Accessing the Underlying Data

Scimap tries to keep controller and presentation logic separate from the underlying data; most of the methods on the XRDMap class retrieve, display and/or store their data without the user’s involvement. Given the complicated nature of scientific analysis, it can sometimes become necessary to retrieve individual diffraction patterns directly, or even to manipulate the data files directly; scimap provides a mechanism for both cases.

Scimap uses HDF5 files to store all the mapping data. This provides two benefits: 1) large datasets can still be analyzed even if they don’t fit into main memory, and 2) the results of analysis can easily be shared or published as one file with accompanying metadata. This comes at the cost of increased time needed to write calculated data to disk, rather than manipulating it in main memory.

Retrieving Common Representations

The following methods of the XRDMap class can be used to retrieve a variety of packaged data.

• XRDMap.diffractogram: Get bulk-averaged diffraction data from all positions.
• XRDMap.get_diffractogram: Get the diffraction data for a single position.

Accessing the XRD Data Store and HDF File

It is possible to interact with the data as numerical arrays. The XRDStore class provides an interface for accessing the defined datasets. It can be retrieved throught the XRDMap().store() method, or instantiated directly.

Warning

The XRDStore class should be used as a context manager whenever possible. Failure to close the underlying HDF5 file, especially if using a writeable mode, is likely to lead to file corruption.

xmap = XRDMap(...)
with xmap.store() as store:
    Is = store.intensities

In the above example, store.intensities gives the intensity (photon counts) for each mapping position. The result will be an m x n array where m is the number of mapping positions and n is the number of angles/scattering vectors.