Re: DDLm, dREL, images and NeXus

Dear Colleagues,

�� This is a distillation of an email conversation James Hester and I

have been having since the Osaka meeting.� We both feel that it

would be helpful if others were to join in and express their views.

We have been discussing the interaction among DDLm, dREL, images and

NeXus.� We agree on most points, and disagree on a few, and hope,

by opening up the discussion, to arrive at a consensus.

�� What is driving this discussion is a need to understand how best to

manage image data in the context of both imgCIF and NeXus, and to do

so in a way that is consistent with the recent adoption of DDLm as

the target framework for new work on CIF dictionaries.

�� It must be clearly understood that it is highly unlikely that a

single standard will ever be adopted for crystallographic diffraction

images, much less for the broader context of pixel-based data in

structural biology.� The best we can hope for right now is to have

some number of clearly defined image data frameworks, and agreed

algorithms for conversion among them.� There are many frameworks

to consider, but two that are very close to achieving the goal of becoming

inter-operable in the immediate future are imgCIF and NeXus.� What is

missing is a formal language within which to specify how to move between

them.

�� We could, of course, just come up with a verbal description of how

to move between imgCIF and NeXus and a couple of example conversion

programs written ad hoc in whatever language might come to mind.� However,

the effort being expended on dREL, the supporting language for DDLm,

suggests the possibility of building on dREL as a base to do this job

by extending dREL to have the capability of working with NeXus (dREL

is already capable of dealing with CIF).� James has made the counter

proposal of leaving dREL as just a CIF-specific language and keeping

the CIF-NeXus conversion algorithm specification as a matter for a

different language and/or API.� James has also suggested the further

step of stripping out the built-in functions from dREL and dealing with

just a very stable dREL language specification in one instance and a

perhaps evolving API (list of builtin functions available in dREL) on the

other:

"My comment at this stage would be that defining a coupling mechanism

between CIF and a given language is not a large task, due to the

simplicity of the CIF syntax, whereas adding lots of stuff to dREL

would be a serious task and has some important downsides (loss of

simplicity being an important one). Apropros the

simplicity of the coupling mechanism, I (predictably) quite like my

Python model of a CIF file as a hash table of CIF data block objects

indexed by datablock name, and the datablock objects are themselves

hash tables of strings/lists of strings indexed by dataname.� This

model would appear to translate pretty easily into most other

languages.� What then remains is some syntactic sugar (the use of

square brackets to do key-based lookup is nice in dREL) which can be

replaced in another language by a few standard methods."

There was a lot more to the discussion, but let us try to settle a

direction:

Should we be trying to extend dREL to support more than just CIF,

specifically NeXus, making something we might call dREL++, or should the�

language for this broader task be something distinct from dREL with a�

distinct name.� In practice, in either case, I suspect all of this will be

built on a python base, or something similar, as James suggests, but

names do matter,

Comments please.

Regards,

�� Herbert

=====================================================

� Herbert J. Bernstein, Professor of Computer Science

� � Dowling College, Kramer Science Center, KSC 121

�� � � � Idle Hour Blvd, Oakdale, NY, 11769

� � � � � � � � � +1-631-244-3035

� � � � � � � � � [email protected]

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