/// <summary>Read a stream for header data.</summary>
/// <param name="dis">The input stream to read the data from.</param>
/// <returns> <CODE>null</CODE> if there was a problem with the header;
/// otherwise return the header read from the input stream.</returns>
/// <exception cref="TruncatedFileException"> </exception>"
public virtual void Read(ArrayDataIO dis)
{
if (dis is RandomAccess)
{
fileOffset = FitsUtil.FindOffset(dis);
}
else
{
fileOffset = - 1;
}
byte[] buffer = new byte[80];
bool firstCard = true;
int count = 0;
bool notEnd = true;
while(notEnd)
{
int need = 80;
// try
// {
for(int len = 1; need > 0 && len > 0;)
{
len = dis.Read(buffer, 80 - need, need);
count += 1;
if(firstCard && len == 0 && need == 80)
{
throw new EndOfStreamException();
}
need -= len;
}
// }
// catch(EndOfStreamException e)
// {
// // Rethrow the EOF if we are at the beginning of the header,
// // otherwise we have a FITS error.
// if(firstCard && need == 80)
// {
// throw e;
// }
// throw new TruncatedFileException(e.Message);
// }
String cbuf = new String(SupportClass.ToCharArray(buffer));
HeaderCard fcard = new HeaderCard(cbuf);
if(firstCard)
{
String key = fcard.Key;
//Console.Out.WriteLine("key = '" + key + "'");
if(key == null || (!key.Equals("SIMPLE") && !key.Equals("XTENSION")))
{
throw new IOException("Not FITS format at " + fileOffset + ":" + cbuf);
}
firstCard = false;
}
String key2 = fcard.Key;
if(key2 != null && cards.ContainsKey(key2))
{
Console.Error.WriteLine("Warning: multiple occurrences of key:" + key2);
}
// save card
AddLine(fcard);
if (cbuf.Substring(0, (8) - (0)).Equals("END "))
{
notEnd = false;
}
}
if (fileOffset >= 0)
{
oldSize = cards.Count;
input = dis;
}
// Read to the end of the current FITS block.
try
{
if(dis.CanSeek)
{
dis.Seek(FitsUtil.Padding(count * 80));
}
else
{
int pad = FitsUtil.Padding(count * 80);
for (int len = dis.Read(buffer, 0, Math.Min(pad, buffer.Length));
pad > 0 && len != -1; )
{
pad -= len;
len = dis.Read(buffer, 0, Math.Min(pad, buffer.Length));
}
}
}
catch(IOException e)
{
throw new TruncatedFileException(e.Message);
}
}
/// <summary>Read the RandomGroupsData.</summary>
public override void Read(ArrayDataIO str)
{
SetFileOffset(str);
try
{
str.ReadArray(dataArray);
}
catch(IOException e)
{
throw new FitsException("IO error reading Random Groups data " + e);
}
int pad = FitsUtil.Padding(TrueSize);
try
{
//System.IO.BinaryReader temp_BinaryReader;
System.Int64 temp_Int64;
//temp_BinaryReader = str;
temp_Int64 = str.Position; //temp_BinaryReader.BaseStream.Position;
temp_Int64 = str.Seek(pad) - temp_Int64; //temp_BinaryReader.BaseStream.Seek(pad, System.IO.SeekOrigin.Current) - temp_Int64;
int generatedAux = (int)temp_Int64;
}
catch(IOException)
{
throw new FitsException("IO error reading padding.");
}
}
/// <summary>
/// Method to read data
/// </summary>
/// <param name="i"></param>
public override void Read(ArrayDataIO i)
{
// Don't need to read null data (noted by Jens Knudstrup)
if (byteSize == 0)
{
return ;
}
SetFileOffset(i);
//if(i is RandomAccess)
if(i.CanSeek)
{
//tiler = new ImageDataTiler(this, (RandomAccess) i, ((RandomAccess) i).FilePointer, dataDescription);
tiler = new ImageDataTiler(this, (RandomAccess) i, ((Stream)i).Position, dataDescription);
try
{
double pos = i.Position;
//pos = i.Seek((int)byteSize) - pos;
i.Seek((int)byteSize);
}
