Stempy H5 Format

This file is present to keep a record of the current layout of the stempy H5 format.

Currently, the structure of the format is as follows:

electron_events
├── frames
└── scan_positions
stem
└── images
frames

• electron_events/frames - Array of arrays, the first index is the scan position ( corresponding to scan_positions ) and the second array holds an array of of indices into the diffractogram where an electron strike was detected.

  • Attributes:

    • Nx: the width of the frame

    • Ny: the height of the frame

• electron_events/scan_positions - Array of shorts holding the scan positions.

  • Attributes:

    • Nx: the width of the scan

    • Ny: the height of the scan

• stem/images - A list of 2D arrays of unsigned integers containing stem images (possibly bright and dark fields).

  • Attributes:

    • names: a list of names assigned to the images

• frames - If present, the raw diffractogram data, where the first index is the scan position index for the 2D diffractogram.

  • Attributes:

    • scan_dimensions: the dimensions (width, height) of the scan

This file can be produced with the script at examples/create_hdf5.py by using a command similar to the following:

python create_hdf5.py -h 40 -w 40 -v 2 -x 2 -d /data/4dstem/electronCounting/stem4d_0000000235_0000000001.dat /data/4dstem/electronCounting/stem4d_0000000236_0000000009.dat --save-raw

Use python create_hdf5.py --help for more information about the options.