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Introduc,on 3 HistoryofAdxv 4 SupportedFileFormats 5 NotesforHDF5files 6 Star,ngAdxv 7 Examples 9 TheAdxvWindows
Control 11 Image 17 Magnify 20 Load 25 Save 31
OutputFileFormats 32
Line/Histogram 35
Info(ImageHeader) 39
Predic,ons 42
Formatofthe.adxfile 44
Sta,s,cs 46
SeUngs 47
Improveddisplayoflowdosedata 50
Proper,es 51
Background 54
SocketInterface 56
BeamCenterFile 59
FrequentlyaskedQues,ons 60
Commandlineop,ons 62
Environmentvariables 69
Introduc,on
Adxv isaprogramtographicallydisplayandanalyze2‐Dareadetectordata. It isop,mizedtodisplayX‐Raycrystallographydiffrac,onimages.Manycommondataformatsarerecognized,includingADSCSMV/IMG,CBFandHDF5.Thedatamaybedisplayedasa1‐Dcrosssec,on,2‐Dimageor3‐Dsurface.Sequen,alimagesmaybedisplayedasananima,on.Themagnifica,on,contrastandcolormappingareadjustable.Displayed datamay be saved in a variety of formats includingASCII,SMV/IMG,TIFF,JPEGandPostscript.
AdxvwillrunonmostversionsofLinuxandOSX.ItisbasedonX11/Mo,fsoanX‐server is required. It will run on Windows if the Cygwin libraries have beeninstalledandanX‐serverisrunning.
Adxv is freely available to everyone. There is no registra,on, license or feerequiredtouseit.Youcandownloaditfrom:
www.scripps.edu/~arvai/adxv.html
Thismanualisavailablehere:
www.scripps.edu/~arvai/adxv/AdxvUserManual.pdf
ThecurrentversionofAdxvis1.9.13.
3
ABriefHistoryofAdxvIn1992TheScrippsResearch Ins,tute (TSRI) gotanewMar ImagePlateScanner. Itwas a great detector, although it used the VMS opera,ng system and the displaysogware(XIPS)wasnotsogreat.SoIwroteaprogramcalledXviptodisplayimagesonourUnix (Sun)worksta,ons.Xvipwaswriien inCandused theX11/Xviewgraphicslibraries.
Our Sunworksta,onsweremonochrome, so grayscale imageswere displayed usingdithering.Whenwegotcolorworksta,ons,ImodifiedXviptoworkwithgrayscaleandcolor.A laterversionofXvipwasgiven toMarResearch,whichevolved intowhat isnowtheirMarViewdisplayprogram.In1993, incollabora,onwithADSC,IcreatedaversionofXvipwhichwasbeiersuitedforSAXSdata.ThisprogramwascalledMarvip.In1994IcombinedthebestfeaturesofXvipandMarvipintothefirstversionofAdxv.ThiswaswriienwiththeX11/Mo,flibraries.OvertheyearsAdxvhasslowlyevolvedby adding more features, suppor,ng more data formats and suppor,ng the latestcomputersandopera,ngsystems.
Adxv.Thereisnosubs,tute.
Xvip,circa1993
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Format
ADSCSMV/IMG(16and32‐bitinteger) .img
Bruker .sfrm
CBF(Standardand“mini‐CBF”) .cbf
EDF .edf
FujiImagePlate .fuji
HDF5 .h5/.hdf5
MarCCD .mccd
MarImagePlate .image/.marxxxx
NUMPY .npy
R‐AXIS .osc
TIFF (8, 16, 32 Bits/Pixel with 1 Sample/Pixel) .tif / .tiff
Rawbinary(8,16,32‐bitintegerand32‐bitfloat) any
Adxvspotfile .adx
Cheetahpixelmapfile .h5
Denzo.xfile .x
SupportedFileFormats
File Extension
Adxvrecognizesmanyfileformatsbasedonthefileheader,sothefileextensioncanbeanything.Fileswhichhavebeencompressedwithgzip,compressorbzipmaybereadwithoutuncompressingthem.
The internal data representa,on of Adxv is 32‐bit signed integer. If an input dataformat isfloa,ngpoint and thedata valuesare very smallor very large, youmaywant to runAdxvwith the–iscale command lineop,on tomul,ply thedatabyascalefactorbeforeconversiontointeger. 5
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HDF5 files are containers for two kinds of objects ‐ Datasets and Groups. Datasetscontainmul,dimensionalarraysofdataandGroupsarecontainerstructureswhichmaycontainDatasetsorotherGroups.GroupsareanalogoustodirectoriesandDatasetsarelikefiles.
BydefaultAdxvwilltrytoopenthefollowingDatasetsinanhdf5file:
Ifnoneofthesearefound,thefirstdatasetwillbeloaded.Ifthereisaproblem,theInfoWindowisraisedandyoucanexaminethefileheadertofindthedatasetname. Youcaneitherdouble‐clickonthedatasetornext,meyoucanstartAdxvwith:
adxv‐hdf5dataset<datasetname>
NotesforHDF5files
IntheInfoWindowtotheright,thedatasetnameis/entry/data/data
An hdf5 file may contain mul,pledatasets, each of which will behighlightedinaboldfontintheInfoWindowFor more informa,on about hdf5files see page 25 (Load Window)andpage39(InfoWindow).
/data /entry/data/data
/data/data /entry_1/data_1/data
/intensi@es /entry_1/image_1/data
/real /entry_1/instrument_1/detector_1/data
/entry/data /entry/instrument/detector/data
Star,ngAdxv
TheusagetostartAdxvfromthecommandlineis:
adxv [op@ons] [file [predic@ons]]
Theop,onswhichmaybe specifiedon the command line are listed star,ngonpage62.Followinganycommandlineop,onsisthenameofanimagefiletoload.Agertheimagefile,afilewithspotposi,onsmayalsobespecified.
Forexampletodisplayanimageyoucando:
adxv test_1_001.img
Twowindowswillappear‐theControlWindowandtheImageWindow.TheImageWindow graphically displays the image using a grayscale colormap. Larger pixelvalues are darker and smaller pixel values are lighter. As the mouse is movedaround the Image Window, the posi,on of the cursor is displayed in bothmillimeters and pixels. The resolu,on (in Angstroms) and I/Sigma of the regionunderthecursorarealsodisplayed.
Inthe ImageWindow,theLegmousebuionmaybepressed,draggedandthenreleasedtoproducea1‐dcross‐sec,onplot.Thisplotwillbedisplayed inanewLineWindow. Themiddlemouse buionmay be pressed and dragged to "pan"around the image.Pressing the rightmousebuionwillmagnifyanddisplay theareaunderthecursorinaseparateMagnifyWindow.
7
The Control Window may be used to modify the appearance of the displayedimage. In the center of this window is a graphical display of the pixel to colormappingandimmediatelytotherightofthisisaver,calslider.Draggingthesliderwilladjustthecontrastoftheimage.Pixelvalueslargerthanthevalueinthetextboxabove the slideraredrawnasblack (or the top color in the colormap), andpixel values smaller than the value below the slider are drawn aswhite (or theboiomcolorinthecolormap).Thereareradiobuionstoadjusttheimagescale,and colormap. The default Scale is Auto and this will scale the image so it fitsinsidetheImageWindow.If100%isselected,theneachpixelintheimagewillbedrawnas1pixelon the screen. If 50% is selected, theneveryotherpixel in theimagewillbedrawn.Thereare3choicesforcolormap(Gray,HeatandRainbow).Eachofthesemaybeinverted.ForexampleiftheGraycolormapisinverted,thenlargepixelsareWhiteandsmallpixelsareBlack.
