Modified AU shearing program xfshear for SPAM echo/antiecho MQMAS
from Bruker BioSpin




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Modified AU program xfshear

The three-pulse z-filter MQMAS pulse sequence generates echo and antiecho, which have the same amplitude with the same sign. In contrast, the SPAM echo/antiecho pulse program generates echo amplitude and antiecho amplitude with opposite signs. Furthermore, the first sequence involves States acquisition procedure whereas the second sequence involves the echo/antiecho procedure. As a result, the shearing AU program should be modified accordingly.

/****************************************************************/
/*    xfshear2005            08.11.1996                         */
/****************************************************************/
/*    Short Description :                                       */
/*                                                              */
/*    Program for shearing of 2D MQMAS spectra of odd half      */
/*    integer quadrupolar nuclei. Data need to be aquired in    */
/*    States Mode                                               */
/*    Program used for shearing of ZQ-TROSY experiments         */
/*    like trosyzqgpphwg                                        */
/****************************************************************/
/*    Keywords :                                                */
/*                                                              */
/*    shear, odd half spin nuclei, multi quantum, mq, MQ        */
/*    ZQ-TROSY                                                  */
/****************************************************************/
/*    Description/Usage :                                       */
/*                                                              */
/*    Program is used                                           */
/*                                                              */
/*    a) for 2D MQ experiments on nuclei with                   */
/*    odd half integer spin for shearing-FT of 2D spectrum      */
/*    including 2DFT and referencing in F1 dimension            */
/*    according to delta(MQ)=delta(iso)+(p-R)delta(qis)         */
/*    It checks for the parameter "nucleus" (AMX) or "NUC1"     */
/*    (Avance) and sets the spin value accordingly.             */
/*    If the nucleus is not in the list it asks for the spin,   */
/*    too. Only most common nuclei are in the list.             */
/*    If the pulse program name matches mpxq, where             */
/*    x corresponds to the multiple quantum order of            */
/*    the experiment, then this is assumed, otherwise           */
/*    it is asked for by the program.                           */
/*    Program asks if abs2 in F2 dimension is desired.          */
/*    If answered with yes, then a Hilbert transform            */
/*    is automatically done, which requires xwinnmr1.3          */
/*    or later. In older versions, this command has to          */
/*    be eliminated from the program code.                      */
/*    A F1 frequency shift in ppm is asked for to compensate    */
/*    for malchosen o1 setting. This value is stored and        */
/*    suggested for any repeated processing.                    */
/*    b) for ZQ-TROSY experiments to eliminate the              */
/*    contribution of proton chemical shift in the              */
/*    F1 direction                                              */
/****************************************************************/
/*    Author(s) :                                               */
/*                                                              */
/*    Name          : Christian Fernandez                       */
/*    Organisation  : Universite de Lille, CNRS-801             */
/*    Email         : christian.fernandez@univ.lille.fr         */
/*                                                              */
/*    Name          : Stefan Steuernagel                        */
/*    Organisation  : Bruker Analytik                           */
/*    Email         : stefan.steuernagel@bruker.de              */
/****************************************************************/
/*    Name        Date       Modification:                      */
/*    ste         960201     created                            */
/*    ste         980813     check xdim's and status sizes      */
/*                           at right time                      */
/*    ste         980813     XHT2 included after XF1 to         */
/*                           allow f2 phase correction after    */
/*                           processing                         */
/*    ste         981101     close of input data files and      */
/*                           "mv temp-file to 2rr" etc          */
/*                           included                           */
/*    ste         000105     XIF2 and XFB included after        */
/*                           shearing to allow apodisation      */
/*                           in F2, set-up to be done prior     */
/*                           to execution of xfshear, all       */
/*                           handling done by this program      */
/*    ber/ste     010909     handling for ZQ-TROSY experiment   */
/*                           included, allows to use strip      */
/*                           transformation in F2 only          */
/*                           not strip-FT for MQMAS!            */
/*    ste         031031     shearing and calibration           */
/*                           of STMAS included                  */
/*                           "xf2 raw" command used to avoid    */
/*                           error if partly processed data     */
/*                           exist                              */
/*    ste         040112     check pparmod for 2D, so it can    */
/*                           be applied to planes from 3D       */
/*                           echo/anti-echo treatment incl.     */
/*    ste         041224     auto function included to          */
/*                           suppress abs2 and F1-shift query   */
/*                           dynamic memory allocation incl.    */
/****************************************************************/
/*
$Id: xfshear,v 1.15.2.2 2005/02/07 14:06:38 es Exp $
*/

