package ij.io;
import ij.util.Tools;
import ij.IJ;
import java.io.*;
import java.util.*;
import java.net.*;
public class TiffDecoder {
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 ORIENTATION = 274;
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 ARTIST = 315;
public static final int HOST_COMPUTER = 316;
public static final int PREDICTOR = 317;
public static final int COLOR_MAP = 320;
public static final int TILE_WIDTH = 322;
public static final int SAMPLE_FORMAT = 339;
public static final int JPEG_TABLES = 347;
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; public static final int META_DATA = 50839;
static final int UNSIGNED = 1;
static final int SIGNED = 2;
static final int FLOATING_POINT = 3;
static final int SHORT = 3;
static final int LONG = 4;
static final int MAGIC_NUMBER = 0x494a494a; static final int INFO = 0x696e666f; static final int LABELS = 0x6c61626c; static final int RANGES = 0x72616e67; static final int LUTS = 0x6c757473; static final int PLOT = 0x706c6f74; static final int ROI = 0x726f6920; static final int OVERLAY = 0x6f766572; static final int PROPERTIES = 0x70726f70;
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;
private String tiffMetadata;
private int photoInterp;
public TiffDecoder(String directory, String name) {
if (directory==null)
directory = "";
directory = IJ.addSeparator(directory);
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);
}
final long getUnsignedInt() throws IOException {
return (long)getInt()&0xffffffffL;
}
final int getShort() throws IOException {
int b1 = in.read();
int b2 = in.read();
if (littleEndian)
return ((b2<<8) + b1);
else
return ((b1<<8) + b2);
}
final long readLong() throws IOException {
if (littleEndian)
return ((long)getInt()&0xffffffffL) + ((long)getInt()<<32);
else
return ((long)getInt()<<32) + ((long)getInt()&0xffffffffL);
}
final double readDouble() throws IOException {
return Double.longBitsToDouble(readLong());
}
long OpenImageFileHeader() throws IOException {
int byteOrder = in.readShort();
if (byteOrder==0x4949) littleEndian = true;
else if (byteOrder==0x4d4d) littleEndian = false;
else {
in.close();
return -1;
}
int magicNumber = getShort(); long offset = ((long)getInt())&0xffffffffL;
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(long offset, FileInfo fi) throws IOException {
byte[] colorTable16 = new byte[768*2];
long saveLoc = in.getLongFilePointer();
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++;
int sum = 0;
for (int i=0; i<256; i++) {
fi.reds[i] = colorTable16[j];
sum += fi.reds[i];
fi.greens[i] = colorTable16[512+j];
sum += fi.greens[i];
fi.blues[i] = colorTable16[1024+j];
sum += fi.blues[i];
j += 2;
}
if (sum!=0 && fi.fileType==FileInfo.GRAY8)
fi.fileType = FileInfo.COLOR8;
}
byte[] getString(int count, long offset) throws IOException {
count--; if (count<=3)
return null;
byte[] bytes = new byte[count];
long saveLoc = in.getLongFilePointer();
in.seek(offset);
in.readFully(bytes);
in.seek(saveLoc);
return bytes;
}
public void saveImageDescription(byte[] description, FileInfo fi) {
String id = new String(description);
boolean createdByImageJ = id.startsWith("ImageJ");
if (!createdByImageJ)
saveMetadata(getName(IMAGE_DESCRIPTION), id);
if (id.length()<7) return;
fi.description = id;
int index1 = id.indexOf("images=");
if (index1>0 && createdByImageJ && id.charAt(7)!='\n') {
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.compression==FileInfo.COMPRESSION_NONE)
fi.nImages = n;
}
}
}
public void saveMetadata(String name, String data) {
if (data==null) return;
String str = name+": "+data+"\n";
if (tiffMetadata==null)
tiffMetadata = str;
else
tiffMetadata += str;
}
void decodeNIHImageHeader(int offset, FileInfo fi) throws IOException {
