SImPA (version 1.3) - TUTORIAL
About the SImPA Tutorial:
The following will guide the first-time user through the steps of a typical SImPA session.
It is assumed that a sample powder X-ray diffraction
image named 'sample.img', distributed with SImPA, is available.
It is particularly useful to view this tutorial using the Windows
95 'Wordpad', Microsoft Word, or other suitable program while
SImPA is running; in this manner the user can easily execute the
different steps by switching back and forth between the tutorial
and the application.
For a full description of what problems SImPA is addressing and of all SImPA commands, the reader should refer to the 'SImPA User Guide', a separate document to be found in the SImPA distribution as file "simpa_gu". The SImPA User Guide and Tutorial are available in different displayable and printable format by anonymous ftp at "joule.physics.uottawa.ca" in "/pub/lpsd/simpa/manual" or by directing your web browser at
"ftp://joule.physics.uottawa.ca/pub/lpsd/simpa/manual",
if ftp is supported.
The following abbreviations are used throughout the SImPA Tutorial:
RMB for 'right mouse button' and LMB for 'left mouse button'.
Copyright and Conditions of use:
'SImPA' is Copyright © 1995-1997 by Ken Lagarec
and Serge Desgreniers. All Rights Reserved.
To registered users, SImPA is provided with limited
technical support. You may direct comments, urgent questions,
or further inquiries to:
Laboratoire de physique des solides denses
Prof. Serge Desgreniers serge@physics.uottawa.ca (preferred)
Département de physique
Université d'Ottawa (613) 562-5800 (ext. 6757)
150, rue Louis PASTEUR (613) 562-5190 (FAX)
OTTAWA, ONTARIO, CANADA. http://joule.physics.uottawa.ca/~lpsd/simpa.htm
K1N 6N5
What is SImPA addressing?
The use of two-dimensional detectors to record X-ray diffraction from solids is becoming a standard practice, at synchrotron radiation facilities around the world as well as in the laboratory.
Due to a large detector area, a good X-ray sensitivity,
and a linear intensity over a large dynamic range, imaging plates
are now regarded de facto as among the best detectors to
record powder X-ray diffraction of a minute amount of sample at
ambient conditions or at very high pressure.
SImPA (Simplified
Imaging
Plate
Analysis)
has been written to bridge the gap between modern two-dimensional
recording of X-ray diffraction and crystalline structure refinement
software packages. More specifically, SImPA provides the necessary
tools to process a powder X-ray diffraction image recorded on
a phosphor imaging plate for further analysis as follows:
And, importantly, SImPA offers
an easy-to-use interface running under Windows 95/NT.
System Requirements
The current version of SImPA (version 1.3) requires
the following (minimum) hardware and operating system to function
properly and efficiently:
486 or faster Intel or alike microprocessor
256-colour SVGA video adapter (1024 x 768 resolution recommended)
16 Mb of RAM (32 Mb recommended)
1.5 Mb of hard disk space (excluding disk space for
image files and possible swap space)
Windows 3.1 (with Win32s), Windows 95, or Windows
NT (3.51 or above)
Installing SImPA
SImPA is distributed as one compressed file. The
SImPA distribution is self-installing. The distribution contains
the executable file, the necessary libraries, this tutorial document
as well as the user guide. In addition, a sample image file accompanies
the distribution ('sample.img'); it is necessary for the tutorial
and is also helpful for testing SImPA upon installation. For
convenience, the sample image should be place in the same directory
as all other SImPA files. After installation, create a shortcut
in Windows for faster access to SImPA.
Initiating a SImPA session
A SImPA session is initiated under Windows 95/NT
by clicking on the SimPA icon or the executable filename in the
File Manager or the Windows Explorer.
Figure 1. Angle-dispersive X-ray diffraction configuration.
X-ray diffraction for a powered sample (at high pressure in a
diamond anvil cell in this case) is recorded by a two-dimensional
detector like a phosphor imaging plate. Debye rings are recorded
as ellipses if the incoming X-ray beam is not perpendicular to
the plane of the imaging plate.
