def abort(Home, Source, winfil): if winfil ==0 : TopCmds.SET_SELECTED_WIN(Source) TopCmds.CLOSEWIN(TopCmds.CURDATA()) TopCmds.SET_SELECTED_WIN(Home) TopCmds.EXIT() if winfil ==1 : TopCmds.RE(Source) TopCmds.CLOSEWIN(TopCmds.CURDATA()) TopCmds.RE(Home) TopCmds.EXIT()
def name(input):
Cname = str("EXPORT_C_C" + input[4] + "_B" + input[5] + "_MAS" + input[2] +
"_np" + input[3] + ".wave")
Nname = str("EXPORT_N_C" + input[4] + "_B" + input[6] + "_MAS" + input[2] +
"_np" + input[3] + ".wave")
Cwave = pul.pulDict['sCexp']
Nwave = pul.pulDict['sNexp']
Wave = str(INPUT_DIALOG("EXPORT Files", "", ["C File = ","C Wave =","N File = ","N Wave =",],\
[Cname,Cwave,Nname,Nwave],["","","",""],["1","1","1","1"],["Accept","Close"], [spc,ret], 30))
if wave == None: TopCmds.EXIT()
Files = Wave[8:len(Wave) - 21] #get rid of Java formatting
i = Files.find(",")
ii = Files[i + 3:].find(",") + 3
iii = Files[i + ii + 3:].find(",") + 3
Cfile = Files[0:i - 1]
Cwave = Files[i + 3:i + ii - 1]
Nfile = Files[i + ii + 3:i + ii + iii - 1]
Nwave = Files[i + ii + iii + 3:]
#MSG( Cfile )
#MSG( Cwave )
#MSG( Nfile )
#MSG( Nwave )
pul.SetPar(str(Cwave), str(Cfile), "")
pul.SetPar(str(Nwave), str(Nfile), "")
return Cfile, Nfile
def HN(MAS0, MAS, units):
p90H = pul.GetPar('pH90', "")
ampH = pul.GetPar('aH', units)
SPH = pul.GetPar('sHhn', "")
ampHCP = pul.GetPar('aHhn', units)
avgH = 1.0
p90X = pul.GetPar('pN90', "")
ampX = pul.GetPar('aN', units)
SPX = pul.GetPar('sNhn', "")
ampXCP = pul.GetPar('aNhn', units)
avgX = 1.0
CNCT = pul.GetPar('pHN', "")
params = TopCmds.INPUT_DIALOG("HN CP MAS adjustment", "Proton Nitrogen Cross Polarization", \
["Old MAS rate","New MAS rate","Old 1H power ("+pul.pulDict['aHhc']+")",\
"Old 15N power ("+pul.pulDict['aNhn']+")","Contact Time ("+pul.pulDict['pHN']+")",\
"H-Ramp ("+pul.pulDict['sHhc']+")","N-Ramp ("+pul.pulDict['sChc']+")"],\
[str(MAS0),str(MAS),str(ampXCP),str(ampHCP),str(CNCT),SPH,SPX],\
["Hz","Hz",units,units,"us","",""],\
["1","1","1","1","1","1","1"],\
["Accept","Close"], [spc,ret], 10)
if params == None: TopCmds.EXIT()
if units == "W":
params[2] = str(Setup.WtodB(float(params[2])))
params[3] = str(Setup.WtodB(float(params[3])))
ampH = Setup.WtodB(ampH)
ampX = Setup.WtodB(ampX)
if SPH != "None" and SPH != None and SPH != "Unused":
avgH = IntShape.Integrate(SPH) / 100.
if SPX != "None" and SPX != None and SPX != "Unused":
avgX = IntShape.Integrate(SPX) / 100.
