//cppwXnut - Obtain an X nutation curve using cross polarization and a 
//           flipback pulse.Characterize B1 homogeneity (R,F),calculate
//           the desired amplitude aX90 to obtain the specification, and
//           calculate the predicted 180-degree null, pwX180. 
 
//           Follow this calibration with cppwXnull to refine aX90.

//===================
// The SETUP macro
//===================

if (($#>0) and ($1='setup')) then   

// Set the Nuclei and Region

   parammodule('setsampleglobals')
   rtppar('Settancpx')
   AhX
   pseq = 'two'
   parammodule('updatesampleglobals')
   parammodule('studydir')

// Set the Region, Force pwr = ''

   $reg='' $pwr='' $nuc=''
   $macroname = $0 + '(\'region\',$2,$3,$4,1):$reg,$pwr,$nuc'
   exec($macroname)
   $pwr=''

// Change Region Defaults

   d1=5.0 nt=4

// Get the Spinrate

   exists('SPspinrateon','parameter','global'):$e
   if ($e<0.5) then 
      create('SPspinrateon','string','global')
      SPspinrateon='n'
   endif
   if (SPspinrateon='y') then 
      $macronamespin = $0 + '(\'spinrate\'):$srate'
      exec($macronamespin)
   else 
      probeparamgroup('getlocal',$reg,'H1','','srateHX'):srate
   endif

   if (srate<500) then 
      write('error','Warning: Error: srate<500, Calibrate srateHX>500 in the Probe File')
      abort
   endif

// Calibrate setddrtc for CP

   exists('ddrpm','parameter'):$e
   if ($e < 0.5) then
      create('ddrpm','string')
      ddrpm='r'
   endif   
   rof2=rd-0.6 alfa=ad

// Check the Spinrate

   probeparamgroup('getlocal',$reg,'H1','','srateHX'):$srate
   if (((srate < 0.995*$srate) or (srate > 1.005*$srate)) and (SPspinrateon='y')) then       
      write('error','Warning: Warning: srate=%f Hz and srateHX=%f Hz in the Probe File Disagree\n',srate,$srate)
   endif

// Obtain Standard CP and Decoupling Parameters from Probe File

   probeparamgroup('getlocal',$reg,$nuc,'','ofX90','dbX90'):$tof,tpwr
   tof=$tof
   probeparamgroup('getlocal',$reg,'H1','','ofX90','dbX90'):$dof,dpwr
   dof=$dof
   probeparamgroup('get',$reg,'H1','HX','ch','sh','to','fr',
                                         'aH','b','d','t','of')
   probeparamgroup('get',$reg,$nuc,'HX','aX')
   probeparamgroup('get','hp'+$reg,'H1','90H','a','pw')
   probeparamgroup('get',$reg,$nuc,'90X','a','pw')
   probeparamgroup('get',$reg,'H1','tppmH','a','pw','ph')
   probeparamgroup('get',$reg,'H1','spinalH','a','pw','ph','alp')
   Hseq = 'spinal'

// Set Decoupler and Acquisition

   phHspinal=0.0 alpHspinal=0.0 phHtppm=0.0
   aHspinal=aH90*pwH90/7.0 aHtppm=aHspinal
   sw=10000.0 at=0.2

// Access Sample Module

   exists('SPsamplefilename','parameter','global'):$e
   if ($e<0.5) then 
      create('SPsamplefilename','string','global')
      SPsamplefilename=''
   endif

   exists('samplefilename','parameter'):$e
   if ($e<0.5) then 
      create('samplefilename','string')
      samplefilename=''
   endif

   samplefilename=''
   $e=0 $e1=0
   if (SPsamplefilename<>'') then 
      $studysamplefilename=archivedir+'/'+sample+'/dirinfo/'+SPsamplefilename
      exists($studysamplefilename,'file'):$e
      if ($e>0.5) then
         shell('touch '+$studysamplefilename):$dum
         fread($studysamplefilename)
         samplefilename=SPsamplefilename
         write('line3','Obtain Sample Module %s from Study',SPsamplefilename)
      else
         $usersamplefilename=userdir+'/modules/'+SPsamplefilename
         exists($usersamplefilename,'file'):$e1
         if ($e1>0.5) then
            shell('touch '+$usersamplefilename):$dum
            fread($usersamplefilename)
            samplefilename=SPsamplefilename
            write('line3','Obtain Sample Module %s from Modules Directory',SPsamplefilename)
         else 
            write('error','ERROR: Sample Module Does Not Exist')
         endif
      endif
   endif 

