View source for 34ID-E Data Analysis Overview

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A wide variety of measurements can be carried out at 34ID-E: white beam or mono beam, step scans or slew scans, with area detectors or point detectors, depth-resolving or not, etc. Hence a collection of tools are developed to tackle different types of data sets.

A majority of analysis and visualization functions are built into '''[[LaueGo]]''', a package developed at 34ID-E based on [[IGOR Pro]] which runs on a single PC or Mac. 

== Data types and formats ==
* Each exposure of an [[34ID-E Detectors|area detector]], if file-saving is turned on, creates a file containing 2D data. By default our detector images are saved in the [[NeXus format]] [http://www.nexusformat.org/ NeXus format], which is based on [[wikipedia:Hierarchical Data Format | HDF-5]]. 
** Note: with special configurations, such as the [[fly-scan mode]], multiple exposures can be saved in a single data file as a 3D array.
* Each scan automatically creates a *.mda file that is sequentially numbered. The mda file stores motor positions and pre-selected scaler counts at each scan step.
** Only the motors that are being scanned are recorded in mda files.
* For multichannel analyzer (MCA) fluorescence detectors, total counts of each window of channels are recorded as scalers, and stored in the mda files.

== Types of Analysis ==
=== Depth-resolved scans (wire scans) === 
Data from depth-resolved measurements requires [[Reconstruction of Depth-Profiling Data | reconstruction]]. A reconstruction takes a depth-profiling wire scan data as input, and generates a series of 2D image files each representing the diffracted intensities from a specific depth along the x-ray's penetration. The process is carried out by a multi-node Linux cluster at APS. Reconstructed image files are also written in NeXus format.

The reconstruction process is the same for white-beam or mono-beam scans.

=== White-beam Laue images ===
===== Single image =====
''Main Article: [[Single Laue Image Analysis with LaueGo]]''

Single Laue images, depth-reconstructed or not, can be indexed with [[LaueGo]]. One can index a single Laue Image and get the crystal orientation, deviatoric strain, predict the energy of specific Bragg peaks, or identify the existence of certain phases.
===== Multiple images =====
Indexing of a large number of images can be automated on the Linux cluster through [[ORNL Client]]. It is recommended that one first try indexing a few images with LaueGo and get all the input parameters optimized before submitting a batch indexing job.

Each multiple-indexing job creates an xml report file that contains the indexing results for each image. This report can be imported to LaueGo for further analysis, such as strain refinement, 2D/3D plotting, pole figures, etc.
=== Monochromatic beam data (energy scans) ===

Mono beam are mostly used for energy scans near specific Bragg peaks to measure lattice d-spacings, they can be done with or without depth-profiling.

Depth-resolved wire scans need to be reconstructed first.

Energy scan data can be analyzed with functions listed in the [[LaueGo#E scans Tab|"E scans" tab of LaueGo]].

=== Scaler data (mda files) ===
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There are a few ways of visualizing scaler scan data:
#Plotting window by MEDM (for 1D scans)
#scanSee (1D and 2D)
#LaueGo has built-in functions for reading and displaying mda files
#An IDL utitlity on beamline PC can display 2D mda data


== See Also ==