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 X11,X12,X13,X14,X15,X16,X17

[The first three optional output parameters (in this example X11,X12,X13) specify register variables that are to receive the sub-pixel coordinates and value of the largest peak found using a center of gravity calculation. The peak location is expressed relative to the location of SPIDER's center if the image. X14 contains the ratio of the first peak relative to the peak # specified for that ratio (option ORIGIN OVERRIDE). The next two registers (here X15 and X16) contain an alternative sub-pixel peak location calculated according to a 9-point parabolic fit. Register variable X17 contains the value of that peak.]

.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 (NSAM/2 + 1, NROW/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 for the next input:

.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 temporary registers if output parameters X11-X17 are specified.

NOTES

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

SUBROUTINES

SPEAKC

CALLER

UTIL1