def CPDparse(Ramp, Nuc):
Dirs = get_dir()
Name = find_file(Dirs, Ramp)
pl_name = ''
pw_name = ''
# There is a problem if the files don't exist.
if os.path.exists(Name) == 1:
f = open(Name, 'r')
text = f.readlines()
f.close()
else:
if Nuc == "1H":
TopCmds.XCMD(pul.pulDict['prgHDec'])
if Nuc == "13C":
TopCmds.XCMD(pul.pulDict['prgCDec'])
if Nuc == "15N":
TopCmds.XCMD(pul.pulDict['prgNDec'])
if Nuc == "2H":
TopCmds.XCMD(pul.pulDict['prgDDec'])
for line in text:
lines = line.rstrip()
#print(lines)
if lines.find("pl") >= 0:
j = lines.find('=')
pl_name = lines[j + 1:]
if lines.find("pcpd") >= 0:
pw_name = "pcpd"
elif lines.find("p31") >= 0:
pw_name = "p31"
elif lines.find("p62") >= 0:
pw_name = "p62"
# Delve into the pulse program if we didn't find our power level in the cpd file
if pl_name == '':
pulprog = TopCmds.GETPAR("PULPROG")
#TopCmds.MSG(pulprog)
ppText = PProgtools.PPparse(pulprog)
#ppText =TopCmds.GET_PULSPROG_TEXT(pulprog)
#TopCmds.MSG(str(ppText))
Lines = devide_into_lines(ppText)
pl_name = get_cpd_plnam(Lines, Nuc)
return pl_name, pw_name
def HDec(units):
Stuff = []
p90H = float(TopCmds.GETPAR("P 3"))
ampH = float(TopCmds.GETPAR("PLdB 2"))
MaxB1H = 1000000. / 4. / p90H
CPD = TopCmds.GETPAR2("CPDPRG 2")
if CPD == "mlev" or CPD == "None":
TopCmds.XCMD("cpdprg2")
CPD = (TopCmds.GETPAR2("CPDPRG 2"))
Stuff = CPDtools.CPDparse(CPD, "1H")
#TopCmds.MSG(str(Stuff))
amp0 = CPDtools.Find_old_pl(Stuff[0])
decpw0 = CPDtools.Find_old_pw(Stuff[1], "1H")
B1_0 = MaxB1H * (math.pow(10, (ampH - amp0) / 20.)) / 1000.
if B1_0 > 1.: B1out = '% .1f' % B1_0
if B1_0 <= 1.: B1out = '75.0'
index = TopCmds.INPUT_DIALOG("Mr Setup Input", "Decoupling Window", \
["Desired 1H Decoupling Amplitude","File"],\
[B1out,CPD],["kHz",""],["1","1",],\
["Accept","Close"], ['a','c'], 10)
TopCmds.PUTPAR("CPDPRG 2", index[1])
#print(index[0], MaxB1H)
adjust = 20 * (math.log10(1000. * float(index[0]) / MaxB1H))
Hamp = ampH - adjust
decpwH = (MaxB1H / 1000. / float(index[0])) * (170. / 180.) * 2 * p90H
if units == "W":
Hamp = dBtoW(Hamp)
value = TopCmds.SELECT("Adjusting the H decoupling parameters:",\
"This will set\n 1H power ("+ Stuff[0] +") to: "+ str('%.2f' %Hamp)+" "+ units+"\n \
Pulse width (" + Stuff[1] +") to: " +str('%3.2f' %decpwH) + units,["Update", "Keep Previous"])
if value != 1:
if Stuff[0] == 'pl12':
TopCmds.PUTPAR("PL" + units + " 12", str('%3.2f' % Hamp))
elif Stuff[0] == 'pl13':
TopCmds.PUTPAR("PL" + units + " 13", str('%3.2f' % Hamp))
elif Stuff[0] == 'pl14':
TopCmds.PUTPAR("PL" + units + " 14", str('%3.2f' % Hamp))
if Stuff[1] == 'pcpd':
TopCmds.PUTPAR("PCPD 2", str('%3.2f' % decpwH))
elif Stuff[1] == 'p31':
TopCmds.PUTPAR("P 31", str('%3.2f' % decpwH))
TopCmds.PUTPAR("P 30", str('%3.2f' % decpwH))
elif Stuff[1] == 'p62':
TopCmds.PUTPAR("P 61", str('%3.2f' % decpwH))
TopCmds.PUTPAR("P 62", str('%3.2f' % decpwH))
def S6purge():
p90C=float(TopCmds.GETPAR("P 1"))
ampC=float(TopCmds.GETPAR("PLdB 1"))
MAS =float(TopCmds.GETPAR("CNST 31"))
MaxB1 = 1000000./4./p90C
p90sC=float(TopCmds.GETPAR("P 6"))
SPname=(TopCmds.GETPAR2("SPNAM 6"))
if p90sC == 0: p90sC = 1500000./MAS
SP=SPname
#Check for existence and default
if SP == "gauss" or SP == "None" :
#TopCmds.MSG("Please set spnam6")
TopCmds.XCMD("spnam6")
SP=(TopCmds.GETPAR2("SPNAM 6"))
offs = float(TopCmds.GETPAR("SPOFFS 6"))
ppm=CFrq.offs2ppm(offs)
if ppm > 140.0 : ppm=55.0
if ppm < -10.0 : ppm=55.0
index = TopCmds.INPUT_DIALOG("CA 90 purge", "S6 soft 90", \
["Duration","Offset","Pulse Name (3pi/2 Sinc)"],\
[str('%3.2f' %p90sC),str('%3.2f' %ppm),SP],\
["us","ppm",""],\
["1","1","1"],\
["Accept","Close"], ['a','c'], 10)
p90sC=float(index[0])
ppm=float(index[1])
SP=index[2]
offs=CFrq.ppm2offs(ppm)
AvgAmp=IntShape.Integrate(SP)/100.
adjust=20*math.log10(p90C/p90sC/AvgAmp)
Power=ampC-adjust
PowerW=pwr.dBtoW(Power)
confirm = TopCmds.SELECT("Adjusting the S6 purge pulse:",\
"This will set\n \
13C amp (pl26) to :" + str('%3.2f' %PowerW)+ " W\n \
Pulse offset to :" + str('%8.0f' %offs) + " Hz\n \
Equivalent to :" + str('%3.1f' %ppm ) + " ppm\n \
p6 to :" + str('%6.1f' %p90sC)+ " us\n "\
,["Update", "Keep Previous"])
if confirm != 1:
TopCmds.PUTPAR("PLdB 26",str('%3.2f' %Power))
TopCmds.PUTPAR("SPNAM 6",SP)
TopCmds.PUTPAR("SPOFFS 6",str('%8.2f' %offs))
TopCmds.PUTPAR("P 6",str('%3.2f' %p90sC))
def load_templt(templt, expname, stan_dir):
"""
Load Topspin parameter set from stand_dir and creates a new dataset.
Args:
templt: Name of topspin parameter set
expname: Name of the new dataset
stand_dir: Directory from where Topspin stores new data set
"""
try:
TC.NEWDATASET([expname, '1', '1', stan_dir])
TC.RE([expname, '1', '1', stan_dir], 'y')
TC.XCMD('rpar %s all' % templt)
except:
TC.MSG(
'''You need to define the parameter set "%s" defining the correct
routing to continue.
First define the correct routing using edasp.
Then save the parmeterset using:
wpar %s all
''' % (templt, templt))
TC.EXIT()
def PPparse(pp):
Dirs = get_dir()
Name = find_file(Dirs, pp)
#TopCmds.MSG(str(Dirs))
#TopCmds.MSG(str(Name))
# There is a problem if the files don't exist.
if os.path.exists(Name) == 1:
f = open(Name, 'r')
text = f.readlines()
f.close()
else:
while os.path.exists(Name) != 1:
TopCmds.XCMD('edpul')
pp = TopCmds.GETPAR("PULPROG")
Name = find_file(Dirs, pp)
if os.path.exists(Name) == 1:
f = open(Name, 'r')
text = f.readlines()
f.close()
kkl = CPDtools.devide_into_lines(text)
#TopCmds.MSG(str(kkl))
for line in kkl:
lines = line.rstrip()
#TopCmds.MSG(lines)
#lines.append=CPDtools.devide_into_lines(lines)
#TopCmds.MSG(str(lines))
for line in text:
lines = line.rstrip()
return text
def CalBSH(p90, ppm, amp, ampD, Cnct, shp, dfltramp, pflp, pflp2k, units, In,
Out):
"""
p90 : Dictionary Key for Nucleus 90 degree pulse; determines Nuc (Decoupling flag)
ppm : float of ppm difference
amp : dict key for CP amp
ampD : dict key for Decoupler (assumed to be 1H) or "empty"
Cnct : dict key for CP contact
shp : dict key of CP shape file
dfltshp: Default pulse shape
pflp : dict key for trim pulse
pflp2k: dict key for flip back pulse
units : Watts (W) or decibel (dB)
In : Title, Subtitle, and Label for Input Dialog
Out : Title and Label for Selection/Confirmation Window
"""
P90 = pul.GetPar(p90, "")
P90D = pul.GetPar('pH90', "")
if p90.find('H') >= 0:
Amp = pul.GetPar('aH', units)
nuc = "1H"
if p90.find('C') >= 0:
Amp = pul.GetPar('aC', units)
nuc = "13C"
if p90.find('N') >= 0:
Amp = pul.GetPar('aN', units)
nuc = "15N"
frq = fq.fq(nuc, 1)
AmpD = pul.GetPar('aH', units)
i = 0
Nucs = NUC.list()
for label in Nucs:
if label == nuc: frq = fq.fq(nuc, i + 1)
i = i + 1
SP = pul.GetPar(shp, "")
MAS = pul.GetPar('MAS', "") / 1000. #kHz not Hz
CNCT = pul.GetPar(Cnct, "")
## Check that the values aren't stupid
if CNCT <= 1.: CNCT = 1000.
if CNCT >= 10000.: CNCT = 10000.
