TiffDecoder.java

package ij.io;
import java.io.*;
import java.util.*;
import java.net.*;

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 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;
    
    //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;
        
    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;
    }

    public void decodeImageDescription(byte[] description, FileInfo fi) {
        if (description.length<7)
            return;
        if (ij.IJ.debugMode)
            ij.IJ.log("Image Description: " + new String(description).replace('\n',' '));
        if (!new String(description,0,6).equals("ImageJ"))
            return;
        fi.description = new String(description);
    }

    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 = 7; break; //Calibration.RODBARD
            }
            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 COLOR_MAP: name="ColorMap"; break; 
            case SAMPLE_FORMAT: name="SampleFormat"; break; 
            case NIH_IMAGE_HDR: name="NIHImageHeader"; break; 
            default: name="???"; break;
        }
        String cs = (count==1)?"":", count=" + count;
        dInfo += "    " + tag + ", \"" + name + "\", value=" + value + cs + "\n";
        //ij.IJ.write(tag + ", \"" + name + "\", value=" + value + cs);
    }

    double getRational(int loc) throws IOException {
        int saveLoc = in.getFilePointer();
        in.seek(loc);
        int numerator = getInt();
        int denominator = getInt();
        in.seek(saveLoc);
        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)
            return null;
        ifdCount++;
        FileInfo fi = new FileInfo();
        for (int i=0; i<nEntries; i++) {
            tag = getShort();
            fieldType = getShort();
            count = getInt();
            value = getValue(fieldType, count);
            if (debugMode) dumpTag(tag, count, value, fi);
            //ij.IJ.write(i+"/"+nEntries+" "+tag + ", count=" + count + ", value=" + value);
            //if (tag==0) return null;
            switch (tag) {
                case IMAGE_WIDTH: 
                    fi.width = value;
                    break;
                case IMAGE_LENGTH: 
                    fi.height = value;
                    break;
                case STRIP_OFFSETS: 
                    if (count==1)
                        fi.offset = value;
                    else {
                        int saveLoc = in.getFilePointer();
                        in.seek(value);
                        fi.offset = getInt(); // Assumes contiguous strips
                        in.seek(saveLoc);
                    }
                    break;
                case PHOTO_INTERP:
                    fi.whiteIsZero = value==0;
                    break;
                case BITS_PER_SAMPLE:
                        if (count==1) {
                            if (value==8)
                                fi.fileType = FileInfo.GRAY8;
                            else if (value==16) {
                                fi.fileType = FileInfo.GRAY16_UNSIGNED;
                                fi.intelByteOrder = littleEndian;
                            }
                            else if (value==32) {
                                fi.fileType = FileInfo.GRAY32_INT;
                                fi.intelByteOrder = littleEndian;
                            } else if (value==1)
                                fi.fileType = FileInfo.BITMAP;
                            else
                                throw new IOException("Unsupported BitsPerSample: " + value);
                        } else if (count==3) {
                            int saveLoc = in.getFilePointer();
                            in.seek(value);
                            int bitDepth = getShort();
                            if (!(bitDepth==8||bitDepth==16))
                                throw new IOException("ImageJ can only open 8 and 16 bit/channel RGB images");
                            if (bitDepth==16) {
                                fi.intelByteOrder = littleEndian;
                                fi.fileType = FileInfo.RGB48;
                            }
                            in.seek(saveLoc);
                        }
                        break;
                case SAMPLES_PER_PIXEL:
                    if (value==3 && fi.fileType!=FileInfo.RGB48)
                        fi.fileType = FileInfo.RGB;
                    else if (!(value==1||value==3)) {
                        String msg = "Unsupported SamplesPerPixel: " + value;
                        if (value==4)
                            msg += " \n \n" + "ImageJ cannot open CMYK and RGB+alpha TIFFs";
                        throw new IOException(msg);
                    }
                    break;
                case X_RESOLUTION:
                    double xScale = getRational(value); 
                    if (xScale!=0.0) fi.pixelWidth = 1.0/xScale; 
                    break;
                case Y_RESOLUTION:
                    double yScale = getRational(value); 
                    if (yScale!=0.0) fi.pixelHeight = 1.0/yScale; 
                    break;
                case RESOLUTION_UNIT:
                    if (value==1&&fi.unit==null)
                        fi.unit = " ";
                    else if (value==2)
                        fi.unit = "inch";
                    else if (value==3)
                        fi.unit = "cm";
                    break;
                case PLANAR_CONFIGURATION:
                    if (value==2 && fi.fileType==FileInfo.RGB48)
                            throw new IOException("ImageJ cannot open planar 48-bit RGB images");
                    if (value==2 && fi.fileType==FileInfo.RGB)
                        fi.fileType = FileInfo.RGB_PLANAR;
                    break;
                case COMPRESSION:
                    if (value!=1 && value!=7) // don't abort with Spot camera compressed (7) thumbnails
                        throw new IOException("ImageJ cannot open compressed TIFF files ("+value+")");
                    break;
                case COLOR_MAP: 
                    if (count==768 && fi.fileType==fi.GRAY8)
                        getColorMap(value, fi);
                    break;
                case SAMPLE_FORMAT:
                    if (fi.fileType==FileInfo.GRAY32_INT && value==FLOATING_POINT)
                        fi.fileType = FileInfo.GRAY32_FLOAT;
                    if (fi.fileType==FileInfo.GRAY16_UNSIGNED && value==SIGNED)
                        fi.fileType = FileInfo.GRAY16_SIGNED;
                    break;
                case IMAGE_DESCRIPTION: 
                    if (ifdCount==1) {
                        byte[] s = getString(count,value);
                        if (s!=null) decodeImageDescription(s,fi);
                    }
                    break;
                case METAMORPH1: case METAMORPH2:
                    if (name.indexOf(".STK")>0 || name.indexOf(".stk")>0) {
                        if (tag==METAMORPH2)
                            fi.nImages=count;
                        else
                            fi.nImages=9999;
                    }
                    break;
                case IPLAB: 
                    fi.nImages=value;
                    break;
                case NIH_IMAGE_HDR: 
                    if (count==256)
                        decodeNIHImageHeader(value, fi);
                    break;
                default:
            }
        }
        fi.fileFormat = fi.TIFF;
        fi.fileName = name;
        fi.directory = directory;
        if (url!=null)
            fi.url = url;
        if (debugMode) dInfo += "    offset=" + fi.offset + "\n";
        return fi;
    }