pulses = p90H, ampH, p90X, ampX, avgH, avgX
SelectorText="Adjust the HN CP parameters:","Calculate New Match for:",\
["Proton","Nitrogen","Maximum for Both"]
ampHCP, ampXCP = FindMatch(params, pulses, SelectorText)
if units == "W":
ampXCP = Setup.dBtoW(ampXCP)
ampHCP = Setup.dBtoW(ampHCP)
value = TopCmds.SELECT("Adjusting the HN CP parameters:",\
"This will set\n 1H power to: " + str('%3.2f' %ampHCP)+ " "+units+"\n \
15N power to: " +str('%3.2f' %ampXCP) + " "+units,["Update", "Keep Previous"])
if value != 1:
pul.SetPar('aHhn', ampHCP, units)
pul.SetPar('aNhn', ampXCP, units)
pul.SetPar('pHN', CNCT, "")
pul.SetPar('sHhn', SPH, "")
pul.SetPar('sNhn', SPX, "")
def dialog():
input = TopCmds.INPUT_DIALOG("DUOinput", "", \
["RF field = ", "MAS = ","steps" ,"B = ", "C = "], \
["100","10000","100","3.5","0.5"],\
["kHz","Hz","","lit=3.5","lit=0.5",], ["1", "1", "1", "1", "1"],\
["Accept","Close"], [spc,ret],10)
if input == None: TopCmds.EXIT()
return input
def Find_PWdec(Text):
while i < len(Text):
about = ''
if Text[i].find("pcpd") >= 0: type = "PCPD"
elif Text[i].find("p31") >= 0: type = "P 31"
elif Text[i].find("p63") >= 0: type = "P 63"
elif Text[i].find("p62") >= 0: type = "P 62"
else:
TopCmds.MSG("File for Decoupling not found; Exiting")
TopCmds.EXIT()
def name(input):
name = str("DUO_C" + input[4] + "_B" + input[3] + "_MAS" + input[1] +
"_np" + input[2] + ".wave")
Wavename = str(
TopCmds.INPUT_DIALOG("DUO File", "", ["Filename = "], [name], [""],
["1"], ["Accept", "Close"], [spc, ret], 30))
if Wavename == None: TopCmds.EXIT()
Filename = Wavename[8:len(Wavename) - 21] #get rid of Java formatting
#MSG( Filename + ' \n is the file name')
return Filename
def dialog():
MAS = TopCmds.GETPAR("CNST 31")
#MSG(MAS)
input = TopCmds.INPUT_DIALOG("EXPORTinput", "", \
["13C field ","15N field ","MAS ", "steps in Export Element", "C(Ix+Sx)=CFx", "B Iy", "B Sy", "Initial Phase"],\
["50","50",str(MAS),"100", "7.0", "0.375", "0.625", "90"],\
["kHz","kHz","Hz","","","","",""],\
["1","1", "1", "1", "1", "1", "1", "1"],\
["Accept","Close"], [spc,ret], 10)
if input == None: TopCmds.EXIT()
return input
def name_confirm(Ttot,RIRO,Sc,Del,Bet,key):
Name = "DRM_" + str('%.0f'%Sc) +"Sc_"+str('%.0f'%Del)+"D_"+str('%.0f'%Bet)+"B.wave"
SP=pul.pulDict[key]
index=TopCmds.INPUT_DIALOG("DREAM Files", "", \
["File = ","Wave =",],[Name,SP],["",""],["1","1"],\
["Accept","Close"], [spc,ret], 30)
if index == None:TopCmds.EXIT()
pul.SetPar(key,index[0],"")
return index[0]
def dialog():
MAS = pul.GetPar('MAS', "")
TauR = float(1000000 / MAS)
Data = TopCmds.INPUT_DIALOG("Tangent Ramp Input", "", \
["Scaling","steps","Ramp (Delta)","Adiabicity (Beta)"],\
["50","500","20","4"],\
["%","","%",""],\
["1","1","1","1"],\
["Accept","Close"], [spc,ret], 10)
if Data == None: TopCmds.EXIT()
return Data
def find_match(input):
import math
NomRF = 1000 * float(input[0])
MAS = float(input[1])
Ioffs = 1000 * float(input[6])
Soffs = 1000 * float(input[7])
m = 1
Match = m * MAS - Ioffs - Soffs
if Match < 0:
m = 2
Match = m * MAS - Ioffs - Soffs
if Match < 0:
TopCmds.MSG("Cannot find match conditions, spinning too slowly")
TopCmds.EXIT()
found = 0
for n in range(10000):
WIeff = math.sqrt(Ioffs * Ioffs + float(n * n))
WSeff = math.sqrt(Soffs * Soffs + float(n * n))
Match = (m * MAS) - WIeff - WSeff
#mm is the amplitude in Hz
if Match > 0.0: mm = n
if Match < 0.0: found = 1
if found == 0:
TopCmds.MSG("Match condition not found within 10kHz, aborting")
TopCmds.EXIT()
YorN = TopCmds.SELECT(
"Scaling",
"The match condition is around %i Hz \n\n Which scaling should be used?"
% mm, ["Calibration", "0.5", "None(1.0)"])
# CONFIRM("Scale Shape Pulse for Match","The amplitude should be approximately %i Hz \n \nUse scaling?" % Match)
if YorN < 0: Scale = 1.0
if YorN == 0: Scale = float(Match) / NomRF
if YorN == 1: Scale = 0.5
if YorN == 2: Scale = 1.0
return Scale
def CPdec(amp, units, In, Out):
"""
amp : dict key for CP decoupling amp
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('pH90', "")
Amp90 = pul.GetPar('aH', "dB")
AmpD0 = pul.GetPar(amp, "dB")
MaxB1D = 1000000. / 4. / P90
B1_0 = MaxB1D * (math.pow(10, (Amp90 - AmpD0) / 20.))
