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CrysTBox - ringGUI step by step


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ringGUI step by step

Here is a list of several steps you typically need to go through with ringGUI (see below) if you are after some more or less reliable results.

1 - Open input image

In order to demonstrate how ringGUI operates, a sample image is provided and loaded by default. This allows you to just press Launch all (described below) and see the correct results in a moment. Your own diffractograms can be loaded using the Browse button in the Image panel or via the menu File / Open image. Either way leads to a dialog box (see aside).

(2 - Optional: Set image resolution)

If the image contains metadata with the image resolution, it is loaded and can be seen in the Image panel. Otherwise, you have to specify the resolution manually.

You can let ringGUI to parse scalebars burnt into the image via Tools / Detect scalebar. If the scalebar is read successfully, the resolution is calculated and after you check it, it can be applied. If there is a conflict between the scalebar resolution and the value stated previously in the GUI, you will be notified and given a choice of whether to use one or another.

Note: The scalebar should be eliminated if it might influence positions of peaks in the intensity profile (circular average). One of the ways how to eliminate it is to perform the scalebar detection even though the resolution is known from the metadata.

3 - Select sample material

The sample material can be changed at any time during the analysis. Details about material database and selection can be found here.

4 - Launch all

The whole analysis can be launched at once using the Launch all button. The individual procedure steps represented by the buttons below are then carried out consecutively. After the whole procedure has been finished successfully, the final results are presented. Each step can be re-launched at any time by pressing respective button below the Launch all button. Partial results of individual steps can be shown via corresponding Show buttons aside. It is advisable to check the partial results to verify relevance of the final findings. Below, the individual steps and expected results are discussed in detail.

4a - Beamstopper detection

A beamstopper must be masked out prior to further processing. This is done using the button Detect beamstopper. The Beamstopper pop-up menu offers several ways of the beamstopper elimination:
None - select if no beamstopper is present.
Auto - an automated algorithm for beamstopper detection.
Manual - beamstopper is outlined manually.

Check: Press the Show button next to the Detect beamstopper to check whether the whole beamstopper is masked.

4b - Rings centre localization

Consequently, the ring centre must be localized via the Centre localization button. This can be done automatically, which should work fine for most cases, or manually. The automatic algorithm works in stages - the more stages the more accurate and time consuming. The manual way employs a user-friendly GUI (see aside).

Check: Press Show button next to the Centre localization or Adjust centre manually to check whether the centre is localized correctly.

4c - Background extraction

After the circular average (intensity profile) is calculated, the background must be estimated and removed by pressing Background extract.. This is done automatically showing the result in the plot below the image. If the resulting background does not follow the intensity profile accurately, the background can be defined manually using a dedicated GUI (see aside) via the button Adjust background manually. The tool allows the user to provide the background points manually. As the user adds or removes individual background points the background is recalculated, subtracted from the intensity profile and the intensity peaks are shown.

Check: Press the Show button next to the Background extract to check whether the background curve fits the intensity profile correctly.

4d - Peak identification and interpretation

After the the background is subtracted from the intensity profile, the peaks are formed, localized and assigned to the theoretical d-spacing values via the Peak identification button. An interactive intensity profile can be seen in the plot below the input image (see aside). Similarly to the diffractGUI, it depicts the theoretical d-spacings specific to the material and d-spacings measured in the image. In the bottom part, there are dark-blue lines corresponding to the theoretical d-spacings. In the upper part, there is the intensity profile (red line) with the localized and identified peaks represented by the dark-blue lines.

An assignment between the theoretical and measured reflections is visualized by the light-blue connector lines. The dotted d-spacings represent very weak or forbidden reflections. By default, these are excluded from the assignment, but can be included via the main menu Settings / Omit weak and forbidden reflections. Similarly to diffractGUI, one can use Calib. coef in the Peak plot panel to align the assignments and to reduce an inaccuracy of the camera length calibration.

To get more information about a particular d-spacing, just select one using a mouse click. The selected d-spacing is highlighted in the plot, corresponding ring is marked in the input image (see aside) and its details can be found in the Cursor panel. Some of the peaks may come from an inaccurate background elimination. This is typical for peaks on the left side of the profile, which corresponds to the central part of the diffraction pattern. Those invalid peaks can be excluded selecting the peaks and unchecking the checkbox Valid peak in the Cursor panel. This way, you can exclude arbitrary reflections from further analysis or visualization.

Check: Press the Show button next to the Peak identification. If there are false (invalid) peaks caused by an inaccurate background estimation, try to eliminate them in the previous step or exclude them using the Valid peak checkbox. If the assignments between the theoretical and measured reflections are biased, adjust the calibration coefficient.

4e - Results and visualization

As you can see below, the input image can be "enhanced" to make the rings more aparent. Use check boxes in the Diffraction image panel to remove the background or beamstopper or to make faint ring visible. Spotty rings can be smoothed using the Average only checkbox.

Original image Background eliminated Beamstopper removed Rings revealed All together
The results can be visualized using the pop-up menu next to the Show overview button (see below). The Quadrant mode allows you to see Miller indices of the depicted rings. You can also place the theoretical and experimetntal rings side by side to see how they match using the Half & Half visualization.
Original image Quadrant visualization (beamstopper and background removed) Half & Half visualization (beamstopper and background removed)
5 - Further features

One of the ringGUI features can be used for an automatic to estimation of the correct calibration coefficient and even for picking a proper sample material from a list of possible candidates. Another functionality allows for a multi-phase analysis, but this feature requires perfect calibration, good knowledge of the sample and some experience with ringGUI. Both features can be found in the tabs Multi-Phase analysis and Estimation of material and calib. coef in the bottom left corner of the window.

6 - Save the results

If you need to save the results, you can generate an HTML report via File / Generate HTML report. The image and visualizations within the image can be exported using File / Export diffraction view. The profile can be exported either as a picture via File / Export peak view or as a data text file File / Export profile data. More about the image export can be found here.

Author contact

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