Laboratoire de physique des solides denses
Université d'Ottawa
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 X-ray diffraction of a minute amount of powdered sample
at ambient conditions or at very high pressure.
SImPA (Simplified
Imaging
Plate
Analysis)
has been elaborated as a software tool to bridge the gap between
modern two-dimensional recording of X-ray diffraction and crystalline
structure refinement software packages. In other words, SImPA
provides the necessary tools to process a powder X-ray diffraction
image recorded on a phosphor imaging plate for subsequent analysis:
And, importantly, SImPA presents an easy-to-use interface
running under Windows95/NT.
System Requirements
The current version of SImPA (version 1.3) requires
the following 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 swap space)
Windows 3.1 (with Win32s), Windows 95, or Windows
NT (3.51 or above).
Copyright and Conditions of use:
SImPA is Copyright © 1995-1997 by Ken Lagarec
and Serge Desgreniers. All Rights Reserved.
In a spirit of scientific collaboration, 'SImPA' is made available at LOW COST by the Laboratoire de physique des solides denses / Université d'Ottawa. SImPA users fees will help to continue its development. The conditions of use of SImPA are as follows:
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
SImPA Distribution and Installation
A working version of SImPA is available free of charge
for evaluation. The free version is fully functional on a sample
image provided as part of the SImPA distribution. To use SImPA
with your images, you will have to register as a SImPA user and
by remitting the associated fee.
The SImPA distribution comes as a one compressed
ZIP file. Decompress in a separate directory on your hard disk.
The distribution contains the executable file, the necessary libraries,
as well as the user guide and the tutorial document. In addition,
a sample image file accompanies the distribution; it is necessary
for the tutorial and is also helpful for testing SImPA upon installation.
After installation, create a shortcut in Windows, for faster access
to SImPA.
To download the evaluation version of SImPA or for
the latest announcements, please consult the SImPA web page at
"http://www.physics.uottawa.ca/~lpsd/simpa.htm".
About the SImPA User Guide
Following an introduction to the problem of reducing
a powder X-ray diffraction image recorded on a two-dimensional
detector to a diffracted intensity versus 2q
plot and the solutions provided by SImPA, this guide documents
all SImPA commands. The SImPA User Guide is supplemented by the
'SImPA Tutorial', which leads the first-time user through the
most important steps of a typical SImPA session using a sample
image provided as part of the SImPA distribution. The 'SImPA Tutorial'
is found as a separate document in the SImPA distribution (file
"simpa_tu.doc"). Different displayable and printable
formats of this guide and the tutorial can be retrieved by an
anonymous ftp from "joule.physics.uottawa.ca" in "/pub/lpsd/simpa/manual".
The problem and its solution:
X-ray diffraction from crystalline material arises when Bragg's relation is satisfied:
where corresponds to the spacing between lattice
planes of a given family, q
is the Bragg angle (the diffraction angle) and is the wavelength
of the incoming X-ray radiation. On a plane placed at a distance
from the diffracting powdered sample and perpendicularly to the
incident X-ray beam, X-ray diffraction from a powdered sample
is recorded as perfectly circular X-ray traces of radii given
by
and with intensities corresponding to the diffraction
conditions. The diffraction configuration is depicted in Figure
1.
In order to extract any useful information from a
diffraction image, i.e., the crystalline structure parameters
of the diffracting sample, one needs to get the diffraction intensity
recorded as a function the diffraction angle 2q.
In principle it would suffice to get the radial intensity profile,
i.e., the pixel counts along a line passing through the image
centre. In order to improve on the signal-to-background ratio,
however, it is desirable to perform an azimuthal summation of
all pixel counts at a given 2q.
With the azimuthal summation, X-ray diffraction from weak X-ray
scatter ers or small amount of material is largely improved.
SImPA provides all the necessary tools to generate an integrated diffraction intensity as a function of 2q from a powder diffraction image. In order to do so, a correction of the plate orientation with respect to the incident X-ray beam and a calibration of the sample-to-plate distance are imperative prior to carrying out the actual reduction of the diffraction image. We briefly review the necessary expressions invoked to solve the problem.
Consider a point P located at coordinates (X,Y) on
a plane of the imaging plate placed at a distance from the diffracting
sample. The image centre, defined by the position of the direct
(undiffracted) beam on the plane of the imaging plate, is located
at (Xc,Yc). Moreover, the incident X-ray
beam makes an angle with the plane of the imaging plate such that
S(Sx, Sy, Sz). The experimental
configuration is shown in Figure 1. Obviously, if the incident
diffraction beam is not perpendicular to the plate of the imaging
plate, the Debye rings are recorded as ellipses. The diffraction
angle 2q
subtended at point P is then given by
Equivalently we write
The last equation is used in SImPA to translate a given position at coordinates (X,Y) into an angle 2q, according to the plate parameters (Xc,Yc), (Sx, Sy), and . For the solution of the current problem, Sz is not needed.