The magnifica,on factor used to display data in the Magnify Window may beadjustedfrom1to128.Forexampleifthisissetto8,theneachpixelintheimagewill be drawn as an 8x8 pixel in theMagnifyWindow. The data in theMagnifyWindowmaybedisplayedasValues,Pixelsor3‐D.IfValuesisselected,thenonlynumberswillbedisplayed.IfPixelsisselected,thenamagnifiedviewofthepixelsisdisplayed. If3‐D is selected, thedata isdisplayedasa three‐dimensionalwiremesh.
OtherAdxvwindowscanbeaccessedfromtheControlWindow.ClickingwiththeLegmousebuiononthemenubaratthetopoftheControlWindowwilldisplayamenuwithchoicesofWindowstodisplay.Eachofthesewindows,aswellastheControlWindowandImageWindow,willbeshownandexplained inmoredetaillater.
IftheControlWindowisnotvisible,simultaneouslypressingthe<SHIFT>keyandthe right mouse buion in either the Image or Magnify Window will raise theControlWindowtothetop.
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Examples
Displayanimageandoverlayspotsfroma.adxfile:
adxv Thau2_1_031.img Spots.adx
Drawresolu,onringsat4specificresolu,ons:
adxv ‐rings 8 3.5 2 1.5 trypsin_2_001.img
Display1152x1152binaryunsignedshortdata,skip2048byteheaderandswapbytes:
adxv ‐ushort ‐nx 1152 ‐ny 1152 ‐skip 2048 ‐swap test_001.raw
Displayanimageanddenzopredic,ons:
adxv nnos6_1_001.img nnos6_1_001.x
SpecifyanexactvisualidanduseOpenGLforthe3‐Ddisplay:
adxv ‐visual 0x26 ‐gl
ReadanHDF5fileandspecifywhichdatasettodisplay:
adxv ‐hdf5dataset /entry_1/image_1/data cxidb‐3.cxi
ConvertanimagefromCBFtoIMG:
adxv ‐smv32bits –sa G8_1_00001.cbf G8_1_00001.img
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Automa,callysaveanimageasa1/10scalejpegfile:
adxv ‐sa ‐jpeg_scale 0.1 nnos6_001.img nnos6_001.jpeg
Cropa100x100pixelregion,wheretheupperlegcornerisatx=200,y=300,fromanhdf5fileandsaveitasa32‐bit.imgfile.
adxv –smv32bits ‐sa ‐sa_crop 100x100+200+300 dark.h5 dark.img
DisplayCSPADdataanduseaCheetahpixelmapfiletocorrecttheimage:
adxv ‐pixelsize 0.110 ‐pixelmap pixelmap.h5 CxiDs1‐image.h5
Usealargerfontfortheresolu,onrings.Thiswillhelpifyouhavealargeimage,scaleto100%andthensaveasjpgor,ff:
adxv ‐rings ‐rfont "‐*‐lucidatypewriter‐bold‐r‐normal‐sans‐180‐*‐*‐*‐*‐*‐*‐*”
Improvethedisplayofdatawhichhavesmallspotsandweakbackground:
adxv –weak_data –small_spots D1_2_0_scr_000061.cbf
Here’sashortscripttomakeamoviefromaseriesofimages:
#! /bin/csh
foreach i ( lyso_*.img )
adxv ‐sa $i /tmp/$i:r.jpg
end
ffmpeg ‐r 25 ‐i /tmp/lyso_%03d.jpg ‐vb 20M lyso.mpg
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TheControlWindow
Adjusts the scale of the image in theImageDisplayWindow. Whenthescaleis100%,everypixel isdisplayedsothat1 pixel in the image is 1 pixel on thescreen.Whenthescaleis25%,every4thpixel in the image is displayed on thescreen. For example if the image is3072x3072 pixels and the scale is 25%,then the imagedisplayedon the screenwill be 768x768 pixels. When Auto isselected, the image is scaled so it fitsinside the ImageWindow. The scale iscalculated as the width of the imagedivided by the width of the ImageWindow. For example if the ImageWindowis600pixelswideandtheimageis 3072 pixels wide the scale will be600/3072=0.195.
Seeexamplesbelow.
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The top row contains a menu bar.Selec,ngoneofthesemenubuionswilldisplay a pull downmenu. The items inthesepulldownmenuswillbediscussedlater.
Auto 25%
50% 100%The ImageWindowshowing the same imagedisplayedatdifferent scales.Whenthe scale is 25% or larger the image does not fit completely inside the ImageWindow. In thiscase,youcanpressandhold theMiddlemousebuiontomovetheimagearound.Thebeamcenterisdrawnasaredcrossineachimage.
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Adjusts the colormap of the imagedisplayed in the Image and MagnifyWindows. For example with Heat, largerpixelvaluesarelightYellow,intermediatevaluesareOrangeandsmallervaluesaredarkRed.
This inverts the colormap. For example, with Gray,largerpixelvaluesareBlack.WhenInvertisselected,largerpixelvaluesareWhite.
Seeexamplesofdifferentcolormapsbelow.
13
Heat Rainbow
Gray+InvertGray
Rainbow + Invert Rainbow
Heat Heat + Invert
Gray Gray + Invert
The Image Window showing different colormaps
14
Pixel values larger than this value are drawn as Black. This may also be set and displayed in the Histogram Window.
If the Right mouse button is pressed in the colormap drawing area, this popup menu appears. Selecting “Fix Contrast” will not automatically update the contrast setting for each image as it is loaded. The Max and Min contrast settings will remain as from the last image loaded or as set by the user. This may also be set in the Settings window. When Fix Contrast is set, the Max and Min contrast values in the textboxes to the right will be drawn in a Bold font.
Graphical display of pixel value vs. color mapping. For example a pixel value of 360 will be drawn in medium gray and a pixel value of 120 will be drawn in light gray. The Middle mouse button may be pressed and dragged in this window to stretch and adjust the colormap. The behavior is analogous to stretching a rubber sheet. Selecting a different colormap or moving the contrast slider will reset the colormap.
Slider to adjust the contrast. Dragging this up increases the contrast and dragging it down decreases the contrast.
15
Pixel values smaller than this are drawn as White. May also be set and displayed in the Histogram Window.
This selects how data is displayed in the Magnify Window. If 3D is selected the data is displayed as a wire mesh. Pixels displays magniQied pixels and Values prints only numbers. See examples on Page 22.
Information about the image which was loaded. MaxI is the largest pixel value in the image. AvgI is the average pixel value. Over4lows is the number of pixels which have overQlowed the linear range of the detector. Spots is the number of groups of contiguous pixels which are overQlowed, i.e. each “spot” may contain multiple overQlowed pixels. Scale factor is how much the image was scaled to Qit in the Image Window when the Scale mode is Auto. In this case the image is 19% the size of the entire image, so about every 5th pixel is displayed.
If Adxv is started with the –verbose Qlag, more information is printed:
‐ The x,y position of the smallest and largest pixels ‐ The number of ‐1 and ‐2 pixels ‐ The standard deviation (sigma) of all the pixels
MagniQication factor of pixels drawn in the Magnify Window. 8 means that each pixel in the raw data is magniQied 8 times and is drawn as an 8x8 pixel box in the Magnify Window. The range of magniQications is from 1 to 128. See examples on Page 21.
There is more information about magniQication types and factors in the Magnify Window section (page 20).
16
TheImageWindow
The The ImageWindow graphically displays the image using a grayscale colormap.Larger pixel valuesare darkerandsmallerpixelvaluesarelighter. AsthemouseismovedaroundtheImageWindow,theposi,onofthecursorisdisplayedinbothmmandpixels.Theresolu,on(inA)andtheI/Sigmaoftheregionunderthecursorisalsodisplayed. The beam center is drawn as a red cross in both the Image andMagnifywindows.
