View

Multipurpose program to analyse CCD images. view can be used for the display of images, peak search, creating boxfiles, examining profiles and various image transformations.

Legenda.
Explanation of colours and argument types.
Menu.
Explanation of menu mode.
Calibration directory.

Start program
Reading data
Display
Peak Search
Reflections
Box
Circle
Profile
Zoom
Window
Command list by context
List of commands
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Version history

You may also visit the explanation of internal commands: aliases, flowcontrol etc.

Starting the program

Once view is started, it checks whether the file view.init exists in the directory where view is installed. If this file exists, it will be executed.
Next, view checks whether the file view.init exists in the current directory. If this file exists, it will be executed.

Reading data

To read an image, use read.
If a dark image is read in before (by dark or trydark), this dark image will be subtracted from each new image until nodark is specified.
You can add(subtract) images to(from) the current image with readadd and readsub.
Use next if you want to read the next image and prev if you want to read the previous image. The similar commands nextadd, nextsub, prevadd and prevsub are available.
Use nextscan and prevscan to switch to other scans. nextscanadd, nextscansub, prevscanadd and prevscansub are also available.
Use frame to change the framenumber (relative or absolute).
There are some wait commands which enable you the read images while they are being measured. wait n will wait until the n'th next image is available, and then reads the next image. readwait file waits until file is available. If you want to wait for the next image, use the command nextwait. If you want to wait for the next scan, use the command nextscanwait. darkwait file waits until file exists, and reads the file with dark.
Dezingering or selection of (multiframed) images is controlled by zinger. Handling of adczero information is controlled by adczero.
You can also read cnt files with contour and contournext. The contour values are multiplied by contourfactor. You may add new contours to the current buffer with contouradd and contournextadd.
Use output read to control the amount of output.

Display

Type plot to display an image. First a sorted array will be build, and then the picture will be created. You may build the sorted array yourself with prepare.

You may select various colour schemes. They are set with mode. Available schemes are equal, jaap, linear, log, sharp and square. All schemes use the value of minimum and maximum. These values are set by prepare, but you may change them. The default minimum and maximum set by prepare is controlled by the value of globalmin and globalmax. The number of colours is set by maxcolour. With the command grey you select colours from white(low) to black(high). With -grey the greycolours are inverted. Pixels with a value less than minimum get the colour set by bgcolour. Pixels with a value higher than maximum get the colour set by fgcolour. If you want to use real colours (instead of grey colours) use colour, (the corresponding background and foreground colours are now called bg2colour and fg2colour) or set your own colours with setcolour.

The commands ajmd, ajmd2 and ajmd3 can be used to change the appearance of the pictures. Note that the data of the image (within view, not the image file) will be changed by these commands. You can also use shade.

postscript/gif/jpg files of windows can be created with ps/gif/jpeg.

If the dimensions of the image file are too big the appearence depends on the value of plotbin. If plotbin is set to zero (the default) the image will be binned (in graphics only, the internal data are maintained). If plotbin is set to a nonzero value the value of plotbin will be used for binning, and the window dimensions will be changed. If the resulting image is still too big, only a part of the image is displayed. You may select which part with part and ll.

Use output plot to control the amount of output.

Peak Search

The maximum number of peaks to be found in one image is set by peaknr. Peaks will not be found in the following regions

theta<thmin
theta>thmax
reso>resomin
reso<resomax
duration>durationmax
behind the beamstop. (see the Beamstop Page)

Peaks are searched from the highest value (or the value set by peakmax) in the image down to a minimum set with peakmin. If a local maximum is found, the center of gravity will be determined in a box with dimensions set by peaksizemm with the minimum value subtracted from each pixel. See the view peak search description whether a peak is considered observed or weak.
Once a peak is found, a box with dimensions set by peakareamm will be used to clear the area around the peak. When there are peakbreak successive weak reflections encountered the peak search stops.

Peaks in one image can be found with peak2.

Use peak3 to search for peaks in multiple images. Now the accepted peaks are stored in an array. The pixel values in the next image will be compared with the stored peak information. If the stored value is larger, the stored value will be used. If the current image value is larger, it will be stored. peakstart clears the array of peaks. In the next peakremove degrees, no peak will be found at the found positions.

If peakrmat is set, a test will be made to check whether a peak fits the lattice. The fit is controlled by round, fitmm and fitrot. If peakfit=on, the new peak has to fit in the lattice. If peakfit=off, the new peak may not fit in the lattice (Using this option, you may search for non-lattice peaks, i.e. in twins). You may want to change the colours of the reflections in the lattice with datcolcolour same.

Use peakfile to set the name of a pk file, use peakopen to create the pk file and peakclose to close it.

The peak search related colours can be set by peakcolour.
peakmark can be used to plot the peak array, peakmarkfile plots all peaks from a .pk file, peakmarkthisfile plots all peaks from a .pk file found in the current image. peakmarkfilesearch reads the appropriate image and plots the n'th peak from a pkfile.
peakchi plots chi-arcs (assuming the current image represents a phi/chi scan) around the peaks in the array and peakchifile plots chi-arcs around the peaks from a pk file. The width of the chi-arcs (in pixels) is set by peakchiwidth.

Labels will be drawn if peaklabel is nonzero.

A DirAxfile can be written. Set the filename with diraxfile, create the file with diraxopen, write c-vectors with various peak2 or peak3 commands, and close the file with diraxclose.

The values of peak variables can be shown with the show peak. Use output peak to control the amount of output. peakstatus will give the number of reflections in the pk and dirax files.
How to use all of this in a phi/chi experiment is explained elsewhere.

Reflections

First of all, an rmatrix (rmat) is needed. Use datcol to display all reflections in the current image. With hkl, you can search for the impact position of a specific reflection. hklplot does the same, but will load the appropriate image if it is available. m2h gives the reflection indices from the mm coordinates of a point on the detector. In menu mode, you can toggle the hkl button, and for subsequent clicks in the image window, the reflection indices will be given.

Datcol generates a list of reflections. The reflection generation process is controlled by various constants.

beamstop
See the Beamstop Page.
resolutionm limits
The resolution limits are set with the commands resomin, resomax, thmin and thmax.
resolution limits set by forbidtheta or forbidreso. Usefull for eliminating reflections close to ice rings.
duration
The maximum duration of a reflection is set with durationmax.
capillary absorption
Capillary absorbed reflections can be excluded with capillaryangle. The capillary axis can be set with capillaryaxis.
mosaicity
If mosaic has been set to a non-negative value, reflections are drawn as circles (with size shapesizea in colour shapecolour) if they are predicted within duration*mosaic degrees of the current frame.
And, if shapeform=circle, and shapeclean=on, the pixels of the (predicted) reflections in the image will be replaced by their average background.

Reflections with an impact on the current image are drawn in white. The minimum value of boxdepth and datcolboxes determines how many reflections of previous and next frames will be plotted. The colours used are blue (<-1 image), cyan (previous image), white (current image), yellow(next image) and goldenrod(>1 image). You may change these colours with datcolcolour.

You may specify more (i.e. rmat2) matrices. In this case the colours are set with matcolour. All commands with an optional matrixnumber are listed under context rmat.

The amount of normal output can be controlled by output datcol.
If reflection boxes are written (boxopen), the reflections impacting the current image will be stored in the box-reflection-list, and the boxdata will be written for each of these reflections. You may open boxfiles for each rmatrix.

Box

Reflection boxes are written with the datcol command. The box dimensions are set with boxsize (horizontal and vertical, pixels) or boxsizemm (horizontal and vertical, mm) and boxdepth (number of frames; or datcolinc).
Create a boxfile with boxopen. Close the file with boxclose. The command boxnext closes the current boxfile, increments the boxnumber and creates a new one. If the actual number of reflections in a boxfile exceeds the value of boxrefl view will execute boxnext automatically.

While building boxfiles, the values of dist, inc, swing and exposuretime are monitored for changes in succeeding images. view will issue a warning if such a change occurs (if abort=on view will terminate with a fatal condition, unless boxcheck=off). If the header contents cannot be trusted, you may have to overrule exposuretime to a fixed value, or increase the value of tolerance exposuretime.

If multiple matrices are available, you can build reflection boxes for the different lattices in one run. Use boxopen2 to create the file. At the end use boxclose2 or close all boxfiles with boxcloseAll.

Use output box to control the amount of output.

Circle

Define circle radii with circledef (2-theta) or circledefr (resolution). You also can use the circleclick command to click a few points on one circle. The radius will be set the the average value of these points. Clear the list with circleclear. Draw the circles with circle. Circles are drawn with an interval of circledelta degrees. You may set the colour with circlecolour.

The other circle related commands are used to determine the detector position with a powder image. You have to define the circles (using circledef. circledefr or circleclick). You may set the relative intensitities with circleint. These intensities will be used as weights in the refinement. The refined values are the sum of the circlesum values for each circle. Set the estimated errors of the detector position with circlefitfactor. Set the refinement exit value with circlefittol. Start refinement with circlefit.
You may inspect the whole circlesum field with circlesearch.
Finally, all circle commands can be abbreviated by substituting c for circle.

Profile

horizontal/vertical profiles.
Profiles can be drawn with profile, profilemm or by using the profile button in menu (with profilegeneralpick=off). If the difference between the horizontal coordinates is greater than the difference in the vertical coordinates, a horizontal profile (at the mean value of the vertical coordinates) is shown (and vice versa for vertical profiles). All pixels within profilewidth (in pixels) from the central profile line are added to the profile.
general profiles.
General profiles can be drawn with generalprofile or by using the profile button in menu (with profilegeneralpick=on). Use profilegeneralwidth to set the width in millimeter. You can rotate to start and end points of the general profile with profilegeneralrot
radial profiles and tangential profiles
The commands profilerad and profiletang create radial and circular profiles. You have to enter four numbers (radialmin, radialmax, tangmin and tangmax). In menu mode you click two points. The radial range is then determined by the minimum and maximum radial value of those two points while the angular part is drawn from the first point to the second point rotating anti clockwise. The zero angular value is at the top of the detector (and coincides with the beam stop shadow).

You may set the colour of the central line with profilecolour profile and the colour of the profilewidth lines with profilecolour width. The profile window will be used to display the result. You may set the colours of the text and axes in this window with profilecolour label. An optional title in the upperleft corner can de set using profiletitle.
profilehor will first ad up all the pixels by column, profilever first adds all pixels by row and profilehalf draws a profile horizontal profile at the center of the detector.

Intensities are corrected for the effective area of a pixel if the value of areafixed is set. If profilenorm is set, the values in the profile are divided by the number of contributing pixels. If not set, the brute sum is shown in the profile. Use profiletangchi to eliminate pixels in a bad chi region

Profiles are scaled between the actual minimum and maximum values. You may select profiletype fixed to limit the scaling between the values set by profilemax and profilemin. Or use profiletype global to limit the scaling between the values set by maximum and minimum. Use profiletype free to return to the free scale setting. With profilemode you can switch between linear and logarithmic scales.

It is possible to calculate an intensity over the profile. More information is available at the netint section.

A profile can be drawn as a profile or as histogram by setting profileconnect to on or off.

Profile information can be written to files. You can create a cnt contour file. Start the saving of the profiles with profile2d. All subsequent profiles are stored, and finally flushed to the file profile.cnt with profileno2d. Radial profiles (intensity versus 2theta) created by profiletang can be written to an x_y file with profilexy file and profilenoxy.

Use output profile to control the amount of output.

Finally, all profile commands can be abbreviated by substituting p for profile.

Zoom

zoom
Specify Lower Left and Upper Right pixel pairs. The size of the zoomwindow is determined from these corners and the value of zoomfactor.
zoomaround
Specify the Central Pixel. The zoomwindowsize can be set with zoomaroundsize. The zoomed part of the image is calculated using zoomaroundsize and zoomfactor.
Use zoomfollow to zoom the same part of every new image. Use zoomfollowhkl to create zoomwindows for every m2h and hkl command.
zoombeamstop
Zooms around the beamstop. The zoomwindowsize can be set with zoomaroundsize. The zoomed part of the image is calculated using zoomaroundsize and zoomfactor.

The colourscheme of the zoom window can be set with zoomscale. Smoothing of the zoomwindow can be set with zoomtype.

Finally, all zoom commands can be abbreviated by substituting z for zoom.

Window

The following windows are available:

Name	description	Activated by
1	the main image window	activate 1
2	the second image window	activate 2
menu	menu window	menu, go
distor	undistorted image window	distor
profile	profile window	profile, profilemm, profilegeneral, profiletangrad etc.
zoom	zoom window	zoom, zoomaround, zoombeamstop

Use activate windowname (or left mouse click in the window in menu mode) to activate a window. The plot command will plot the current image in the last activated window. Windows can be removed with close, iconized with icon and made unvisible with unmap. Use map or raise to restore an iconized or unmapped window.
The window dimensions and position can be changed with the window command and windowinfo will print all window related information.

Finally, to disable all window output use graphics off.

Commandlist by context

Context	Commands
Badmask	badmask badmaskarea badmaskcircle badmaskcolumn badmaskcorner badmaskid badmaskinit badmaskpixel badmaskrow badmaskwithreso badpixelforce
Box	badresponsthreshold boxcheck boxclose boxdepth boxnext boxopen boxrefl boxsize boxsizemm datcol datcolinc datcolwalk focuschange focusstart gainfactor polarquotient tolerance
Circle	circle circleclear circleclick circlecolour circledef circledefr circledelta circlefit circlefitfactor circlefittol circleint circleprofile circlesearch circlesum circlewidth circlewidthcolour save circle show circle
Colour	beamstopcolour bgcolour bg2colour centrecolour circlecolour circlewidthcolour colour datcolcolour durationclour fgcolour fg2colour forbidthetacolour fibrecolour gridcolour hklcolour markcolour matcolour maxcolour menucolour peakcolour pickcolour primarybeamcolour profilecolour setcolour shapecolour show colour zoomcolour
Constants	capillaryangle capilaryaxis circledelta contourfactor cornersize durationmax globalmax globalmin gridsize gridsizex gridsizey jaap marksize maxcolour mergefactor noglobalmax resomax resomin sharp smoothfactor thmax thmin
Contour	contour contouradd contourfactor contourframe contournext contournextadd
Conversion	angle2m angle2p anglem anglep cone fm2p fp2m m2p m2x m2mid mid2m p2m x2m x2p
Detector	beamstop beamstop2 beamstopangle beamstopangle2 beamstopclick beamstopid beamstopcolour beamstopdiameter beamstopdiameter2 beamstopdistance, beamstopdistance2, beamstoprot beamstoprot2 beamstopset beamstopshift beamstopshift2 beamstopwidth beamstopwidth2 detectoroffset detectorshift gaintest goniostatchange goniostatprint goniostattype nodetectorshift permutate setprimary
Display	autorefresh capilaryplot datcolboxes datcollabel datcollabelboxes datcolshrinkboxes drawbeamstop drawlinemm grid ll markbeamstop markprimary markcentre markm markp markprimary maximum minimum mode part plot plotbin refresh
Fibre	cell fibre fibreall fibrecolour fibrecrit fibrehkl fibremaxindex fibreorient fibrerot
Files	diraxclose diraxfile diraxopen displayhc drxpk gif jpeg netintappend netintclose netintfile netintopen peakchifile peakclose peakfile peakmarkfile peakmarkfilesearch peakmarkthisfile peakopen profile2d profileno2d profilenosc profilenoxy profilexy ps psframe redirect save scatterfile shapeend write
Header	contigframes dictheader dist header lambda nooverrule overrule swing
HKL	datcol datcolboxes datcolwalk denzox forbidlist forbidnone forbidreso forbidtheta fp2h hkl hklmatrix hklplot laue m2h mosaic normat p2h peakrmat pg qvp qvpoff qvpon qvprint rmat scanlength shapeclean xtal zoomfollowhkl
Info	corner display displayhistogram echo ek examine histo imagesigma ke m2c mean meanaround merge monitor resocorner resohalf qvp qvprint search show showcell thcorner thhalf
Intensity	bpbfixed bpbfraction netint shape shapeend shapeform shapeinit shapemargin shapemaximum shapemm shapesize shapesizea shapesizeb weak
Menu	go menu menucolour
Miscellaneous	abort correct dict dictheader dictname end evpylog exit goniostatoutputlevel help output quit reset
Peak	diraxclose diraxfile diraxopen drxpk fitmm fitrot forbidlist forbidnone forbidreso forbidtheta peak2 peak3 peakareamm peakbg peakbg2 peakbg3 peakbreak peakchi peakchifile peakchiwidth peakclose peakfile peakfit peaklabel peakmark peakmarkfile peakmarkfilesearch peakmarkthisfile peakmax peakmin peaknr peakopen peakremove peakrmat peaksizemm peaksmallsize peakstart peakstatus round save
Processing	ajmd ajmd2 ajmd3 badmask distor distorsquare lowerresolution plane radial respons smooth smooth2 timfilt
Profile	areafixed profile profile2d profilecolour profileconnect profilefactor profilefit profilegeneral profilegeneralpick profilegeneralwidth profilehalf profilehor profilemax profilemin profilemm profilemode profilenoh2d profilenorm profilenosc profilenoxy profilerad profileradr profilesc profiletang profiletangchi profiletangfull profiletangr profiletangrad profiletangradr profiletitle profiletype profilexy profilewidth save
Read	addconstant adczero addfactor badpixel baseline checknext dark darkwait frame imagefiletype next nextadd nextaddwait nextscan nextscanadd nextscansub nextscanwait nextsub nextwait nodark norespons prev prevadd prevscan prevscanadd prevscansub prevsub read readadd readsub readwait responsread scaledark subfactor trydark wait
Rmat	boxclose boxopen laue matcolour normat peakrmat pg rmat showcell
Still	flex still stilltheta stilltype
Test	area boxdb cosines dirty durationplot gravity limits lorplot polarplot polarquotient prepare trans
Window	activate close flush graphics graphicsmod icon imageon imageoff map raise title unmap window windowinfo
Zoom	save zoom zoomaround zoomaroundfrac zoomaroundmm zoomaroundsize zoombeamstop zoomecho zoomfactor zoomfollow zoomfollowhkl zoomscale zoomtype