if B1_0 > 100.: Dcond = '% .1f' % B1_0
if B1_0 > MaxB1D: Dcond = '85000.0'
if B1_0 <= 100.: Dcond = '85000.0'
Val = [str('%3.3f' % (float(Dcond) / 1000.))]
index=TopCmds.INPUT_DIALOG(In[0],In[1],In[2],\
Val,["kHz"],["1"],\
["Accept","Close"], [spc,ret], 10)
if index == None:
TopCmds.EXIT()
#Safety
Damp = DecSafely(1000. * float(index[0]), amp, MaxB1D, 150000., Amp90,
units)
if units == "W":
Damp = dBtoW(Damp)
value = TopCmds.SELECT(Out[0],"This will set\n "+\
Out[1]+" power to: " + str('%3.2f' %Damp)+" "+ units,\
["Update", "Keep Previous"],[spc,ret])
if value != 1:
pul.SetPar(amp, Damp, units)
return
def name_confirm():
adbname = pul.GetPar('sCadb', "")
if adbname == "gauss": adbname = "TanhTan"
SP = pul.pulDict['sCadb']
Wave = str(TopCmds.INPUT_DIALOG("Adiabatic TOBSY", "",\
["SP File = ","SP Wave =",],\
[adbname,SP],["",""],["1","1"],["Accept","Close"], [spc,ret], 30))
if Wave == None: TopCmds.EXIT()
Files = Wave[8:len(Wave) - 21] #get rid of Java formatting
i = Files.find(",")
File = Files[0:i - 1]
SP = Files[i + 3:]
pul.SetPar(SP, str(File), "")
pul.SetPar('sCadb', File, "")
def LoadDefault(units):
#
# Read the Prosol data (Defaults remain if no Prosol)
# Still under development :(
p90H = 2.5
p90C = 3.0
p90N = 5.0
if units == "W":
ampH = 100.
ampC = 200.
ampN = 400.
else:
ampH = 0.
ampC = 0.
ampN = 0.
MAS = 10000
#Read the Prosol data if it exists
#XCMD('rprosol')
#p90H, p90C, p90N, ampH, ampC, ampN, MAS = ReadHPFromData(units)
index = TopCmds.INPUT_DIALOG("Mr Setup Input", "Pulse Widths and Power", \
["1H 90 pw","1H ampl","13C 90 pw","13C ampl","15N 90 pw","15N ampl","MAS"],\
[str(p90H),str(ampH),str(p90C),str(ampC),str(p90N),str(ampN),str(MAS)],\
["us",units,"us",units,"us",units," Hz"],\
["1","1","1","1","1","1","1"],\
["Accept","Close"], [spc,ret], 10)
if index == None: TopCmds.EXIT()
p90H = float(index[0])
ampH = float(index[1])
p90C = float(index[2])
ampC = float(index[3])
p90N = float(index[4])
ampN = float(index[5])
MAS = float(index[6])
TauR = 1000000. / MAS
PutPars(p90H, ampH, p90C, ampC, p90N, ampN, MAS, units)
def MakeRamp(Scale, Delta, Beta, Nuc):
MAS =pul.GetPar('MAS',"")
TauR=float(1000000/MAS)
if Nuc=="1H" :
MaxB1=1000./4./(pul.GetPar('pH90',""))
Amp=pul.GetPar('aH','dB')
Time=pul.GetPar('pHdrm',"")
TimeKey='pHdrm'
key='sHdrm'
if Nuc=="13C":
MaxB1=1000./4./(pul.GetPar('pC90',""))
Amp=pul.GetPar('aC','dB')
Time=pul.GetPar('pCdrm',"")
TimeKey='pCdrm'
key='sCdrm'
PctScal=Scale/MaxB1
PctRamp=2.*Delta/MaxB1
PctAdia=Beta/MaxB1
Index = TopCmds.INPUT_DIALOG("DREAM RAMP", "", \
["Total Contact","Read-In/Out","Ampl","Ramp","Adiabicity"],\
[str(Time/1000.),str( '%3.2f' % (2*TauR)),str('%3.1f'%(Scale/1000.)),\
str('%3.1f'%(Delta/1000.)),str('%3.1f' % Beta)],\
["ms" ,"us" ,"kHz" ,"+/- kHz","Hz"],\
["1" ,"1" ,"1" ,"1" ,"1"],\
["Accept","Close"], [spc,ret], 10)
if Index == None:TopCmds.EXIT()
PctAmpl=100.*float(Index[2])/MaxB1
PctDel=PctAmpl*float(Index[3])
PctBet=float(Index[2])*float(Index[4])/MaxB1/10.