Thelegmousebuionmaybepressed,draggedalongthewindowandthenreleasedtoproducea1‐dplot inaseparateLineWindow. Themiddlemousebuionmaybepressed and dragged to "pan” the image if the image does not fit in the window.Pressingtherightmousebuionwillmagnifyanddisplaytheareaunderthecursorinaseparate Magnify Window. If the <SHIFT> key and Right mouse buion are pressedsimultaneously, the ControlWindowwill be raised. If themouse has a scroll wheel,theninPixels and3‐D modethescrollwheelcanbeusedtoadjustthemagnifica,onfactorintheMagnifyWindowfrom1to128.
Ifthe<SHIFT>keyandLegmousebuionarepressedsimultaneously,aposi,onontheimageisselected.Oncethreeposi,onshavebeenselected,theanglebetweentwo consecu,ve lines described by those three posi,ons will be printed to thestandardoutput.Iftwoofthethreeposi,onsareiden,cal,thehorizontalandver,calangle(rela,vetothecrystalorigin)betweenthetwopointsisprinted.Ifallthreepointsare iden,cal, thehorizontal and ver,cal angle requiredtorotate thatpoint to thebeamcenterisprinted. Theseop,onswereusefulinthe old days tomeasure theanglesofalaUceores,matehowfartorotateacrystaltoalignazone.
If the <SHIFT> key andMiddlemouse buion are pressed simultaneously, the beamcenterwillbesettothecursorposi,on.ThismayalsobedoneintheMagnifyWindow.
With the cursor is in the ImageWindow, twonumbers followedbya carriage returnmaybe typedand theMagnifyWindowwillbe raisedandcenteredon that x,ypixelposi,on. If theRightmousebuionispressedwhilethe<SHIFT>key isalsopressed,thenthedistancebetweensuccessiveclicks (inpixelsandmm)willbeprintedto theterminal.
17
Image showing resolution rings. Notice that the beam center is drawn as a red cross. For this image 2‐theta is non‐zero, so the resolution rings are not circular. Resolution rings may be turned on or off in the Properties Window, which is discussed later. The font used for the rings may be set with the –rfont command line option. If you want to draw only the rings, without the resolutions printed, you can use the –rings_only command line option. Rings may also be drawn at specific resolutions with the –rings command line option.
18
f RaisetheLoadWindow.TheFileLoadWindowisdisplayed.
h Adjust thehistogramcontrast in the ImageWindow.Thecontrastof the visible por@on of thedataintheImage Windowisautoma,callyadjusted.Notethatiftheen,reimageisnotvisible,onlythepixelsvisibleintheImageWindowareusedtoadjustthecontrast.
l Toggle ligh,ng on and off in the Magnify Window. When using OpenGLgraphics,thiswilltoggleturningligh,ngonandoff.
m AdjustthehistogramcontrastintheMagnifyWindow.ThecontrastoftheMagnifyWindowisautoma,callyadjusted.
P|p Toggle turning predic,ons on and off.When predic,ons are displayed, this willtoggledisplayingthemornotdisplayingthem.
r Resetthedisplayinthe3‐dmagnifywindow.Theposi,onandorienta,onof thedatainthe3‐dmagnifywindowisresettoitsoriginalstate.
s TogglesmoothingintheMagnifyWindow.WhenusingOpenGLgraphicsinlinemode (‐gl_lines), thiswill toggle between drawing thewiremeshwith smoothlines (slower) or aliased lines (faster).When a surface is displayed this willtogglebetweendrawingaliasedandan,‐aliasedpolygons.
w Toggle between wiremeshand surfacedisplay in theMagnifyWindow.WhenusingOpenGLgraphics,this will togglebetweenawiremeshandsurfacedisplayofthedata.
Arrow Keys Adjustthecursorposi,on.Pressing the arrowkeys (up, down, leg,right) willmovethecursorbyonepixel. Ifthe Plot Type is Circle (set underEdit‐>Proper,es),thearrowkeyswilltranslatethecenterofthecirclebyonepixel.
? Printhelp.Thiswillprintasummaryofthekeyswhichmaybepressed.
<SHIFT> + Middle mouse bulon
Setthebeamcentertothecurrentcursorposi,on
<SHIFT> + Right mouse bulon
Raises the Control Window. Also prints the distance between successive Rightmousebuionclickstotheterminal.
The following keys may be typed while the cursor is in the Image Window
19
TheMagnifyWindow
The Magnify Windowdisplaysamagnifiedpor,onofthedatafromtheImageWindow.Pressing the right mouse buion in the Image Window draws a box and displays amagnifiedviewofthedatawithinthatboxinaseparateMagnifyWindow.Theformatofthe displayed data may be selected by toggle buions in the Control Window (seeexamplesbelow).Thedefault is"Pixels"whereeach pixel in the image isscaledbyamagnifica,onfactoranddisplayed.Ifthemagnifica,onfactoris32orlarger,thevalueofeachpixelwillalsobeprintedwithineachpixel.If"Values"isselectedthenonlypixelvalues will be printed, not a magnified image. If "3‐D" is selected then a threedimensionalwiremeshrepresenta,onofthedatawillbedisplayed.Thefunc,onofthemousebuionsisdifferentwiththedifferentdisplaymodes.
InValues modetheLegandRightmousebuionshavenoeffect.TheMiddlemousebuionwillpanthedisplayeddataaroundtheimage.
InPixels modetheLegmousebuionwilldrawalineorcircle (depending on the PlotTypeseUngintheProper,esWindow).TheMiddlemousebuionagainpansaroundtheimageandtheRightbuionhasnoeffect.
In 3‐Dmode the Legmousebuion rotates thewiremesh. TheMiddlemousebuiontranslates themesh (inX‐Y) within theMagnify Window. TheRightmousebuion isusedtoscalethewiremeshintheZdirec,on.IfControl‐Right mouse buionispressedthiswillscalethewiremeshinalldimensions.
Ifthemousehasascrollwheel,theninPixels and3‐D modethescrollwheelcanbeusedtoadjustthemagnifica,onfactorfrom1to128.
If Adxv is started with the ‐gl command line, thenOpenGLgraphics isused for3‐Dmode.
20
x1 x2 x4
x8 x16 x32
x64 x128
Magnify Window display as the magniQication is increased from 1 to 128. The magniQication mode is Pixels.
21
Notice that when the magniQication is 32 or larger, the pixel values are printed in each pixel. Depending on the number of digits needed for each value, a larger or smaller font may be used so that the value will Qit within a pixel . For Values the magniQication setting is disabled. The magniQication depends on how many pixels can be Qit in the Magnify Window and is usually about 32.
Comparison between Pixels, 3D and Values.
22
3D Pixels
Pixels Values
The same data is shown with MagniQication set to Pixels (left) and 3‐D (right). The magniQication is 4 in both cases.
The Magnify Window when using GL (gl command line option)
Pixels. The colormap is Heat.
3‐D Wire Mesh. Type “w” to toggle between wire mesh and surface display.
3‐D Surface. Type “l” to toggle lighting on and off.
23
l Thiswilltoggleturningligh,ngonandoff.
r Theposi,onandorienta,onofthedatainthe3‐DMagnifyWindowwillberesettoitsoriginalstate.
S Inlinemode(‐gl_lines),thiswilltogglebetweendrawingthewiremeshwith smooth lines (slower) or aliased lines (faster).When a surface isdisplayed this will toggle between drawing aliased and an,‐aliasedpolygons.
w Thiswilltogglebetweenawiremeshandsurfacedisplayofthedata.