MaxB1 = 1000000. / 4. / P90
MaxB1D = 1000000. / 4. / P90D
##Set Decoupler if Appropriate
if nuc != "1H":
AmpD0 = pul.GetPar(ampD, "dB")
B1_0 = MaxB1D * (math.pow(10, (AmpD - AmpD0) / 20.))
if B1_0 > 100.: Dcond = '% .1f' % B1_0
if B1_0 > MaxB1D: Dcond = '85000.0'
if B1_0 <= 100.: Dcond = '85000.0'
#Use a reasonable ramp name (passed in as dfltramp)
if SP == "gauss" or SP == "None" or SP == "" or SP == "0":
pul.SetPar(shp, dfltramp, "")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict[shp]))
SP = pul.GetPar(shp, "")
## change everything into dB for calculations.
if units == "W":
Amp = Setup.WtodB(Amp)
AmpD = Setup.WtodB(AmpD)
bf = math.floor(float(frq.bf))
ppm = float(str('%.0f' % ppm))
changedPPM = 'y'
while changedPPM == 'y':
#TopCmds.MSG(str(ppm)+":ppm bf:"+str(bf))
DHz = (float(ppm) * bf) / 1000.
bshkHz = round(float(((MAS * MAS) - ((DHz * DHz) / 4)) / MAS), 2)
if nuc != "1H":
index=TopCmds.INPUT_DIALOG(In[0],In[1],In[2],\
[str('%.2f' %bshkHz),SP,str('%.0f' %ppm),\
str('%.0f' %(CNCT/1000.)),str('%.2f' %(float(Dcond)/1000.))],\
["kHz","","ppm","ms","kHz"],\
["1","1","1","1","1"],\
["Accept","Close"], [spc,ret], 10)
Dcond = float(index[4]) * 1000.
if nuc == "1H":
index=TopCmds.INPUT_DIALOG(In[0],In[1],In[2],\
[str('%.2f' %bshkHz),str(SP),str('%.2f' %ppm),\
str('%.0f' %(Cnct/1000.))],\
["kHz","","ppm","ms"],\
["1","1","1","1"],\
["Accept","Close"], [spc,ret], 10)
bshkHz = float(index[0])
SP = index[1]
Cnct = float(index[3]) * 1000.
if str('%.2f' % ppm) == str('%.2f' % float(index[2])): changedPPM = 'n'
if str('%.2f' % ppm) != str('%.2f' % float(index[2])):
changedPPM = 'y'
ppm = float(index[2])
DHz = (float(ppm) * bf) / 1000.
flip = (math.atan(DHz / bshkHz) * 180) / 3.1415
pflip = round(((P90 * flip) / 90.), 2)
#TopCmds.MSG(str(P90)+" "+str(flip)+" "+str(pflip)+" "+str(DHz)+" "+str(bshkHz))
flip2k = (DHz * DHz) / bshkHz
pflip2k = round(((0.25 / flip2k) * 1000), 2)
w1bsh = float(index[0])
adjust = 20 * (math.log10(w1bsh * 1000 / MaxB1))
AmpBsh = Amp - adjust
# Adjust for the ramp.
if SP == "Unused":
AvgAmp = 1.
else:
AvgAmp = IntShape.Integrate(SP) / 100.
AmpBsh = AmpBsh - 20 * (math.log10(1. / AvgAmp))
# For the Decoupling
if nuc != "1H":
AmpDec = Setup.DecSafely(Dcond, ampD, MaxB1D, 150000., AmpD, units)
# Convert to Watts, if wanted
if units == "W":
AmpBsh = Setup.dBtoW(AmpBsh)
if nuc != "1H": Damp = Setup.dBtoW(AmpDec)
if nuc == "1H":
value = TopCmds.SELECT(Out[0],"This will set\n "+\
Out[1]+" power ("+pul.pulDict[amp]+") to: " + str('%3.2f' %AmpBsh)+" "+ units+"\n"+\
"With shape (" + pul.pulDict[shp] + ") of "+ str(SP) +"\n"\
"Flip pulse (" + pul.pulDict[pflp] + ") of "+ str(pflip) +"us\n"\
"Flip pulse 2k(" + pul.pulDict[pflp2k] + ") of "+ str(pflip2k) +"us\n",\
["Update", "Keep Previous"],[spc,ret])
else:
value = TopCmds.SELECT(Out[0],\
"This will set\n "+\
Out[1][0]+" power ("+pul.pulDict[amp]+") to: " + str('%3.2f' %AmpBsh)+" "+ units+"\n"+\
Out[1][1]+" power ("+pul.pulDict[ampD]+") to: " + str('%3.2f' %AmpD)+" "+ units+"\n"+\
"With shape (" + pul.pulDict[shp] + ") of "+ str(SP) +"\n"\
"Flip pulse (" + pul.pulDict[pflp] + ") of "+ str(pflip) +"us\n"\
"Flip pulse 2k(" + pul.pulDict[pflp2k] + ") of "+ str(pflip2k) +"us\n",\
["Update", "Keep Previous"],[spc,ret])
if value != 1:
pul.SetPar(amp, AmpBsh, units)
pul.SetPar(shp, SP, units)
pul.SetPar(pflp, pflip, units)
pul.SetPar(pflp2k, pflip2k, units)
if nuc == "1H":
pul.SetPar(ampD, AmpD, units)
return
def CalCP(p90H, p90L, ampH, ampL, ampD, Cnct, shH, shL, HXorXY, iGuess, units,
In, Out):
P90H = pul.GetPar(p90H, "")
P90L = pul.GetPar(p90L, "")
P90D = pul.GetPar('pH90', "")
#Use Definitions to find hard pulse powers
if p90H.find('H') >= 0: AmpH = pul.GetPar('aH', units)
if p90H.find('C') >= 0: AmpH = pul.GetPar('aC', units)
if p90H.find('N') >= 0: AmpH = pul.GetPar('aN', units)
if p90L.find('H') >= 0: AmpL = pul.GetPar('aH', units)
if p90L.find('C') >= 0: AmpL = pul.GetPar('aC', units)
if p90L.find('N') >= 0: AmpL = pul.GetPar('aN', units)
SPH = pul.GetPar(shH, "")
SPL = pul.GetPar(shL, "")
MAS = pul.GetPar('MAS', "")
CNCT = pul.GetPar(Cnct, "")
if CNCT <= 1.: CNCT = 1000.
if CNCT >= 10000.: CNCT = 10000.
MaxB1H = 1000000. / 4. / P90H
MaxB1L = 1000000. / 4. / P90L
MaxB1D = 1000000. / 4. / P90D
#Set Decoupler if Appropriate
if HXorXY == "XY":
AmpD = pul.GetPar('aH', "dB")
AmpD0 = pul.GetPar(ampD, "dB")
B1_0 = MaxB1D * (math.pow(10, (AmpD - AmpD0) / 20.))
if B1_0 > 100.: Dcond = '% .1f' % B1_0
if B1_0 > MaxB1D: Dcond = '85000.0'
if B1_0 <= 100.: Dcond = '85000.0'
if units == "W":
AmpH = WtodB(AmpH)
AmpL = WtodB(AmpL)
if pul.GetPar(shH,"") == "gauss" or pul.GetPar(shH,"") == "None" or \
pul.GetPar(shH,"") == "" or pul.GetPar(shH,"") == "0" :
pul.SetPar(shH, "ramp.100", "")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict[shH]))
SPH = pul.GetPar(shH, "")
if pul.GetPar(shL,"") == "gauss" or pul.GetPar(shL,"") == "None" or \
pul.GetPar(shL,"") == "" or pul.GetPar(shL,"") == "0" :
pul.SetPar(shL, "square.100", "")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict[shL]))
SPH = pul.GetPar(shL, "")
if iGuess == "Max":
#find the channel with the lowest B1
if MaxB1L < MaxB1H:
Ratio = int(math.floor(MaxB1L / MAS))
HCond = (Ratio + 0.5) * MAS
LCond = (Ratio - 0.5) * MAS
if MaxB1L >= MaxB1H:
Ratio = int(math.floor(MaxB1H / MAS))
HCond = (Ratio - 0.5) * MAS
LCond = (Ratio + 0.5) * MAS
while HCond > MaxB1H or LCond > MaxB1L:
Ratio = Ratio - 1
if MaxB1L < MaxB1H:
HCond = (Ratio + 0.5) * MAS
LCond = (Ratio - 0.5) * MAS
if MaxB1L >= MaxB1H:
HCond = (Ratio - 0.5) * MAS
LCond = (Ratio + 0.5) * MAS
# If spinning very fast or using weak B1s
if Ratio == 2:
LCond = 0.75 * MAS
HCond = 1.75 * MAS
if Ratio <= 1 or HCond > MaxB1H or LCond > MaxB1L:
LCond = .25 * MAS
HCond = .75 * MAS
else:
LCond = (5. / 2.) * MAS
if iGuess == "Low":
HCond = (3. / 2.) * MAS
else:
#iGuess == "High":
HCond = (7. / 2.) * MAS
while LCond > MaxB1L:
LCond = LCond - MAS
CCond = LCond + MAS
while HCond > MaxB1H:
LCond = LCond - MAS
CCond = LCond + MAS
if LCond < MAS:
LCond = 0.25 * MAS
HCond = 0.75 * MAS
adjust = 20 * (math.log10(LCond / MaxB1L))
Lamp = AmpL - adjust
adjust = 20 * (math.log10(HCond / MaxB1H))
Hamp = AmpH - adjust
if HXorXY == "HX":
index=TopCmds.INPUT_DIALOG(In[0],In[1],In[2],\
[str(HCond),str(SPH),str(LCond),str(SPL),str(CNCT)],\
["Hz","","Hz","","us"],\
["1","1","1","1","1"],\
["Accept","Close"], ['a','c'], 10)
if HXorXY == "XY":
index=TopCmds.INPUT_DIALOG(In[0],In[1],In[2],\
[str(HCond),str(SPH),str(LCond),str(SPL),str(CNCT),str(Dcond)],\
["Hz","","Hz","","us","Hz"],\
["1","1","1","1","1","1"],\
["Accept","Close"], ['a','c'], 10)
adjust = 20 * (math.log10(float(index[0]) / MaxB1H))
Hamp1 = AmpH - adjust
if SPH == "Unused":
AvgAmp = 1.
else:
AvgAmp = IntShape.Integrate(index[1]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Hamp = Hamp1 - adjust
adjust = 20 * (math.log10(float(index[2]) / MaxB1L))
Lamp1 = AmpL - adjust
if SPL == "Unused":
AvgAmp = 1.
else:
AvgAmp = IntShape.Integrate(index[3]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Lamp = Lamp1 - adjust
CNCT = float(index[4])
if HXorXY == "XY":
adjust = 20 * (math.log10(float(index[5]) / MaxB1D))
Damp = AmpD - adjust
if units == "W":
Hamp = dBtoW(Hamp)
Lamp = dBtoW(Lamp)
if HXorXY == "XY": Damp = dBtoW(Damp)
if HXorXY == "HX":
value = TopCmds.SELECT(Out[0],\
"This will set\n "+\
Out[1][0]+" power to: " + str('%3.2f' %Hamp)+" "+ units+"\n"+\
Out[1][1]+" power to: " + str('%3.2f' %Lamp)+" "+ units,\
["Update", "Keep Previous"])
if HXorXY == "XY":
value = TopCmds.SELECT(Out[0],\
"This will set\n "+\
Out[1][0]+" power to: " + str('%3.2f' %Hamp)+" "+ units+"\n"+\
Out[1][1]+" power to: " + str('%3.2f' %Lamp)+" "+ units+"\n"+\
Out[1][2]+" power to: " + str('%3.2f' %Damp)+" "+ units,\
["Update", "Keep Previous"])
if value != 1:
pul.SetPar(ampH, Hamp, units)
pul.SetPar(ampL, Lamp, units)
if HXorXY == "XY":
pul.SetPar(ampD, Damp, units)
pul.SetPar(Cnct, CNCT, "")
if SPH != "Unused":
pul.SetPar(shH, index[1], "")
if SPL != "Unused":
pul.SetPar(shL, index[3], "")
return
def DDec(units):
Stuff = []
p90 = pul.GetPar('pD90', "")
amp = pul.GetPar('aD', units)
CPD = pul.GetPar('prgDDec', "")
MaxB1 = 1000000. / 4. / p90
if units == "W":
amp = WtodB(amp)
if CPD == "mlev" or CPD == "None":
TopCmds.XCMD(pul.xcmd_name(pul.pulDict['prgDDec']))
CPD = pul.GetPar('prgDDec', "")
Stuff = CPDtools.CPDparse(CPD, "2H")
amp0 = CPDtools.Find_old_pl(Stuff[0])
decpw0 = CPDtools.Find_old_pw(Stuff[1], "2H")
B1_0 = MaxB1 * (math.pow(10, (amp - amp0) / 20.)) / 1000.
