Table of Contents
marView - image display and analysis program for images collected on
a mar research Imaging Plate Detector System
marView [ -a (--autoload)
] [ -b (--browser) name ] [ -c (--colors) N ] [ -f (--follow) file ] [ -g (--geometry)
[WxH][+X+Y] ] [ -h (--help) [ -i (--invert) ] [ -p (--pixelsize) size ] [ -v (--verbose)
] [ -z (--zoom) N ] [ filename ]
marView is a Motif-based graphical
user interface for display and analysis of images collected on mar research
Detector Systems (scanners and CCDs). The program can:
- display images using
several color schemes.
- display magnified areas of the image.
- display cross
sections.
- display and manipulate spot files.
- estimate cell constants.
The behaviour of image display can be configured in a configuration file
/etc/marrc or $HOME/.marrc. See the marrc man page for details.
- -a
(--autoload)
- The program looks once per second for file "$MARVIEWDIR/marview.com"
or "$MARLOGDIR/marview.com" or "./marview.com". If available, the file is
read. This ASCII file may contain one or two lines with a filename specifying
an image file or a spot file to be loaded. If the given files exist, they
are loaded directly by marView and the
- -b (--browser) name
- Uses program ’name’
as help browser instead of the default (netscape).
- -c (--colors) N
- Uses N colors
instead of the default (64).
- -g (--geometry) [WxH][+X+Y]
- Gives the initial
geometry of the marView window. You may specify the width (W) and height
(H) of the window as well as the coordinates X and Y of the upper left
corner. It is useful to set an alias to marView with a certain default geometry
depending on your window manager.
- -f (--follow) filename
- The program looks
for image file "filename". If available, the image is loaded. The image no.
is increased and the program tries to load the next image, etc.. If the image
cannot be found, the program waits until it becomes available.
- -h (--help)
- Prints a summary of program command line options.
- -i (--invert)
- Inverts colors
(Grey and Blue scales only, see COLORS).
- -p (--pixelsize) size
- The size of
one pixel in mm. The default is: 0.150 mm
- -v (--verbose)
- Increases verbosity
level (up to 2) for more program output.
- -z (--zoom) N
- Chooses another default
zoom mode (see below). Valid choices for N are 0, 1 and 2. The default is:
0
- filename
- The program directly loads the image "filename". See section
INPUT FILE for a description of currently supported image formats.
The main window controls the most important display functions. If
consists of the following areas:
- Menubar:
- see sections FILE MENU, OPTION
MENU and HELP
- Image display area:
- see section MOUSE ACTIONS
- Color area:
- see section COLORS.
- Image load buttons:
- Buttons to load images with image
numbers decremented by 1 (>) or incremented by 1 (>) or continuous incrementing
(>>). There is also a "Stop" button to stop continuous incrementation.
- Magnification
buttons:
- see section MAGNIFICATION.
- Image save button:
- This button saves
the part of the image currently displayed in the image display area into
a graphics file with the default file name "$IMAGENAME.xwd" where $IMAGENAME
is the name of the currently loaded image. The file format corresponds to
the "X Windows system window dump" format. It can be converted into any
desired graphics format (tiff, jpg, gif) with standard freeware utilities
(xv, convert from the ImageMagick suite) or into PostScript with program
"xpr" (SGI, DEC Unix).
- Spot buttons:
- Toggles display of spots loaded from
a spot file. When the "Edit" button is pressed, an additional set of buttons
shows up in the upper left corner of the image display area that allows
to add and remove spots from the spot file. Always press "Done" when finished
editing.
Displayed coordinates are always with the origin in the lower left
corner, x being the horizontal axis (running from left to right) and y
being the vertical axis (running upwards).
The "File" menu can
be obtained by pressing the "File"-button or by typing: "Alt+f". The following
choices are offered:
- Open File:
- Pops up the ’File selection’ window. Shortcut:
Ctrl+o. See OPEN FILE.