Importing an X-ray diffraction image file
Import the sample powder X-ray diffraction image in SImPA by clicking on icon or by selecting item 'Open' in the 'File' menu. Then select filename "sample.img". The sample image represents a powder X-ray diffraction image of stainless steel AISI T301, recorded at room conditions after a compression in a diamond anvil cell. The major phase presents the body-centered cubic structure (BCC). A second minor phase presents the hexagonal close-packed structure (HCP). The reminder of this tutorial will refer to the sample image.
Depending on your system hardware, the full image
should be imported in SImPA and displayed in less than 60 seconds.
Once the image is displayed, a cursor should follow the mouse
movement. Cartesian coordinates as well as the pixel intensity
at the cursor position appear at the bottom of the active window.
The sample powder X-ray diffraction image is shown in Figure 2.
Figure 2. A view of the SImPA graphical interface
displaying the powder X-ray diffraction image 'sample.img'.
Note that SImPA currently reads two different image
formats: a custom binary format (labeled as '.img') used by FUJI
or the modified TIFF format (labeled as '.gel') used by MOLECULAR
DYNAMICS.
Changing the displayed X-ray diffraction image intensity
The X-ray diffraction image is displayed in greyscale. Image intensity enhancements are achieved by varying the contrast and/or brightness intensity (gamma equalization). For the sample image, a contrast defined by 0 and 100, as the lower and upper intensity limits, respectively, should provide a suitable display. To set the contrast, click on icon and enter the lower and upper limits, 0 and 100, separated by a space. Then hit 'Enter'. You can do the same by first selecting item 'Contrast' in the 'View' menu. The brightness is adjusted by first clicking on icon and sliding the displayed cursor to the desired setting. Note that the default brightness setting is appropriate for the sample image.
Zooming in and out an X-ray diffraction image
area
An area of the image is zoomed by the 'Zoom' tools,
activated by their respective icons, in the icon bar, or items
in the 'View' menu. By clicking on the 'Zoom in' icon, ,
a Zoom window displays the selected area
of the image magnified four times. The magnified area, outlined
by a contrasted frame on the full image, is selected by first
pointing the cursor at its centre and then by clicking with the
right mouse button (RMB). This can be done in the full display
or the Zoom window. Further magnification or demagnification is
achieved by clicking on the 'Zoom in' or 'Zoom out' icons, respectively.
Finding the X-ray diffraction image centre
Zoom in 2-3 times around the image centre (in this case, in the central area where the X-rays were attenuated). The attenuated direct beam should clearly appear as a contrasted dot. Activate the zoom window by clicking in its area with the RMB. Initiate the centre finding routine by clicking on icon . In the Zoom window, define a more or less square frame around the beam spot by dragging diagonally the cursor while holding the LMB; release the LMB upon frame completion (Figure 3). In a short period, results of the centre finding operation should be displayed as in Figure 4.
Figure 3. Image area defined to find Figure 4. Centre point fitting results.
the diffraction image centre point.
Coordinates of the beam centre (Xc, Yc)
of the X-ray diffraction image are (rounded off): (986, 1271).
The other parameters are related to the actual two-dimensional
Gaussian fit. After hitting 'Ok', a cross locates the centre on
the Zoom area.
Correcting for the imaging plate orientation and
calibrating the sample-to-plate distance
Correction for the imaging plate orientation with
respect to the incident X-ray beam and calibration of the sample-to-plate
distance are accomplished by refining the parameters of the equation
describing a given Debye ring (ellipse in our case) recorded by
the detector. This is obtained by first defining points along
one Debye ring (ellipse) corresponding to a known Bragg angle
2q. Refer
to Figure 1 for the recording geometry.
In the following sections, we first define points manually for the purpose of finding the proper plate orientation correction and the sample-to-plate distance calibration. Further parameter refinements will then be carried out using auxiliary methods.
