34ID-E Data Analysis Overview - Revision history

Ruqingxu: /* Data types and formats */ linke to wikipedia nexus data format page

2013-10-21T18:39:33Z

Data types and formats: linke to wikipedia nexus data format page

← Older revision		Revision as of 18:39, 21 October 2013
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	== 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.

Ruqingxu: /* Scaler data (mda files) */

2013-08-22T16:30:08Z

Scaler data (mda files)

← Older revision		Revision as of 16:30, 22 August 2013
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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 ==

Ruqingxu: /* Depth-resolved scans (wire scans) */

2013-08-22T16:19:49Z

Depth-resolved scans (wire scans)

← Older revision		Revision as of 16:19, 22 August 2013
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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 the computer cluster~~. 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 ===

Ruqingxu: /* Single image */

2013-08-22T16:14:47Z

Single image

← Older revision		Revision as of 16:14, 22 August 2013
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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.

Ruqingxu at 22:21, 21 August 2013

2013-08-21T22:21:15Z

← Older revision		Revision as of 22:21, 21 August 2013
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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 ==
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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. Reconstructed image files are also written in NeXus format.

	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.

Ruqingxu: /* See Also */

2013-08-21T22:17:33Z

Ruqingxu at 22:16, 21 August 2013

2013-08-21T22:16:02Z

← Older revision		Revision as of 22:16, 21 August 2013
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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]], ~~which~~ is carried out by a multi-node Linux cluster at APS.		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 ===		=== White-beam Laue images ===
	===== Single image =====		===== Single image =====
	[[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.
	===== 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.

			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) ===		=== 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) ===		=== Scaler data (mda files) ===
			{{Incomplete}}
			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 ==		== See Also ==

Ruqingxu at 23:15, 19 August 2013

2013-08-19T23:15:56Z

← Older revision		Revision as of 23:15, 19 August 2013
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	{{Incomplete}}		{{Incomplete}}
	* Overview
	* Depth-~~resolved~~ data analysis, ~~reconstruction~~		<!-- Overview -->
	* ~~White~~-~~beam Laue image analysis~~		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.
	** single ~~image~~
	** ~~multiple~~ images		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.
	* Monochromatic ~~scan analysis~~
			== 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]], which is carried out by a multi-node Linux cluster at APS.
			=== White-beam Laue images ===
			===== Single image =====
			[[Single Laue Image Analysis with LaueGo]]
			===== Multiple images =====
			=== Monochromatic beam data (energy scans) ===
			=== Scaler data (mda files) ===

			== See Also ==

Ruqingxu: moved 34ID-E Data Analysis Overivew to 34ID-E Data Analysis Overview: title typo corrected

2013-08-19T19:55:54Z

moved 34ID-E Data Analysis Overivew to 34ID-E Data Analysis Overview: title typo corrected

← Older revision	Revision as of 19:55, 19 August 2013
(No difference)

Ruqingxu: Created page with "{{Incomplete}} * Overview * Depth-resolved data analysis, reconstruction * White-beam Laue image analysis single image multiple images * Monochromatic scan analysis"

2013-08-19T19:54:05Z

Created page with "{{Incomplete}} * Overview * Depth-resolved data analysis, reconstruction * White-beam Laue image analysis ** single image ** multiple images * Monochromatic scan analysis"

New page

{{Incomplete}}
* Overview
* Depth-resolved data analysis, reconstruction
* White-beam Laue image analysis
** single image
** multiple images
* Monochromatic scan analysis

← Older revision		Revision as of 22:17, 21 August 2013
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	== See Also ==		== See Also ==
			* [[LaueGo]]
			* [[Reconstruction]]
			* [[peakSearch program]] and [[Euler program]]