[Nexus] NeXus update

[Osborn, Raymond]

Hi Mark,
That is a slightly different issue, which was resolved in your favor, I believe, at the NIAC meeting, i.e., we have formally removed the requirement to create dummy axes when none exist. I have modified NeXpy so that it will plot data, whether there are axes or not (I’ll need to check if that’s been released yet). The issue that Armando and I have been discussing is a requirement that additional attributes be added to identify which axes to use when they do exist. The new requirement is to add two extra group attributes, when in nearly all cases, only one is necessary. 

Ray

On Jan 21, 2015, at 11:49 AM, Mark Rivers <rivers at cars.uchicago.edu> wrote:

> The case I ran into with Ray's program was simply visualizing a 2-D image from a camera stored in NeXus format.  As I recall I got an error because I did not have any axes specified in my NeXus file.  
> 
> In many cases an image really does not need to have axis definitions to be useful.  And in most cases simply being able to specify an offset and pixel size is sufficient to describe the axis.  But NeXus wants a 1-D array, not an offset and size.
> 
> Mark
> 
> 
> -----Original Message-----
> From: NeXus [mailto:nexus-bounces at nexusformat.org] On Behalf Of V. Armando Sole
> Sent: Wednesday, January 21, 2015 11:26 AM
> To: Discussion forum for the NeXus data format
> Subject: Re: [Nexus] NeXus update
> 
> On 21.01.2015 17:48, Osborn, Raymond wrote:
>> On Jan 7, 2015, at 3:45 AM, V. Armando Solé <sole at esrf.fr> wrote:
>> 
>>> I think you should take into consideration the advice of people 
>>> actually writing data visualization software (Ray, myself and even 
>>> Eugen was thinking about whether the generic solution specifying 
>>> points would not be the best).
>>> 
>>> I doubt I will ever add support to the new indices stuff. I can 
>>> default to the current situation where the user can specify what he 
>>> actually want to visualize.
>> 
>> Armando,
>> Sorry I didn’t reply at the time you wrote, but I think that your
>> comment about not supporting the new indices stuff is critically
>> important to the reasons behind my own objections. Adding this support
>> to NeXpy will require me to divert my time from other things. I don’t
>> object to changes per se, but it’s frustrating when the change is for
>> something that is not needed 99% of the time. Currently, it is low on
>> my priority list because I have many other things to do first.
>> 
> 
> Yep. It's the same with me.
> 
> One thing is to specify a *simple* default plot and other one to ask 
> every code to be able to generate the actual axes because the actual 
> data are not there.
> 
> For multidimensional visualization software it is much simpler to get 
> the x and y (and eventually z) coordinates at which something was 
> measured and needs to be plotted than to get a reduced amount x, y (and 
> eventually z) values from which to generate all the coordinates. In one 
> case you need a visualization software. In the other you need a "NeXus 
> interpreter" plus a visualization software.
> 
> If one makes a n_points two dimensional scan, with a motor for the x 
> positions and a motor for the y positions, the simplest is to save 
> n_points values for the x positions and n_points values for the y 
> position with shape (npoints,). To store x and y as (n_rows, ncolumns) 
> with the product n_rows * n_columns equal to n_points is *not* 
> convenient. The same applies to storing x as (n_rows) and y as 
> (n_columns). Why? Because not only due to visualization issues. The data 
> will be taken sequentially, if the user interrupts the scan *because of 
> any reason*, one can end up with a non regular grid. The solution with 
> shapes (npoints,) for the motors and (n_points, 
> whatever_dimensions_needed_for_the_measured_data) will *always* be 
> possible to visualize.
> 
> So, either one specifies *simple* cases in NXdata (and for that the 
> interpretation attribute helps a lot) or one writes the data properly to 
> make the (very few) complex cases for which you would need the new 
> indices simple. Basically one wants coordinates at which something has 
> to be plotted. That something can be a set of scalars, of spectra, of 
> images, of whatever and for that we have the interpretation attribute. I 
> do not think that is difficult to understand or to interpret.
> 
> Armando
> 
> 
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-- 
Ray Osborn, Senior Scientist
Materials Science Division
Argonne National Laboratory
Argonne, IL 60439, USA
Phone: +1 (630) 252-9011
Email: ROsborn at anl.gov