? Printhelp.Thiswillprintasummaryofthekeyswhichmaybepressed.
The following keys may be typed in the Magnify Window
The following keys may be typed when using OpenGL graphics (‐gl)
f RaisetheLoadWindow
h Adjustthecontrasttoop,mizedisplayofthecontentsoftheMagnifyWindow
p Toggledisplayofspotson/off
r Resetorienta,onof3‐Ddisplay
Arrow Keys Adjustthecursorposi,on.Pressingthearrowwillmovethecursorbyonepixel.
? Printhelp.Thiswillprintasummaryofthekeyswhichmaybepressed
<SHIFT> + Middle mouse bulon
Setthebeamcentertothecurrentmouseposi,on
<SHIFT> + Right mouse bulon
PrintsthedistancebetweensuccessiveRightmousebuionclickstotheterminal
24
TheLoadWindow
ThiswindowisaccessedbyclickingFile‐>Load fromtheControlWindowandis used to load Qiles. Image Qiles, Adxv spot (.adx) and denzo output (.x) Qiles may also be loaded.
Regular expression(s) to Qilter which Qiles are listed in the scrolling window to the right. Some examples of patterns:
*0.img [A‐C]*.h5 lys3_?_*.cbf
If Pattern is blank or *, all Qiles are listed. Directories are always listed.
Typing a carriage return will re‐scan the Directory for Qiles matching the Pattern. 25
Pressing the List button will list all Qiles which match the regular expression in the Pattern text Qield.
About 20000 Qiles may be listed at once. However, if there are too many Qiles, you can list every 100’th Qile by making the pattern
*01.img
Directory where Qiles are located
Directories are listed Qirst, followed by Qiles. Directory names have a trailing “/”.
Single‐clicking a directory will change into that directory. Clicking the “..” directory will move one directory up.
Double‐clicking on a Qile will load and display that Qile.
Pressing the Right mouse button in the Qile list section brings up a menu where you can choose to sort Qiles alphabetically or by modiQication time. The default is alphabetical.
26
Load and display the Qile in the text Qield to the left.
You can type a Qile name into this text Qield or select one with the mouse from the list on the right. To load a Qile you can either click the Load button, type a carriage return in the text Qield or double‐click on the Qile in the list on the right
Specify the number of Qiles to load. If Files is 5, then 5 consecutive Qiles will be loaded, summed and displayed as one image. See the next page for more information.
Whenfilesarelisted,theyarenotsortedabsolutelyalphabe,cally.Sor,ngalsotakes into account run numbers and these are sorted from small to large. Forexample,filesaresortedlikethis:
data_1_001.imgdata_2_001.imgdata_10_001.imgdata_11_001.img
notlikethis:
data_10_001.imgdata_11_001.imgdata_1_001.imgdata_2_001.img
WhenSort by Timeisselected,morerecentfilesarelistedfirst,regardlessoffilename.Directoriesares,lllistedfirst.
Tore‐scanfilesinadirectory,presstheList buionortypeacarriagereturninthePaierntextfield.
IftheFiles textfieldis>1,thenmul,pleconsecu,vefileswillbeloaded,summedanddisplayedasoneimage.Filesareareloadedinconsecu,venumericalorder.Ifafileisunavailable,thenfilesindecreasingconsecu,venumericalorderwillaiempttobeloadedun,lthetotalnumberoffilesspecifiedisloaded.
Thenumberoffilessummedwillbeshowninthe,tlebar.
27
Movie mode. Continually load and display the next Qile. Press again to stop. In this case the Stride is 5, so every 5’th Qile (8, 13, 18, etc) will be continually loaded and displayed. If Qiles are displayed too quickly, a pause can be added between them with the –delay command line option.
Load and display the next Qile. In this case, the next Qile to load will be C3_1_00013.img. This is because the current Qile is number 8 and the stride is 5. If instead the left (previous) arrow button is pressed, then Qile number 3 would be loaded.
When a new Qile is loaded, if the Line or Magnify Windows are displayed, their contents will be updated to reQlect the data in the new Qile. This also applies to movie mode.
Specify every n’th Qile to load. For example if the Stride is 5, then every 5’th Qile will be loaded. If the Stride is 1, then every Qile will be loaded.
28
With three‐dimensional hdf5 data, the Load Window will automatically show two additional text Qields and a checkbox. These are used to select which slab(s) to display.
Number of slabs to combine and display. If Slabs is 5, then 5 slabs are summed and displayed. How to combine slabs (sum or average) may be speciQied in the Properties Window.
If this checkbox is checked, then the forward and backward arrows will display the next slab of data, not the next Qile. For example if you are displaying slab #1, the stride is 3, and you click the forward arrow button, then slab #4 will be displayed. If there are no more slabs, then the next Qile will be displayed.
Specify the Qirst slab to display. Each slab is a 2‐d array of data. If the data is 100x2527x2463 pixels, then there are 100 slabs of data, where each slab is 2527x2463 pixels.
29
Here a Qile (G4_2_00001.h5) is loaded which contains a total of 5 slabs. The Qirst slab to display is 2 and the number of slabs to combine is 3. Thus, slabs 2‐4 are combined and displayed.
The title bar of the Image Window shows that slabs 2‐4 are displayed out of a total of 5 slabs in the Qile.
30
Directory and File where the saved data will be written.
Selects which window data will be saved from.
Selects which format the data will be saved as. See Output File Formats (below) for more information about these choices.
31
TheSaveWindow
Thiswindow isaccessedbyclickingFile‐>Save in theControlWindow.Data from the Image, Magnify and Line windows may be saved to a Qile in various formats. The Line window may display either a histogram or a 1‐d cross section of the data. Whichever is displayed in the Line window will be saved.
OutputFileFormats
For the Image andMagnify Windows, the output is NX columns and NY rows,whereNX is thewidth (inpixels) andNY is theheight. For example, here is theoutputofa5x5pixelregiondisplayedintheMagnifyWindow:
443462387439413439215615664724254882560019114757420451563609483431396415410440424
FortheLinewindow,thereisashortheader,followedbypairsofX,Yvalues,whereXisthedistance(inpixels)andYisthevalue.Forexample:
#Linefromimage:/home/arvai/test_images/pilatus.cbf#Start:12801119#End:12901119#Linewidth:1#Interpola,on:1#0406.0000001469.0000002449.0000003488.000000425600.000000519114.0000006420.0000007410.0000008393.0000009434.000000
Notethatthex‐coordinate(distance)isrela,vetotheStartposi,onintheheader.
• Ascii
32
Thisisonlyanop,onfortheImageWindow.Theen,reimageiswriien,regardlessofhowmuch isvisible.Theoutputformat isADSC imgformat.There isanASCIIheaderwhichlookslikethis:
{HEADER_BYTES=512;DIM=2;SIZE1=2463;SIZE2=2527;TYPE=unsigned_short;BYTE_ORDER=liile_endian;DISTANCE=80.001;PIXEL_SIZE=0.172000;WAVELENGTH=0.980800;}^L
Theheader ispadded toHEADER_BYTESbytesand is then followedby the rawdata,whichis16‐bitunsignedshprt.Theoutputdatawillbesigned32‐bitintegerifAdxvisstartedwith the –smv32bits command line op,on. In this case theheader is slightlydifferent,with:
TYPE=long_integer;
• Binary
33
Images may also be converted to and saved as .img files with the –sa command line option. See examples on pages 9 and 10.
Here is a library and documentation to read/write ADSC SMV/IMG files:
http://www.scripps.edu/~arvai/adxv/data/smv.tar.gz
Taggedimagefileformat.