long saveLoc = in.getLongFilePointer();
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;
}
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;
}
in.seek(offset+182);
int fitType = in.read();
int unused = in.read();
int nCoefficients = in.readShort();
if (fitType==11) {
fi.calibrationFunction = 21; fi.valueUnit = "U. OD";
} else if (fitType>=0 && fitType<=8 && nCoefficients>=1 && nCoefficients<=5) {
switch (fitType) {
case 0: fi.calibrationFunction = 0; break; case 1: fi.calibrationFunction = 1; break; case 2: fi.calibrationFunction = 2; break; case 3: fi.calibrationFunction = 3; break; case 5: fi.calibrationFunction = 4; break; case 6: fi.calibrationFunction = 5; break; case 7: fi.calibrationFunction = 6; break; case 8: fi.calibrationFunction = 10; break; }
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(); int skip = in.readShort(); fi.frameInterval = in.readFloat();
}
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) {
long lvalue = ((long)value)&0xffffffffL;
String name = getName(tag);
String cs = (count==1)?"":", count=" + count;
dInfo += " " + tag + ", \"" + name + "\", value=" + lvalue + cs + "\n";
}
String getName(int tag) {
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 ORIENTATION: name="Orientation"; 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 ARTIST: name="Artist"; break;
case HOST_COMPUTER: name="HostComputer"; 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 JPEG_TABLES: name="JPEGTables"; 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;
}
return name;
}
double getRational(long loc) throws IOException {
long saveLoc = in.getLongFilePointer();
in.seek(loc);
double numerator = getUnsignedInt();
double denominator = getUnsignedInt();
in.seek(saveLoc);
if (denominator!=0.0)
return numerator/denominator;
else
return 0.0;
}
FileInfo OpenIFD() throws IOException {
int tag, fieldType, count, value;
int nEntries = getShort();
if (nEntries<1 || nEntries>1000)
return null;
ifdCount++;
if ((ifdCount%50)==0 && ifdCount>0)
ij.IJ.showStatus("Opening IFDs: "+ifdCount);
FileInfo fi = new FileInfo();
fi.fileType = FileInfo.BITMAP; for (int i=0; i<nEntries; i++) {
tag = getShort();
fieldType = getShort();
count = getInt();
value = getValue(fieldType, count);
long lvalue = ((long)value)&0xffffffffL;
if (debugMode && ifdCount<10) dumpTag(tag, count, value, fi);
switch (tag) {
case IMAGE_WIDTH:
fi.width = value;
fi.intelByteOrder = littleEndian;
break;
case IMAGE_LENGTH:
fi.height = value;
break;
case STRIP_OFFSETS:
if (count==1)
fi.stripOffsets = new int[] {value};
else {
long saveLoc = in.getLongFilePointer();
in.seek(lvalue);
fi.stripOffsets = new int[count];
for (int c=0; c<count; c++)
fi.stripOffsets[c] = getInt();
in.seek(saveLoc);
}
fi.offset = count>0?fi.stripOffsets[0]:value;
if (count>1 && (((long)fi.stripOffsets[count-1])&0xffffffffL)<(((long)fi.stripOffsets[0])&0xffffffffL))
fi.offset = fi.stripOffsets[count-1];
break;
case STRIP_BYTE_COUNT:
if (count==1)
fi.stripLengths = new int[] {value};
else {
long saveLoc = in.getLongFilePointer();
in.seek(lvalue);
fi.stripLengths = new int[count];
for (int c=0; c<count; c++) {
if (fieldType==SHORT)
fi.stripLengths[c] = getShort();
else
fi.stripLengths[c] = getInt();
}
in.seek(saveLoc);
}
break;
case PHOTO_INTERP:
photoInterp = value;
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;
else if (value==32)
fi.fileType = FileInfo.GRAY32_INT;
else if (value==12)
fi.fileType = FileInfo.GRAY12_UNSIGNED;
else if (value==1)
fi.fileType = FileInfo.BITMAP;
else
error("Unsupported BitsPerSample: " + value);
} else if (count>1) {
long saveLoc = in.getLongFilePointer();
in.seek(lvalue);
int bitDepth = getShort();