   if (samplefilename<>'') then 
      if (tn='C13') then
         if (C13d1>0.0) then d1=C13d1 endif
         if (C13nt>0.0) then nt=C13nt endif
         if (C13sw>0.0) then sw=C13sw endif
         if (C13at>0.0) then at=C13at endif
         if (C13np>0.0) then np=C13np endif
      endif

      if (tn='N15') then
         if (N15d1>0.0) then d1=N15d1 endif
         if (N15nt>0.0) then nt=N15nt endif
         if (N15sw>0.0) then sw=N15sw endif
         if (N15at>0.0) then at=N15at endif
         if (N15np>0.0) then np=N15np endif
      endif
   endif

// Save Sample Module with Study

   $e=0
   if (SPsamplefilename<>'') then
      $studysamplefiledir=archivedir+'/'+sample+'/dirinfo'
      exists($studysamplefiledir,'directory'):$e
      if ($e>0.5) then
         module('list',SPsamplefilename):$list
         writeparam(archivedir+'/'+sample+'/dirinfo/'+SPsamplefilename,$list,'current')
         write('line3','Write Sample Module %s to Study',SPsamplefilename)
      else
         write('line3','Sample Module not Written')
      endif
   endif

// Set the Auto Display to Absolute Value

   $macroname = $0 + '(\'maxamp\',100)'
   wnt='vp=0 sb=\'y\' wft setref av ' + $macroname + ' noislm(1.0) dssh'

// Set Macro-Specific Processing and Plotting 

   wexp = 'chempackQ'
   execprocess = $0 + '(\'process\',\''+$2+'\',\''+$3+'\',\''+$4+'\',0)'
   execplot = ''
   clear(2)
//   au
   return
endif

//===========================
// Macro-Specific Processing
//===========================

if (($# > 0) and ($1 = 'process')) then 

// Analyze the 1H Nutation Curve

   $macroname = $0 + '(\'refx\',$2,$3,$4,0)'
   exec($macroname)  
endif

//==========================
// Macro-Specific Plotting
//==========================

if (($# > 0) and ($1 = 'plot')) then 
   wc = 50 sc = 50
   plot1d
   return  
endif 

//==================================
// Begin AutoCalibration Utilities
//==================================

//--------------------
// The maxamp function
//--------------------

if (($# > 0) and ($1 = 'maxamp')) then
   select(celem) 
   if (celem=1) then 
      vsadj($2) 
   endif
   peak:$ht
   if ($ht>$2) then 
      vsadj($2) 
   endif 
   return    
endif  

//--------------------------
// The  minmaxfit function
//--------------------------

if (($# > 0) and ($1 = 'minmaxfit')) then 

   $bestone=$2
   $lim=2
   if ($#>3) then $lim=$4 endif

// Prepare 'analyze.inp'

   $file=curexp+'/analyze.inp'
   exists($file,'file'):$a
   if ($a>0.5) then 
      write('reset',$file) 
   endif

   format((2*$lim+1),2,0):$sizes

   write('file',$file,'AMPLITUDE')
   write('file',$file,'INTENSITY')
   write('file',$file,'%12s%13s%7s%7s\n','1',$sizes,'linear','linear')
   format((2*$lim+1),2,0):$sizes
   write('file',$file,'%8s%5s','NEXT',$sizes)
   write('file',$file,'1')

   $step=$bestone-$lim
   repeat
      select($step)
      peak:$ht
      write('file',$file,'%14.1f%12.2f',$step,$ht)
      $step=$step+1
   until ($step>$bestone+$lim)

