protected void createInstance(uint numPlane, TiffInfoCollection tifInfo)
{
allInfo = tifInfo.InfoCollection;
this.numPlane = Convert.ToInt32(numPlane);
StkInfoCollection stkInfo = null;
if (tifInfo is StkInfoCollection)
{
stkInfo = tifInfo as StkInfoCollection;
}
if (stkInfo != null && stkInfo.NumberOfPlanes == numPlane)
{
for (uint i = 0; i < this.numPlane; i++)
{
zDistance.Add(stkInfo.ZDistance[i].Clone() as TiffInfo);
creationTime.Add(stkInfo.CreationTime[i].Clone() as TiffInfo);
modifiedTime.Add(stkInfo.ModifiedTime[i].Clone() as TiffInfo);
wavelength.Add(stkInfo.Wavelength[i].Clone() as TiffInfo);
}
UIC1 = stkInfo.UIC1DataDeepCopy;
UIC4 = stkInfo.UIC4DataDeepCopy;
uint[] num, denom;
if (!UIC4.ContainsKey(AbsoluteZ))
{
num = new uint[numPlane];
denom = new uint[numPlane];
for (int i = 0; i < numPlane; i++)
{
denom[i] = 1;
}
setAbsoluteZUIC4(num, denom);
setAbsoluteZUIC1(num, denom);
}
else
{
try {
getAbsoluteZUIC4(out num, out denom);
setAbsoluteZUIC1(num, denom);
} catch {
num = new uint[numPlane];
denom = new uint[numPlane];
for (int i = 0; i < numPlane; i++)
{
denom[i] = 1;
}
setAbsoluteZUIC4(num, denom);
setAbsoluteZUIC1(num, denom);
}
}
}
else
{
createUICtagInfo();
}
}
/// <summary>
/// Write RGB image data to a stack image. Also test the availability of required info. May throw WriteFileException.
/// </summary>
/// <param name="data">Image data in a 3D jagged array, with dimesion number of planes * 3 * (height * width).</param>
/// <param name="allInfo">Info collection to be written in the stack file.</param>
public void writeRGBstack(byte[][][] data, int width, int height, StkInfoCollection allInfo)
{
if (data == null)
{
throw new WriteFileException("Invalid image data");
}
if (allInfo == null)
{
throw new WriteFileException("Info collection is NULL");
}
System.IO.Stream stream = writer.BaseStream;
int planeNum = data.Length;
if (planeNum != allInfo.NumberOfPlanes)
{
throw new WriteFileException("Incompatible image data and image info collection: Inconsistent plane number");
}
int size = width * height;
for (int i = 0; i < planeNum; i++)
{
if (data[i] == null || data[i].Length != 3)
{
throw new WriteFileException("Invalid image data");
}
for (int k = 0; k < 3; k++)
{
if (data[i][k].Length != size)
{
throw new WriteFileException("Invalid image data");
}
}
}
prepareWriteRGBstack(allInfo, width, height, planeNum);
if (numberOfBits != 8)
{
throw new WriteFileException("Can only write 8bit RGB image.");
}
if (!isPrepared)
{
throw new WriteFileException("Failed to pre-write data");
}
if (BufferSize < MIN_BUFFER_SIZE)
{
BufferSize = MIN_BUFFER_SIZE;
}
writeRGBImageDataStrips(data, byteCountsPerPlane, (uint)width, (uint)height, allInfo);
finalizeImageWriting(allInfo, new StkStruct());
}
/// <summary>
/// Write grayscale image data to a stack image. Also test the availability of required info. May throw WriteFileException.
