[Nexus] question about NeXus classes
darren.dale at cornell.edu
Tue Aug 26 16:22:53 BST 2008
I think my last message might have been overlooked since I posted it on a
weekend. I'd like to try to revive the discussion and ask a couple more
On Saturday 26 July 2008 09:42:04 am Darren Dale wrote:
> On Friday 25 July 2008 13:35:13 Peterson, Peter F. wrote:
> > -----Original Message-----
> > From: nexus-bounces at nexusformat.org
> > [mailto:nexus-bounces at nexusformat.org] On Behalf Of Darren Dale
> > I have a question regarding specialization of the generic class
> > definitions listed at http://www.nexusformat.org/Design#NeXus_Classes .
> > Is it acceptable to create a subclass of NXdetector that is specific to a
> > single- or multi-element energy-dispersive detector, called NX_Vortex90EX
> > for example, and save that class name to NX_class? If that is not
> > advisable, I guess I could use an additional attribute like NX_subclass.
> > I'm just trying to get asense of the intended use of the NX_class
> > attribute and its limitations.
> > Thank you for the question.
> > The current philosophy of classes is that they are to be thought of as
> > dictionaries. If you are familiar with xml schema (xsd) the "any" tag is
> > appropriate. This means that there is one NXdetector which covers all
> > the various types of detectors in existence. If a particular detector
> > needs another field that isn't in the current NXdetector, then it should
> > be added. Subclassing is not an idea that can be applied to the base
> > classes.
> Thanks for responding. I have almost no experience with xml, so please
> excuse my ignorance: if I need additional fields, I can add them, but I
> should continue to use the existing classes. Is that correct?
> > However, the NIAC has noted the similarities in several of classes and
> > applying the object oriented design techniques such as subclassing. The
> > committee agreed that this is the direction for the future, but are
> > waiting until the current definitions (v2.0) can be finalized.
Is there any news on this subject?
> I'd like to explain what I'm working on. I have been developing a program
> for acquisition and analysis at my beamline, and have been generating hdf5
> files using pytables. I am now working on updating my data model to format
> the files according to the nexus guidelines, and am starting at the
> foundation: an object-oriented interface to the hdf5 file and tree. This
> foundation is not built on the nexus api or the official nexus python
> bindings, nonetheless I want to make sure my files adhere to the standard.
> For example:
> t = NXfile('NXtest.h5')
> vortex = t['entry']['instrument']['vortex']
> That currently inspects the node's attributes and returns an instance of
> the NXdetector python class. In the future I can also inspect the nodes
> "type" and "description" attributes to find a more specialized constructor
> if necessary, one that provides additional methods and a richer interface
> to the same underlying NXdetector data.
The basic foundation of my project is essentially in place, thanks to the new
h5py project: http://h5py.alfven.org/ , which provides a simple and intuitive
interface to the hdf5 library. h5py similar to (and somewhat deriving from)
pytables, but unlike pytables h5py supports links and is threadsafe. I think
it is a great foundation for building an interface geared towards working
with NeXus data interactively in python, or with simple python scripts.
I'm not trying to interfere with the official nexus python bindings, which
provide a NAPI-ish interface. But I do see an opportunity that I felt I had
to explore. I hope nobody feels like I am stepping on anyone's toes.
> I'm just getting started, so right now I can access the data in a pythonic
> way and return basic NX* object instances, but the objects are all
> featureless aside from providing access to the underlying data. Since I'm
> just getting started, it would be helpful if you could share any
> information concerning the future of nexus' definitions and organization.
> Are the committee's discussions available on the web? Do you think my
> approach is one that the nexus developers could be comfortable with, or
> should I be considering another approach? My hope is that the project would
> eventually be useful to the wider community.
Today I discovered nxvalidate in the nexus trunk and tried running it on some
of the test files in test/data. They either did not conform to the new 3.0
schema or the perhaps the schema does not include all the definitions needed
to validate these files. nexus_defs/schema/testfile.xml does validate. Is
there any additional information available concerning the new organization of
NeXus classes/subclasses, new features, etc?
At my beamline, we do some scanning X-ray fluorescence microscopy, and we
process the data in real time. I would like to group the processed data
together as a child group of the NXentry, something like:
NXentry/element_maps/NXdata for each element modeled
It looks like the class I am looking for to provide the element_maps grouping
is described in NXprocessed.xml or PROCESSED.xsd, which is not present in the
class list at http://www.nexusformat.org/Design. I am still trying to get my
bearings, can NXentry contain a NXprocessed group and still conform, or does
NXprocessed have to exist under NXroot? Can NXprocessed contain additional
metadata besides what is listed in NXprocessed.xml, like links to NXdetector
MCA data, or should that information be stored in NXprocessed/NXprocess? Is
there documentation answering basic questions like these?
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