tiffdecoder.java

本公司开发项目中本人做的公共类文件。如文件的操作

/**
 * 
 */
package com.intohotel.util;

import java.io.IOException;
import java.io.InputStream;
import java.io.RandomAccessFile;
import java.util.Vector;

/**
 * @author majh
 *
 */
public class TiffDecoder {
//	 tags
    public static final int NEW_SUBFILE_TYPE = 254;
    public static final int IMAGE_WIDTH = 256;
    public static final int IMAGE_LENGTH = 257;
    public static final int BITS_PER_SAMPLE = 258;
    public static final int COMPRESSION = 259;
    public static final int PHOTO_INTERP = 262;
    public static final int IMAGE_DESCRIPTION = 270;
    public static final int STRIP_OFFSETS = 273;
    public static final int SAMPLES_PER_PIXEL = 277;
    public static final int ROWS_PER_STRIP = 278;
    public static final int STRIP_BYTE_COUNT = 279;
    public static final int X_RESOLUTION = 282;
    public static final int Y_RESOLUTION = 283;
    public static final int PLANAR_CONFIGURATION = 284;
    public static final int RESOLUTION_UNIT = 296;
    public static final int SOFTWARE = 305;
    public static final int DATE_TIME = 306;
    public static final int PREDICTOR = 317;
    public static final int COLOR_MAP = 320;
    public static final int SAMPLE_FORMAT = 339;
    public static final int METAMORPH1 = 33628;
    public static final int METAMORPH2 = 33629;
    public static final int IPLAB = 34122;
    public static final int NIH_IMAGE_HDR = 43314;
    public static final int META_DATA_BYTE_COUNTS = 50838; // private tag registered with Adobe
    public static final int META_DATA = 50839; // private tag registered with Adobe
    
    //constants
    static final int UNSIGNED = 1;
    static final int SIGNED = 2;
    static final int FLOATING_POINT = 3;

    //field types
    static final int SHORT = 3;
    static final int LONG = 4;

    private String directory;
    private String name;
    private String url;
    protected RandomAccessStream in;
    protected boolean debugMode;
    private boolean littleEndian;
    private String dInfo;
    private int ifdCount;
    private int[] metaDataCounts;
        
    public TiffDecoder(String directory, String name) {
        this.directory = directory;
        this.name = name;
    }

    public TiffDecoder(InputStream in, String name) {
        directory = "";
        this.name = name;
        url = "";
        this.in = new RandomAccessStream(in);
    }

    final int getInt() throws IOException {
        int b1 = in.read();
        int b2 = in.read();
        int b3 = in.read();
        int b4 = in.read();
        if (littleEndian)
            return ((b4 << 24) + (b3 << 16) + (b2 << 8) + (b1 << 0));
        else
            return ((b1 << 24) + (b2 << 16) + (b3 << 8) + b4);
    }

    int getShort() throws IOException {
        int b1 = in.read();
        int b2 = in.read();
        if (littleEndian)
            return ((b2 << 8) + b1);
        else
            return ((b1 << 8) + b2);
    }

    int OpenImageFileHeader() throws IOException {
    // Open 8-byte Image File Header at start of file.
    // Returns the offset in bytes to the first IFD or -1
    // if this is not a valid tiff file.
        int byteOrder = in.readShort();
        if (byteOrder==0x4949) // "II"
            littleEndian = true;
        else if (byteOrder==0x4d4d) // "MM"
            littleEndian = false;
        else {
            in.close();
            return -1;
        }
        int magicNumber = getShort(); // 42
        int offset = getInt();
        return offset;
    }
        
    int getValue(int fieldType, int count) throws IOException {
        int value = 0;
        int unused;
        if (fieldType==SHORT && count==1) {
                value = getShort();
                unused = getShort();
        }
        else
            value = getInt();
        return value;
    }   
    
