internal override void read(System.IO.BinaryReader reader)
{
preRead(reader);
if (dirArray == null)
{
throw new ReadFileException("Not a TIFF file.");
}
TiffDirData uic2 = search(StkInfoCollection.UIC2Tag);
if (uic2 == null)
{
throw new ReadFileException("Not a stack file.");
}
TiffDirData uic3 = search(StkInfoCollection.UIC3Tag);
if (uic3 == null)
{
throw new ReadFileException("Not a stack file.");
}
numPlane = uic3.Data.Count;
if (numPlane <= 0)
{
throw new ReadFileException("Not a stack file.");
}
postRead(reader);
}
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);
}
// Not all STK file info can be read : The STK documentation I used might be out of date?
internal override void postRead(System.IO.BinaryReader reader)
{
System.IO.Stream stream = reader.BaseStream;
List <TiffDirData> dirTemp = new List <TiffDirData>();
TiffDirData dir = search(StkInfoCollection.UIC2Tag);
if (dir != null)
{
if (dir.Offset < 0)
{
throw new ReadFileException("Corrupted stack file.");
}
try
{
stream.Seek(dir.Offset, System.IO.SeekOrigin.Begin);
UIC2data = new TiffData(TiffData.TIFFdataType.Rational, 3 * numPlane);
UIC2data.read(reader);
dirTemp.Add(dir);
}
catch
{
throw new ReadFileException("Corrupted stack file.");
}
}
dir = search(StkInfoCollection.UIC3Tag);
if (dir != null)
{
try
{
stream.Seek(dir.Offset, System.IO.SeekOrigin.Begin);
UIC3data = new TiffData(TiffData.TIFFdataType.Rational, numPlane);
UIC3data.read(reader);
dirTemp.Add(dir);
}
catch
{
UIC3data = null;
}
}
dir = search(StkInfoCollection.UIC4Tag);
if (dir != null)
{
try
{
stream.Seek(dir.Offset, System.IO.SeekOrigin.Begin);
readUIC4tagData(reader);
dirTemp.Add(dir);
}
catch
{
UIC4data = null;
}
}
dir = search(StkInfoCollection.UIC1Tag);
if (dir != null)
{
try
{
stream.Seek(dir.Offset, System.IO.SeekOrigin.Begin);
readUIC1tagData(reader, dir.Data.Count);
dirTemp.Add(dir);
}
catch
{
UIC1data = null;
}
}
for (int i = 0; i < dirArray.Length; i++)
{
if (dirArray[i].Tag == StkInfoCollection.UIC1Tag)
{
continue;
}
else if (dirArray[i].Tag == StkInfoCollection.UIC2Tag)
{
continue;
}
else if (dirArray[i].Tag == StkInfoCollection.UIC3Tag)
{
continue;
}
else if (dirArray[i].Tag == StkInfoCollection.UIC4Tag)
{
continue;
}
else if (dirArray[i].Offset > 0)
{
try
{
stream.Seek(dirArray[i].Offset, System.IO.SeekOrigin.Begin);
dirArray[i].readData(reader);
}
catch
{
continue;
}
}
dirTemp.Add(dirArray[i]);
}
dirArray = dirTemp.ToArray();
this.sort();
}
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);
}
