wiki:DemoCalibrateTilted

Calibration of an area detector in GSAS-II

In this demo, data collected with a Perkin-Elmer area detector at APS 11-ID-C with a wavelength 0.10798 A, where the detector was intentionally tilted at 45 degrees, are used. Note that menu entries are listed in bold face below as Help/About? GSAS-II, which lists first the name of the menu (here "Help") and second the name of the entry in the menu (here "About GSAS-II").

Step 1: download the data file

Download the sample data file from one of these links:

https://subversion.xray.aps.anl.gov/trac/pyGSAS/browser/Examples/images/tilt-11ID/La_hex_%2B45deg-00015.tif?format=raw or https://subversion.xray.aps.anl.gov/pyGSAS/Examples/images/tilt-11ID/La_hex_+45deg-00015.tif

Step 2: Start GSAS-II

This is done in different ways, depending on your OS and how GSAS-II is installed. A console window is opened (if necessary) and displays some information about the version of python and the packages used by GSAS-II. This console window will display important information as data processing by GSAS-II proceeds. You may wish to cut-and-paste parts of this window to another place if desired.

apsvisit24d:demo1 toby$ python ~/software/work/GSASII/GSASII.py
Available python module versions for GSASII:
python:      2.7.1
wxpython:    2.8.10.1
matplotlib:  1.0.1
numpy:       1.5.1
scipy:       0.9.0rc2
OpenGL:      3.0.1
Max threads  1

The GSAS-II program has now been started and an empty project file is created. The project file contains all data and results related to the project you are working on. (Exception: image files are not stored in the project; to save space only the file name is saved.) You should see three windows, two of which are empty. One, in the upper right, is labeled GSASII data tree, the second, immediately under the first is labeled GSAS-II data display and the third on the left is labeled GSAS-II Plots. These windows may be moved anywhere on the screen but many GSAS-II operations will restore the first two to their default locations. On Linux and Windows a menu bar appears on the data tree and data display windows; on a Mac these menus will appear in the system menu bar location (usually at the screen top) depending on which GSAS-II window has the focus.

Step 3: read in the data file

Use the Data/Read? image data menu item to read the data file into the current GSAS-II project. (view). Select the La_hex_+45deg-00015.tif data file and press Open.

At this point the data tree window will have several entries (view); the plot window shows a faint image (view) and a new window is opened to edit the image controls (view).

Step 4: Edit image parameters

Note that, alas, very few image formats contain all of the important metadata about the image, so it needs to be added manually. In this case set the wavelength to 0.10798. It is also helpful to change the display of the image so that it is easier to see the diffraction rings. Lowering the maximum intensity to 10,000 to 20,000 counts will help (note that this can be done by moving the slider, or by typing a value in the box and then clicking on another control or the typing the Enter/return key). You may also wish to select another color scheme using the Color bar selector.

Alternately, the view of the image can be enhanced by displaying it on a logarithmic scale. Click on the window and press the upper or lowercase "L" key to toggle logarithmic plotting, or use the keypress selector button at the lower left of this window.

Step 5: Calibrate

First:

Set the material used as a sample in the box labeled Calibrant

Second:

Use the Image Operations/Calibrate? menu item (note this menu is on the Image Controls window or for the Mac, the Image Controls window must be active to place this into the system menu bar). At this point the status line on the bottom of the Image Controls window changes with a prompt to select points for calibration. (view).

Third:

Use the left mouse button to click on at least five locations on the innermost ring. As each point is defined, a red "+" is added to the plot (view).

To remove a point added in error click on that point with the right mouse button [on the Mac, if you have a single-button mouse, hold the Command (⌘) key down and click].

Fourth:

When done, press the right mouse button well away from any points that have been added [on the Mac, if you have a single-button mouse, hold the Command (⌘) key down and click].

The calibration is then performed. First the rings are located and an ellipse is optimized for each ring. The indexed rings are first shown in red as the calibration proceeds and center of each ellipse is noted with a blue "+". When all rings have been fitted, the entire ensemble of rings are refitted to the detector parameters and the rings are then shown in blue. (view). The derived calibration results are shown in the Image Controls window. (view). and the console window shows details of the fit; a trial refinement for the wavelength is also given for you to consider. To see the actual points selected by the program, click on the "show ring picks?" check button (view). When this is done, it becomes clear that the points selected for the outermost ring are scattered between that and the next ring. This can be repaired by changing the "pixel search range" to 10 and then repeating the last calibration step (using the right mouse button) (view). This produces very slightly better calibration constants (view).

Assuming that these calibration results will be applied to other images in the same GSAS-II project, click on "Use as default for all images." To save the project, including the now-derived calibration information, use the File/Save? Project menu item associated with the data tree window.

Next step: Integrate the Data

Last modified 9 years ago Last modified on Sep 6, 2012 4:12:21 PM