catch(IOException e)
{
throw new FitsException("Unable to skip over data:" + e);
}
}
else
{
dataArray = ArrayFuncs.NewInstance(dataDescription.type, dataDescription.dims);
try
{
i.ReadArray(dataArray);
}
catch(IOException e)
{
throw new FitsException("Unable to read image data:" + e);
}
tiler = new ImageDataTiler(this, null, 0, dataDescription);
}
int pad = FitsUtil.Padding(TrueSize);
try
{
long pos = i.Seek(pad);
if(pos != pad)
{
throw new FitsException("Error skipping padding");
}
}
catch(IOException e)
{
throw new FitsException("Error reading image padding:" + e);
}
}
/// <summary>Read table, heap and padding</summary>
protected internal void ReadTrueData(ArrayDataIO i)
{
int len;
try
{
len = table.Read(i);
// IO.BinaryReader temp_BinaryReader;
Int64 temp_Int64;
//temp_BinaryReader = i;
temp_Int64 = i.Position; //temp_BinaryReader.BaseStream.Position;
temp_Int64 = i.Seek(heapOffset, SeekOrigin.Current) - temp_Int64; //temp_BinaryReader.BaseStream.Seek(heapOffset, IO.SeekOrigin.Current) - temp_Int64;
int generatedAux = (int)temp_Int64;
heap.Read(i);
//IO.BinaryReader temp_BinaryReader2;
Int64 temp_Int65;
//temp_BinaryReader2 = i;
temp_Int65 = i.Position; //temp_BinaryReader2.BaseStream.Position;
temp_Int65 = i.Seek(FitsUtil.Padding(TrueSize), SeekOrigin.Current) - temp_Int65; //temp_BinaryReader2.BaseStream.Seek(FitsUtil.padding(TrueSize), IO.SeekOrigin.Current) - temp_Int65;
int generatedAux2 = (int)temp_Int65;
}
catch(IOException e)
{
throw new FitsException("Error reading binary table data:" + e);
}
}
/// <summary>Read the data -- or defer reading on random access</summary>
public override void Read(ArrayDataIO i)
{
SetFileOffset(i);
currInput = i;
if (i is RandomAccess)
{
try
{
//BinaryReader temp_BinaryReader;
Int64 temp_Int64;
//temp_BinaryReader = i;
temp_Int64 = i.Position;//temp_BinaryReader.BaseStream.Position;
temp_Int64 = i.Seek(TrueSize, SeekOrigin.Current) - temp_Int64; //temp_BinaryReader.BaseStream.Seek(TrueSize, IO.SeekOrigin.Current) - temp_Int64;
int generatedAux = (int)temp_Int64;
//IO.BinaryReader temp_BinaryReader2;
Int64 temp_Int65;
//temp_BinaryReader2 = i;
temp_Int65 = i.Position;//temp_BinaryReader2.BaseStream.Position;
temp_Int65 = i.Seek(FitsUtil.Padding(TrueSize), SeekOrigin.Current) - temp_Int65;//temp_BinaryReader2.BaseStream.Seek(FitsUtil.padding(TrueSize), IO.SeekOrigin.Current) - temp_Int65;
int generatedAux2 = (int)temp_Int65;
}
catch(IOException e)
{
throw new FitsException("Unable to skip binary table HDU:" + e);
}
}
else
{
if (table == null)
{
table = CreateTable();
}
ReadTrueData(i);
}
}
/// <summary>
/// Writes this binary table in one pass,
/// then seeks back to fix NAXIS2. Requires
/// s to be seekable and
/// either no strings or truncated string output.
/// </summary>
/// <param name="s">The destination stream.</param>
protected void WriteThenFix(ArrayDataIO s)
{
long headerMark = s.Position;
int nRows = WriteTable(s);
long endMark = s.Position;
myHeader.RemoveCard("NAXIS2");
myHeader.SetNaxis(2, nRows);
myHeader.InsertComment("No comment.", "THEAP");
myHeader.RemoveCard("THEAP");
s.Seek(headerMark, SeekOrigin.Begin);
myHeader.Write(s);
s.Seek(endMark, SeekOrigin.Begin);
}
/// <summary>
/// Writes this binary table with heap temp file if necessary,
/// then fixing nRows and PCOUNT in header,
/// then if necessary copying heap file to destination stream.
