PK C - Peak search - Center of gravity

PURPOSE

Searches for center of gravity of local peaks in image.

SEE ALSO

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

USAGE

.OPERATION: PK C [x],[y],[pk],[ratio],[xp],[yp],[pkp]

[The first three optional output parameters (in this example [x],[y],[pk]) specify registers that are to receive the sub-pixel coordinates and the value of the largest peak found in this operation. The peak location is

expressed relative to the location of SPIDER's center if the image. The 4th register (here [ratio]) contains the ratio

of the first peak relative to the peak # specified for that ratio (option: ORIGIN OVERRIDE). The 5th & 6th registers (here [xp],[yp]) return the sub-pixel coordinates according to a 9-point parabolic fit, and the last register (here [pkp] here) contains the value of that maximum.]

.INPUT FILE: PIC001
[Enter the name of the image file.]

.ENTER NUMBER OF PEAKS, CENTER ORIGIN OVERRIDE (0/1): 12, 0
[Enter the number of peaks to be searched for. If an origin position other than at the picture's center (NX/2 + 1, NY/2 + 1) is desired, enter '1' in the second position. The system will then allow you to enter the X,Y coordinates of the origin to be used.]

If the option 'CENTER ORIGIN OVERRIDE' is specified, SPIDER asks:

.NEW ORIGIN COORDINATES: 1,1
[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.]

.ELLIPSE AXES (X,Y) FOR CGR CALCULATION: 2.5, 3.5
[Enter the axes of the ellipse limiting the area around each peak, that is used for the center of gravity calculation. (Default for Y=0 is X=Y, assuming a circular area.)

.POSITIVITY ENFORCED? (Y/N): N
[If 'Y' is answered, first the minimum in the area used for the CGR calculation is determined and subtracted from all pixels in that area]

.NEIGHBORHOOD DISTANCE: 5.0
[Only peaks with a distance greater than the specified neighborhood distance will be reported.]

.EDGE EXCLUSION WIDTH X, Y: 4, 3
[Enter the minimum distance (in pixels (integer)) of peaks towards the edge of the image. The program uses the length of the ellipse half-axes for the edge exclusion if values lower than the ones for the CGR elliptical area are given]

[In the above example, the computer will find the 12 largest peaks. Their positions will be printed in the RESULTS file, and the value position of the largest peak will be printed to the user's terminal. In addition, the peak positions and values will be put into the register variables if requested.

NOTES

1. The register variables from the command line (if any) can be used as input to a subsequent 'SH' (SHIFT) operation.

SUBROUTINES

SPEAKC, PARABL

CALLER

UTIL1