Alphabetical List of commands

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

abort

Syntax: abort state
Default: abort off
Context: miscellaneous
If state=off, warnings are not fatal. If state=on, a warning will abort the program. Examples of warnings are: datcol with no cell defined, errors while creating files, reading nonexisting files and unknown commands. abort on is useful in scripts.
Related commands: checknext, boxcheck

activate

Syntax: activate 1/2/zoom/profile/distor/menu
Context: window
Activate a specific window. n is the window number (1-2). Drawing is done in the selected window.
Also available in menu by selecting the window with the left mouse button.

addconstant

Syntax: addconstant n
Default: addconstant 0
Context: read
Add the value of n to every pixel while reading an image.
Note, the value of n will effectively be subtracted with the subtract variants of read (readsub, prevsub, prevscansubsub, nextsub and nextscansub).
Warning: modifying pixel values may interfere with badresponsthreshold

adczero

Syntax: adczero state
Context: read
Default: adczero on
Some kappa ccd images contain information on the adczero of the image readout (images with 625 and 1344 horizontal pixels: the last two columns, images with 672 horizontal pixels: the last column)
If state=on (the default for kcd files), the relevant columns of an image are used to determine the adczero of the image readout which will be subtracted from all pixel values.

addfactor

Syntax: addfactor f
Default: addfactor 1.0
Context: read
When adding images (readadd, prevadd, nextadd, prevscanadd and nextscanadd) the pixel values of the new image will be multiplied by f.
Related command: subfactor.

ajmd

Syntax: ajmd
Context: processing
The current image will be changed. V_x,y = V_x+1,y + V_x,y+1 - 2*V_x,y
You may have to set the minimum to init. shade uses ajmd to create a nice picture.

ajmd2

Syntax: ajmd2
Context: processing
The current image will be changed. V_x,y = √ [ ( V_x,y-1-V_x,y+1 )² + ( V_x-1,y-V_x+1,y )²]
You may have to set the minimum to init.

ajmd3

Syntax: ajmd3
Context: processing
The current image will be changed. V_x,y = V_x,y-1-V_x,y+1 + V_x-1,y-V_x+1,y
You may have to set the minimum to init.

ajmd4

Syntax: ajmd4
Context: processing
The current image will be changed. V_x,y = V_x,y+1 V_x,y
You may have to set the minimum to init.

ajmd5

Syntax: ajmd5
Context: processing
The current image will be changed. V_x,y = V_x+1,y V_x,y
You may have to set the minimum to init.

angle2m

Syntax: angle2m x1 y1 x2 y2
Context: conversion
Output angle (x1 y1) - crystal - (x2 y2).

angle2p

Syntax: angle2p px1 py1 px2 py2
Context: conversion
Output angle (px1 py1) - crystal - (px2 py2).

anglem

Syntax: anglem x y
Context: conversion
Stores: hormm vermm
Output angle PrimaryBeam - crystal - (x y). (i.e. 2theta).

anglep

Syntax: anglep px py
Context: conversion
Stores: horpx verpx hormm vermm
Output angle PrimaryBeam - crystal - (px py). (i.e. 2theta).

area

Syntax: area px py
Context: test
Stores: horpx verpx
Displays the effective area of a pixel. See areafixed. The area of a pixel is used in profiletang, profilerad and profiletangrad.

areafixed

Syntax: areafixed state
Default: areafixed on
Context: profile
If state=on, the area of all pixels is set to 1.0. Otherwise, the effective area of a pixel is calculated from the viewpoint of the crystal. The area of a pixel is used in profiletang, profilerad and profiletangrad.

autorefresh

Syntax: autorefresh state
Default: autorefresh on
Context: display
If state=on, the refresh command is executed when:

a peaksearch is done (peak2 peak3 peak4)
This will clear the window from all boxes drawn by previous peak search commands
the beamstop is modified (beamstop beamstopangle beamstopdiameter beamstopdistance, beamstoprot beamstopset beamstopshift beamstopwidth)
This will clear the window from previous beamstops.
reflections are predicted (datcol)
This will clear the window from all boxes drawn by previous datcol commands

badmask

Syntax: badmask
Context: badmask
Apply the bad mask array to the current image.

If badresponsthreshold is active (for ADSC and MARCCD detectors by default, or by an explicit invocation) the pixels below this threshold will be changed into badresponsvalue. You may even change some pixels to a value belowe the threshold first by invoking patch.
You do not have to apply this command when creating boxfiles, as the badmask information is always added to the boxfile.
The currect imagedata will be changed by badmask. It is not possible to undo these changes; you will have to read the image again.

Related command: patch.
More information on the Badmask Page.

badmaskarea

Syntax: badmaskarea px1 py1 px2 py2
Context: badmask
After an initialisation of the bad mask array (badmaskinit) you may use this command to disable a block of pixels. px1 and py1 specify the lower left and px2 and py2 the upper right.
More information on the Badmask Page.

badmaskcircle

Syntax: badmaskcircle px py r
Context: badmask
After an initialisation of the bad mask array (badmaskinit) you may use this command to disable a filled circle of pixels. px and py specify the center of the circle and r the radius (all in pixels).
More information on the Badmask Page.

badmaskcolumn

Syntax: badmaskcolumn px py1 py2
Context: badmask
After an initialisation of the bad mask array (badmaskinit) you may use this command to disable a column of pixels. px is the column number, and all pixels between py1 and py2 will be disabled.
More information on the Badmask Page.

badmaskcorner

Syntax: badmaskcorner n
Context: badmask
After an initialisation of the bad mask array (badmaskinit) you may use this command to disable pixels in the corners of the detector. n is the size of the triangles (horizontal and vertical)
More information on the Badmask Page.

badmaskid

Syntax: badmaskid s
Default: badmaskid unknown
Context: badmask detector
Sets the badmask id to s. The badmask id is compared with the detector id for each new image. If the two id's are different, view tries to load the file badmask.vic from the calibration directory.
If s=*, the badmaskid will be set when reading the next image (and thus view will avoid searching badmask.vic at every read).
The badmask.vic file can be used to set bad pixels.
More information on the Badmask Page.

badmaskinit

Syntax: badmaskinit
Context: badmask
Initialises the badmask array to all ones. You may later use the following commands to disable pixels: badmaskarea, badmaskcircle, badmaskcolumn, badmaskcorner, badmaskpixel, badmaskrow. Use badmask to apply the bad mask array to the current image.

badmask pixels are added to boxfiles.
More information on the Badmask Page.

badmaskpixel

Syntax: badmaskpixel px py
Context: badmask
After an initialisation of the badmask array badmaskinit) you may use this command to disable pixel px py.
More information on the Badmask Page.

badmaskrow

Syntax: badmaskrow py px1 px2
Context: badmask
After an initialisation of the bad mask array badmaskinit) you may use this command to disable a row of pixels. py is the row number, and all pixels between px1 and px2 will be disabled.
More information on the Badmask Page.

badmaskwithreso

Syntax: badmaskwithreso state
Default: badmaskwithreso on
Context: badmask
If on, the bad mask array will be initialized with resolution limits (resocorner resohalf resomax resomin thcorner thhalf thmax thmin) before every peak search.
The datcol command will set badmaskwithreso off

badpixel

Syntax: badpixel state
Context: read
Default: badpixel off
If state=on, an image will be corrected for badpixels when it is read in. The badpixels are listed in files badpixel.* in the calibration directory.
Related commands: badpixelforce badpixelmonitor badpixelneighbourhood badpixelprint

badpixelforce

Syntax: badpixelforce state
Context: badmask
Default: badpixelforce off
If state=on, all badpixels (in files badpixel.* in the calibration directory) will be treated as badmaskpixels (and thus ignored)

badpixelmonitor

Syntax: badpixelmonitor ph pv
Default: badpixelmonitor -1 -1
ph and pv are set the valid pixel numbers, every badpixel correction related to this pixel will be printed (for debugging purposes).

badpixelneighbourhood

Syntax: badpixelneighbourhood 4/8
Default: badpixelneighbourhood 4
badpixels can be corrected using the values of neighbour pixels. The possible neighbour pixels are specified as X:

4
```
0 X 0
X . X
0 X O
```
8
```
X X X
X . X
X X X
```

badpixelprint

Syntax: badpixelprint
Print a list of all badpixels.

badresponsthreshold

Syntax: badresponsthreshold n
Default: badresponsthreshold 0
Context: box
Sets a threshold for bad respons pixels for the ADSC and PILATUS detectors.

Pixels with a value less than or equal to n are considered bad. badresponsthreshold is used by peak search (peak2 or peak3) and boxfile creation.
In older versions of view (before 20090317), BADRESP pixels were set in the boxfile. Now only the value of badresponsthreshold is propagated into the boxfiles, and the integrating programs will handle the threshold themselves.
You may want to use the badmask command to apply the threshold to the current image. All pixels beneath the threshold will be changed into badresponsvalue.
The default value is only set for ADSC and PILATUS detectors. For other types of detectors, you have to explicitly use the command badresponsthreshold 0.0 to activate the threshold.

More information on the Badmask Page.

badresponsvalue

Syntax: badresponsvalue n
Default: badresponsvalue 0
Context: box
If the badresponsthreshold has been set, the command badmask will change all pixels with a value less than or equal to the threshold into n.
More information on the Badmask Page.

baseline

Syntax: baseline state
Default: baseline on
Context: read
If on: subtract the baseline from the image. (baseline is only nonzero in Bruker images)

beamstop

Syntax: beamstop x y
Syntax: beamstop2 x y
Default: beamstop 0.0 0.0
Default: beamstop2 0.0 0.0
Context: detector
The beamstop is positioned (x y) from the PrimaryBeam position. Use beamstopshift and beamstopshift2 to move the circular part of the beamstop relative to the beamstop mount. Use drawbeamstop to plot the beamstop. You can plot the beamstopposition with markbeamstop and plot the primary beam impact with markprimary. Use save beamstop to save the beamstop parameters in the file beamstop.vic.
See also the Beamstop Page.
For multiple beamstops, you may use beamstop2 to define the second beamstopposition, but beamstoprot and beamstoprot2 are probably better suited for this purpose.
Related commands: beamstopangle, beamstopdiameter, beamstopdistance, beamstoprot, beamstopshift, beamstopwidth.

beamstopangle

Syntax: beamstopangle d
Syntax: beamstopangle2 d
Default: beamstopangle 0.0
Default: beamstopangle2 0.0
Context: detector
Sets the angle of the beamstop mount with respect to the primary beam. to d degrees. A value of zero sets a vertical beamstop mount. The rotation direction is counter-clockwise. The default value depends on the goniostattype (extracted from the image header). Use drawbeamstop to plot the beamstop. Use save beamstop to save the beamstop parameters in the file beamstop.vic.
See also the Beamstop Page.
Related commands: beamstop, beamstopdiameter, beamstopdistance, beamstoprot, beamstopshift, beamstopwidth.

beamstopclick

Syntax: beamstopclick
Context: detector
You left mouse click various points at the edge of the beamstop. Finish the list with a right mouse click. The position of the beamstop will be set to the average of the clicked points, and the beasmtopdiameter will be set to 2*average_distance. You may want to use save beamstop to save the new values for later use.
See also the Beamstop Page.

beamstopcolour

Syntax: beamstopcolour colourname
Context: colour, detector
Default: beamstopcolour cyan
Set beam stop colour. Use drawbeamstop to plot the beamstop.

beamstopconnect

Syntax: beamstopconnect state
Default: beamstopconnect on
Context: detector
Only used if more than one beamstop is defined (so both beamstopdiameter and beamstopdiameter2 should be larger than zero). If on, the two beamstops will be connected by two lines. The area between these lines will obscure the image. The lines are drawn from the first beamstop with a width of abs(beamstopwidth ) to the second beamstop with a width of abs(beamstopwidth2 ).
See also the Beamstop Page.

beamstopdiameter

Syntax: beamstopdiameter x
Syntax: beamstopdiameter2 x
Default: beamstopdiameter 2.5
Default: beamstopdiameter2 -1.0
Context: detector
Sets the beamstop diameter to x. Use beamstopwidth to set the diameter of the beamstop mount. Specify a negative value to disable the beamstop. Use drawbeamstop to plot the beamstop. Use save beamstop to save the beamstop parameters in the file beamstop.vic.
See also the Beamstop Page.
Related commands: beamstop, beamstopangle, beamstopdistance, beamstoprot, beamstopshift, beamstopwidth.

beamstopdistance

Syntax: beamstopdistance x
Syntax: beamstopdistance2 x
Default: beamstopdistance -1
Default: beamstopdistance2 -1.0
Context: detector
Specifies the distance (in mm) between the beamstop and the crystal.
A negative or zero value specifies a beamstopdistance relative to the detector distance.
Related commands: beamstop, beamstopangle, beamstopdiameter, beamstoprot, beamstopshift, beamstopwidth.

beamstopid

Syntax: beamstopid s
Default: beamstopid *
Context: detector
Sets the beamstop id to s. The beamstop id is compared with the detector id for each new image. If the two id's are different, view tries to load the file beamstop.vic from the calibration directory. The beamstop.vic file can be used to set beamstop, beamstopangle, beamstopdiameter, beamstopdistance, beamstoprot, beamstopshift, beamstopwidth.

beamstoprot

Syntax: beamstoprot a
Syntax: beamstoprot2 a
Default: beamstoprot 0.0
Default: beamstoprot2 0.0
Context: detector
The position of the beamstop is defined by beamstop and beamstopshift. This defines the position of the beamstop with respect to the primary beam. With beamstoprot, the beamstop will be rotated around the z-axis (vertical axis through the crystal, pointing up) over a degrees. This can be useful if you want to describe a beamstopsystem with two beamstops.
See also the Beamstop Page.
Related commands: beamstop, beamstopangle, beamstopdiameter, beamstopdistance, beamstopshift, beamstopwidth.

beamstopset

Syntax: beamstopset
Context: detector
Stores: horpx verpx hormm vermm
You left mouse click the position of the beamstop. You may want to use save beamstop to save the new values for later use.
See also the Beamstop Page.

beamstopshift

Syntax: beamstopshift x y
Syntax: beamstopshift2 x y
Default: beamstopshift 0.0 0.0
Default: beamstopshift2 0.0 0.0
Context: detector
The beamstop position is set by the beamstop command. The circular part of the beamstop can be shifted relative to the beamstop mount using beamstopshift. Use drawbeamstop to plot the beamstop. You can plot the beamstopposition with markbeamstop and plot the primary beam impact with markprimary. Use save beamstop to save the beamstop parameters in the file beamstop.vic.
See also the Beamstop Page.
Related commands: beamstop, beamstopangle, beamstopdiameter, beamstopdistance, beamstoprot, beamstopwidth,

beamstopwidth

Syntax: beamstopwidth x
Syntax: beamstopwidth2 x
Default: beamstopwidth 1.0
Default: beamstopwidth2 1.0
Context: detector
Sets the width of the beamstop mount to x. Use beamstopdiameter to set the diameter of the beamstop. Use drawbeamstop to plot the beamstop. Use save beamstop to save the beamstop parameters in the file beamstop.vic.
For multiple beamstops with only one beamstopholder, specify a negative value for x to disable that holder.
See also the Beamstop Page.
Related commands: beamstop, beamstopangle, beamstopdiameter, beamstopdistance, beamstoprot, beamstopshift.

bgcolour

Syntax: bgcolour colourname
Default: bgcolour darkslateblue
Context: colour
Sets the background colour of all windows. In grey or -grey mode, pixels with a value less than minimum will be drawn with the bgcolour colour.
Use bg2colour to set the background colour in colour mode.
Related commands: bg2colour, fgcolour, fg2colour.

bg2colour

Syntax: bg2colour colourname
Default: bg2colour black
Context: colour
In colour mode, pixels with a value less than minimum will be drawn with the bg2colour colour.
Use bgcolour to set the background colour in grey and -grey mode.
Related commands: bgcolour, fgcolour, fg2colour.

boxcheck

Syntax: boxcheck state
Default: boxcheck on
Context: box
While building boxfiles, the values of dist, inc, swing and exposuretime are monitored for changes in succeeding images. Such changes will be printed to screen. If state=on and abort=on view will terminate with an error.
Related commands: checknext, overrule exposuretime, overrule dxstart, tolerance.

boxclose

Syntax: boxclose
Context: box, rmat
Closes boxfile.
See also boxopen.
You may specify a specific boxfile by adding a number to the command (i.e. boxclose2). Use boxcloseall to close all boxfiles.

boxdb

Syntax: boxdb
Context: test
Prints the internal box database.

boxdepth

Syntax: boxdepth n
Default: boxdepth 3
Context: box
Sets the number of images in one reflectionbox.
Related command: datcolinc.

boxnext

Syntax: boxnext
Context: box
Close current boxfile, and creates a new one.
See also boxopen.
You may add a number to this command if you want to apply boxnext to other boxfiles.
boxnextall will perform a boxnext to all open boxfiles. If you set the boxrefl boxfiles will be closed and opened automatically.

boxopen

Syntax: boxopen file
Context: box, rmat
Activates box. Creates a boxfile. If fibre is active (in the menu), then each selected point is written to file box.lis. Boxdata are also written with datcol. Specify the number of images with boxdepth. Set the size of the boxes with boxsize or boxsizemm. And finish writing the boxfile with boxclose. If responsread has been called, the data in the boxfile will be corrected for nonuniformity.
See also boxnext.
You can create multiple boxfiles by adding a number to the command (i.e. boxopen2 file). A warning (see abort) will be given if the matrix is not available.

boxrefl

Syntax: boxrefl n
Default: boxrefl 999999
Context: box
Sets maximum number of reflections in a boxfile. If, after processing an image, the number of reflections in a boxfile exceeds this number, the file is closed and a boxnext is executed. With still data, the boxfile is closed after processing each image.

boxsize

Syntax: boxsize nhor nver
Context: box
Sets box size. The arguments are expressed in pixels. The default values depend on the default value of boxsizemm (which can be used to set the size in millimeters).
Note: nhor and nver will be re-evaluated by the boxsizemm command.

