C**************************      PICKPROFK    **********************************
C
C  Program for e.d. spot integration, using least-squares profile-fitting.
C       Many features of this program are similar to those found in the old 
C       programs PICKOFF, PICKYCOR and PICKAUTO.  The main change is the 
C       introduction of profile-fitting, which might help the accuracy of 
C       measurement of weaker spots.
C
C        remember to change version number if you update.
C       VX1.00  19.4.92         RH      original version
C       VX1.01  22.5.92         RH      substantial general debugging
C       VX1.02  19.3.96         RH      tidy up small raster performance
C       VX1.03  22.3.96         RH      debug lack of NSTEP some headers
C       VX2.00  23.3.96         RH      renamed as PICKPROFA - add unbend option
C                                       for use with CCD + tapered fibre optics
C       VX2.01  14.4.96         RH      substantial debugging e.g. subr CENTRE
C       VX2.02  25.6.96         RH      increase spots to 5000 and debug LOSCAL
C       VX2.03  28.6.96         RH      substantial debugging of profile fitting
C       VX2.04   4.7.96         RH      profile flattened prior to normalisation
C       VX2.05   6.5.97         RH      change PEN(2) to PEN(1)
C       VX2.06  8.11.97         RH      add rough code for tilted e.d. LPTYPE=3
C       VX2.07 20.11.97         RH      extensive debugging of old and new code
C                                       remove all JLOOK.le.0
C       VX3.00 24.11.97         RH      input B3, NCYC added; rename PICKPROFB
C       VX3.01 25.11.97         RH      option for global background averaging 
C       VX3.02  1.12.97         RH      radius of gyration, tilted deconvolution
C                                       profile LPTYPE=3 has shrink calculated 
C                                       by deconvoluting radii of gyration
C       VX3.03 24.12.97         RH      apply TILTDIR after lattice refinement
C                                       debug plotting of lattice vectors
C       VX3.04 29.12.97         RH      debug GLOBAL, check spot is present
C       VX4.00 30.12.97         RH      subroutine_reindex added, PICKPROFC
C       VX4.01  17.7.98         RH      check input OD range is < NLOOKUP=1500
C       VX4.02  29.8.98         RH      improved description of ATANGL,ATAXIS
C       VX5.00  22.8.00         RH      convert to plot2000 -> PICKPROFK
C         "     13.6.01         TSH     P2K_FONT needed string terminator
C                                                                              
C
C  Data cards are :
C
C  1.  A,B,G,ANGDIS,SHRINK,TILTDIR,KV,LPRINT
C       Real space cell dimensions and gamma angle,
C         angle on film perpendicular to which a shrinkage by factor SHRINK is
C         applied before calculating tiltaxis and tiltangle (using EMTILT).
C         TILTDIR - direction of tilt on microscope.
C                   -1 = clockwise on goniometer
C                   +1 = counterclockwise
C         LPRINT -  T  = comprehensive printout.
C
C  2.  LUNBEND,LGLOBL,NGLOBL
C        LUNBEND - T read in distortion correction table TABLEIN and use it to
C                     to correct predicted spot positions.
C                - F use the input file directly.
C        LGLOBL  - T OR F, apply wider global background subtraction
C        NGLOBL  - number of nearby spots to include global background correct.
C
C  3.  LPROFIT,LPTYPE,LPRANGE,INTERLEAVE,IFLATTEN,PROFMIN,TSIGMA
C        LPROFIT - T perform profile fitting
C                - F simple old-fashioned raster
C        LPTYPE - 0 use single profile for whole film.
C                 - 1 learn total of 5 profiles (4 outside quarters and centre)
C                      stored in APROF
C                 - 2 calculate profiles on a spot-by-spot basis, with LPRANGE
C                 - 3 learn 3 profiles for tilted e.d. with convolution to
C                      different parts of film, stored in TPROF - could be
C                      increased to 5 profiles if necessary later.
C        LPRANGE - Spots within LPRANGE pixels are used to perform local
C                    profile averaging, with option LPTYPE = 2.
C        INTERLEAVE - (T/F)  Apply odd/even scan line offset to eliminate 
C                      effects of densitometer zig-zag offset.
C        IFLATTEN - (T/F)  Flatten profile when density falls below PROFMIN.
