#! /usr/bin/perl 
# ./NH-jmod4edit.pl dir_name increment_param
#increment_param is the parameter in the third dimension (for example relaxT)
#
#In stage I it will produce the ft2.com to be manipulated in nmrDraw: 
#>NH-jmod4edit.pl dir_name/ increment_param (NOTE: the neccesity of the slash after the dir_name may be OS dependent)
#
#In stage II, after we set the phase it will copy ft2.com to all increments and will convert to sparky:
#>NH-jmod4edit.pl dir_name/ increment_param spark (NOTE: the neccesity of the slash after the dir_name may be OS dependent)


open (IN,"<$ARGV[0]../procpar")||
                    die "cannot open file filename: $!";
my @timelistparam;		   
		    
while (<IN>) {
	$line=$_;
	
  	if ($line =~ /^sw /) {    # match line against "HUMAN"
       		$line = <IN>;
		chomp($line);
		my @listparam = split (" ",$line);
		$sw=$listparam[1];
	}
	if ($line =~ /^sw1 /) {    # match line against "HUMAN"
                $line = <IN>;
                chomp($line);
                my @listparam = split (" ",$line);
                $sw1=$listparam[1];
        }
  	if ($line =~ /^sfrq /) {    # match line against "HUMAN"
       		$line = <IN>;
		chomp($line);
		my @listparam = split (" ",$line);
		$sfrq=$listparam[1];
	}
  
	if ($line =~ /^dfrq2 /) {    # match line against "HUMAN"
       		$line = <IN>;
		chomp($line);
		@listparam = split (" ",$line);
		$dfrq2=$listparam[1];
	}
	
	
  	if ($line =~ /^ni /) {    # match line against "HUMAN"
       		$line = <IN>;
		chomp($line);
		my @listparam = split (" ",$line);
		$ni=$listparam[1];
       		print "$line\n";
	}
  	if ($line =~ /^np /) {    # match line against "HUMAN"
       		$line = <IN>;
		chomp($line);
		my @listparam = split (" ",$line);
		$np=$listparam[1];
       		print "$line\n";
	}
  	if ($line =~ /^$ARGV[1] /) {    # match line against "HUMAN"
       		$line = <IN>;
		chomp($line);
		@timelistparam = split (" ",$line);
		$T=$timelistparam[0];
       		print "$line\n";           # print line if matches
		#last;
	}
}
    
close(IN);

if($ARGV[2] ne "spark") # for starting with the processing
{

open (IN, ">$ARGV[0]/separate_2d.c")||
                    die "cannot open file filename $A1: $!";
		    
    		print IN "/* separate_3d.c

   This program takes data of the form array='f_Iz, phase2, phase'
   with f_Iz = 'n,y' and makes two data sets. The first
   is f_Iz ='n' and the second is f_Iz='y'.

   It also can be used for other interleaved experiments.  For example, Kappa = 0, 2.  
   January 10, 1997. Daiwen Yang 

mod by TC
array: phase,phase2,kappa

*/
#include <stdio.h>
#include <math.h>
#include <stdlib.h>


#define MAXDATA (16384*2)
  main(argc,argv)
     int argc;
     char *argv[];

  {
    FILE *fi,";
    for ($count=1; $count < $T;$count++)
    { print IN "*fi$count, ";}
     print IN "*fi$T;\n 
     char head_1[50],head_2[50];
    int ni,ni2,np,i,j,k,m;
    static int data_1[MAXDATA],data_2[MAXDATA], dataout_1[MAXDATA], dataout_2[MAXDATA];


 \n";

	print IN  "fi  = fopen(argv[1]\,\"r\")\;\n";
for ($count=1; $count< $T+1; $count++)
{
	$count2=$count+1;
	print IN  "fi$count  = fopen(argv[$count2]\,\"w\")\;\n";
}
$count=$count+1;
$count2=$count+1;
print IN    "if (fi==NULL) {
        fprintf(stderr,\"file 1 cannot \open\\n\");
        exit(1);
    }
    ni = atoi(argv[$count]);
    np = atoi(argv[$count2]);

    if (np > MAXDATA) {
 	fprintf(stderr,\"t3 point exeeds limit \%d\\n\",MAXDATA);
	exit(1);
    }\n";
print IN "    /* read header */\n
	  fread(head_1,1,32,fi);\n";
for ($count=1; $count< $T+1; $count++)
{
	$count2=$count+1;
	print IN  "	fwrite(head_1,1,32,fi$count);\n";
}

print IN "
    for(j=1; j<= ni; j++) 
    {\n";

for ($count=1; $count< $T+1; $count++)
{
print IN "
       	fread(head_1,1,28,fi);
       	fread(&data_1[1],4,np,fi);
       	fwrite(head_1,1,28,fi$count);
       	fwrite(&data_1[1],4,np,fi$count);

 	fread(head_2,1,28,fi);
	fread(&data_2[1],4,np,fi);
       	fwrite(head_2,1,28,fi$count);
       	fwrite(&data_2[1],4,np,fi$count);\n";
}

print IN "} \n fclose(fi);\n";
for ($count=1; $count< $T+1; $count++)
{ print IN "fclose(fi$count); ";}
print IN "}\n";
close(IN);

chdir("$ARGV[0]");
system("gcc separate_2d.c");
for ($count=1; $count< $T+1; $count++)
{ @fids[$count-1]="fid$count";}
$cut=join(" ","./a.out" ,"../fid", @fids,$ni,$np);
system("$cut");
print "$cut\n";
#system("varian");
open (IN, ">fid.com")||
                    die "cannot open file filename $A1: $!";


print IN "#!/bin/csh
\n";
$xT=$np/2;
$yN=2*$ni;

for ($count=1; $count< $T+1; $count++)
{
print IN "var2pipe -in ./fid$count -noaswap  \\
  -xN              $np  -yN               $yN  \\
  -xT              $xT  -yT                $ni  \\
  -xMODE        Complex  -yMODE        Complex  \\
";
printf IN "  -xSW        %8.3f  -ySW         %8.3f  \\\n", $sw, $sw1;
printf IN "  -xOBS         %6.3f  -yOBS          %5.3f  \\\n", $sfrq,$dfrq2;
print IN "  -xCAR           4.775  -yCAR         118.044  \\
  -xLAB              H1  -yLAB             N15  \\
  -ndim               2  -aq2D          States  \\
  -out ./test$count.fid -verb -ov
\n";
}
close(IN);
system("chmod +x fid.com");
system("fid.com");