The first task in processing a diffraction image
in SImPA is to establish the location of the beam centre. Assuming
that an attenuated direct X-ray beam has been recorded along with
the diffraction Debye rings (ellipses), a least-squares fit to
a two-dimensional Gaussian function is performed on user-selected
pixels surrounding the beam spot on the image. This results in
reproducible and accurate coordinates (Xc,Yc)
corresponding to the location of the beam centre.
The best plate orientation parameters (Sx,
Sy) and sample-to-plate distance are achieved using
the following methods:
The latter method is based on a scheme proposed by Piltz et al. 4 The diffraction image is divided azimuthally in n sectors, bounded by and as selected by the user. Pixels in a given sector are then binned using previously estimated Sx and Sy parameters to a give an integrated intensity I. In order to refine the plate orientation correction, an optimization routine is initiated, based on the maximization of the variance of the integrated intensity
with respect to the plate orientation parameters
(Sx, Sy).
In principle, the best plate parameters are found with one of the mentioned methods. In practice, however, a combination of methods is utilized to achieve a fast convergence to acceptable parameters.
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 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.
Once the imaging plate orientation correction and the sample-to-plate distance calibration are satisfactory, SImPA performs a proper azimuthal summation, as a function of 2q, of all intensities for pixels falling between and . The final 2q profile is further corrected for the Lorentz (L) factor as to provide diffraction intensities similar to what one obtains from a diffractometer operating in the Bragg-Brentano configuration:
For diffraction images recorded using synchrotron
radiation, no intensity correction for the X-ray beam polarization
is introduced. Finally, the azimuthally integrated intensity is
normalized to take into account the number of pixels in a ring
(ellipse) encompassed by and . In any cases, one can always modified
the final integrated intensities (in a spreadsheet program for
instance) to apply other specific corrections.
An example of a 2q
profile, generated by SImPA from the powder X-ray diffraction
image presented on the cover page of this guide, is given in Figure
2.
Along with the routines necessary to reduce the image
to a 2q
profile, various commands useful in image processing are available
in SImPA. All SImPA commands are described in the following section.
Figure 2. Powder X-ray diffraction pattern of HfO2 (P21/c, Z=2) and Mo contained in a diamond anvil high pressure cell. The samples are at an hydrostatic pressure of 1.2 GPa. The image, shown on the cover page of this guide, was recorded at the D-line station of the Cornell High Energy Synchrotron Source (USA) using 25.261 keV radiation. The pattern was obtained from the corresponding diffraction image using SImPA. The crystalline structures may be refined from the resulting X-ray diffraction pattern using the Rietveld method.
Input Image
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.
It is imperative to note that SImPA assumes that
the input image does not present noticeable field distortion.
If this were not the case, the input image would have to be processed
to correct for any distortion prior to its analysis in SImPA.
SImPA does not correct for intensity variation introduced during image scanning due to the finite phosphor excitation time. SImPA does, however, take into account an uniform pixel aspect ratio different than 1, treating this as a user-input parameter.
Description of SImPA Commands
The following is a list of all SImPA commands as
they appear in the different SImPA menus. If existing, a corresponding
command icon is indicated. The reader may consult Figure 1 for
the definition of terms and symbols used in the descriptions of
the different SImPA commands. We also refer the reader to the
SImPA Tutorial document for further details regarding the usage
of most of the commands described below.
File: Open
Opens an image file. Multiple images can be opened at the expense of a slower process speed, due to possible memory shortage and consequently use of the swap disk space. SImPA recognizes two different image file formats: a custom binary format (labeled as '.img') used by FUJI or the modified TIFF format (labeled as '.gel') used by MOLECULAR DYNAMICS. 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.
File: Close
Closes an image file. Further images can then be
retrieved.
File: Print Preview
Displays the hardcopy output of the main display
window generated by the 'Print' command.
File: Print
Produces a hardcopy of the main display window, i.e.,
the full image.
File: Print Setup
Brings a dialog box for page layout and printer selection.
File: Exit
Exits SImPA. Information regarding the image analysis
should be transcribed as it will be lost upon exiting.
Edit: Copy
Copies the content of the main display window to
the Windows Clipboard.
View: Zoom in
Magnifies 4 times the area delimited by a contrasted
frame in the main display window. The area to be magnified is
selected by moving the cursor to its centre and by depressing
the RMB.
