Image data in the HDF format

For more information about the HDF file format, please go to http://www.hdfgroup.org/.

For more information about the NeXus file format, please go to http://www.nexusformat.org/.

The Tomography Nexus format (which is stored in HDF5) is described as follows from the Pandata Europe Deliverable 5.3

5.3 Tomography Raw Data

This is again a scan around the sample rotation axis. However, in tomography it is common to collect dark field and bright field images before, during and after the actual sample scan in order to be able to correct the data for detector effects. For data reduction the order in which those images have been collected is important.

• entry:NXentry
  • title
  • start_time
  • end_time
  • definition
  • instrument:NXinstrument
    • NXsource
      • type
      • name
      • probe
    • detector:NXdetector
      • data[nFrames,xsize,ysize]
        • @signal=1
      • image_key[nFrames]
      • x_pixel_size
      • y_pixel_size
      • distance
  • sample:NXsample
    • name
    • rotation_angle[nFrames]
      • @axis=1
    • x_translation[nFrames]
    • y_translation[nFrames]
    • z_translation[nFrames]
  • control:NXmonitor
    • data[nFrames]
  • data:NXdata
    • data --> /NXentry/NXinstrument/data:NXdetector/data
    • rotation_angle --> /NXentry/NXsample/rotation_angle

Where image_key is an array which holds for each image either 0,1 or 2 depending if it is a sample, bright field or dark field image.

Tomo Entry

See http://www.nexusformat.org/http://download.nexusformat.org/sphinx/classes/applications/NXtomo.html.

An example NeXus scan file, viewed in hdfview, is presented below:

Please note that the following items are currently essential for running tomography reconstruction with the help of Tomo Recon GUI in Dawn:

1. tomo_entry/data/data
2. tomo_entry/data/rotation_angle
3. tomo_entry/instrument/detector/image_key

The above Nexus paths are also used as default locations in the tomo-centre & tomo-recon commands and in Savu Reconstruction Pipeline. For more information about tomography reconstruction in DLS, see Reconstruction from image data in the HDF format.