if B1_0 > 1.: B1out = '% .1f' % B1_0
if B1_0 <= 1.: B1out = '15.0'
index = TopCmds.INPUT_DIALOG("Mr Setup Input", "Decoupling Window", \
["Desired 2H Decoupling Amplitude","File"],\
[B1out,CPD],["kHz",""],["1","1",],\
["Accept","Close"], ['a','c'], 10)
pul.SetPar('aDdec', index[1], "")
adjust = 20 * (math.log10(1000. * float(index[0]) / MaxB1))
ampli = amp - adjust
decpw = (MaxB1 / 1000. / float(index[0])) * 2 * p90
if units == "W":
ampli = dBtoW(ampli)
value = TopCmds.SELECT("Adjusting the 2H decoupling parameters:",\
"This will set\n 2H power ("+ Stuff[0] +") to: "+ str('%3.2f' %ampli)+" "+ units+"\n \
Pulse width (" + Stuff[1] +"= 180deg) to: " +str('%3.2f' %decpw) + " us",["Update", "Keep Previous"])
if value != 1:
pl = ""
if Stuff[0] != "": pl = pul.pp_2_xcmd(Stuff[0], "")
if pl == "":
pul.SetPar('aDdec', ampli, units)
elif pl == pul.pulDict['aDdec']:
pul.SetPar('aDdec', ampli, units)
elif pl == pul.pulDict['aHdec']:
DecError('aHdec', "13C")
elif pl == pul.pulDict['aHdec2']:
DecError('aHdec2', "13C")
elif pl == pul.pulDict['aHdec3']:
DecError('aHdec3', "13C")
if Stuff[1] == 'pcpd':
pul.SetPar("PCPD 3", decpw, "")
elif Stuff[1] == 'p31':
pul.SetPar("P31", decpw, "")
pul.SetPar("P30", decpw, "")
elif Stuff[1] == 'p62':
pul.SetPar("P61", decpw, "")
pul.SetPar("P62", decpw, "")
def HDec(units):
Stuff = []
p90 = pul.GetPar('pH90', "")
amp = pul.GetPar('aH', units)
CPD = pul.GetPar('prgHDec', "")
MaxB1 = 1000000. / 4. / p90
if CPD == "mlev" or CPD == "None":
pul.SetPar('prgHDec', "tppm15", "")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict['prgHDec']))
CPD = pul.GetPar('prgHDec', "")
TopCmds.MSG(str(CPD) + " CPD")
Stuff = CPDtools.CPDparse(CPD, "1H")
TopCmds.MSG(str(Stuff) + " Stuff")
amp0 = CPDtools.Find_old_pl(Stuff[0], units)
TopCmds.MSG(str(amp0) + " amp0")
if units == "W":
amp = WtodB(amp)
amp0 = WtodB(amp0)
decpw0 = CPDtools.Find_old_pw(Stuff[1], "1H")
B1_0 = MaxB1 * (math.pow(10, (amp - amp0) / 20.)) / 1000.
if B1_0 > 1.: B1out = '% .1f' % B1_0
if B1_0 > MaxB1 / 1000.: B1out = '75.0'
if B1_0 <= 1.: B1out = '75.0'
index = TopCmds.INPUT_DIALOG("Mr Setup Input", "Decoupling Window", \
["Desired 1H Decoupling Amplitude","File"],\
[B1out,CPD],["kHz",""],["1","1",],\
["Accept","Close"], ['a','c'], 10)
pul.SetPar('prgHDec', index[1], "")
adjust = 20 * (math.log10(1000. * float(index[0]) / MaxB1))
Hamp = amp - adjust
decpwH = (MaxB1 / 1000. / float(index[0])) * (170. / 180.) * 2 * p90
if units == "W":
Hamp = dBtoW(Hamp)
value = TopCmds.SELECT("Adjusting the H decoupling parameters:",\
"This will set\n 1H power ("+ Stuff[0] +") to: "+ str('%.2f' %Hamp)+" "+ units+"\n \
Pulse width (" + Stuff[1] +") to: " +str('%3.2f' %decpwH)+" us",["Update", "Keep Previous"])
if value != 1:
pl = ""
if Stuff[0] != "": pl = pul.pp_2_xcmd(Stuff[0], "")
if pl == pul.pulDict['aHdec']:
pul.SetPar('aHdec', Hamp, units)
elif pl == pul.pulDict['aHdec2']:
pul.SetPar('aHdec2', Hamp, units)
elif pl == pul.pulDict['aHdec3']:
pul.SetPar('aHdec3', Hamp, units)
if Stuff[1] == 'pcpd':
pul.SetPar("PCPD 2", decpwH, "")
elif Stuff[1] == 'p31':
pul.SetPar("P31", decpwH, "")
pul.SetPar("P30", decpwH, "")
elif Stuff[1] == 'p62':
pul.SetPar("P61", decpwH, "")
pul.SetPar("P62", decpwH, "")
def HC(units):
#44,45
p90H = float(TopCmds.GETPAR("P 3"))
ampH = float(TopCmds.GETPAR("PLdB 2"))
p90C = float(TopCmds.GETPAR("P 1"))
ampC = float(TopCmds.GETPAR("PLdB 1"))
MAS = float(TopCmds.GETPAR("CNST 31"))
SPH = TopCmds.GETPAR2("SPNAM 44")
SPH0 = TopCmds.GETPAR2("SPNAM 40")
CNCT = float(TopCmds.GETPAR("P 44"))
CNCT0 = float(TopCmds.GETPAR("P 15"))
MaxB1H = 1000000. / 4. / p90H
MaxB1C = 1000000. / 4. / p90C
if CNCT <= 1.00: CNCT = CNCT0
if SPH == "gauss" or SPH == "None" or SPH == "":
SPH = SPH0
TopCmds.PUTPAR("SPNAM 44", SPH)
TopCmds.XCMD("spnam44")
SPH = (TopCmds.GETPAR2("SPNAM 44"))
SPH.join()
Hav = IntShape.Integrate(SPH)
Hav0 = IntShape.Integrate(SPH0)
Hint = 0.01 * ((Hav)**2) / Hav0
#TopCmds.MSG("Hint "+str(Hint))
Hamp0 = float(TopCmds.GETPAR("SPdB 40"))
Camp0 = float(TopCmds.GETPAR("SPdB 41"))
B1H = MaxB1H * Hint * math.pow(10, (ampH - Hamp0) / 20.)
B1C = MaxB1C * math.pow(10, (ampC - Camp0) / 20.)
index = TopCmds.INPUT_DIALOG("H-C CP", "Contact and Ramp", \
["Proton B1 Field","H Ramp","Carbon B1 Field","Contact Time(P44)"],\
[str('%3.0f' %B1H),SPH,str('%3.0f' %B1C),str(CNCT)],\
["kHz","","kHz","us"],\
["1","1","1","1"],\
["Accept","Close"], ['a','c'], 10)
SP = index[1]
CNCT = float(index[3])
adjust = 20 * (math.log10(float(index[0]) / MaxB1H))
Hamp1 = ampH - adjust
AvgAmp = IntShape.Integrate(index[1]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Hamp = Hamp1 - adjust
adjust = 20 * (math.log10(float(index[2]) / MaxB1C))
Camp = ampC - adjust
if units == "W":
Hamp = Setup.dBtoW(Hamp)
Camp = Setup.dBtoW(Camp)
value = TopCmds.SELECT("Adjusting the CH CP parameters:",\
"This will set\n 1H power to: " + str('%3.2f' %Hamp)+" "+units+"\n \
13C power to: " +str('%3.2f' %Camp) + units,["Update", "Keep Previous"])
if value != 1:
TopCmds.PUTPAR("SP" + units + " 44", str('%3.2f' % Hamp))
TopCmds.PUTPAR("SP" + units + " 45", str('%3.2f' % Camp))
TopCmds.PUTPAR("PL" + units + " 44", str('%3.2f' % Hamp))
TopCmds.PUTPAR("PL" + units + " 45", str('%3.2f' % Camp))
TopCmds.PUTPAR("P 44", str('%3.2f' % CNCT))
TopCmds.PUTPAR("SPNAM 44", SP)
def DDec(units):
Stuff = []
p90 = float(TopCmds.GETPAR("P 32"))
amp = float(TopCmds.GETPAR("PLdB 31"))
MaxB1 = 1000000. / 4. / p90
CPD = TopCmds.GETPAR2("CPDPRG 5")
if CPD == "mlev" or CPD == "None":
TopCmds.XCMD("cpdprg5")
CPD = (TopCmds.GETPAR2("CPDPRG 5"))
Stuff = CPDtools.CPDparse(CPD, "2D")
TopCmds.MSG(str(Stuff))
amp0 = CPDtools.Find_old_pl(Stuff[0])
decpw0 = CPDtools.Find_old_pw(Stuff[1], "2D")
B1_0 = MaxB1 * (math.pow(10, (amp - amp0) / 20.)) / 1000.
if B1_0 > 1.: B1out = '% .1f' % B1_0
if B1_0 <= 1.: B1out = '5.0'
index = TopCmds.INPUT_DIALOG("Mr Setup Input", "Decoupling Window", \
["Desired 2H Decoupling Amplitude","File"],\
[B1out,CPD],["kHz",""],["1","1",],\
["Accept","Close"], ['a','c'], 10)
TopCmds.PUTPAR("CPDPRG 5", index[1])
adjust = 20 * (math.log10(1000. * float(index[0]) / MaxB1))
ampli = amp - adjust
decpw = (MaxB1 / 1000. / float(index[0])) * 2 * p90
if units == "W":
ampli = dBtoW(ampli)
value = TopCmds.SELECT("Adjusting the D decoupling parameters:",\
"This will set\n 2H power ("+ Stuff[0] +") to: "+ str('%3.2f' %ampli)+" "+ units+"\n \
Pulse width (" + Stuff[1] +"= 180deg) to: " +str('%3.2f' %decpw) + " us",["Update", "Keep Previous"])
if value != 1:
if Stuff[0] == '':
TopCmds.PUTPAR("PL" + units + " 25", str('%3.2f' % ampli))
elif Stuff[0] == 'pl25':
TopCmds.PUTPAR("PL" + units + " 25", str('%3.2f' % ampli))
elif Stuff[0] == 'pl12':
TopCmds.MSG(
"You are using pl12 for 2H decouling. It is usually reserved for 1H \n Please verify"
)
#TopCmds.PUTPAR("PLdB 12",str('%3.2f' %ampli))
elif Stuff[0] == 'pl13':
TopCmds.MSG(
"You are using pl13 for 2H decouling. It is usually reserved for 1H \n Please verify"
)
#TopCmds.PUTPAR("PLdB 13",str('%3.2f' %ampli))
elif Stuff[0] == 'pl14':
TopCmds.MSG(
"You are using pl14 for 2H decouling. It is usually reserved for 1H \n Please verify"
)
#TopCmds.PUTPAR("PLdB 14",str('%3.2f' %ampli))
if Stuff[1] == 'pcpd':
TopCmds.PUTPAR("PCPD 5", str('%3.2f' % decpw))
elif Stuff[1] == 'p31':
TopCmds.PUTPAR("P 31", str('%3.2f' % decpw))
TopCmds.PUTPAR("P 30", str('%3.2f' % decpw))
elif Stuff[1] == 'p62':
TopCmds.PUTPAR("P 61", str('%3.2f' % decpw))
TopCmds.PUTPAR("P 62", str('%3.2f' % decpw))
def NCO(units):
p90C = float(TopCmds.GETPAR("P 1"))
ampC = float(TopCmds.GETPAR("PLdB 1"))
p90N = float(TopCmds.GETPAR("P 21"))
ampN = float(TopCmds.GETPAR("PLdB 3"))
MAS = float(TopCmds.GETPAR("CNST 31"))
SP = TopCmds.GETPAR2("SPNAM 51")
CNCT = float(TopCmds.GETPAR("P 17"))
if CNCT <= 1.: CNCT = 3500.
