[Nexus] How to access data

[Tobias.Richter at diamond.ac.uk]

Hi Tim,

The simple version to read the data is NXgetdata which will read all of it. That may well run out of memory.
With NXgetslab you can bite off chunks the size you can chew. Slab_start and Slab_size need to be of the same rank as the data.
Slab_size tells the API how big the data volume is you want and Slab_start tells it where to get it from.

For example: So if you want to read the 35st image out of a stack of 150, with a data shape like this: (150, 640, 480) You pick slab_start as (34,0,0) and slab_size as (1, 640,480).

If I just needed to dump out the data somehow I'd use python/h5py or nexpy: http://nexpy.github.io/nexpy/ unless there was a particular other reason to use C. That may just be my preference though.

Regards,

Tobias


-----Original Message-----
From: NeXus [mailto:nexus-bounces at nexusformat.org] On Behalf Of Tim Gruene
Sent: 12 June 2014 21:13
To: nexus at nexusformat.org
Subject: [Nexus] How to access data

Dear all,

I have a file in Nexus format (HDF v.5) and I would like to access the data at /run_466/tof_detector_1/single_events_time
/run_466/tof_detector_1/single_events_x
/run_466/tof_detector_1/single_events_y

from a C or C++ program.
So far I got stepwise into the groups so that
	NXopendata (myfile, (dir_tof1 + "/single_events_x").c_str()); returned NX_OK.

At this point I don't know how to proceed. I looked at the online API documentation and the example file napi_test.c

I assume for the 3x1.5 million numbers, the functionNXgetslab would be helpful. In napi_test.c the calls are:
 NXgetslab (fileid, data_buffer, slab_start, slab_size)

the data_buffer is the memory block where the data get stored, I assume.
It was allocated with
NXmalloc ((void **) &data_buffer, NXrank, NXdims, NXtype)

Question 1: does this allocate the memory for the entire data? If so, what if there is too much data for the RAM of my computer?

I also don't understand the roles of slab_start and slab_size. In napi_test.c, these are two-dimensional arrays.

Question 2: Is it correct that for my one-dimensional data "single_events_time" I require a one-dimesional
	int slab_start[1], slab_size[1];
respectively?

Question 3: I would think that NXgetslab reads data according to the rank of the data beginning at entries number slab_start[0], slab_start[1], ... and reads a total number of slab_size[0], slab_size[1], ... into memory at once. Is this correct?

Question 4: Is there a simple way to access the one-dimensional data  in single_events_time, single_events_x, and single_events_y?
I used the DUMP command in the utility nxbrowse in order to create plain text files containing the data just to test my ideas, which work greatly. So all I need is a C-version of dumping the data out of the nexus-container.

I greatly appreciate any help, maybe a link to a decent tutorial (for C or C++) on how to read nexus format. Many of the tutorials start with how to write nexus, which is confusing to me and something I don't need.

Regards,
Tim Gruene
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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