if (bitDepth==8)
fi.fileType = FileInfo.GRAY8;
else if (bitDepth==16)
fi.fileType = FileInfo.GRAY16_UNSIGNED;
else
error("ImageJ cannot open interleaved "+bitDepth+"-bit images.");
in.seek(saveLoc);
}
break;
case SAMPLES_PER_PIXEL:
fi.samplesPerPixel = value;
if (value==3 && fi.fileType==FileInfo.GRAY8)
fi.fileType = FileInfo.RGB;
else if (value==3 && fi.fileType==FileInfo.GRAY16_UNSIGNED)
fi.fileType = FileInfo.RGB48;
else if (value==4 && fi.fileType==FileInfo.GRAY8)
fi.fileType = photoInterp==5?FileInfo.CMYK:FileInfo.ARGB;
else if (value==4 && fi.fileType==FileInfo.GRAY16_UNSIGNED) {
fi.fileType = FileInfo.RGB48;
if (photoInterp==5) fi.whiteIsZero = true;
}
break;
case ROWS_PER_STRIP:
fi.rowsPerStrip = value;
break;
case X_RESOLUTION:
double xScale = getRational(lvalue);
if (xScale!=0.0) fi.pixelWidth = 1.0/xScale;
break;
case Y_RESOLUTION:
double yScale = getRational(lvalue);
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) {
if (fi.pixelWidth==1.0/72.0) {
fi.pixelWidth = 1.0;
fi.pixelHeight = 1.0;
} else
fi.unit = "inch";
} else if (value==3)
fi.unit = "cm";
break;
case PLANAR_CONFIGURATION: if (value==2 && fi.fileType==FileInfo.RGB48)
fi.fileType = FileInfo.RGB48_PLANAR;
else if (value==2 && fi.fileType==FileInfo.RGB)
fi.fileType = FileInfo.RGB_PLANAR;
else if (value!=2 && !(fi.samplesPerPixel==1||fi.samplesPerPixel==3||fi.samplesPerPixel==4)) {
String msg = "Unsupported SamplesPerPixel: " + fi.samplesPerPixel;
error(msg);
}
break;
case COMPRESSION:
if (value==5) { fi.compression = FileInfo.LZW;
if (fi.fileType==FileInfo.GRAY12_UNSIGNED)
error("ImageJ cannot open 12-bit LZW-compressed TIFFs");
} else if (value==32773) fi.compression = FileInfo.PACK_BITS;
else if (value==32946 || value==8) fi.compression = FileInfo.ZIP;
else if (value!=1 && value!=0 && !(value==7&&fi.width<500)) {
fi.compression = FileInfo.COMPRESSION_UNKNOWN;
error("ImageJ cannot open TIFF files " +
"compressed in this fashion ("+value+")");
}
break;
case SOFTWARE: case DATE_TIME: case HOST_COMPUTER: case ARTIST:
if (ifdCount==1) {
byte[] bytes = getString(count, lvalue);
String s = bytes!=null?new String(bytes):null;
saveMetadata(getName(tag), s);
}
break;
case PREDICTOR:
if (value==2 && fi.compression==FileInfo.LZW)
fi.compression = FileInfo.LZW_WITH_DIFFERENCING;
if (value==3)
IJ.log("TiffDecoder: unsupported predictor value of 3");
break;
case COLOR_MAP:
if (count==768)
getColorMap(lvalue, fi);
break;
case TILE_WIDTH:
error("ImageJ cannot open tiled TIFFs.\nTry using the Bio-Formats plugin.");
break;
case SAMPLE_FORMAT:
if (fi.fileType==FileInfo.GRAY32_INT && value==FLOATING_POINT)
fi.fileType = FileInfo.GRAY32_FLOAT;
if (fi.fileType==FileInfo.GRAY16_UNSIGNED) {
if (value==SIGNED)
fi.fileType = FileInfo.GRAY16_SIGNED;
if (value==FLOATING_POINT)
error("ImageJ cannot open 16-bit float TIFFs");
}
break;
case JPEG_TABLES:
if (fi.compression==FileInfo.JPEG)
error("Cannot open JPEG-compressed TIFFs with separate tables");
break;
case IMAGE_DESCRIPTION:
if (ifdCount==1) {
byte[] s = getString(count, lvalue);
if (s!=null) saveImageDescription(s,fi);
}
break;
case ORIENTATION:
fi.nImages = 0; break;
case METAMORPH1: case METAMORPH2:
if ((name.indexOf(".STK")>0||name.indexOf(".stk")>0) && fi.compression==FileInfo.COMPRESSION_NONE) {
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;
case META_DATA_BYTE_COUNTS:
long saveLoc = in.getLongFilePointer();
in.seek(lvalue);
metaDataCounts = new int[count];
for (int c=0; c<count; c++)
metaDataCounts[c] = getInt();
in.seek(saveLoc);
break;
case META_DATA:
getMetaData(value, fi);
break;
default:
if (tag>10000 && tag<32768 && ifdCount>1)
return null;
}
}
fi.fileFormat = fi.TIFF;
fi.fileName = name;
fi.directory = directory;