• Postscript
Writes level2 color postscript. If Adxv is startedwith the –level1 command lineop,on,thenlevel1postscriptwillbewriien.
• Tiff
StandardJPEGformat.
• Jpeg
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TheLine/HistogramWindow
The horizontal scale ismillimeters and the ver,cal scale is pixel value. The totallength of the displayed data (in millimeters) is shown in the upper right. Anes,mateofthecrystal laUcelengthbasedondistancebetweenadjacentpeaksisalsoshown.
The Line Window displays a 1‐D cross‐sec,on plot of data from the Image orMagnifyWindows.Pressinganddraggingthelegmouse buionin the ImageorMagnifyWindowwilldrawarubberbandline.Whenthemousebuionisreleased,thedataselectedbythatlinewillbedisplayedasa1‐DplotintheLineWindow.
Totallengthofdata(millimeters).
Thisspotspacing,correspondstothisreciprocallaUcespacing.
Pressing theLegmousebuionwilldisplay theXandYcoordinates.PressinganddraggingtheMiddlemousebuionwilladjustthever,calscaleoftheplot
35
The LineWindowmay also display a histogram of the data in the Image orMagnifyWindows. This is selected from the View‐>Histogram pulldown menu in the ControlWindow.ThehistogramofeithertheMagnifyWindow(View‐>Histogram‐>Magnify)ortheen,reimage(View‐>Histogram‐>Image)maybeselected.
Thehorizontalscaleispixelvalueandthever,calscaleisnumberofpixels.
Twover,caldashedlinesaredrawnatthepixelvaluesdisplayedaboveand belowthecontrast sliderintheControlWindowandrepresenttheminandmaxpixelsvaluesinthecolormap.Valuesbelowtheminpixelvaluearedrawnaswhiteandvaluesabovethemaxvaluearedrawnasblack.Pixelvaluesintermediateto thesevaluesaredrawnasagrayscale
The LegMouse buion can beused to adjust the min pixelvalue slider and the RightMouse buion will adjust themax value. TheMiddle mousebuion will adjust the ver,calscaleoftheplot.
Asmallredcrossisdrawnatthehorizontalposi,onofthecursor.TheX‐andY‐valuesofthiscoordinatearedisplayedintheupperright.Thelegandrightarrowkeysmaybepressedtomovethecursor1pixelineachdirec,on.
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TheInfoWindow
ThiswindowisaccessedbyclickingView‐>Image Header intheControlWindow.Thiswillshowtheimageheaderforthedisplayedimage.Belowaresomeexampleimageheadersforvariousimageformats.
mini‐CBF 39
ADSC img
Bruker
Withanhdf5file,headerentrieswith2ormoredimensionsaredisplayedinaboldfont.Ifyoudouble‐clickoneofthesewiththeLegmousebuion,thenAdxvwillloadthatdataset.Adxvwillalsorememberthedatasetnameandwilltrytoloaditfromfuturehdf5files.
41
Dataset name. If star,ng Adxvwiththe-hdf5dataset command line argument, this is the name you would use.
Dimensionsofthedataarrayinpixels.
Data type. In thiscase,F32LEis floa,ng point, 32‐bit, liileendian.
Filter(ifany)neededtodecompressthedata.Inaddi,onstothestandardHDF5filters,Adxvwill also recognize the LZ4 and Bit Shufflefilters.
Double‐clicktoloadthisdataset
ThePredic,onsWindow
This window is accessed by clicking View‐>Predic@ons in the Control Window.Spotscanbeautoma,callyormanuallypickedanddisplayed.
Max # of Spots specifies the maximumnumber of spots to find. All the foundspotsaresortedbasedonI/Sigmaandthelargestaresaved.IfMaxissetto0,thenallspotsarekept.
Min I/Sigma saves only spots larger thanthespecifiedI/Sigma.
Min. Spot Spacingsavesonlythelargeroftwospotsiftheyaretooclose.Distanceisinpixels.
Ignore Ice Rings willnotusespotsnearicerings.
Fast Peak Search uses a different peaksearchalgorithm.
Avoid Zero Pixels ignoresspotsnearpixelswhichhaveavalueof0
When Find Peaks is clicked, spots will besearched, saved inafiles calledpeaks.file and then displayed on the image with aboxaroundeachspot
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The first line of thepeaks.file file is “DPS‐PF A1.0”. This is followed bypairsofY,Xvalues.Forexample:
DPS‐PFA1.0614.36796.76542.30798.36579.09791.72672.28573.30...
If Adxv is started with the –peaks_adx command line op,on, then apeaks.adx fileisalsowriien.ThiscontainsX,Y,I/Sigma:
796.76614.36362.67798.36542.30231.83791.72579.09202.38573.30672.28172.72...
Inbothcases,theX,Yvaluesareinpixels.
Both the peaks.file and peaks.adx files are recognized by Adxv as spotfilesandmaybeusedtodisplayspotposi,ons.Forexample:
adxv test_1_001.img peaks.file
or
adxv test_1_001.img peaks.adx
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Adxvwillautoma,callyrecognize3differentfileformatsfor.adxfilesbasedonthenumberoffieldsoneachline.
1.Pairsofx,ypixelvalues:
796.76614.36798.36542.30791.72579.09573.30672.28677.11516.26
2.PairsofpixelvaluesfollowedbyI/Sigma:
290.36631.90123.73172.98610.93120.76566.94384.87120.17658.17370.86117.85329.97425.34115.47
ThisistheformatwriienbyAdxvwhenthe‐peaks_adxcommandlineop,onisused.
3.PairsofpixelvaluesfollowedbyH,K,Lvalues:
794.92696.092833‐5671.00426.982833‐3379.34861.092834‐7562.18323.032834‐6367.02821.112834‐5
Thisistheformatwriienbythegenerate_adxprogram.
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Formatofthe.adxfile
Add Peaks – Select this to manually addspots. Click on a spot in either the ImageorMagnifyWindowswith the Legmousebuiontoaddaspot.
Spot Info –ClickingonaspotdisplaystheX and Y posi,on of the spot in the textboxesbelow.
Remove Spots – Clicking on a spot withtheLegmousebuionwillremoveit.
Whenadenzo.xfile is loaded,clickingona spot with the Leg mouse buion willdisplaytheHKLandX,Yvalueofthatspot.
ThedisplayedX,Yvaluemaybeselectedtobemmorpixels,buttheoutputpeaks.fileisalwayspixels.
Un‐checkingthisboxwillturnoffthedisplayofspots.Sameastyping“p”intheImageorMagnifyWindows.
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TheSta,s,csWindow
ThiswindowisaccessedbyclickingView‐>Sta@s@cs intheControlWindow.
WhentheRightmousebuionisclickedineithertheImageorMagnifyWindows,sta,s,csofdatainaboxcenteredonthemouseposi,onarecalculatedanddisplayed.
Box Size specifiestheareaoftheregionoverwhichtocalculatesta,s,cs.IftheareaoftheBoxis0,thenallthepixelsintheMagnifyWindowareused.
TheCenter of MassisdisplayedinbothPixelsandmm.
TheAverage pixelvalueaswellastheStandard Devia@on arecalculatedanddisplayed.
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TheSeUngsWindow
ThiswindowisaccessedbyclickingEdit‐>Serngs intheControlWindow.Distanceand Pixel Size are in millimeters,Wavelength is in Angstroms and 2‐Theta is indegrees.Thebeamcentermaybeenteredanddisplayedinpixelsormillimeters,dependingontheseUngoftheadjacentradiobox.