Name=name_confirm(Index[0],Index[1],str(PctAmpl),str(PctDel),str(PctBet),key)
make(Index[0],Index[1],str(PctAmpl),str(PctRamp),PctBet,Name,key)
pul.SetPar(TimeKey,1000.*float(Index[0]),"")
return Name, Index[0]
def find_file(dirs, name):
found = 0
i = 0
path = ''
while i <= (len(dirs) - 1):
#print (dirs[i], found )
if found == 0:
search = str(dirs[i]) + '/' + str(name)
"""
TopCmds.MSG("This is here to remind you that the os package is removed")
found=1
path=search
"""
if os.path.exists(search) == 1:
found = 1
path = search
i = i + 1
if found == 0:
TopCmds.MSG("File named " + name + " not found\n Exiting")
TopCmds.EXIT()
return path
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 SPC5(MASR, MAS, units):
oldC5 = pul.GetPar('aCc5', units)
LoopC5 = pul.GetPar('lC5', "")
index = TopCmds.INPUT_DIALOG("SPC5 MAS", "SPC5 changes for MAS change", \
["Old MAS rate","New MAS rate","Old 13C power ("+pul.pulDict['aCc5']+")",\
"Mixing Loop ("+pul.pulDict['lC5']+")"],\
[str(MASR),str(MAS),str(oldC5),str(LoopC5)],\
["kHz","kHz",units,""],\
["1","1","1","1"],\
["Accept","Close"], [spc,ret], 10)
if index == None: TopCmds.EXIT()
OldMAS = float(index[0])
NewMAS = float(index[1])
oldC = float(index[2])
newL = float(index[3])
if units == "W":
oldC = Setup.WtodB(oldC)
adjust = 20 * (math.log10(NewMAS / OldMAS))
newC = oldC - adjust
if units == "W":
newC = Setup.dBtoW(newC)
value = TopCmds.SELECT("Adjusting the SPC5 parameters:",\
"This will set\n 13C power "+pul.pulDict['aCc5']+" to: " +\
str('%3.2f' %newC)+ " "+units+"\n"+\
"Loop "+pul.pulDict['lC5']+" to: "+ str(newL)\
,["Update", "Keep Previous"])
if value != 1:
pul.SetPar('aCc5', newC, units)
pul.SetPar('lC5', newL, "")
def LoadFromData(units):
p90H, p90C, p90N, ampH, ampC, ampN, MAS = ReadHPFromData(units)
index = TopCmds.INPUT_DIALOG("Mr Setup Input", "Pulse Widths and Power", \
["1H 90 pw","1H ampl","13C 90 pw","13C ampl","15N 90 pw","15N ampl","MAS"],\
[str('%.2f' %p90H),str('%.2f' %ampH),str('%.2f' %p90C),str('%.2f' %ampC),\
str('%.2f' %p90N),str('%.2f' %ampN),str('%.2f' %MAS)],\
["us",units,"us",units,"us",units," Hz"],\
["1","1","1","1","1","1","1"],\
["Accept","Close"], [spc,ret], 10)
if index == None: TopCmds.EXIT()
p90H = float(index[0])
ampH = float(index[1])
p90C = float(index[2])
ampC = float(index[3])
p90N = float(index[4])
ampN = float(index[5])
MAS = float(index[6])
TauR = 1000000. / MAS
PutPars(p90H, ampH, p90C, ampC, p90N, ampN, MAS, units)
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 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 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 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 CMatch():
#Nuc is a string such as 1H or 13C
Nucs = NUC.list()
if Nucs[0] == "13C":
Frq = fq.O1()
elif Nucs[1] == "13C":
Frq = fq.O2()
elif Nucs[2] == "13C":
Frq = fq.O3()
p90 = float(TopCmds.GETPAR("P 1"))
MAS = float(TopCmds.GETPAR("CNST 31"))
NomRF = 1000000. / 4. / p90
nomatch = []
Af = []
Bf = []
Ap = []
Bp = []
Condition = []
mfaa = []
#message=[]
# It should default to CA-CB matching for DREAM, and CA-CO for R2T
# I'm not sure the best way to select these but I'm putting it in as a dialog
aa, Ap, Bp = Nucl()
#TopCmds.MSG(str(aa))
#TopCmds.MSG(str(Ap))
#TopCmds.MSG(str(Bp))
# Now we'll convert the ppm averages from above into frequencies
hits = 0
mm = 1
SPOFF = float(TopCmds.GETPAR("SPOFFS 5"))
for i in range(len(aa)):
Af.append(SPOFF + Frq.ppm2offs(Ap[i]))
Bf.append(SPOFF + Frq.ppm2offs(Bp[i]))
