DICOM format detection

[Burkhard Hoeckendorf]

Dear List,

I apologize in case I am posting this mail twice. The first attempt at 
the end of last week came with an attachment and I assume it was 
probably scrubbed (and rightly so).

We recently ran into an issue with DICOM format detection. We use a 
custom file format that is completely unrelated to DICOM and that is 
implemented for SCIFIO such that the file name extension alone is 
necessary and sufficient to recognize it. This works well, except for a 
single file which we couldn't open in Fiji. Reading it by other means 
(C++, MATLAB) worked fine.

As it turns out, even before looking at its file name extension, SCIFIO 
opened the file and tried to detect whether its header is in DICOM 
format. I am unfamiliar with the DICOM standard and not a professional 
Programmer, but from the SCIFIO implementation 
(io.scif.formats.DICOMFormat) it appears to me that the magic 'DICM' 
string in the header is treated as optional. If it is not found, SCIFIO 
tries to read a single header field, and if successful considers the 
file a DICOM file. In our case, we got unlucky and by accident SCIFIO 
retrieved a valid-enough result when reading the corresponding position 
in the non-DICOM file. Hence, it was wrongly detected as a DICOM file.

For the time being, we are now running our own, locally modified SCIFIO 
that does not try harder when the 'DICM' string is missing, and this 
solved our problem. For reference, we modified line 1079 in 
io.scif.formats.DICOMFormat. I am also happy to send this as a pull 
request, but I am not a DICOM user, so can not comment whether or not 
this is actually a workable solution.

More generally though, this experience has led me to wonder whether the 
order in which file formats are detected could be tweaked such that the 
ones requiring the most work are only attempted when the easier ones 
fail. DICOM format detection would thus only occur when the file name 
extension does not match that of any format where the extension alone is 
necessary and sufficient. This may help prevent similar conflicts in the 
future and may additionally contribute a little bit to a much needed 
performance increase.

Cheers,
Burkhard