- Colors:
- Pops up the ’Color’ window. Shortcut: Ctrl+c.
See COLORS.
- Save:
- Pops up the ’Save’ window. Shortcut: Ctrl+v. See SAVE.
- Set:
- Pops up the ’Set’ window. Shortcut: Ctrl+s. See SET.
- Quit:
- Quits program. Shortcut:
Ctrl+q.
The "Options" menu can be obtained by pressing the
"Options"-button or by typing: "Alt+o". The following options can be set:
- Show/Hide resolution rings:
- The center of diffraction can be set in the
"Set"-window (see SET).
- Show/Hide statistics (average and max. intensity).
-
- Keep/Do not keep color scales:
- When loading a new image, the image will
be drawn in the same way as the previous image (see COLORS).
- Turn ON/OFF
3-D plot:
- When working at magnifications > 4, the displayed magnified area
will be drawn in 3-D style. Note: this option may take considerable CPU-time.
- Next image:
- Loads next image, i.e. with its image number incremented by
1.
- Previous image:
- Loads previous image, i.e. with its image number decremented
by 1.
- Zoom modes:
- Choice of N’th pixel, average or maximum pixel. This affects
the way the image looks at magnfication factors < 1.0 only. If one pixel
on the monitor corresponds to more than one pixel in the image, the program
will take only one image pixel to display and ignore the neighbours (n’th
pixel) or take the average of the neighbours or their maximum, respectively.
Note, that "N’th pixel" mode is faster than the others, since no calculation
is involved.
- Integrate:
- The contents of the displayed image area is integrated.
Only available at magnifications > 1.0!
The "Help" button can be activated
by pressing it or by typing: "Alt+h". The option "Contents" calls an instance
of the desired web browser that directly loads this man page from $MARVIEWDIR/marview.htm
or $MARMANDIR/html/marview.htm or ./marview.htm (in the order given).
To
change magnification factors, select the "Full Image", "Zoom +" or "Zoom
-" buttons on the left hand side of the main window. Available magnifications
factors are 0.25, 0.5, 0.75, 1, 2, 4, 8, 16, 32, 64 and 128, where 1 means:
1 pixel on the screen is 1 pixel in the image. If the full image fits within
the window, no further demagnification will be achieved. Magnification levels
>= 1.0 are shown in the upper left corner of the image display area.
In the image area, the 3 mouse buttons have certain
functions depending on the magnification level.
- Left mouse button:
- Draws
a line from point A to point B and displays the pixel values along that
line in a separate window (see CROSS-SECTION). This works for all magnification
levels.
- Center mouse button:
- Displays x,y-coordinates, intensity and resolution
of the selected pixel (upper left area of the window). At magnifications
<= 1.0 the contents of an box (red) around the cursor is integrated. The
minimum, maximum, average and sigma of the pixels contained in the red
box will be displayed in the upper right area. The size of the integration
box may be changed (see SET).
- Right mouse button:
- At magnification levels
< 1.0, a box is drawn from cursor position A to position B. If the mouse button
is released, the image area within that box will be displayed in the same
window with the corresponding magnification factor. Once the magnification
level is >= 1.0, the right mouse button will not further zoom in, but recenter
the displayed around around the mouse pointer position. By this method,
you can move around within the image!
marView offers choices
for drawing plain cross-sections, for circular and for radial plots (see
SET for details). The default choice is a plain cross-section. This corresponds
to "Single Crystal"-plot mode.
Plots can be obtained by pressing the left
mouse button in the image area of the display window. The cross-section
plot can be used for measuring distances and thus getting an estimate
of cell constants. In the plot area two dashed lines can be moved around
by pressing the left (left bar) and right (right bar) mouse button, respectively.
The distance between bars is given in pixels and mm. The upper horizontal
scale in the plot area is the length of line in pixel units, the lower
one the length in mm.
In "Texture" mode, the plot shows the intensities
along the circumference. The upper horizontal scale in the plot area is
the position on the circumference in degrees with the starting point of
the circumference in the 3 o’clock position (as usual). The lower scale shows
the corresponding position in mm.
