PK 3R - Peak search - 3D, Restricted neighborhood, output to Document file

PURPOSE

Searches for local peaks in an volume with neighbourhood exclusion and stores the output in document file.

SEE ALSO

PK	[Peak search]
PK 3	[Peak search - 3D]
PK C	[Peak search - Center of gravity]
PK D	[Peak search - output to Document file]
PK DC	[Peak search - Center of gravity, output to Document file]

USAGE

.OPERATION: PK 3R X11,X12,X13,X14,X15,X16,X17

[The first three registers pass the integer coordinates of the highest peak, the next three registers pass the floating point coordinates calculated within a 3x3x3 box. The last register passes the absolute height of the peak.]

.INPUT FILE: REC001
[Enter the name of the volume file.]

.MAXIMA(+) OR MINIMA(-)?: +
[Enter '+' if you want the local maxima and '-' if you want the local minima. Default: + for maxima.]

.ENTER NUMBER OF PEAKS, CENTER ORIGIN OVERRIDE (1/0): 80, 0
[Enter the number of maxima or minima sought. The default origin is assumed at the volume's center (NSAM/2 + 1, NROW/2 + 1, NSLICE/2 + 1). If a different origin position is desired, enter '1' in the second position. The system will then allow you to enter the x,y,z coordinates of the origin to be used. In addition, a reference peak may be specified, and the ratio of the height of each data peak to this peak value will be calculated. Default reference peak number is 1.]

.X, Y, & Z RADII OF EXCLUSION NEIGHBORHOOD ELLIPSOID: 5.3, 4.5, 3.2
[Enter the X, Y & Z radii of the ellipsoid determining the spatial region around the highest peak where smaller peaks are excluded.]

If 'Center of Origin' override option was chosen, SPIDER asks the next question:

.X, Y, & Z ORIGIN COORDINATES: 12,15,11
[Enter the new origin coordinates.]

.ENTER PEAK NUMBER FOR RATIO: 1
[Enter the number of the peak relative to which the heights of the other peaks are calculated. This ratio is printed out and listed in the document file along with the other parameters of the peaks.]

.BOX SELECTION (Y/N): Y
[Enter 'Y' if you want to confine the search within a box smaller than the 3-D volume.]

If 'Y' is specified, SPIDER asks the next three questions:

.LOWER,UPPER SLICE: 10,50
[Enter lower and upper z coordinates of confining box]

.LOWER,UPPER ROW: 0,60
[Enter lower, upper y coordinates of confining box.]

.LOWER,UPPER SAMPLE: 12,48
[Enter lower, upper x coordinates of confining box.]

.DOCUMENT FILE: DOC001
[Enter name of output document file]

NOTES

1. This routine does NOT find "maximum" location when image has plateaus. It may find the "last" value along the plateau. To overcome this, use low pass filtration first or use 'PK M'.

SUBROUTINES

SPEAK3, PKSR3, ROUT

CALLER

UTIL1