SImPA (version 1.3) - USER GUIDE

Laboratoire de physique des solides denses

Université d'Ottawa

© Serge Desgreniers 1997

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:

  1. Image display and manipulation, e.g. pixel intensity readout, image enhancement and enlargement;
  2. Sample-to-plate distance calibration for the analysis of the X-ray diffraction image;
  3. Imaging plate orientation correction;
  4. Removal of spurious high intensity spots (e.g. Bragg spots from large single grains);
  5. Azimuthal summation for the construction of a high signal-to-background intensity profile as a function of the diffraction angle.

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:

  1. The evaluation version of 'SImPA' is free of charge and can be kept and used as long as needed.
  2. The official version of SImPA is available to registered users following the remittance of the indicated fees.
  3. Proper credits should be given to the authors of this program in any scientific publications which could result from the use of 'SImPA'.
  4. This software, in its evaluation or official version, is provided "AS IS," and you, its user, assume the entire risk as to the quality and performance when you use it.
  5. The authors of this program, the Laboratoire de physique des solides denses, and the Université d'Ottawa accept no responsibility for damages resulting from the use of this software, in its evaluation or official version, and makes no warranty or representation, either express or implied, including but not limited to, any implied warranty of merchantability or fitness for a particular purpose.
  6. You may not decompile, disassemble, reverse engineer, or modify the evaluation or official version of the software. This includes, but is not limited to modifying/changing any icons, menus, or displays associated with the software, in its evaluation or official version.
  7. This software, in its evaluation or official version, cannot be sold or be repackaged for resale without a written authorization from the authors.

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.

We define a vector S(Sx, Sy, Sz) representing the direction of the incoming X-ray beam with respect to a unit vector normal to the plane of the imaging plate. A vector S with components (0,0,0) corresponds to the situation where the incoming X-ray beam is perfectly normal to the plane of the imaging plate.

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:

  1. Manually entry of the appropriate plate parameters;
  2. Optimization by a least-squares fit to the equation of an ellipse of user-defined data points on a Debye ring (ellipse) corresponding to a known 2q;
  3. Optimization by a least-squares fit to the equation of an ellipse of automatically defined data points on a Debye ring (ellipse) corresponding to a known 2q;
  4. Optimization by the refinement of the diffraction linewidths as obtained by an azimuthal summation in a sectored image.

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.