if SP == "gauss" or SP == "None" or SP == "":
#TopCmds.MSG("Please set spnam2")
TopCmds.XCMD("spnam51")
SP = (TopCmds.GETPAR2("SPNAM 51"))
SP.join()
MaxB1N = 1000000. / 4. / p90N
MaxB1C = 1000000. / 4. / p90C
#find the channel with the lowest B1
NCond = (5. / 2.) * MAS
CCond = (7. / 2.) * MAS
while NCond > MaxB1N:
NCond = NCond - MAS
CCond = NCond + MAS
while CCond > MaxB1C:
NCond = NCond - MAS
CCond = NCond + MAS
if NCond < MAS:
NCond = 0.25 * MAS
CCond = 0.75 * MAS
index = TopCmds.INPUT_DIALOG("NCO CP Input", "N-CO SPECIFIC 7/2*C; 5/2*N", \
["Carbon B1 field","Nitrogen B1 field","Contact Time(P15)","Ramp Name"],\
[str(CCond),str(NCond),str(CNCT),SP],\
["kHz","kHz","us",""],\
["1","1","1","1"],\
["Accept","Close"], ['a','c'], 10)
adjust = 20 * (math.log10(float(index[0]) / MaxB1C))
Camp = ampC - adjust
adjust = 20 * (math.log10(float(index[1]) / MaxB1N))
Namp = ampN - adjust
#Insert ramp calibration here
AvgAmp = IntShape.Integrate(SP) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Camp = Camp - adjust
CNCT = float(index[2])
if units == "W":
Namp = dBtoW(Namp)
Camp = dBtoW(Camp)
value = TopCmds.SELECT("Adjusting the NC CP parameters:",\
"This will set\n 13C power to: " + str('%3.2f' %Camp)+" "+ units+"\n \
15N power to: " +str('%3.2f' %Namp) + units,["Update", "Keep Previous"])
if value != 1:
TopCmds.PUTPAR("PL" + units + " 6", str('%3.2f' % Namp))
TopCmds.PUTPAR("PL" + units + " 51", str('%3.2f' % Camp))
TopCmds.PUTPAR("SP" + units + " 51", str('%3.2f' % Camp))
TopCmds.PUTPAR("P 17", str('%3.2f' % CNCT))
TopCmds.PUTPAR("SPNAM 51", SP)
def HC(units):
p90H = float(TopCmds.GETPAR("P 3"))
ampH = float(TopCmds.GETPAR("PLdB 2"))
p90C = float(TopCmds.GETPAR("P 1"))
ampC = float(TopCmds.GETPAR("PLdB 1"))
MAS = float(TopCmds.GETPAR("CNST 31"))
CNCT = float(TopCmds.GETPAR("P 15"))
SPH = TopCmds.GETPAR2("SPNAM 40")
SPX = TopCmds.GETPAR2("SPNAM 41")
if CNCT <= 1.: CNCT = 1000.
if SPH == "gauss" or SPH == "None" or SPH == "":
#TopCmds.MSG("Please set spnam40")
TopCmds.PUTPAR("SPNAM 40", "ramp.100")
TopCmds.XCMD("spnam40")
SPH = (TopCmds.GETPAR2("SPNAM 40"))
SPH.join()
if SPX == "gauss" or SPX == "None" or SPX == "":
#TopCmds.MSG("Please set spnam10")
TopCmds.PUTPAR("SPNAM 41", "square.100")
TopCmds.XCMD("spnam41")
SPX = (TopCmds.GETPAR2("SPNAM 41"))
SPX.join()
MaxB1H = 1000000. / 4. / p90H
MaxB1C = 1000000. / 4. / p90C
#find the channel with the lowest B1
if MaxB1C < MaxB1H:
Ratio = int(math.floor(MaxB1C / MAS))
#TopCmds.MSG(str(Ratio))
CCond = (Ratio - 0.5) * MAS
HCond = (Ratio + 0.5) * MAS
if HCond > MaxB1H:
Ratio = Ratio - 1
CCond = (Ratio - 0.5) * MAS
HCond = (Ratio + 0.5) * MAS
# If spinning very fast or using weak B1s
if Ratio <= 1:
CCond = .25 * MAS
HCond = .75 * MAS
if MaxB1C >= MaxB1H:
Ratio = int(math.floor(MaxB1H / MAS))
HCond = (Ratio - 0.5) * MAS
CCond = (Ratio + 0.5) * MAS
if CCond > MaxB1C:
Ratio = Ratio - 1
HCond = (Ratio - 0.5) * MAS
CCond = (Ratio + 0.5) * MAS
# If spinning very fast or using weak B1s
if Ratio <= 1:
CCond = .75 * MAS
HCond = .25 * MAS
adjust = 20 * (math.log10(CCond / MaxB1C))
Camp = ampC - adjust
adjust = 20 * (math.log10(HCond / MaxB1H))
Hamp = ampH - adjust
index = TopCmds.INPUT_DIALOG("HC CP Input", "Proton Carbon Cross Polarization", \
["Proton B1 Field","H Ramp","Carbon B1 Field","C Ramp","Contact Time(P15)"],\
[str(HCond),SPH,str(CCond),SPX,str(CNCT)],\
["kHz","","kHz","","us"],\
["1","1","1","1","1"],\
["Accept","Close"], ['a','c'], 10)
adjust = 20 * (math.log10(float(index[0]) / MaxB1H))
Hamp1 = ampH - adjust
AvgAmp = IntShape.Integrate(index[1]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Hamp = Hamp1 - adjust
adjust = 20 * (math.log10(float(index[2]) / MaxB1C))
Camp1 = ampC - adjust
#Ramp integration adjustment
AvgAmp = IntShape.Integrate(index[3]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Camp = Camp1 - adjust
CNCT = float(index[4])
if units == "W":
Hamp = dBtoW(Hamp)
Camp = dBtoW(Camp)
value = TopCmds.SELECT("Adjusting the HC CP parameters:",\
"This will set\n 1H power to: " + str('%3.2f' %Hamp)+" "+ units+"\n \
13C power to: " +str('%3.2f' %Camp) + units,["Update", "Keep Previous"])
if value != 1:
TopCmds.PUTPAR("SP" + units + " 40", str('%3.2f' % Hamp))
TopCmds.PUTPAR("SP" + units + " 41", str('%3.2f' % Camp))
TopCmds.PUTPAR("PL" + units + " 40", str('%3.2f' % Hamp))
TopCmds.PUTPAR("PL" + units + " 41", str('%3.2f' % Camp))
TopCmds.PUTPAR("P 15", str('%3.2f' % CNCT))
TopCmds.PUTPAR("SPNAM 40", index[1])
TopCmds.PUTPAR("SPNAM 41", index[3])
def CalNCO():
p90C=float(TopCmds.GETPAR("P 1"))
ampC=float(TopCmds.GETPAR("PLdB 1"))
p90N=float(TopCmds.GETPAR("P 21"))
ampN=float(TopCmds.GETPAR("PLdB 21"))
MAS =float(TopCmds.GETPAR("CNST 31"))
SP=TopCmds.GETPAR("SPNAM 3")
CNCT=float(TopCmds.GETPAR("P 16"))
if CNCT <= 1.: CNCT = 3500.
if SP == "gauss" or SP == "None" :
#TopCmds.MSG("Please set spnam3")
TopCmds.XCMD("spnam3")
SP=(TopCmds.GETPAR2("SPNAM 3"))
MaxB1N = 1000000./4./p90N
MaxB1C = 1000000./4./p90C
Coffs=Cfrq.ppm2offs(170.0)
NCond=(5./2.)*MAS
CCond=(7./2.)*MAS
while NCond > MaxB1N :
NCond=NCond - MAS
CCond=NCond + MAS
while CCond > MaxB1C :
NCond=NCond - MAS
CCond=NCond + MAS
if NCond < MAS :
NCond= 0.25*MAS
CCond= 0.75*MAS
index = TopCmds.INPUT_DIALOG("NCO off-resonance CP Input",\
"N-CO SPECIFIC-CP w1C=7/2*wr; w1N=5/2*wr", \
["Carbon B1 field","Carbon offset (170ppm)","Nitrogen B1 field","Contact Time(P16)","Ramp Name"],\
[str(CCond),str(Coffs),str(NCond),str(CNCT),SP],\
["Hz","Hz","Hz","us",""],\
["1","1","1","1","1"],\
["Accept","Close"], ['a','c'], 10)
NCond=(float(index[2]))*MAS
CCond=math.sqrt( (float(index[0]))**2 - (float(index[1]))**2))
adjust=20*(math.log10(CCond/MaxB1C))
Camp = ampC-adjust
adjust=20*(math.log10(NCond/MaxB1N))
Namp = ampN-adjust
#Insert ramp calibration here
AvgAmp=IntShape.Integrate(SP)/100.
adjust=20*(math.log10(1./AvgAmp))
Camp = Camp-adjust
CNCT = float(index[3])
CampW=pwr.dBtoW(Camp)
NampW=pwr.dBtoW(Namp)
value = TopCmds.SELECT("Adjusting the NC CP parameters:",\
"This will set\n 13C power to: " + str('%3.2f' %CampW)+ " W\n \
15N power to: " +str('%3.2f' %NampW) + " W",["Update", "Keep Previous"])
if value != 1:
TopCmds.PUTPAR("PLdB 17",str('%3.2f' %Namp))
TopCmds.PUTPAR("PLdB 16",str('%3.2f' %Camp))
TopCmds.PUTPAR("P 16",str('%3.2f' %CNCT))
TopCmds.PUTPAR("SPNAM 3",SP)
def copyCP(aH,sH,aL,sL,pCP,aH0,sH0,aL0,sL0,pCP0,Input,Output,units):
"""
aH/L(0) : dict key for High/Low G CP amp (0 for default)
pCP(0) : dict key for CP contact (0 default)
shH/L(0) : dict key of CP shape files
units : Watts (W) or decibel (dB)
In : Title, Subtitle, and Label for Input Dialog
Out : Title and Label for Selection/Confirmation Window
"""
#Use Dictionary Definitions to find hard pulse powers
if aH.find('H') >= 0:AmpH=pul.GetPar('aH',"dB"); P90H=pul.GetPar('pH90',""); Hnuc="1H"
if aH.find('C') >= 0:AmpH=pul.GetPar('aC',"dB"); P90H=pul.GetPar('pC90',""); Hnuc="13C"
if aH.find('N') >= 0:AmpH=pul.GetPar('aN',"dB"); P90H=pul.GetPar('pN90',""); Hnuc="15N"
if aL.find('H') >= 0:AmpL=pul.GetPar('aH',"dB"); P90L=pul.GetPar('pH90',""); Lnuc="1H"
if aL.find('C') >= 0:AmpL=pul.GetPar('aC',"dB"); P90L=pul.GetPar('pC90',""); Lnuc="13C"
if aL.find('N') >= 0:AmpL=pul.GetPar('aN',"dB"); P90L=pul.GetPar('pN90',""); Lnuc="15N"
MaxB1H=1000000./4./P90H
MaxB1L=1000000./4./P90L
SPH =pul.GetPar(sH,"")
SPL =pul.GetPar(sL,"")
Hamp0=pul.GetPar(aH0,"dB")
Lamp0=pul.GetPar(aL0,"dB")
if pul.GetPar(pCP,"") <= 1.00 :
pul.SetPar(pCP,pul.GetPar(pCP0,""),"")
CNCT = pul.GetPar(pCP,"")/1000.
if SPH == "gauss" or SPH == "None" or SPH == "" or SPH == "0" :
pul.SetPar(sH,pul.GetPar(sH0,""),"")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict[sH]))
SPH = pul.GetPar(sH,"")
if SPL == "gauss" or SPL == "None" or SPL == "" or SPL == "0":
pul.SetPar(sL,pul.GetPar(sL0,""),"")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict[sL]))
SPX=pul.GetPar(sL0,"")
if SPH == "Unused":
Hav = 1.