#include <math.h>

int parmode, si2, si1, outexpno, tempfile2rr, infile2rr,
    tempfile2ir, infile2ir;

int *in2rr, *in2ir, *temp2rr, *temp2ir, *temp2rr2,
    *temp2ir2, *temp2rrB, *temp2irB, *temp2rrB2,
    *temp2irB2;

int dummy, nbytes, sizeofint, nbytesread, xdim2, xdim1, loopcount4,
    sig, mq, nspin, wdw2, bcmod, phmod, stsr2, stsi1, stsi2, fnmode, mc2;

int option1=0, option2=0;

double sw1, sw2, ratio, ph, ph1, ph2, ph3, phc1, phc2,
       in0, sfo1, sfo12, sfo11, bf11, bf12;

float Noise, spin, offset1, offset2, off2, off1, sr2, sr1, swh1;

char  inname2rr[PATH_LENGTH], tempname2rr[PATH_LENGTH],
      inname2ir[PATH_LENGTH], tempname2ir[PATH_LENGTH],
      imfile[8],
      outname[PATH_LENGTH], nucl[80], yes[20],
      pulprog[80], ti[80], ShearOpt[PATH_MAX];

/* select current dataset
   ====================== */
   GETCURDATA;
   (void) strcpy (yes,"yes");

/* is-it a 2D spectrum and taken in States, States-TPPI or EA?
   ===================== */
   FETCHPARS("PPARMOD",&parmode);
   if ( parmode != 1 )
   { STOPMSG("Program is only suitable for 2D data!");}

   FETCHPAR1S("FnMODE",&fnmode);
   if ( fnmode == 0 ) {
     FETCHPAR("MC2",&mc2);
     if ( mc2 != 3 && mc2 != 4 && mc2 != 5 )
       STOPMSG("mc2 must be States, States-TPPI, or Echo-Antiecho!");
   }
   else if ( fnmode != 4 && fnmode != 5 && fnmode != 6) 
     STOPMSG("FnMode must be in States, States-TPPI, or Echo-Antiecho!");

/* prepare for automatic execution and other ratio
   =============================================== */
   sprintf(ShearOpt,"%s",cmd);
   if ( strstr(ShearOpt,"auto")) option1 = 1;
   if ( strstr(ShearOpt,"ratio")) option2 = 1;

/* if auto selected, don't aks for ABS2 and additional F1 shift
   ============================================================ */
   if (option1 == 1)
   {
     f1=0.;
     FETCHPAR1S("NOISF1",&Noise);
     FETCHPARS("TI",ti);
     if (!strcmp(ti,"shearing done")) f1=Noise;
   }

   if (option1 == 0) 
   {

/* automatic baseline correction for MQMAS and STMAS ?
   =================================================== */
     if (mq != 1) GETSTRING("Apply ABS2 ? : ",yes);

/* additional F1 shift ?
   ===================== */
     f1=0.;
     FETCHPAR1S("NOISF1",&Noise);
     FETCHPARS("TI",ti);
     if (!strcmp(ti,"shearing done")) f1=Noise;
     if (mq != 1) GETFLOAT(" F1 shift in ppm ? : ",f1);
   }

/* init some variables
   =================== */
   FETCHPARS("PULPROG",pulprog);
   FETCHPARS("SFO1",&sfo1);
   FETCHPAR("WDW",&wdw2)
   STOREPAR("WDW",0)