In "Powder Diffraction" mode, the plot
shows the average intensities of all pixels along the circumference of
a ring at a given radius The upper horizontal scale in the plot area gives
the radial position in pixels, the lower one the radial position in mm.
In "Single Crystal" mode, to calculate cell constants, the no. of peaks
between the left and the right distance measuring bar must be entered. Place
the bars on top of two peaks. The no. of peaks must include the first and
last one.
One can save the contents of the current plot as ASCII file by
pressing the corresponding button in the "Cross-section" window. The contents
of the ASCII file are "x,y,interpolated intensity", one line per value
in FORTRAN-format 2F8.1,F10.1 (C-Format %8.1f%8.1f%10.1f). The origin is in the
lower left corner, x is horizontal, y vertical. The file name is set automatically
as "$IMAGENAME.lis" where $IMAGENAME is the name of the currently loaded
image.
One can also save the contents of the current plot as graphics file
by pressing the corresponding button in the "Cross-section" window. The graphics
file is in "X Windows system window dump" format and the output file name
always is "crossplot.xwd". ".xwd" files can be converted into any desired
graphics format (tiff, jpg, gif) with standard freeware utilities (xv,
convert from the ImageMagick suite) or into PostScript with program "xpr"
(SGI, DEC Unix).
By default, 64 colors are distributed in equidistant intensity
bins between a minimum (Min) and maximum (Max) value. All pixel values >
Max are drawn in one color and all values < Min in another color. Min usually
is 0, but Max is calculated such that 99.998 % of all pixels in the image
have intensities <= Max. The Max and Min can be entered on the left hand
side of the image display window (upper left and lower left corner, respectively)
or in the "Colors"-window which can be obtained by selecting the "Colors"
option in the "File"-menu or by typing "Ctrl+c". In the "Colors"-window, the
histogram of the pixel values in the image is displayed, i.e. the intensity
of a pixel versus its frequency. In the histogram plot, two dashed bars
mark the Min and Max values. To change Min or Max, enter values in the corresponding
fields (and press RETURN!) or move the left or right bar using the left
or right mouse button, respectively. Warning: each operation requires recalculation
of the whole image (CPU!). Note also, that by entering values in the text
fields and pressing RETURN, the aspect of the plot will be changed: the
plot will now start at a value slightly smaller than Min and end at a value
slightly larger than Max. Placing the bars with the mouse will just redraw
all colors accordingly.
To change color schemes, select "Gray scales" or
"Blue scales" or "Rainbow". By dragging the middle mouse button in the histogram
plot or in the color area of the image display window, colors can be redistributed.
This option works for 8-bit color displays, only.
This window
allows for selection of an image or spot file to be displayed. The "Search
Pattern" consists of a search path (i.e. directory) and a search string
(e.g. *.*). Press return to apply the search pattern. In the "Images" listing
a file may be selected by pressing the left mouse button. A double click
is equivalent to pressing the "Load" button.
The "Follow" button is a utility
to automaticatillay load images after increasing image numbers. If pressed
once, the "Follow" button changes its label to "Stop". Press "Stop" to leave
the automatic image loading mode.
The program automatically determines wether
a selected file is an implemented image format or an implemented spot format
and loads the files accordingly. See section INPUT FILES for a list of implemented
formats.
This window is used mainly for setting parameters affecting
the cross-section plot but also has input fields for distance, wavelength
and phi as well as choices affecting the size of the integration box in
the image display area.
- Distance, wavelength, starting and ending PHI:
- Distance, wavelength, starting and ending PHI are usually taken from image
headers. If these values are missing or just wrong, the values may be given
here. They are needed for correct calculation of the resolution rings and/or
display of spot files. When an image is loaded, the entries found in the
image header will always update the values given here, unless the "Fix"-option
is set.
- Integration box:
- The size of the integration box that shows up
when the middle mouse button is pressed defaults to 50 by 50 pixels. In
the "Integration box" input field you may alter this value.