    public void enableDebugging() {
        debugMode = true;
    }
    
    
    public FileInfo[] getTiffInfo() throws IOException {
        int ifdOffset;
        Vector info;
                
        if (in==null)
            in = new RandomAccessStream(new RandomAccessFile(directory + name, "r"));
        info = new Vector();
        ifdOffset = OpenImageFileHeader();
        if (ifdOffset<0) {
            in.close();
            return null;
        }
        if (debugMode) dInfo = "\n  " + name + ": opening\n";
        while (ifdOffset>0) {
            in.seek(ifdOffset);
            FileInfo fi = OpenIFD();
            //ij.IJ.write(""+fi);
            if (fi!=null)
                info.addElement(fi);
            ifdOffset = getInt();
            if (debugMode) dInfo += "  nextIFD=" + ifdOffset + "\n";
            if (fi!=null && fi.nImages>1) // ignore extra IFDs in ImageJ and NIH Image stacks
                ifdOffset = 0;
        }
        if (info.size()==0) {
            in.close();
            return null;
        } else {
            FileInfo[] fi = new FileInfo[info.size()];
            info.copyInto((Object[])fi);
            if (debugMode) fi[0].info = dInfo;
            if (url!=null) {
                in.seek(0);
                fi[0].inputStream = in;
            } else
                in.close();
            return fi;
        }
    }

}