# The offsets should be less than 1/2 (or 1*) the MAS frequency, or we can't match.
# We will store a list for those aa's that we can't match.
m = 1
Match = m * MAS - math.fabs(Af[i]) - (math.fabs(Bf[i]))
if Match < 0:
m = 2
mm = 2
Match = m * MAS - (math.fabs(Af[i])) - (math.fabs(Bf[i]))
#TopCmds.MSG(str(Match)+" "+str(math.fabs(Af[i]))+" "+str(math.fabs(Bf[i])))
if Match < 0: nomatch.append(aa[i])
if Match >= 0: hits = hits + 1
#TopCmds.MSG(str(len(nomatch)))
if len(nomatch) > 0:
TopCmds.MSG("Cannot find match conditions for:\n "\
+ str(nomatch)+ "\n at this carrier or spinning frequency")
if hits == 0:
TopCmds.MSG(
"Cannot find any match conditions, please consider changing frequencies"
)
TopCmds.EXIT()
# Now, we want to determine the matches and store the results and extrema,
# but not for things we know can't be matched
Upper = 0
Lower = MAS * 2
NotCount = len(nomatch)
#Determine if we want to skip
for i in range(len(aa)):
skip = 0
found = 0
for j in range(NotCount):
if nomatch[j] == aa[i]: skip = 1
if not skip:
for n in range(MAS * 2):
if not found:
WAeff = math.sqrt(Af[i] * Af[i] + float(n * n))
WBeff = math.sqrt(Bf[i] * Bf[i] + float(n * n))
Match = (mm * MAS) - WAeff - WBeff
#mm is the match multiplier
if Match <= 0.0:
found = 1
mfaa.append(aa[i])
Condition.append(n)
if n > Upper: Upper = n
if n < Lower: Lower = n
if not found:
nomatch.append(aa[i])
#Condition.append('N/A')
#TopCmds.MSG(str(nomatch))
#TopCmds.MSG(aa[i]+ " " + str(Ap[i]) + " " +str(Bp[i]) + " " + str(Upper) + " " +str(Lower))
if len(nomatch) > 0:
TopCmds.MSG("Cannot find match conditions for:\n "\
+ str(nomatch)+ "\n at this carrier or spinning frequency")
# Now I want to report what we've found. I'll start with an average, deviation and the extremes,
# And offer a detailed report after a dialog.
# I guess these numbers could be used to generate a wave file
Avg = 0.0
Dev = 0.0
for i in range(len(Condition)):
Avg = Avg + float(Condition[i])
Avg = Avg / float(len(Condition))
for i in range(len(Condition)):
Dev = Dev + (float(Condition[i]) - Avg)**2
Dev = math.sqrt(Dev / float(len(Condition) - 1))
#TopCmds.MSG("DEV(DONE): " + str(Dev))
#TopCmds.MSG(str(Avg)+":Average \n"+str(Dev) +":StDev")
Continue=TopCmds.SELECT("Scaling",\
"The mean match is %.2f Hz" % Avg \
+ " \n With a deviation of %.2f Hz" % Dev \
+ "\n with a maximum at %i Hz " % Upper\
+ "\n and a minimum at %i Hz " % Lower\
,["Details","Proceed"]) #0,1
#TopCmds.MSG(str(SeeMore))
if not Continue:
for i in range(math.ceil(len(mfaa) / 20.)):
message = "Here is set #" + str(
i +
1) + " of the match conditions alphabetically by nucleus\n\n"
for j in range(i * 20, min((i + 1) * 20, len(mfaa))):
message = message + str(mfaa[j]) + ": " + str(
Condition[j]) + "Hz\n "
TopCmds.MSG(message)
# Now I want to sort into order by increasing match
for i in range(len(aa)):
for j in range(len(aa)):
if Condition[j] > Condition[i]:
Condition[j], Condition[i] = Condition[i], Condition[j]
mfaa[j], mfaa[i] = mfaa[i], mfaa[j]
for i in range(math.ceil(len(mfaa) / 20.)):
message = "Here is set #" + str(
i + 1) + " of the match conditions by match\n\n"
for j in range(i * 20, min((i + 1) * 20, len(mfaa))):
message = message + str(Condition[j]) + " Hz : " + str(
mfaa[j]) + "\n "
TopCmds.MSG(message)
#TopCmds.MSG(str(NomRF))