View: Zoom out
Demagnifies 4 times the area delimited by a contrasted
frame in the main display window. The area to be demagnified is
selected by moving the cursor to its centre and by depressing
the RMB.
View: Cross Section…
Generates an intensity profile, in a separate window,
along the cross-sectional line drawn on the main display. When
the cursor meets the cross-sectional line, a double vertical arrow
appears indicating the line can be displaced while the LMB is
depressed.
View: Contrast
Adjusts the image contrast. This command brings a
dialog box in which the minimum and the maximum pixel intensities
are entered, separated by a space.
View: Brightness
Adjusts the image brightness. This command brings
a sliding cursor to change the intensity equalization. For each
displacement of the sliding cursor, the image is redisplayed.
View: Draw Ellipse...
Draws an ellipse on the main display image at a specified
value of 2q
according to the ellipse parameters and the sample-to-plate distance.
This command brings a dialog box in which 2q
and the pixel aspect ratio are entered separated by a space (e.g.,
8.5 1.005).
Tools: Flip Horizontal
Flips the main display image horizontally.
Tools: Flip Vertical
Flips the main display image vertically.
Tools: Exclude Region
This tool allows the user to exclude regions on the
image from the final summation of counts along the Debye rings.
In effect, the 'Exclude region' tool brings to zero the pixel
intensities in the selected regions. For powder X-ray diffraction
images recorded from samples at high pressure, this tool is particularly
useful for removing Bragg spots arising from diamond single crystal
diffraction.
Tools: Remove Points
Removes unwanted points selected manually or automatically
on one Debye ring (ellipse) prior to a fitting for imaging plate
orientation correction.
Tools: Integrate Peak for PO...
Generates an azimuthal intensity profile for a given
Debye ring. Useful to address preferred powder orientation in
X-ray diffraction. The output file is written in an (x,y) format.
Tools: Integrate...
This command activates the azimuthal summation of
counts for pixels falling between 2q
and 2q +
Dq,
as a function of 2q.
Correction for the imaging plate orientation with respect to the
incident X-ray beam and calibration of the sample-to-plate distance
are taken into account. No angular factor is introduced for synchrotron
beam polarization. The intensities are, however, corrected for
the Lorentz factor as to have a final data set compatible with
that obtained by a conventional powder diffractometer in the Bragg-Brentano
configuration. The final result is a data set containing azimuthally
integrated and corrected intensities as a function of 2q.
In the dialog box, the output data filename, the minimum intensity
above which a pixel intensity will be included in the summation,
the start and the end angles (2q),
the angular step size (Dq),
and the output data format are indicated.
Fit: Optimize Finesse...
Activates a refinement routine for the plate orientation
parameters. Parameters Sx and Sy are varied
to optimize the linewidth of the diffraction lines.
Fit: Fit Centre
Activates an image centre finding routine. A two-dimensional Gaussian is fitted (c2 -minimization) to the data contained in a user-delimited area around the beam central spot. It is assumed that a well defined spot has been recorded on the image from the properly attenuated direct X-ray beam. The routine output indicates the location of the beam centre in pixel units as a well as relevant fitting parameters.
Fit: Select Points
This command allows the user to manually select points
along a selected Debye ring (ellipse). All points hence defined
will be used in a c2-minimization
to find the ellipse parameters and to calibrate the sample-to-plate
distance (Fit: Execute Fit...). This assumes that the 2q
value for the selected Debye ring (ellipse) is well known.
Fit: Auto Points Selection...
This command allows the user to automatically define
points along a selected Debye ring (ellipse).
Fit: Execute Fit...
Initiates a fitting routine to find the imaging plate
orientation correction parameters and the sample-to-plate distance.
Points are first selected manually (Fit: Select Points)
or automatically (Fit: Auto Points Selection...) along
one Debye ring (ellipse), corresponding to a known 2q.
Fit: Distance Fit...
Using two X-ray diffraction images, recorded from
the same sample at two different sample-to-plate distances, this
command calibrates the sample-to-plate distance. The distance
between the two images must be known with a good accuracy (better
than 2 pixel units).
Fit: Enter Parameters...
Displays a dialog box containing all the pertinent
plate parameters, if available: beam centre coordinates (Xc
and Yc, in pixels) , ellipse parameters (Sx,
Sy), sample-to-plate distance (r
in pixel unit), and r tan
2q (in pixel
unit) for the ring used to obtain the ellipse parameters. If needed,
all values can be modified before exiting the dialog box.
Window: Cascade
Aranges all displayed windows in a "cascade"
manner.
Window: Tile
Aranges all displayed windows in a "tile"
manner.
Window: Arange Icons
Aranges icons.
Window: Close All
Closes all windows.
Help: About
Provides limited information regarding SImPA.