edu.emory.mathcs.nlp.zzz.CSVRadiology.java Source code

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Here is the source code for edu.emory.mathcs.nlp.zzz.CSVRadiology.java

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/**
 * Copyright 2015, Emory University
 * 
 * Licensed 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 edu.emory.mathcs.nlp.zzz;

import edu.emory.mathcs.nlp.common.collection.tuple.Pair;
import edu.emory.mathcs.nlp.common.util.FileUtils;
import edu.emory.mathcs.nlp.common.util.IOUtils;
import edu.emory.mathcs.nlp.common.util.Joiner;
import edu.emory.mathcs.nlp.component.tokenizer.EnglishTokenizer;
import edu.emory.mathcs.nlp.component.tokenizer.Tokenizer;
import edu.emory.mathcs.nlp.component.tokenizer.token.Token;

import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVParser;
import org.apache.commons.csv.CSVRecord;

import java.io.PrintStream;
import java.util.ArrayList;
import java.util.List;
import java.util.StringJoiner;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

/**
 * @author Jinho D. Choi ({@code jinho.choi@emory.edu})
 */
public class CSVRadiology {
    final String[] BEFORE = { "Patient Name :", "DOB :", "SEX :", "Ordering Physician :", "Exam :", "HEAD CT",
            "CLINICAL", "TECHNIQUE :", "COMPARISON :", "FINDINGS :", "IMPRESSION :" };
    final String[] AFTER = { "INDICATION :", "TECHNIQUE :", "COMPARISON :", "FINDINGS :", "IMPRESSION :" };
    List<Pair<Pattern, String>> P_BEFORE, P_AFTER;
    Pattern NEW_LINE = Pattern.compile("\n");

    public void categorize(String inputFile) throws Exception {
        CSVParser parser = new CSVParser(IOUtils.createBufferedReader(inputFile), CSVFormat.DEFAULT);
        List<CSVRecord> records = parser.getRecords();
        StringJoiner join;
        CSVRecord record;

        for (int i = 0; i <= 500; i++) {
            if (i == 0)
                continue;
            record = records.get(i);
            join = new StringJoiner(" ");

            for (int j = 2; j < 7; j++)
                join.add(record.get(j));

            System.out.println(join.toString());
        }

        parser.close();
    }

    public void tokenize(String inputFile, int outputStart) throws Exception {
        CSVParser parser = new CSVParser(IOUtils.createBufferedReader(inputFile), CSVFormat.DEFAULT);
        String inputPath = FileUtils.getPath(inputFile) + "/";
        List<CSVRecord> records = parser.getRecords();
        Tokenizer tokenizer = new EnglishTokenizer();

        P_BEFORE = new ArrayList<>();
        P_AFTER = new ArrayList<>();
        for (String s : BEFORE)
            P_BEFORE.add(new Pair<>(Pattern.compile(s), "\n" + s));
        for (String s : AFTER)
            P_AFTER.add(new Pair<>(Pattern.compile(s), s + "\n"));

        for (int i = 0; i < records.size(); i++) {
            PrintStream fout = IOUtils.createBufferedPrintStream(getOuputFilename(inputPath, i + outputStart));

            for (List<Token> tokens : tokenizer.segmentize(records.get(i).get(0)))
                print(fout, tokens);

            fout.close();
        }

        parser.close();
    }

    String getOuputFilename(String inputPath, int index) {
        StringBuilder build = new StringBuilder();

        build.append(inputPath);
        if (index < 1000)
            build.append(0);
        if (index < 100)
            build.append(0);
        if (index < 10)
            build.append(0);
        build.append(index);
        build.append(".txt");

        return build.toString();
    }

    void print(PrintStream fout, List<Token> tokens) {
        String s = Joiner.join(tokens, " ");

        for (Pair<Pattern, String> p : P_BEFORE) {
            Matcher m = p.o1.matcher(s);
            if (m.find())
                s = m.replaceAll(p.o2);
        }

        for (Pair<Pattern, String> p : P_AFTER) {
            Matcher m = p.o1.matcher(s);
            if (m.find())
                s = m.replaceAll(p.o2);
        }

        for (String t : NEW_LINE.split(s)) {
            t = t.trim();
            if (!t.isEmpty())
                fout.println(t.trim());
        }
    }

    static public void main(String[] args) {
        //      String inputFile = "/Users/jdchoi/Emory/radiology/tools/500/500-original.csv";
        //      String inputFile = "/Users/jdchoi/Emory/radiology/dat/radiology_report_151112_lemmon.csv";

        String inputFile = "/Users/jdchoi/Emory/radiology/de-identification/1986/Remaining_1986Reports_FULL.csv";

        try {
            CSVRadiology cvs = new CSVRadiology();
            cvs.tokenize(inputFile, 500);
            //         cvs.categorize(inputFile);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
}