/// </summary>
/// <param name="s">The destination stream.</param>
/// steps:
/// 1) write the header to the main stream
/// write the table to the main stream
/// byterenderers write data to the heap if necessary
/// byterenderers return heap positions and lengths if necessary
/// these are returned as a byte sequence like any other data
/// and are written to the table like any other data
/// 2) fix the header
/// 3) write the heap tempfile to the main stream
/// what a pain
protected void WriteHeapOutputWithTempHeapFile(ArrayDataIO s)
{
String heapFilename = CreateTempFilename() + "heap.tmp";
HeapStream heapS = null;
int[] maxColWidths = null;
if(_hasStrings)
{
maxColWidths = new int[_byteRenderers.Length];
heapS = new HeapStream(new FileStream(heapFilename, FileMode.Create));
for(int col = 0; col < _byteRenderers.Length; ++col)
{
_byteRenderers[col].Heap = heapS;
maxColWidths[col] = -1;
}
}
#region 1) write the header and the table
// prep header to make sure it will line up properly with the table later on.
// since we made the header, we know that anything we add later
// (except THEAP, accounted for here) will already have been there,
// so we're not inflating the header
myHeader.RemoveCard("THEAP");
if(_hasStrings && _writeMode == StringWriteMode.HEAP)
{
myHeader.AddValue("THEAP", 0, null);
}
long headerMark = s.Position;
myHeader.Write(s);
int nRows = 0;
for(Array[] els = _rs.GetNextRow(ref _row); els != null;)
{
++nRows;
for(int col = 0; col < _byteRenderers.Length; ++col)
{
_byteRenderers[col].Write(els[col], s);
if(els[col] is String[])
{
maxColWidths[col] = maxColWidths[col] < ((String[])els[col])[0].Length ?
((String[])els[col])[0].Length : maxColWidths[col];
}
}
els = _rs.GetNextRow(ref _row);
}
// pad the table. if there's a heap, pad the heap instead
if(!_hasStrings)
{
int pad = FitsUtil.Padding((long)nRows * (long)_rowSizeInBytes);
s.Write(new byte[pad], 0, pad);
}
s.Flush();
#endregion
#region 2) fix the header and write it to the main stream
myHeader.RemoveCard("NAXIS2");
myHeader.SetNaxis(2, nRows);
// shoehorn correct heap information into header
// PCOUNT, THEAP, and TFORMn
// fix NAXIS1
if(_hasStrings)
{
long theap = (long)nRows * (long)_rowSizeInBytes;
int pad = FitsUtil.Padding(theap + heapS.Position);
int pcount = (int)heapS.Position + pad;
// here we correct for swapping out actual strings with heap indices/lengths
myHeader.RemoveCard("NAXIS1");
myHeader.InsertCard(new HeaderCard("NAXIS1", _rowSizeInBytes, null), "NAXIS2");
myHeader.RemoveCard("PCOUNT");
myHeader.InsertCard(new HeaderCard("PCOUNT", pcount, "Length of heap area in bytes"),
"GCOUNT");
myHeader.RemoveCard("THEAP");
// can't fit a long in here!
if(pcount > 0 && _writeMode == StringWriteMode.HEAP)
{
myHeader.AddValue("THEAP", (int)theap, "Position of heap wrt start of binary table");
}
// fix the TFORMn entries for string columns
IEnumerator ie = null;
bool found = false;
for(int i = 0; i < maxColWidths.Length; ++i, found = false)
{
if(maxColWidths[i] > -1)
{
ie = myHeader.GetEnumerator();
ie.MoveNext();
for(int j = 0; !found && ie.Current != null; ++j, ie.MoveNext())
{
if(("TFORM" + (i + 1)).Equals(((DictionaryEntry)ie.Current).Key))
{
myHeader.RemoveCard(j);
myHeader.