// 'poly2 Analysis with 'expfit'

   analyze('expfit','regression','poly2')
   $file=curexp+'/analyze.out'
   lookup('file',$file)
   lookup('seek','NEXT','skip', '2','read','4'):$a0s,$a1s,$a2s
   format($a0s,8,4):$a0
   format($a1s,8,4):$a1
   format($a2s,8,4):$a2
   $inf=-$a1/(2.0*$a2)
   $infval=$a0+$a1*$inf+$a2*$inf*$inf

// Mean Value from 'poly0' 

   analyze('expfit','regression','poly0')
   lookup('file',$file)
   lookup('seek','NEXT','skip', '2','read','4'):$a0s,$a1s,$a2s
   format($a0s,8,4):$a0
   $mean=$a0
//   write('line3','$inf=%f $infval=%f $mean=%f',$inf,$infval,$mean)
//   write('line3','$2 = %f',$2)

// Min ($minmax<0) or Max ($minmax>0) or none ($minmax=0)

   $minmax=0 $ret=0.0
   if (($bestone-$lim)<$inf)and($inf<($bestone+$lim)) then 
      $ret=$inf
      if ($infval<$mean) then 
         $minmax=-1
      else
         $minmax=1
      endif
   endif

//   write('line3','$xmin = %f $ret = %f $xmax = %f $minmax=%f',$bestone-$lim,$ret,$bestone+$lim,$minmax)

// Return the new $bestone and a Fraction After $bestone,
// else Return $bestone=$2 and $remainder=0.0 

   $remainder=0 
   if (($3='min')and($minmax<0)) then 
      $bestone=trunc($ret) 
      $remainder=$ret-$bestone
   endif
   if (($3='max')and($minmax>0)) then 
      $bestone=trunc($ret) 
      $remainder=$ret-$bestone
   endif
   if ($minmax=0) then
      $bestone=$2 
      $remainder=0.0
   endif
//   write('line3','$bestone=%f',$bestone)
   return($bestone,$remainder)
endif 

//---------------------
// The refx Macro
//---------------------

if (($# > 0) and ($1 = 'refx')) then

// Set the Region

   $reg='' $pwr='' $nuc=''
   $macroname = $0 + '(\'region\',$2,$3,$4,0):$reg,$pwr,$nuc'
   exec($macroname)
  
// Auto Phase

   fn=16*np sb='n' ph wft lp=4 vsadj(100) noislm(1.0)
   aph0:$aphok
   if ($aphok=1) then
      aph0
      peak:$int
      if ($int<-10) then rp=rp+180 endif
   endif

// Find Peak

   peak:$ht,cr

// Set Reference Mode if Possible

   exists('uselockref','parameter','global'):$e
   if ($e < 0) then 
      write('line3','Error: Reference Software not Enabled')
      return
   endif
   uselockref='n'
   if ($reg ='HC') then 
      setBaseref(37.77p)
   else 
      write('line3', 'Reference Value not Available\n')
   endif

//   $H1baserefstring=''
//   substr(userbaseref[5],10,14):$H1baserefstring
   write('line3','H1reffrq = %f\n',H1reffrq)
   probeparamgroup('setlocal',$reg,$nuc,'','baserefX',H1reffrq)
endif
 