Whenanewimageisdisplayed,thesevaluesmaybeoverwriienbyvaluesintheimageheader.Toavoidthisandkeepthevaluesastheyare,checktheboxunderFixandnexttotherelevantparameter
Here theWavelength is fixed,soavalueread in fromanewimagewillnotchangethis.
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2‐theta may be Horizontal orVer,cal.WhenHorizontal, thedetector rotates about aver,calaxisandwhenVer,calthe detector rotates about ahorizontalaxis.
When Fix Contrast is checked, the image contrast is not automa,callyadjustedforeachimageasitisloaded.ThemayalsobesetfromapulldownmenuselectedbyclickingtheRightmousebuion inthecolormapdrawingareaoftheControlWindow.
When Small Spots is checked, there is more smoothing of the datadisplayedintheImageWindow.Ifspotsaresmallandeveryn’thpixelis simplydisplayedwithout smoothing, then some spotsmaynotbevisible. This only affects the display in the Image Window, not theMagnifyWindow.Seeexamplesonthenextpage.
Theposi,onofthebeamcentermay be moved by 1 pixel byclicking the appropriate arrowbuion
The coordinates of the beamcenter may be entered anddisplayed in the text boxes tothe leg in either millimeters orpixelsbyselec,ngmmorpixels,respec,vely.
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WhenWeakDataischecked,thedisplay of data with very weakbackground (< 5 counts)will beimproved. See page 50 for anexample.
Effect of smoothing on an image which is scaled to 50%
No smoothing (every other pixel is displayed). This can be selected with the –nosmooth command line option.
This is the default setting. There is no smoothing when the image is scaled to 100% and there is progressively more smoothing as the image scale is decreased.
More smoothing (about twice the default). This can be selected with the –small_spots command line option or by checking the Small Spots checkbox in the Settings Window.
Data with small spots and very low background
Default image display. The average background intensity is about 1 count. Notice that not even the shadow of the beamstop is visible
The same image with Weak Data set. This can be set with the –weak_data command line option or in the Settings window with the Weak Data check box.
The same image with both Weak Data and Small Spots set
TheProper,esWindow
Thiswindow isaccessedbyclickingEdit‐>Proper@es in theControlWindow.Theupper setofproper,esaffect thedisplayof theLineWindowand the lower setaffectthedisplayoftheImageWindow
Numberofpixelsorthogonal to thelinedirec,onwhichareaveragedtoform each point displayed in theLineWindow.
Numberofpointsdrawnperpixeloflength.
Whenapointfallsbetweenpixels,it’svaluemay be either the closest pixelorinterpolatedfromclosepixels.
The line may be displayed asindividual points, a line connec,ngpoints, or a stair‐step centered oneachpixel.
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The Leg mouse buion will selectthecenterofacircle.Asthemouseis dragged, the radius of the circleincreases.When themouse buionisreleased,acirculararcofdatawillbe drawn, from 0 to 360 degreesaround the circle. The plot iscounter‐clockwise star,ng from therightside.
Same as above, except the edge ofthecircleisselectedandthemouseisthendraggedtoselectthecenter.
As above, the center of a circle is selectedwith the Legmouse buion and themouseisdraggedtoselecttheradius.Thehorizontalaxisoftheplotisradius(i.e.distance from the centerof the circle). The valueat each radius is the circularlyaveragedpixelintensityatthatradius.MaybeusefulforSAXS.
The plotwill be a straight line, where the first point is selectedwith the Legmousebuion.Themouseisthendraggedandtheendpointiswherethemousebuionisreleased
52
Draw circles on the ImageWindowshowing the resolu,on.Default is5circles. See the –rings and –rfontcommand line flags for moreop,ons. Notethattheseresolu,onringsarenotcircularwhen2‐thetaisnon‐zero. When Anchor1 isselected,acircleisdrawnaboutthebeamcenter,throughthenextpointselected with the Leg mousebuion.Thediameterofthisringwillchange as the beam center ischanged.ThisisusefulforfiUngthebeam center from ice rings orcheckinganisotropicscaiering.
Number of colors to use for thecolormap when displaying theimage.
53
Selects how to combine slabswhenmul,pleslabs fromanhdf5filearedisplayed.
TheBackgroundWindow
ThiswindowisaccessedbyclickingEdit‐>Background intheControlWindow.Youcandisplaythebackgroundofanimageaswellassubtractordividethebackgroundfromanimage.Thismayalsobeusedtoaddorsubtractimages.
Display will calculate anddisplay the background of thecurrentimage.
Divide willdividethecurrentimagebyeitherafileoracalculatedbackground.
Subtract will subtract thebackground (either calculatedor read from a file) from thecurrent image. The percentageof the background to subtractmaybespecified.50%specifieshalf the background will besubtracted. If thepercentage isnega,ve, the background isadded. For example ‐100% canbeusedtosumtwoimages.
Selectwhetherthebackgroundisreadfromafileorcalculatedfromthecurrentimage.
54
Select whether thebackground is applied tothe Original image or thecurrently Displayed image.The difference is that thecurrently displayed imagemayalreadyhavehadsomebackgroundsubtracted.
ThebackgroundmaybecalculatedusingaLocal movingaverageorbasedonRadial symmetryaboutthebeamcenter.Forthelater,makesurethebeamcenteriscorrect.
55
If File is selected as theSource, then the Directory andFile arespecifiedhere.
TheSocketinterface
When Adxv is started with the –socket command line op,on, it will listen for aconnec,on on port 8100. Commands may be sent to Adxv over this connec,on.Commandscanbesenttoloadimages,displayspotsorraisewindows.Belowisalistofcommandswhichcanbesent.
box x y Sizeofboxdrawnaroundspots.
colors Gray|Heat|Rainbow|Invert Adjustthecolormap
contrast_max N Imagecontrast,Maxthreshold
contrast_min N Imagecontrast,Minthreshold
define_type n color <color> radius <radius>
Defineaspottype.Colorisoneofred,greenorBlue.Radiusisinpixels.
end_of_pack ClosesaWindow.<window>mustbeoneofControl,Image,Magnify,Line,orLoad.
group N Numberofconsecu,vefilestoloadandsumtogether
increment_files StepthroughFiles
increment_slabs StepthroughSlabs
load_image <image file> Loadanimagefile
load_spots N ReadNspots
x y type Spotatpixelposi,onxy
lower_window <window> ClosesaWindow.<window>mustbeoneofControl,Image,Magnify,Line,orLoad.
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print_header [keyword] Printtheimageheader.Ifkeywordisspecified,onlyprintlinesmatchingkeyword.
raise_window <window> RaisesaWindow.<window>mustbeoneofControl,Image,Magnify,Line,orLoad.
rings on|off Turndisplayofresolu,onringsonoroff
rings [res1, res2, …] Drawringsatspecifiedresolu,ons
save_image <image_file> Saveanimagefile(jpegor,ff)
small_spots 0|1 Beier image display for images with smallspots.0=False,1=True.
slab N DisplayslabN
set_slab N Sameasslab,butdon’tloadtheimage
set_slabs N Numberofslabsofamul,‐dimensionalhdf5datatomergeanddisplay
slabs N Slabthicknesstodisplay
Stride N Number of Slabs/Files to stepwhen loadingthenextimage
weak_data 0|1 Beier image display for images with smallspotsandlowbackground.
exit ExitAdxv
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Hereisanexampleofusingthesocketinterface:
hip://www.scripps.edu/~arvai/adxv/data/adxv_socket_example.c
Torun:
cc‐oadxv_socket_exampleadxv_socket_example.cadxv‐socket&./adxv_socket_example
Thiswillloadanimagefile,display4spotsofvarioussizesandcolorsandraisetheLoadWindow.Youwillneedtochangethenameoftheimagefile inthecode.Anexampleimageisavailablehere:
hip://www.scripps.edu/~arvai/adxv/data/q1.img.gz
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TheBeamCenterFile
WheneverAdxvreadsanimagefile,itcheckstoseeifthereisa.adxv_beam_center fileinthedirectorywheretheimageisbeingloadedfrom.Ifthisfileexists,thenitwillbeusedtosetthebeamcenter.Thereasonforthisisthatsome,mesthebeamcenterwriienintheimageheaderisnotcorrect.Ifitisadjustedone,me,thenallimagesinthatdirectorywillbedisplayedwiththecorrectbeamcenter.