/// </summary>
/// <param name="data">Image data in a 2D jagged array, with dimesion number of planes * (height * width).</param>
/// <param name="allInfo">Info collection to be written in the stack file.</param>
public void writeGrayscaleStack(Array[] data, int width, int height, StkInfoCollection allInfo)
{
if (data == null || data.Length == 0)
{
throw new WriteFileException("Empty image data");
}
if (allInfo == null)
{
throw new WriteFileException("Info collection is NULL");
}
System.IO.Stream stream = writer.BaseStream;
int planeNum = data.Length;
if (planeNum != allInfo.NumberOfPlanes)
{
throw new WriteFileException("Incompatible image data and image info collection: Inconsistent plane number");
}
int size = width * height;
for (int i = 0; i < planeNum; i++)
{
if (data[i] == null || data[i].Length != size)
{
throw new WriteFileException("Invalid image data");
}
}
prepareWriteGrayscaleStack(allInfo, width, height, TiffWriter.getArrayDataType(data[0]), planeNum);
if (!isPrepared)
{
throw new WriteFileException("Failed to pre-write data");
}
if (BufferSize < MIN_BUFFER_SIZE)
{
BufferSize = MIN_BUFFER_SIZE;
}
BufferSize = BufferSize / 4 * 4;
writeGrayScaleImageDataStrips(data, byteCountsPerPlane, (uint)width, (uint)height, allInfo);
finalizeImageWriting(allInfo, new StkStruct());
}
protected void prepareWriteStack(StkInfoCollection allInfo, int width, int height, ImageDataType dataType, int planeNum, ushort photometricInterpretation)
{
if (allInfo == null)
{
return;
}
stkInfo = allInfo;
TiffWriter.getDataTypeInfo(dataType, out numberOfBits, out isFloatPoint);
isPrepared = false;
planeCounter = 0;
if (width <= 0 || height <= 0 || planeNum <= 0)
{
throw new WriteFileException("Invalid image parameters");
}
this.width = width;
this.height = height;
this.planeNum = planeNum;
System.IO.Stream stream = writer.BaseStream;
prepareWriteFile();
allInfo.forceAdd(new TiffInfo(TiffInfoCollection.PhotometricInterpretation, "", photometricInterpretation));
allInfo.add(new TiffInfo(TiffInfoCollection.XResolution, "", (uint)1, (uint)1));
allInfo.add(new TiffInfo(TiffInfoCollection.YResolution, "", (uint)1, (uint)1));
allInfo.add(new TiffInfo(TiffInfoCollection.ResolutionUnit, "", (ushort)1));
if (isFloatPoint)
{
allInfo.setSampleFormat(TiffInfoCollection.SampleFormatType.FloatPoint);
}
else
{
allInfo.setSampleFormat(TiffInfoCollection.SampleFormatType.UnsignedInteger);
}
if (photometricInterpretation <= 1 || photometricInterpretation == 3)
{
allInfo.forceAdd(new TiffInfo(TiffInfoCollection.BitsPerSample, "Bits per Sample", (ushort)numberOfBits));
byteCountsPerPlane = (uint)(width * height * numberOfBits / 8);
}
else if (photometricInterpretation == 2)
{
allInfo.forceAdd(new TiffInfo(TiffInfoCollection.BitsPerSample, "Bits per Sample", new ushort[] { (ushort)8, (ushort)8, (ushort)8 }));
allInfo.forceAdd(new TiffInfo(TiffInfoCollection.SamplesPerPixel, "Sample per Pixel", (ushort)3));
allInfo.forceAdd(new TiffInfo(TiffInfoCollection.PlanarConfiguration, "", (ushort)1));
byteCountsPerPlane = (uint)(width * height * 3);
}
else
{
throw new Exception("Only support grayscale, palette-color, or RGB images.");
}
stripOffset = (uint)stream.Position;
allInfo.forceAdd(new TiffInfo(TiffInfoCollection.ImageWidth, "width", (uint)width));
allInfo.forceAdd(new TiffInfo(TiffInfoCollection.ImageLength, "height", (uint)height));
allInfo.forceAdd(new TiffInfo(TiffInfoCollection.StripOffsets, "strip Offsets", stripOffset));