Hav0 = 1.
else:
Hav = IntShape.Integrate(pul.GetPar(sH,""))/100.
Hav0 = IntShape.Integrate(pul.GetPar(sH0,""))/100.
if SPL == "Unused":
Lav = 1.
Lav0 = 1.
else:
Lav = IntShape.Integrate(pul.GetPar(sL,""))/100.
Lav0 = IntShape.Integrate(pul.GetPar(sL0,""))/100.
#This is the new integration times the change in new/old
Hint = ((Hav)**2)/Hav0
Lint = ((Lav)**2)/Lav0
B1H = MaxB1H*Hint*math.pow(10,(AmpH-Hamp0)/20.)
B1L = MaxB1L*Lint*math.pow(10,(AmpL-Lamp0)/20.)
index=TopCmds.INPUT_DIALOG(Input[0],Input[1],Input[2],\
[str('%.3f' %(B1H/1000.)),SPH,str('%.3f' %(B1L/1000.)),SPL,str(CNCT)],\
["kHz","","kHz","","ms"],\
["1","1","1","1","1",],\
["Accept","Close"], [spc,ret], 10)
if index == None:TopCmds.EXIT()
SPH=index[1]
SPX=index[3]
CNCT=1000*float(index[4])
adjust=20*(math.log10(1000.*float(index[0])/MaxB1H))
Hamp1 = AmpH-adjust
if SPH == "Unused":
AvgAmp=1.
else:
AvgAmp=IntShape.Integrate(index[1])/100.
adjust=20*(math.log10(1./AvgAmp))
Hamp = Hamp1-adjust
adjust=20*(math.log10(1000.*float(index[2])/MaxB1L))
Lamp = AmpL-adjust
if SPL == "Unused":
AvgAmp=1.
else:
AvgAmp=IntShape.Integrate(index[3])/100.
adjust=20*(math.log10(1./AvgAmp))
Lamp = Lamp-adjust
if units == "W":
Hamp=Setup.dBtoW(Hamp)
Lamp=Setup.dBtoW(Lamp)
value = TopCmds.SELECT(Output[0],\
"This will set\n"+\
Hnuc+" power to: " + str('%3.2f' %Hamp)+" "+units+"\n"+ \
Lnuc+" power to: " +str('%3.2f' %Lamp) + units,\
["Update", "Keep Previous"],[spc,ret])
if value != 1:
pul.SetPar(aH,Hamp,units)
pul.SetPar(aL,Lamp,units)
pul.SetPar(pCP,CNCT,"")
if SPH != "Unused":
pul.SetPar(sH,index[1],"")
if SPX != "Unused":
pul.SetPar(sL,index[3],"")
def CalcSym(CorR, N, n, v, mult, p90, amp, Wave, time, dfltT, nuc, dec, units):
"""
CorR : Symmetry Element
N : Step Number
n : Space Winding Number
v : Spin Winding Number (not used here, yet)
mult : Mulitplier for Composite Pulses
p90 : Dict key for Hard Pulse of Nucleus
amp : Dict key for recoupling Amplitude
Wave : Shaped pulse (None or Unused)
nuc : Recoupled Nucleus
dec : Dict key for Decoupler Nucleus
dfltT : Default Time or Loop
"""
value = 0
if pul.pulDict[time].find("D") >= 0:
lblT = "Delay", "s"
elif pul.pulDict[time].find("L") >= 0:
lblT = "Loop", "cycles"
elif pul.pulDict[time].find("P") >= 0:
lblT = "Pulse", "us"
#Use Dictionary Definitions to find hard pulse powers
if p90.find('H') >= 0: Amp = pul.GetPar('aH', "dB")
if p90.find('C') >= 0: Amp = pul.GetPar('aC', "dB")
if p90.find('N') >= 0: Amp = pul.GetPar('aN', "dB")
#Assume 1H decoupling if neccessary
P90 = pul.GetPar(p90, "")
P90D = pul.GetPar('pH90', "")
MAS = pul.GetPar('MAS', "")
Tau_r = 1. / float(MAS)
MaxB1 = 1000000. / 4. / P90
MaxB1D = 1000000. / 4. / P90D
#Calculate the RF field
if CorR == "C":
Cond = mult * 1. * N * MAS / n
if CorR == "R":
Cond = mult * 2. * N * MAS / n
#Set Decoupler if Appropriate
if dec != "None":
AmpD = pul.GetPar('aH', "dB")
AmpD0 = pul.GetPar(dec, "dB")
B1_0 = MaxB1D * (math.pow(10, (AmpD - AmpD0) / 20.))
if B1_0 > 100.: Dcond = B1_0
if B1_0 > MaxB1D: Dcond = 85000.0
if B1_0 <= 100.: Dcond = 85000.0
if Cond > MaxB1:
TopCmds.MSG("The match condition for " + CorR+str(N)+unb+str(n)+crt+str(v)+" is "+\
str('%.3f' %(Cond/1000.))+" kHz \n\nIt is greater than the Max B1 ("+ str('%.3f' %(MaxB1/1000.))+" kHz)\n\n"+\
pul.pulDict[amp]+" will NOT be set ")
TopCmds.EXIT()
else:
if dec == "None":
Title = "Adjusting " + nuc + " Power for Symmetry-Based Recoupling"
Subtit = CorR + str(N) + unb + str(n) + crt + str(
v) + "Symmetry Match"
Label = [nuc + " Amplitude", lblT[0] + " " + pul.pulDict[time]]
Values = [str('%.3f' % (Cond / 1000.)), str(dfltT)]
Units = ["kHz", lblT[1]]
Types = ["1", "1"]
Buttons = ["Accept", "Cancel"]
ShortCuts = [spc, ret]
columns = 10
else:
Title = "Adjusting " + nuc + " Power for Symmetry-Based Recoupling"
Subtit = CorR + str(N) + unb + str(n) + crt + str(
v) + " Symmetry Match"
Label = [nuc+" Amplitude",lblT[0]+" "+pul.pulDict[time],\
"1H decoupling field"]
temp1 = Cond / 1000.
temp2 = Dcond / 1000.
Values = [str('%.3f' % temp1), str(dfltT), str('%.3f' % temp2)]
Units = ["kHz", lblT[1], "kHz"]
Types = ["1", "1", "1"]
Buttons = ["Accept", "Cancel"]
ShortCuts = [spc, ret]
columns = 10
index = TopCmds.INPUT_DIALOG(Title, Subtit, Label, Values, Units,
Types, Buttons, ShortCuts, columns)
if index == None:
TopCmds.EXIT()
if index != None:
Cond = float(index[0]) * 1000.
Time = str(index[1])
if dec != "None":
#Safety
Damp = DecSafely(1000. * float(index[2]), dec, MaxB1D, 150000.,
AmpD, units)
#Calculate the power
adjust = 20 * (math.log10(Cond / MaxB1))
Condition = Amp - adjust
#Calculate the Integration if shaped pulses are used
if Wave != "None" and Wave != "Unused":
if pul.GetPar(Wave,"") == "gauss" or pul.GetPar(Wave,"") == "None" or \
pul.GetPar(Wave,"") == "" or pul.GetPar(Wave,"") == "0" :
pul.SetPar(Wave, "square.100", "")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict[Wave]))
SP = pul.GetPar(Wave, "")
AvgAmp = IntShape.Integrate(SP) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Condition = Condition - adjust
if units == "W":
Condition = dBtoW(Condition)
if dec != "None": Damp = dBtoW(Damp)
if dec == "None":
Confirm = nuc + " Power for " + CorR + str(N) + "_" + str(
n) + "^" + str(v) + "Symmetry Match"
Power ="Set\n "+ pul.pulDict[amp]+" to: "+str('%3.2f' %Condition)+" "+ units+"\n"+\
pul.pulDict[time]+" "+lblT[1]+" to: "+index[1]
else:
Confirm = "Adjusting " + nuc + " and 1H Power for " + CorR + str(
N) + "_" + str(n) + "^" + str(v) + "Symmetry Match"
Power ="Set\n "+ pul.pulDict[amp]+" to: "+str('%3.2f' %Condition)+" "+ units+"\n"+\
pul.pulDict[dec]+" (Dec) power to: "+str('%3.2f' %Damp)+" "+ units+"\n"+\
pul.pulDict[time]+" "+lblT[1]+" to: "+index[1]
if Confirm == "None":
value = 1
else:
value = TopCmds.SELECT(Confirm, Power, ["Update", "Keep Previous"],
[spc, ret])
if value != 1:
pul.SetPar(amp, Condition, units)
pul.SetPar(time, index[1], "")
if dec != "None": pul.SetPar(dec, Damp, units)
def CalDec(p90, amp, cpd, nuc, units, dfltWave, dfltB0, dfltPH, aOption,
aFaults):
"""
p90 : Dict key for Hard Pulse of Decoupled Nucleus
amp : Dict key for Hard Pulse Amplitude
cpd : Dict key for CPD file
nuc : Decoupled Nucleus
units : Watts (W) or Decibels (dB)
dfltWave: Default CPD
dfltB0 : Default field
dfltPH : Default tip angle used in CPD
aOption : List of accepted amplitude dict keys
aFaults : List of amplitude dict keys that will cause a PLEASE CONFIRM Message
"""
Stuff = []
P90 = pul.GetPar(p90, "")
Amp = pul.GetPar(amp, units)
CPD = pul.GetPar(cpd, "")
MaxB1 = 1000000. / 4. / P90
if CPD == "mlev" or CPD == "None" or CPD == None or CPD == "":
pul.SetPar(cpd, dfltWave, "")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict[cpd]))
CPD = pul.GetPar(cpd, "")
Stuff = CPDtools.CPDparse(CPD, nuc)
Amp0 = CPDtools.Find_old_pl(Stuff[0], units)
if units == "W":
Amp = WtodB(Amp)
Amp0 = WtodB(Amp0)
decpw0 = CPDtools.Find_old_pw(Stuff[1], nuc)
B1_0 = MaxB1 * (math.pow(10, (Amp - Amp0) / 20.)) / 1000.
