/* xf3d_hmsIST au program written by Sven G. Hyberts from a template by Wolfgang Bermel */
/* further developed by Clemens Anklin clemens.anklin@bruker.com                       */
/* the present implementation is limited to reconstruction of 3-dimensional spectra    */
/* 150602 - cga: nc_proc = 0 option with xf2 nd2d works around scaling issue
optional transform in f2 and f1
added abs2.water to the result of xf2 nd2d
Requires  brr2pipe.exe, hmsIST.exe and pipe2brr.exe in <TOPSPINHOME>/prog/bin
These biary programs are available on request and for MacOS, Linux and Windows7
*/


#undef DEBUG

int argc;
char **args;

/*
the present implementation is limited to reconstruction of 3-dimensional NUSpectroscopy,  /cga
*/


int fntype;
char path1[1024];
char path2[1024];
char path4[1024];

FILE *fptr3;

/* 
xf2 nd2d does a transform along the acquisition dimension irrespective of the 
dimensionality of the dataset (it always produces a 2rr and 2ri). 
Spectra in f2 are packed and in the order of nuslist
*/ 

GETCURDATA
char answer[8], answer2[8];

/* ask for ABS after f3 transform. Use standard code from abs2.water */
float dwater=4.7, delta=0.1;

			GETSTRING( "Perform f2 and f1 transform after reconstruction (y , n)",answer2);	
			GETSTRING( "Perform ABS after f3 transform (y , n)", answer );
			
	if (( strcmp( answer, "yes" ) == 0 ) || ( strcmp( answer, "y" ) == 0 ))
 {

GETFLOAT("Enter chemical shift of water in ppm :  ",dwater);
GETFLOAT("Enter distance from water in ppm :  ",delta);
 }
 



/*FETCHPAR ("FnTYPE", &fntype)
FETCHPARS ("FnTYPE", &fntype)
STOREPAR( "FnTYPE", 0 )
STOREPARS( "FnTYPE", 0 ) */
 

/*STOREPAR( "FnTYPE", fntype)
STOREPARS( "FnTYPE", fntype)*/

/* Setup of parameters in proc*s to be consistent with 3rrr that will be returned from reconstruction */

int xN, yN, dN;
FETCHPARN( 1, "SI", &yN ); 
FETCHPARN( 2, "SI", &xN ); 
FETCHPARN( 3, "SI", &dN );

int xTD, yTD, dTD;
FETCHPARN( 1, "TD", &yTD ); 
FETCHPARN( 2, "TD", &xTD ); 
FETCHPARN( 3, "TD", &dTD );


STOREPARNS( 1, "SI", yN );
STOREPARNS( 2, "SI", xN );
STOREPARNS( 3, "SI", dN );

STOREPARNS( 1,"STSI", yN );
STOREPARNS( 2,"STSI", xN );
STOREPARNS( 3,"STSI", dN );

STOREPARNS( 1, "TDeff", yTD);
STOREPARNS( 2, "TDeff", yTD);
STOREPARNS( 3, "TDeff", dTD );

STOREPARNS( 1, "FT_mod", 0);
STOREPARNS( 2, "FT_mod", 0);
STOREPARNS( 1, "XDIM", yN);
STOREPARNS( 2, "XDIM", xN);
STOREPARNS( 3, "XDIM", dN); 
STOREPARNS( 1, "WDW", 0);
STOREPARNS( 2, "WDW", 0);
STOREPARNS( 1, "PH_mod", 0);
STOREPARNS( 2, "PH_mod", 0);
STOREPARNS( 1, "ME_mod", 0);
STOREPARNS( 2, "ME_mod", 0);
yN /=2;
xN /=2;
yTD /=2;
xTD /=2;

(void)strcpy(path1, PROCPATH(""));
(void)chdir(path1);

#ifdef DEBUG
fprintf( stderr, "%s\n", path1);
#endif

if ( CPR_exec("xf2 nd2d nc_proc 0 1000",WAIT_TERM) )
   ABORT 
   
   DATASET(name, expno, 1000, disk, user);
   