if (url!=null)
fi.url = url;
return fi;
}
void getMetaData(int loc, FileInfo fi) throws IOException {
if (metaDataCounts==null || metaDataCounts.length==0)
return;
int maxTypes = 10;
long saveLoc = in.getLongFilePointer();
in.seek(loc);
int n = metaDataCounts.length;
int hdrSize = metaDataCounts[0];
if (hdrSize<12 || hdrSize>804) {
in.seek(saveLoc);
return;
}
int magicNumber = getInt();
if (magicNumber!=MAGIC_NUMBER) { in.seek(saveLoc);
return;
}
int nTypes = (hdrSize-4)/8;
int[] types = new int[nTypes];
int[] counts = new int[nTypes];
if (debugMode) {
dInfo += "Metadata:\n";
dInfo += " Entries: "+(metaDataCounts.length-1)+"\n";
dInfo += " Types: "+nTypes+"\n";
}
int extraMetaDataEntries = 0;
int index = 1;
for (int i=0; i<nTypes; i++) {
types[i] = getInt();
counts[i] = getInt();
if (types[i]<0xffffff)
extraMetaDataEntries += counts[i];
if (debugMode) {
String id = "unknown";
if (types[i]==INFO) id = "Info property";
if (types[i]==LABELS) id = "slice labels";
if (types[i]==RANGES) id = "display ranges";
if (types[i]==LUTS) id = "luts";
if (types[i]==PLOT) id = "plot";
if (types[i]==ROI) id = "roi";
if (types[i]==OVERLAY) id = "overlay";
if (types[i]==PROPERTIES) id = "properties";
int len = metaDataCounts[index];
int count = counts[i];
index += count;
if (index>=metaDataCounts.length) index=1;
String lenstr = count==1?", length=":", length[0]=";
dInfo += " "+i+", type="+id+", count="+count+lenstr+len+"\n";
}
}
fi.metaDataTypes = new int[extraMetaDataEntries];
fi.metaData = new byte[extraMetaDataEntries][];
int start = 1;
int eMDindex = 0;
for (int i=0; i<nTypes; i++) {
if (types[i]==INFO)
getInfoProperty(start, fi);
else if (types[i]==LABELS)
getSliceLabels(start, start+counts[i]-1, fi);
else if (types[i]==RANGES)
getDisplayRanges(start, fi);
else if (types[i]==LUTS)
getLuts(start, start+counts[i]-1, fi);
else if (types[i]==PLOT)
getPlot(start, fi);
else if (types[i]==ROI)
getRoi(start, fi);
else if (types[i]==OVERLAY)
getOverlay(start, start+counts[i]-1, fi);
else if (types[i]==PROPERTIES)
getProperties(start, start+counts[i]-1, fi);
else if (types[i]<0xffffff) {
for (int j=start; j<start+counts[i]; j++) {
int len = metaDataCounts[j];
fi.metaData[eMDindex] = new byte[len];
in.readFully(fi.metaData[eMDindex], len);
fi.metaDataTypes[eMDindex] = types[i];
eMDindex++;
}
} else
skipUnknownType(start, start+counts[i]-1);
start += counts[i];
}
in.seek(saveLoc);
}
void getInfoProperty(int first, FileInfo fi) throws IOException {
int len = metaDataCounts[first];
byte[] buffer = new byte[len];
in.readFully(buffer, len);
len /= 2;
char[] chars = new char[len];
if (littleEndian) {
for (int j=0, k=0; j<len; j++)
chars[j] = (char)(buffer[k++]&255 + ((buffer[k++]&255)<<8));
} else {
for (int j=0, k=0; j<len; j++)
chars[j] = (char)(((buffer[k++]&255)<<8) + (buffer[k++]&255));
}
fi.info = new String(chars);
}
void getSliceLabels(int first, int last, FileInfo fi) throws IOException {
fi.sliceLabels = new String[last-first+1];
int index = 0;
byte[] buffer = new byte[metaDataCounts[first]];
for (int i=first; i<=last; i++) {
int len = metaDataCounts[i];
if (len>0) {
if (len>buffer.length)
buffer = new byte[len];
in.readFully(buffer, len);
len /= 2;
char[] chars = new char[len];
if (littleEndian) {
for (int j=0, k=0; j<len; j++)
chars[j] = (char)(buffer[k++]&255 + ((buffer[k++]&255)<<8));
} else {
for (int j=0, k=0; j<len; j++)
chars[j] = (char)(((buffer[k++]&255)<<8) + (buffer[k++]&255));
}
fi.sliceLabels[index++] = new String(chars);
} else
fi.sliceLabels[index++] = null;
}
}
void getDisplayRanges(int first, FileInfo fi) throws IOException {
int n = metaDataCounts[first]/8;
fi.displayRanges = new double[n];
for (int i=0; i<n; i++)