- Line width:
- The width of lines of a cross-section usually should be 1 pixel, but you
are allowed to increase this number if not working in "Powder Diffraction"
mode.
- Center of diffraction:
- By default, the values for the center of diffraction
will be taken from image headers. In many cases, there will be dummy values
only corresponding to the actual center of the image. The values given for
the center of diffraction affect only the display of resolution rings.
For convenience, one can take the center values directly from the "[x,y]
at start" and "[x,y] at end"-fields which are updated automatically by
pressing the left mouse button.
There are 3 different types of drawing
plots:
- Single Crystal:
- Draws a straight line from the position of the
left mouse button press to the position of the left mouse button release.
If the line width is larger than 1, the interpolated values of neighbouring
pixels are summed up and averaged.
- Textures:
- Draws a circle centered at
the position of the left mouse button press with a radius corresponding
to the position of the left mouse button release. The resulting "texture"
plot shows the intensities along the circle circumference. If the line
width is larger than 1, the interpolated values of neighbouring pixels
are summed up and averaged.
This mode is called "Texture" mode since in
texture analysis one typically looks at intensity variations (modulations)
along the circumference of diffraction rings.
- Powder Diffraction:
- Draws
a circle centered at the position of the left mouse button press with a
radius corresponding to the position of the left mouse button release. The
resulting plot shows the average intensities of all pixels along the circumference
of a ring at a given radius starting at the mouse button press with a radius
of 1 pixel and ending at the mouse button release with a radius corresponding
to the distance between mouse press and release.
In this mode, only a line
width of 1 is allowed.
This mode is called "Powder Diffraction" mode since
in powder diffraction one typically looks at integrated intensities of
powder rings. Reflections show up as peaks in the "powder diffraction plot
and can easily be integrated.
For each plot type one can use the left mouse
button for selecting the starting and the ending point of the plot. However,
one can also fix the starting point of the plot as well as the ending point.
It is certainly useful in "Texture" or "Powder Diffraction" mode to set
the starting point to the center of diffraction. The values may be entered
manually in the "[x,y] at start"-fields. You must select the "Fix"-button
on the right hand side of those fields to fix the coordinates, otherwise
by pressing the left mouse button always the current x,y-coordinates are
entered automatically. In "Single Crystal"-mode one can set the ending coordinates
by fixing the "[x,y] at end" and entering the desired x,y coordinates or
by fixing the "Length & angle" and entering the desired length of the line
and the angle (where 0 degrees = 3 o’clock). In "Texture" and "Powder Diffraction"
modes only "Length & angle" can be fixed.
This window is used
for writing complete or partial images out to disk in several formats:
- PostScript:
- Whole image only (colors or grey scales).
- Tiff:
- Whole image
only. Scale factors may be applied to reduce size of output file. A factor
of 1.0 means: no loss of information.
- SGI Image:
- Whole Image or Zoom Area.
Scale factor may be applied. The output file ("rgb") can be manipulated
using programs imgview, imgworks and the tools from SGI’s imgtools suite.
Otherwise standard freeware utilities (xv, convert from the ImageMagick
suite) are available for manipulation and format conversion.
The
following logical names affect program function, but are all optional
- MARVIEWDIR
- Directory containing file marview.htm. Directory to look for file marview.com
to be used with option --autoload.
- MARMANDIR
- Directory containing file html/marview.htm.
- MARLOGDIR
- Directory to look for file marview.com to be used with option
--autoload.
If MARVIEWDIR is assigned, MARMANDIR and MARLOGDIR will be ignored.
If neither MARVIEWDIR nor MARMANDIR are assigned, marview.htm may be taken
from the current directory. If neither MARVIEWDIR nor MARLOGDIR are assigned,
marview.com will be taken from the current directory.
The program
automatically determines wether a selected file is an implemented image
format or an implemented spot format and loads the files accordingly. The
following image formats are implemented:
- mar345:
- Images in mar345 format.
