputStream); | ||
| BufferedReader bufferedReader = new BufferedReader(inputStreamReader); | ||
| // read header | ||
| String line = bufferedReader.readLine(); | ||
| if (line == null) { | ||
| return null; | ||
| } | ||
| while (line.indexOf(':') > 0) { | ||
| String name = line.substring(0, line.indexOf(':')); | ||
| odeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(name)); | ||
| line = line.substring(line.indexOf(':') + 1); | ||
| } | ||
| // read data | ||
| while ((line = bufferedReader.readLine()) != null) { | ||
| line = line + " "; | ||
| double[] values = new double[odeSolverResultSet.getDataColumnCount()]; | ||
| boolean bCompleteRow = true; | ||
| for (int i = 0; i < odeSolverResultSet.getDataColumnCount(); i++) { | ||
| if (line.indexOf(' ')==-1) { // here and below we assume separator is ' ', in other cases might also be '\t' | ||
| bCompleteRow = false; | ||
| break; | ||
| }else{ | ||
| String value = line.substring(0, line.indexOf(' ')).trim(); | ||
| values[i] = Double.valueOf(value).doubleValue(); | ||
| line = line.substring(line.indexOf(' ') + 1); | ||
| } | ||
| } | ||
| if (bCompleteRow){ | ||
| odeSolverResultSet.addRow(values); | ||
| }else{ | ||
| break; | ||
| } | ||
| } | ||
| return odeSolverResultSet; | ||
| } | ||
| } |
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