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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
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
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.
- -s SIGMA
- Sigma cutoff for separating background from signal. The
default is 10.
- -t TARGET
- 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
- -f INPUT
- 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.
- -l LOG-FILE
- The default log file
name is MARPEAKS.LP. This default is overwritten by the LOG-FILE name given
with the -l option.
- -o OUTPUT
- By default, spot output files carry the prefix
<root>. With this option prefix OUTPUT will be used instead.
- -e EXTENSION
images will have file name extension EXTENSION.
- -n NFRM
- A series of NFRM
images will be processed starting with image_file.
- image_file [ffrm lfrm
- 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>
to be written.
Default: TITLE MARPEAKS: Spot search.
- ROOT <root> [<extension>]
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).
- 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".
- 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
|PEAK||XBOX/YOX||MIN|| MAX|| DXDY|| SIZE|
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
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>]
- 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
- ANGL*es TWO*theta <twotheta> CHI <chi> OMEGA <omega>
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>]
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.
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>.
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 BEAM*stop
- Exclude spots within a circle of radius <r> pixels centered at center of
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
POLY*gon <x1> <y1> <x2> <y2> <x3> <y3> <x4> <y4>
Exclude spots within a polygon spanned between pixels <x1>,<y1>, <x2>,<y2>, <x3>,<y3>
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
If no command
line option is given (except option -f INPUT), the program requires the
input file PEAKS.DATA in the local directory (./).
- 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.
- 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.
the program produces the following output file:
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).
- Log file.
- Contains spot list in AUTOMAR format. This format can be processed by program
- 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.
The index.pks output file has the following format:
mar300_formats, mar345_formats, marIndex, automar
- Some header lines (usually
19) with keyworded information about used distance and wavelength, etc.
- Each image starts with one header line marking the contents of the spot
line columns. This line may not be removed!
- Per spot one line.
- Each spot
line contains the following items:
- spot number
- spot flag (0=fully, 1=partial,
- x coordinate in pixel units
- y coordinate in pixel units
- PHI value
- integrated intensity
- first image on which spot occurs
- last image on which
- no. of pixels contributing to spot
- ratio intensity/average background
- The spot line format is:
- 2i5, 3f8.2, f10.1, 3i5, f10.2 (FORTRAN)
Klein, marXperts GmbH, Norderstedt, Germany
© Copyright 1997-2016
marXperts GmbH, Norderstedt, Germany
|marXperts GmbH||Phone: +49
- (40) - 529 884-0 |
|Werkstr. 3|| FAX: +49 - (40) - 529 884-20|
|D-22844 Norderstedt -
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