C                          this is compulsory for LPTYPE=3
C        PROFMIN  - Density threshold for profile flattening - normally 0.03
C        TSIGMA   - Throw out outliers from background that deviate by more
C                    than TSIGMA*stndev from the fitted value, and refit.
C
C
C  4.  J,K 
C       Look-up table for optical density: LOOKUP(J)=K
C         This is linearly interpolated for J=1,1500.  The first card must have
C         J=1 and the last J=1500. 
C
C  5.  Description of source of above look-up table - TITLE.
C
C
C  6.  NPLATE  plate number, used on output file
C
C  7.  TITLE  Title of diffraction pattern, for use on output file.
C
C  8.  LREINDEX, ATANGL, ATAXIS
C       Attempt to reindex the lattice parameters so that the titlangle and
C         tiltaxis are close to the expected values given by ATANGL and ATAXIS
C         ATANGL always positive, ATAXIS measured relative to the XY-axis
C
C  9.  X0,Y0,TLTAXA,TLTANG,B3
C       Coordinates of centre, position of tiltaxis (angle from tiltaxis to
C         A-axis in direction A to B positive), size of tiltangle. If non-zero,
C         X0,Y0 as well as TLTAXA and TLTANG and B3 override values calculated 
C         internally or taken from header of digitised pattern. Note that
C         TLTAXA here is angle between tiltaxis and astar ON FILM, not in 3D 
C         as in ORIGTILT.  B3 is the pincushion distortion value (0.00000000240)
C
C  10. DX1,DY1,DX2,DY2  
C       Position of (1,0) and (0,1) relative to centre.  If non-zero, these 
C         values override the values on the input file header (from AUTOINDEX).
C
C  11. ROUT,RIN,PRPMAX  
C       Outer and inner radii in Angstroms, converted to pixels in the program
C         using cell dimensions on card 1.  PRPMAX is the maximum perpendicular
C         resolution from the tiltaxis.
C
C  12. NXM,NYM,    NXMT,NYMT
C       sizes for peak integration, peak raster sizes  used for initial 
C         lattice parameter refinement, near and far from tiltaxis.
C
C  13. FRACT,ABSOL,XAMINE,NCYC
C       Reflections with Friedel differences greater than FRACT and ABSOL are
C         rejected.  Weak reflections are rejected from the centre of gravity
C         and lattice parameter calculations by a criterion using XAMINE applied
C         to the peak rasters.  NCYC is maximum number of cycles of refinement 
C         of lattice parameters.   NCYC=0 indicates no refinement, where program
C         goes straight to integration - allows strict comparisons to be made.
C
C
C
C INPUT AND OUTPUT**************************************************************
C
C 'IN'     (1) : INPUT densitometered film array, any size.
C      FOR002  : OUTPUT of profile-fitted intensity values.
C 'RADIAL' (3) : INPUT radial density curve for background correction.
C 'YCORR'  (4) : INPUT Y-axis densitometer drift curve for background correction.
C      FOR005  : INPUT control cards.
C      FOR006  : OUTPUT datastream.
C 'PLOTOUT'    : PLOTTER OUTPUT of spot positions and c. of gravity deviations.
C 'INPARAM'(9) : INPUT header of image file with autoindexed lattice parameters
C 'DENOUT'(10) : OUTPUT of film density with radial background, ycorr, zigzag
C                      offset and profile fitted peaks subtracted - should be 
C                      completely flat.
C 'TABLEIN'(11): INPUT of position distortion correction table from ccunbende.for
C
C*******************************************************************************
C  Notes on meaning of some of the variables:
C       GSBACK,GPBACK   - global backgrounds derived from simple fit and profile
C       SINT,BACK       - simple raster integrated peak and background density
C       ICORR           - background-corrected raster integrated intensity
C       IPROF           - profile-fitted integrated intensity
C       XCOORD,YCOORD   - distortion corrected coordinates of spots.
C       X0,Y0           - coordinates of pattern centre.
C       JPROF           - exact interpolated raster of density around each spot.
C       LPROF           - logical array which flags over- or underloaded pixels.
C       TPROF           - three profiles for convolution in tilted patterns
C       APROF           - profile to be used for measurement in PROFMEAS
C       JSTORE          - raw densities transferred from input array.
C
C*******************************************************************************
C