boxsizemm

Syntax: boxsizemm x
Default: boxsizemm 2.3
Context: box
Sets box size (both horizontal and vertical) in millimeters. Use boxsize to set the size in pixels.

bpbfixed

Syntax: bpbfixed state
Default: bpbfixed on
Context: intensity
Used if intensities of profiles are calculated. (This calculation can be set with netint).
If state=off, the boundaries of the background region are determined from the profile. If the resulting intensity/sigma is less than weak, there intensity and sigma will be set to zero.
If state=on, the fixed boundaries (specified with bpbfraction) are used.

bpbfraction

Syntax: bpbfraction f
Default: bpbfraction 0.16
Context: intensity
Used if intensities of profiles are calculated. (This calculation can be set with netint). If bpbfixed=on, the value of f is used to set the boundaries of the background in the profile. A value of 0.1 sets to background limits at 0.1 and 0.9, leaving 0.8 for the peak, and 0.2 for the (total) background).

capillaryangle

Syntax: capillaryangle d
Default: capillaryangle -1.0
Context: constants
If set to a positive value, reflections within d° of the capillaryaxis will be excluded from the list of reflections generated by the datcol command. Use capillaryplot to draw the excluded region.

capillaryaxis

Syntax: capillaryaxis vx vy vz
Default: capillaryaxis 0 0 1
Context: constants
Sets the components of the capillary axis. Set capillaryangle to a positive value to exclude capillary absorbed reflections.

capillaryplot

Syntax: capillaryplot
Context: display
Valid only if capilaryangle is set to a positive value.
Draws the region (using durationcolour) with impacts close (within capilaryangle°) to the capillaryaxis. view uses circledelta to create the outline of the obscured region.

cell

Syntax: cell a b c alpha beta gamma
Context: fibre
Calculates DMAT and RMAT from cell parameters. Used for fibres only. A warning (see abort) will be given if the matrices cannot be build. The matrices will be printed with output misc full. You can save the rmatrix to a file using the save rmat command.
For single crystal data, use the rmat command to load a cell.

centrecolour

Syntax: centrecolour colourname
Default: centrecolour red
Context: colour
Set centre colour. Use markcentre to draw the centre of the detector.

checknext

Syntax: checknext state
Default: checknext off
Context: read
After a next command the end value of the rotation angle of the previous frame is checked against the start value of the new frame. If the difference is nonzero, a warning (see abort) is given if checknext=on.

circle

Syntax: circle
Context: circle
draws circles around PrimaryBeam. Define circle radii with circledef or circledefr. The colour of the circles can be set with circlecolour. The width of the circles (see circlewidth) will be plotted with circlewidthcolour.
Also available in menu mode.

circleclear

Syntax: circleclear
Context: circle
Removes all definitions of circles. Define new circle radii with circledef, circledefr or circleclick.

circleclick

Syntax: circleclick
Context: circle
Defines the radius for one new circle. You click an several points on the circle using the left mouse or middle mouse button. Finish the definition with a click with the right mouse button. The circle radius will be set the the average value of the clicked positions. Use circledefr to set radii in Å or circledef to set radii in degrees. New definitions are appended to the existing list. circleclear will clear the list.

circlecolour

Syntax: circlecolour colourname
Default: circlecolour yellow
Context: circle, colour
Set colour for circle.
Related command: circlewidthcolour.

circledef

Syntax: circledef d d d d ....
Context: circle
Sets radii for circles. The arguments are angles between the primary beam and the cone of outrays (i.e. 2theta values). Use circledefr to set radii in Å or circleclick to point to a circle. New definitions are appended to the existing list. circleclear will clear the list.

circledefr

Syntax: circledefr t t t t ....
Context: circle
Sets radii for circles. t in Å. Use circledef to set radii in degrees or circleclick to point to a circle. New definitions are appended to the existing list. circleclear will clear the list.

circledelta

Syntax: circledelta d
Default: circledelta 1.0
Context: circle, constants
Set circle interval angle to d degrees. This is the stepsize used to draw circles.

circlefit

Syntax: circlefit
Context: circle
Fit the detector position to a maximum circlesum. The detector position is initially read from detalign.vic. circlefit will refine the position.
If you have changed the detector position manually (with detectorshift), you cannot go back to the original position (with nodetectorshift) after refinement with circlefit.
The amount of output can be set with output circle
Related commands: circledef, circledefr, circleint, circlefitfactor, circlefittol, circleprofile and circlewidth.

circlefitfactor

Syntax: circlefitfactor fx fy fz
Default: circlefitfactor 0.2 0.2 0.2
Context: circle
Set estimated errors for detector shifts (in mm). If you set a factor to zero, the corresponding variable will not be refined by the circlefit command.

circlefittol

Syntax: circlefittol f
Default: circlefittol 0.005
Context: circle
Set refine exit criterium for circlefit.

circleint

Syntax: circleint f f f ....
Default: circleint 1.0 1.0 1.0 ....
Context: circle
Sets the relative intensities for powder circles. The intensities are used as a weight (1.0/f) in the calculation of circlesum. You have to enter intensities for all circles previously defined by circledef or circledefr.

circleprofile

Syntax: circleprofile state
Default: circleprofile on
Context: circle
Controls how circlesum calculates the intensities of circles.

circlesearch

Syntax: circlesearch DistStart DistEnd DistIncr HorStart HorEnd HorIncr VerStart VerEnd VerInc
Default: circlesearch -2 2 0.1 -2 2 0.1 -2 2 0.1 Context: circle
This creates the whole circlesum field. Circles have to be defined. You enter: start, end and increment values for detector position (distance, horizontal and vertical).
Finally the files field.cnt and atlas.init will be created. field.cnt will contain nx maps (along distance) of nz lines (vertical) with ny columns (horizontal).

circlesum

Syntax: circlesum
Context: circle
Display sum of intensities over all circles.
Circles are defined with circledef and circledefr commands. The width of the circles is set by circlewidth.
All pixels within circlewidth of each circle are considered. The contribution of the pixel intensity depends on the value of circleprofile:

circleprofile off
The contribution is the pixel intensity. The circlesum for each circle will correspond to the intensity of the powder circle.
circleprofile on
The contribution is the pixel intensity, weighted with the distance from the circle, and the intensity of the circle as set by circleint:
```
   r = distance from circle_i
   f = 1-r/circlewidth
   contrib = PixelIntensity*f/circleint_i
```
The circlesum is suitable for refinement with circlefit

These contributings are summed for each circle, and the number of contributing pixels is counted.
The intensity of each circle is this sum divided by the number of contributing pixels.
circlesum is the total summed intensitites divided by the total number of contributing pixels.
circlesum is used in the refinement procedure circlefit
The amount of output can be set with output circle

circlewidth

Syntax: circlewidth d
Default: circlewidth 0.15
Context: circle
Set the width (in degrees) of a circle area. Pixels within each circle ± d are used in the calculation of circlesum. The width of the circles will be plotted with circlewidthcolour.

circlewidthcolour

Syntax: circlewidthcolour colourname
Default: circlewidthcolour NONE
Context: circle, colour
Set colour for circlewidth.
Related command: circlecolour.

close

Syntax: close 2/zoom/profile/distor
Context: window
Delete a specific window. You cannot close window 1.

colour

Syntax: colour
Context: colour
Define a colour table with length maxcolour. All colours are different. The colours are set from darkblue RGB(0,0,50) through red RGB(125,0,0) to yellow RGB(0,255,255).
The resulting table can be displayed with show colour map, and you may change individual colours with setcolour.
Related commands: bgcolour, bg2colour, fgcolour, fg2colour, grey, -grey, setcolour.

cone

Syntax: cone px py
Context: conversion
Stores: horpx verpx
Calculated are the angles rho and tau. rho is the angle PrimaryBeam-crystal-(x y) (i.e. 2theta). tau is the angle between PrimaryBeam-(x y) and the vertical axis.

contigframes

Syntax: contigframes state
Default: contigframes off
Context: header
This command is a nasty trick to circumvent bad image header values of some broken datacollection packages.
If set to off nothing happens. If set to on the start-angle of the current image will be changed into the sum of the start-angle of the current image and the end-angle of the previous image. And the end-angle of the current image will be changed into to sum of the end-angle of the current image and the end-angle of the previous image.

contour

Syntax: contour file
Context: contour
Reads the first map from a cnt contourfile. A warning (see abort) will be given if the file cannot be opened.
Each point is multiplied by contourfactor. Use contournext to read subsequent maps. Use contouradd and contournextadd to add a contour map to the current buffer.

contouradd

Syntax: contouradd file
Context: contour
Reads the first map from a cnt contourfile, multiply each point by contourfactor and add the result to the existing buffer. A warning (see abort) will be given if the file cannot be opened.

contourbadmask

Syntax: contourbadmask f
Context: constour
Creates a file badmask.vic, marking all the pixels with a value larger than f as badpixels.

contourfactor

Syntax: contourfactor f
Default: contourfactor 1.0
Context: constants, contour
Every point in a contourfile will be multiplied by f.

contourframe

Syntax: contourframe n
Default: contourframe 1
Context: contour
Contourfiles can contain more than one map. After opening the contour file (with contour) set n to the requested map.
By opening a new contour file (contour (contouradd (contournext (contournextadd) contourframe will be set to 1

contournext

Syntax: contournext
Context: contour
Reads the following map from a cnt contourfile, multiply each point by contourfactor.

contournextadd

Syntax: contournextadd
Context: contour
Reads the following map from a cnt contourfile, multiply each point by contourfactor and add the result to the existing buffer.

corner

Syntax: corner
Context: info
Display minima, maxima and average in the four corners. The corners are defined with cornersize.

cornersize

Syntax: cornersize n1 n2
Default: cornersize 50 50
Context: constants
Set size of corners. In each corner a box with sides of n1 pixels is defined. The centre is defined between n2 and bufdim-n2. Corner shows extremes and averages in those areas.

correct

Syntax: correct none/normal/full/debug
Default: correct normal
Context: miscellaneous
Allows command and option corrections. Commands and options are only corrected if input originates from the keyboard, and output is sent to the screen.

none
No correction will be applied
normal
Commands and options will be corrected.
full
As before plus possible corrections are printed
debug
As before plus all available commands/options are printed

cosines

Syntax: cosines h k l
Context: test
This command is for testing purposes only.
Prints direction corsines for the specified reflection.

dark

Syntax: dark file
Context: read
Reads a dark image. The default filename is *drk.type with type the type set by imagefiletype (if no such file exist, the default is changed to *.dark).
From all subsequent images, the dark image will be subtracted. If scaledark=on, the dark subtraction will be scaled by the ratio of the exposuretime of the new image and the dark image.
Related commands: darkwait, read, trydark.
Disable dark subtraction with nodark.

darkwait

Syntax: darkwait file
Context: read
Waits for file and executes dark file.

datcol

Syntax: datcol
Context: hkl, box
The first time this command is used a list of reflections is build. See the Reflections Section above.
If boxopen had been called, boxfiles will be written for all the reflections in the current image. The reflection boxes will be corrected for nonuniformity if responsread has been called.
If boxopen has not been called, the reflections are stored in a list. This list can be excluded from a peak search. See peak3.
If mosaic has been set to a non-negative value, the behaviour of datcol is different. Reflections will be drawn as circles (with size shapesizea in colour shapecolour) if they are predicted within duration*mosaic degrees of the current frame. Also, if shapeform=circle, and shapeclean=on, the pixels of the (predicted) reflections in the image will be replaced by their average background.
You can control the amount of screen output with output datcol.
Also available in menu mode.

datcolboxes

Syntax: datcolboxes n
Context: display
With the command datcol reflections will be displayed on the screen. The value of boxdepth determines how many previous and next images will be considered. Set datcolboxes to a value less than boxdepth to limit the display of reflections to ±n images.
Note: This command does not limit the size of boxfiles. It is for display purposes only.

datcolcolour

Syntax: datcolcolour all 7 colournames
Syntax: datcolcolour reset
Syntax: datcolcolour same colourname
Syntax: datcolcolour option colourname
Default: datcolcolour all navy blue lightblue white khaki goldenrod goldenrod4
Context: colour
Sets the colours for reflections generated by datcol in current-3, current-2, previous, current, next, current+2 and current+3 images.

datcolcolour all
You have to enter seven colournames.
datcolcolour same
You have to enter one colourname All datcolcolours will be set to this colour.
datcolcolour reset
Sets datcolcolours to the initial values.
datcolcolour option
option can be one of -3 -2 -1 0 +1 +2 +3. You have to enter one colourname.

If boxdepth is set to a number less than 7, or if datcolboxes is set to a number less than 3, then some of the colours defined here will not be used.

datcolinc

Syntax: datcolinc d
Context: box
Calculates boxdepth = d/image_inc

datcollabel

Syntax: datcollabel state
Context: display
If state=on a call of datcol will plot the reflection indices (for reflections within datcollabelboxes neighbouring images).

datcollabelboxes

Syntax: datcollabelboxes n
Default: datcollabelboxes 0
Context: display
Sets the number of neighbouring images for the datcollabel command.

datcolshrinkboxes

Syntax: datcolshrinkboxes state
Default: datcolshrinkboxes on
Context: display
If state=on the size of the box (on the screen) will depend on the mtraix number (higher matrix, smaller box).

datcolwalk

Syntax: datcolwalk state
Default: datcolwalk off
Context: hkl, box
Builds a reflections list with virtual reflections. The detector is split into sections with dimensions set by boxsize. For each of these sections reflections indices hkl (floating numbers) will be generated. The rotation value of these reflections is the rotvalue of the current image. Once the reflection list is generated, shoeboxes can be build using datcol. As the current image most likely will be the central image of each box, you probably want to first read another image.

Example

rmat ir
boxsize 48 48
boxdepth 5
read s01f0003
datcolwalk on
read s01f0001
boxopen1 dummy/s01f001.shoe.Z
output datcol full
output box full
read s01f0001 plot datcol
\repeat 4 next plot datcol
boxclose1

denzox

Syntax: denzox
Context: hkl
view opens a denzo .x file (with the same name as the current image file) and calculates the impacts for all reflections in the denzo file.

detectoroffset

Syntax: detectoroffset dist hor ver
Context: detector
Sets the detector offset to dist hor ver. The default values originate from the file detalign.vic). Use detectorshift to add a shift to the detector offset.

detectorshift

Syntax: detectorshift dist hor ver
Context: detector
The values of dist hor ver will be added to the detector offset (as found in the file detalign.vic). You can remove the (accumulated) shifts with the command nodetectorshift (but see the remark at circlefit). Multiple invocations of detectorshift will accumulate. Use detectoroffset to modify the offset.

dict

Syntax: dict state
Default: dict off
Context: miscellaneous
If state=on the output of

dictheader
peak search commands (peak2, peak3)
resolution commands (thmin, thmax resomin, resomax, thhalf, resohalf)

will contain a list of keyword/value pairs. The keywords start with dictname. This output can be used to parse the output of any into another program.

dictheader

Syntax: dictheader
Context: header miscellaneous
If dict is on print a dictionary of image header variables

dictname

Syntax: dictname label
Default: dictname !!view-
Context: miscellaneous
Sets the leading part of keywords of dictionary output (if dict =on).

diraxclose

Syntax: diraxclose
Context: peak, files
Closes the DirAx file (opened with diraxopen).

diraxfile

Syntax: diraxfile file
Context: peak, files
Specifies the name of the DirAx file. See also drxpk.

diraxopen

Syntax: diraxopen
Context: peak, files
Creates a DirAx file. The name of the file can be specified with diraxfile. A warning (see abort) will be given if the file cannot be created.
c-vectors will be written to this file. These c-vectors are the results from peak2 and peak3.
A description of the dirax program can be found here. See also drxpk.

dirty

Syntax: dirty
Context: test
Flag current image data as dirty. The next execution of the plot command will trigger a call to prepare.

display

Syntax: display px py [nx ny]
Context: info
Stores: horpx verpx
Display images content around px py. Specify nx ny to change the size of the region.
Use displayhc on to save the selected image contents to a file.
Also available in menu mode.
Related commands: displayhistogram, examine, search.

displayhc

Syntax: displayhc on filename
Syntax: displayhc off
Context: files
If state=on, a file filename will be created. A warning (see abort) will be given if the file cannot be created.
Every succeeding execution of display (either as command or via menu) will write the screen output to the file. If state=off, the file filename will be closed.

displayhistogram

Syntax: displayhistogram state
Default: displayhistogram off
Context: info
If on, invocation of the display command (by the command itself or by using menu mode) will also print a histogram of the displayed image part.

dist

Syntax: dist x
Context: header
Set crystal-detector distance in mm. The value is normally extracted from image file.
Note, the final detector distance will be different if the dist components of detectoroffset and/or detectorshift have nonzero values.

distor

Syntax: distor
Context: processing
Calculate distortion corrected image. The image will be plotted in the distor window. Set the width and height of that window to appropriate values (using window distor W width H height). Use distorsquare to set square decay correction.

distorsquare

Syntax: distorsquare state
Default: distorsquare off
Context: processing
Set/reset correction in distor for square decay.

drawbeamstop

Syntax: drawbeamstop
Context: detector display
Draws the beamstop.
See also the Beamstop Page.

drawlinemm

Syntax: drawlinemm x1 y1 x2 y2
Context: display Draws a line from x1 y1 to x2 y2

drxpk

Syntax: drxpk file
Context: peak, files
This will set both diraxfile as peakfile to file. Then diraxopen and peakopen are executed.

durationcolour

Syntax: durationcolour colourname
Default: durationcolour orange
Context: colour
Set the colour of the duration arc. These are the pixels with a duration = durationmax. The same colour is used by capillaryplot.

durationmax

Syntax: durationmax f
Default: durationmax 5.0
Context: constants
Set the maximum value of the duration. Definition:

variable	definition	length	description
rotax		1.0	vector along rotation axis
inray		1.0	vector pointing to primary beam
lorvec	vecprod(rotax,inray)	sin(rotax,inray)	lorentz vector (does not change during one scan)
c		2*sin(θ)/λ	c-vector in diffracting position
lor	\|(1.0/scalprod(c,lorvec)\|		the lorentz correction
duration	\|c\|*lor		theta corrected lorentz correction

Used by datcol, peak2 and peak3.

durationplot

Syntax: durationplot vx vy vz
Context: test
Calculates and plots the duration map with the current detector settings. The rotation axis is defined with vx vy vz. The values are multiplied by 100. (After durationplot, you have to reread the image.)

echo

Syntax: echo arg.....
Context: info
Echoes all args. The whole line will be parsed, unless an argument nop or ; is encountered.
If arg starts with $ arg will be substituted.