allInfo.forceAdd(new TiffInfo(TiffInfoCollection.StripByteCounts, "strip Byte Counts", byteCountsPerPlane));
allInfo.forceAdd(new TiffInfo(TiffInfoCollection.RowsPerStrip, "Rows per strip", (uint)height));
MyTiffCompression.setCompressionTag(allInfo, CompressMethod, CompressLevel);
MyTiffCompression.setHorizontalDifferencing(allInfo, HorizontalDifferencing);
int[] missing;
if (photometricInterpretation <= 1)
{
missing = allInfo.missingInfoGrayscale();
}
else if (photometricInterpretation == 2)
{
missing = allInfo.missingInfoRGB();
}
else
{
missing = allInfo.missingInfoPaletteColor();
}
if (missing.Length > 0)
{
String msg = "Missing tags: ";
for (int i = 0; i < missing.Length; i++)
{
msg += missing[i] + " ";
}
throw new WriteFileException(msg);
}
if (!allInfo.validUIC2tag())
{
throw new WriteFileException("Invalid UIC2 data");
}
isPrepared = true;
}
public void prepareWriteRGBstack(StkInfoCollection allInfo, int width, int height)
{
prepareWriteStack(allInfo, width, height, ImageDataType.Byte, (ushort)2);
}
public void prepareWritePaletteColorStack(StkInfoCollection allInfo, int width, int height, ImageDataType dataType, byte[][] colormap)
{
addColormapToTiffInfo(allInfo, colormap);
prepareWriteStack(allInfo, width, height, dataType, (ushort)3);
}
public void prepareWriteGrayscaleStack(StkInfoCollection allInfo, int width, int height, ImageDataType dataType)
{
prepareWriteStack(allInfo, width, height, dataType, (ushort)1);
}
internal override TiffInfoCollection toInfoCollection()
{
StkInfoCollection infoC = new StkInfoCollection(Convert.ToUInt32(numPlane), base.toInfoCollection());
TiffDirData uic2test = search(StkInfoCollection.UIC2Tag);
if (uic2test == null || UIC2data == null)
{
return(infoC);
}
uint[] uicContent = (uint[])UIC2data.getContent();
if (uicContent.Length < 6 * numPlane)
{
return(infoC);
}
for (int i = 0; i < numPlane; i++)
{
infoC.setZdistance(uicContent[6 * i], uicContent[6 * i + 1], i);
infoC.setCreationDatetime(uicContent[6 * i + 2], uicContent[6 * i + 3], i);
infoC.setModifiedDatetime(uicContent[6 * i + 4], uicContent[6 * i + 5], i);
}
TiffDirData uic3test = search(StkInfoCollection.UIC3Tag);
if (uic3test != null && UIC3data != null)
{
uicContent = (uint[])UIC3data.getContent();
if (uicContent.Length < 2 * numPlane)
{
return(infoC);
}
for (int i = 0; i < numPlane; i++)
{
infoC.setWavelength(uicContent[2 * i], uicContent[2 * i + 1], i);
}
}
TiffDirData uic4test = search(StkInfoCollection.UIC4Tag);
if (uic4test != null && UIC4data != null && UIC4data.Count > 0)
{
foreach (KeyValuePair <ushort, TiffData[]> pair in UIC4data)
{
if (pair.Value.Length != numPlane)
{
continue;
}
TiffInfo[] temp = new TiffInfo[numPlane];
for (int j = 0; j < numPlane; j++)
{
temp[j] = new TiffInfo(StkInfoCollection.UIC4Tag, "UIC4", (pair.Value)[j]);
}
infoC.forceAddUIC4Data(pair.Key, temp);
}
}
TiffDirData uic1test = search(StkInfoCollection.UIC1Tag);
if (uic1test != null && UIC1data != null && UIC1data.Count > 0)
{
foreach (KeyValuePair <uint, TiffData[]> pair in UIC1data)
{
TiffInfo[] uic1info = new TiffInfo[pair.Value.Length];
for (int i = 0; i < pair.Value.Length; i++)
{
uic1info[i] = new TiffInfo(StkInfoCollection.UIC1Tag, "UIC1", pair.Value[i]);
}
infoC.forceAddUIC1Data(pair.Key, uic1info);
}
}
return(infoC);
}
internal override void setFromInfoCollection(TiffInfoCollection info)
{
base.setFromInfoCollection(info);
StkInfoCollection allInfo = info as StkInfoCollection;