fi.displayRanges[i] = readDouble();
}
void getLuts(int first, int last, FileInfo fi) throws IOException {
fi.channelLuts = new byte[last-first+1][];
int index = 0;
for (int i=first; i<=last; i++) {
int len = metaDataCounts[i];
fi.channelLuts[index] = new byte[len];
in.readFully(fi.channelLuts[index], len);
index++;
}
}
void getRoi(int first, FileInfo fi) throws IOException {
int len = metaDataCounts[first];
fi.roi = new byte[len];
in.readFully(fi.roi, len);
}
void getPlot(int first, FileInfo fi) throws IOException {
int len = metaDataCounts[first];
fi.plot = new byte[len];
in.readFully(fi.plot, len);
}
void getOverlay(int first, int last, FileInfo fi) throws IOException {
fi.overlay = new byte[last-first+1][];
int index = 0;
for (int i=first; i<=last; i++) {
int len = metaDataCounts[i];
fi.overlay[index] = new byte[len];
in.readFully(fi.overlay[index], len);
index++;
}
}
void getProperties(int first, int last, FileInfo fi) throws IOException {
fi.properties = new String[last-first+1];
int index = 0;
byte[] buffer = new byte[metaDataCounts[first]];
for (int i=first; i<=last; i++) {
int len = metaDataCounts[i];
if (len>buffer.length)
buffer = new byte[len];
in.readFully(buffer, len);
len /= 2;
char[] chars = new char[len];
if (littleEndian) {
for (int j=0, k=0; j<len; j++)
chars[j] = (char)(buffer[k++]&255 + ((buffer[k++]&255)<<8));
} else {
for (int j=0, k=0; j<len; j++)
chars[j] = (char)(((buffer[k++]&255)<<8) + (buffer[k++]&255));
}
fi.properties[index++] = new String(chars);
}
}
void error(String message) throws IOException {
if (in!=null) in.close();
throw new IOException(message);
}
void skipUnknownType(int first, int last) throws IOException {
byte[] buffer = new byte[metaDataCounts[first]];
for (int i=first; i<=last; i++) {
int len = metaDataCounts[i];
if (len>buffer.length)
buffer = new byte[len];
in.readFully(buffer, len);
}
}
public void enableDebugging() {
debugMode = true;
}
public FileInfo[] getTiffInfo() throws IOException {
long ifdOffset;
ArrayList list = new ArrayList();
if (in==null)
in = new RandomAccessStream(new RandomAccessFile(new File(directory+name), "r"));
ifdOffset = OpenImageFileHeader();
if (ifdOffset<0L) {
in.close();
return null;
}
if (debugMode) dInfo = "\n " + name + ": opening\n";
while (ifdOffset>0L) {
in.seek(ifdOffset);
FileInfo fi = OpenIFD();
if (fi!=null) {
list.add(fi);
ifdOffset = ((long)getInt())&0xffffffffL;
} else
ifdOffset = 0L;
if (debugMode && ifdCount<10) dInfo += "nextIFD=" + ifdOffset + "\n";
if (fi!=null && fi.nImages>1)
ifdOffset = 0L; }
if (list.size()==0) {
in.close();
return null;
} else {
FileInfo[] info = (FileInfo[])list.toArray(new FileInfo[list.size()]);
if (debugMode) info[0].debugInfo = dInfo;
if (url!=null) {
in.seek(0);
info[0].inputStream = in;
} else
in.close();
if (info[0].info==null)
info[0].info = tiffMetadata;
FileInfo fi = info[0];
if (fi.fileType==FileInfo.GRAY16_UNSIGNED && fi.description==null)
fi.lutSize = 0; if (debugMode) {
int n = info.length;
fi.debugInfo += "number of IFDs: "+ n + "\n";
fi.debugInfo += "offset to first image: "+fi.getOffset()+ "\n";
fi.debugInfo += "gap between images: "+getGapInfo(info) + "\n";
fi.debugInfo += "little-endian byte order: "+fi.intelByteOrder + "\n";
}
return info;
}
}
String getGapInfo(FileInfo[] fi) {
if (fi.length<2) return "0";
long minGap = Long.MAX_VALUE;
long maxGap = -Long.MAX_VALUE;
for (int i=1; i<fi.length; i++) {
long gap = fi[i].getOffset()-fi[i-1].getOffset();
if (gap<minGap) minGap = gap;
if (gap>maxGap) maxGap = gap;
}
long imageSize = fi[0].width*fi[0].height*fi[0].getBytesPerPixel();
minGap -= imageSize;
maxGap -= imageSize;
if (minGap==maxGap)
return ""+minGap;
else
return "varies ("+minGap+" to "+maxGap+")";
}
}