If arg starts with $imh, a substitution with information from the image header will be tried. Available names are (in alphabetical order):

imhadc imhadded imhalpha1 imhalpha2 imhalpharatio imhautooverflow imhaxis imhbaseline imhbeamhor imhbeamver imhbeamcatcherdiameter imhbeamcatcherdistance imhbin imhbinned imhcalibrationid imhchiinterval imhchirange imhchiscan imhchistart imhcircular imhcomment imhcorrected imhcryoactualtemperature imhcryotemperature imhdatatype imhdatetime imhdetectorid imhdetectortype imhdetgain imhdetrot imhdist imhdoswapheader imhdoswapdata imhdxinterval imhdxrange imhdxscan imhdxstart imhendpos imhexposuretime imhformat imhgoniostat imhgoniostatid imhgoniostattype imhhv imhid imhimagefixedadczero imhimagemedianadczero imhimagereadoutnoise imhinc imhintegrationtime imhkappainterval imhkapparange imhkappascan imhkappastart imhma imhmodel imhmodetime imhmultiplied imhnoverflow imhnoverflow1 imhnoverflow2 imhnunderflow imhomegainterval imhomegarange imhomegascan imhomegastart imhoverflowtrigger imhpadding imhphiinterval imhphirange imhphiscan imhphistart imhpixelxsize imhpixelysize imhpolarisation imhradiationtype imhrescanfactor imhrescanlevel imhrotaxis imhrotend imhrotstart imhrotvalue imhscale imhstartpos imhswing imhtarget imhthetainterval imhthetarange imhthetascan imhthetastart imhtotaleposuretime imhtotalintegrationtime imhunderflowsize imhunwarped

If arg is $imhall, all available header variables will be displayed.
Try the stored values from \listeval.
Try an \alias.

Examples

The image $fullimagefilename was collected at $imhdatetime

The image s01f0001.sfrm was collected at 12/19/13 13:04:45

\eval pi/3
echo pi divided by three is $eval_result

\eval pi/3
   1.0471975511965976     
pi divided by three = 1.047197551196598

output read none
read s01f0001
\repeat 20 next echo image $imagefilename started at $imhstartpos

View> output none
View> read s01f0001
s01f0001 
View> \repeat 20 next echo image $imagefilename started at $imhstartpos      
s01f0002 
image s01f0002 started at 0.0 90.0 -0.5
s01f0003 
image s01f0003 started at 0.0 90.0 -1.0
s01f0004 
image s01f0004 started at 0.0 90.0 -1.5
s01f0005 
image s01f0005 started at 0.0 90.0 -2.0
s01f0006 
image s01f0006 started at 0.0 90.0 -2.5
s01f0007 
image s01f0007 started at 0.0 90.0 -3.0
s01f0008 
image s01f0008 started at 0.0 90.0 -3.5
s01f0009 
image s01f0009 started at 0.0 90.0 -4.0
s01f0010 
image s01f0010 started at 0.0 90.0 -4.5
s01f0011 
image s01f0011 started at 0.0 90.0 -5.0
s01f0012 
image s01f0012 started at 0.0 90.0 -5.5
s01f0013 
image s01f0013 started at 0.0 90.0 -6.0
s01f0014 
image s01f0014 started at 0.0 90.0 -6.5
s01f0015 
image s01f0015 started at 0.0 90.0 -7.0
s01f0016 
image s01f0016 started at 0.0 90.0 -7.5
s01f0017 
image s01f0017 started at 0.0 90.0 -8.0
s01f0018 
image s01f0018 started at 0.0 90.0 -8.5
s01f0019 
image s01f0019 started at 0.0 90.0 -9.0
s01f0020 
image s01f0020 started at 0.0 90.0 -9.5
s01f0021 
image s01f0021 started at 0.0 90.0 -10.0

ek

Syntax: ek
Context: info
This will print the Euler and Kappa angles for the starting, mean and ending goniometer values of the current image.

end

Syntax: end
Context: miscellaneous
Finish program. Alternatives: exit, quit.

evpylog

Syntax: yvpylog string
Context: miscellaneous
Try to locate a file evpy.log in the current or parent directories. If found, append a timestamp and string to that file.

examine

Syntax: examine [n1 [n2]]
Context: info
Prints part of the sorted sorted array. This array is created by prepare and contains the data that will be plotted.

examine prompts for two numbers and displays the values between these two arraypositions n1 to n2.
examine n displays the values around arrayposition n
examine n1 n2 displays the values for arraypositions n1 to n2
examine last display the last values.

The format of the output is: Index Value WinH WinV Hor Ver Image

name	description
Index	the index number in the sorted array
Value	the value in the sorted array
WinH	horizontal pixel coordinate in the window
WinV	vertical pixel coordinate in the window
Hor	Corresponding horizontal pixel coordinate in image
Ver	Corresponding vertical pixel coordinate in image
Image	Image value on Hor Ver

Note: the values of Value and Image will differ if plotbin unequals 1.
Related commands: display, search.

exit

Syntax: exit
Context: miscellaneous
Finish program. Alternatives: end, quit.

fgcolour

Syntax: fgcolour colourname
Default: fgcolour red
Context: colour
In grey or -grey mode, pixels with a value greater than maximum will be drawn with the fgcolour colour.
Use fg2colour to set the foreground colour in colour mode.
Related commands: bgcolour, bg2colour, fg2colour.

fg2colour

Syntax: fg2colour colourname
Default: fg2colour white
Context: colour
In colour mode, pixels with a value greater than maximum will be drawn with the fg2colour colour.
Use fgcolour to set the foreground colour in grey and -grey mode.
Related commands: bgcolour, bg2colour, fgcolour.

fibre

Syntax: fibre and you pick a point using the mouse
Syntax: fibre x y
Context: fibre
Show names and plot positions (colours walk from fibrecolour 0 to fibrecolour 7) of neighbouring reflections. Use fibrecrit to set the distance criterium.
If boxopen is activated, then a boxfile will be written.
Also available in menu mode.

fibreall

Syntax: fibreall
Context: fibre
Generates reflections -n<h<n, -n<k<n, -n<l<n, with n a number set by fibremaxindex (default=10). Plots positions of these generated reflections in the active window with fibrecolour 0.

fibrecolour

Syntax: fibrecolour all 8 colournames
Syntax: fibrecolour reset
Syntax: fibrecolour option colourname
Default: fibrecolour all red orange gold yellow green palegreen aquamarine cyan
Context: colour, fibre
Sets the colours for reflections generated by fibre (fibrecolour 0 to 7) and fibreall (fibrecolour 0)

fibrecolour all
You have to enter eight colournames.
fibrecolour same
You have to enter one colourname. All fibrecolours will be set to this colour.
fibrecolour reset
Sets fibrecolours to the initial values.
fibrecolour option
option can be one of 0 1 2 3 4 5 6 7. You have to enter one colourname.

fibrecrit

Syntax: fibrecrit f
Default: fibrecrit 0.3
Context: fibre
Set Fibre neighbour criterium The value of f is used by fibre. f = the maximum allowed distance in mm between the selected position and the neighbour reflections (on the detector).

fibrehkl

Syntax: fibrehkl h k l
Context: fibre
You enter h k l and view displays the impact position with colour fibrecolour 0.

fibremaxindex

Syntax: fibremaxindex n
Default: fibremaxindex 10
Context: fibre
Sets the reflection generator limits for the fibreall command.

fibreorient

Syntax: fibreorient vx vy vz
Default: fibreorient 0.0 0.0 1.0
Context: fibre
Describes the orientation of the fibre axis. The default is along laboratory z-axis.

fibrerot

Syntax: fibrerot x/y/z d
Context: fibre
This command will rotate the fibre orientation around the x/y/z axis over d degrees.

fitmm

Syntax: fitmm f
Context: peak
Specifies the distance (in mm) between observed and calculated reflections. Used by m2h, HKL in menu mode, peak2 and peak3. The impact position is converted to reciprocal indices using the rmatrix resulting in 3 floating numbers. If they are close to integer (how close is controlled by round) they are rounded to integer, and a new impact position will be calculated. The difference in millimeter and the difference in rotation (fitrot) determines whether the observed impact fits the lattice.
If multiple matrices (rmatR) are available, they are all tested, except in the case of a peaksearch where the rmatrix is set with peakrmat.
Related commands: fitrot, peakfit.

fitrot

Syntax: fitrot f
Context: peak
Specifies the difference (in degrees) between observed and calculated reflections. Used by m2h, HKL in menu mode, peak2 and peak3. The impact position is converted to reciprocal indices using the rmatrix resulting in 3 floating numbers. If they are close to integer (how close is controlled by round) they are rounded to integer, and a new impact position will be calculated. The difference in millimeter (fitmm) and the difference in rotation determines whether the observed impact fits the lattice.
If multiple matrices (rmatR) are available, they are all tested, except in the case of a peaksearch where the rmatrix is set with peakrmat.
Related commands: fitmm. peakfit.

flex

Syntax: flex f
Default: flex 0.5
Context: still
The impact will be something between the η and θ impact. flex will only be used if stilltype equals flexible.

flush

Syntax: flush
Context: window
Flush the X-window buffers. Normally not to be used.

fm2p

Syntax: fm2p x y
Context: conversion
Stores: hormm vermm
Convert mm to pixels. Pixels are expressed as floating point numbers.
Related command: m2p.

focuschange

Syntax: focuschange s
Context: box
Change one or more of the focus parameters.
These parameters are not used in view, but they will propagate into boxfiles.
Enter a semicolon ; or nop to return back to the view-command prompt.

focusstart

Syntax: focusstart s
Context: box
Similar to focuschange

forbidlist

Syntax: forbidlist
Context: peak hkl
Print all forbidden theta/resolution areas, defined by forbidreso or forbidtheta).

forbidnone

Syntax: forbidnone
Context: peak hkl
Removes all forbidden theta regions (defined by forbidreso or forbidtheta).

forbidreso

Syntax: forbidreso d1 d2
Context: peak hkl
Adds a forbidden resolution region. These regions are used during peak search and the generation of reflection during datcol. The maximum number of regions is 10. d1 is then lowest resolution, d2 is the highest resolution Use forbidnone to remove the regions. Use forbidlist to print the regions. The resolution circles will be drawn with forbidthetacolour.
See also forbidtheta.

forbidtheta

Syntax: forbidtheta d1 d2
Context: peak hkl
Adds a forbidden theta region. These regions are used during peak search and the generation of reflection during datcol. The maximum number of regions is 10. d1 is thetamin, d2 is thetamax. Use forbidnone to remove the regions. Use forbidlist to print the regions. The theta circles will be drawn with forbidthetacolour.
See also forbidreso.

forbidthetacolour

Syntax: forbidthetacolour colourname
Default: forbidthetacolour green
Context: peak hkl colour
Set colour for forbidtheta and forbidreso circles.

fp2h

Syntax: fp2h fx fy
Context: hkl
You enter fx fy (in pixels). view shows the reflection indices for that impact position. The fit is controlled by round, fitmm and fitrot.
Also available in menu mode (where it is called HKL).

Related command: p2h.

fp2m

Syntax: fp2m fx fy
Context: conversion
Stores: hormm vermm
Convert pixels to mm. Pixels are expressed as floating point numbers. The resulting coordinate is stored (via addeval) in hormm and vermm
Related command: p2m.

frame

Syntax: frame n
Context: read
n is interpreted as relative if it starts with a + or -, otherwise n is an absolute frame number. If the new image exists, it will be read.

-grey

Syntax: -grey
Context: colour
Define grey colour table with length maxcolour. All colours are different. Grey scale from black (low) to white (high).
The resulting table can be displayed with show colour map, and you may change individual colours with setcolour.
Related commands: bgcolour, bg2colour, colour, fgcolour, fg2colour, grey, setcolour.

gainfactor

Syntax: gainfactor f
Default: gainfactor 1
Context: box
Multiply the gain from the imageheader with f. The result is written to the boxfile.

gaintest

Syntax: gaintest f g
Default: gaintest 0.1 10
Context: detector
Select four areas of size g at positions specified by the fractional number f.

Area	LowerLeft	LowerRight	UpperRight	UpperLeft
1	f*Nhor	f*Nhor+g	f*Nver	f*Nver+g
2	(1-f)*Nhor	(1-f)*Nhor-g	f*Nver	f*Nver+g
3	(1-f)*Nhor	(1-f)*Nhor-g	(1-f)*Nver	(1-f)*Nver-g
4	f*Nhor	f*Nhor+g	(1-f)*Nver	(1-f)*Nver-g

In each of these areas, calculate Mean, Sigma and Sigma²/Mean (=Gain)

gif

Syntax: gif file
Context: files
Create a gif file from the active window (see activate). The gif file is created using the import program of the ImageMagick program suite. A warning (see abort) will be given if the file cannot be created.
The filename depends on the selected window. image .gif, image profile.gif, image zoom.gif or image distor.gif. If psframe=on, a frame of the window will be included.
Related commands: jpeg, ps.

globalmax

Syntax: globalmax n
Default: noglobalmax
Context: constants
Set maximum for all images to n.
Use noglobalmax to use the actual maximum of an image.
Related command: globalmin

globalmin

Syntax: globalmin posmin/init/n
Default: globalmin posmin
Context: constants
Set default minimum.

globalmin posmin will set minimum value for each new image to its lowest positive value.
globalmin init will set minimum value for each new image to its lowest value.
globalmin n will set a fixed minimum value n.

Related command: globalmax

go

Syntax: go
Context: menu
Start event loop. Select quit in the menu to return to command mode or press the right mouse button. Equivalent to menu

gonio

Syntax: gonio
Context: info
Prints goniostat angles (average position and position with rotangle=0).
Prints transformation matrices ToZero (from Goniostat to Zero angles), ToGoniostatRotZero (from Zero position to goniostat with rotangle=0) and ToMean (from Zero position to average position).
Prints the laboratory vectors of the goniometer head axes at average goniostat position.

goniostatchange

Change one or more attributes of the goniostat. See the goniostat page for more information.

goniostatid

Syntax: goniostatid s
Default: goniostatid *
Context: detector
Obsolete command to set the goniostat id to s. You should use goniostatchange id instead.
The goniostat id is compared with the detector id for each new image. If the two id's are different, view tries to load the file goniostat.vic from the calibration directory.

goniostatoffset

Syntax: goniostatoffset a a a
Default: goniostatoffset 0.0 0.0 0.0
Context: detector
Obsolete command to set the goniostat offset. You should use: goniostatchange offset instead.

goniostatoutputlevel

Syntax: goniostatoutputlevel none/normal/full/debug
Default: goniostatoutputlevel normal
Context: miscellaneous
Sets the amount of output, related to goniostat routines.

goniostatprint

Prints the parameters of the goniostat. See the goniostat page for more information.

goniostattype

Sets the goniostat type. See the goniostat page for more information.

graphics

Syntax: graphics state
Default: graphics on
Context: window
If on, all graphics commands will be executed. If off, the graphics commands will be ignored. Use graphics off to process images if no graphics is needed or possible.
Here is a list of commands ignored by graphics: capillaryplot, circle, distor, drawbeamstop, durationplot, grid, plot, refresh, title
The following commands will be executed but the graphics related output will be omitted: durationmax, hkl, hklplot, all profile variants, zoom, zoomaround, zoomaroundmm, zoombeamstop, zoomfollow, zoomfollowhkl.Br> Also available in menu mode.

graphicsmod

Syntax: graphicsmod n
Default: graphicsmod 1
Context: window
Only every n'th plot command will be honoured.
Related commands: imageoff, imageon.

gravity

Syntax: gravity px py
Context: test
Stores: horpx verpx
Determine the center of gravity in the neigbourhood of the specified pixel px py. This is for testing only. The gravity command is implicitly used by the various peaksearch commands, and by middle mouse clicks.

grey

Syntax: grey
Context: colour
Define grey colour table with length maxcolour. All colours are different. Grey scale from white (low) to black (high).
The resulting table can be displayed with show colour map, and you may change individual colours with setcolour.
Related commands: bgcolour, bg2colour, colour, fgcolour, fg2colour, -grey, setcolour.

grid

Syntax: grid
Context: display
Draw a grid with the colour specified with gridcolour. Use gridsize, gridsizex or gridsizey to set the grid size.

gridcolour

Syntax: gridcolour colourname
Default: gridcolour yellow
Context: colour
Set grid colour.

gridsize

Syntax: gridsize f
Default: gridsize 1.5
Context: constants
Set grid interval in mm for both directions for the grid command.
Related commands: gridsizex, gridsizey.

gridsizex

Syntax: gridsizex f
Default: gridsizex 1.5
Context: constants
Set x gridsize to f mm for the grid command.
Related commands: gridsize, gridsizey.

gridsizey

Syntax: gridsizey f
Default: gridsizey 1.5
Context: constants
Set y gridsize to f mm for the grid command.
Related commands: gridsize, gridsizex.

gui

Syntax: gui variable
This command is to be used by GUI programs to access some variables in view. The return code is the type and value of variable.
Variable type is one of:

F float
A angle in degrees
I integer
L true or false
S string

guiactive

Syntax: guiactive state
Default: guiactive off
To be used only by a gui-program. If on, menu or go will terminate after the first click. If off, menu or go will terminate only with a right mouse button click.

header

Syntax: header
Context: info
show header information of last image file.

help

Syntax: help [command]
Context: miscellaneous
Start webbrowser with help on view. The following browsers are tried: (GETENV BROWSER), iceweasel, firefox, mozilla, netscape. You may add the optional command; if possible, the browser will jump to the appropriate section.

histo

Syntax: histo
Context: info
Prints a histogram of the values in the current image. Only the pixels betweem minimum and maximum are used. The number of intervals is fixed to 50.
Related commands: displayhistogram combined with display

hkl

Syntax: hkl h k l
Syntax: hkl h k l qvp
Context: hkl
Calculates impacts for the specified reflection. The reflection indices are based on the matrix specified with hklmatrix. If qvectors are defined, you have to enter qvp (qvector pointer).
view calculates the impact positions of all equivalent reflections (symmetry set by the rmat or the laue or pg commands). If available, the name of the images containing predicted reflections are printed. The reflections predicted in the current image will be plotted with a box of dimensions set by marksize in hklcolour. The command hklplot will first read the appropriate image. A warning (see abort) will be given if no rmatrix is available.

hklcolour

Syntax: hklcolour colourname
Default: hklcolour red
Context: colour
Set colour for hkl and hklplot.

hklmatrix

Syntax: hklmatrix n
Default: hklmatrix 1
Context: hkl
Set the hklmatrix number to n. A warning (see abort) will be given if the specified matrix is not available.
hklmatrix is used by hkl, hklplot qvp, qvpoff, qvpon.

hklpick

Syntax: hklpick
Context: hkl
Every mouse click will try to determine the reflection indices of the selected pixel.

hklplot

Syntax: hklplot h k l
Syntax: hklplot h k l qvp
Context: hkl
Works similar to hkl, and will load the appropriate image if it is available.

icon

Syntax: icon 1/2/zoom/profile/distor/menu
Context: window
This command will iconize a window. Use map to restore the window.
Related command: unmap.

imagefiletype

Syntax: imagefiletype s
Context: read
Use string s as the default filetype. Is the filetype is set, you don't have the specify it at the various read commands. The defaults depend on the version of view:

program	default
view	kcd
view2000	kcd
viewadsc	img
viewmar	mar2300
viewmarccd	mccd
viewsmart	sfrm
viewraxis	osc
viewcbf	cbf

If an imagefile cannot be found, view will try to append compression filetypes (.Z .gz .bz2) to the name.
See the Detectors Page.

imageoff

Syntax: imageoff n
Default: imageoff 0
Context: window

ImageOff	ImageOn	Action
0	0	Ignore all plot commands.
>0	0	Ignore all plot commands.
0	>0	Honour all plot commands.
>0	>0	Ignore ImageOff plot commands. Then honour ImageOn plot commands. Repeat this scheme.

