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marPeaks - program for finding spots on images to be used for indexing


marPeaks [ -h ] [ -e EXTENSION ] [ -f INPUT ] [ -l LOG-FILE ] [ ] [ -n NFRM ] [ -o OUTPUT ] [ -s SIGMA ] [ -t TARGET ] image_file [ ffrm lfrm suffix ]


marPeaks is a program for finding spots on images collected on marXperts Imaging Plate Detector Systems. The program integrates the spots and determines their centroids. The spot coordinates and intensities are written to output in several formats to be used by the indexing routines of programs marIndex, DENZO, XDS and MOSFLM. The program accepts images collected by the 180, 300 and 345 mm scanners, respectively, as well as by Rayonix CCD detector.

Default input is a standard image format with extension (.image) and default output is AUTOMAR format to be used by programs marIndex.

Although there is a number of options, the default settings should cover most types of diffraction ranging from small molecule crystals to virus crystals.

The program should be used by giving command line arguments only. The full range of keywords, however, is read from file PEAKS.DATA if no command line options are supplied, except when using option -f INPUT and when running marPeaks with option marPeaks.ctrl. When "marPeaks.ctrl" is given on the command line, parameters are taken from that file, so this type of input is equivalent to -f marPeaks.ctrl.

The program can be run stand-alone but usage within the graphical user interface automar is highly recommended.


Sigma cutoff for separating background from signal. The default is 10.
Number of spots to be expected in the output file. The sigma level will be automatically adjusted, so any input sigma value will be ignored. The amount of extracted spots will never be smaller than TARGET.
If no command line options are given, the program requires a keyworded input file PEAKS.DATA. If option -f INPUT is given, the program reads file INPUT instead of file PEAKS.DATA.
The default log file name is MARPEAKS.LP. This default is overwritten by the LOG-FILE name given with the -l option.
By default, spot output files carry the prefix <root>. With this option prefix OUTPUT will be used instead.
All images will have file name extension EXTENSION.
A series of NFRM images will be processed starting with image_file.
image_file [ffrm lfrm suffix]
The root name of the image files can be entered in 3 ways: either the root name and a three-digit image number, e.g. "xtal_001" or the root name and image number and extension, .e.g. "xtal_001.mar1200" or just the root name, e.g. "xtal". In the first 2 cases, the optional argument -n NFRM tells the program to process NFRM images starting with the one given by "image_file". In the latter case, two more arguments must be given: the starting ("ffrm") and ending ("lfrm") image number. The "suffix" string may contain an identifier for the image number consisting of "####" , i.e. a 4-digit number (as used by CCD images). For a more general way of specifying image names the image_file name may consist of strings with some variable amount of digits (represented by 0’s) placed withing <brackets>. The string with the digits embraced by <brackets> is then broken up into its components (prefix, image number and suffix). E.g.: "marPeaks xtal_<0000>.ccd 1 20" will process images xtal_0001.ccd to xtal_0020.ccd. If no extension is given, extension ".pck" will be used. If <name>.pck doesn’t exist, <name>.image will be tried.


TITL*e <title>
Title to be written.
Default: TITLE MARPEAKS: Spot search.

ROOT <root> [<extension>]
Filename root of images, i.e. the part before the three-digit image number leaving out the underscore but including full path name, e.g. to process a file /data/images/lyso_001.image, enter ROOT /data/images/lyso.
Default: root=none; extension="image"

EXTE*nsion <extension>
Extension <extension> overrides the defaults, which is "pck" or "image" for the 300 mm scanners and "marXXXX" for the 345mm scanners (where XXXX is the 1200, 1600, 1800, 2000, 2300, 2400, 3000 or 3450).
Default: "pck".

OUTP*ut <type>
Choice of type of spot output format. Options for <type> are: AUT*omar, MAR*peaks, XDS, DEN*zo, MOS*flm. If <type> does not fit into these options, <type> is assumed to be the extension for the output files. The default extension is "pks".
Default: AUTOMAR.

SPOT <maxspot> <type>
Gives the maximum no. of spots to be extracted from images. <type> is the typical size of spots to be expected. This depends on the type of diffraction of experiment and can be set to "huge", "large", "medium", "small" or "tiny". Depending on the choice given here, internal parameters set by keyword PEAK subkey receive the following defaults:

Default: SPOT 10000.

DIST*ance <distance>
Distance crystal-detector in mm. This information is read by default from the image header. Note that this information may get lost when transferring images between different computer architectures.
Default: get it from image header.

PIXE*lsize <pixelsize>
Pixelsize in mm.
Default: Taken from image header.

IMAG*e <ffrm> <lfrm> [OSC <dphi> START <phibeg>] [BIN n]
Process images <ffrm> to <lfrm>. By default, the PHI range of this image is looked up in the image header, but if subkeys OSC and START are given, the corresponding values will be used instead. Up to 10 IMAGE cards may be used. For BIN n, when n is > 1 the pixels in the image will be binned by the given factor. Binning can help to make spot search on diffraction patterns with very large spots. When not given, no binning is applied
Default: none.

ANGL*es TWO*theta <twotheta> CHI <chi> OMEGA <omega>
Specicifies goniometer settings for two-theta, chi and omega of images. Values are not used by marPeaks, but copied into the peak file header.
Default: TWOTHETA 0.0 CHI 0.0 OMEGA 0.0.

CENT*er <xcen> <ycen>
Center of diffraction in pixel units. Normally diameter/2. Should be used in indexing programs rather than here.
Default: IP diameter/2.

PRINT <nprint> or <@spot_file>
Prints profiles of up to <nprint> spots in image. If <@spot_file> is given, the profiles of all spots in file <spot_file> are printed. Format of this file must be MARPEAKS or AUTOMAR.
Default: PRINT 0.