Usual extensions: .marXXXX where XXXX is 1200, 1600, 1800, 2000, 2300, 2400,
3000 or 3450
- image:
- Images in mar "image" format (also mar300). Usual extensions:
.image
- pck:
- Images in mar "pck" format. Usual extensions: .pck
- cbf:
- Images
in "CBF" format. Usual extensions: .cbfXXXX where XXXX is 1200, 1600, 1800,
2000, 2300, 2400, 3000 or 3450
- cbf:
- Images in "CIF" format. Usual extensions:
.cifXXXX where XXXX is 1200, 1600, 1800, 2000, 2300, 2400, 3000 or 3450
- marCCD:
- Images in marCCD format. No standard extension
- raw:
- Images in raw
16-bit format. The name extension must be (at least) ".raw". This file format
is supposed to contain a raw array of 16-bit values (2-bytes) without header,
trailer or high intensity records. It is supposed to contain sqrt( total_bytes/2
) pixels in x-direction and the same in y-direction. The first pixel is in
the upper left corner and the fast varying axis is horizontal.
Besides
image files, the following spot file formats are implemented:
- MARPEAKS:
- Spot files produced by programs marpeaks/marPeaks to be used for indexing
with marIndex and marrefix. Usual extensions: .mar or .pks
- MARPREDICT:
- Spot
predictions produced by program marPredict. Usual extension: .prd
- XDISP:
- Spot search list produced by program XDISP (HKL suite). Usual extension:
.file
- DENZO X:
- Integrated spots produced by program DENZO (York format only).
Usual extension: .x
- MOSFLM:
- Spot prediction produced by program ipmosflm.
Usual extension: .gen
- XDS COLSPOT:
- Spot search list produced by program
XDS, step COLSPOT. Usual extension: .SPT
- XDS IDXREF:
- Indexed spot search
list produced by program XDS, step IDXREF. Usual extension: .SPT
- XDS COLPROF:
- Integrated spots produced by program XDS, step COLPROF. Mandatory name:
XREC.XDS
- XDS CORRECT:
- Integrated and scaled spots produced by program XDS,
step CORRECT. Mandatory name: XDS.HKL
From the list of spot formats, only
MARPEAKS, XDISP, and XDS COLSPOT are editable.
Some spot file formats
contain images from more than one images. For those formats only selected
spots will be displayed. In the case of MARPEAKS, only spots will be displayed
where the range for the first and last image covers the current image number
(as deduced by the image number in the image name). In the case of the
XDS formats, the starting and ending PHI of the current image as given
in the "SET" window (see SET) will be used and compared to the PHI value
in the spot file. In the case of MOSFLM, the image number in the spot file
header must match the current image number.
For all spot formats, fully
recorded spots are drawn as red crosses and partials are drawn in green.
PHI overlaps are drawn in blue (MARPREDICT only) and split spots from a
second wavelength contribution are drawn in orange (MARPREDICT only). XDS
formats don’t carry information about partiality, so in this case a spot
is assumed to be partial if the PHI value of the centroid +/- 0.5 degrees
is smaller or larger than the starting and ending PHI, respectively.
From the SAVE WINDOW one can produce output files in several formats:
PostScript, TIFF or SGI Image (see above). From the CROSS-SECTION WINDOW
and the MAIN WINDOW one can also produce "X windows system window dump"
files (see above).
mar345, marpeaks, mar345_formats, mar300_formats,
marrc
Claudio Klein, Marresearch G.m.b.H., Norderstedt, Germany
©
Copyright 2000-2004 Marresearch G.m.b.H., Norderstedt, Germany
|
| Marresearch
G.m.b.H. | Phone: +49 - (40) - 529 884-0 |
| Hans-Boeckler-Ring 17 | FAX: +49 - (40) - 529 884-20 |
| D-22851
Norderstedt - GERMANY | info@marresearch.com |
| www.marrresearch.com |
Table of Contents