Related command: graphicsmod.

imageon

Syntax: imageon n
Default: imageon 1
Context: window
See imageoff

imagesigma

Syntax: imagesigma
Context: info
Calculates and prints the mean and sigma of all pixels in the image. The imagename and total exposuretime will also be printed with output misc full.
badmask will be invoked to eliminate bad pixels.
The value of sigma can be used to set adcnoise in pixel15.

jaap

Syntax: jaap f1 f2
Default: jaap 0.9 1.5
Context: constants
Sets the values for the mode jaap option.

jpeg

Syntax: jpeg file
Context: files
Create a jpeg file from the active window (see activate). The jpeg file is created using the import program of the ImageMagick program suite. A warning (see abort) will be given if the file cannot be created.
The filename depends on the selected window. image .jpeg, image profile.jpeg, image zoom.jpeg or image distor.jpeg. If psframe=on, a frame of the window will be included.
Related commands: gif, ps.

ke

Syntax: ke
Context: info
This will display the Euler angles for the starting, mean and ending goniometer values of the current image.

lambda

Syntax: lambda mo/cu/ag
Syntax: lambda mo1/mo2/cu1/cu2/ag1/ag2/f
Context: header
Set wavelength.

target	α₁	α₂	ratio	λ_mean	λ_mid
mo	0.70930	0.71359	2.0	0.71073	0.71144
cu	1.54056	1.54439	2.0	1.54184	1.54247
ag	0.559407	0.563798	2.0	0.56087	0.56160
mo1	-	-	-	0.70930	0.70930
mo2	-	-	-	0.71359	0.71359
cu1	-	-	-	1.54056	1.54056
cu2	-	-	-	1.54439	1.54439
ag1	-	-	-	0.559407	0.559407
ag2	-	-	-	0.563798	0.563798
f	-	-	-	f	f

λ_mean = (ratio*α₁ + α₂)/(ratio+1)
λ_mid = (α₁ + α₂)/2
λ_mean is used for all wavelength dependent calculations. λ_mid is never used.

laue

Syntax: laue s
Context: hkl, rmat
Sets the laue group to s. The default pointgroup is extracted from the rmat file. If no pointgroup information is available, an educated guess based on the cell parameters is done.
overview of laue groups.
You may add a number to the command (i.e. laue2) to set the laue group for a different lattice. A warning (see abort) will be given if the matrix is not available. Use laueall to change all available lattices. The reflection relations will be printed with output misc normal.
Related command: pg.

limits

Syntax: limits
Context: test
Prints various hardcoded program limits. More output will be given with output misc full

Item	Description
DatcolRefl	Maximum number of reflections for datcol
BoxRefls	Maximum number of active box reflections
BoxData	Maximum number of bytes available for box data
BoxNovp	Maximum number of overflow pixels for box data
hklRmat	space needed for matrices
Rmatlist	space needed for matrices
BadPixel	Maximum number of badpixels in one image
Screen	Space needed for graphics
Ovp	Maximum number of overflow pixels in one image
Bufdim	space needed for image buffers (dark,data,scratch...)
Peak	Maximum number of peaknr
Peakremove	Maximum number of refls within peakremove

ll

Syntax: ll px py
Context: display
If an image is too big for the window only a part of the image will be displayed. You may select which part. px py are the pixel coordinates of the lower left part of the displayed image. You can also use part or change the value of plotbin.

lorplot

Syntax: lorplot vx vy vz
Context: test
Calculates and plots the Lorentz factor for every pixel. The rotation axis is defined with vx vy vz. The values are multiplied by 1000. (After lorplot, you have to reread the image.)

lowerresolution

Syntax: lowerresolution n
Context: processing Set pixelvalues to mean value of a n*n square. lowerresolution 1 will do nothing. lowerresolution 256 creates a map of 4 regions.

m2c

Syntax: m2c x y
Context: info
Stores: hormm vermm
You enter x y (in mm). view prints theta, chi and the c-vector.

m2h

Syntax: m2h x y
Context: hkl
Stores: horpx verpx hormm vermm
You enter x y (in mm). view shows the reflection indices for that impact position. The fit is controlled by round, fitmm and fitrot.
Also available in menu mode (where it is called HKL).

m2mid

Syntax: m2mid x y
Context: conversion
Converts the millimeter coordinates x y to idealized millimeter coordinates (= coordinates of an ideal positioned detector)

m2p

Syntax: m2p x y
Context: conversion
Stores: horpx verpx hormm vermm
Convert mm to pixels. The resulting pixel values are printed.
Related command: fm2p.

map

Syntax: map 1/2/zoom/profile/distor/menu
Context: window
This command will pop up the selected window. Synonymous with raise.
Related commands: icon, unmap.

markbeamstop

Syntax: markbeamstop
Context: display
Draws a cross at the position of the beamstop. The position of the beamstop is influenced by the detector position parameters and the value of beamstop. The size of the cross can be set with marksize. The colour can be set with beamcolour. Use drawbeam to plot the beamstop.
Also available in menu mode.

markcentre

Syntax: markcentre
Context: display
Draws centre cross at the centre of the detector. The centre of the detector depends only on the distortion function of the detector. The size of the cross can be set with marksize. The colour can be set with centrecolour.
Also available in menu mode.

markcolour

Syntax: markcolour colourname
Default: markcolour yellow
Context: colour
Set colour for markm and markp.

markm

Syntax: markm x y
Context: display
Stores: horpx verpx hormm vermm
Draws a cross at x y (mm). The size of the cross can be set with marksize. The colour can be set with markcolour.
Also available in menu mode.

markp

Syntax: markp px py
Context: display
Stores: horpx verpx
Draws a cross at px py (pixels). The size of the cross can be set with marksize. The colour can be set with markcolour.
Also available in menu mode.

markprimary

Syntax: markprimary
Context: display
Draws a cross at the position of the primary beam. The position of the primary beam is influenced by the detector position parameters but not by the value of beamstop. The size of the cross can be set with marksize. The colour can be set with primarybeamcolour.
Related commands: markbeamstop, drawbeamstop, permutate, setprimary

marksize

Syntax: marksize n
Default: marksize 7
Context: constants
Set size (in pixels) of crosses, stars etc...

matcolour

Syntax: matcolour 3 colournames
Default:matcolour white wheat1 wheat4
Default:matcolour2 deepskyblue dodgerblue3 dodgerblue4
Default:matcolour3 seagreen1 seagreen4 darkgreen
Default:matcolour4 violet magenta magenta4
Default:matcolour5 yellow yellow3 yellow4
Context: colour, rmat
Sets the datcolcolours if there is more than one lattice. The first colour will be used to highlight reflections in the current frame, the second is used to draw reflections in neighbouring frames and the third one is used for all other frames. You may add a number to the command (i.e. matcolour2) to specify colours for different lattices. Use matcolourall to change all colours.
If only one matrix is defined, the matcolour colours will not be used, but the colours specified with datcolcolour.

maxcolour

Syntax: maxcolour n
Default: maxcolour 48
Context: colour, constants
Set maximum number of colours. The maximum number = 200, but 50 grey colours give nice pictures. Use grey and -grey to define the the greyscale colours. Use colour to define non-grey colours.

maximum

Syntax: maximum n
Default: maximum maximum_value_in_image
Context: display
Pixels with a value greater than n will not be drawn according to the colour scheme (see mode), but with the colour set by fgcolour (in grey and -grey mode) or fg2colour (in colour mode).
This value is also used when drawing profile with profiletype=global.
Use globalmax to set the maximum for succeeding images.

mean

Syntax: mean px1 py1 px2 py2
Context: info
Calculate mean and minimum,maximum in a specified area.
px1 py1 = pixel coordinates of lower left of area.
px2 py2 = pixel coordinates of uper right of area.
Related commands: meanaround, merge.

meanaround

Syntax: meanaround px py nx ny
Context: info
Stores: horpx verpx
Calculate mean and minimum,maximum in a specified area.
px py = pixel coordinates of centre of area.
nx ny = size of area.
Related commands: mean, merge.

menucolour

Syntax: menucolour option colourname
Context: colour, menu.
Sets menu window colours.

option	default	description
active	red	background of active item
choice	steelblue	choice items
fg	green	text foreground
normal	navyblue	command items

merge

Syntax: merge
Context: info
Calculate mean values and extremes in parts of the image. The image is divided into mergefactor * mergefactor blocks. A value of 2 for mergefactor will give means and extremes for four parts (Upper Left, Upper Right, Lower left and Lower Right). Always included are the means and extremes for the sum of rows and sum of columns.
Note: Only pixels with a value between minimum and maximum will be counted.
Related commands: mean, meanaround.

mergefactor

Syntax: mergefactor n
Default: mergefactor 4
Context: constants
Set mergefactor. See merge.

minimum

Syntax: minimum init/posmin/n
Default: minimum posmin
Context: display
Pixels with a value less than n will not be drawn according to the colour scheme (see mode), but with the colour set by bgcolour (in grey and -grey mode) or bg2colour (in colour mode).

minimum n
n is an number.
minimum init
minimum is set to then minimum of the image.
minimum posmin
minimum is set to the lowest positive value of the image.

Use globalmin to set the minimum for succeeding images. minimum is also used when drawing profiles with profiletype=global.
Also available in menu mode.

mid2m

Syntax: mid2m x y
Context: conversion
Stores: hormm vermm
Converts the idealized millimeter coordinates x y to detector millimeter coordinates (= coordinates of detector positioned as it now is).

mode

Syntax: mode log/square/equal/linear/sharp/jaap
Default: mode linear
Context: display
Set display mode.
Also available in menu mode.
The sharp value can be set with sharp. The jaap values can be set with jaap.

mode square
Syntax: mode square
Set square colour scheme.
Delta = maximum - minimum) / (maxcolour*maxcolour).

Level  Value
  1    minimum
  2    level1 + Delta
  3    level2 + 3*Delta
  4    level3 + 5*Delta
  5    level4 + 7*Delta
etc

mode equal
Syntax: mode equal
Set equal colour scheme. Each level will have an equal number of pixels.

mode linear
Syntax: mode linear
Set linear colour scheme.
Delta = (maximum - minimum) / maxcolour.

Level  Value
  1    minimum
  2    minimum +   Delta
  3    minimum + 2*Delta
  4    minimum + 3*Delta
  5    minimum + 4*Delta
etc

mode log
Syntax: mode log
Set logarithmic colour scheme.
Delta = ln(maximum / minimum)/maxcolour.

Level  Value
  1    minimum
  2    minimum*exp(Delta)
  3    minimum*exp(2*Delta)
  4    minimum*exp(3*Delta)
  5    minimum*exp(4*Delta)
etc

mode sharp
Syntax: mode sharp
Set colour scheme. Sharp value can be set with sharp.
f = (maximum - minimum)**(1-sharp)
Delta = (maximum - minimum+1) / maxcolour

Level  Value
  1    minimum
  2    minimum + (f*Delta)**sharp
  3    minimum + (2*f*Delta)**sharp
  4    minimum + (3*f*Delta)**sharp
  5    minimum + (4*f*Delta)**sharp
etc

mode jaap
Syntax: mode jaap
Set colour scheme. m1 is set to jaap1*mean. m2 is set to jaap2*mean. See jaap for the values of jaap1 and jaap2. Between m1 and m2 a linear colour scheme is used. All pixels larger than the m2 will be coloured with the highest colour.
Delta = (m2 - m1) / maxcolour.
```
Level  Value
  1    m1
  2    m1 +   Delta
  3    m1 + 2*Delta
  4    m1 + 3*Delta
  5    m1 + 4*Delta
etc
```

monitor

Syntax: monitor option value
Default:monitor clear
Context: info
Controls more or less output while reading image headers.

monitor add what
adds what to the monitor list. The header lines corresponding to what will be echoed to the screen together with derived values.
monitor clear
Remove all monitors.
monitor remove what
Removes what from the monitor list
monitor print
prints the monitor list

The value of what depends on the image-header-type. A list of possible what's can be obtained by reading an image with output read full.

mosaic

Syntax: mosaic f
Default:mosaic -1
Context: hkl
Sets the mosaicity to f. This will change the behaviour of the datcol command. Instead of drawing square boxes on impact positions, it will draw circles (with size shapesizea in colour shapecolour). A circle is drawn if the reflection is within duration*f degrees of the current frame.
Use a negative value for f to disable mosaic

netint

Syntax: netint state
Default: netint off
Context: intensity, profile
Set/unset the calculation of intensities in profiles.
The intensity is based on a B(ackground)P(eak)B(ackground) model. If state=off netint calculations are disabled.
If state=on the calculation depends on the setting of bpbfixed. If bpbfixed=on, the positions of left and right background are calculated from the value of bpbfraction, otherwise these positions are calculated from the profile itself. In this case, no intensity is given if the left or right side of the profile can not be found or if the intensity is less than the value specified by weak. Use profilecolour netint to set the colour of the background positions in the profile window. The amount of output is controlled by output misc.

The values of netint can be written to a file. Specify the file with netintfile, start writing with netintopen or netintappend and finish with netintclose.

netintappend

Syntax: netintappend
Context: files
Opens the netint file. If the file does not exist, it will be created. A warning (see abort) will be given if the file cannot be created.
Set the filename with netintfile. Close the file with netintclose.
Related command: netintopen.

netintclose

Syntax: netintclose
Context: profile, files
Close the netint output file (created with netintopen).

netintfile

Syntax: netintfile file
Default: netintfile netint.txt
Context: files
Set the netint filename to file. Use netintopen to create the file.

netintopen

Syntax: netintopen
Context: files
Creates the the netint file. A warning (see abort) will be given if the file cannot be created.
Set the filename with netintfile. Close the file with netintclose.
Related command: netintappend.

Syntax: next
Context: read
Reads the next image. The end value of the rotation angle of the previous frame is checked against the start value of the new frame. If the difference is nonzero, a warning (see abort) is given if checknext=on.

