public static MapHeader ReadFromFile(BinaryReader reader, FileInfo info, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType)
{
MapHeader Header = null;
if (info.Extension.ToLower() == ".mrc" || info.Extension.ToLower() == ".mrcs" || info.Extension.ToLower() == ".ali" || info.Extension.ToLower() == ".rec" || info.Extension.ToLower() == ".st")
{
Header = new HeaderMRC(reader);
}
else if (info.Extension.ToLower() == ".em")
{
Header = new HeaderEM(reader);
}
else if (info.Extension.ToLower() == ".tif" || info.Extension.ToLower() == ".tiff")
{
Header = new HeaderTiff(info.FullName);
}
else if (info.Extension.ToLower() == ".dat")
{
long SliceElements = headerlessSliceDims.Elements() * ImageFormatsHelper.SizeOf(headerlessType);
long Slices = (info.Length - headerlessOffset) / SliceElements;
int3 Dims3 = new int3(headerlessSliceDims.X, headerlessSliceDims.Y, (int)Slices);
Header = new HeaderRaw(Dims3, headerlessOffset, headerlessType);
}
else
{
throw new Exception("File type not supported.");
}
return(Header);
}
public static MapHeader ReadFromFile(BinaryReader reader, string path, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType, Stream stream = null)
{
MapHeader Header = null;
string Extension = Helper.PathToExtension(path).ToLower();
if (Extension == ".mrc" || Extension == ".mrcs" || Extension == ".rec" || Extension == ".st")
Header = new HeaderMRC(reader);
else if (Extension == ".em")
Header = new HeaderEM(reader);
else if (Extension == ".dm4" || Extension == ".dm3")
Header = new HeaderDM4(reader);
else if (Extension == ".tif" || Extension == ".tiff")
Header = new HeaderTiff(path, stream);
else if (Extension == ".eer")
Header = new HeaderEER(path, stream);
else if (Extension == ".dat")
{
FileInfo info = new FileInfo(path);
long SliceElements = headerlessSliceDims.Elements() * ImageFormatsHelper.SizeOf(headerlessType);
long Slices = (info.Length - headerlessOffset) / SliceElements;
int3 Dims3 = new int3(headerlessSliceDims.X, headerlessSliceDims.Y, (int)Slices);
Header = new HeaderRaw(Dims3, headerlessOffset, headerlessType);
}
else
throw new Exception("File type not supported.");
return Header;
}
public HeaderDM4(BinaryReader reader)
{
Reader = new BinaryReaderMixedEndian(reader);
pixelOffset = 0;
//LOGGER.info("Verifying Gatan format");
littleEndian = false;
pixelSizes = new List <Double>();
units = new List <String>();
Reader.SetEndian(littleEndian);
// only support version 3
version = Reader.ReadInt32();
if (version != 3 && version != 4)
{
throw new FormatException("invalid header");
}
//LOGGER.info("Reading tags");
Reader.ReadBytes(4);
skipPadding(Reader);
littleEndian = Reader.ReadInt32() != 1;
Reader.SetEndian(littleEndian);
// TagGroup instance
Reader.ReadBytes(2);
skipPadding(Reader);
int numTags = Reader.ReadInt32();
if (numTags > Reader.BaseStream.Length)
{
littleEndian = !littleEndian;
Reader.SetEndian(littleEndian);
adjustEndianness = false;
}
//LOGGER.debug("tags ({}) {", numTags);
try
{
parseTags(Reader, numTags, null, " ");
}
catch (Exception e)
{
throw new FormatException("Unable to parse metadata tag", e);
}
//LOGGER.debug("}");
//LOGGER.info("Populating metadata");
littleEndian = true;
if (Dimensions.X == 0 || Dimensions.Y == 0)
{
throw new FormatException("Dimensions information not found");
}
if (Dimensions.Z == 0)
{
Dimensions.Z = 1;
}
//m.sizeC = 1;
//m.sizeT = 1;
//m.dimensionOrder = "XYZTC";
//m.imageCount = getSizeZ() * getSizeC() * getSizeT();
int bytes = (int)(numPixelBytes / Dimensions.Elements());
if (bytes != ImageFormatsHelper.SizeOf(ValueType))
{
throw new Exception("Bytes per pixel does not match the actual size of image data.");
}
reader.BaseStream.Seek(pixelOffset, SeekOrigin.Begin);
}
