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CrysTBox ringGUI - ring diffraction analysis


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General information

The main purpose of this tool is to automatically identify crystallographic planes corresponding to the rings depicted in the ring diffractogram. If the sample material is not exactly known, ringGUI can select the sample material from a list of candidate materials given by the user. The tool can also automatically enumerate the camera length incaccuracy, so it can be very helpful during the camera length calibration.


Video >>
Examples>>

Input image > ringGUI > Result

Input

Image

  • ring diffraction image (rings does not need to be complete - even very spotty patterns can be processed)
  • rings should not be significantly elliptical (if they are, you can look for some correction tools at Dave Mitchell's website)
  • multi-phase diffractograms not supported
  • supported file formats: DM3 (prefered as it contains scaling information) and all common image formats (JPG, PNG, TIF,...)
Sample material
  • defined by unit cell
  • supported file formats: .CIF, .CELL
  • some materials are predefined, but user can specify arbitrary material (details...)

Examples

If you are interested how ringGUI copes with various input images, see examples.

Window description

ringGUI window

The application window consists of two figures and several panels. The figures allow the user to see the input image and a graphical interpretation of some results. The surrounding panels allow to control the analysis procedure and list some results.

A detailed description of the graphical user interface follows.

Diffraction image
Diffraction image

This figure shows the input image and/or some graphical visualization of some results. This particular example shows an identification of diffraction rings and can be obtained using button Show overview.

Peak plot
Peak plot

The diffraction profile is plotted here once it is known. The profile is a circular average of the image intensity as function of distance from the ring center. The left border of the plot corresponds to the ring center, while the right one corresponds to the image border. Vertical blue lines in the bottom part of the plot stand for the theoretical ring radii specific to the sample material. Vertical blue lines in the upper part (in the profile) represent the ring radii measured in the experimental image. Light-blue lines in between illustrate the assignment between the measured radii and their theoretical counterparts. This plot is interactive. You can click the blue lines corresponding to either theoretical or experimental d-spacing and you should see details in Cursor panel and a visualization in the Diffraction image.

Input panel
Input panel

This panel contains information about the input image.

Browse
This button allows you to find the input image in the directory structure.
Load
Loads given input image.
Resolution
The image resolution can be set manually here.
Material
The sample material can be specified using this field.

Diffraction evaluation panel
Diffraction evaluation panel

The analysis procedure can be controled using this panel. The whole procedure can be launched at once by single click on the Launch all button or it can be performed step by step clicking on the buttons corresponding to individual steps. Partial results of individual steps can be displayed using corresponding Show buttons.

Launch all
This button launches all the analysis steps at once.
Detect beamstopper
The algorithm requires the beamstopper to be detected. This can be done manually or automatically for the known beamstoppers. Resulting beamstopper mask is shown once this step is completed. If the mask does not fit the beamstopper correctly, the user shall outline the beamstopper manually. Manual localization can be performed by setting the pop-up menu Beamstopper to "Manual" and then clicking the button Detect beamstopper.
Beamstopper
This pop-up menu specifies type of the beamstopper for automatic detection or manual localization.
Center localization
This step localizes center of the diffraction rings. This can be done automatically in several stages (see Num. of stages) or manually.
Num. of stages
This pop-up menu defines number of stages for the automatic centre localization. The higher is the number of stages, the more precise and time consuming the localization is. User can also localize the centre manually setting the value to "Manual"
Background extract.
Typically, there is some background in the diffraction image - central parts of the image are brighter compared to the image borders. This button is used to extract the background from the image, which is necessary for precise and reliable ring localization.
Num. of points
The background is approximated by a hyperbolic function touching the diffraction profile from bellow. Number of points, where the hyperbola should touch the diffraction profile is specified here.
Peak identification
This step localizes certain number of the highest peaks in the profile.
Num. of peaks
Number of the highest peaks to be localized (and subsequently crystallographically identified) in the diffraction profile can be specified in this field.
Show overview
Shows an assignment of the plane indices to the diffraction rings into the diffraction view.

Panel for Estimation of material and calib. coef.
Panel for Estimation of material and calib. coef.

If the sample material is not known, the tool can select the most appropriate one from the list given by the user. Similarly, the calibration coefficient can be determined - the user can specify a range of possible values and the algorithm automatically finds the one which best fits the experimental data. Both functionalities can be combined together, so that ringGUI searches for the most appropriate material and calibration coefficient at once.

Possible materials
Comma-separated list of possible sample materials (see Material for details).
Possible calilb.coefs
Range of possible calibration coefficients (see Calib. coef. for details).
Estimate
Button launching the estimation of the material and/or calibration coefficient.
MgO 1.005 (pop-up menu with estimation results)
Several best-scored combinations of the material and calibration coefficient are stated in this pop-up menu. Selection of particular menu entry automatically sets given sample material and calibration coefficient (calibration coefficient is adjusted, theoretical ring radii are redrawn and assignments to the experimental radii are recalculated).

Peak plot and Diffraction image panels
Peak plot and Diffraction image panels

These two panels adjust the Peak plot and Diffraction image.

Background elimination (Peak plot panel)
This checkbox specifies whether to eliminate the background from the Peak plot (and from the Diffraction image if Show in the image is selected).
Show in the image (Peak plot panel)
The checkbox controls whether the diffraction profile is shown in the Diffraction image.
Calib. coef. (Peak plot panel)
This value allows for an adjustment of the camera length calibration inaccuracies. The measured ring radii are multiplied by this coefficient prior to the comparison with the theoretical ones.
Background elimination (Diffraction image panel)
Allows for a removal of the background from the diffraction image (see figure below).
Beamstopper removal (Diffraction image panel)
Removes the beamstopper from the image (see figure below).
Average only (Diffraction image panel)
Shows the intensities calculated from the circular average instead of the input image. This makes the image smoother.
Ring revelation (Diffraction image panel)
Makes the weaker beams more apparent (see figure below).

Original image Background eliminated Beamstopper removed Rings revealed All together
Cursor panel

Cursor panel In this panel, one can see the details about the theoretical and experimental ring radii chosen using a mouse-click into the Peak plot.

Plane
Miller indices corresponding to the given radius.
Meas radius
Radius measured in the experimental image.
Theor. radius
The theoretical radius specific to the sample material.
Valid peak
This checkbox allows to exclude currently selected peak from the evaluation. Excluded peaks (denoted by small cross in the Peak plot) are not displayed in the overview (see Show overview) and they are not taken into account during the estimation of material or calibration coefficient (see Panel for Estimation of material and calib. coef..
Score
Score reflecting relative height of the peak.
Conf.
Confidence measure reflecting how the tool is confident, that current peak correspond to a ring in the image.

Author contact

If you have any questions, offers or comments, please feel free to contact me:
Miloslav Klinger
e-mail: klingeratpost [dot] cz