Adxv

Visualizing XDS data reduction

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.

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!):

! Task: generate .adx files from existing XDS.INP and XDS_ASCII.HKL
!       to be able to visualize where XDS finds/expects reflections
! The latest beta versions of ADXV (from http://www.scripps.edu/~arvai/adxv/) 
! can read these .adx files and display them together with the frames.
! Compilation: save this code as "generate_adx.f90" and compile with e.g.
! gfortran -O -C generate_adx.f90 -o generate_adx
! Then move the resulting binary to /usr/local/bin or ~/bin 
! Usage: go to the directory which has XDS_ASCII.HKL and run generate_adx
! - the resulting files will be written to the directory where the frames are
! - which means you need write permission for that directory
! - which also means that the program might overwrite your frames if something goes wrong
! If you don't want this then just change the NAME_TEMPLATE_OF_DATA_FRAMES= line.
! Kay Diederichs 6/2009
! 
     implicit none
     integer :: hkl(3),iframe,j=-10000,mini=huge(mini),maxi=-huge(maxi),&
                nref=0,i,i1,i2,num
     real intensity,sigi,x,y,z
     character :: string*80,frmnam*80,form*6='(i0.0)'
     logical :: back=.true.

100  format(5i5)
101  format(a)

! find out NAME_TEMPLATE_OF_DATA_FRAMES
     open(1,file='XDS.INP')
       do
         read(1,101,end=98) string
         string=adjustl(string)
         if (string(:29)=='NAME_TEMPLATE_OF_DATA_FRAMES=') then
           frmnam=adjustl(string(30:))
           i1=index(frmnam,'!')
           if (i1>0) frmnam=frmnam(:i1-1)
           if (index(frmnam,'.',back)>index(frmnam,'?',back)) then
             frmnam=frmnam(:index(frmnam,'.',back))//'adx' ! exchange extension
           else
             frmnam=frmnam(:len_trim(frmnam))//'.adx'  ! add extension
           endif
         endif
       end do
 98  close(1)
     print*,'.adx names :',frmnam(:len_trim(frmnam))
! prepare modification of framename
     i1=index(frmnam,'?')
     i2=0
     do i=i1,80
       if (frmnam(i:i)=='?') then
         i2=i
       else
         exit
       endif
     end do
     if (i2==0) stop 'template should contain a ?'
     write(form(3:3),'(i1)') i2-i1+1
     form(5:5)=form(3:3)

! sort XDS_ASCII.HKL by frame number
     print*,'sorting XDS_ASCII.HKL ...'
     call system('grep -v \! XDS_ASCII.HKL | sort -k 8n > temp_adx.sort')
     open(1,file='temp_adx.sort')
     print*,'sorting XDS_ASCII.HKL done'
     
     num=10000
     do 
       read(1,*,end=99)hkl,intensity,sigi,x,y,z
       iframe=int(z)+1
       mini=min(iframe,mini)
       maxi=max(iframe,maxi)
       nref=nref+1
       if (mod(nref,num)==0) then
         print*,'working',num
         num=num*2
       endif
       if (iframe/=j) then  ! new frame
         write(frmnam(i1:i2),form) iframe
         if (j/=-10000) close(2)
         open(2,file=frmnam)
         j=iframe
       endif
! XDS starts counting at 1, whereas ADXV starts at 0:
       write(string,100) nint(x)-1,nint(y)-1,hkl
       call removeblanks(string)
       write(2,101)string(:len_trim(string))
     end do
 99  print*,'first frame, last frame, nref=',mini,maxi,nref
     close(1,status='delete')
     close(2)
     end      
!
     subroutine removeblanks(string)
! Removes leading and trailing blanks, and turns multiple blanks into one blank.
     implicit none
     character string*(*),copy*80
     integer i,j
     logical first

     j=0
     first=.false.
     do i=1,len_trim(string)
       if (string(i:i) /= ' ') then
         j=j+1
         copy(j:j)=string(i:i)
         first=.true.
       elseif (first) then
         j=j+1
         copy(j:j)=string(i:i)
         first=.false.
       endif
     end do
     string=copy(1:j)
     end