Nexus Format

The structure of the HDF5 files written by the Nexus writer is compliant with the Nexus standard. You can refer to the Nexus documentation for a full description.

Here, we show an example of an HDF5 file, which contains the data of three scans:

  1. ascan(samy, 0, 9, 9, 0.1, diode1, basler1, xmap1), where diode1 is a diode, basler1 is a camera with one ROI defined and xmap1 an MCA controller with one channel
  2. Unspecified scan
  3. A scan with two independent subscans (for example, one subscan can be a temperature monitor scan)
sample_dataset.h5
 ├ 1.1    # first scan
 |  ├ instrument
 |  |  ├ samy(@NXpositioner)
 |  |  |  └ value (10)   # motor positions during scan
 |  |  ├ diode1(@NXdetector)
 |  |  |  └ data  (10)
 |  |  ├ basler1(@NXdetector)
 |  |  |  ├ data  (10, 2048, 2048)
 |  |  |  ├ acq_parameters   # camera metadata
 |  |  |  |  └ ...
 |  |  |  └ ctrl_parameters  # camera metadata
 |  |  |     └ ...
 |  |  ├ basler1_roi1(@NXdetector)
 |  |  |  ├ data (10)
 |  |  |  ├ avg  (10)
 |  |  |  ├ std  (10)
 |  |  |  ├ min  (10)
 |  |  |  ├ max  (10)
 |  |  |  └ selection   # ROI metadata
 |  |  |     └ ...
 |  |  ├ xmap1_det0(@NXdetector)
 |  |  |  ├ data          (10, 2048)
 |  |  |  ├ elapsed_time  (10)
 |  |  |  ├ live_time     (10)
 |  |  |  ├ dead_time     (10)
 |  |  |  ├ input_counts  (10)
 |  |  |  ├ input_rate    (10)
 |  |  |  ├ output_counts (10)
 |  |  |  └ output_rate   (10)
 |  |  ├ positioners
 |  |  |  ├ samx (1)   # motor position at start
 |  |  |  ├ samy (10)  # motor positions during scan
 |  |  |  └ samz (1)   # motor position at start
 |  |  ├ start_positioners
 |  |  |  ├ samx (1)  # motor position at start
 |  |  |  ├ samy (1)  # motor positions at start
 |  |  |  └ samz (1)  # motor position at start
 |  └ measurement
 |     ├ samy (10)
 |     ├ diode1 (10)
 |     ├ basler1 (10, 2048, 2048)
 |     ├ basler1_roi1 (10)
 |     ├ basler1_roi1_avg (10)
 |     ├ basler1_roi1_std (10)
 |     ├ basler1_roi1_min (10)
 |     ├ basler1_roi1_max (10)
 |     ├ xmap1_det0 (10, 2048)
 |     ├ xmap1_det0_elapsed_time (10)
 |     ├ xmap1_det0_live_time (10)
 |     ├ xmap1_det0_dead_time (10)
 |     ├ xmap1_det0_input_counts (10)
 |     ├ xmap1_det0_input_rate (10)
 |     ├ xmap1_det0_output_counts (10)
 |     └ xmap1_det0_output_rate (10)
 ├ 2.1   # second scan
 ├ 3.1   # third scan
 └ 3.2   # also third scan

Each scan contains two groups (plots and application definitions are not shown).

  • instrument:
    • all motors moving during the scan (NXpositioner: distance, time, energy, …)
    • all detectors enabled for the scan (NXdetector)
    • start_positioners: snapshot of all motors before the scan
    • positioners: like start_positioners
  • measurement: flat list of all NXpositioner and NXdetector data

Note that each NXdetector contains one primary value called data and each NXpositioner contains one primary value called value. Additional datasets and groups represent secondary detector/positioner data or metadata such as detector settings.