    void getColorMap(int offset, FileInfo fi) throws IOException {
        byte[] colorTable16 = new byte[768*2];
        int saveLoc = in.getFilePointer();
        in.seek(offset);
        in.readFully(colorTable16);
        in.seek(saveLoc);
        fi.lutSize = 256;
        fi.reds = new byte[256];
        fi.greens = new byte[256];
        fi.blues = new byte[256];
        int j = 0;
        if (littleEndian)
            j++;
        for (int i=0; i<256; i++) {
            fi.reds[i] = colorTable16[j];
            fi.greens[i] = colorTable16[512+j];
            fi.blues[i] = colorTable16[1024+j];
            j += 2;
        }
        fi.fileType = FileInfo.COLOR8;
    }
    
    byte[] getString(int count, int offset) throws IOException {
        count--; // skip null byte at end of string
        if (count<=0)
            return null;
        byte[] bytes = new byte[count];
        int saveLoc = in.getFilePointer();
        in.seek(offset);
        in.readFully(bytes);
        in.seek(saveLoc);
        return bytes;
    }

    /** Save the image description in the specified FileInfo. ImageJ
        saves spatial and density calibration data in this string. For
        stacks, it also saves the number of images to avoid having to
        decode an IFD for each image. */
    public void saveImageDescription(byte[] description, FileInfo fi) {
        if (description.length<7)
            return;
        //if (ij.IJ.debugMode)
        //    ij.IJ.log("Image Description: " + new String(description).replace('\n',' '));
        String id = new String(description);
        fi.description = id;
        int index1 = id.indexOf("images=");
        if (index1>0) {
            int index2 = id.indexOf("\n", index1);
            if (index2>0) {
                String images = id.substring(index1+7,index2);
                int n = (int)Tools.parseDouble(images, 0.0);
                if (n>1) fi.nImages = n;
            }
        }
    }

    void decodeNIHImageHeader(int offset, FileInfo fi) throws IOException {
        int saveLoc = in.getFilePointer();
        
        in.seek(offset+12);
        int version = in.readShort();
        
        in.seek(offset+160);
        double scale = in.readDouble();
        if (version>106 && scale!=0.0) {
            fi.pixelWidth = 1.0/scale;
            fi.pixelHeight = fi.pixelWidth;
        } 

        // spatial calibration
        in.seek(offset+172);
        int units = in.readShort();
        if (version<=153) units += 5;
        switch (units) {
            case 5: fi.unit = "nanometer"; break;
            case 6: fi.unit = "micrometer"; break;
            case 7: fi.unit = "mm"; break;
            case 8: fi.unit = "cm"; break;
            case 9: fi.unit = "meter"; break;
            case 10: fi.unit = "km"; break;
            case 11: fi.unit = "inch"; break;
            case 12: fi.unit = "ft"; break;
            case 13: fi.unit = "mi"; break;
        }

        // density calibration
        in.seek(offset+182);
        int fitType = in.read();
        int unused = in.read();
        int nCoefficients = in.readShort();
        if (fitType==11) {
            fi.calibrationFunction = 21; //Calibration.UNCALIBRATED_OD
            fi.valueUnit = "U. OD";
        } else if (fitType>=0 && fitType<=8 && nCoefficients>=1 && nCoefficients<=5) {
            switch (fitType) {
                case 0: fi.calibrationFunction = 0; break; //Calibration.STRAIGHT_LINE
                case 1: fi.calibrationFunction = 1; break; //Calibration.POLY2
                case 2: fi.calibrationFunction = 2; break; //Calibration.POLY3
                case 3: fi.calibrationFunction = 3; break; //Calibration.POLY4
                case 5: fi.calibrationFunction = 4; break; //Calibration.EXPONENTIAL
                case 6: fi.calibrationFunction = 5; break; //Calibration.POWER
                case 7: fi.calibrationFunction = 6; break; //Calibration.LOG
                case 8: fi.calibrationFunction = 10; break; //Calibration.RODBARD2 (NIH Image)
            }
            fi.coefficients = new double[nCoefficients];
            for (int i=0; i<nCoefficients; i++) {
                fi.coefficients[i] = in.readDouble();
            }
            in.seek(offset+234);
            int size = in.read();
            StringBuffer sb = new StringBuffer();
            if (size>=1 && size<=16) {
                for (int i=0; i<size; i++)
                    sb.append((char)(in.read()));
                fi.valueUnit = new String(sb);
            } else
                fi.valueUnit = " ";
        }
            