/* shearing ratio calculation for quadrupolar nuclei
   set mq and spin to 1 for 1H
   ==================================================*/
   spin=5./2.;
   mq=3;
   FETCHPARS("NUC1",nucl)
   if(!strcmp(nucl,"off")) FETCHPARS ("NUCLEUS",nucl)
   if(!strcmp(nucl,"7Li")) spin=1.5;
   else if(!strcmp(nucl,"11B"))   spin=1.5;
   else if(!strcmp(nucl,"17O"))   spin=2.5;
   else if(!strcmp(nucl,"23Na"))  spin=1.5;
   else if(!strcmp(nucl,"27Al"))  spin=2.5;
   else if(!strcmp(nucl,"35Cl"))  spin=1.5;
   else if(!strcmp(nucl,"39K"))   spin=1.5;
   else if(!strcmp(nucl,"45Sc"))  spin=3.5;
   else if(!strcmp(nucl,"51V"))   spin=3.5;
   else if(!strcmp(nucl,"55Mn"))  spin=2.5;
   else if(!strcmp(nucl,"63Cu"))  spin=1.5;
   else if(!strcmp(nucl,"65Cu"))  spin=1.5;
   else if(!strcmp(nucl,"69Ga"))  spin=1.5;
   else if(!strcmp(nucl,"71Ga"))  spin=1.5;
   else if(!strcmp(nucl,"85Rb"))  spin=2.5;
   else if(!strcmp(nucl,"87Rb"))  spin=1.5;
   else if(!strcmp(nucl,"93Nb"))  spin=4.5;
   else if(!strcmp(nucl,"121Sb")) spin=2.5;
   else if(!strcmp(nucl,"209Bi")) spin=4.5;
   else if(!strcmp(nucl,"1H"))    spin=1.0;
   else GETFLOAT(" Enter spin number  : ",spin);
   nspin = (int) ceil ( (double)(2*spin) );
   if ( nspin == 3 && !strncmp(pulprog,"mp3q",4) )
     { mq = -3;
       ratio = 7./9.; }
   else
     { if (!strncmp(pulprog,"mp3q",4))           mq=3;
       else if(!strncmp(pulprog,"mp5q",4))       mq=5;
       else if(!strncmp(pulprog,"mp7q",4))       mq=7;
       else if(!strncmp(pulprog,"mp9q",4))       mq=9;
       else if(!strcmp(pulprog,"trosyzqgpphwg")) mq=1;
       else if(!strncmp(pulprog,"stmas",5))
         {
         mq=0;
         if(nspin == 3) ratio=-8./9.;
         if(nspin == 5) ratio=7./24.;
         if(nspin == 7) ratio=28./45.;
         if(nspin == 9) ratio=55./72.;
         }
       else GETINT(  " Enter the pQ order : ",mq);
       mq = (int) ceil ( (double)mq );
       if ( mq == nspin ) mq = -mq; 
       if ( nspin == 5 && mq == -5) ratio = 25./12.;
       if ( nspin == 5 && mq ==  3) ratio = 19./12.;
       if ( nspin == 7 && mq == -7) ratio = 161./45.;
       if ( nspin == 7 && mq ==  5) ratio = 11./9.;
       if ( nspin == 7 && mq ==  3) ratio = 101./45.;
       if ( nspin == 9 && mq == -9) ratio = 31./6.;
       if ( nspin == 9 && mq ==  7) ratio = 7./18.;
       if ( nspin == 9 && mq ==  5) ratio = 95./36.;
       if ( nspin == 9 && mq ==  3) ratio = 91./36.;
       if ( mq == 1 ) ratio = -1.; } ;
       if ( option2 == 1) GETDOUBLE(" Enter different shearing ratio :",ratio);

/* ignore strip parameters in F1 for 1H spectra!
   ============================================= */
   if (mq == 1 )  {
     FETCHPAR1("STSI",&stsi1);
     STOREPAR1("STSR",0);
     STOREPAR1("STSI",0);
     if (stsi1 != 0)
       Proc_err(0,"F1 Strip-FT not yet implemented,\nparameters disabled");
   }

/* ignore all strip parameters for MQMAS spectra !
   =============================================== */
   if ( mq != 1)  {
     FETCHPAR("STSI",&stsi2);
     FETCHPAR1("STSI",&stsi1);
     STOREPAR("STSR",0);
     STOREPAR("STSI",0);
     STOREPAR1("STSR",0);
     STOREPAR1("STSI",0);
     if (stsi2 != 0 || stsi1 != 0) 
       Proc_err(0,"Strip-FT not yet implemented,\nparameters disabled");
   }

/* calculate F2 transform 
   ====================== */
   SETCURDATA AUERR=CPR_exec( "xf2 raw",WAIT_TERM);
   if ( yes[0]=='y') {ABS2 XHT2}

/* get required status parameters after F2 transform
   ================================================= */
   FETCHPARS("SW_p",&sw2);
   FETCHPARS("SI",&si2);
   FETCHPARS("STSR", &stsr2);
   FETCHPAR1S("SWH", &swh1);
   FETCHPAR1S("SI",&si1);
   FETCHPAR1S("XDIM",&xdim1);
   FETCHPARS("XDIM",&xdim2);
   sizeofint=sizeof(int);
   nbytes=sizeofint*xdim2*2;

/* calculate phase for shearing and scaling for MQMAS/STMAS F1
   =========================================================== */
   ph1= -2.*3.141529*ratio*sw2 / swh1 / (double)(si2);

/* for MQMAS */
   if ( mq<0 ) ph1= -ph1;
   d1= fabs(ratio - (double)mq);

/* for TROSY */
   if ( mq==1 ) d1=1.0;

/* for STMAS of inner satellite */
   if ( mq==0 ) d1=fabs(ratio - 1.0);
   sfo11=d1*sfo1;

