Skip to content

Latest commit

 

History

History
20 lines (13 loc) · 3.79 KB

docs-outputs.md

File metadata and controls

20 lines (13 loc) · 3.79 KB
Raw
title subtitle
Output File Format
The HDF5 output file format of Prismatic

Outputs are written to HDF5 files with a format compatible with the analysis package py4DSTEM. All output from Prismatic is packed into a single file, according to the EMD file format description and directly compatible with the py4DSTEM analysis package. There are potentially 2D, 3D, and 4D outputs, as well as calculations of DPC center of mass and the calculated projected potential slices. For all outputs, there are at least two dimensions corresponding to X and Y probe positions. At each position, Prismatic can output the full probe (4D), a radially integrated output placed into virtual detector bins (3D), an image further integrated over a range of detector bins to produce a single value for each scan position (2D), the differential phase contrast center of mass, and the projected potential. The 3D output is considered to be the primary result and is the only output produced by default; however, any combination of 2D, 3D, 4D, DPC, and potential slice outputs may be produced with a single simulation. The metadata parameter filename_output is set with "-o" at the command line.

  • 2D output: Produced by adding the command line option "-2D ang_min ang_max" where "ang_min" and "ang_max" are the inner and outer integration angles in mrad. By default this is off. The 2D output is saved into a single array in the HDF5 file under /4DSTEM_experiment/data/realslices/annular_detector_depth####/realslice, where #### is the output layer (always 0000 if using the PRISM algorithm).
  • 3D output: Controlled by command line option "-3D 0/1" where 0 or 1 is a boolean on/off. The 3D output is saved to filename_output. By default this is on. The 3D output is saved into a series of realslice arrays in the HDF5 file under /4DSTEM_experiment/data/realslices/virtual_detector_depth####/bin$$$$where #### is the output layer (always 0000 if using the PRISM algorithm) and $$$$ is the virtual detector bin.
  • 4D output: Controlled by command line option "-4D 0/1" where 0 or 1 is a boolean on/off. By default this is off. The 4D output is saved into a single, chunked array in the HDF5 file under /4DSTEM_experiment/data/datacubes/CBED_array_depth####/datacube, where #### is the output layer (always 0000 if using the PRISM algorithm).
  • DPC Center of Mass: Controlled by command line option "-DPC 0/1" where 0 or 1 is a boolean on/off. By default this is off. The DPC output is saved into two realslice arrays in the HDF5 file under /4DSTEM_experiment/data/realslices/DPC_CoM_depth####/DPC_CoM_$, where #### is the output layer (always 0000 if using the PRISM algorithm) and $ is either x or y.
  • Potential Slices: Controlled by command line option "-ps 0/1" where 0 or 1 is a boolean on/off. By default this is off. The potential slice output is saved into a series of realslice arrays in the HDF5 file under /4DSTEM_experiment/data/realslices/ppotential/slice_####where #### is the potential slice (increasing in Z).

For example, the prismatic command ./prismatic -i atoms.XYZ -2D 0 10 -4D 1 -3D 1 -o example.h5 will produce "prism_2Doutput_example.h5" with the 2D bright field image integrated from 0-10 mrad, the 3D output, and the 4D output, but will not include the DPC calculation nor potential slices. Physically relevant metadata from the simulation is saved into the metadata group under /4DSTEM_experiment/metadata/metadata_0/original/simulation_parameters as a series of attributes that can be accessed as key-value pairs. A parameter file is also generated at the end of the simulation and placed into the home directory of the user.