Defining points manually:
Select a well defined Debye ring for which 2q
is known as accurately as possible. For the current example, choose
the 7th ellipse from the centre, i.e., the second most
intense from the centre, which corresponds to the (211) line of
the BCC phase of the stainless steel sample. Click on icon or
select item 'Select Points' in the 'Fit' menu. Define a minimum
of 8 points along the ring with the help of the Zoom tool: centre
the zoom area on the appropriate portion of the selected ellipse
with the RMB and mark a point with the LMB. Keep marking points
along the same Debye ring (ellipse). For the current example,
define about 16 points along the ellipse, roughly spaced azimuthally
by 22 degrees.
Fitting points on an ellipse:
With points now defined on a selected ellipse, click
on the 'Execute Fit' icon, , or select the corresponding item
in the 'Tools' menu. Indicate the 2q
value for the selected Debye ring (ellipse), in this case 24.489°.
Initiate the fitting routine by hitting 'Ok'. After a short period,
the fitting results will appear in a dialog box as depicted in
Figure 5.
Figure 5. Plate parameters resulting from the fit.
Figure 6. Simulated ellipse (in red) .
Hit 'Ok'. This is followed by the trace on the image of the simulated ellipse at the 2q which was entered, as shown in Figure 6. It is important to note that the plate parameters you will obtain might differ from those given in Figure 5 due to a different selection of points on the ellipse. The variation of plate parameters should however be slight and most likely not significant. After calibration, the cursor Cartesian coordinates are now translated in a 2q value, as shown at the bottom of the main display and the zoom windows.
In order to verify the "goodness of the fit", inspect the elliptical trace at different azimuthal angles, for higher values of 2q. This is accomplished by clicking on the 'Ellipse' icon , followed by a 2q value. Try 2q = 28.24°. Inspect the new trace with the Zoom tools. You may notice that, with the plate parameters given in Figure 5, the simulated ellipse does not fit correctly the Debye ring. The ellipse parameters consequently need further refinement.
The fit parameters are redisplayed in a dialog box by selecting item 'Parameters' in the 'Fit' menu. In order to refine the ellipse parameters, values are modified, assuming that the sample-to-plate distance is correct, by
The latter is based on the optimization of the final
linewidths in a sectored image. Consult the SImPA User Guide for
a detailed description of the optimization routine.
To improve the ellipse parameters, we will now define
points on another Debye ring (ellipse) using the automatic point
selection routine, as follows.
Defining points automatically:
Alternatively, it is possible to mark points automatically
along a selected Debye ring (ellipse). The following indicates
how to proceed. A Debye ring (ellipse) is first selected by marking
the lower and upper bound radii which encompass the desired Debye
ring (ellipse). We will now select the 10th ellipse
from the centre at 2q
= 28.33°. Click on icon or select item 'Auto Points Selection
'
in the 'Fit' menu. By bringing back the cursor on the main display
window, a first circle is provided to mark, with the LMB, the
lower bound radius for the 10th ellipse. A second circle
then marks with the LMB the upper bound radius to encompass the
desired ellipse. Next, in the dialog box, indicate 60 as the number
of points to be automatically found and marked on the ellipse.
After a short period, 60 points will appear in colour on the selected
ellipse. If all points are satisfactory, i.e., if they fall exactly
on the ellipse (by inspection with the 'Zoom tool'), proceed by
fitting all the thus defined points, following the steps described
in the previous section, using 2q
= 28.33°. Note that it is also possible to remove points
which were defined automatically prior to executing a fit. To
do so click on icon or select item 'Remove Points' from the 'Tools'
menu. An "eraser" will appear in the main display window.
Drag it on top of a point to be discarded and hit the LMB: the
selected point is then removed from the fitting dataset. When
all undesirable points have been removed, deactivate the 'Remove
Points' routine be clicking on icon and
proceed with the fit. For the current example, removal of any
points should not be necessary.
It is also possible to use the "finesse optimization"
routine to refine the plate parameters as described in the following
section.
