private static NiftiHeader ReadHeader(Stream stream)
{
bool reverseBytes = false;
//var memstrem = new MemoryStream();
//stream.CopyTo(memstrem);
var streamLen = stream.Length;
NiftiHeader hdr = new NiftiHeader();
hdr.sizeof_hdr = ReadInt(stream, reverseBytes);
reverseBytes = hdr.SourceIsBigEndian();
hdr.data_type = ReadBytes(stream, 10);
hdr.db_name = ReadBytes(stream, 18);
hdr.extents = ReadInt(stream, reverseBytes);
hdr.session_error = ReadShort(stream, reverseBytes);
hdr.regular = ReadByte(stream);
hdr.dim_info = ReadByte(stream);
hdr.dim = ReadMyShorts(stream, 8, reverseBytes);
hdr.intent_p1 = ReadFloat(stream, reverseBytes);
hdr.intent_p2 = ReadFloat(stream, reverseBytes);
hdr.intent_p3 = ReadFloat(stream, reverseBytes);
hdr.intent_code = ReadShort(stream, reverseBytes);
hdr.datatype = ReadShort(stream, reverseBytes);
hdr.bitpix = ReadShort(stream, reverseBytes);
hdr.slice_start = ReadShort(stream, reverseBytes);
hdr.pixdim = ReadFloats(stream, 8, reverseBytes);
hdr.vox_offset = ReadFloat(stream, reverseBytes);
hdr.scl_slope = ReadFloat(stream, reverseBytes);
hdr.scl_inter = ReadFloat(stream, reverseBytes);
hdr.slice_end = ReadShort(stream, reverseBytes);
hdr.slice_code = ReadByte(stream);
hdr.xyzt_units = ReadByte(stream);
hdr.cal_max = ReadFloat(stream, reverseBytes);
hdr.cal_min = ReadFloat(stream, reverseBytes);
hdr.slice_duration = ReadFloat(stream, reverseBytes);
hdr.toffset = ReadFloat(stream, reverseBytes);
hdr.glmax = ReadInt(stream, reverseBytes);
hdr.glmin = ReadInt(stream, reverseBytes);
hdr.descrip = ReadBytes(stream, 80);
hdr.aux_file = ReadBytes(stream, 24);
hdr.qform_code = ReadShort(stream, reverseBytes);
hdr.sform_code = ReadShort(stream, reverseBytes);
hdr.quatern_b = ReadFloat(stream, reverseBytes);
hdr.quatern_c = ReadFloat(stream, reverseBytes);
hdr.quatern_d = ReadFloat(stream, reverseBytes);
hdr.qoffset_x = ReadFloat(stream, reverseBytes);
hdr.qoffset_y = ReadFloat(stream, reverseBytes);
hdr.qoffset_z = ReadFloat(stream, reverseBytes);
hdr.srow_x = ReadFloats(stream, 4, reverseBytes);
hdr.srow_y = ReadFloats(stream, 4, reverseBytes);
hdr.srow_z = ReadFloats(stream, 4, reverseBytes);
hdr.intent_name = ReadBytes(stream, 16);
hdr.magic = ReadBytes(stream, 4);
if (streamLen >= 352)
{
hdr.extension = ReadBytes(stream, 4);
if (hdr.extension[0] == 1) // Extension is present
{
hdr.esize = ReadInt(stream, reverseBytes);
hdr.ecode = ReadInt(stream, reverseBytes);
hdr.edata = ReadBytes(stream, hdr.esize - 8);
}
}
if (TypeOf(hdr) == FileType.UNKNOWN)
{
throw new InvalidDataException("Not a NIfTI file (no magic bytes)");
}
if (hdr.dim[0] > 7)
{
throw new InvalidDataException("NIFTI header is using more than 7 dimensions. I don't really know how to handle that :\\");
}
else if (hdr.dim[0] < 0)
{
throw new InvalidDataException("Somethings broken with the dimensions...");
}
return(hdr);
}
private static dynamic ReadData(Stream stream, NiftiHeader hdr, short forceType)
{
var datatype = forceType != NiftiHeader.DT_UNKNOWN ? forceType : hdr.datatype;
var reverseBytes = hdr.SourceIsBigEndian();
var bytelen = stream.Length - stream.Position;
var data = InitData(datatype, bytelen);
switch (datatype)
{
case NiftiHeader.DT_FLOAT32:
for (int i = 0; i < data.Length; ++i)
{
data[i] = ReadFloat(stream, reverseBytes);
}
break;
case NiftiHeader.DT_INT32:
for (int i = 0; i < data.Length; ++i)
{
data[i] = ReadInt(stream, reverseBytes);
}
break;
case NiftiHeader.DT_UINT32:
for (int i = 0; i < data.Length; ++i)
{
data[i] = ReadInt(stream, reverseBytes);
}
break;
case NiftiHeader.DT_INT16:
for (int i = 0; i < data.Length; ++i)
{
data[i] = ReadShort(stream, reverseBytes);
}
break;
case NiftiHeader.DT_UINT16:
for (int i = 0; i < data.Length; ++i)
{
data[i] = ReadUShort(stream, reverseBytes);
}
break;
case NiftiHeader.DT_DOUBLE:
for (int i = 0; i < data.Length; ++i)
{
data[i] = ReadDouble(stream, reverseBytes);
}
break;
case NiftiHeader.DT_COMPLEX:
for (int i = 0; i < data.Length; ++i)
{
data[i] = ReadLong(stream, reverseBytes);
}
break;
case NiftiHeader.DT_RGB24:
for (int i = 0; i < data.Length; ++i)
{
data[i] = ReadRGB(stream, reverseBytes);
}
break;
case NiftiHeader.DT_RGBA32:
for (int i = 0; i < data.Length; ++i)
{
data[i] = ReadRGBA(stream, reverseBytes);
}
break;
default:
for (int i = 0; i < data.Length; ++i)
{
data[i] = ReadByte(stream);
}
break;
}
return(data);
}