dtprocess on-line help

Find spots for autoindexing and refinement

The Find menu prepares a dtfind command and runs it. The peak criteria include a Sigma value, a Minimum value and a Peak filter or size value.

Select a header from the top list. Usually this is dtprocess.head.
Select one or more images from the bottom list. Either click or click-and-drag to select images. Use ctrl-click and/or ctrl-click-and-drag to make changes in your selection.
Set the menu options described below.
Select Run find
View the dtfind log file and dismiss it when finished.

Find menu options

Image sequence: The first and last image to search for spots. Multiple non-adjacent sequences may be selected, but ONLY from the bottom images list and not with the text fields in the menu.
Sigma: The minimum value for a pixel to be consider a spot in units of sigma (standard deviation) above the background average. If Sigma is 0, then no background average is calculated and spot finding is faster. The actual threshold is the maximum of Sigma and Minimum.
Minimum: The minimum value for a pixel to be considered a spot. The actual threshold is the maximum of Sigma and Minimum.
Resolution: Only reflections within the resolution limits in Angstroms are found. If either limit is 0.0, then the resolution of found reflections is not checked. WARNING: The resolution is calculated based on the detector position and wavelength which may have been specified incorrectly.
Peak filter: The minimum number of pixels in a 3x3 area that must be above the Threshold (see Sigma and Minimum) for the central pixel to be considered a spot.
Box size: The size of a box or window in pixel units that encompasses a spot completely. If the Box size is 0, 0, then an appropriate size will be automatically determined, but will take more time.
Padding: The number of images to include in a 3-dimensional box before and after a peak. Tip: If you set the threshold high, set the padding larger. This value should probably be no higher than 3. It is not used for 2-dimensional searches.
Display: If set, dtfind will send messages to dtdisplay to display the images and the found spots. Dtdisplay must have File/Respond to updates/Others set.
2D search: If set, a 2-dimensional search is done on a scan of images. The default for a contiguous set of images is a 3D search. The default a single image or non-contiguous images is a 2D search.
Show more options: If set, the advanced options below are displayed.
Background rect: Rectangle size of a region of pixels for determining the background averaged and standard deviation used by the Sigma option. The default is to divide the image into 64 regions with width and height one-eighth of the full size.
Circle limit: Center of the search circle and inner and outer radii in pixels. dtfind will search for peaks only within the specified annulus. The default is to search the entire image.
Rect limit: Search rectangle specified as start1, start2, end1, end2 in pixels. dtfind will search for peaks only within the specified rectangle. The default is to search the entire image, less a small border of 1% around the edges.
Dump interval: In 3D search mode only, specifies how often to write shoeboxes to disk files for viewing later with dtdisplay. If greater than 0, every Dump intervalth shoebox will be written to disk as a non-uniformity corrected image file with the naming convention dtfindref????.img.

Advanced options

Not written yet.