Refining the plate parameters by optimization
of the diffraction line "finesse"
The optimization routine is initiated by clicking on icon or selecting item 'Optimize Finesse ' in the 'Fit' menu. The optimization is done over several Debye rings (ellipses) for best results. With the main display window activated, select a range of 2q which encompasses several Debye rings. In the current sample image, a circle with a lower bond radius is set at 2q = 12.7° with the LMB and a second circle corresponding to the upper bound radius is set at 2q = 25.1° again by depressing the LMB. These actions are followed by a dialog box asking for the number of sectors into which the image will be divided for the purpose of optimization. Enter 60 and hit 'Ok'. The actual optimization can take several minutes, depending on your hardware. Upon completion, the updated plate parameters are displayed in a dialog box. After hitting 'Ok', the trace of the simulated ellipse will be displayed as before. It should be emphasized that only the plate orientation parameters are refined with the optimization routine, assuming that the sample-to-plate distance has been already defined and is adequate.
At this point, you should have a satisfactory plate
orientation correction and sample-to-plate distance calibration.
If this were not the case, you could manually enter the following
(acceptable) plate parameters: Sx = -0.002; Sy
= 0.004, r
= 1701 pixel units.
With the plate parameters now set, one last step
remains to be done before the final data reduction: removing unwanted
spots on the image.
Correcting for unwanted diffraction spots on the X-ray diffraction image
As you may have noticed, the sample X-ray diffraction image contains high intensity spots, arising for single crystal diffraction. These spots are unwanted as they will contaminate during the next step, i.e., the reduction through the azimuthal summation process. The spots can be "erased" by clicking on icon or by selecting item 'Exclude Region' in the 'Tools' menu. Once activated, the function displays an "eraser" which follows the movement of the mouse. In either the main display or the zoom window, depressing the LMB brings the pixel intensity at the cursor location to zero. Moreover, dragging the mouse while the LMB is depressed is similar to "rubbing" the eraser against the image. Individual pixels can also be excluded by punctually clicking with the LMB. The 'Exclude region' function is deactivated by clicking on icon again.
In the current image, "erase" spots located
at around (1047,566), (1705,822), and (1481,1968). Other minor
spots and streaks can also be excluded; if not removed, however,
they will contribute to a lesser extent to the final X-ray diffraction
pattern.
Summing along the Debye rings (ellipses)
Once the image centre has been defined, the image
plate orientation has been corrected, the sample-to-plate distance
has been calibrated, and all unwanted spots have been excluded,
the final step is to generate the 2q
intensity profile. In order to increase the signal-to-noise ratio,
an azimuthal summation of all the X-ray diffraction counts falling
between 2q'
and 2q'
+ Dq
will be performed as a function of 2q.
To do this click on icon or select item 'Integrate
' in
the 'Tools' menu. In the dialog box, indicate the output data
filename (sample.dat), the minimum intensity above which a pixel
intensity will be included in the summation (115), the start and
the end 2q
angles (6 and 40, respectively), the angular step size (0.02),
and the output data format (X,Y).
The azimuthal summation is initiated by hitting 'Ok'.
The summation may take up to several minutes, depending on your
hardware. The output data is written in ASCII, in a two-column
format, i.e., 2q
and intensity, separated by a comma. The output data can then
be imported in an appropriate X-ray diffraction analysis program
(like XRDA) or a Rietveld refinement package (for this it could
be more appropriate to select the "8-column" diffractometer
style output format prior to carrying out the azimuthal summation.
The final output data could require a further modification to
be readable by your Rietveld refinement package). The output data
may also be graphed using a common plotting software (e.g. Excel,
Origin, etc.); it should look as in Figure 7.
Figure 7. Powder X-ray diffraction pattern obtained from "sample.img"
using SImPA.
If the output 2q-intensity
profile is not satisfactory, for instance if the diffraction lines
are not sharp or present asymmetries, further refinements of the
sample-to-plate distance and/or imaging plate orientation corrections
could be necessary, following the steps previously outlined.
Ending a SImPA session
Quitting SImPA is simply done by selecting item 'Exit' in the 'File' menu. It should be noted that the plate parameters are not retained upon exiting SImPA. If important, the plate parameters should be transcribed separately.