[ome-users] BigTIFF OME-TIFFs do not meet the BigTIFF standard

[Melissa Linkert]

Hi Matthias,

> I have used your code snippet but I get the same result with it:
> Libtiff 4.0.2 fails to open BigTIFF OME-TIFFs with big endian byte order. 
> 
> According to the BigTIFF specification, the first eight bytes are grouped in four groups with two bytes each (datatype = word). 
> For me, it seems that the first eight bytes of BigTIFF OME-TIFFs only consist of three groups. Two two-byte groups and one four-byte group. 
> Therefore, BigTIFF OME-TIFFs with little endian byte order are valid because the position of the number 8 is correct. 
> But for BigTIFF OME-TIFFs with big endian byte order, the number 8 should be two positions towards the left side. 

Thank you for clarifying - the critical detail is that this is only a
problem when writing big-endian files.

> In the Java class "TiffSaver", I found the following line in the writeHeader() method: 
>     out.writeInt(8); 
> As this line will always write four bytes at once, I think it should be replaced by: 
>     if (bigTiff) { 
>         out.writeShort(8); 
>         out.writeShort(0); 
>     }else out.writeInt(8); 

This works for me as well, and so has been turned into a patch to be reviewed
for inclusion:

https://github.com/openmicroscopy/bioformats/pull/258

Regards,
-Melissa

On Wed, Nov 28, 2012 at 11:46:10PM +0100, Matthias Baldauf wrote:
> Hi Melissa, 
> 
> thank you for your response!
> I have used your code snippet but I get the same result with it:
> Libtiff 4.0.2 fails to open BigTIFF OME-TIFFs with big endian byte order. 
> 
> According to the BigTIFF specification, the first eight bytes are grouped in four groups with two bytes each (datatype = word). 
> For me, it seems that the first eight bytes of BigTIFF OME-TIFFs only consist of three groups. Two two-byte groups and one four-byte group. 
> Therefore, BigTIFF OME-TIFFs with little endian byte order are valid because the position of the number 8 is correct. 
> But for BigTIFF OME-TIFFs with big endian byte order, the number 8 should be two positions towards the left side. 
> 
> In the Java class "TiffSaver", I found the following line in the writeHeader() method: 
>     out.writeInt(8); 
> As this line will always write four bytes at once, I think it should be replaced by: 
>     if (bigTiff) { 
>         out.writeShort(8); 
>         out.writeShort(0); 
>     }else out.writeInt(8); 
> 
> After changing these lines, TiffSaver creates valid BigTIFFs for both, big & little endian byte order. 
> I use the following code snippet to read the first eight bytes: 
> 
> // -- begin -- 
> RandomAccessFile ra = new RandomAccessFile(new File(bigometiff), "r"); 
> for(int i=0; i<8; i++) 
>     System.out.println(ra.read()); 
> ra.close(); 
> // -- end -- 
> 
> I hope I can help you with this information.
> 
> Kind regards, 
> Matthias
>