/* additional F1 shift
   =================== */
   ph2= (double)f1;
   phc2= -2.*3.141529*ph2*sfo11/(double)swh1; 

/* compensate for strip transformation of 1H spectra
   ================================================= */
   if ( mq == 1 ) {
     ph3 = - ph1 * stsr2;
     phc2 += ph3;
   }

/* decide 2ii or 2ir file
   ====================== */
   if ( fnmode == 1 ) (void)sprintf(imfile,"2ii");
   else (void)sprintf(imfile,"2ir");

/* Open source file RR and IR
   ========================== */
   (void)sprintf( inname2rr,"%s/data/%s/nmr/%s/%d/pdata/%d/2rr",
                  disk,user,name,expno,procno);
   if ((infile2rr=open(inname2rr,0))==-1)
     { (void)sprintf(text," I/O Error (Open) \n%s ",inname2rr);
       STOPMSG(text);}
   (void)sprintf( inname2ir,"%s/data/%s/nmr/%s/%d/pdata/%d/%s",
                  disk,user,name,expno,procno,imfile);
   if ((infile2ir=open(inname2ir,0))==-1)
     { (void)sprintf(text," I/O Error (Open) \n%s ",inname2ir);
       STOPMSG(text);}

/* Create temporary files : 2rrtemp et 2irtemp 
   =========================================== */
   (void)sprintf( tempname2rr,"%s/data/%s/nmr/%s/%d/2rrtemp",
                  disk,user,name,expno);
   if ((tempfile2rr=creat(tempname2rr,0664))==-1)
     { (void)sprintf(text," I/O Error (Create) \n%s ",tempname2rr); 
       STOPMSG(text);}
   (void)sprintf( tempname2ir,"%s/data/%s/nmr/%s/%d/2irtemp",
                  disk,user,name,expno);
   if ((tempfile2ir=creat(tempname2ir,0664))==-1)
     { (void)sprintf(text," I/O Error (Create) \n%s ",tempname2ir);
       STOPMSG(text);}
   (void)sprintf(text,"shear : calculating");
   Show_status(text);

/* allocate memory for array */
   in2rr = (int*)malloc(nbytes*10);
   if (in2rr == 0) STOPMSG("Not enough memory");
   in2ir = in2rr + nbytes/sizeofint;
   temp2rr= in2ir + nbytes/sizeofint;
   temp2ir= temp2rr + nbytes/sizeofint;
   temp2rr2= temp2ir + nbytes/sizeofint;
   temp2ir2= temp2rr2 + nbytes/sizeofint;
   temp2rrB= temp2ir2 + nbytes/sizeofint;
   temp2irB= temp2rrB + nbytes/sizeofint;
   temp2rrB2= temp2irB + nbytes/sizeofint;
   temp2irB2= temp2rrB2 + nbytes/sizeofint;

/* Read data in submatrix 
   ====================== */
   TIMES(si1/xdim1)
     TIMES2 (si2/xdim2)
       TIMES3 (xdim1/2)
         if ((nbytesread=read(infile2rr,in2rr,nbytes))<=0)
                                                  /* Read 2 rows ! */
           {(void)remove(tempname2rr);
            STOPMSG(" 2rr file corrupted! ");}

         if ((nbytesread=read(infile2ir,in2ir,nbytes))<=0)
           {(void)remove(tempname2ir);
            STOPMSG(" 2ir file corrupted! ");}

         /* Store Sx */
         for (loopcount4=0;loopcount4<xdim2;loopcount4++)
         { temp2rr[loopcount4]= in2rr[loopcount4];
           temp2ir[loopcount4]= in2ir[loopcount4];}

         /* Store iSy */
         for (loopcount4=0;loopcount4<xdim2;loopcount4++)
         { temp2rr2[loopcount4]= in2rr[loopcount4+xdim2];
           temp2ir2[loopcount4]= in2ir[loopcount4+xdim2];}

         /* combine Sx and iSy to create ... 
            ================================ */
         for (loopcount4=0;loopcount4<xdim2;loopcount4++)
         {
           /* echo
              ==== */
            temp2rrB[loopcount4]=(temp2rr[loopcount4]
              -temp2ir2[loopcount4])/2;
            temp2irB[loopcount4]=(temp2ir[loopcount4]
              +temp2rr2[loopcount4])/2;

            /* and antiecho
               ============ */
            temp2rrB2[loopcount4]=(temp2rr[loopcount4]
              +temp2ir2[loopcount4])/2;
            temp2irB2[loopcount4]=(temp2ir[loopcount4]
              -temp2rr2[loopcount4])/2;
         }