# Finally I'm going to pass the result back
# It is best to do this as a percentage to suggest a pulse shape.
# I need a delta, beta, and scale.
#TopCmds.MSG(str(Avg))
AvgPC = 100. * Avg / NomRF
DeltaPC = 100. * (Upper - Lower) / NomRF
BetaPC = 100. * Dev / NomRF
return AvgPC, DeltaPC, BetaPC
def PPDIM():
ppdim = 1
aqseq = ""
ph2D = ""
ph3D = ""
ph4D = ""
Nucl1D = ""
Nucl2D = ""
Nucl3D = ""
Nucl4D = ""
#Acquisition dimension from acq file
Nucl1D = "".join(letter for letter in Nuc.list()[0] if letter.isalpha())
#TopCmds.MSG(Nucl1D)
pp = TopCmds.GETPAR("PULPROG")
dir = get_dir("PP_DIRS")
Name = find_file(dir, pp)
#TopCmds.MSG(Name)
if os.path.exists(Name) == 1:
f = open(Name, 'r')
text = f.readlines()
f.close()
else:
TopCmds.MSG("Pulse Program not found: Exiting")
TopCmds.EXIT()
# Determine pulse sequence dimension and TPPI phases
for line in text:
lines = line.rstrip()
if lines.find("aqseq") >= 0:
#Check for comments
if lines.find(";") < 0:
aqseq = "".join(letter for letter in lines if letter.isdigit())
elif lines.find(";") > lines.find("aqseq"):
aqseq = "".join(letter for letter in lines if letter.isdigit())
if lines.find("F1PH") >= 0 or lines.find("F1EA") >= 0:
if lines.find("F1PH") >= 0: search = "F1PH"
if lines.find("F1EA") >= 0: search = "F1EA"
#Check for comments
if lines.find(";") < 0:
if ppdim < 2: ppdim = 2
ph2D = find_phase(lines, search)
ph2Dp = ph2D + ")"
ph2D = ph2D + " "
elif lines.find(";") > lines.find(search):
if ppdim < 2: ppdim = 2
ph2D = find_phase(lines, search)
ph2Dp = ph2D + ")"
ph2D = ph2D + " "
if lines.find("F1QF") >= 0:
#Check for comments
if lines.find(";") < 0:
if ppdim < 2: ppdim = 2
Nucl2D = "_"
elif lines.find(";") > lines.find("F1QF"):
if ppdim < 2: ppdim = 2
Nucl2D = "_"
if lines.find("F2PH") >= 0 or lines.find("F2EA") >= 0:
if lines.find("F2PH") >= 0: search = "F2PH"
if lines.find("F2EA") >= 0: search = "F2EA"
#Check for comments
if lines.find(";") < 0:
if ppdim < 3: ppdim = 3
ph3D = find_phase(lines, search)
ph3Dp = ph3D + ")"
ph3D = ph3D + " "
elif lines.find(";") > lines.find(search):
if ppdim < 3: ppdim = 3
ph3D = find_phase(lines, search)
ph3Dp = ph3D + ")"
ph3D = ph3D + " "
if lines.find("F2QF") >= 0:
#Check for comments
if lines.find(";") < 0:
if ppdim < 3: ppdim = 3
Nucl3D = "_"
elif lines.find(";") > lines.find("F2QF"):
if ppdim < 3: ppdim = 3
Nucl3D = "_"
if lines.find("F3PH") >= 0 or lines.find("F3EA") >= 0:
if lines.find("F3PH") >= 0: search = "F3PH"
if lines.find("F3EA") >= 0: search = "F3EA"
#Check for comments
if lines.find(";") < 0:
if ppdim < 4: ppdim = 4
ph4D = find_phase(lines, search)
ph4Dp = ph4D + ")"
ph4D = ph4D + " "
elif lines.find(";") > lines.find("F3PH"):
if ppdim < 4: ppdim = 4
ph4D = find_phase(lines, search)
ph4Dp = ph4D + ")"
ph4D = ph4D + " "
if lines.find("F3QF") >= 0:
#Check for comments
if lines.find(";") < 0:
if ppdim < 4: ppdim = 4
Nucl4D = "_"
elif lines.find(";") > lines.find("F3QF"):
if ppdim < 4: ppdim = 4
Nucl4D = "_"
#TopCmds.MSG(ph2D+":2D\n"+ph3D+": 3D\n"+ph4D+": 4D")
#TopCmds.MSG(str(ppdim)+" ppdim\n"+str(ph2D)+" ph2D")
# From TPPI phases make a string corresponding to pulse nucleus
for line in text:
lines = line.rstrip()
