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

(9/4/09)

PURPOSE

Searches for local peaks in an volume with neighbourhood exclusion and stores the output in document file. Does NOT find "maximum" location when image has plateaus. It may even find the "last" value along the plateau! To overcome this, low pass filter the volume first.   Example.

SEE ALSO

PK 3D [Peak search - 3D, output to Document file]
PK [Peak search]

USAGE

.OPERATION: PK 3R [x],[y],[z],[xp],[yp],[zp],[pk]
[Find peak info. This operation can return up to 7 optional register variables which contain info on the highest peak:
Variable Example Receives
First [x] Peak X location (integer)
Second [y] Peak Y location (integer)
Third [x] Peak Z location (integer)
Fourth [xf] Peak X subpixel location
Fifth [yf] Peak Y subpixel location
Sixth [xf] Peak Z subpixel location
Seventh [pk] Peak height
[The subpixel coordinates are calculated within a 3x3x3 box.]

.INPUT FILE: VOL001
[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 is: '+'.]

.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 (NX/2 + 1, NY/2 + 1, NZ/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 EXCLUDED NEIGHBORHOOD: 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 two questions:

.X, Y, & Z ORIGIN COORDINATES: 1, 1, 1
[Enter the new origin coordinates.]

.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. Enter '*' if no document file is wanted.]

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.

SUBROUTINES

SPEAK3, PKSR3

CALLER

UTIL3

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