         /* perform shearing transformation  
         =============================== */
         i1= loopcount3 +(loopcount1)*xdim1/2;
         for (loopcount4=0;loopcount4<xdim2;loopcount4++)
           { i2= loopcount4+(loopcount2)*xdim2;
             phc1= ph1*(double)((i2-si2/2)*i1); 
             phc1+=phc2*(double)i1;
             in2rr[loopcount4]= 
               (int)(((double)temp2rrB[loopcount4])*cos(phc1)
                +((double)temp2irB[loopcount4])*sin(phc1))/2;
             in2ir[loopcount4]= 
               (int)(((double)temp2irB[loopcount4])*cos(phc1)
                -((double)temp2rrB[loopcount4])*sin(phc1))/2;
             in2rr[loopcount4+xdim2]= 
               (int)(((double)temp2rrB2[loopcount4])*cos(phc1)
                -((double)temp2irB2[loopcount4])*sin(phc1))/2;
             in2ir[loopcount4+xdim2]= 
               (int)(((double)temp2irB2[loopcount4])*cos(phc1)
                +((double)temp2rrB2[loopcount4])*sin(phc1))/2;
           }
         for (loopcount4=0;loopcount4<xdim2;loopcount4++)
           {temp2rr[loopcount4]=0.5*( 
              in2rr[loopcount4]+in2rr[loopcount4+xdim2]);
            temp2ir[loopcount4]=0.5*( 
              in2ir[loopcount4]+in2ir[loopcount4+xdim2]);
            temp2irB[loopcount4]=0.5*( 
              in2rr[loopcount4]-in2rr[loopcount4+xdim2]);
            temp2rrB[loopcount4]=0.5*( 
              in2ir[loopcount4]-in2ir[loopcount4+xdim2]);
           }
         for (loopcount4=0;loopcount4<xdim2;loopcount4++)
           {in2rr[loopcount4]= temp2rr[loopcount4];
            in2ir[loopcount4]= temp2ir[loopcount4];
            in2rr[loopcount4+xdim2]= temp2rrB[loopcount4];
            in2ir[loopcount4+xdim2]= temp2irB2[loopcount4];
           }

         /* Save
            ==== */
         write(tempfile2rr,in2rr,nbytesread);
         write(tempfile2ir,in2ir,nbytesread);
       END ; /* loop3 */
     END; /* loop2 */
   END; /*loop1 */

   close(tempfile2rr);
   close(tempfile2ir);  
   close(infile2rr);
   close(infile2ir);

/* Copy  
   ==== */
   (void)remove(inname2rr);
   if (rename(tempname2rr,inname2rr)!=0) Proc_err(1,"error %d",errno);
   (void)remove(inname2ir);
   if (rename(tempname2ir,inname2ir)!=0) Proc_err(1,"error %d",errno);
   (void)sprintf(text,"shear : finished");
   Show_status(text);

/* F1 Scaling for MQ MAS experiments
   ================================= */
   if ( option2 == 0) {
     if ( d1 != 1.0 ) {
       FETCHPARS("BF1",&bf12);
       FETCHPARS("SR",&sr2);
       bf11= d1*bf12;
       sr1=  (float)(d1*sr2);
       STOREPAR1S("BF1",bf11);
       STOREPAR1("BF1",bf11);
#if 1
       STOREPAR1S("SF",bf11 + sr1 * 1e-6);
       STOREPAR1("SF",bf11 + sr1 * 1e-6);
#endif
#if 0
       STOREPAR1S("SR",sr1 );
       STOREPAR1("SR",sr1);
#endif
       STOREPAR1S("SFO1",sfo11);
       STOREPAR1("SFO1",sfo11);
       FETCHPAR1S("OFFSET",&offset1);
       offset1=offset1-ph2;
       STOREPAR1S("OFFSET",offset1);
     }
   }

/* store TI to recall shearing and shifting
   ======================================== */
   STOREPARS("TI","shearing done");
   STOREPAR1S("NOISF1",f1);

/* inverse F2 and subsequent F2+F1 transform
    ========================================= */
   XHT2
   XIF2
   FETCHPAR("PH_mod",&phmod)
   STOREPAR("PH_mod",0)
   STOREPAR("WDW",wdw2)
   FETCHPAR("BC_mod",&bcmod)
   STOREPAR("BC_mod",0)
   CPR_exec("xfb nc_proc 0",WAIT_TERM);
   STOREPAR("PH_mod",phmod)
   STOREPAR("BC_mod",bcmod)
   VIEWDATA
   QUITMSG(" Shearing-FT done!")

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