it.crs4.features.BioImgRecordReader.java Source code

Introduction

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

Source

/**
 * BEGIN_COPYRIGHT
 *
 * Copyright (C) 2014-2017 Open Microscopy Environment:
 *   - University of Dundee
 *   - 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.IOException;

import org.apache.commons.logging.LogFactory;
import org.apache.commons.logging.Log;

import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.NullWritable;
import org.apache.hadoop.mapreduce.InputSplit;
import org.apache.hadoop.mapreduce.RecordReader;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.mapreduce.lib.input.FileSplit;

import org.apache.avro.generic.IndexedRecord;

import loci.formats.ImageReader;
import loci.formats.FormatException;

public class BioImgRecordReader extends RecordReader<NullWritable, IndexedRecord> {

    private static final Log LOG = LogFactory.getLog(BioImgRecordReader.class);

    private ImageReader reader;
    private BioImgFactory factory;
    private int globalPlaneIdx;
    private int planeCounter;
    private int nPlanes;
    private int planesPerSeries;
    private String name;
    private IndexedRecord value;

    public void initialize(InputSplit genericSplit, TaskAttemptContext context) throws IOException {
        FileSplit split = (FileSplit) genericSplit;
        globalPlaneIdx = (int) split.getStart();
        nPlanes = (int) split.getLength();
        Path file = split.getPath();
        FileSystem fs = file.getFileSystem(context.getConfiguration());
        String absPathName = fs.getFileStatus(file).getPath().toString();
        reader = new ImageReader();
        try {
            reader.setId(absPathName);
        } catch (FormatException e) {
            throw new RuntimeException("FormatException: " + e.getMessage());
        }
        planesPerSeries = reader.getImageCount();
        factory = new BioImgFactory(reader, absPathName);
        name = PathTools.stripext(PathTools.basename(absPathName));
        planeCounter = 0;
    }

    public boolean nextKeyValue() throws IOException {
        if (planeCounter >= nPlanes) {
            value = null;
            return false;
        }
        int seriesIdx = globalPlaneIdx / planesPerSeries;
        int planeIdx = globalPlaneIdx % planesPerSeries;
        LOG.debug(String.format("series: %d, plane: %d", seriesIdx, planeIdx));
        factory.setSeries(seriesIdx);
        try {
            // TODO: support x/y slicing
            value = factory.build(String.format("%s_%d", name, seriesIdx), planeIdx);
        } catch (FormatException e) {
            throw new RuntimeException("FormatException: " + e.getMessage());
        }
        planeCounter++;
        globalPlaneIdx++;
        return true;
    }

    @Override
    public NullWritable getCurrentKey() {
        return NullWritable.get();
    }

    @Override
    public IndexedRecord getCurrentValue() {
        return value;
    }

    public float getProgress() throws IOException {
        return Math.min(1.0f, (planeCounter + 1) / (float) nPlanes);
    }

    public synchronized void close() throws IOException {
        if (reader != null) {
            reader.close();
        }
    }
}