Changes between Initial Version and Version 1 of DemoCalibrateTilted


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Timestamp:
Jul 28, 2011 9:01:51 AM (11 years ago)
Author:
toby
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  • DemoCalibrateTilted

    v1 v1  
     1= Calibration of an area detector in GSAS-II =
     2
     3''In this demo, data collected with a GE(?) area detector, intentionally tilted at 45 degrees, are used. Note that menu entries are listed 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").''
     4
     5=== Step 1: download the data file  ===
     6Download the sample data file from one of these links:
     7    https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/images/tilt-11ID/La_hex_%2B45deg-00015.tif?format=raw
     8    or https://subversion.xor.aps.anl.gov/pyGSAS/Examples/images/tilt-11ID/La_hex_+45deg-00015.tif
     9
     10=== Step 2: Start GSAS-II ===
     11
     12 This is done in different ways, depending on your OS and how GSAS-II is installed.
     13
     14   {{{
     15apsvisit24d:demo1 toby$ python ~/software/work/GSASII/GSASII.py
     16Available python module versions for GSASII:
     17python:      2.7.1
     18wxpython:    2.8.10.1
     19matplotlib:  1.0.1
     20numpy:       1.5.1
     21scipy:       0.9.0rc2
     22OpenGL:      3.0.1
     23Max threads  1
     24}}}
     25
     26 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.)
     27You should see two windows, both empty. One, in the upper left, is labeled GSASII Plots, the other, in the upper right, is labeled GSAS-II data tree. On Linux and Windows a menu bar appears on the latter data tree window; on a Mac the menu is in the system menu bar location (usually at the screen top).
     28
     29=== Step 3: read in the data file ===
     30
     31 Use the Data/Read image data menu item to read the data file into the current GSAS-II project.
     32 ([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoIntegrateTilted/d1m1.png view]).
     33 Select the La_hex_+45deg-00015.tif data file and press Open.
     34
     35 At this point the data tree window will have several entries
     36 ([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoIntegrateTilted/d1w1.png view]); the plot window
     37 shows a faint image
     38 ([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoIntegrateTilted/d1w2.png view]) and a new window
     39 is opened to edit the image controls
     40 ([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoIntegrateTilted/d1w3.png view]). 
     41
     42=== Step 4: Edit image parameters ===
     43
     44 Note that, alas, very few image formats allow for storage of important metadata about the image, so this information 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). You may also wish to select another color scheme using the color bar selector.
     45
     46 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.
     47
     48=== Step 5: Calibrate ===
     49
     50 First:
     51   Set the material used as a sample in the box labeled Calibrant
     52
     53 Second:
     54   Use the Image Operations/Calibrate menu item (note this menu is on the Image Controls window or for the Mac, the Image
     55   Controls window must be active to place this into the system menu bar). At this point the status line on the bottom of the
     56   Image Controls window changes with a prompt to select points for calibration.
     57   ([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoIntegrateTilted/d1w4.png view]).
     58
     59 Third:
     60  Use the left mouse button to click on at least four locations on the innermost ring. As each point is defined a red "+" is added to the plot
     61  ([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoIntegrateTilted/d1w5.jpg view]). 
     62
     63  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].
     64
     65 Fourth:
     66  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 Control key down and click].
     67
     68 The calibration is then performed. First the rings are located and an ellipse is optimized for each ring. The indexed rings are shown in blue and center of each ellipse is noted with a blue "+"
     69 ([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoIntegrateTilted/d1w6.jpg view]).
     70 The derived calibration results are shown in the Image Controls window.
     71 ([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoIntegrateTilted/d1w7.jpg view]).
     72
     73 To see the actual points selected by the program, click on the "show ring picks?" check button
     74 ([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoIntegrateTilted/d1w8.jpg view]).
     75 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 using the Image Operations/Clear Calibration menu item, lowering the area the program uses for searching for points by changing the "pixel search range" to 10 and then repeating the calibration steps (selecting points again on the first ring and then using the right mouse button)
     76 ([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoIntegrateTilted/d1w10.jpg view]).
     77 This produces very slightly better calibration constants
     78 ([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoIntegrateTilted/d1w9.jpg view]).
     79
     80 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.
     81
     82== Next step: [DemoIntegrateTilted Integrate the Data] ==