PK DR - Peak search - Restricted neighborhood, output to Document file

(12/04/12)

PURPOSE

Searches for local peaks in an image with neighbourhood exclusion and stores the output in document file. This operation does NOT find "maximum" location when image has plateaus. It may even find the "last" value along the plateau. To overcome this use low pass filtration first or use 'PK M'.   Example.

SEE ALSO

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

USAGE

.OPERATION: PK DR [xi],[yi],[pk],[ratio], [xs],[ys],[pkp]
[This operation can return up to seven optional register variables:
Variable Example Receives
First [xi] X integral location relative to the image
Second [yi] Y integral location relative to the image
Third [pk] Peak height of maximum pixel
Fourth [ratio] Ratio of the peak height relative to highest peak
Fifth [xs] X sub-pixel location relative to origin
Sixth [ys] Y sub-pixel location relative to origin
Seventh [pkp] Fitted peak height at sub-pixel location

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

.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. In this example, SPIDER 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 are specified. The registers can be used as input to a subsequent shift ("SH") operation.

.NEIGHBOURHOOD EXCLUSION DISTANCE : 130
[Enter the neighbourhood distance for peak exclusion. Starting with the highest peak, only peaks with a distance larger than the specified neighborhood distance will be written into a document file. In this case the number of peaks returned may be less than the requested number.

.DOCUMENT FILE: DOC001
[Enter name for the output document file. The maxima positions will be placed in the document file rregisters as follows:

XO YO HEIGHT RATIO

Where each value has following contents:

XO: X integer peak location relative to origin
YO: Y integer peak location relative to origin
HEIGHT: Peak height
RATIO: Peak height relative to highest or specified peak

NOTES

  1. In the above example, the computer will find the 12 largest peaks. These positions will be printed in the RESULTS file labeled as follows:
    NO IX IY XO YO HEIGHT RATIO
    Where each value has following contents:
    NO: Peak number
    IX: X integer peak location relative to image
    IY: Y integer peak location relative to image
    XO: X integer peak location relative to origin
    YO: Y integer peak location relative to origin
    HEIGHT: Peak height
    RATIO: Peak height relative to highest or specified peak
    The sub-pixel offset of a parabolically fitted peak and height of this peak will also be printed in the results file.

  2. Maxima occuring on the boundary of the image are IGNORED.

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

SUBROUTINES

SPEAKR, PARABL

CALLER

UTIL1

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