Difference between revisions of "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 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.  
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. A few heavier tasks require using a multi-node Linux cluster at APS.


== Data types and formats ==
== 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]].  
* 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 [[wikipedia:Nexus (data format)|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.
** 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.
* 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.
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== Types of Analysis ==
== Types of Analysis ==
=== Depth-resolved scans (wire scans) ===  
=== 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.
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 the computer cluster, and can be submitted through [[ORNL Client]].  


The reconstruction process is the same for white-beam or mono-beam scans.
The reconstruction process is the same for white-beam or mono-beam scans. Reconstructed image files are also written in NeXus format.


=== White-beam Laue images ===
=== White-beam Laue images ===
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''Main Article: [[Single Laue Image Analysis with LaueGo]]''
''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.
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 energies of specific Bragg peaks, or identify the existence of certain phases.
 
===== Multiple images =====
===== 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.
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.
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=== Scaler data (mda files) ===
=== Scaler data (mda files) ===
{{Incomplete}}
{{Incomplete}}
There are a few ways of visualizing scaler scan data:
There are a few ways to visualize scaler scan data:
#Plotting window by MEDM (for 1D scans)
#Plotting window by MEDM (for 1D scans only)
#scanSee (1D and 2D)
#scanSee (1D and 2D)
#LaueGo has built-in functions for reading and displaying mda files
#LaueGo has built-in functions for reading and displaying mda files
#An IDL utitlity on beamline PC can display 2D mda data
#An IDL utitlity on beamline PC can display 2D mda data


== See Also ==
== See Also ==

Latest revision as of 18:39, 21 October 2013

(This article/section is incomplete, please check back again or help expanding it)

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. A few heavier tasks require using a multi-node Linux cluster at APS.

Data types and formats

  • Each exposure of an 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, which is based on 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. 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 the computer cluster, and can be submitted through ORNL Client.

The reconstruction process is the same for white-beam or mono-beam scans. Reconstructed image files are also written in NeXus format.

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 energies 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 "E scans" tab of LaueGo.

Scaler data (mda files)

(This article/section is incomplete, please check back again or help expanding it)

There are a few ways to visualize scaler scan data:

  1. Plotting window by MEDM (for 1D scans only)
  2. scanSee (1D and 2D)
  3. LaueGo has built-in functions for reading and displaying mda files
  4. An IDL utitlity on beamline PC can display 2D mda data

See Also