Sastool Parameters Table
This table is a simplified reference for the Sastool parameters. The detailed explanation of each parameter can be found Parameters submenu.
| Parameter | Required? | Default | Arguments | Comments |
| -a | yes/no | no | [no|yes] [points|angle] value_pairs |
This parameter is required if -m is not set to "yes" and will be ignored otherwise. The first item takes values of yes or no. "yes" means to integrate the larger area that is defined by the rest of the parameter value, and "no" means to integrate the smaller area. The second item is either "points" or "angle". If "points", values of two points (in pixels) follow. If "angle", starting angle and angle range (in degrees) are required. |
| -c | yes | row column | X-ray beam center coordinates in pixels. | |
| -d | no | no | two value pairs | Use different detector offsets for four individual quadrants. |
| -e | no | circular | [rectangular|circular] | For MarCCD and MX images. |
| -f | yes | sample_file_name [num_sample_frames] [buffer_file_name] [num_buffer_frames] | Files to be processed. This is required.
If two sets of file names are given, the first file name is assumed to be the buffer, and the second the sample. The file name is the first image file that will be processed, and num_buffer_frames or num_sample_frames defines how many subsequent frames to be processed. |
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| -i | no | no | no | No normalization based on i1 or i2 intensities. |
| yes i1|i2 [base_value] | Use i1 or i2 intensities to normalize the data. The base_value is used to normalize multiple series of data. If no base_value is given, the i1 or i2 intensity of the first image frame will be used as the base_value. | |||
| -l | yes | file_name | Log file name. This needs to be the first in the parameters file. | |
| -m | no | no | no | Do not use a mask file for image processing. |
| yes file_name | Use the file as a mask file for image processing. If this parameter is set to yes, the -a parameter will be ignored. | |||
| -n | no | no | [start_num [end_num]] | Use the buffer and sample naming convention. This is not required, and default is no. If "yes", two numbers may follow. The first number is the starting number, and the second ending number. SasTool will process data from the start number to the end number. If no start or end num is given, it starts from 1 to 999. If only one number is given, it is assumed to be the start num. This will allow data processing of a whole directory with one -f parameter file. |
| -o | no | 10.0 | value | Detector offset. If not defined, the default value of 10.0 is used. For Pilatus images, use the paramter and set the value to 0.0. |
| -q | no | no | no | No q conversion from number of pixels. |
| yes p1 q1 p2 q2 ... | Linear mapping of number of pixels to q. | |||
| wide photon_energy camera_len | Convert number of pixels to q using q=4π/λ * sin(0.5 atan(x/D)). Photon energy in EV, and camera length in mm. | |||
| -r | no | no | no | No rejection of individual image frames from the summation of the whole series based on its standard deviation compared with the reference frame. |
| yes factor | Reject frame if its standard deviation relative to the reference frame is larger than the product of the "factor" and the average of the standard deviations of all the buffer frames. | |||
| -s | no | no | no | No subtraction of buffer intensity from individual sample frame. |
| yes | The average buffer intensity will be subtracted from individual sample frames in their .dat files. | |||
| -t | no | no | no | Do not re-use the existing buffer .tot file for sample data processing. |
| yes | Re-use the existing buffer .tot file, if it exists, for sample data processing. | |||
| -u | no | no | no | Do not process the image file as acquired by the push-thru method. |
| yes | Process the image files as acquired by the push-thru method. | |||
| -v | no | threshold_factor [image_offset] [reference_offset] |
Decide whether to exclude an image frame from integration based on transmission. The threshold transmission value is calculated using {threshold = transm_low + threshold_factor * (trans_high - transm_low)}. If the beam intensity of a frame is higher than the threshold, the frame will be excluded from the integration. Image_offset is an integer, the number of frames that will be excluded from integration even though they have acceptable transmission values but they are next to the images with high transmission. The default value is 1. Reference_offset is also an integer, and is to indicate which frame is to be used as the reference to compute deviations that are used to reject frames in data integration via the –r parameter. The default value is 1 |
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| -z | no | no | no |
No dezinger operation is perform on the images. |
| yes [factor] | Perform dezinger operation on images. If no factor is given for "yes", default factor is 3.0. | |||
| -E | no | photon_energy | Specify the photon energy of the beam when the images were acquired. The number is the photon energy in eV. This parameter is not required. However, with this parameter, the -q yes parameter is essentially the same as -q wide. | |
| -L | no | no | yes | List number of pixels at different distances from the beam center. This parameter is not required, and the default is no. If "yes", SaxsTool will generate .dat files that contain three columns: first is the distance from the beam center with the unit of a pixel length, then the number of pixels at that distance, and finally the average value of all the pixels at that distance. |