com.marcolotz.lung.debug.InputTester.java Source code

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Here is the source code for com.marcolotz.lung.debug.InputTester.java

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/*******************************************************************************
 * Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
 * 
 * Copyright (c) 2014 Marco Aurelio Barbosa Fagnani Gomes Lotz (marcolotz.com)
 * 
 * The source code in this document is licensed under Creative Commons
 * Attribution-NonCommercial-ShareAlike 4.0 International License. You must 
 * credit the author of the source code in the way specified by the author or
 * licenser (but not in a way to suggest that the author or licenser has given 
 * you allowance to you or to your use of the source code). If you modify,
 * transform or create using this source code as basis, you can only distribute
 * the new source code under the same license or a similar license to this one.
 * 
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 * 
 * To see a copy of the license, access:
 * creativecommons.org/licenses/by-nc-sa/4.0/legalcode
 ******************************************************************************/
package com.marcolotz.lung.debug;

import ij.plugin.DICOM;

import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;

import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.BytesWritable;
import org.apache.hadoop.io.NullWritable;
import org.apache.hadoop.mapreduce.InputFormat;
import org.apache.hadoop.mapreduce.RecordReader;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.mapreduce.TaskAttemptID;
import org.apache.hadoop.mapreduce.lib.input.FileSplit;
import org.apache.hadoop.mapreduce.task.TaskAttemptContextImpl;
import org.apache.hadoop.util.ReflectionUtils;

import com.marcolotz.lung.io.inputFormat.WholeFileInputFormat;

/**
 * Class used for debuging the input given by the record reader.
 * 
 * @author Marco Aurelio Lotz
 * 
 */
@SuppressWarnings("deprecation")
public class InputTester {

    public InputTester() {
    };

    /***
     * Method used for local testing the record reader and the Input format. It
     * generates an input split from the local file system file.
     * 
     * @param filePath
     */
    public void localTest(String filePath) {
        DICOM image;
        Configuration testConf = new Configuration(false);

        /* Reads the local file system */
        testConf.set("fs.default.name", "file:///");

        File testFile = new File(filePath);

        Path path = new Path(testFile.getAbsoluteFile().toURI());
        FileSplit split = new FileSplit(path, 0, testFile.length(), null);

        InputFormat<NullWritable, BytesWritable> inputFormat = ReflectionUtils
                .newInstance(WholeFileInputFormat.class, testConf);
        TaskAttemptContext context = new TaskAttemptContextImpl(testConf, new TaskAttemptID());

        try {
            RecordReader<NullWritable, BytesWritable> reader = inputFormat.createRecordReader(split, context);
            while (reader.nextKeyValue()) {
                /* get the bytes array */
                BytesWritable inputBytesWritable = (BytesWritable) reader.getCurrentValue();
                byte[] inputContent = inputBytesWritable.getBytes();

                /* Check for Correct value */
                // generateLocalOutput("path/to/output");

                InputStream is = new ByteArrayInputStream(inputContent);

                image = new DICOM(is);
                image.run("Dicom Test");

                /* Prints the bytes as an ImagePlus image */
                ImageViewer debug = new ImageViewer();
                debug.setImage(image);
            }
        } catch (Exception e) {

        }
    }

    /***
     * Writes the byte content of the input stream to the local file system.
     * @param filePath
     * @param outputContent
     */
    public void generateLocalOutput(String filePath, byte[] outputContent) {
        try {
            FileOutputStream output = new FileOutputStream(new File(filePath));
            IOUtils.write(outputContent, output);
        } catch (IOException e) {
            System.err.println("Error during debug output process.");
            e.printStackTrace();
        }
    }
}