if (allInfo == null)
{
return;
}
List <TiffDirData> dirTemp = new List <TiffDirData>();
numPlane = allInfo.NumberOfPlanes;
uint[] uic2 = new uint[6 * numPlane];
if (allInfo.validUIC2tag())
{
for (int i = 0; i < Math.Min(numPlane, allInfo.ZDistance.Length); i++)
{
if (allInfo.ZDistance[i] != null)
{
Array content = allInfo.ZDistance[i].Data.getContent();
if (content == null || content.Length <= 0)
{
continue;
}
uint[] temp = (uint[])content;
uic2[6 * i] = temp[0];
uic2[6 * i + 1] = temp[1];
}
else
{
uic2[6 * i] = 0;
uic2[6 * i + 1] = 0;
}
}
for (int i = 0; i < Math.Min(numPlane, allInfo.CreationTime.Length); i++)
{
if (allInfo.CreationTime[i] != null)
{
Array content = allInfo.CreationTime[i].Data.getContent();
if (content == null || content.Length <= 0)
{
continue;
}
uint[] temp = (uint[])content;
uic2[6 * i + 2] = temp[0];
uic2[6 * i + 3] = temp[1];
}
else
{
uic2[6 * i + 2] = 0;
uic2[6 * i + 3] = 0;
}
}
for (int i = 0; i < Math.Min(numPlane, allInfo.ModifiedTime.Length); i++)
{
if (allInfo.ModifiedTime[i] != null)
{
Array content = allInfo.ModifiedTime[i].Data.getContent();
if (content == null || content.Length <= 0)
{
continue;
}
uint[] temp = (uint[])(content);
uic2[6 * i + 4] = temp[0];
uic2[6 * i + 5] = temp[1];
}
else
{
uic2[6 * i + 4] = 0;
uic2[6 * i + 5] = 0;
}
}
}
UIC2data = new TiffData(TiffData.TIFFdataType.Rational);
UIC2data.setContent(uic2);
TiffDirData ddTemp = new TiffDirData();
ddTemp.Tag = StkInfoCollection.UIC2Tag;
ddTemp.Data = new TiffData(TiffData.TIFFdataType.Rational, numPlane);
dirTemp.Add(ddTemp);
if (allInfo.validUIC3tag())
{
uint[] uic3 = new uint[2 * numPlane];
for (int i = 0; i < numPlane; i++)
{
if (allInfo.Wavelength[i] != null)
{
uint[] temp = (uint[])(allInfo.Wavelength[i].Data.getContent());
uic3[2 * i] = temp[0];
uic3[2 * i + 1] = temp[1];
}
else
{
uic3[2 * i] = 0;
uic3[2 * i + 1] = 0;
}
}
UIC3data = new TiffData(TiffData.TIFFdataType.Rational);
UIC3data.setContent(uic3);
ddTemp = new TiffDirData();
ddTemp.Tag = StkInfoCollection.UIC3Tag;
ddTemp.Data = new TiffData(TiffData.TIFFdataType.Rational, numPlane);
dirTemp.Add(ddTemp);
}
UIC4data = new SortedList <ushort, TiffData[]>();
if (allInfo.validUIC4tag())
{
ddTemp = new TiffDirData();
ddTemp.Tag = StkInfoCollection.UIC4Tag;
ddTemp.Data = new TiffData(TiffData.TIFFdataType.Byte, numPlane);
dirTemp.Add(ddTemp);
foreach (KeyValuePair <ushort, List <TiffInfo> > pair in allInfo.UIC4DataDeepCopy)
{
if (pair.Value.Count != numPlane)
{
continue;
}
TiffData[] temp = new TiffData[numPlane];
for (int j = 0; j < numPlane; j++)
{
temp[j] = (pair.Value)[j].Data;
}
UIC4data.Add(pair.Key, temp);
}
}
UIC1data = new SortedList <uint, TiffData[]>();
if (allInfo.validUIC1tag())
{
ddTemp = new TiffDirData();
ddTemp.Tag = StkInfoCollection.UIC1Tag;
SortedList <uint, List <TiffInfo> > uic1Copy = allInfo.UIC1DataDeepCopy;
ddTemp.Data = new TiffData(TiffData.TIFFdataType.Byte, uic1Copy.Count);
dirTemp.Add(ddTemp);
foreach (KeyValuePair <uint, List <TiffInfo> > pair in uic1Copy)
{
TiffData[] temp = new TiffData[pair.Value.Count];
for (int i = 0; i < pair.Value.Count; i++)
{
temp[i] = pair.Value[i].Data;
}
UIC1data.Add(pair.Key, temp);
}
}
TiffDirData[] newDir = new TiffDirData[dirArray.Length + dirTemp.Count];
for (int i = 0; i < dirArray.Length; i++)
{
newDir[i] = dirArray[i];
}
for (int i = dirArray.Length; i < newDir.Length; i++)
{
newDir[i] = dirTemp[i - dirArray.Length];
}
dirArray = newDir;
Array.Sort(dirArray);
}