if ppdim >= 2:
if lines.find(ph2D) >= 0 and Nucl2D == "":
#TopCmds.MSG(lines)
Nucl2D = find_nuc(lines, ph2D)
#TopCmds.MSG(Nucl2D)
elif lines.find(ph2Dp) >= 0 and Nucl2D == "":
#TopCmds.MSG(lines)
Nucl2D = find_nuc(lines, ph2Dp)
#TopCmds.MSG(Nucl2D)
if ppdim >= 3:
if lines.find(ph3D) >= 0 and Nucl3D == "":
#TopCmds.MSG(lines)
Nucl3D = find_nuc(lines, ph3D)
#TopCmds.MSG(Nucl3D)
elif lines.find(ph3Dp) >= 0 and Nucl3D == "":
#TopCmds.MSG(lines)
Nucl3D = find_nuc(lines, ph3Dp)
#TopCmds.MSG(Nucl3D)
if ppdim >= 4:
if lines.find(ph4D) >= 0 and Nucl4D == "":
#TopCmds.MSG(lines)
Nucl4D = find_nuc(lines, ph4D)
elif lines.find(ph4Dp) >= 0 and Nucl4D == "":
#TopCmds.MSG(lines)
Nucl4D = find_nuc(lines, ph4Dp)
#TopCmds.MSG(str(ppdim)+" :ppdim\n"+Nucl2D+" :Nucl2D\n"+Nucl3D+" :Nucl3D\n"+Nucl4D+" :Nucl4D\n")
# Translate, Concatenate and return the Nucls
if ppdim >= 4 and Nucl4D.isdigit():
Nucl4D = "".join(letter for letter in Nuc.list()[int(Nucl4D) - 1]
if letter.isalpha())
if ppdim >= 3 and Nucl3D.isdigit():
Nucl3D = "".join(letter for letter in Nuc.list()[int(Nucl3D) - 1]
if letter.isalpha())
if ppdim >= 2 and Nucl2D.isdigit():
Nucl2D = "".join(letter for letter in Nuc.list()[int(Nucl2D) - 1]
if letter.isalpha())
#TopCmds.MSG(Nucl1D+" :Nucl1D\n"+Nucl2D+" :Nucl2D\n"+Nucl3D+" :Nucl3D\n"+Nucl4D+" :Nucl4D\n")
if ppdim == 4:
EXP = Nucl4D + Nucl3D + Nucl2D
aqseq = "4321"
if ppdim == 3:
if aqseq == "321": EXP = Nucl3D + Nucl2D
if aqseq == "312": EXP = Nucl2D + Nucl3D
if aqseq == "":
EXP = Nucl3D + Nucl2D
aqseq = "321"
if ppdim == 2:
EXP = Nucl2D
aqseq = "21"
return ppdim, aqseq, Nucl1D + EXP
def NCO(MAS0,MAS,units):
p90X=float(TopCmds.GETPAR("P 1"))
ampX=float(TopCmds.GETPAR("PL"+units+" 1"))
ampXdB=float(TopCmds.GETPAR("PLdB 1"))
ampXCP0=float(TopCmds.GETPAR("SP"+units+" 51"))
ampXCP0dB=float(TopCmds.GETPAR("SPdB 51"))
#ampXCP0=float(TopCmds.GETPAR("PL"+units+" 50"))
#ampXCP0dB=float(TopCmds.GETPAR("PLdB 50"))
SPX=TopCmds.GETPAR2("SPNAM 51")
p90Y=float(TopCmds.GETPAR("P 21"))
ampY=float(TopCmds.GETPAR("PL"+units+" 3"))
ampYdB=float(TopCmds.GETPAR("PLdB 3"))
ampYCP0=float(TopCmds.GETPAR("PL"+units+" 6"))
ampYCP0dB=float(TopCmds.GETPAR("PLdB 6"))
SPY="None"
avgY0=1.
# Get the integration before possibly changing the shape.
if SPX != "None" and SPX != None:
avgX0=IntShape.Integrate(SPX)/100.
if SPX == "None" or SPX == None:
avgX0=1.
CNCT=float(TopCmds.GETPAR("P 17"))
#Interact with user about MAS and power levels, likely not needed
params = TopCmds.INPUT_DIALOG("NCO CP MAS adjustment", "Nitrogen Carbonyl Cross Polarization", \
["Old MAS rate","New MAS rate","Old 13C power","Old 15N power","Contact Time(P16)","C-Ramp"],\
[str(MAS0),str(MAS),str(ampXCP0),str(ampYCP0),str(CNCT),SPX],\
["kHz","kHz",units,units,"us",""],\
["1","1","1","1","1","1"],\
["Accept","Close"], ['a','c'], 10)
if params == None: TopCmds.EXIT()
params.append(SPY)
# Everything is written with dB, so we might have to convert
if units == "W":
params[2]=str(Setup.WtodB(float(params[2])))
params[3]=str(Setup.WtodB(float(params[3])))
if SPX != "None" and SPX != None:
avgX0=IntShape.Integrate(SPX)/100.
if SPX == "None" or SPX == None:
avgX0=1.