WAVE*length <lambda> [ALPHA1 <lambda1> ALPHA2 <lambda2>]
Wavelength of radiation in Ang. This information is read by default from the image header. Note that this information may get lost when transferring images between different computer architectures. <lambda> can be Cu, Mo, Ag or a value. When WAVE Mo or WAVE Ag are given, ALPHA1 and ALPHA2 are assumed automatically. The program features an algorithm capable of finding spots that originate from alpha1/alpha2 splitting.
Default: Cu

TARGET <n> or "TINY", "SMALL", "MEDIUM", "LARGE", "HUGE" or "VIRUS" Number of spots to be expected in output file. The sigma threshold used for separating peaks from background will be adjusted automatically so that the expected number of spots will end up in the output file. The target number of spots can be given as a numerical value, or by the given strings, where TINY=25, SMALL=50, MEDIUM=100, LARGE=200, HUGE=500 and VIRUS=1000 spots
Default: not used

PEAK [MIN <minpix>] [MAX <maxpix>]

[XBOX <xbox>] [YBOX <ybox>]
[IMIN <imin>] [SIZE <size>]
[BKG <bkg> ] [SIGMA <sigma>]
[#S/#B <s2b>] [DXDY <dxdy>]
Parameters for peak selection. Keep the defaults where ever possible. The single most important parameter is PEAK SIGMA that determines, which pixels are selected for forming spots. All other parameters set thresholds for spots during or after integration.:

Accepted spots must consist of at least <minpix> pixels and at most <maxpix> pixels. Default: 5 and 1000.
The total size of the integration box must not exceed <xbox> and <ybox> pixels. Default: 33 for both.
The minimum intensity of a single pixel to be used in a spot must be <imin>. Default: 10.0.
The minimum ratio of signal over noise must be <sigma>*e.s.d. for a single pixel. Default: 10.0.
The minimum ratio of signal over average background in the integration box must be <bkg>*e.s.d. Default: 2.0.
The ratio of signal to background pixels in the integration box must be at least <s2b>. Default: 1.0.
The max. allowed ratio of integration box sides x/y is <dxdy>. Default: 2.0.
The average diameter of a spot is <size> pixels in each direction. The value should be smaller than the integration box size. Default: 15.

REJE*ct [SEPA*ration <dmin>] [IMIN <imin>] [<which>]
Set spot rejection criteria. Spots are rejected if they are too close together (< dmin pixels). If 2 spots are too close together, one may choose <which> one to reject: the WEAKEST, STRONGEST, BOTH, INNER or OUTER of both. If the total integrated intensity is smaller than <imin> the spot also is rejected.
Default: dmin = 5 pixels, imin = 100.0, which = WEAKEST.

RADIUS <rmin> <rmax>
Minimum and maximum radius threshold for spots in pixels.
Default: rmin = 15 pixels, rmax = edge of plate - 5 pixels.

Exclude spots within a circle of radius <r> pixels centered at center of diffraction.
CIRC*le <x> <y> <r>
Exclude spots within a circle of radius <r> pixels centered at pixels <x>,<y>.
RING <r1> <r2>
Exclude spots within a ring between radius <r1> and <r2> pixels centered at center of diffraction.
RECT*angle <x1> <y1> <x2> <y2> [<width>]
Exclude spots within a rectangle spanned between pixels <x1>,<y1> and <x2>,<y2>. If an optional width is given, the rectangle is tilted. The given coordinates then represent the middle of two opposite sides (with length <width>) of the rectangle.
POLY*gon <x1> <y1> <x2> <y2> <x3> <y3> <x4> <y4>
Exclude spots within a polygon spanned between pixels <x1>,<y1>, <x2>,<y2>, <x3>,<y3> and <x4>,<y4>.
ICE <d1> <d2> <d3> <d4> <d5>
Exclude spots within ice rings at 3.89 A, 3.67 A, 3.44 A, 2.67 A and 2.25 A.
Default: no exclusions


The program reads parameters from file PEAKS.DATA in the local directory.
marPeaks marPeaks.ctrl
The program reads parameters from file marPeaks.ctrl in the local directory.

marPeaks -f MY.DATA
The program reads parameters from file MY.DATA in the local directory.

marPeaks -e mar1200 xtal 1 20
Processes files xtal_001.mar1200 to xtal_020.mar1200.

marPeaks -s 5.0 -e mar2300 -nfrm 6 xtal_005
Processes files xtal_005.mar2300 to xtal_010.mar2300 and applies a cutoff of 5.0 * e.s.d.

Input Files

If no command line option is given (except option -f INPUT), the program requires the input file PEAKS.DATA in the local directory (./).

Output Files

By default, the program produces the following output file:
Log file.
Contains spot list in AUTOMAR format. This format can be processed by program marIndex.
Contains spot list in MARPEAKS format. This format can be processed by program marIndex and marrefix.
Contains spot list in DENZO format. This format can be processed by program DENZO and can make program xdisp obsolete.

If keywords OUTPUT MOSFLM and OUTPUT XDS are given, marPeaks writes files peaks.spt and peaks.xds, respectively.

Automar/Marpeaks Output Format

For AUTOMAR, the coordinate system is defined in such a way that the origin is in the lower left corner of the image, x runs horizontally (to the right corner) and y runs vertically up. The older marPeaks format differs from the AUTOMAR format only by the axis definition: the origin here is in the lower left corner of the image, x runs vertically (up!!!) and y runs horizontally (to the right corner).
The index.pks output file has the following format:

See Also

mar300_formats, mar345_formats, marIndex, automar


Claudio Klein, marXperts GmbH, Norderstedt, Germany


© Copyright 1997-2016 marXperts GmbH, Norderstedt, Germany


marXperts GmbHPhone: +49 - (40) - 529 884-0
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