Related commands: frame, read, nextadd, nextsub, nextwait.
Also available in menu mode.

nextadd

Syntax: nextadd
Context: read
Adds the next image to the current one. Before adding, the pixel values will be multiplied by addfactor.
The end value of the rotation angle of the previous frame is checked against the start value of the new frame. If the difference is nonzero, a warning (see abort) is given if checknext=on.
Related commands: next, nextaddwait, nextsub.

nextaddwait

Syntax: nexaddwaitt
Context: read
Waits for the next image and add this one to the current one.
The end value of the rotation angle of the previous frame is checked against the start value of the new frame. If the difference is nonzero, a warning (see abort) is given if checknext=on.
Related commands: nextadd, nextsub.

nextscan

Syntax: nextscan
Context: read
Read the first image of the next scan. (i.e. the result of s04f0123 will be s05f0001).
Related commands: read, prevscan, nextscanwait.

nextscanadd

Syntax: nextscanadd
Context: read
Read the first image of the next scan. (i.e. the result of s04f0123 will be s05f0001) and add the content to the current data.

nextscansub

Syntax: nextscansub
Context: read
Read the first image of the next scan (i.e. the result of s04f0123 will be s05f0001) and subtract the content from the current data.

nextscanwait

Syntax: nextscanwait
Context: read
Waits for the same image of the next scan and reads it.
Related commands: nextscan.

nextsub

Syntax: nextsub
Context: read
Subtracts the next image to the current one. Before subtracting, the pixel values will be multiplied by subfactor.
The end value of the rotation angle of the previous frame is checked against the start value of the new frame. If the difference is nonzero, a warning (see abort) is given if checknext=on.
Related commands: next, nextadd.

nextsubwait

Syntax: nextsubwait
Context: read
Waits for the next image and subtracts the it from the current one. Before subtracting, the pixel values will be multiplied by subfactor.
The end value of the rotation angle of the previous frame is checked against the start value of the new frame. If the difference is nonzero, a warning (see abort) is given if checknext=on.
Related commands: next, nextadd.

nextwait

Syntax: nextwait
Context: read
Wait for the next image and read it.
The end value of the rotation angle of the previous frame is checked against the start value of the new frame. If the difference is nonzero, a warning (see abort) is given if checknext=on.
Related commands: next, nextadd, nextsub.

nodark

Syntax: nodark
Context: read
Disable subtracting of dark data.

nodetectorshift

Syntax: nodetectorshift
Context: detector
Subtract the accumulated values of detectorshift from the detector position parameters (but see the remark at circlefit).

noglobalmax

Syntax: noglobalmax
Context: constants
Disable globalmax.

nooverrule

Syntax: nooverrule variable
Context: header
Disable overrule commands. variable is one of dxstart thetastart omegastart kappastart chistart phistart exposuretime integrationtime alpha1 alpha2 alpharatio omegarange kapparange chirange phirange.

norespons

Syntax: norespons
Context: read
Disable correction with responsdata data.
Related commands: respons, responsread.

normat

Syntax: normat
Context: hkl, rmat
Disable a lattice. See rmat. You may add a number to the command (i.e. normat2. Use normatall to remove all available matrices.

output

Syntax: output option value
Default:output normal
Context: miscellaneous
Controls more or less output.
option is one of box circle convert datcol misc peak plot profile read x zoom
value is on of none normal full debug

option	normal	full	debug
badmask	badmaskfill	bad mask actions: beamstop, box, circle, corner, column, row	changes in badmaskstatus, trace of routine badmaskagain
box	file open and close	datcol pointers	respons correction, trace, box database
circle	nothing	per circle results for circlesum, intermediate results for cirlefit		complete circlefit process
convert	nothing	mm/pixel conversion	pixel/window conversion
datcol	range changes, theta changes	range calculation, theta calculation	pointers, matrices, rejected reasons, full hkl listing
misc		limits, shape netint
peak	useful peaks	rejected peaks	gravity search, one by one accept, rmat fit
plot	nothing	active window change, prepare, pointers	pointers per colour, durationarc, colourtable, drawline
profile
range	badpixel replacement, read, dark subtraction	extremes	extremes
read	badpixel replacement, read, dark subtraction	badpixel load, read, goniostat changes	distorpol, detalign, goniostat matrices
respons	read of respons image
x	nothing	window close, init, window open	menu creation, window setup, menu update
zoom	section dimensions, zoomfactor	window dimensions, prepare, extremes

If you not specify an option, the value will be set for all options.

overrule

Syntax: overrule variable value
Context: header
The values supplied in some types of image headers are non-trust-able. Use the overrule command to set the correct values.
variable is one of alpha1 alpha2 alpharatio chirange chistart dxrange dxstart exposuretime integrationtime kapparange kappastart omegarange omegastart overflow phirange phistart pixelxsize pixelysize polarisation rotateframe smartdatatype target thetarange thetastart
Use nooverrule arg to switch off overrules.
If you specify no arguments to overrule the current overrules will be shown.

alpha1
Set a fixed wavelength to value (in Å).
Related command: lambda.
alpha2
Set a fixed wavelength to value (in Å).
Related command: lambda.
alpharatio
Set a fixed wavelength to value (in Å).
Related command: lambda.
chirange
Set the increment of the chiscan to value (degrees).
chistart
Set the startvalue of chi to value (degrees).
dxrange
Set the increment of the dxscan to value (degrees).
dxstart
Set detectordistance to value (in mm).
Related command: dist.
exposuretime
Set a fixed exposuretime to value (in seconds).
Related commands: tolerance, boxcheck.
integrationtime
Set a fixed integrationtime to value (in seconds).
integrationtime is never used. The value is passed through the boxfiles.
kapparange
Set the increment of the kappascan to value (degrees).
kappastart
Set the startvalue of kappa to value (degrees).
omegarange
Set the increment of the omegascan to value (degrees).
omegastart
Set the startvalue of omega to value (degrees).
overflow
Set the overflowlevel to value (degrees).
phirange
Set the increment of the phiscan to value (degrees).
phistart
Set the startvalue of phi to value (degrees).
pixelxsize
Set the horizontal pixel size to value (micrometer).
pixelysize
Set the vertical pixel size to value (micrometer).
polarisation
Set the polarisation to value (string).
rotateframe
This will not overwrite a header value, but allows rotation of the images with respect to the detector-normal, while they are read, thus interchanging horizontal and vertical pixels. The number of horizontal and vertical pixels will be interchanged. Useful if the detector and goniostat have been rotated with respect to the laboratory system. rotateframe -1 is a counterclockwise rotation. rotateframe 1 is a clockwise rotation. Any other value corresponds to no rotation.
smartdatatype
A nonzero value forces the data type of smart images (when written) to u16. A zero value allows the writing routines to select u8, u16 or u32 whichever gives the smallest imagefile.
target
Set the target material (Mo, Cu or Ag). This will ignore target names AND wavelengths from the header.
thetarange
Set the increment of the thetascan to value (degrees).
thetastart
Thetastart is the start value of theta. Swing will be evaluated as 2*thetastart. Related command: swing.

Note, values will only be overruled if they are encountered in the header of the image. If, for example, the command overrule omegarange 1.0 is given, and the image is part of a phiscan, the overruled value for omegarange will not be used.

p2h

Syntax: p2h px py
Context: hkl
Stores: horpx verpx hormm vermm
You enter px py (in pixels). view shows the reflection indices for that impact position. The fit is controlled by round, fitmm and fitrot.
Also available in menu mode (where it is called HKL).

Related command: fp2h.

p2m

Syntax: p2m px py
Context: conversion
Stores: horpx verpx hormm vermm
Convert pixels to mm. Pixels are expressed as integers. The resulting coordinate is stored (via addeval) in hormm and vermm The resulting coordinate is also stored (via addeval) in horpx and verpx
Related command: fp2m.

patch

Syntax: patch px1 py1 px2 py2 v
Context: read
Fill the pixels in the area from px1 py1 to px2 py2 with v. This can be usefull to mark some pixels as bad, by setting their value to something below the badresponsthreshold.

part

Syntax: part ll/lr/ur/ul/centre/left/right/up/low
Default:part ll
Context: display
If an image is too big for the window only a part of the image will be displayed. You may select which part. The options are

option	part
ll	Lower Left
lr	Lower Right
ur	Upper Right
ul	Upper Left
centre	Centre
left	Left side
right	Right side
up	Top side
low	Bottom side

You can also use ll to specify the pixel coordinates of the lower left of the displayed part or change the value of plotbin.

peak2

Syntax: peak2
Context: peak
Search for peaks in one frame. Peaksearch is controlled by the variables peaksizemm, peakareamm, peaknr, peakmin, peakmax and peakbreak.
Found peaks are plotted with peakcolour found.
Peaks are rejected if:

weak
See the view peak search description when a peak is considered observed or weak.
duration > durationmax
theta < thetamin
theta > thetamax
theta in one of the forbidtheta ranges or resolution in one of the forbidreso ranges.
peak position is behind beamstop (See the Beamstop Page)
one or more badpixels are found in the peakarea (See the Badmask Page)
peak fits rmat and peakfit=on.
peak does not fit rmat and peakfit=off.

Rejected peaks are plotted with peakcolour bad. Rejected peaks will be printed if output peak=full.

After evaluation of a peak, the area in the image around the peak with dimensions peakareamm will be set to zero.

The peaksearch continues until peaknr peaks have been found, or when peakbreak successive weak peaks have been found.

Create output files with peakfile, peakopen and peakclose.
Use peakrmat, fitmm, fitrot, round and peakfit to do a peak search in combination with a rmat.
Use peak3 to do a peak search on multiple images.

peak3

Syntax: peak3
Context: peak
Search for peaks in more images. Use peakstart to initialise the peaksearch for a new set of images.

Consider a box with dimensions peaksizemm around a maximum. The minimum value within this box (or the value specified with peakmin if this is larger) will be subtracted from al pixels in the box. The sum is defined as the sum of the pixel values in this box. The smallsum is defined as the sum of the central pixel and the eight neighbouring pixels.
Peaks are rejected if:

weak
See the view peak search description when a peak is considered observed or weak.
duration > durationmax
theta < thetamin
theta > thetamax
theta in one of the forbidtheta ranges or resolution in one of the forbidreso ranges.
peak position is behind beamstop (See the Beamstop Page)
one or more badpixels are found in the peakarea (See the Badmask Page)
peak fits rmat and peakfit=on.
peak does not fit rmat and peakfit=off.

Rejected peaks are plotted with peakcolour bad. Rejected peaks will be printed if output peak=full.

If a peak is found:

Store peak information. Plot with peakcolour possible.
Read next image.
Evaluate the intensity at the stored positions.
- Increase: store new peak information. Plot with peakcolour improving.
- Decrease: if the saved peak was on the first image, ignore it. (plot with peakcolour first) otherwise the stored peak is a good peak (plot with peakcolour found).
goto step 2

The peaksearch continues until peaknr peaks have been found, or when peakbreak successive weak peaks have been found.
If a peak was found, the program will not find a new peak at the same position for the next peakremove degrees (plot with peakcolour ignored).

After evaluation of a peak, the area in the image around the peak with dimensions peakareamm will be set to zero.

Create output files with peakfile, peakopen and peakclose.
Use peakrmat, fitmm, fitrot, round and peakfit to do a peak search in combination with a rmat.
Use peak2 to do a peak search in one image.

peakareamm

Syntax: peakareamm f
Default: peakareamm -1
Context: peak
After a peak has been evaluated, the area around the peak in the image with dimensions f will be set to zero (so no more peaks will be found within this area).
If f is negative, the value of peaksizemm will be used.

peakbg

Syntax: peakbg f
Default: peakbg 3.0
Context: peak
See the view peak search description when a peak is considered observed or weak.
Related commands: peakbg2, peakbg3.

peakbg2

Syntax: peakbg2 f
Default: peakbg2 3.0
Context: peak
See the view peak search description when a peak is considered observed or weak.
Related commands: peakbg, peakbg3.

peakbg3

Syntax: peakbg3 f
Default: peakbg3 100.0
Context: peak
See the view peak search description when a peak is considered observed or weak.
Related commands: peakbg, peakbg2.

peakbreak

Syntax: peakbreak n
Default: peakbreak 30
Context: peak
Stop searching for peaks (peak2 or peak3) if n successive weak peaks have been found.

peakchi

Syntax: peakchi
Context: peak
Used for phi/chi scans. First read the phi scan. Do a peak search with peak2. Then read the corresponding phi/chi scan. Plot the peakpositions (of the phiscan) with peakmark. The command peakchi will plot the chi-arcs around the peak positions in colour peakcolour chi. The width of the chi-arc can be set by peakchiwidth.
See also the view phi/chi description
Related command: peakchifile

peakchifile

Syntax: peakchifile file
Context: files, peak
Used for phi/chi scans. Reads peak information from file (this file should contain peak information of the phi scan). A warning (see abort) will be given if the file cannot be opened.
Read the corresponding phi/chi scan. Plot the peakpositions (of the phiscan) with peakmarkfile file. The command peakchifile file will plot the chi-arcs around the peak positions in colour peakcolour chi. The width of the chi-arc can be set by peakchiwidth.
See also the view phi/chi description
Related command: peakchi

peakchiwidth

Syntax: peakchiwidth n
Default: peakchiwidth 4
Context: peak
Sets the width (in pixels) of the chi-arcs drawn by the commands peakchi and peakchifile.

peakclose

Syntax: peakclose
Context: peak, files
Close a peak output file. Use peakopen to create the file.

peakcolour

Syntax: peakcolour option colourname
Context: colour
Sets peak colours.

option	default	description
bad	red	weak, bad theta, bad duration...
chi	yellow	Colour of chi arc in peakchi and peakchifile
first	cyan	first image of a peak3 search
fit	steelblue	fitting/notfitting a peakrmat matrix
found	green	accepted in peak2 and peak3. also peakmark peakmarkfile peakmarkthisfile.
ignored	forestgreen	within peakbreak images of a previous peak
improving	cyan	improving peak in peak3 search
possible	yellow	promising peak in peak3 search

peakcolour may be abreviated to pc.

peakfile

Syntax: peakfile file
Default: peakfile scan.pk
Context: peak, files
Specifies the name of a peakfile. See peakopen and drxpk.
The filetype is .pk. The format is pk format.

peakfit

Syntax: peakfit state
Default: peakfit off
Context: peak
If state=on, new peaks have to fit to the lattice specified with peakrmat. If state=off, new peaks may not fit to the lattice specified with peakrmat.
Related commands: fitmm, fitrot.

peaklabel

Syntax: peaklabel n
Default: peaklabel 0
Context: peak
If nonzero, peaks (from peak2, peak3, peakmark, peakmarkfile, peakmarkfilesearch or peakmarkthisfile) will be labeled with the sequence number.
In the case of peakmarkfilesearch or peakmarkthisfile the labelvalue depends on n:

1: set the label to the sequence number in this frame
2: set the label to the number from the pk file

peakmark

Syntax: peakmark
Context: peak
Draws the stored peaks. These peaks are found by peak3.
Related commands: peakmarkfile, peakmarkthisfile.

peakmarkfile

Syntax: peakmarkfile file
Context: files, peak
Draws all the peaks from file. A warning (see abort) will be given if the file cannot be opened.
The filetype is .pk. The format is pk format.
Related commands: peakmark, peakmarkfilesearch, peakmarkthisfile.

peakmarkfilesearch

Syntax: peakmarkfilesearch file n
Context: files, peak
Extracts the image name for peak n from pkfile file. The image will be drawn, and peak n will be marked. You may want to use peaklabel to draw the n too. The filetype is .pk. The format is pk format.
Related commands: peakmarkfile. peakmarkthisfile

peakmarkthisfile

Syntax: peakmarkfile file
Context: files, peak
Draws the peaks from file. A warning (see abort) will be given if the file cannot be opened.
Only peaks found in the current image will be plotted. The filetype is .pk. The format is pk format.
Related commands: peakmark, peakmarkfile, peakmarkfilesearch.

peakmax

Syntax: peakmax n
Default: peakmax -1
Context: peak
Do not search peaks above the given value. A negative value will set peakmax to the maximum of the image.

peakmin

Syntax: peakmin n
Default: peakmin 30
Context: peak
Do not search peaks below the given value. peakmin is also used for the determination of weak peaks (See view peak search description).

peaknr

Syntax: peaknr n
Default: peaknr 5
Context: peak
Sets maximum number of peaks to search for the commands peak2 and peak3.

peakopen

Syntax: peakopen
Context: peak, files
Creates a peak output file. A warning (see abort) will be given if the file cannot be created.
The format is pk format. The commands peak2 and peak3. will write peak information to this file. Specify the filename with peakfile. Close the file with peakclose. See also drxpk.

peakremove

Syntax: peakremove d
Default: peakremove 1.0
Context: peak
Once a peak has been found, the same location will be ignored during the next d degrees. Used with peak3. The ignored areas are plotted with peakcolour ignored.

peakrmat

Syntax: peakrmat n/all/none
Default: peakrmat none
Context: hkl, peak, rmat
Specifies which rmat should be used in conjunction with a peak search.

command	description
peakrmat 1	use rmat1
peakrmat 2	use rmat2
peakrmat all	use all available rmat's
peakrmat none	no rmat used

Use peakfit to specify whether a peak has to fit or may not fit to the specified peakrmat. Use round, fitmm and fitrot to set the fit parameters.

peaksizemm

Syntax: peaksizemm f
Default: peaksizemm 1.2
Context: peak
Sets the size of a box around a peak to f. peaksizemm is used for determining whether a peak is weak or not (See view peak search description).
Related command: peakareamm

peaksmallsize

Syntax: peaksmallsize n
Default: peaksmallsize 1
Context: peak
Sets the size of a central part of a peak to n. (See view peak search description)

peakstart

Syntax: peakstart
Context: peak
Initialises the peak information arrays for peak3.

peakstatus

Syntax: peakstatus
Context: peak
Print the number of peaks in the peak arrays (peak3) and the number of peaks in the pkfile (peakopen) and diraxfile (diraxopen).

permutate

Syntax: permutate n
Context: detector
view tries to extract to position of the primary beam from the header of the image. Two offsets are used, and it is not always clear how these offsets are defined (+/- hor, +/- ver). This command draws all 8 permuations. You select the correct one. You may want to use save detalign to save the choice.
Related commands: detectoroffset, markprimary

pg

Syntax: pg s
Context: hkl, rmat
Sets the point group to s. The default pointgroup is extracted from the rmat file. If no pointgroup information is available, an educated guess based on the cell parameters is done.
overview of point groups.
You may add a number to the command (i.e. pg2) to specify the pointgroup for a different lattice. A warning (see abort) will be given if the matrix is not available. Use pgall to change all available lattices. The reflection relations will be printed with output misc normal.
Related command: laue.

pickcolour

Syntax: pickcolour colourname
Default: pickcolour gold
Context: colour
Set colour for echo of mouse-picking in menu mode.

plane

Syntax: plane f1 f2
Default: plane 2.5 2.5
Context: processing
Calculates least-squares plane through whole image. If a pixelvalue lies outside f1*SigmaPlane, the pixel is excluded from the plane calculation. The whole procedue is repeated until less than 4 pixels are excluded.
Then, if the observed value is less than the calculated value plus f2*SigmaPlane, the value is set to zero.

plot

Syntax: plot
Context: display
Draw a picture in the last activated window. Use refresh to redraw a picture.
Also available in menu mode.

plotbin

Syntax: plotbin n
Default: plotbin 0
Context: display
Sets the binning for the displayed image. A value of zero (the default) triggers autobinning (the binning value will be calculated from the image dimensions and the window dimensions). A nonzero value overrides this calculation. If the (binned) image is too big for the window, only a part of the image will be shown. You may select which part with part and ll.

polarplot

Syntax: polarplot perpendicular/parallel/antiparallel/none/synchrotron/synchrotronz/osmic
Context: test
Calculates and plots the polarisation with the current detector settings. The values are multiplied by 100. You may want to change the value of polarquotient for the synchrotron and synchrotronz polarisation types.
(After using the polarplot command, you have to reread the image.)

polarquotient

Syntax: polarquotient f
Context: box, test
Sets the quotient Weak/Strong for the polarisation of the synchrotron and synchrotronz types. The polarisation type is set by the information in the image header.

