Name

Synopsis

Description

• 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.

Options

-555 (--mar555)

marView now cooperates with the mar555 data collection programs, in particular with program mar555prc, which produces Cartesian output files from the mar555 flatpanel detector. When started with option -mar555, marView reads a file $HOME/.mar555prc which is updated by program mar555prc and contains timestamps and filenames. marView automatically loads new images as soon as they become available.

-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).

-m (--minmax) N

Use N as max. value for the histogram of a newly loaded image. Usually, marView determines automatically how to distribute colors for showing an image based on the histogram of pixel values. The max. histogram value used for scaling can thus be restrained to a certain value.

-p (--pixelsize) size

The size of one pixel in mm. The default is: 0.150 mm -sc (--scale) linear|square|log|cubic|fwhm This keyword overrides the values given on keyword display_scale read from the marrc file (see marrc man page for more details).

-v (--verbose)

Increases verbosity level (up to 2) for more program output.

-x (--fastaxis) NX

-y (--slowaxis) NX marView can read raw binary arrays of NX*NY 16-bit pixel values. In order to display them correctly, you need to tell the program how many pixels are to be found in 1 horizontal line ("fastaxis") and how many in vertical line ("slowaxis").

-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.

Main Window

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).

File Menu

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.

Histogram:

Pops up the ’Color’ window with a histogram only of the image area. Shortcut: Ctrl+h. 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.

Options Menu

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.

Resize on zoom:

When selecting a zoom area with the right mouse button, the marView window will automatically be resized according to the boxed area. The default is to leave the original window‘ size;

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! From version 7.5 on a histogram is plotted from the pixels contained within the display area.

Help

Magnifications

Mouse Actions in Image Area

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!

Cross-section

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).

Colors

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.

The "Colors"-window will also open when the choice "Histogram" has been selected from the "File"-menu. Thist time, though, the pixel value histogram in the color window is based only on the pixels shown in the image area and NOT on all pixels in the image.

Open File

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.

Set

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.

Save Window

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.

Environment

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.

Input Files

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.

Output Files

See Also

marrc

Author

Copyright

Address

Table of Contents

• Name
• Synopsis
• Description
• Options
• Main Window
• File Menu
• Options Menu
• Help
• Magnifications
• Mouse Actions in Image Area
• Cross-section
• Colors
• Open File
• Set
• Save Window
• Environment
• Input Files
• Output Files
• See Also
• Author
• Copyright
• Address