InsertCard(new HeaderCard("TFORM" + (i + 1),
"1PA(" + maxColWidths[i] + ")",
null), j);
found = true;
}
}
}
}
}
// rewrite the header
long heapMark = s.Position;
s.Seek(headerMark, SeekOrigin.Begin);
myHeader.Write(s);
#endregion
#region 3) write the heap tempfile to the main stream
if(_hasStrings)
{
// calculate the pad
int pad = FitsUtil.Padding((long)nRows * (long)_rowSizeInBytes + heapS.Position);
s.Seek(heapMark, SeekOrigin.Begin);
// write heap to the main stream
heapS.Seek(0, SeekOrigin.Begin);
for(int nRead = heapS.Read(_buf, 0, _buf.Length); nRead > 0;)
{
s.Write(_buf, 0, nRead);
nRead = heapS.Read(_buf, 0, _buf.Length);
}
heapS.Close();
File.Delete(heapFilename);
// pad the file
s.Write(new byte[pad], 0, pad);
}
#endregion
}
/// <summary>
/// Method to read the ArrayDataIO
/// </summary>
/// <param name="i"></param>
public override void Read(ArrayDataIO i)
{
SetFileOffset(i);
if (i is RandomAccess)
{
try
{
//BinaryReader temp_BinaryReader;
System.Int64 temp_Int64;
//temp_BinaryReader = i;
temp_Int64 = i.Position; //temp_BinaryReader.BaseStream.Position;
temp_Int64 = i.Seek((int)byteSize) - temp_Int64; //temp_BinaryReader.BaseStream.Seek((int) byteSize, SeekOrigin.Current) - temp_Int64;
int generatedAux = (int)temp_Int64;
}
catch (IOException e)
{
throw new FitsException("Unable to skip over data:" + e);
}
}
else
{
try
{
i.Read(data);
}
catch (IOException e)
{
throw new FitsException("Unable to read unknown data:" + e);
}
}
int pad = FitsUtil.Padding(TrueSize);
try
{
//BinaryReader temp_BinaryReader2;
System.Int64 temp_Int65;
//temp_BinaryReader2 = i;
temp_Int65 = i.Position; //temp_BinaryReader2.BaseStream.Position;
temp_Int65 = i.Seek(pad) - temp_Int65; //temp_BinaryReader2.BaseStream.Seek(pad, SeekOrigin.Current) - temp_Int65;
// if (temp_Int65 != pad)
if (i.Seek(pad) != pad)
{
throw new FitsException("Error skipping padding");
}
}
catch (IOException e)
{
throw new FitsException("Error reading unknown padding:" + e);
}
}
/// <summary>Read in an ASCII table. Reading is deferred if
/// we are reading from a random access device</summary>
public override void Read(ArrayDataIO str)
{
SetFileOffset(str);
currInput = str;
//if(str is RandomAccess)
if(str.CanSeek)
{
try
{
//BinaryReader temp_BinaryReader;
Int64 temp_Int64;
//temp_BinaryReader = str;
temp_Int64 = str.Position; //temp_BinaryReader.BaseStream.Position;
temp_Int64 = str.Seek(nRows * rowLen) - temp_Int64;//temp_BinaryReader.BaseStream.Seek(nRows * rowLen, SeekOrigin.Current) - temp_Int64;
int generatedAux = (int)temp_Int64;
}
catch(IOException e)
{
throw new FitsException("Error skipping data: " + e);
}
}
else
{
try
{
GetBuffer(rowLen * nRows, 0);
}
catch (IOException e)
{
throw new FitsException("Error reading ASCII table:" + e);
}
}
try
{
//BinaryReader temp_BinaryReader2;
Int64 temp_Int65;
//temp_BinaryReader2 = str;
temp_Int65 = str.Position;//temp_BinaryReader2.BaseStream.Position;
temp_Int65 = str.Seek(FitsUtil.Padding(nRows * rowLen)) - temp_Int65;
//temp_BinaryReader2.BaseStream.Seek(FitsUtil.padding(nRows * rowLen), SeekOrigin.Current) - temp_Int65;
int generatedAux2 = (int)temp_Int65;
}
catch (IOException e)
{
throw new FitsException("Error skipping padding:" + e);
}
}
/// <summary>Skip the Data object immediately after the given Header object on
/// the given stream object.</summary>
/// <param name="stream">the stream which contains the data.</param>
/// <param name="hdr">template indicating length of Data section</param>
/// <exception cref="IOException"> IOException if the Data object could not be skipped.</exception>
public static void SkipData(ArrayDataIO stream, Header hdr)
{
//System.IO.BinaryReader temp_BinaryReader;
Int64 temp_Int64;
//temp_BinaryReader = stream;
temp_Int64 = stream.Position; //temp_BinaryReader.BaseStream.Position;
temp_Int64 = stream.Seek((int)hdr.DataSize) - temp_Int64; //temp_BinaryReader.BaseStream.Seek((int) hdr.DataSize, System.IO.SeekOrigin.Current) - temp_Int64;
int generatedAux = (int)temp_Int64;
}