com.marcolotz.lung.posprocesser.core.JSONExtractor.java Source code

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Here is the source code for com.marcolotz.lung.posprocesser.core.JSONExtractor.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.posprocesser.core;

import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;

import org.apache.log4j.Logger;

import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonStreamParser;
import com.marcolotz.lung.io.outputFormat.SeriesDataWritable;

/**
 * This objects deals with an input in a non-stardard JSON format file (since
 * there will be many JSON files inside only one output) and retrieves each of
 * the original JSON files (that are processed DICOM series) from it. It returns
 * a series at a time until the end of the file
 * 
 * @author Marco Aurelio Lotz
 * 
 */
public class JSONExtractor {

    @SuppressWarnings("unused")
    private static final Logger LOG = Logger.getLogger(JSONExtractor.class);

    /***
     * Path to the MapReduce json file.
     */
    String inputPath;

    Gson gson = new GsonBuilder().setPrettyPrinting().create();

    JsonStreamParser parser;

    SeriesDataWritable currentSeries;

    /***
     * Number of series found so far.
     */
    private int numberOfExtractedSeries = 0;

    public JSONExtractor(String inputPath) {
        this.inputPath = inputPath;
    }

    /***
     * Make possible initializations for the object. In this case the only
     * initialization is open the input file
     */
    public void initialize() {

        openFile();
    }

    /***
     * Opens the input File
     */
    private void openFile() {

        try {
            parser = new JsonStreamParser(new FileReader(inputPath));
        } catch (FileNotFoundException e) {
            System.err.println("Error openning file.");
            e.printStackTrace();
        }
    }

    /***
     * Unserializes the next JSON object and sets as a temporary element that
     * will be returned by the getSeries() method. More references on:
     * http://stackoverflow
     * .com/questions/11253476/reading-multiple-elements-from-json-file
     * 
     * @throws IOException
     */
    public boolean hasNext() {

        if (parser.hasNext()) {

            currentSeries = gson.fromJson(parser.next(), SeriesDataWritable.class);
            numberOfExtractedSeries++;
            return true;
        }
        return false;
    }

    public SeriesDataWritable getSeries() {
        return currentSeries;
    }

    /**
     * @return the numberOfExtractedSeries
     */
    public int getNumberOfExtractedSeries() {
        return numberOfExtractedSeries;
    }
}