it.crs4.features.ImageToAvro.java Source code

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Here is the source code for it.crs4.features.ImageToAvro.java

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/**
 * BEGIN_COPYRIGHT
 *
 * Copyright (C) 2014-2015 CRS4.
 *
 * 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.
 *
 * END_COPYRIGHT
 */

package it.crs4.features;

import java.io.File;

import loci.formats.ImageReader;

import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.GnuParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.ParseException;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public final class ImageToAvro {

    private static final Logger LOGGER = LoggerFactory.getLogger(ImageToAvro.class);

    private ImageToAvro() {
    }

    private static CommandLine parseCmdLine(Options opts, String[] args) throws ParseException {
        opts.addOption("o", "outdir", true, "write avro files to this dir");
        CommandLineParser parser = new GnuParser();
        return parser.parse(opts, args);
    }

    public static void main(String[] args) throws Exception {
        Options opts = new Options();
        CommandLine cmd = null;
        try {
            cmd = parseCmdLine(opts, args);
        } catch (ParseException e) {
            System.err.println("ERROR: " + e.getMessage());
            System.exit(1);
        }
        String fn = null;
        try {
            fn = cmd.getArgs()[0];
        } catch (ArrayIndexOutOfBoundsException e) {
            HelpFormatter fmt = new HelpFormatter();
            fmt.printHelp("java ImageToAvro IMG_FILE", opts);
            System.exit(2);
        }
        String outDirName = null;
        if (cmd.hasOption("outdir")) {
            outDirName = cmd.getOptionValue("outdir");
            File outDir = new File(outDirName);
            if (!outDir.exists()) {
                boolean ret = outDir.mkdirs();
                if (!ret) {
                    System.err.format("ERROR: can't create %s\n", outDirName);
                    System.exit(3);
                }
            }
        }

        String name = PathTools.stripext(PathTools.basename(fn));
        ImageReader reader = new ImageReader();
        reader.setId(fn);
        LOGGER.info("Reading from {}", fn);
        BioImgFactory factory = new BioImgFactory(reader);
        int seriesCount = factory.getSeriesCount();

        // FIXME: add support for XY slicing
        String seriesName;
        String outFn;
        for (int i = 0; i < seriesCount; i++) {
            seriesName = String.format("%s_%d", name, i);
            outFn = new File(outDirName, seriesName + ".avro").getPath();
            factory.setSeries(i);
            factory.writeSeries(seriesName, outFn);
            LOGGER.info("Writing to {}", outFn);
        }
        reader.close();
        LOGGER.info("All done");
    }

}