#--------------------------- writing the first ft2.com file for nmrDraw
open (IN, ">ft2.com")||
                    die "cannot open file filename $A1: $!";


print IN "#!/bin/csh
\n";
print IN "
nmrPipe -in test1.fid                                       \\
|nmrPipe -fn  SOL                                           \\
#| nmrPipe  -fn MAC -macro \$NMRTXT/ranceY.M -noRd -noWr     \\
| nmrPipe  -fn SP -off 0.5 -end 1.00 -pow 1 -c 0.5          \\
| nmrPipe  -fn ZF -auto                                     \\
| nmrPipe  -fn FT -auto                                     \\
| nmrPipe  -fn PS -p0 0.0 -p1 0.0 -di -verb                 \\
| nmrPipe  -fn EXT -x1 6ppm -xn 12ppm -sw                   \\
| nmrPipe  -fn TP                                           \\
#| nmrPipe -fn LP -fb -ord 12                                \\
#| nmrPipe -fn LP -x1 1 -xn 60 -pred 30 -after -verb         \\
| nmrPipe  -fn SP -off 0.5 -end 1.00 -pow 1 -c 1.0          \\
| nmrPipe  -fn ZF -auto -size 1024                          \\
| nmrPipe  -fn FT -auto                                     \\
| nmrPipe  -fn PS -p0 -68.0  -p1 135.0 -di -verb            \\
| nmrPipe -fn REV                                           \\
#| nmrPipe -fn CS -ls 1.7ppm -sw                             \\
| nmrPipe  -fn POLY -auto                                   \\
| nmrPipe  -fn TP                                           \\
| nmrPipe  -fn POLY -auto                                   \\
   -ov -out test1.ft2\n";
close(IN);
system("chmod +x *");
system("ft2.com");	   
}

#-------------------------- writing the new ft2.com file, extracting the phase values from the previous ft2.com file in the nmrpipe folder.
if($ARGV[2]eq "spark")
{

chdir("$ARGV[0]");
system("ls");
	open (IN,"<ft2.com")||
                    die "cannot open file filename: $!";
	$flag=1;
		    
	while (<IN>) {
		$line=$_;
  		if ($line =~ /-fn PS -p0 /) {    
			if($flag)				#for f1
			{
				chomp($line);
				@listparam = split (" ",$line);
				$ph0_1=$listparam[5];
				$ph1_1=$listparam[7];
				print "$line\n";
				$flag=0;
			}else{					# for f2
				chomp($line);
				@listparam = split (" ",$line);
				$ph0_2=$listparam[5];
				$ph1_2=$listparam[7];
				print "$ph0_2 $ph1_2\n";
			last;
			}

		}
	}
	close(IN);
	open (IN, ">ft2.com")||
                    die "cannot open file filename $A1: $!";


	print IN "#!/bin/csh
	\n";
	
	for ($count=1; $count< $T+1; $count++)
	{
	print IN "
nmrPipe -in test$count.fid                                    \\
|nmrPipe -fn  SOL                                             \\
#| nmrPipe  -fn MAC -macro \$NMRTXT/ranceY.M -noRd -noWr       \\
| nmrPipe  -fn SP -off 0.5 -end 1.00 -pow 1 -c 0.5            \\
| nmrPipe  -fn ZF -auto                                       \\
| nmrPipe  -fn FT -auto                                       \\\n"; 
printf IN "| nmrPipe  -fn PS -p0 %3.1f  -p1 %3.1f -di -verb   \\\n", $ph0_1,$ph1_1;
print IN "| nmrPipe  -fn EXT -x1 6ppm -xn 12ppm -sw           \\
| nmrPipe  -fn TP                                             \\
#| nmrPipe -fn LP -fb -ord 12                                  \\
#| nmrPipe -fn LP -x1 1 -xn 60 -pred 30 -after -verb           \\
| nmrPipe  -fn SP -off 0.5 -end 1.00 -pow 1 -c 1.0            \\
| nmrPipe  -fn ZF -size 1024                                  \\
| nmrPipe  -fn FT -auto                                       \\\n";
printf IN "| nmrPipe  -fn PS -p0 %3.1f  -p1 %3.1f -di -verb   \\\n", $ph0_2,$ph1_2;
print IN "| nmrPipe  -fn POLY -auto                           \\
| nmrPipe -fn REV                                             \\
#| nmrPipe -fn CS -ls 1.7ppm -sw                               \\
| nmrPipe  -fn TP                                             \\
| nmrPipe  -fn POLY -auto                                     \\
   -ov -out test$count.ft2\n";
	   }
	close(IN);
	system("ft2.com");	   
	for ($count=1; $count< $T+1; $count++)
	{
		$k=$timelistparam[$count]*1000;
		$cmd="pipe2ucsf test$count.ft2 $k.lista.ct-NHjmod_media.ucsf";
#must be sure that pipe2ucsf is aliased in the /usr/local/bin directory			
		system("$cmd");
	}
}

##while(<IN>){
## chomp($_);