if B1_0 > 1.: B1out = '% .3f' % B1_0
if B1_0 > MaxB1 / 1000.: B1out = '% .3f' % dfltB0
if B1_0 <= 1.: B1out = '% .3f' % dfltB0
index = TopCmds.INPUT_DIALOG("Mr Setup Input", "Decoupling Window", \
["Desired "+nuc+" Decoupling Amplitude","File"],\
[B1out,CPD],["kHz",""],["1","1"],\
["Accept","Close"], [spc,ret], 10)
if index == None:
TopCmds.EXIT()
pul.SetPar(cpd, index[1], "")
pl = pul.pp_2_xcmd(Stuff[0], "")
matched = 0
for a in aOption:
if pl == pul.pulDict[a]:
matched = 1
Hamp = DecSafely(
float(index[0]) * 1000, a, MaxB1, 2 * 1000. * dfltB0, Amp,
units)
if matched == 0:
Hamp = DecSafely(
float(index[0]) * 1000, aOption[0], MaxB1, 2 * 1000. * dfltB0, Amp,
units)
decpw = (MaxB1 / 1000. / float(index[0])) * (dfltPH / 180.) * 2 * P90
if units == "W":
Hamp = dBtoW(Hamp)
value = TopCmds.SELECT("Adjusting the "+nuc+" decoupling parameters:",\
"This will set\n "+nuc+" power ("+ Stuff[0] +") to: "+ str('%.2f' %Hamp)+" "+ units+"\n \
Pulse width (" + Stuff[1] +") to: " +str('%3.2f' %decpw)+" us",["Update", "Keep Previous"])
if value != 1:
if Stuff[0] == "":
pul.SetPar(aOption[0], Hamp, units)
for i in aFaults:
if pl == pul.pulDict[i]:
DecError(f, nuc)
for a in aOption:
if pl == pul.pulDict[a]:
pul.SetPar(a, Hamp, units)
return Stuff[1], decpw
def CalCP(p90H, p90L, ampH, ampL, ampD, Cnct, shH, shL, HXorXY, iGuess, units,
offsCP, In, Out):
"""
p90H/L: Dictionary Key for High/Low Gamma Nucleus 90 degree pulse
ampH/L: dict key for High/Low G CP amp
ampD : dict key for Decoupler (assumed to be 1H) or "empty"
Cnct : dict key for CP contact
shH/L : dict key of CP shape files
HXorXY: Determines whether decoupling is used
iGuess: "Max", "High", "Low", "LG"
Max : determine highest allowed condition
High : High G = 3/2 Wr Low G = 5/2 Wr
Low : High G = 7/2 Wr Low G = 5/2 Wr
LG : Use Max, but adjust for Lee-Goldburg
units : Watts (W) or decibel (dB)
offsCP: offset for CP in Hz (LG or off-resonance CP)
In : Title, Subtitle, and Label for Input Dialog
Out : Title and Label for Selection/Confirmation Window
"""
P90H = pul.GetPar(p90H, "")
P90L = pul.GetPar(p90L, "")
P90D = pul.GetPar('pH90', "")
#Use Dictionary Definitions to find hard pulse powers
if p90H.find('H') >= 0: AmpH = pul.GetPar('aH', units)
if p90H.find('C') >= 0: AmpH = pul.GetPar('aC', units)
if p90H.find('N') >= 0: AmpH = pul.GetPar('aN', units)
if p90L.find('H') >= 0: AmpL = pul.GetPar('aH', units)
if p90L.find('C') >= 0: AmpL = pul.GetPar('aC', units)
if p90L.find('N') >= 0: AmpL = pul.GetPar('aN', units)
SPH = pul.GetPar(shH, "")
SPL = pul.GetPar(shL, "")
MAS = pul.GetPar('MAS', "")
CNCT = pul.GetPar(Cnct, "")
if CNCT <= 1.: CNCT = 1000.
if CNCT >= 10000.: CNCT = 10000.
MaxB1H = 1000000. / 4. / P90H
MaxB1L = 1000000. / 4. / P90L
MaxB1D = 1000000. / 4. / P90D
#Set Decoupler if Appropriate
if HXorXY == "XY":
AmpD = pul.GetPar('aH', "dB")
AmpD0 = pul.GetPar(ampD, "dB")
B1_0 = MaxB1D * (math.pow(10, (AmpD - AmpD0) / 20.))
if B1_0 > 100.: Dcond = '% .1f' % B1_0
if B1_0 > MaxB1D: Dcond = '85000.0'
if B1_0 <= 100.: Dcond = '85000.0'
if units == "W":
AmpH = WtodB(AmpH)
AmpL = WtodB(AmpL)
if pul.GetPar(shH,"") == "gauss" or pul.GetPar(shH,"") == "None" or \
pul.GetPar(shH,"") == "" or pul.GetPar(shH,"") == "0" :
pul.SetPar(shH, "ramp.100", "")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict[shH]))
SPH = pul.GetPar(shH, "")
if pul.GetPar(shL,"") == "gauss" or pul.GetPar(shL,"") == "None" or \
pul.GetPar(shL,"") == "" or pul.GetPar(shL,"") == "0" :
pul.SetPar(shL, "square.100", "")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict[shL]))
SPH = pul.GetPar(shL, "")
if iGuess == "LG":
#Adjust MaxB1H for Lee-Goldburg
MaxB1H = MaxB1H * math.sqrt(3.0 / 2.)
if iGuess == "Max" or iGuess == "LG":
#find the channel with the lowest B1
if MaxB1L < MaxB1H:
Ratio = int(math.floor(MaxB1L / MAS))
HCond = (Ratio + 0.5) * MAS
LCond = (Ratio - 0.5) * MAS
if MaxB1L >= MaxB1H:
Ratio = int(math.floor(MaxB1H / MAS))
HCond = (Ratio - 0.5) * MAS
LCond = (Ratio + 0.5) * MAS
while HCond > MaxB1H or LCond > MaxB1L:
Ratio = Ratio - 1
if MaxB1L < MaxB1H:
HCond = (Ratio + 0.5) * MAS
LCond = (Ratio - 0.5) * MAS
if MaxB1L >= MaxB1H:
HCond = (Ratio - 0.5) * MAS
LCond = (Ratio + 0.5) * MAS
# If spinning very fast or using weak B1s
if Ratio == 2:
LCond = 0.75 * MAS
HCond = 1.75 * MAS
if Ratio <= 1 or HCond > MaxB1H or LCond > MaxB1L:
LCond = .25 * MAS
HCond = .75 * MAS
else:
LCond = (5. / 2.) * MAS
if iGuess == "Low":
HCond = (3. / 2.) * MAS
else:
#iGuess == "High":
HCond = (7. / 2.) * MAS
while LCond > MaxB1L:
LCond = LCond - MAS
HCond = LCond + MAS
while HCond > MaxB1H:
LCond = LCond - MAS
HCond = LCond + MAS
if LCond < MAS:
LCond = 0.25 * MAS
HCond = 0.75 * MAS
if iGuess == "LG":
#Change MaxB1H back for proper conversion
MaxB1H = 1000000. / 4. / P90H
if HXorXY == "HX":
index=TopCmds.INPUT_DIALOG(In[0],In[1],In[2],\
[str('%.3f' %(HCond/1000.)),str(SPH),str('%.3f' %(LCond/1000.)),str(SPL),\
str('%.3f' %(CNCT/1000.))],\
["kHz","","kHz","","ms"],\
["1","1","1","1","1"],\
["Accept","Close"], [spc,ret], 10)
if HXorXY == "XY":
index=TopCmds.INPUT_DIALOG(In[0],In[1],In[2],\
[str('%.3f' %(HCond/1000.)),str(SPH),str('%.3f' %(LCond/1000.)),str(SPL),\
str('%.3f' %(CNCT/1000.)),str('%.3f' %(float(Dcond)/1000.))],\
["kHz","","kHz","","ms","kHz"],\
["1","1","1","1","1","1"],\
["Accept","Close"], [spc,ret], 10)
if index == None:
TopCmds.EXIT()
if iGuess == "LG":
w1H = float(index[0]) * math.sqrt(2. / 3.)
LGoffs = 1000 * float(index[0]) / math.sqrt(3.)
else:
w1H = float(index[0])
#TopCmds.MSG("w1H "+str('%.2f' %(w1H*1000.))+" MaxB1H: "+str('%.2f' %(MaxB1H)))
adjust = 20 * (math.log10(w1H * 1000. / MaxB1H))
Hamp1 = AmpH - adjust
if SPH == "Unused":
AvgAmp = 1.
else:
AvgAmp = IntShape.Integrate(index[1]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Hamp = Hamp1 - adjust
adjust = 20 * (math.log10(float(index[2]) * 1000. / MaxB1L))
Lamp1 = AmpL - adjust
if SPL == "Unused":
AvgAmp = 1.
else:
AvgAmp = IntShape.Integrate(index[3]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Lamp = Lamp1 - adjust
CNCT = float(index[4]) * 1000.
if HXorXY == "XY":
#Decouple Safely
Damp = DecSafely(1000. * float(index[5]), ampD, MaxB1D, 150000., AmpD,
units)
if units == "W":
Hamp = dBtoW(Hamp)
Lamp = dBtoW(Lamp)
if HXorXY == "XY": Damp = dBtoW(Damp)
if HXorXY == "HX":
if iGuess == "LG":
value = TopCmds.SELECT(Out[0],\
"This will set\n "+\
Out[1][0]+" power ("+ pul.pulDict[ampH] +") to: " + str('%3.2f' %Hamp)+" "+ units+"\n"+\
Out[1][1]+" power ("+ pul.pulDict[ampL] +") to: " + str('%3.2f' %Lamp)+" "+ units+"\n"+\
"1H LG offset ("+ pul.pulDict[offsCP] +") to: "+ str('%3.2f' %LGoffs)+ " Hz",\
["Update", "Keep Previous"],[spc,ret])
else:
value = TopCmds.SELECT(Out[0],\
"This will set\n "+\
Out[1][0]+" power ("+ pul.pulDict[ampH] +") to: " + str('%3.2f' %Hamp)+" "+ units+"\n"+\
Out[1][1]+" power ("+ pul.pulDict[ampL] +") to: " + str('%3.2f' %Lamp)+" "+ units,\
["Update", "Keep Previous"],[spc,ret])
if HXorXY == "XY":
value = TopCmds.SELECT(Out[0],\
"This will set\n "+\
Out[1][0]+" power ("+ pul.pulDict[ampH] +") to: " + str('%3.2f' %Hamp)+" "+ units+"\n"+\
Out[1][1]+" power ("+ pul.pulDict[ampL] +") to: " + str('%3.2f' %Lamp)+" "+ units+"\n"+\
Out[1][2]+" power ("+ pul.pulDict[ampD] +") to: " + str('%3.2f' %Damp)+" "+ units,\
["Update", "Keep Previous"],[spc,ret])
if value != 1:
pul.SetPar(ampH, Hamp, units)
pul.SetPar(ampL, Lamp, units)
pul.SetPar(Cnct, CNCT, "")
if iGuess == "LG":
pul.SetPar(offsCP, LGoffs, "")
if HXorXY == "XY":
pul.SetPar(ampD, Damp, units)
if SPH != "Unused":
pul.SetPar(shH, index[1], "")
if SPL != "Unused":
pul.SetPar(shL, index[3], "")
return
def HN(units):
p90H = float(TopCmds.GETPAR("P 3"))
ampH = float(TopCmds.GETPAR("PLdB 2"))
p90N = float(TopCmds.GETPAR("P 21"))
ampN = float(TopCmds.GETPAR("PLdB 3"))
MAS = float(TopCmds.GETPAR("CNST 31"))
CNCT = float(TopCmds.GETPAR("P 25"))
SPH = TopCmds.GETPAR2("SPNAM 42")
SPX = TopCmds.GETPAR2("SPNAM 43")
if CNCT <= 1.: CNCT = 1000.
