C*******************************************************************************
C
C TTREFINE : refines defocus, astigmatism, tiltaxis and tiltangle in images
C            of thin tilted crystals.
C         VERY IMPORTANT NOTE : The quality of image data required for success
C            in this type of least squares refinement is high, particularly
C            if more than one parameter is to be refined. BE VERY CAREFUL.
C
C       Version 1.01    9 Dec 1985      RH
C       Version 1.02    27 Dec 1985     RH
C       Version 1.03    13 Sep 1986     JMB     Corr stat interm output.
C       Version 1.04    1 May 1987      RH      Allows points off curve
C       Version 1.05    1 July 1987     RH      Allows NX.ne. NY
C       Version 1.06    2 July 1987     JMB     Allows up to 800 spots
C       Version 1.07    28 Oct 1987     JMB     ISHIFT option on card 1
C       Version 1.08    2  Nov 1987     JMB     IREF=0 option on card 1
C       Version 1.09    7  Dec 1987     JMB     Some tidying
C       Version 1.10    30 Dec 1987     RH      Correction to TANGL sign
C       Version 1.11    19 Feb 1988     JMB     Some Format alterations
C       Version 1.12    30 Mar 1989     RH      FSHIFT drops if oscill.
C       Version 1.13     8.Jun 1989     JMB     Better converg. test & formats.
C       Version 1.14    14 Jun 1989     RH      IQ=9 added.
C       Version 2.00     3 Jan 1992     RH      Convert to UNIX for Alliant
C       Version 2.01    25 Jul 1995     RH      Convert to Alpha, extraneous bit
C       Version 2.02     4 Jul 1999     RH      add mtz input, remove all lcf
C       Version 2.03    30 Oct 1999     RH      STOP if ISHIFT=T and NCYC.gt.1
C       Version 2.04    29 Mar 2000    JMS      irtorg mod to include zorigin
C       Version 2.05    29 Oct 2001     RH      change FILIN to CHARACTER*80
C       Version 3.00    30 Oct 2005     HS      2dx
C
C DATACARDS :
C
C  1.   IMODE,NCYC,FSHIFT,LIST,MTZ,MAXIM,LISTS,ISHIFT,IREF        (*)
C
C  2.   FILIN -- full name of input file (.FFT)
C
C  3.   ISIZEX,ISIZEY,DSTEP,XMAG,CS,KVOLT           (*)
C
C  4.   NUMSPOT, NOH, NOK, NHOR, NVERT              (*)
C
C  5.   RESMIN, RESMAX                              (*)
C
C  6.   AX, AY, BX, BY                              (*)
C
C  7.   ISPGRP,ORIGH,ORIGK,REVHK,ROT180,SGNXCH      (*)
C
C  8.   DFMID1,DFMID2,ANGAST,TLTAXIS,TLTANGL   (*)  These are parameters which
C                                                       can be refined.
C  9.   LABIN FC=F SIGFC=SIGF PHCAL=PHS FOM=FOM ##      Program uses SIGFC as test for
C                                                       the presence of F and FOM as
C                                                       test for presence of phase. This
C                                                       data is input on stream HKLIN
C
C
C     IMODE       if = 1 Defocus refined
C                    = 2 Defocus and astigmatism refined.
C                    = 3 Tiltaxis refined.
C                    = 4 Tiltangle refined.
C                    = 5 All five parameters refined.
C     NCYC        Maximum number of cycles of refinement.
C     FSHIFT      Fractional shifts to be applied at each cycle.
C     LIST        if T, list spots whose amps and phases will be used,
C                       and list their resulting details.
C     MTZ         if T, reads in ref amplitudes from MTZ(or non-MTZ) file.
C                 if F, uses dummy amplitudes, in which case the various
C                       R-factors and residuals do not mean a lot.
C     MAXIM       IF T, the program simply maximises the corrected diffraction
C                        spot intensities.
C                 if F, the program minimises the rms R-factor against MTZ amps.
C     LISTS     IF T, write output to data set 10 for use in statistics 
C                 program
C     ISHIFT    IF T, adds 1/3(ax + bx); 1/3(ay +by) to lattice points for use
C                 in control calculations. If F does nothing. As an added 
C                 caution, ISHIFT.eq.T requires NCYC.lt.2
C     IREF        if = 0 Set IREF=0. Read formatted data h,k,a,p; not MTZ file
C                    = 1 Use MTZ file ---- only needed if MTZ.eq.T
C
C     ISIZEX      size of image, used to check against image file-header.
C     ISIZEY
C     DSTEP       densitometer stepsize in microns.
C     XMAG        magnification of micrograph.
C     CS          spherical aberration coefficient in mm.
C     KVOLT       microscope voltage in KV, used to calculate wavelength. 
C     NUMSPOT     number of spots to be printed out at each cycle.
C     NOH, NOK    number of orders of spots in H & K directions to be generated.
C     NHOR, NVERT box size in grid units in horizontal & vertical directions,
C                 i.e. X & Y resp. ( up to 20 grid units in each
C                 direction).
C     RESMIN, RESMAX inner & outer resolution limits in Angstroms within which
C                        spots(centre of box) must fall.
C     AX,AY,BX,BY coordinates in grid units of 1,0 & 0,1 spots
C                 respectively.
C     DFMID1      defocus in one direction (underfocus +ve) 
C     DFMID2      defocus at 90-degs to above
C     ANGAST      direction for DFMID1 in degrees relative to x,y in transform.
C     TLTAXIS     direction of tiltaxis in degrees relative to x,y in transform,
C                   should be between -90 and +90 degrees.
C     TLTANGL     magnitude of tiltangle.
C                       (+ve for less underfocus at start of scan(y=0))
C                          (or if TLTAXIS is parallel to y, at x=0)
C     ISPGRP      two-dimensional space group number (1 - 17)
C     ORIGH,ORIGK phase origin shifts for (1,0) and (0,1) reflection to bring
C                 phases to the precise crystallographic origin (from ORIGMERG).
C     REVHK       reverses H and K before comparing to reference data.
C     ROT180      rotates by 180 degs about c-axis. (needed in p3)
C     SGNXCH      rotates by 180 degs about a-axis. (needed in p121)
C
C  The function which this program minimises (when MTZ=.TRUE. and MAXIM=.FALSE.)
C    is :-
C
C    L = Sum of [1/sigma**2]*[Aobs-Aed*]**2
C
C                                       where Aed is the scaled (sf+tf)
C                                          electron diffraction data.
C                                       and Aobs is the result of con-
C                                          volution of the F.T. of the
C                                          image with the F.T. of the
C                                          function of ctf with position.
C                                       See Henderson et al, Utramic.(1986).
C
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C