Ifthe.adxv_beam_centerfiledoesnotexistoriftheuseradjuststhebeamcenterinAdxv,thenthisfilewillbewriien.Thefilecontains4asciinumbers:
beam_x beam_y nx ny
beam_x andbeam_y arethecoordinatesofthebeamcenterandnx andny aretheimage dimensions. For the beam center to be used, the image dimensions of thedisplayedimagemustmatchnxandny.
Tonotreadorwritethe.adxv_beam_centerfile,Adxvcaneitherbestartedwiththe‐no_adxv_beam_center command line op,on or the NO_ADXV_BEAM_CENTER environmentvariablemaybeset.
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FrequentlyaskedQues,ons
Is there any license or fee for using Adxv?
No,itisfreeforanyonetouse.
Where can I download adxv from?
www.scripps.edu/~arvai/adxv.html
What if Adxv complains about missing fonts?
Youcaninstallthemissingfontsfromthesepackages:
xorg‐x11‐fonts‐75dpi.noarch
xorg‐x11‐fonts‐ISO8859‐1‐75dpi.noarch
YoucanalsodownloadallthefontsAdxvneedsfrom:
hip://www.scripps.edu/~arvai/adxv/fonts.tar.gz
Putthisfileinadirectory(i.e./usr/share/adxvfonts/)andtype:
gunzip‐‐stdoutfonts.tar.gz|tarxvf–
ThenrunAdxvwiththefontpathop,on:
adxv‐fp/usr/share/adxvfonts
What if I download Adxv and get "./adxv: Permission denied."?
chmod+x./adxv 60
What if the Image Window doesn't refresh correctly under NX?
ThisisabuginNXandshouldbefixedinnewerversionsoftheNXserver.
TrytypingCtrl + Alt + E totogglelazyencoding.
DependingontheversionofNX,tryaddingoneofthefollowing op,onsonthemachinewhichisrunningthenxserver:
/usr/NX/etc/node.cfgAgentExtraOp,ons="‐defer0"
/etc/nxserver/node.confAGENT_EXTRA_OPTIONS_X="‐defer0"
Otherthingstotry:
adxv‐nopixmapadxv‐nopixmap‐nobsComplaintonomachine(hips://www.nomachine.com/report‐issues)Asalastresort,contactme([email protected])
Is there a version of Adxv which runs under Windows?
Ifyouinstallcygwin(hip://www.cygwin.com/)andthex‐serverpackages(hip://x.cygwin.com/docs/ug/setup‐cygwin‐x‐installing.html)thentheCygwinversionofAdxvshouldwork.AdxvwascompiledunderWindows8.ThiswillalsorununderWindows7,butonlyifyouinstallthe32‐bit versionofcygwin.ThankstoDr.IlyaFrantsuzovforthisfeedback.
Adxv crashes with "Library not loaded: /usr/X11/lib/libXt.6.dylib”
InOSX10.10(Yosemite)theX11librariesweremovedfrom/usr/X11to/opt/X11.Youcanmakeasymboliclinkfrom/opt/X11to/usr/X11:
ln ‐s /opt/X11 /usr/X11
What if none of the binaries run on my machine or I find a bug?
What if I want to donate money to fund Adxv support and development?
Definitelycontactme.
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Commandlineop,ons
‐autoload Automa,cally load images listed in the file$XFORMSTATUSFILE. Thisfile shouldcontainonelinewithtwovalues,an integernumberandfilename.Thisfile ischeckedeverytwosecondsandwhentheintegernumber changes, the specifiedfile name is loaded anddisplayed.
‐auto_sigma As the cursor moves across the ImageWindow, the I/Sigmaoftheregionunderthecursoriscalculatedmoreaccurately,butmoreslowly. This isdonebydefault intheMagnifyWindow.
‐beam_center x y Specifythebeamcenterinmm.Defaultisreadfromtheimageheader.
‐beam_center_pixels x y Specifythebeamcenterinpixels.Defaultisreadfromtheimageheader.
‐border Drawa1pixelborderaroundtheimage.
‐bruker InputfileisBruker(.sfrm)format.
‐char Inputfileisbinarysignedchars
‐colormap Createanewcolormapinsteadofusingthedefaultone.
‐colors Gray|Heat|Rainbow Definestheini,alcolormapcolors.DefaultisGray.
‐contrast Min Max Settheini,alvaluesforthecontrastseUng.Defaultisautoma,c.
‐debug Printdebugginginforma,on.
‐dectris_kludge Treatunsigned16‐bitdataassigned(default).Thissothat65535isdisplayedas‐1atmoduleboundaries.
‐delay t Delay(inmilliseconds)fordisplayingimagesinmoviemode.
‐display DISPLAY X11displaytouse
‐distance x Specifythecrystaltodetectordistanceinmm.Defaultisreadfromtheimageheader. 62
‐double Inputfileisbinarydoubles
‐edf InputfileisEDFformat
‐fast_scan_mm H|V Specifythefastscanningdirec,onformmcoordinatesdisplayedintheImageWindow.DefaultisH(Horizontal).Seealso‐scan_origin_mm
‐fast_scan_px H|V Specifythefastscanningdirec,onforpixelcoordinatesdisplayedintheImageWindow.DefaultisH(Horizontal).Seealso‐scan_origin_px
‐find_peaks Runpeaksearchandexit
‐fix_contrast Donotautoma,callyre‐adjustthecontrastaseachnewimage is read in. Thismayalsobe set in theSeUngsWindow.
‐flip H|V FliptheimageaboutaHorizontalorVer,calaxis.
‐flip_beam H|V FlipthebeamcenteraboutaHorizontalorVer,calaxis.
‐float Inputfileisbinaryfloats
‐fp FontPath TheFontPath
‐fuji InputfileisaFujiimageplateimage.
‐fuji10bit InputfileisaFuji10bitimageplateimage.
‐gl ‐use_gl
Ifavailable,useOpenGLtorender3‐dgraphicsintheMagnifyWindow.
‐gl_lines DrawOpenGL3‐dgraphicsasawiremesh.Typing"w"intheMagnifyWindowwillalsotogglebetweenawiremeshorpolygonalsurfacerepresenta,on.
‐gl_quad_strip_bug Drawthe3‐dpolygonalsurfaceusingGL_QUADSinstead ofGL_QUAD_STRIP.ThisworksaroundabuginsomeX‐Servers.
‐group N Numberofconsecu,vefilestoloadandsumtogether
‐hdf5dataset <dataset> NameofHDF5dataset(i.e./data)
63
‐ifont <fontname> TextfonttouseintheImageWindow
‐int Inputfileisrawbinarysignedintegers(4bytes/pixel).
‐invert_colors Invertthecolormapcolors
‐iscale X Scalefactortomul,plypixelvaluesby
‐itext Drawtextinimagewindowwithwhitebackground
‐jpeg_quality N Outputjpegquality.0isworst,100isbest,defaultis75.
‐jpeg_scale X Outputjpegand,fscale.0‐1.0,defaultis1.0.Onlyworkswith–sacommandlineop,on.