        in.seek(offset+260);
        int nImages = in.readShort();
        if(nImages>=2 && (fi.fileType==FileInfo.GRAY8||fi.fileType==FileInfo.COLOR8)) {
            fi.nImages = nImages;
            fi.pixelDepth = in.readFloat(); //SliceSpacing
            int skip = in.readShort();      //CurrentSlice
            fi.frameInterval = in.readFloat();
            //ij.IJ.write("fi.pixelDepth: "+fi.pixelDepth);
        }
            
        in.seek(offset+272);
        float aspectRatio = in.readFloat();
        if (version>140 && aspectRatio!=0.0)
            fi.pixelHeight = fi.pixelWidth/aspectRatio;
        
        in.seek(saveLoc);
    }
    
    void dumpTag(int tag, int count, int value, FileInfo fi) {
        String name;
        switch (tag) {
            case NEW_SUBFILE_TYPE: name="NewSubfileType"; break;
            case IMAGE_WIDTH: name="ImageWidth"; break;
            case IMAGE_LENGTH: name="ImageLength"; break;
            case STRIP_OFFSETS: name="StripOffsets"; break;
            case PHOTO_INTERP: name="PhotoInterp"; break;
            case IMAGE_DESCRIPTION: name="ImageDescription"; break;
            case BITS_PER_SAMPLE: name="BitsPerSample"; break;
            case SAMPLES_PER_PIXEL: name="SamplesPerPixel"; break;
            case ROWS_PER_STRIP: name="RowsPerStrip"; break;
            case STRIP_BYTE_COUNT: name="StripByteCount"; break;
            case X_RESOLUTION: name="XResolution"; break;
            case Y_RESOLUTION: name="YResolution"; break;
            case RESOLUTION_UNIT: name="ResolutionUnit"; break;
            case SOFTWARE: name="Software"; break;
            case DATE_TIME: name="DateTime"; break;
            case PLANAR_CONFIGURATION: name="PlanarConfiguration"; break;
            case COMPRESSION: name="Compression"; break; 
            case PREDICTOR: name="Predictor"; break; 
            case COLOR_MAP: name="ColorMap"; break; 
            case SAMPLE_FORMAT: name="SampleFormat"; break; 
            case NIH_IMAGE_HDR: name="NIHImageHeader"; break; 
            case META_DATA_BYTE_COUNTS: name="MetaDataByteCounts"; break; 
            case META_DATA: name="MetaData"; break; 
            default: name="???"; break;
        }
        String cs = (count==1)?"":", count=" + count;
        dInfo += "    " + tag + ", \"" + name + "\", value=" + value + cs + "\n";
        //ij.IJ.log(tag + ", \"" + name + "\", value=" + value + cs + "\n");
    }

    double getRational(int loc) throws IOException {
        int saveLoc = in.getFilePointer();
        in.seek(loc);
        int numerator = getInt();
        int denominator = getInt();
        in.seek(saveLoc);
        //System.out.println("numerator: "+numerator);
        //System.out.println("denominator: "+denominator);
        if (denominator!=0)
            return (double)numerator/denominator;
        else
            return 0.0;
    }
    
    FileInfo OpenIFD() throws IOException {
    // Get Image File Directory data
        int tag, fieldType, count, value;
        int nEntries = getShort();
        if (nEntries<1 || nEntries>1000)
            return null;
        ifdCount++;
        FileInfo fi = new FileInfo();