//-------------------
// The Region Macro
//-------------------

if (($# > 0) and ($1 = 'region')) then
   $nuc=$2
   $reg=''
   $pwr=$4
   if (($# > 4) and ($5 = 1)) then 
      if ($2='C13') then 
         tn='C13' dn='H1' dn2='N15' dn3=''   
         wc = 200 sc =10
         ad=4.0 rd=4.0 ddrtc=8.0 rp=0 lp=0 d1=2.0 nt=1 ss=2 bs=4
         sw=100000.0 at=0.01 fn=16.0*np sb=at/2.0 sb='y' sbs='n' lb=50 gain=30
         ofHX=0.0
         if ($3='alpha') then
            d1=2.0 nt=1
            setref(tn) setoffset('C13',63):$tof tof=0.1*trunc($tof/0.1 + 0.5) sp=38p wp=50p
            $reg='HCa'
        elseif ($3='salpha') then
            d1=2.0 nt=1
            setref(tn) setoffset('C13',175):$tof tof=0.1*trunc($tof/0.1 + 0.5) sp=38p wp=50p
            $reg='sHCa'
         elseif ($3='carbonyl') then 
            d1=2.0 nt=1
            setref(tn) setoffset('C13',175):$tof tof=0.1*trunc($tof/0.1 + 0.5) sp=165p wp=20p
            $reg='HCO'
         elseif ($3='scarbonyl') then 
            d1=2.0 nt=1
            setref(tn) setoffset('C13',63):$tof tof=0.1*trunc($tof/0.1 + 0.5) sp=165p wp=20p
            $reg='sHCO'
         elseif ($3='adam') then 
            d1=2.0 nt=1.0
            setref(tn) setoffset('C13',33.3):$tof tof=0.1*trunc($tof/0.1 + 0.5) sp=28p wp=20p
            $reg='HC'
         endif
      elseif ($2='N15') then 
         tn='N15' dn='H1' dn2='C13'  dn3=''   
         wc = 200 sc =10
         ad=16.0 rd=4.0 ddrtc=20.0 rp=0 lp=0 ss=2 bs=4
         sw=100000.0 at=0.01 fn=16.0*np sb=at/2.0 sb='y' sbs='n' lb=0  lb='n' gain=30  
         ofHX=0.0
         if ($3='amide') then
            d1=2.0 nt=4
            setref(tn) setoffset('N15',115):$tof tof=0.1*trunc($tof/0.1 + 0.5) sp=90p wp=50p
            $reg='HNai'
         elseif ($3='amine') then
            d1=2.0 nt=1 
            setref(tn) setoffset('N15',35):$tof tof=0.1*trunc($tof/0.1 + 0.5) sp=15p wp=40p
            $reg='HNam'
         elseif ($3='amino') then 
            d1=2.0 nt=1
            setref(tn) setoffset('N15',35):$tof tof=0.1*trunc($tof/0.1 + 0.5) sp=15p wp=40p
            $reg='HN'
         endif         
      endif
      probeparamgroup('setlocal',$reg,$nuc,'','ofX90',tof)
   else
      if ($2='C13') then 
         if ($3='alpha') then
            $reg='HCa'
         elseif ($3='salpha') then
            $reg='sHCa'
         elseif ($3='carbonyl') then 
            $reg='HCO'
         elseif ($3='scarbonyl') then 
            $reg='sHCO'
         elseif ($3='adam') then 
            $reg='HC'
         endif
      elseif ($2='N15') then 
         if ($3='amide') then
            $reg='HNai'
         elseif ($3='amine') then 
            $reg='HNam'
         elseif ($3='amino') then 
            $reg='HN'
         endif
      endif
   endif
   return($reg,$pwr,$nuc)
endif

//---------------------
// The Spin Rate Macro
//---------------------

if (($# > 0) and ($1 = 'spinrate')) then

// Get the Current Spin Rate with an Average of 10

   banner('Measuring Spinning Rate and Stability')
   $count=1 srate=0
   repeat
      $index=''
      if ($count<10) then
         format($count,1,0):$index
      else
         format($count,2,0):$index
      endif
      $dest=curexp+'/stat'+$index
      shell('showstat > ',$dest):$dummy
 
      lookup('file',$dest,'currently', 'at:','read'):$masrate,$ret 
      if $ret then
         format($masrate,5,0):srate[$count]
      endif
      echo($masrate)
      shell('sleep 1')
      $count=$count+1
   until ($count>10)

   averag(srate[1],srate[2],srate[3],srate[4],srate[5],srate[6],
       srate[7],srate[8],srate[9],srate[10]):$avgsrate,$dev

   $avgsrate = trunc($avgsrate + 0.5)  

//Check the Spin Rate 

   if ($avgsrate<500) then 
      $message='MAS Spin Rate Measurement is Less Than 500 Hz - Aborting with 0.0 '
      banner($message)
      srate = 0.0
//      abort
   else
      srate = $avgsrate
      return($avgsrate)
   endif 

// Remove Files Generated by the Spin Rate Measurement

   $count=1
   repeat
      $index=''
      if ($count<10) then
         format($count,1,0):$index
      else
         format($count,2,0):$index
      endif
      $dest=curexp+'/stat'+$index
      rm($dest):$dummy
      $count=$count+1
   until ($count>10)
   return(srate)
endif 

