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Merge pull request #1 from wsp-sag/bart-feat-omx-read
Feature - Add OMX Read
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119 changes: 119 additions & 0 deletions
119
core/cmf/common-base/src/java/com/pb/common/matrix/OMXMatrixReader.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,119 @@ | ||
| package com.pb.common.matrix; | ||
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| import java.io.File; | ||
| import java.util.Set; | ||
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| import org.apache.log4j.Logger; | ||
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| import omx.OmxFile; | ||
| import omx.OmxMatrix; | ||
| import omx.OmxMatrix.OmxDoubleMatrix; | ||
| import omx.OmxLookup; | ||
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| /** | ||
| * Implements an OMX MatrixReader | ||
| * | ||
| * @author Ben Stabler | ||
| * @version 1.0, 02/11/15 | ||
| */ | ||
| public class OMXMatrixReader extends MatrixReader { | ||
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| private OmxFile omxFile = null; | ||
| protected static Logger logger = Logger.getLogger("com.pb.common.matrix"); | ||
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| /** | ||
| * Prevent outside classes from instantiating the default constructor. | ||
| */ | ||
| private OMXMatrixReader() {} | ||
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| /** | ||
| * @param file represents the physical matrix file | ||
| */ | ||
| public OMXMatrixReader(File file) throws MatrixException { | ||
| this.file = file; | ||
| openOMXFile(); | ||
| } | ||
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| public Matrix readMatrix() throws MatrixException { | ||
| return readMatrix(""); | ||
| } | ||
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| public Matrix readMatrix(String name) throws MatrixException { | ||
| if(omxFile.getMatrixNames().contains(name)){ | ||
| return readData(name); | ||
| } | ||
| else{ | ||
| logger.info("No matrix in " + file.getPath() + " with name " + name); | ||
| throw new MatrixException(MatrixException.INVALID_TABLE_NAME + " " + name); | ||
| } | ||
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| } | ||
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| private void openOMXFile() throws MatrixException { | ||
| try { | ||
| omxFile = new OmxFile(file.getPath()); | ||
| omxFile.openReadWrite(); | ||
| } | ||
| catch (Exception e) { | ||
| throw new MatrixException(e, MatrixException.FILE_CANNOT_BE_OPENED + ", "+ file.getPath()); | ||
| } | ||
| } | ||
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| /** | ||
| * Reads and returns an entire matrix | ||
| * | ||
| */ | ||
| public Matrix[] readMatrices() throws MatrixException { | ||
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| Matrix[] m = null; | ||
| Set<String> matNames = omxFile.getMatrixNames(); | ||
| m = new Matrix[matNames.size()]; | ||
| int i = 0; | ||
| for(String matName : omxFile.getMatrixNames()){ | ||
| m[i] = readMatrix(matName); | ||
| i++; | ||
| } | ||
| return m; | ||
| }; | ||
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| /** | ||
| * Returns a matrix. | ||
| * | ||
| */ | ||
| private Matrix readData(String name) { | ||
| OmxMatrix.OmxDoubleMatrix omxMat = null; | ||
| try { | ||
| omxMat = (OmxDoubleMatrix) omxFile.getMatrix(name); | ||
| double[][] values = omxMat.getData(); | ||
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| //convert to Matrix float[][] | ||
| float[][] valuesFloat = new float[values.length][values[0].length]; | ||
| for (int i = 0 ; i < values.length; i++) { | ||
| for (int j = 0 ; j < values[0].length; j++) { | ||
| valuesFloat[i][j] = (float) values[i][j]; | ||
| } | ||
| } | ||
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| Matrix m = new Matrix(name, name, valuesFloat); | ||
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| //set zone numbers if found | ||
| //CUBE - 1 to X | ||
| //VISUM - 'NO' | ||
| //EMME - 'zone number' | ||
| //TransCAD - ? | ||
| if (omxFile.getLookupNames().contains("NO")) { | ||
| OmxLookup.OmxIntLookup omxZoneNums = (OmxLookup.OmxIntLookup)omxFile.getLookup("NO"); | ||
| m.setExternalNumbersZeroBased(omxZoneNums.getLookup()); | ||
| } | ||
| if (omxFile.getLookupNames().contains("zone number")) { | ||
| OmxLookup.OmxIntLookup omxZoneNums = (OmxLookup.OmxIntLookup)omxFile.getLookup("zone number"); | ||
| m.setExternalNumbersZeroBased(omxZoneNums.getLookup()); | ||
| } | ||
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| return m; | ||
| } | ||
| catch (Exception e) { | ||
| throw new MatrixException("Matrix not found: " + name); | ||
| } | ||
| } | ||
| } |
110 changes: 110 additions & 0 deletions
110
core/cmf/common-base/src/java/com/pb/common/matrix/OMXMatrixWriter.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,110 @@ | ||
| package com.pb.common.matrix; | ||
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| import java.io.File; | ||
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| import org.apache.log4j.Logger; | ||
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| import omx.OmxFile; | ||
| import omx.OmxLookup; | ||
| import omx.OmxMatrix; | ||
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| /** | ||
| * Implements an OMX MatrixWriter | ||
| * | ||
| * @author Ben Stabler | ||
| * @version 1.0, 02/11/15 | ||
| */ | ||
| public class OMXMatrixWriter extends MatrixWriter { | ||
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| private OmxFile omxFile = null; | ||
