RawDataLoader.java

package azgracompress.io.loader;

import azgracompress.data.ImageU16;
import azgracompress.data.V3i;
import azgracompress.io.FileInputData;
import azgracompress.io.InputData;
import azgracompress.utilities.TypeConverter;

import java.io.*;
import java.util.Arrays;

public class RawDataLoader implements IPlaneLoader {
    private final FileInputData inputDataInfo;

    public RawDataLoader(final FileInputData inputDataInfo) {
        this.inputDataInfo = inputDataInfo;
    }

    @Override
    public ImageU16 loadPlaneU16(int plane) throws IOException {
        byte[] buffer;
        final V3i rawDataDimension = inputDataInfo.getDimensions();

        try (FileInputStream fileStream = new FileInputStream(inputDataInfo.getFilePath())) {
            final long planeSize = (long) rawDataDimension.getX() * (long) rawDataDimension.getY() * 2;
            final long expectedFileSize = planeSize * rawDataDimension.getZ();
            final long fileSize = fileStream.getChannel().size();


            if (expectedFileSize != fileSize) {
                throw new IOException(
                        "File specified by `rawFile` doesn't contains raw data for image of dimensions " +
                                "`rawDataDimension`");
            }

            final long planeOffset = plane * planeSize;

            buffer = new byte[(int) planeSize];
            if (fileStream.skip(planeOffset) != planeOffset) {
                throw new IOException("Failed to skip.");
            }
            if (fileStream.read(buffer, 0, (int) planeSize) != planeSize) {
                throw new IOException("Read wrong number of bytes.");
            }
        }

        return new ImageU16(rawDataDimension.getX(),
                            rawDataDimension.getY(),
                            TypeConverter.unsignedShortBytesToIntArray(buffer));
    }

    @Override
    public int[] loadPlanesU16Data(int[] planes) throws IOException {
        if (planes.length < 1) {
            return new int[0];
        } else if (planes.length == 1) {
            return loadPlaneU16(planes[0]).getData();
        }

        final int planeValueCount = inputDataInfo.getDimensions().getX() * inputDataInfo.getDimensions().getY();
        final long planeDataSize = 2 * (long) planeValueCount;

        final long totalValueCount = (long) planeValueCount * planes.length;

        if (totalValueCount > (long) Integer.MAX_VALUE) {
            throw new IOException("Integer count is too big.");
        }

        int[] values = new int[(int) totalValueCount];

        Arrays.sort(planes);

        try (FileInputStream fileStream = new FileInputStream(inputDataInfo.getFilePath());
             DataInputStream dis = new DataInputStream(new BufferedInputStream(fileStream, 8192))) {

            int lastIndex = 0;
            int valIndex = 0;

            for (final int planeIndex : planes) {
                // Skip specific number of bytes to get to the next plane.
                final int requestedSkip = (planeIndex == 0) ? 0 : ((planeIndex - lastIndex) - 1) * (int) planeDataSize;
                lastIndex = planeIndex;

                final int actualSkip = dis.skipBytes(requestedSkip);
                if (requestedSkip != actualSkip) {
                    throw new IOException("Skip operation failed.");
                }

                for (int i = 0; i < planeValueCount; i++) {
                    values[valIndex++] = dis.readUnsignedShort();
                }

            }
        }

        return values;
    }

    @Override
    public int[] loadAllPlanesU16Data() throws IOException {
        final V3i imageDims = inputDataInfo.getDimensions();
        final long dataSize = (long) imageDims.getX() * (long) imageDims.getY() * (long) imageDims.getZ();

        if (dataSize > (long) Integer.MAX_VALUE) {
            throw new IOException("RawFile size is too big.");
        }

        int[] values = new int[(int) dataSize];

        try (FileInputStream fileStream = new FileInputStream(inputDataInfo.getFilePath());
             DataInputStream dis = new DataInputStream(new BufferedInputStream(fileStream, 8192))) {

            for (int i = 0; i < (int) dataSize; i++) {
                values[i] = dis.readUnsignedShort();
            }
        }

        return values;
    }
}