Normal2 = X-axis*Normal1
Polar = 1/(1+PolarQuotient)

Polarisation Type	Normal1	Normal2	Quotient
none	0 1 0	0 0 1	1.0
synchrotron	0 1 0	0 0 1	5.0/95.0 = 0.05263 (This value will be set by polarquotient)
synchrotronz	0 0 1	0 1 0	5.0/95.0 = 0.05263 (This value will be set by polarquotient)
osmic	0 1 0	0 0 1	1.0
perpendicular	0 0 1	0 1 0	(cos(2*ThetaMonochromator))^2 = 0.95706
parallel	0 1 0	0 0 1	(cos(2*ThetaMonochromator))^2 = 0.95706
antiparallel	0 1 0	0 0 1	(cos(2*ThetaMonochromator))^2 = 0.95706

The polarisation is only used by the polarplot command. The value of polarquotient is propagated to boxfiles.

prad

This is short for profilerad.

prepare

Syntax: prepare
Context: test
Force interpretation of image. Result is an array containing x and y coordinates sorted on intensity. Plot will invoke prepare if necessary.

Syntax: prev
Context: read
Reads the previous image.
Related comands: prevadd, prevsub.
Also available in menu mode.

prevadd

Syntax: prevadd
Context: read
Adds the previous image to the current one. Before adding, the pixel values will be multiplied by addfactor.
Related commands: prev, prevsub.

prevscan

Syntax: prevscan
Context: read
Reads the first image of the previous scan. (i.e. the result of s04f0123 will be s03f0001)

prevscanadd

Syntax: prevscanadd
Context: read
Read the first image of the previous scan (i.e. the result of s04f0123 will be s03f0001) and add the content to the current data.

prevscansub

Syntax: prevscansub
Context: read
Read the firstimage of the previous scan (i.e. the result of s04f0123 will be s03f0001) and subtract the content from the current image.

prevsub

Syntax: prevsub
Context: read
Subtracts the previous image from the current one. Before subtracting, the pixel values will be multiplied by subfactor.
Related commands: prev, prevadd.

primarybeamcolour

Syntax: primarybeamcolour colourname
Default: primarybeamcolour blue
Context: colour
Set primary beam colour. Use markprmary to draw the impact of the primary beam.

profile

Syntax: profile px1 py1 px2 py2
Context: profile
Display a line profile.
px1 py1 = starting point
px2 py2 = end point.
If |px2-px1| > |py2-py1| a horizontal profile will be calculated from px1,py to px2,py with py=(py1+py2)/2
otherwise the result will be a vertical profile from px,py1 to px,py2 with px=(px1+px2)/2.
Use profilegeneral to avoid this behaviour.
Also available in menu mode.

If netint is set, a net intensity is calculated. ( See bpbfixed, bpbfactor, netint, netintpx and weak).

profile2d

Syntax: profile2d
Context: files, profile
Save all following profiles in a 2-dimensional array. You can write this array to a file with profileno2d.

profilecolour

Syntax: profilecolour option colourname
Context: colour, profile
option is one of profile bg fg fit label netint width.
Sets profile colours.

option	default	description
profile	yellow	profile line in image window
bg	navyblue	background in profile window
fg	yellow	foreground in profile window
fit	red	fitted profile if profilefit=on
label	cyan	labels and axes in profile window
netint	magenta	peak bounderies in profile window
width	seagreen	profile width lines in image window

profileconnect

Syntax: profileconnect state
Default: profileconnect off
Context: profile
If on, profiles are drawn as a connected set of lines. If off, profiles are drawn in a histogram like shape.

profilefactor

Syntax: profilefactor f
Default: profilefactor 1.0
Context: profile
If profilenorm=on the tangential and radial profiles (profilerad, profiletang and profiletangrad) will be normalized and multiplied with f.

profilefit

Syntax: profilefit state
Default: profilefit off
Context: profile
If on, a gaussian will be fitted into profiles.

y = Baseline + Scale*exp( -(x-Mean)²/(2*Sigma²))
FWHM = 2.3548*Sigma

The values of Scale, Mean, Sigma, Baseline and FWHM will be printed.
The fitted profile will be plotted in the profile window with profilecolour fit, together with the Full-Width line at Half-Maximum.

profilegeneral

Syntax: profilegeneral x1 y1 x2 y2
Context: profile
Display a general profile.
x1 y1 = starting point
x2 y2 = end point.
Use profilegeneralwidth to set the width of the profile in mm. You can rotate the profile endpoints around the centre of the profile with profilegeneralrot. See profilenorm to control the normalization of the profile.

If netint is set, a net intensity is calculated. See bpbfixed, bpbfactor, netint, netintpx and weak.

profilegeneralpick

Syntax: profilegeneralpick state
Default: profilegeneralpick off

off. If profiles are drawn using the profile button, calculate horizontal/vertical profiles, similar to profile.
on. If profiles are drawn using the profile button, calculate general profiles, similar to profilegeneral.

profilegeneralrot

Syntax: profilegeneralrot d
Context: profile
Rotate the start and end points of a profilegeneral around the centre of the profile. The rotation is counter-clockwise.

profilegeneralwidth

Syntax: profilegeneralwidth x
Default: profilegeneralwidth 5.0
Context: profile
Set the width for profilegeneral.

profilehalf

Syntax: profilehalf
Context: profile
Draws a profile halfway the detector.
Also available in menu mode.

profilehor

Syntax: profilehor
Context: profile
Show accumulated profile. A mean value is calculated for each column and the resulting (horizontal) set of numbers is displayed in the profile window.
Also available in menu mode.

profilemax

Syntax: profilemax n
Default: profilemax -1
Context: profile
Sets the maximum profile value. Only used if profiletype=fixed: if profilemax>profilemin both are used for scaling, otherwise set values of maximum and minimum are used.

profilemin

Syntax: profilemin n
Default: profilemin 0
Context: profile
Sets the minimum profile value. Only used if profiletype=fixed: if profilemax>profilemin both are used for scaling, otherwise set values of maximum and minimum are used.

profilemm

Syntax: profilemm x1 y1 x2 y2
Context: profile
Convert the mm coordinates x1 y1 x2 y2 to pixels and invokes profile.

profilemode

Syntax: profilemode linear/log
Default: profilemode linear
Context: profile
Sets the scaling mode of profiles.

profileno2d

Syntax: profileno2d
Context: files, profile
Writes 2d profile array to scan .cnt.
A warning (see abort) will be given if the file cannot be created.
You can start filling the array with profile2d.

profilenorm

Syntax: profilenorm state
Syntax: profilenorm on
Context: profile

state=on
All values in a radial or tangential profile (profilerad, profiletang and profiletangrad) will be divided by the number of contributing pixels (and multiplied with profilefactor.
All values in a profilegeneral will be divided by the number of contributing pixels.
state=off
Radial, tangential and general profiles consist of the brute sums of intensities only with no normalization.

profilenosc

Syntax: profilenosc
Context: files, profile
Close the scatter file created by profilesc.

profilenoxy

Syntax: profilenoxy
Context: files, profile
Close the x-y file created by profilexy.

profilerad

Syntax: profilerad r1 r2 t1 t2
Context: profile
Create a radial profile.
r1 = minimum radial value (i.e. 2theta)
r2 = maximum radial value
t1 = minimum tangential value (t1=0 is on top of display. The tangent moves counterclockwise)
t2 = maximum tangential value
Use profileradr to express r1 and r2 in Å (resolution).
Use profiletangchi to eliminate pixels in a bad chi region. Use profilenorm to set the normalization of the profile. If areafixed=off the pixel values will be divided by the effective pixel area.
Related commands: profiletang, profiletangrad.

profileradr

Syntax: profileradr r1 r2 t1 t2
Context: profile
Similar to profilerad but with r1 r2 expressed in Å (resolution) instead of 2theta.

profileradtang

See profiletangrad.

profileradtangr

See profiletangradr.

profilesc

Syntax: profilesc
Context: files, profile
Create a profile scatter file. A warning (see abort) will be given if the file cannot be created.
The filename can be set with scatterfile. Subsequent profiles are copied to this file.
The format is: pixhor pixhor mmhor mmver ang value sum

variable	description
pixhor	horizontal pixel
pixver	vertical pixel
hor	horizontal coordinate in mm
ver	vertical coordinate in mm
ang	angle between primary beam and outray through hor,ver
value	value at pixhor,pixver
sum	sum of values in one column/row

Use profilenosc to close the file.

profiletang

Syntax: profiletang r1 r2 t1 t2
Context: profile
Create a tangential profile.
r1 = minimum radial value (i.e. 2theta)
r2 = maximum radial value
t1 = minimum tangential value (t1=0 is on top of display, behind beam stop. The tangent moves counterclockwise)
t2 = maximum tangential value
Use profiletangr to express r1 and r2 in Å (resolution).
Use profiletangchi to eliminate pixels in a bad chi region. Use profilenorm to set the normalization of the profile. If areafixed=off the pixel values will be divided by the effective pixel area.
Related commands: profilerad, profiletangrad.

profiletangchi

Syntax: profiletangchi d
Default: profiletangchi 90
Context: profile
Specify the chimax value to eliminate pixels in profiletang. The default value will include all pixels.

profiletangfull

Syntax: profiletangfull
Context: profile
Executes: profiletangrad r1 r2 3.0 357 with r1=2*thmin and r2=2*(minimum theta on the edges of the image).

profiletangr

Syntax: profiletangr r1 r2 t1 t2
Context: profile
Similar to profiletang but with r1 r2 expressed in Å (resolution) instead of 2theta.

profiletangrad

Syntax: profiletangrad r1 r2 t1 t2
Context: profile
Create a radial and a tangential profile.
r1 = minimum radial value (i.e. 2theta)
r2 = maximum radial value
t1 = minimum tangential value (t1=0 is on top of display, behind beam stop. The tangent moves counterclockwise)
t2 = maximum tangential value
Use profiletangradr to express r1 and r2 in Å (resolution).
Use profiletangchi to eliminate pixels in a bad chi region. Use profilenorm to set the normalization of the profile. If areafixed=off the pixel values will be divided by the effective pixel area.
Related commands: profilerad, profiletang.
Also available in menu mode.

profiletangradr

Syntax: profiletangradr r1 r2 t1 t2
Context: profile
Similar to profiletangrad but with r1 r2 expressed in Å (resolution) instead of 2theta.

profiletickmm

Syntax: profiletickmm state
Default: profiletickmm on
Only used for horizontal/vertical profiles.

off. Horizontal labels in the profile window are pixel coordinates.
on. Horizontal labels in the profile window are mm coordinates.

profiletitle

Syntax: profiletitle text
Default: profiletitle
Context: profile
Sets a title for the profile window. The title will be drawn in the upper right corner of the window. You may include the following keywords surrounded by square brackets in the string.

Keyword	Source	Description
datetime	header	date and time
dist	header, dist	crystal to detector distance
exposuretime	header	image exposure time
gonioendn	header	(n=1,2,3) goniostat end angle
gonioend	header	3 goniostat end angles
goniostartn	header	(n=1,2,3) goniostat start angle
goniostart	header	3 goniostat start angles
goniostatn	header	(n=1,2,3) mean goniostat angle
goniostat	header	3 mean goniostat angles
hv	header	Generator High Voltage
image	read	image filename
ma	header	Generator Current
rotend	header	rotation end
rotinc	header	rotation increment
rotstart	header	rotation start value
rotvalue	header	mean rotation value
scan	read	imagefilename with scannumber
shortimage	read	image filename without filetype
swing	header, swing	detector swing angle
temperature	header	the (cryo) temperature
totalexposuretime	header	image total exposure time

profiletype

Syntax: profiletype free/fixed/global
Default: profiletype free
Context: profile
Set profile scaling.

free = automatic scaling.
global = scaling is done based on the values specified with minimum and maximum.
fixed = scaling is done based on the values specified with profilemin and profilemax.

Also available in menu mode.

profilever

Syntax: profilever
Context: profile
Show accumulated profile. A mean value is calculated for each row and the resulting (vertical) set of numbers is displayed in the profile window.
Also available in menu mode.

profilewidth

Syntax: profilewidth n
Default: profilewidth 15
Context: profile
Set profile width to n. The width of the profiles will be plotted with colour profilecolour width.

profilexy

Syntax: profilexy file
Default: profilexy image .x_y
Context: files, profile
Creates file. A warning (see abort) will be given if the file cannot be created.
The succeeding profilerad and profiletang profiles will be written to this file (Note, the double profile profiletangrad is not allowed). Close the file with profilenoxy.

ps

Syntax: ps file
Context: files
Creates a postscript file of the active window. (Use activate). The ps file is created using the import program of the ImageMagick program suite. A warning (see abort) will be given if the file cannot be created.
The filename depends on the selected window. image .ps, image profile.ps, image zoom.ps or image distor.ps. Use psframe to include or exclude the window frame in the plot.
Related commands: gif, jpeg.

psframe

Syntax: psframe state
Default: psframe on
Context: files
Includes the window frame in the ps command.

ptang

This is short for profiletang.

quit

Syntax: quit
Context: miscellaneous
Finish program. Alternatives: end, exit

qvp

Syntax: qvp n
Context: hkl, info
Valid only if qvectors are defined. n is a qvector pointer (pointing to a qvector combination; see the description of a rmat file). view will print the qvector combination and the resulting (floating) hkl indices.
Select hklmatrix if multiple matrices are defined.
Use qvprint to print all qvector pointers.

qvpoff

Syntax: qvpoff list
Context: hkl
Disables a set of qvector pointers. Valid only if qvectors are defined. Enter a list of qvector pointers (pointing to a qvector combination, see the description of a rmatfile).

argument	description
all	all qvector pointers
n	qvector pointer n
: n	all qvector from last selected until n
:	all remaining qvector pointers

Select hklmatrix if multiple matrices are defined.
Use qvpon to activate a set of qvector pointers.

qvpon

Syntax: qvpon list
Default: qvpon all
Context: hkl
Activates a set of qvector pointers. Valid only if qvectors are defined. Enter a list of qvector pointers (pointing to a qvector combination, see the description of a rmatfile).

argument	description
all	all qvector pointers
n	qvector pointer n
: n	all qvector from last selected until n
:	all remaining qvector pointers

Select hklmatrix if multiple matrices are defined.
Use qvpoff to disable a set of qvector pointers.

qvprint

Syntax: qvprint Context: hkl, info
Prints the set of qvector pointers. Use qvpon and qvpoff to define a selection.
Select hklmatrix if multiple matrices are defined.
Use qvp to print one qvector pointer.

radial

Syntax: radial margin size maxfrac subfrac
Default: radial 20 125 0.5 0.9. Context: processing
Determine a radial background around PrimaryBeam. margin is the number of pixels excluded from the edges of the image. A radial profile (with size elements) is calculated using pixels less than maxfrac*maximum. The profile will be drawn. Then subfrac*PROFILEVALUE is subtracted from each pixel.

raise

Syntax: raise 1/2/zoom/profile/distor/menu
Context: window
This command will pop up the selected window. Synonymous with map.
Related commands: icon, unmap.

read

Syntax: read file
Context: read

Read data from file.
See imagefiletype for the default file types.
If responsread has been called, the appropriate responsfile will be read if necessary, and the image will be reread.
If the file badmask.vic is found in the calibration directory, the commands in this file will be executed after reading the first image.
If the ID of the distortionfile (distorpol.vic) differs from the imageheader detectorid, the distortionfile will be loaded from the calibration directory.
If the ID of the detector alignmentfile (detalign.vic) differs from the imageheader detectorid, the alignmentfile will be loaded from the calibration directory.
If badpixel=on and the ID of the badpixel files(badpixel.*) differ from the imageheader detectorid, the badpixel files will be loaded from the calibration directory.
If the ID of the beamstopfile (beamstop.vic) differs from the imageheader detectorid, the beamstopfile will be loaded from the calibration directory.
If the ID of the goniostatfile (goniostat.vic) differs from the imageheader detectorid, the goniostatfile will be loaded from the calibration directory.
If file .vic exists, it will be excuted after the image has been read.
If a dark image has been read, it will be subtracted from the new image.
If badpixels are available, the image is corrected for them.
If the file view.post exists, it will be executed after the image has been read.
If the file image .vic exists, it will be executed after the image has been read.

