PK D - Peak search - output to Document file

PURPOSE

Searches for local peaks in an image. Places location in a SPIDER 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 3	[Peak search - 3D]
PK DR	[Peak search - Restricted neighborhood, output to Document file]

USAGE

.OPERATION: PK D [ix],[iy], [pk],[ratio], [xs],[ys], [pkp]

[This operation can return up to seven optional register variables:

Variable	Example	Receives
First	[ix]	X integral location, relative to the image
Second	[iy]	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 specified origin
Sixth	[ys]	Y sub-pixel location relative to specified origin
Seventh	[pkp]	Peak height of parabolically fitted peak

.INPUT FILE: IMG001
[Enter name of the input 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 image's center (NX/2 + 1, NY/2 + 1) is desired, enter '1' in the second position.]

If the option "CENTER ORIGIN OVERRIDE" is specified, SPIDER asks the next two questions:

.NEW ORIGIN COORDINATES: 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.]

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

2. The sub-pixel offset of a parabolically fitted peak and height of this peak will also be printed in the results file.

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

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

SUBROUTINES

SPEAK, PARABL

CALLER

UTIL1