‐level1 Outputlevel1postscript(defaultislevel2)
‐log Takethelogofallthepixels:p=log(p)*1000
‐long Inputfileisbinarysignedlongs(8bytes/pixel)
‐marccd Marccdimage
‐minicbf Assumecbffilesareinminicbfformat
‐minval N Pixelswithvalue<=Narenotvaliddatapixels
‐mosflm MimicMosflm'scoordinatesystem.Shortcutfor:‐rotate90‐flipV‐scan_origin_pxUL‐scan_origin_mmUL
‐ncolors N Use N colors for the colormap. Default is 1024. If N=0,usethemaximumpossible
‐newpixmap Create a new pixmap when a new image is read. Thedefaultistoonlycreateanewpixmapifthenewimageisadifferentsize
‐no_adxv_beam_center Neitherreadnorcreatethe.adxv_beam_centerfile.
‐noborder Donotdrawaborderaroundtheimage(default)
‐nobs DonotuseBackingStoreonthedisplay
‐no_dectris_kludge Leave16‐bitunsigneddataasunsigned.Invalidpixels(‐1)aredisplayedas65535.
‐nofp Donottrytosetupfontpath(default)
‐no_default_win_pos Allowthewindowmanagertoplacewindows64
‐nodisplay Donotdisplaytheimage
‐nopixmap UseaWindowinsteadofaPixmapintheImageWindow.
‐norotate Donotrotatemar.imagefiles90degreesbeforedisplaying.
‐nosmooth When the image scale factor is less than 0.25, do notsmooth the displayed image. When a large image isscaled down, small spots may not be visible if simplyeveryn'thpixelisdisplayed.Smoothingisonbydefault.
‐nolabelPixmap LabelsarenotdrawnfromPixmaps
‐numpy InputfileisNUMPYformat
‐nx N Numberofpixelsinhorizontal(fast)direc,on
‐ny N Numberofpixelsinver,cal(slow)direc,on
‐o_direct OpenfileswithO_DIRECTforfasterI/O
‐offset N Constanttoaddtoallpixelvalues
‐oldcontrast Useolderautoma,ccontrastadjustment.
‐overload N Pixeloverloadvalue.Pixelslargerthanthisaredrawnasyellow.ThismayalsobesetintheProper,esWindow
‐parallel Usemul,pleprocessors(upto16)
‐peaks_adx Writepeaks.adx(XYI/Sigma)forpeaksearch.
‐pixelmap <pixelmapfile> Cheetahpixelmapfile(hdf5format)
‐pixelsize X Pixelsize(mm)
‐printheader Printimageheadertothestandardoutput
‐ps DisplaythePredic,onWindowatstartup.
‐q LineWindowhorizontalscaleisinq‐spaceunits
‐rfont <fontname> Fonttouseforresolu,onrings.
‐rings [res1, res2, ...] Displayresolu,onrings
‐rings_only Drawonlytherings,nottheresolu,ons65
66
‐rotate 90 | 180 | 270 Rotatetheimage90,180or270degreesbeforedisplayingit
‐sa Standalonemode.Thisreadsanimagefile,automa,callywritesajpeg,,fforimg file andthenexits. Itrequiresan input imagefileandoutputfilenameasthe lasttwoarguments, respec,vely. The output filename extension(.,ff,.jpegor.img)specifiestheoutputformat.
‐sa_crop WxH+X+Y In standalone mode (‐sa), this will crop the outputimage. The upper leg corner is X,Y and the outputdimensionsareWxH(pixels).
‐scandir Usestat()insteadofd_typefieldtodeterminethefiletype
‐scan_origin_mm UL|UR|LL|LR
The scan origin for mmcoordinatesdisplayedintheImageWindow.DefaultisLL(LowerLeg).Seealso‐fast_scan_mm.
‐scan_origin_px UL|UR|LL|LR
The scan origin for pixel coordinates displayed in theImageWindow.DefaultisUL(UpperLeg).Seealso‐fast_scan_px.
‐short ‐sshort
Inputfileisrawbinarysignedshorts(2bytes/pixel).
‐show_underload Showpixelsbelowathreshold.SeeProper,esWindow.
‐skip N Skip N bytes before readingrawbinarydata.Maybeusedtoskipafileheader.
‐slab_combine Sum|Avg Sum or Average data when combining mul,ple slabs.DefaultisSum.Appliestomul,‐dimensionalhdf5data.
‐slab N Firstslabofmul,‐dimensionalhdf5datatodisplay
‐slabs N Numberofslabsofmul,‐dimensionalhdf5datatomergeanddisplay
‐slowcbf Slowerrou,netoopenCBFfiles
‐small_cursor UseasmallercrosshaircursorintheImageWindow
‐small_spots Beierimagedisplayforimageswithsmallspots
‐smv32bits Output imgfileswillbe32‐bit signed integer, insteadof16‐bitunsignedshort
‐socket [port_number] Adxvwill listen fora socket connec,ononportnumber8100. The port number may be set with theADXV_DISPLAY_PORTenvironmentvariable.
‐spindle_orient H|V SpindleOrienta,on(forDPS)
‐spindle_rot clock|an@ SpindleRota,on(forDPS)
‐stride N NumberofSlabs/Filestostepwhenloadingthenextimage
‐swab ‐swap ‐swapbytes
Swapthetwo8‐bithalvesofeach16‐bitword
‐swap_beam_center Swapxandyposi,onofthebeamcenter
‐swaw Swapthetwo16‐bithalvesofeach32‐bitword
‐swadw Swapthetwo32‐bithalvesofeach64‐bitword
‐@ff InputfileformatisTIFF
‐@ff32 OutputTIFFfileformatwillbe32‐bitinteger
‐twotheta X 2‐Thetaangleindegrees.Defaultisreadfromtheimageheader
‐uchar Inputfileisrawbinaryunsignedchars(1byte/pixel)
‐underload N Thresholdbelowwhich to show small pixel values.MayalsobesetinProper,esWindow.
‐uint Inputfileisbinaryunsignedintegers(4bytes/pixel)
‐ushort Inputfileisrawbinaryunsignedshorts(2bytes/pixel)
‐verbose Moreverbosetextmessages
‐visual Visual VisualClassorIDtouse.Seexdpyinfo(1)orglxinfo(1).
‐wavelength X X‐Ray wavelengthinangstroms.Defaultisreadfromtheimageheader.
‐weak_data Beierimagedisplayfordatawithlowbackground67
‐win_pos_delta_x N Translate all default horizontal window posi,ons by Npixels
‐win_pos_delta_y N Translatealldefaultver,calwindowposi,onsbyNpixels
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EnvironmentVariables
ADXV_DISPLAY_PORT Porttolistenforasocketconnec,on.Defaultis8100.Alsosetwith–socketcommandlineargument
ADXV_PATTERN PaierntolistnewimagesintheLoadWindow.Defaultis*.img.
ADXV_SHOW_PIXELS Pixeloverloadvalue.Pixelslargerthanthisaredrawninyellow. Default is 65000, but may be changed in thePropertyWindow.
DISPLAY Setthedefaulthostanddisplaynumber.
MARHOME If$MARHOME/fontsexiststhenthiswillbeprependedtotheXFontPath.See‐nofp.
NO_ADXV_BEAM_CENTER Donotreadorwritethe.adxv_beam_centerfile
XFORMSTATUSFILE Filewhichspecifiesimagestoautoma,callyload(seethe‐autoloadcommandlineop,on).
OMP_NUM_THREADS Maximum number of threads to use when the ‐parallelcommandlineop,onisused.Maxis16.
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