Help for Parameters Tab of the SasTool GUI Version

The Parameters tab is where you set most of your parameters that SasToolDLG will use to analyse your images. You generally need to set the parameters in this tab before you can do the analyses. The Parameters tab looks like the image below (with annotations for easier reference in this help document).

The user can use previously created parameters file by check the "Use Parameters File" box (1). Once the file is imported by using the "Import" button, the fields will be populated according to values of the parameters in the file. The parameters file can be created by modifying the sample parameters file included in the software package, or by saving the values of current parameters into a file using the "Save" button (16). If (1) is checked, and a file name is given, the results from the processing will be saved in the same directory as the parameters file.

The "Log File Name" field (2) is required. The file name can be typed in or filled in by using the "Browse" button. This is the -l parameter in the parameters file. If (1) is checked, the file name can be relative to the directory of the parameters file. If (1) is not checked, the results from the processing will be saved in the same directory as the log file.

If "Convert to Q" box (3) is checked, SasTool will convert distance in pixels to q in the results, and pairs of pixel-q values are required for linear least squares regression to convert pixels into q. This is the -q parameter in the parameters file.

The "Beam Center" position (4) in pixels is required, and can be obtained by examining the images with Fit2D. This is the -c parameter in the parameters file.

The "Integration Area" is mostly for the -a parameter in the parameters file. There are three components for the parameter: "Integrate the Larger Area" (5), "Use Angle" (6), and "Use Points" (7). The component (5) is for setting the first value of the -a parameter, and if it is checked, the value is "yes", meaning the integration area will be the larger area that was defined either by angle or points, otherwise the value is "no", meaning the integration area is the smaller area. Only one of the components (6) and (7) can be selected. If (6) is selected, the integration area is defined by two numbers, "Start Angle" and angle "Range", in degrees. Angle starts from the horizontal line that passes through the beam center, and increases ccw, and the angle range should be always positive and less than 180. If (7) is selected, positions of two points, in column and row pixels, are needed. These two points and the beam center define the integration area. If box (14) is checked, however, all the selections and values in the "Integration Area" (components (5), (6), (7), (8)) will be ignored.

Choose the shape of the exposed area for the images (8). They are either a circle (for images acquired using MarCCD 165) or a rectangle (for images acquired using MX225-HE). This is the -e parameter in the parameters file.

Check "Use I1/I2" box (9) is you want to use i1 or i2 for data normalization. If checked, please specify whether to use i1 or i2, and the grand base for i1 or i2. This grand base is used for multiple series of data so that they can have the same normalization factor for better comparison. For best results, the grand base i1 or i2 should be equal to or slightly greater than the actual i1 or i2. If the base is too big, it may result in standard errors that are too big, producing incorrect results. If the grand base is not supplied, but (9) is checked, the value of the grand base will be set to equal to the i1/i2 value of the first frame of the first buffer series.

Check "Reject Frames Using Factor Value of" box (10) if you want to exclude frames that are statistically significantly different from the other frames in summation of the whole series. If checked, please give a factor. The larger the factor, the larger the tolerance you place on the statistical variation. The average standard deviation of the buffer series is used as the reference to reject frames of the sample series. If the standard deviation of the sample frame is larger than the product of buffer average standard deviation and the factor, the sample frame is excluded from the summation of the sample series. This is the -r parameter in the parameters file.

Check "Re-use Buffer .tot File" box (11) if you want to use the .tot file that was already existent for the buffer series. If the .tot file is not available, SasTool will do a full analysis of the buffer series, and create the .tot file. This parameter is meant to save processing time if the same buffer series is used for multiple sample series. However, if you are trying to re-analyse the series and have changed the other parameters, you should NOT check this box (11), because the values in the buffer .tot file may change as well, resulting in wrong final results. This is the -t parameter in the parameters file.

Check "Subtract Buffer from Individual Sample Frame" box (12, to the right of 11) if you want to get, for each sample frame, the .dat file that has the buffer counts subtracted. If there is no buffer series specified, checking this box (12) will generate an error, and analysis will not generate any results for the sample series. This is the -s parameter in the parameters file.

The "Detector Offset" (13) is the value SasTool uses to remove the offset MarCCD detector added to the intensity when the image files were written. If no value is given in the field, the default value of 10.0 will be used. This value will be ignored if the box (15) is checked. This is the -o parameter in the parameters file.

Check "Use Mask File" box (14) if you want to specify which pixels to be included in the integration of the images. The mask file can be created using Fit2D. The pixel that has the value of 1 will be included in the integration, and the pixel with the value of 0 will be discarded. This potentially allows more useful pixels of data to be integrated. If box (14) is checked, the selections and values associated with (5), (6), (7), (8) will be ignored. This is the -m parameter in the parameters file.

Check "Use Different Offset for Four Quadrants" box (15) if you want to have a better handle with the offset. The numbers in "Offset Areas" and "Integration Area" are in pixels. Care should be taken as not to include exposed areas in the "Offset Areas". If box (15) is checked, the value in (13) is ignored. This is the -d parameter in the parameters file.

Check "De-zinger Using Factor Value of" box (16) if you want to exclude abnormal pixels in the frames. If checked, please give a factor. The larger the factor, the larger the tolerance you place on the variation for pixel exclusion. If the difference between the intensity at the pixel and the average of all the pixels at the same distance is larger than the product of average and the factor, the pixel is considered to be a zinger and is excluded from the data integration. This is the -z parameter in the parameters file.

After you make changes, click the "Apply" button (17) to make the change effective in subsequent data analyses, but the user interface will stay in the "Parameters" tab.

If you want to save the parameters into a parameters file for later use (or for use by the command line version, SasTool.exe), click the "Save" button (18).

If you want to make the changes effective and go back to the "Main" tab, click the "OK" button (19). If you do not want the changes to be effective, click the "Cancel" button (20), the program will go to the "Main" tab.

To exit the program, click the "Exit" button (21).

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