if SPH == "gauss" or SPH == "None" or SPH == "":
#TopCmds.MSG("Please set spnam1")
TopCmds.PUTPAR("SPNAM 42", "ramp.100")
TopCmds.XCMD("spnam42")
SPH = (TopCmds.GETPAR2("SPNAM 42"))
SPH.join()
if SPX == "gauss" or SPX == "None" or SPX == "":
#TopCmds.MSG("Please set spnam11")
TopCmds.PUTPAR("SPNAM 43", "square.100")
TopCmds.XCMD("spnam43")
SPX = (TopCmds.GETPAR2("SPNAM 43"))
SPX.join()
MaxB1H = 1000000. / 4. / p90H
MaxB1N = 1000000. / 4. / p90N
#find the channel with the lowest B1
if MaxB1N < MaxB1H:
Ratio = int(math.floor(MaxB1N / MAS))
NCond = (Ratio - 0.5) * MAS
HCond = (Ratio + 0.5) * MAS
if HCond > MaxB1H:
Ratio = Ratio - 1
NCond = (Ratio - 0.5) * MAS
HCond = (Ratio + 0.5) * MAS
# If spinning very fast or using weak B1s
if Ratio <= 1:
NCond = .25 * MAS
HCond = .75 * MAS
if MaxB1N >= MaxB1H:
Ratio = int(math.floor(MaxB1H / MAS))
HCond = (Ratio - 0.5) * MAS
NCond = (Ratio + 0.5) * MAS
if NCond > MaxB1N:
Ratio = Ratio - 1
HCond = (Ratio - 0.5) * MAS
NCond = (Ratio + 0.5) * MAS
# If spinning very fast or using weak B1s
if Ratio <= 1:
NCond = .25 * MAS
HCond = .75 * MAS
adjust = 20 * (math.log10(NCond / MaxB1N))
Namp = ampN - adjust
adjust = 20 * (math.log10(HCond / MaxB1H))
Hamp = ampH - adjust
index = TopCmds.INPUT_DIALOG("HN CP Input", "Proton Nitrogen Cross Polarization", \
["Proton B1 Field","H Ramp","Nitrogen B1 Field","N Ramp","Contact Time(P25)"],\
[str(HCond),SPH,str(NCond),SPX,str(CNCT)],\
["kHz","","kHz","","us"],\
["1","1","1","1","1"],\
["Accept","Close"], ['a','c'], 10)
adjust = 20 * (math.log10(float(index[0]) / MaxB1H))
Hamp1 = ampH - adjust
AvgAmp = IntShape.Integrate(index[1]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Hamp = Hamp1 - adjust
adjust = 20 * (math.log10(float(index[2]) / MaxB1N))
Namp = ampN - adjust
#Ramp integration adjustment
AvgAmp = IntShape.Integrate(index[3]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Namp = Namp - adjust
CNCT = float(index[4])
#TopCmds.MSG("Adjusting the HC CP parameters:\n Your Proton Amplitude is set to " + str('%3.2f' %Hamp)+ "dB\n Your Nitrogen Ammplitude is set to " +str('%3.2f' %Namp))
if units == "W":
Hamp = dBtoW(Hamp)
Namp = dBtoW(Namp)
value = TopCmds.SELECT("Adjusting the HN CP parameters:",\
"This will set\n 1H power to: " + str('%3.2f' %Hamp)+" "+ units+"\n \
15N power to: " +str('%3.2f' %Namp) + units,["Update", "Keep Previous"])
if value != 1:
TopCmds.PUTPAR("SP" + units + " 42", str('%3.2f' % Hamp))
TopCmds.PUTPAR("SP" + units + " 43", str('%3.2f' % Namp))
TopCmds.PUTPAR("PL" + units + " 42", str('%3.2f' % Hamp))
TopCmds.PUTPAR("PL" + units + " 43", str('%3.2f' % Namp))
TopCmds.PUTPAR("P 25", str('%.2f' % CNCT))
TopCmds.PUTPAR("SPNAM 42", index[1])
TopCmds.PUTPAR("SPNAM 43", index[3])
def HC(units):
p90H = pul.GetPar('pH90', "")
p90C = pul.GetPar('pC90', "")
ampH = pul.GetPar('aH', units)
ampC = pul.GetPar('aC', units)
MAS = pul.GetPar('MAS', "")
CNCT = pul.GetPar('pHC', "")
SPH = pul.GetPar('sHhc', "")
SPX = pul.GetPar('sChc', "")
if units == "W":
ampH = WtodB(ampH)
ampC = WtodB(ampC)
if CNCT <= 1.: CNCT = 1000.
if SPH == "gauss" or SPH == "None" or SPH == "" or SPH == "0":
pul.SetPar('sHhc', "ramp.100", "")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict['sHhc']))
SPH = pul.GetPar('sHhc', "")
if SPX == "gauss" or SPX == "None" or SPX == "" or SPX == "0":
pul.SetPar('sChc', "square.100", "")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict['sChc']))
SPX = pul.GetPar('sChc', "")
MaxB1H = 1000000. / 4. / p90H
MaxB1C = 1000000. / 4. / p90C
#find the channel with the lowest B1
if MaxB1C < MaxB1H:
Ratio = int(math.floor(MaxB1C / MAS))
CCond = (Ratio - 0.5) * MAS
HCond = (Ratio + 0.5) * MAS
if HCond > MaxB1H:
Ratio = Ratio - 1
CCond = (Ratio - 0.5) * MAS
HCond = (Ratio + 0.5) * MAS
# If spinning very fast or using weak B1s
if Ratio <= 1:
CCond = .25 * MAS
HCond = .75 * MAS
if MaxB1C >= MaxB1H:
Ratio = int(math.floor(MaxB1H / MAS))
HCond = (Ratio - 0.5) * MAS
CCond = (Ratio + 0.5) * MAS
if CCond > MaxB1C:
Ratio = Ratio - 1
HCond = (Ratio - 0.5) * MAS
CCond = (Ratio + 0.5) * MAS
# If spinning very fast or using weak B1s
if Ratio <= 1:
CCond = .75 * MAS
HCond = .25 * MAS
adjust = 20 * (math.log10(CCond / MaxB1C))
Camp = ampC - adjust
adjust = 20 * (math.log10(HCond / MaxB1H))
Hamp = ampH - adjust
index = TopCmds.INPUT_DIALOG("HC CP Input", "Proton Carbon Cross Polarization", \
["Proton B1 Field","H Ramp","Carbon B1 Field","C Ramp","Contact Time(P15)"],\
[str(HCond),str(SPH),str(CCond),str(SPX),str(CNCT)],\
["Hz","","Hz","","us"],\
["1","1","1","1","1"],\
["Accept","Close"], ['a','c'], 10)
adjust = 20 * (math.log10(float(index[0]) / MaxB1H))
Hamp1 = ampH - adjust
if SPH == "Unused":
AvgAmp = 1.
else:
AvgAmp = IntShape.Integrate(index[1]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Hamp = Hamp1 - adjust
adjust = 20 * (math.log10(float(index[2]) / MaxB1C))
Camp1 = ampC - adjust
if SPX == "Unused":
AvgAmp = 1.
else:
AvgAmp = IntShape.Integrate(index[3]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Camp = Camp1 - adjust
CNCT = float(index[4])
if units == "W":
Hamp = dBtoW(Hamp)
Camp = dBtoW(Camp)
value = TopCmds.SELECT("Adjusting the HC CP parameters:",\
"This will set\n 1H power to: " + str('%3.2f' %Hamp)+" "+ units+"\n \
13C power to: " +str('%3.2f' %Camp) + " "+units,["Update", "Keep Previous"])
if value != 1:
pul.SetPar('aHhc', Hamp, units)
pul.SetPar('aChc', Camp, units)
pul.SetPar('pHC', CNCT, "")
if SPH != "Unused":
pul.SetPar('sHhc', index[1], "")
if SPX != "Unused":
pul.SetPar('sChc', index[3], "")
def HN(units):
p90H = pul.GetPar('pH90', "")
p90N = pul.GetPar('pN90', "")
ampH = pul.GetPar('aH', units)
ampN = pul.GetPar('aN', units)
MAS = pul.GetPar('MAS', "")
CNCT = pul.GetPar('pHN', "")
SPH = pul.GetPar('sHhn', "")
SPX = pul.GetPar('sNhn', "")
if units == "W":
ampH = WtodB(ampH)
ampN = WtodB(ampN)
if CNCT <= 1.: CNCT = 1000.
if SPH == "gauss" or SPH == "None" or SPH == "" or SPH == "0":
pul.SetPar('sHhn', "ramp.100", "")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict['sHhn']))
SPH = pul.GetPar('sHhn', "")
if SPX == "gauss" or SPX == "None" or SPX == "" or SPX == "0":
pul.SetPar('sNhn', "square.100", "")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict['sNhn']))
SPX = pul.GetPar('sNhn', "")
MaxB1H = 1000000. / 4. / p90H
MaxB1N = 1000000. / 4. / p90N
#find the channel with the lowest B1
if MaxB1N < MaxB1H:
Ratio = int(math.floor(MaxB1N / MAS))
NCond = (Ratio - 0.5) * MAS
HCond = (Ratio + 0.5) * MAS
if HCond > MaxB1H:
Ratio = Ratio - 1
NCond = (Ratio - 0.5) * MAS
HCond = (Ratio + 0.5) * MAS
# If spinning very fast or using weak B1s
if Ratio <= 1:
NCond = .25 * MAS
HCond = .75 * MAS
if MaxB1N >= MaxB1H:
Ratio = int(math.floor(MaxB1H / MAS))
HCond = (Ratio - 0.5) * MAS
NCond = (Ratio + 0.5) * MAS
if NCond > MaxB1N:
Ratio = Ratio - 1
HCond = (Ratio - 0.5) * MAS
NCond = (Ratio + 0.5) * MAS
# If spinning very fast or using weak B1s
if Ratio <= 1:
NCond = .25 * MAS
HCond = .75 * MAS
adjust = 20 * (math.log10(NCond / MaxB1N))
Namp = ampN - adjust
adjust = 20 * (math.log10(HCond / MaxB1H))
Hamp = ampH - adjust
index = TopCmds.INPUT_DIALOG("HN CP Input", "Proton Nitrogen Cross Polarization", \
["Proton B1 Field","H Ramp","Nitrogen B1 Field","N Ramp","Contact Time(P25)"],\
[str(HCond),SPH,str(NCond),SPX,str(CNCT)],\
["Hz","","Hz","","us"],\
["1","1","1","1","1"],\
["Accept","Close"], ['a','c'], 10)
adjust = 20 * (math.log10(float(index[0]) / MaxB1H))
Hamp1 = ampH - adjust
if SPH == "Unused":
AvgAmp = 1.
else:
AvgAmp = IntShape.Integrate(index[1]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Hamp = Hamp1 - adjust
adjust = 20 * (math.log10(float(index[2]) / MaxB1N))
Namp = ampN - adjust
if SPX == "Unused":
AvgAmp = 1.