| protected static Logger logger = Logger.getLogger("com.pb.common.matrix"); | ||
| private double defaultNA = Double.valueOf(0); | ||
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| /** | ||
| * Prevent outside classes from instantiating the default constructor. | ||
| */ | ||
| private OMXMatrixWriter() {} | ||
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| /** | ||
| * @param file represents the physical matrix file | ||
| */ | ||
| public OMXMatrixWriter(File file) throws MatrixException { | ||
| this.file = file; | ||
| } | ||
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| public void writeMatrix(Matrix m) throws MatrixException { | ||
| writeMatrix(m.name, m); | ||
| } | ||
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| public void writeMatrix(String name, Matrix m) throws MatrixException { | ||
| writeData(name, m); | ||
| } | ||
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| /** | ||
| * Writes a matrix to the underlying file. | ||
| * | ||
| *@param name matrix name | ||
| *@param m the matrix to write | ||
| * | ||
| */ | ||
| private void writeData(String name, Matrix m) { | ||
| omxFile = new OmxFile(file.getPath()); | ||
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| try { | ||
| if(file.exists()) { | ||
| omxFile.openReadWrite(); | ||
| } else { | ||
| int[] shape = new int[2]; | ||
| shape[0] = m.getRowCount(); | ||
| shape[1] = m.getColumnCount(); | ||
| omxFile.openNew(shape); | ||
| } | ||
| } catch (Exception e) { | ||
| throw new MatrixException(e, MatrixException.FILE_NOT_FOUND + ", "+ file); | ||
| } | ||
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| try { | ||
| //convert to double[][] | ||
| float[][] values = m.getValues(); | ||
| double[][] valuesDouble = new double[values.length][values[0].length]; | ||
| for (int i = 0 ; i < values.length; i++) { | ||
| for (int j = 0 ; j < values[0].length; j++) { | ||
| valuesDouble[i][j] = (double) values[i][j]; | ||
| } | ||
| } | ||
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| //create sequential CUBE_MAT_NUMBER attribute for use with Cube | ||
| int count = 1; | ||
| for (String matName : omxFile.getMatrixNames()) { | ||
| count = count + 1; | ||
| } | ||
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| //add matrix to file | ||
| OmxMatrix.OmxDoubleMatrix mat = new OmxMatrix.OmxDoubleMatrix(name,valuesDouble,defaultNA); | ||
| omxFile.addMatrix(mat); | ||
| mat.setAttribute("CUBE_MAT_NUMBER",count); | ||
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| //add external zone numbers as NO lookup | ||
| if (!omxFile.getLookupNames().contains("NO")) { | ||
| OmxLookup.OmxIntLookup omxZoneNums = new OmxLookup.OmxIntLookup("NO", m.getExternalColumnNumbersZeroBased(), 0); | ||
| omxFile.addLookup(omxZoneNums); | ||
| } | ||
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| //save file | ||
| omxFile.save(); | ||
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| } catch (Exception e) { | ||
| throw new MatrixException(e, MatrixException.ERROR_WRITING_FILE); | ||
| } | ||
| } | ||
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| /** Writes all tables of an entire matrix | ||
| * | ||
| */ | ||
| public void writeMatrices(String[] names, Matrix[] m) throws MatrixException { | ||
| for(int i=0; i<names.length; i++) { | ||
| writeData(names[i],m[i]); | ||
| } | ||
| } | ||
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| } |
41 changes: 41 additions & 0 deletions
41
core/cmf/common-base/src/java/com/pb/common/matrix/OMXTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| package com.pb.common.matrix; | ||
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| import java.io.File; | ||
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| import omx.OmxLookup; | ||
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| /** | ||
| * Test basic OMX Matrix Reader and writer | ||
| * java -classpath "omx.jar;common-base.jar" -Djava.library.path="jhdfdllFolder" com.pb.common.matrix.OMXTest | ||
| * requires omx.jar in classpath and jhdf5.dll,jhdf.dll in the java.library.path | ||
| * @author Ben Stabler | ||
| * @version 1.0, 02/11/15 | ||
| */ | ||
| public class OMXTest { | ||
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| private OMXTest() {} | ||
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| public static void main(String[] args) { | ||
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| int[] zoneNames = {100,101,102,103,104}; | ||
| File testFile = new File("test.omx"); | ||
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| Matrix mat = new Matrix("test","test",zoneNames.length,zoneNames.length); | ||
| mat.fill(2); | ||
| mat.setExternalNumbersZeroBased(zoneNames); | ||
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| OMXMatrixWriter writer = new OMXMatrixWriter(testFile); | ||
| writer.writeMatrix(mat); | ||
| System.out.println("write test matrix sum:" + Double.valueOf(mat.getSum())); | ||
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| OMXMatrixReader reader = new OMXMatrixReader(testFile); | ||
| Matrix matIn = reader.readMatrix("test"); | ||
| System.out.println("read test matrix sum:" + Double.valueOf(matIn.getSum())); | ||
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| for (int j = 0 ; j < matIn.getExternalRowNumbersZeroBased().length; j++) { | ||
| System.out.println("zone " + String.valueOf(matIn.getExternalRowNumbersZeroBased()[j])); | ||
| } | ||
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| } | ||
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| } |
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