HDF5 files

HDF5 files

HDF5 files are used as input and output of the simulation. They store the information of the previous simulation steps as well as information of intermediate calculations of this detector. Inside of such files an hierachical structure with groups and data sets exsists. data sets contain data and groups contain other groups or data sets.

Requirements and datastructures of the input HDF5 file

In front of a detector is usually a diffraction area. Here the output of the singFEL diffractor is used. Its output file has the following structure:

HDF5 path	Datatype	Content
/data/data	2D numpy array	integrated intensity per pixel
/data/diffr	2D numpy array	integrated intensity per pixel converted to photon count (Poissonized)
/data/angle		Euler angles applied to atomic positions
/history/parent/detail	ExternalLink	Details of parent data
/history/parent/parent	ExternalLink	Parent data, hierarchical
/info/package_version		Backengine code version
/info/contact		Support contact
/info/data_description		Data documentation
/info/method_description		Method documentation
/params/geom/detectorDist	float	Detector distance
/params/geom/pixelWidth	float	Pixel width (x)
/params/geom/pixelHeight	float	Pixel height (y)
/params/geom/mask		Masked pixels
/params/beam/photonEnergy		Central photon energy
/params/beam/photons		Number of photons in beam
/params/beam/focusArea		Beam focus area
/params/info		Input parameter for backengine code

Requirements and datastructures of the output HDF5 file

HDF5 path	Datatype	Content
/data/data	2D numpy array	each element is a charge detected at that spot of the detector
/data/photons	2D numpy array	each element contains the number of photon it has
/data/interaction	m x 5 numpy array	each row is an interaction of a photon at the detector
/history/parent	ExternalLink	Link to the input file
/info/package_version	string	Backengine code version
/params/geom/detectorDist	numpy float_	Detector distance
/params/geom/pixelWidth	numpy float_	Pixel width (x)
/params/geom/pixelHeight	numpy float_	Pixel height (y)
/params/beam/photonEnergy	numpy float_	Central photon energy

Description of the arrays

data/data

This data set includes an array such as data/data, where the simulated and propagated charge per detector pixel is stored in

data/photons

the data/data of the input file but converted to a numpy array

data/interactions

This numpy array (m x 5) recordes the interactions of the photons with the detector. Each row (j elem m) represents an interaction:

- [i,0] = position at the detector of the deposited energy in x
- [i,1] = position at the detector of the deposited energy in y
- [i,2] = position at the detector of the deposited energy in z
- [i,3] = time of the deposition of energy
- [i,4] = deposited energy of the photon at the detector