else:
AvgAmp = IntShape.Integrate(index[3]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Namp = Namp - adjust
CNCT = float(index[4])
#TopCmds.MSG("Adjusting the HC CP parameters:\n Your Proton Amplitude is set to " + str('%3.2f' %Hamp)+ "dB\n Your Nitrogen Ammplitude is set to " +str('%3.2f' %Namp))
if units == "W":
Hamp = dBtoW(Hamp)
Namp = dBtoW(Namp)
value = TopCmds.SELECT("Adjusting the HN CP parameters:",\
"This will set\n 1H power to: " + str('%3.2f' %Hamp)+" "+ units+"\n \
15N power to: " +str('%3.2f' %Namp) + units,["Update", "Keep Previous"])
if value != 1:
pul.SetPar('aHhn', Hamp, units)
pul.SetPar('aNhn', Namp, units)
pul.SetPar('pHN', CNCT, "")
if SPH != "Unused":
pul.SetPar('sHhn', index[1], "")
if SPX != "Unused":
pul.SetPar('sNhn', index[3], "")
def NCO(units):
p90H = pul.GetPar('pH90', "")
p90C = pul.GetPar('pC90', "")
p90N = pul.GetPar('pN90', "")
ampH = pul.GetPar('aH', units)
ampC = pul.GetPar('aC', units)
ampN = pul.GetPar('aN', units)
MAS = pul.GetPar('MAS', "")
CNCT = pul.GetPar('pNCO', "")
SPX = pul.GetPar('sCnco', "")
SPY = pul.GetPar('sNnco', "")
#TopCmds.MSG(str(CNCT))
MaxB1H = 1000000. / 4. / p90H
if units == "W":
ampN = WtodB(ampN)
ampC = WtodB(ampC)
ampH = WtodB(ampH)
if CNCT <= 1.: CNCT = 3500.
if SPX == "gauss" or SPX == "None" or SPX == "" or SPX == "0":
pul.SetPar('sCnco', "ramp.100", "")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict['sCnco']))
SPX = pul.GetPar('sCnco', "")
if SPY == "gauss" or SPY == "None" or SPY == "" or SPY == "0":
pul.SetPar('sNnco', "ramp.100", "")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict['sNnco']))
SPY = pul.GetPar('sNnco', "")
MaxB1N = 1000000. / 4. / p90N
MaxB1C = 1000000. / 4. / p90C
#find the channel with the lowest B1
NCond = (5. / 2.) * MAS
CCond = (7. / 2.) * MAS
while NCond > MaxB1N:
NCond = NCond - MAS
CCond = NCond + MAS
while CCond > MaxB1C:
NCond = NCond - MAS
CCond = NCond + MAS
if NCond < MAS:
NCond = 0.25 * MAS
CCond = 0.75 * MAS
index = TopCmds.INPUT_DIALOG("NCO CP Input", "N-CO SPECIFIC 7/2*C; 5/2*N", \
["CO B1 field","N B1 field","H B1 decoupler","Contact Time","Carbon Ramp","Nitrogen Ramp"],\
[str(CCond),str(NCond),"85000.0",str(CNCT),SPX,SPY],\
["Hz","Hz","Hz","us","",""],\
["1","1","1","1","1","1"],\
["Accept","Close"], ['a','c'], 10)
adjust = 20 * (math.log10(float(index[0]) / MaxB1C))
Camp = ampC - adjust
adjust = 20 * (math.log10(float(index[1]) / MaxB1N))
Namp = ampN - adjust
adjust = 20 * (math.log10(float(index[2]) / MaxB1H))
Hamp = ampH - adjust
CNCT = float(index[3])
#Insert ramp calibration here
if SPX == "Unused":
AvgAmp = 1.
else:
AvgAmp = IntShape.Integrate(index[4]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Camp = Camp - adjust
if SPY == "Unused":
AvgAmp = 1.
else:
AvgAmp = IntShape.Integrate(index[5]) / 100.
adjust = 20 * (math.log10(1. / AvgAmp))
Namp = Namp - adjust
if units == "W":
Namp = dBtoW(Namp)
Camp = dBtoW(Camp)
Hamp = dBtoW(Hamp)
value = TopCmds.SELECT("Adjusting the NCO CP parameters:",\
"This will set\n \
13C power to: " + str('%3.2f' %Camp) + " " + units +"\n \
15N power to: " + str('%3.2f' %Namp) + " " + units +"\n \
1H power to: " + str('%3.2f' %Hamp) + " " + units,["Update", "Keep Previous"])
if value != 1:
pul.SetPar('aNnco', Namp, units)
pul.SetPar('aCnco', Camp, units)
pul.SetPar('aHnco', Hamp, units)
pul.SetPar('pNCO', CNCT, "")
if SPX != "Unused":
pul.SetPar('sCnco', index[4], "")
if SPY != "Unused":
pul.SetPar('sNnco', index[5], "")
def CalSP(nuc,units,para,dflt,limits,dia,conf,tip):
"""
nuc : Nucleus, 13C or 1H
units : Watts (W) or Decibels (dB)
para : Dict keys for soft pulse wave (time,amp,shape,offs)
dflt : Defaults (time,shape,offs(in ppm))
limits : ppm frequency limits (upper, lower)
"""
if nuc=="13C":p90=pul.GetPar('pC90',""); amp=pul.GetPar('aC',units)
if nuc=="1H": p90=pul.GetPar('pH90',""); amp=pul.GetPar('aH',units)
MAS =pul.GetPar('MAS',"")
if units == "W":
amp=Setup.WtodB(amp)
MaxB1 = 1000000./4./p90
pSft = pul.GetPar(para[0],"")
if pSft == 0: pSft = dflt[0]
SP=pul.GetPar(para[2],"")
offs0 = pul.GetPar(para[3],"")
#Check for existence and default
if SP == "gauss" or SP == "None" or SP == "0" or SP == "" :
pul.SetPar(para[2],dflt[1],"")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict[para[2]]))
SP=pul.GetPar(para[2],"")
if pul.pulDict['uoffs']=='ppm':
ppm=offs0
offs=Cfrq.ppm2offs(offs0)
else:
#offs0 is in Hz
ppm=Cfrq.offs2ppm(offs0)
offs=offs0
if ppm > limits[0] : ppm=dflt[2]
if ppm < limits[1] : ppm=dflt[2]
index = TopCmds.INPUT_DIALOG(dia[0],dia[1],dia[2],\
[str('%3.2f' %pSft),str('%3.2f' %ppm),SP],\
dia[3],["1","1","1"],\
["Accept","Close"], [spc,ret], 10)
if index == None:TopCmds.EXIT()
pSft=float(index[0])
ppm=float(index[1])
SP=index[2]
offs=Cfrq.ppm2offs(ppm)
AvgAmp=IntShape.Integrate(SP)/100.
adjust=20*math.log10((tip/90.)*p90/pSft/AvgAmp)
Power =amp-adjust
if units == "W":
Power=Setup.dBtoW(Power)
confirm = TopCmds.SELECT(conf,\
"This will set\n "+\
nuc+" amp "+pul.pulDict[para[1]]+" to : " + str('%3.2f' %Power)+ " "+units+"\n \
Pulse offset to : " + str('%8.0f' %offs) + " Hz\n \
Equivalent to : " + str('%3.1f' %ppm ) + " ppm\n "+\
pul.pulDict[para[0]]+" to :" + str('%6.1f' %pSft)+ " us\n "\
,["Update", "Keep Previous"])
if confirm != 1:
pul.SetPar(para[0],pSft,"")
pul.SetPar(para[1],Power,units)
pul.SetPar(para[2],SP,"")
if pul.pulDict['uoffs']=='ppm':
pul.SetPar(para[3],ppm,"")
elif pul.pulDict['uoffs']=='Hz':
pul.SetPar(para[3],offs,"")
else :
pul.SetPar(para[3],ppm,"")
def CalDREAM(p90,match,amp,ampD,Cnct,SP,dfltSP,shpdict,units,In,Out):
"""
p90 : Dictionary Key for Nucleus 90 degree pulse; determines Nuc (Decoupling flag)
match : float of precalculated match
amp : dict key for DREAM amp
ampD : dict key for Decoupler (assumed to be 1H) or "empty"
Cnct : dict key for DREAM contact
shp : dict key of DREAM shape file
dfltSP: Default pulse shape
shpdict:dict key for DREAM shape
units : Watts (W) or decibel (dB)
In : Title, Subtitle, and Label for Input Dialog
Out : Title and Label for Selection/Confirmation Window
"""
MAS=pul.GetPar('MAS',"")
TauR=float(1000000/MAS)
P90D=pul.GetPar('pH90',"")
AmpD =pul.GetPar('aH',"dB")
MaxB1D = 1000000./4./P90D
if p90.find('H') >=0:MaxB1=1000000./4./(pul.GetPar('pH90',""));Amp=pul.GetPar('aH','dB')
if p90.find('C') >=0:MaxB1=1000000./4./(pul.GetPar('pC90',""));Amp=pul.GetPar('aC','dB')
CNCT=pul.GetPar(Cnct,"")
if CNCT <= 1. : CNCT = 1000.
if CNCT >= 10000.: CNCT = 10000.
if p90.find('H') <=0:
AmpD0=pul.GetPar(ampD,'dB')
B1_0 = MaxB1D*(math.pow(10,(AmpD-AmpD0)/20.))
if B1_0 > 100. : Dcond='% .1f' % B1_0
if B1_0 > MaxB1D: Dcond='85000.0'
if B1_0 <= 100. : Dcond='85000.0'
if units == "W":
Amp=WtodB(Amp)
if SP == "gauss" or SP == "None" or SP=="" or SP == "0" :
SP=dfltSP
pul.SetPar(shpdict,SP,"")
TopCmds.XCMD(pul.xcmd_name(pul.pulDict[shpdict]))
SP=pul.GetPar(shp,"")
if p90.find('H') >=0:
index=TopCmds.INPUT_DIALOG(In[0],In[1],In[2],\
[str('%.3f' %(match/1000.)),str(SP),str('%.3f' %(CNCT/1000.))],\
["kHz","","ms"],\
["1","1","1"],\
["Accept","Close"], [spc,ret], 10)
if index== None: TopCmds.EXIT()
else:
index=TopCmds.INPUT_DIALOG(In[0],In[1],In[2],\
[str('%.3f' %(match/1000.)),str(SP),str('%.3f' %(CNCT/1000.)),\
str('%.3f' %(float(Dcond)/1000.))],\
["kHz","","ms","kHz"],\
["1","1","1","1"],\
["Accept","Close"], [spc,ret], 10)
if index== None: TopCmds.EXIT()
wD=float(index[3])
w1=float(index[0])
SP=index[1]
CNCT=float(index[2])*1000.
#Integrate Dream ramp
adjust=20*(math.log10(w1*1000./MaxB1))
Amp1 = Amp-adjust
AvgAmp=(IntShape.Integrate(SP))/100.
adjust=20*(math.log10(1./AvgAmp))
AmpX = Amp1-adjust
if units == "W": AmpX=dBtoW(AmpX)
#TopCmds.MSG(str(Out))
if p90.find('H') <=0:
AmpD = Setup.DecSafely(1000.*wD,ampD,MaxB1D,150000.,AmpD,units)
value = TopCmds.SELECT(Out[0],\
"This will set\n "+\
Out[1][1]+" power ("+ pul.pulDict[amp] +") to: " + str('%3.2f' %AmpX)+" "+ units+"\n"+\
Out[1][0]+" power ("+ pul.pulDict[ampD] +") to: " + str('%3.2f' %AmpD)+" "+ units,\
["Update", "Keep Previous"],[spc,ret])
else:
value = TopCmds.SELECT(Out[0],\
"This will set\n "+\
Out[1][0]+" power ("+ pul.pulDict[amp] +") to: " + str('%3.2f' %Hamp)+" "+ units+"\n"+\
["Update", "Keep Previous"],[spc,ret])
if value != 1:
pul.SetPar(amp,AmpX,units)
pul.SetPar(Cnct,CNCT,"")
if p90.find('H') <=0:
pul.SetPar(ampD,AmpD,"dB")