The following aliases are created:

alias	description
NX	number of horizontal pixels
NY	number of vertical pixels
HX	'NX'/2
HY	'NY'/2
scan	scan

Use 'alias' to use these aliases. (see alias substitutions).
Related commands: dark, frame, next, prev, readadd, readsub, readwait, trydark, wait, and zinger.

readadd

Syntax: readadd file
Context: read
Read data from file and add them to the current data. Before adding, the pixel values will be multiplied by addfactor.
Related commands: read, readsub.

readsub

Syntax: readsub file
Context: read
Read data from file and subtract them from the current data. Before subtracting, the pixel values will be multiplied by subfactor.
Related commands: read, readadd

readwait

Syntax: readwait file
Context: read
Wait for file and read data from file.
Related commands: read, wait.

redirect

Syntax: redirect screen/file
Default: redirect screen
Context: files
Write all output to file (append if file already exists). A warning (see abort) will be given if the file cannot be created.
Use redirect screen to direct output to screen.

refresh

Syntax: refresh
Context: display
Redraws the current window, as if it was picked by the shift-left-mouse button. This will result in a clean picture (profile lines, zoom boxes, circles and gridlines are removed). refresh works much faster than plot.
Related command: autorefresh

reset

Syntax: reset option
Context: miscellaneous
initialise some variables. options is one of all circle colour data detalign detector dirax distor fibre hkl image misc peak profile view xlib zoom.

resocorner

Syntax: resocorner
Context: info
Prints resolution values of the four corners of the image. and sets resomax to the maximum of the four values.
Related commands: resohalf, thhalf, thcorner.

resohalf

Syntax: resohalf
Context: info
Prints resolution values at the center of the four edges of the image and sets resomax to the maximum of the four values.
Related commands: resocorner, thhalf, thcorner.

resomax

Syntax: resomax f
Context: constants
Specify the maximum resolution (in Å). Used by peak2, peak3 and datcol. The resolution circle will be drawn in circlecolour.
Related commands: resomin, thmax, thmin.

resomin

Syntax: resomin f
Context: constants
Specify the minimum resolution (in Å). Used by peak2, peak3 and datcol. The resolution circle will be drawn in circlecolour.
Related commands: resomax, thmax, thmin.

respons

Syntax: respons
Context: processing
Correct the image for nonuniformity. The responsfile must have been read (see responsread). If you have read the responsfile, the correction for nonuniformity will be done automatically if you are writing boxfiles.
See the Detectors Page.

responsread

Syntax: responsread
Context: read
Reads the responsfile. The name of the respons file is respons target with target the name of the target material of the xray source (i.e. MO, CU).
view searches for the file in the calibration directory. If the file cannot be located, view tries to locate sensi detid with detid the id of the detector.
If the responsfile has been read successfully, view tries to locate the Incidence Correction file in the calibration directory.
The incidencefilename is target -incidence.coefficient or incidence.coefficient. If found, the first line of this file contains the incidence coefficient.

If an image has been read, the image will be reread; otherwise the execution of responsread will be postponed until the first image has been read.
You then may correct images for nonuniformity with respons. The correction for nonuniformity will be done automatically if you are writing boxfiles. Use norespons to disable respons correction.
See the Detectors Page.

rmat

Syntax: rmat file
Context: hkl, rmat
Default file type is .rmat The format is rmat format. Specify orientation matrix for cell parameters. You may add a number to the command (i.e. rmat2) to specify more lattices. A warning (see abort) will be given if the matrix number is illegal.
If trans=on, the rmatrix will be multiplied with the transformation matrix. Use normat to disable a lattice.

round

Syntax: round f
Default: round .3
Context: peak
An impact on the detector (detector coordinates combined with a rotation angle) can be expressed in relation to a rmat. In general the indices are floating numbers. The value of f determines if rounding will be applied to the floating indices. The (default) value of 0.3 will allow rounding of 5.19 and 4.81 to 5 but 5.31 will not be rounded.
Round is used in a peaksearch in conjunction with peakrmat, with m2h and on mouse clicks (if the menu option HKL is switched on).
Related commands: fitmm, fitrot, peakfit.

save

Syntax: save beamstop/circle/detalign/distorpol/goniostat/peak/profile/zoom [filename].
Syntax: save rmat nr filename.
Context: files

beamstop
Creates a file beamstop.vic with all beamstop related parameters. The file beamstop.vic will be loaded automatically at the next invocation of view (see calibration directory).
circle
Creates a file circlesetup.vic containing all circle related parameters.
detalign
Creates a file detalign.vic with commands describing the alignment of the detector. This file will be loaded automatically at the next invocation of view (see calibration directory).
distorpol
Creates a file distorpol.vic with commands describing the distortion correction of the detector. This file will be loaded automatically at the next invocation of view (see calibration directory).
goniostat
Creates a file goniostat.vic with commands describing the distortion correction of the detector. This file will be loaded automatically at the next invocation of view (see calibration directory).
peak
Creates a file peaksetup.vic containing all peak related parameters.
profile
Creates a file profilesetup.vic containing all profile related parameters.
rmat
Saves a rmatrix to a file. Specify the matrix number nr and the filename.
zoom
Creates a file zoomsetup.vic containing all zoom related parameters.

scaledark

Syntax: scaledark status
Default: scaledark on
Context: hkl
If scaledark=on, the dark subtraction will be scaled by the ratio of the exposuretime of the new image and the dark image.
Related commands: dark, read.

scanlength

Syntax: scanlength d
Default: scanlength 360
Context: hkl
The first call of datcol will create a list of reflections given the current settings of detector, cell, goniostat etc... The maximum length of this list is limited (i.e. 100,000 reflections). If there are too many reflections, the rotation range of the prediction will be shortened (it defaults to -180 to 180 degrees) and the generation of reflections will be repeated.
You may change the default values of scanlength to avoid the overflow of the generation process.

scatterfile

Syntax: scatterfile file
Default: scatterfile profile.scatter
Context: files
Sets the name of the scatterfile. The file will be created with profilesc and closed with profilenosc.

search

Syntax: search n
Context: info
Prints part of the sorted sorted array. This array is created by prepare and contains the data that will be plotted.
The format of the output is described at the examine command.
Related commands: display, examine.

setcolour

Syntax: setcolour n colourname
Context: colour
Set a colour. n is number between one and maxcolour. The changed colournames will be reset by the commands: grey, -grey, colour.

setprimary

Syntax: setprimary
Context: detector
Stores: horpx verpx hormm vermm
You left mouse click the position of the primary beam. New values for the detector aligment are calculated. You may want to use save detalign to save the new values for later use.

shade

This is an alias in view.init (see view start) for the following sequence of commands:
ajmd prepare minimum init mode equal grey plot

shape

Syntax: shape px py
Context: intensity
Stores: horpx verpx
Calculates intensities. Start with defining the shapeform and shapesize. A warning (see abort) will be given if shapeform=none.
If shapemaximum=on the intensity is determined around the local maximum around the provided coordinates. The figure will be plotted with shapecolour. The amount of output is controlled by output misc.
If shapeform is set, the intensity calculation is also done for all mouse clicks in menu mode.
Related command: shapemm.

shapeclean

Syntax: shapeclean state
Default: shapeclean off
Context: hkl
If on, and shapeform=circle the data wihtin the image will be changed. The central part, limited by shapesize, will be changed into the average background (determined by shapesize plus shapemargin.
This will also happen with the command if mosaic is set ta a positive value.
You may want to save the modified image with write.

shapecolour

Syntax: shapecolour colourname
Default: shapecolour cyan
Context: colour
Set colour for shape figures and the circles of datcol if mosaic is set to a non-negative value.

shapeend

Syntax: shapeend
Context: files, intensity
Write collected shape profiles to the file netint.pos. A warning (see abort) will be given if the file cannot be created.
Intermediate shape results are only stored for shapeform=loop.

shapeform

Syntax: shapeform best/box/circle/loop/none
Default: shapeform none
Context: intensity
Set form of shape figures.

best
Similar as loop (see below). The final intensity (and shape radius) is calculated from the loop results. The optimal values are those where the intensity change is less than 1%.
box
1. integrate a box of dimensions shapesizeA and shapesizeB around px py. N1 = nr of pixels, I1 = integrated intensity.
2. integrate a box of dimensions shapesizeA+1 and shapesizeB+1 around px py. N2 = nr of pixels, I2 = integrated intensity
3. BP = background/pixel = (I2-I1 / (N2-N1)
4. netint = I1 - N1*BP.
circle
1. integrate a circle if radius ShapesizeA around px py. N1 = nr of pixels, I1 = integrated intensity
2. integrate a circle of radius shapesizeA+1 around px py. N2 = nr of pixels, I2 = integrated intensity
3. BP = background/pixel = (I2-I1) / (N2-N1)
4. netint = I1 - N1*BP
loop
Same result as circle, but the intermediate numbers (circle radius from 1 to ShapesizeA) are printed. With this table you can select the proper value of ShapesizeA (where background/pixel becomes constant).
All shape loop results are stored. Use shapeinit to clear the storage. Use shapeend to write the stored data to file netint.pos.

If shapeform is set, the intensity calculation is also done for all mouse clicks in menu mode.

shapeinit

Syntax: shapeinit
Context: intensity
Clear the shape data array. The array is used to store intermediate results of shape, but only for shapeform=loop. Use shapeend to write the data to file.

shapemargin

Syntax: shapemargin n
Default: shapemargin 1
Context: intensity
If shapeform is not none, the background will be estimated by increasing the shapesize with n. The extra pixels and then assumed to be part of the background. An average background/pixel is calculated. This value will be used if shapeclean=on.

shapemaximum

Syntax: shapemaximum state
Default: shapemaximum off
Context: intensity
Used by the shape command or on mouseclicks (if shapeform is set).
If on, the intensity will be calculated around a local maximum in the neighbourhood of the provided coordinates.
If off, the actual position will be used.

shapemm

Syntax: shapemm x y
Context: intensity
Stores: horpx verpx hormm vermm
Calculates intensities. Start by defining the shapeform and shapesize. A warning (see abort) will be given if shapeform=none.
If shapemaximum=on the intensity is determined around the local maximum around the provided coordinates. The figure will be plotted with shapecolour. The amount of output is controlled by output misc.
If shapeform is set, the intensity calculation is also done for all mouse clicks in menu mode.
Related command: shape.

shapesize

Syntax: shapesize n
Default: shapesize 9. Context: intensity
Set size of shape figures. Both shapesizea and shapesizeb are set.

shapesizea

Syntax: shapesizea n
Default: shapesizea 9. Context: intensity
Set size of shape figures and the circles of datcol if mosaic is set to a non-negative value.

shapesizeb

Syntax: shapesizeb n
Default: shapesizeb 9. Context: intensity
Set size of shape figures.

sharp

Syntax: sharp f
Default: sharp 4.0
Context: constants
Sets the value for the mode sharp option. The default value is 4.0

show

Syntax: show all/beamstop/box/circle/colour/datcol/detpos/detector/fibre/goniostat/id/image/peak/profile/rmat/shape/zoom.
Syntax: show colour all/misc/datcol/fibre/menu/peak/profile/mat/map
Context: info
Display program parameters
Also available in menu.

showcell

Syntax: showcell
Context: info, rmat
Print rmat informaton. You may add a number to this command if you want to print other rmats. showcellA will print all available rmats.

smooth

Syntax: smooth
Context: processing
Smooth an image by averaging every pixel with ±smoothfactor neighbours.

smooth2

Syntax: smooth2
Context: processing
Smooth an image using the algoritm described by Sjolin and Wlodawer, Acta Cryst A37 1981 670-679.

smoothfactor

Syntax: smoothfactor n
Context: constants
Default: smoothfactor 0
Set factor smooth.

still

Syntax: still f
Default: still -1.0
Context: still
If positive, sets the epsilon threshold for still data to f. datcol will generate reflections if the absolute difference between η and θ is less than f.

stilltheta

Syntax: stilltheta f g
Default: stilltheta
Context: still
Decrease the epsilon threshold for still data with increasing theta. f is the stillvalue (in degrees) for theta = g. If f0 is the value as set by still, the epsilon threshold will be
f0 + theta*(f-f0)/g
For theta values larger than g, still will be set to f.

stilltype

Syntax: stilltype close/eta/flexible
Default: stilltype flexible
Context: still
Controlls the way outrays (and thus impact piositions) are calculated for still data.

close
outray_close = c - inray
eta
outray_η = rotate inray around c over 180 degrees
flexible
Calculate an outray with an angle of 2*θ with the primary beam:
- rotax = inray x c
- outray_θ = rotate inray around rotax over 180-2*θ
- f is the value of flex
- (1-f)*outray_η + f*outray_θ
- If f=0.0 the result coincides with the eta-impact.
- If f=1.0 the result coincides with the theta-impact.

See the still page of eval15

subfactor

Syntax: subfactor f
Default: subfactor 1.0
Context: read
When subtracting images (readsub, prevsub, nextsub, prevscansub and nextscansub) the pixel values of the new image will be multiplied by f.
Related command: addfactor.

swing

Syntax: swing d
Default swing 0
Context: detector
Enters detector swing angle in degrees. Value is normally extracted from image file.

thcorner

Syntax: thcorner
Context: info
Prints theta values of the four corners of the image. and sets thmax to the maximum of the four values.
Related commands: resocorner, resohalf, thhalf.

thhalf

Syntax: thhalf
Context: info
Prints theta values at the center of the four edges of the image and sets thmax to the maximum of the four values.
Related commands: resocorner, resohalf, thcorner.

thmax

Syntax: thmax d
Context: constants
Specify the maximum resolution (in degrees theta). Used by peak2, peak3 and datcol. The theta max circle will be drawn with circlecolour.
Related commands: resomax, resomin, thmin.

thmin

Syntax: thmin d
Context: constants
Specify the minimum resolution (in degrees theta). Used by peak2, peak3 and datcol. The theta min circle will be drawn in circlecolour.
Related commands: resomax, resomin, thmax.

timfilt

Syntax: timfilt boxsize subtracttype
Default: timfilt 21 1
Context: processing
Determine background by mode-filter. boxsize

subtracttype 1 subtract estimated background from current image
subtracttype -1 replace current image by estimated background

title

Syntax: title s
Context: window
Sets the title for the active window.

tolerance

Syntax: tolerance boxdist/exposure f
Default: tolerance distance 0.001
Default: tolerance exposuretime 0.01
(Default: tolerance exposuretime 1.01 (for MAR and MARCCD))
Context: box
Sets tolerances for detectordistance or exposuretime. Within a scan, detector distance and exposuretime of each image is compared with the value used in the boxfile. If the difference exceeds the value of f, a warning (see abort) is given if checknext=on.

distance
Set a tolerance for detectordistance to f mm.
exposuretime
Set a tolerance for exposuretime to f seconds. This is to avoid a bug in some image headers where the exposuretime is not to be trusted.

Related commands: overrule dxstart, overrule exposuretime, boxcheck.
See the Detectors Page.

trans

Syntax: trans state
Default: trans on
Context: test
If on, an optional transformation matrix will be applied to the rmatrix.

trydark

Syntax: trydark state [min]
Default: trydark off
Context: read
If on, view will try to read a drk or low image before the next image will be read. After the next read, state will always be set off. If min is given and the dark image is found, the command globalmin min is executed.

unmap

Syntax: unmap 1/2/zoom/profile/distor/menu
Context: window
This command will unmap a window. The window will not be visable anymore, but it still exists. Use map to restore the window.
Related commands: icon, map, raise.

wait

Syntax: wait n
Context: read
n is an interval. Suppose, the current file = imagexxxx.kcd (with xxxx a number). view will wait for the file image(xxxx+n).kcd. If this exists. file image(xxxx+1) is read.
Related commands: read, readwait.

weak

Syntax: weak f
Default: weak 5.0
Context: intensity
Set less thans criterium for netint calculations with bpbfixed=off. If the final intensity/sigma is less than f, the unreliable results will be rejected (i.e. resulting intensity amd sigma will be set to 0.0)

example

read s04f0275

\alias

SCAN=>s04f
FRAMENUMBER=>0275
FULLIMAGEFILENAME=>s04f0275.sfrm
IMAGEFILENAME=>s04f0275

write imagefilename (dangerous: this will create a new file with the same name)
write new'imagefilename' (use single quotes to force substitution)
mkdir subdir
write subdir/'imagefilename' (note the single quotes)

x2m

Syntax: x2m vx vy vz
Context: conversion
Stores: hormm vermm
Convert laboratory vector to mm. The resulting coordinate is stored (via addeval) in hormm and vermm
Related command: x2p.

x2p

Syntax: x2p vx vy vz
Context: conversion
Stores: horpx verpx hormm vermm
Convert laboratory vector to pixels. The resulting pixel values are printed. They are also stored in the aliases LASTX and LASTY. Refer to these aliases using 'LASTX' resp. 'LASTY'. The resulting coordinate is also stored (via addeval) in horpx and verpx
Related command: x2m.

xtal

Syntax: xtal vx vy vz
Default: xtal 0.0 0.0 0.0
Context: hkl
Define xtal coordinates in laboratory system with all goniostat angles zero. Used by datcol, hkl, hklplot.

zinger

Syntax: zinger n
Default: zinger 0
Context: read
Sets dezinger option.

Value	Frames	Explanation
0	all	Dezinger
-1	all	Mean
-2	all	Minimum
-3	available	Dezinger
n	n	One Frame

zoom

Syntax: zoom px1 py1 px2 py2
Context: zoom
Show specified section multiplied by zoomfactor. px1 py1 = Lower Left, px2 py2 = Upper Right.
Also available in menu.

zoomaround

Syntax: zoomaround px py
Context: zoom
Stores: horpx verpx
Use current zoomfactor and zoomaroundsize to create a zoomed image.
The initial defaults for px and py are calculated from zoomaroundfrac.
Related commands: zoomfollow, zoomfollowhkl.
Also available in menu.

zoomaroundfrac

Syntax: zoomaroundfrac fx fy
Context: zoom
fx and fy are the fractional detector coordinates of the default zoomaround window. zoomaroundfrac can be used to set these defaults before any image is read (for example in view.init. Use zoomaround = = to create the zoomwindow using the fractional defaults.

Syntax: zoomfollowhkl state
Default: zoomfollowhkl off
Context: hkl, zoom
If on the execution the commands m2h and hkl (if the reflection is found on the current image) will trigger a zoomaround. The same will happen in menu HKL.
If zoomfollowhkl=on, zoomfollow will be switched off.

1.4
- New commands: badmask badmaskarea badmaskcircle badmaskcolumn badmaskcorner badmaskid badmaskinit badmaskpixel badmaskrow profilefit profilegeneralpick profilemm profiletickmm zoomaroundmmmm
- Modified commands:
1.3
- New commands: badresponsthreshold capillaryaxis circleclick contigframes resocorner resohalf
- Modified commands:
  - save new options: circle/peak/profilezoom
- adczero subtraction in float
- faster startup: directorynosort in SetImageFileType
1.2 2003012900
- follow has fractional coordinates
- added command/option correction
- correct on/off changed to correct none/normal/full/debug
1.1 2002090500
1.0 2002080100

EVPY Suite Overview

Contents

Example

Examples