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| | The adxv program can be downloaded from http://www.scripps.edu/tainer/arvai/adxv.html |
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| | == What if the Image Window doesn't refresh correctly under NX? == |
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| | This is a bug in NX and should be fixed in newer versions of the NX server. |
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| | Depending on the version of NX you have try adding one of the following options: |
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| | /usr/NX/etc/node.cfg |
| | AgentExtraOptions="-defer 0" |
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| | /etc/nxserver/node.conf |
| | AGENT_EXTRA_OPTIONS_X="-defer 0" |
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| | If this doesn't work try setting the Link Type to "LAN". This may be slower, but may also work. |
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| | Finally, try using "adxv -nopixmap" |
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| == Visualizing XDS data reduction == | | == Visualizing XDS data reduction == |
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| The latest beta versions of ADXV (from http://www.scripps.edu/~arvai/adxv/) can read spot files (whose name ends with .adx) and display them together with the frames. | | The latest beta versions of ADXV (from http://www.scripps.edu/~arvai/adxv/) can read spot files (whose name ends with .adx) and display them together with the frames. |
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| This is Fortran code for generating these files in the same directory where the frames are (i.e. you need write permission in that directory!):
| | These spot files can be written by [[generate_adx]]. In adxv's file selection window, it is useful to change the filename pattern from e.g. "*.cbf" to just "*" which then gives you the possibility to load frames and spot files at will. |
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| ! Task: generate .adx files from existing XDS.INP and XDS_ASCII.HKL
| | If using ADXV on a NoMachine (NX) desktop, it is useful to know that one needs the -nopixmap commandline option if the frame is not correctly displayed (I found that the zoom window still does not display correctly). |
| ! to be able to visualize where XDS finds/expects reflections
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| ! The latest beta versions of ADXV (from http://www.scripps.edu/~arvai/adxv/)
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| ! can read these .adx files and display them together with the frames.
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| ! Compilation: save this code as "generate_adx.f90" and compile with e.g.
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| ! gfortran -O -C generate_adx.f90 -o generate_adx
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| ! Then move the resulting binary to /usr/local/bin or ~/bin
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| ! Usage: go to the directory which has XDS_ASCII.HKL and run generate_adx
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| ! - the resulting files will be written to the directory where the frames are
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| ! - which means you need write permission for that directory
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| ! - which also means that the program might overwrite your frames if something goes wrong
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| ! If you don't want this then just change the NAME_TEMPLATE_OF_DATA_FRAMES= line.
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| ! Kay Diederichs 6/2009
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| !
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| implicit none
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| integer :: hkl(3),iframe,j=-10000,mini=huge(mini),maxi=-huge(maxi),&
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| nref=0,i,i1,i2,num
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| real intensity,sigi,x,y,z
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| character :: string*80,frmnam*80,form*6='(i0.0)'
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| logical :: back=.true.
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|
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| 100 format(5i5)
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| 101 format(a)
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|
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| ! find out NAME_TEMPLATE_OF_DATA_FRAMES
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| open(1,file='XDS.INP',status='old')
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| do
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| read(1,101,end=98) string
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| string=adjustl(string)
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| if (string(:29)=='NAME_TEMPLATE_OF_DATA_FRAMES=') then
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| frmnam=adjustl(string(30:))
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| i1=index(frmnam,'!')
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| if (i1>0) frmnam=frmnam(:i1-1)
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| if (index(frmnam,'.',back)>index(frmnam,'?',back)) then
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| frmnam=frmnam(:index(frmnam,'.',back))//'adx' ! exchange extension
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| else
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| frmnam=frmnam(:len_trim(frmnam))//'.adx' ! add extension
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| endif
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| endif
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| end do
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| 98 close(1)
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| print*,'.adx names :',frmnam(:len_trim(frmnam))
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| ! prepare modification of framename
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| i1=index(frmnam,'?')
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| i2=0
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| do i=i1,80
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| if (frmnam(i:i)=='?') then
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| i2=i
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| else
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| exit
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| endif
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| end do
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| if (i2==0) stop 'template should contain a ?'
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| write(form(3:3),'(i1)') i2-i1+1
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| form(5:5)=form(3:3)
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|
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| ! sort XDS_ASCII.HKL by frame number
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| print*,'sorting XDS_ASCII.HKL ...'
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| call system('grep -v \! XDS_ASCII.HKL | sort -k 8n > temp_adx.sort')
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| open(1,file='temp_adx.sort')
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| print*,'sorting XDS_ASCII.HKL done'
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|
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| num=10000
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| do
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| read(1,*,end=99)hkl,intensity,sigi,x,y,z
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| iframe=int(z)+1
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| mini=min(iframe,mini)
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| maxi=max(iframe,maxi)
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| nref=nref+1
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| if (mod(nref,num)==0) then
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| print*,'working',num
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| num=num*2
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| endif
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| if (iframe/=j) then ! new frame
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| write(frmnam(i1:i2),form) iframe
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| if (j/=-10000) close(2)
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| open(2,file=frmnam)
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| j=iframe
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| endif
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| ! XDS starts counting at 1, whereas ADXV starts at 0:
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| write(string,100) nint(x)-1,nint(y)-1,hkl
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| call removeblanks(string)
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| write(2,101)string(:len_trim(string))
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| end do
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| 99 print*,'first frame, last frame, nref=',mini,maxi,nref
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| close(1,status='delete')
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| close(2)
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| end
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| !
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| subroutine removeblanks(string)
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| ! Removes leading and trailing blanks, and turns multiple blanks into one blank.
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| implicit none
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| character string*(*),copy*80
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| integer i,j
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| logical first
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|
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| j=0
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| first=.false.
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| do i=1,len_trim(string)
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| if (string(i:i) /= ' ') then
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| j=j+1
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| copy(j:j)=string(i:i)
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| first=.true.
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| elseif (first) then
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| j=j+1
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| copy(j:j)=string(i:i)
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| first=.false.
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| endif
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| end do
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| string=copy(1:j)
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| end
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