SETCURDATA


/* do abs2.water on dataset created by xf2 nd2d */

	if (( strcmp( answer, "yes" ) == 0 ) || ( strcmp( answer, "y" ) == 0 )) 
{
STOREPAR("ABSF1",100.0)
STOREPAR("ABSF2",dwater+delta)
ABS2
STOREPAR("ABSF1",dwater-delta)
STOREPAR("ABSF2",-100.0)
ABS2
}
   
   int stsi3;
   FETCHPARS("STSI", &stsi3);
   
(void)strcpy(path2, ACQUPATH("pdata"));
(void)strcat(path2, "/1000/");

(void)chdir(path2);

#ifdef DEBUG
fprintf( stderr, "%s\n", path2);
#endif
/***** check and execute brr2pipe *****/

char path[1024];

char args_arg[1024];
char nuslist[1024];

Show_status( "Reconstruction with hmsIST...");

(void)sprintf(path,"%s/bin/brr2pipe.exe", PathXWinNMRProg() );

if (access(path, F_OK))
   {
   (void)sprintf(text, "file %s does not exist", path);
   STOPMSG(text);
   }


(void)sprintf( args_arg, "%s %s", path, "-in 2rr -dim 2 -out .test.nus" );


if ( system( args_arg ) < 0 )
   STOP
 
/***** check and execute hmsIST *****/


(void)sprintf(path,"%s/bin/hmsIST.exe", PathXWinNMRProg() );

if (access(path, F_OK))
   {
   (void)sprintf(text, "file %s does not exist", path);
   STOPMSG(text);
   }


(void)strcpy(nuslist, ACQUPATH("nuslist") );


(void)sprintf( args_arg, "%s -in .test.nus -over 1 -i_mult 0.70 -e_mult 0.70 -itr 25 -out .test.phf -dim 2 -xN %d -yN %d -sched %s", path, xTD, yTD, nuslist );
#ifdef DEBUG
fprintf( stderr, args_arg ); fprintf( stderr, "\n");
#endif

if ( system( args_arg ) < 0 )
   STOP

/***** check and execute pipe2brr *****/

(void)sprintf(path,"%s/bin/pipe2brr.exe", PathXWinNMRProg() );
 
if (access(path, F_OK))
   {
   (void)sprintf(text, "file %s does not exist", path);
   STOPMSG(text);
   }


#ifdef DEBUG 
fprintf( stderr, "%s\n", path2);
#endif

(void)chdir(path1);


(void)sprintf( args_arg, "%s -in %s/.test.phf -dim 2 -xTD %d -yTD %d -xN %d -yN %d -out 3rrr", path, path2, xTD, yTD, xN, yN );
#ifdef DEBUG
fprintf( stderr, args_arg ); fprintf( stderr, "\n");
#endif


if ( system( args_arg ) < 0 )
   STOP

/* switchback to original procnoand check if TD is larger or smaller than processed size, adjust tdeff in f1 and f2
 Process in f2 und f1 if desired */

DATASET(name, expno, 1, disk, user);
   
SETCURDATA
VIEWDATA

int tdeff1, tdeff2;

 if (  yTD > yN )
 { 
 	tdeff1 = yN*2;
 }
else
 {
 	  tdeff1 = yTD*2;
 }
 
  if (  xTD > xN )
 { 
 	tdeff2 = xN*2;
 }
else
 {
 	  tdeff2 = xTD*2;
 }
 


STOREPARNS( 1, "TDeff", tdeff1 );
STOREPARNS( 2, "TDeff", tdeff2 );

STOREPARS("STSI", stsi3);

(void)sprintf(path4,PROCPATH("title"));
fptr3 = fopen(path4,"at");
fprintf(fptr3,"This NUS data was reconstructed using hmsIST \n please cite \n Sven G. Hyberts, Alexander G. Milbrandt, Andreas B. Wagner, Haribabu Arthanari and Gerhard Wagner, \n Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling \n J Biomol NMR 52, 315-327 (2012). http://dx.doi.org/10.1007/s10858-012-9611-z ");

fclose(fptr3);

	if (( strcmp( answer2, "yes" ) == 0 ) || ( strcmp( answer2, "y" ) == 0 ))
 {
XCMD("ftnd 2")
XCMD("ftnd 1")
 }

QUIT