dtprocess on-line help

Integrate: Integrate a scan of images to h,k,l,Intensity, SigmaI.

1. Select a header from the top list. Usually this is dtrefine.head.
2. Set the menu options described below.
3. Select Run integrate
4. View the dtintegrate log file.

Integrate menu options

Image sequence

The first and last image in a scan to to integrate. If you do not use the Images list, you can set the sequence of images to integrate by entering their numbers.

Resolution range:

Sets the resolution of reflections to predict and integrate. Remember that low resolution reflections may be blocked by the beam stop, while high resolution reflections may be limited by the detector swing or corners. If you specify equal min and max, then all reflections on the detector are predicted and integrated.

Box size

The integration box size in pixels. A local background is calculated from pixels within this box after peak pixels are excluded. It is normal and OK if neighboring reflections intrude into this box. Be sure the chosen box completely encloses the Bragg reflection. Good starting values are 3 to 4 times the spot size as listed in the dtfind.log output (View / Log file ...). Or decide on a box size by examining the spots with dtdisplay. If the Box size is 0, 0, then 4 times the sizes found in the header keyword DTFIND_SPOTSIZE are used, if the keyword is found in the header, otherwise 4 times the value 7.5 is used (that is, 30). If the Box size is less than 0, then abs(Box_size) * DTFIND_SPOTSIZE is used. For example, a Box size of -5, -5 will use 5 times the DTFIND_SPOTSIZE.

Padding

The number of images to include in a shoebox both before and after the predicted rotation width of the Bragg peak. Padding allows for a shift of the predicted peak position and for background pixels before and after the Bragg peak lies on the Ewald sphere.

Minimum peak radius

The minimum radius of a reflection in pixels. Since spot shape is automatically determined, this radius should be smaller than the actual spot, so that the algorithm can use it as a seed from which to grow the spot shape. The shape of weak reflections is determined from nearby strong reflections.

Profile size

Sizes of the transformed local Kabsch 3D profile in degrees. The first value is the angular spread of a reflection in directions tangent to the Ewald sphere, while the second is angular spread of a reflection in the direction perpendicular to the reciprocal lattice vector in the diffracting condition and passing through the origin of the sphere. Good starting values are 0.5 * arctan(spot_size / crystal_to_detector_distance) and max(crystal_mosaicity/3, 2 * image_rotation_width). These are the same as Kabsch parameters DIVRAD and DIVBET. If a value of 0 is used, then an appropriate value is calculated. If a negative value is used, then profile analysis is not performed.

Images per batch

The number of images treated as a batch. Refinement is done after every batch of images with the centroids of non-weak reflections found in the images. Reflections in the batch of images will all have the same sBatch field in the dtintegrate.ref and dtprofit.ref files.

Prerefine

This option allows one to refine parameters before integration starts with a reflnlist derived as follows: predict reflections in designated images and determine the centroids of the the predicted reflections. The designated images are chosen by the option menu:

None

No prerefine will be done.

First image

The first image of the scan is searched for reflections.

First & last images

The first and last images of the scan are searched for reflections.

First, last, & middle images

The first, last, and middle images of the scan are searched for reflections.

1st images of 3 batches

The first image, then 2 more images each nImagesPerBatch further along in the scan are searched for reflections.

Batch prefix

A prefix to use for batch ids given to reflections in the output reflection list. In the dtscalemerge program a separate scaling factor will be refined for each batch. The prefix should not be longer than 4 characters. Default prefix is no prefix.

No purge

If toggled on, then use the -nopurge option which prevents dtintegrate from deleting scratch files created during integration. Usually dtintegrate deletes these files when it finishes normally. This option is not always available.

Wait limit

Maximum number of seconds to wait for a required image before stopping. Default 0, that is do not wait.

Dump interval

Specifies when to dump or write reflection shoeboxes to disk. The non-uniformity corrected data of every nthRefln will be written to disk as an image file with name D?????.raw, if nthRefln > 0. The dumped shoeboxes can be viewed with the dtdisplay program.