C ++********************************************************************
C                                                                      *
C                                                                      *
C                                                                      *
C **********************************************************************
C=* FROM: SPIDER - MODULAR IMAGE PROCESSING SYSTEM.   AUTHOR: J.FRANK  *
C=* Copyright (C) 1985-2005  Health Research Inc.                      *
C=*                                                                    *
C=* HEALTH RESEARCH INCORPORATED (HRI),                                *   
C=* ONE UNIVERSITY PLACE, RENSSELAER, NY 12144-3455.                   *
C=*                                                                    *
C=* Email:  spider@wadsworth.org                                       *
C=*                                                                    *
C=* This program is free software; you can redistribute it and/or      *
C=* modify it under the terms of the GNU General Public License as     *
C=* published by the Free Software Foundation; either version 2 of the *
C=* License, or (at your option) any later version.                    *
C=*                                                                    *
C=* This program is distributed in the hope that it will be useful,    *
C=* but WITHOUT ANY WARRANTY; without even the implied warranty of     *
C=* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU  *
C=* General Public License for more details.                           *
C=*                                                                    *
C=* You should have received a copy of the GNU General Public License  *
C=* along with this program; if not, write to the                      *
C=* Free Software Foundation, Inc.,                                    *
C=* 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.      *
C=*                                                                    *
C **********************************************************************
C                                                                      *
C                                                                      *
C                                                                      *
C  PURPOSE:                                                            *
C                                                                      *
C  PARAMETERS:                                                         *
C                                                                      *
C        0         2         3         4         5         6         7 *
C23456789012345678901234567890123456789012345678901234567890123456789012
C***********************************************************************

      SUBROUTINE MRALIGN(XYPTS,PRJ,ANGLE,SHIFT,SCALE,PTACTIVE,ls)


C TAKES IMAGES XYPTS AND TRANSFORMS THEM BY ROTATING ABOUT THE
C GEOMETRICAL CENTER (NOT CENTER OF MASS) AND TRANSLATING IT
C BY SHFT.
C
C INPUT:
C     XYPTS(2,LS,LV)= COORDS OF POINTS TO BE TRANSFORMED
C     ANGLE(3,LV)= EULER ANGLES. ANGLE(2) IS TILT AND ANGLE(1) IS
C                  FINAL ROTATION CORRECTION (APPLIED HERE)
C     SHIFT(2,LV)= SHIFT (X,Y) THAT THE IMAGE MUST UNDERGO
C     SCALE(LV)= MULTIPLICATIVE SCALING FACTOR
C COMMON INPUT:
C     NUMPTS(LV)= MAXIMUM INDEX OF POINTS USED IN AN IMAGE
C     NTVW= TOTAL NUMBER OF VIEWS IN SERIES
C     NTPT= TOTAL NUMBER OF DISTINCT MARKERS USED
C     CIR(2)= COORDS OF CENTER OF IMAGE
C
C OUTPUT:
C     PRJ(2,LS,LV)= COORDS OF CORRECTED POINTS
      LOGICAL*1   PTACTIVE(LS)
      DIMENSION   XYPTS(2,LS), PRJ(2,LS)
      DIMENSION   SHIFT(2)

C
        CA = COS(ANGLE)
        SA = SIN(ANGLE)
C
C     Image center (CIR) WAS already subtracted in MRGETINFO.
C     ROTATION IS MEANT TO BE AROUND THE CENTER OF THE IMAGE
C     NOT AROUND THE CORNER OR CENTER OF MASS
C    _                 _   _
C    X' = Scale*R(psi)*X + Shift
C
        DO  IPT=1,ls
	if(ptactive(ipt))  then
c
c  this provision will make it work for prj == xypts
	qt=XYPTS(1,IPT)
      PRJ(1,IPT)= SCALE*( qt*CA + XYPTS(2,IPT)*SA) + SHIFT(1)
      PRJ(2,IPT)= SCALE*(-qt*SA + XYPTS(2,IPT)*CA) + SHIFT(2)
	endif
	ENDDO
      END