Binary3DImage.java

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package theba.core.gui;

import java.io.FileInputStream;
import java.io.RandomAccessFile;
import java.nio.ByteBuffer;
import java.nio.channels.FileChannel;
import java.util.StringTokenizer;

import theba.core.RegionMask;


public class Binary3DImage {
        private int x;

        private int y;

        private int z;

        public byte[] image;

        public int[] image2;

        private String filepath;

        private String filepathRLC;

        private RegionMask regionMask;

        public Binary3DImage(String pathname, int x, int y, int z) {
                this.x = x;
                this.y = y;
                this.z = z;
                regionMask = null;
                this.image = new byte[x * y * z / Byte.SIZE];
                this.image2 = new int[x * y * z / Integer.SIZE];
                this.filepath = pathname;
                StringTokenizer stringTokenizer = new StringTokenizer(pathname, ".");
                filepathRLC = new String(stringTokenizer.nextToken() + "_RLC."
                                + stringTokenizer.nextToken());
                System.out.println("image.length = " + image.length);
        }

        public Binary3DImage(RegionMask regionMask, int x, int y, int z) {
                this.x = x;
                this.y = y;
                this.z = z;
                this.regionMask = regionMask;
                this.image = new byte[x * y * z / Byte.SIZE];
                this.image2 = new int[x * y * z / Integer.SIZE];
                // this.filepath = pathname;
                // StringTokenizer stringTokenizer = new StringTokenizer(pathname, ".");
                // filepathRLC = new String(stringTokenizer.nextToken() + "_RLC." +
                // stringTokenizer.nextToken());
                System.out.println("image.length = " + image.length);
        }

        public boolean readImageFile() {
                ByteBuffer byteBuffer;
                FileChannel fileChannel;
                FileInputStream fileInputStream;
                byte[] bufData;

                try {
                        bufData = new byte[this.x * this.y / Byte.SIZE];
                        byteBuffer = ByteBuffer.wrap(bufData);
                        fileInputStream = new FileInputStream(filepath);
                        fileChannel = fileInputStream.getChannel();
                        int counter = 0;
                        for (int i = 0; i < this.z; i++) {
                                fileChannel.position(i * this.x * this.y / Byte.SIZE);
                                byteBuffer.position(0);
                                // Save position
                                int pos = byteBuffer.position();
                                // Set position to zero
                                byteBuffer.position(0);
                                while (byteBuffer.hasRemaining()) {
                                        byte b = byteBuffer.get();
                                        image[counter++] = b;
                                        // System.out.println(b & 0xFF);
                                }
                                byteBuffer.position(pos);
                        }
                        fileChannel.close();
                        fileInputStream.close();
                        System.out.println("Voxels read = " + counter);
                } catch (Exception e) {
                        e.printStackTrace();
                        return false;
                }
                return true;
        }

        public boolean readRLCCompressedImageFile() {
                RandomAccessFile raf;
                try {
                        raf = new RandomAccessFile(filepathRLC, "r");
                        int current = 0;
                        long size = raf.length() / 2;
                        int counter = 0;
                        int bitpos = 7;
                        byte b = 0;
                        for (int i = 0; i < size; i++) {
                                int a = raf.readUnsignedShort();
                                // System.out.println(a);
                                for (int j = 0; j < a; j++) {
                                        b |= (current << bitpos--);
                                        if (bitpos == -1) {
                                                image[counter++] = b;
                                                // System.out.println(b & 0xFF);
                                                // if (counter < 5230 && counter > 5220)
                                                // System.out.println(b & 0xFF);
                                                b = 0;
                                                bitpos = 7;
                                        }
                                }
                                current = (current == 0) ? 1 : 0;
                        }
                        raf.close();
                        System.out.println("Voxels read (RLC) = " + counter);
                } catch (Exception e) {
                        e.printStackTrace();
                        return false;
                }
                return true;
        }

        public void printImageArray() {
                for (int i = 0; i < image.length; i++) {
                        printByteContent(image[i]);
                }
        }

        public int compareByteArrays() {
                int a = 0;
                for (int i = 0; i < image.length; i++) {
                        if (image[i] != image2[i]) {
                                a++;
                                System.out.println(i + " " + image[i] + " " + image2[i]);
                        }
                }
                return a;
        }

        public byte getVoxelValue(int x, int y, int z) {
                int a = (x + this.x * y + this.x * this.y * z);
                // System.out.print( " " + a + " " );
                byte b = image[a / Byte.SIZE];
                // if (b > 0) System.out.println(b);
                int i = a % Byte.SIZE;
                byte c = (byte) (b >> (Byte.SIZE - 1 - i) & 0x01);
                // if (c == en) System.out.println("yeah");
                return c;
        }

        public int getVoxelValueInt(int x, int y, int z) {
                int a = (x + this.x * y + this.x * this.y * z);
                int b = image2[a / Integer.SIZE];
                int i = a % Integer.SIZE;
                int c = (b >> (Integer.SIZE - 1 - i) & 0x0001);
                return c;
        }

        public int[] getCell(int x, int y, int z) {
                int[] b = new int[8];
                if (regionMask == null) {
                        b[0] = getVoxelValue(x, y, z);
                        b[1] = getVoxelValue(x + 1, y, z);
                        b[2] = getVoxelValue(x, y + 1, z);
                        b[3] = getVoxelValue(x + 1, y + 1, z);
                        b[4] = getVoxelValue(x, y, z + 1);
                        b[5] = getVoxelValue(x + 1, y, z + 1);
                        b[6] = getVoxelValue(x, y + 1, z + 1);
                        b[7] = getVoxelValue(x + 1, y + 1, z + 1);
                } else {
                        b[0] = regionMask.isSet(x, y, z) ? 1 : 0;
                        b[1] = regionMask.isSet(x + 1, y, z) ? 1 : 0;
                        b[2] = regionMask.isSet(x, y + 1, z) ? 1 : 0;
                        b[3] = regionMask.isSet(x + 1, y + 1, z) ? 1 : 0;
                        b[4] = regionMask.isSet(x, y, z + 1) ? 1 : 0;
                        b[5] = regionMask.isSet(x + 1, y, z + 1) ? 1 : 0;
                        b[6] = regionMask.isSet(x, y + 1, z + 1) ? 1 : 0;
                        b[7] = regionMask.isSet(x + 1, y + 1, z + 1) ? 1 : 0;
                }
                return b;
        }

        public byte getByte(int position) {
                if (position >= x * y * z / Byte.SIZE)
                        throw new ArrayIndexOutOfBoundsException(
                                        "Position greater than size of image: " + position);
                // throw new ArrayIndexOutOfBoundsException();
                return image[position];
        }

        public static byte[] getByteList(byte bits) {
                byte[] b = new byte[Byte.SIZE];
                for (int i = 0; i < Byte.SIZE; i++) {
                        b[i] = (byte) (bits >> (Byte.SIZE - 1 - i) & 0x01);
                }
                return b;
        }

        public static void printByteContent(byte b) {
                for (int i = 0; i < Byte.SIZE; i++) {
                        System.out.print((b >> (Byte.SIZE - 1 - i) & 0x01) + " ");
                }
                System.out.println(" = " + (b & 0xFF));
        }

        public int getX() {
                return x;
        }

        public int getY() {
                return y;
        }

        public int getZ() {
                return z;
        }
}