pulses=p90X,ampXdB,p90Y,ampYdB,avgX0,avgY0
SelectorText="Adjust the NCA CP parameters:","Calculate New Power Level for:",\
["Carbon","Nitrogen","Both"]
ampXCPdB, ampYCPdB = FindMatch(params,pulses,SelectorText)
if units == "W":
ampXCP=Setup.dBtoW(ampXCPdB)
ampYCP=Setup.dBtoW(ampYCPdB)
value = TopCmds.SELECT("Adjusting the NCO CP parameters:",\
"This will set\n 13C power to: " + str('%3.2f' %ampXCP)+ " "+units+"\n \
15N power to: " +str('%3.2f' %ampYCP) + " "+units,["Update", "Keep Previous"])
if value != 1:
TopCmds.PUTPAR("PLdB 51",str('%3.2f' %ampXCPdB))
TopCmds.PUTPAR("SPdB 51",str('%3.2f' %ampXCPdB))
TopCmds.PUTPAR("PLdB 6",str('%3.2f' %ampYCPdB))
TopCmds.PUTPAR("P 17" ,str('%3.2f' %CNCT))
TopCmds.PUTPAR("SPNAM 51",SPX)
def HN(MAS0,MAS,units):
p90H=float(TopCmds.GETPAR("P 3"))
ampH=float(TopCmds.GETPAR("PL"+units+" 2"))
ampHdB=float(TopCmds.GETPAR("PLdB 2"))
ampHCP0=float(TopCmds.GETPAR("SP"+units+" 42"))
ampHCP0dB=float(TopCmds.GETPAR("SPdB 42"))
#ampHCP0=float(TopCmds.GETPAR("PL"+units+" 42"))
#ampHCP0dB=float(TopCmds.GETPAR("PLdB 42"))
SPH=TopCmds.GETPAR2("SPNAM 42")
p90X=float(TopCmds.GETPAR("P 21"))
ampX=float(TopCmds.GETPAR("PL"+units+" 3"))
ampXdB=float(TopCmds.GETPAR("PLdB 3"))
ampXCP0=float(TopCmds.GETPAR("SP"+units+" 43"))
ampXCP0dB=float(TopCmds.GETPAR("SPdB 43"))
#ampXCP0=float(TopCmds.GETPAR("PL"+units+" 43"))
#ampXCP0dB=float(TopCmds.GETPAR("PLdB 43"))
SPX=TopCmds.GETPAR2("SPNAM 43")
CNCT=float(TopCmds.GETPAR("P 25"))
#Interact with user about MAS and power levels, likely not needed
params = TopCmds.INPUT_DIALOG("HN CP MAS adjustment", "Proton Nitrogen Cross Polarization", \
["Old MAS rate","New MAS rate","Old 15N power","Old 1H power","Contact Time(P15)","H-Ramp","N-Ramp"],\
[str(MAS0),str(MAS),str(ampXCP0),str(ampHCP0),str(CNCT),SPH,SPX],\
["kHz","kHz",units,units,"us","",""],\
["1","1","1","1","1","1","1"],\
["Accept","Close"], ['a','c'], 10)
if params == None: TopCmds.EXIT()
# Everything is written with dB, so we might have to convert
if units == "W":
params[2]=str(Setup.WtodB(float(params[2])))
params[3]=str(Setup.WtodB(float(params[3])))
if SPH != "None" and SPH != None:
avgH0=1.
avgH0=IntShape.Integrate(SPH)/100.
if SPX != "None" and SPX != None:
avgX0=1.
avgX0=IntShape.Integrate(SPX)/100.
pulses=p90H,ampHdB,p90X,ampXdB,avgH0,avgX0
SelectorText="Adjust the HN CP parameters:","Calculate New Match for:",\
["Proton","Nitrogen","Maximum for Both"]
ampHCPdB, ampXCPdB = FindMatch(params,pulses,SelectorText)
if units == "W":
ampXCP=Setup.dBtoW(ampXCPdB)
ampHCP=Setup.dBtoW(ampHCPdB)
value = TopCmds.SELECT("Adjusting the HN CP parameters:",\
"This will set\n 1H power to: " + str('%3.2f' %ampHCP)+ " "+units+"\n \
15N power to: " +str('%3.2f' %ampXCP) + " "+units,["Update", "Keep Previous"])
if value != 1:
TopCmds.PUTPAR("PLdB 42",str('%3.2f' %ampHCPdB))
TopCmds.PUTPAR("SPdB 42",str('%3.2f' %ampHCPdB))
TopCmds.PUTPAR("PLdB 43",str('%3.2f' %ampXCPdB))
TopCmds.PUTPAR("SPdB 43",str('%3.2f' %ampXCPdB))
TopCmds.PUTPAR("P 25" ,str('%3.2f' %CNCT))
TopCmds.PUTPAR("SPNAM 42",SPH)
TopCmds.PUTPAR("SPNAM 43",SPX)
def FindMatch(params,pulses,Dia):
p90H,ampHdB,p90X,ampXdB,avgH0,avgX0=pulses
MAS0 =float(params[0])
MAS =float(params[1])
ampXCP0dB=float(params[2])
ampHCP0dB=float(params[3])
CNCT =float(params[4])
SPH =params[5]
SPX =params[6]
avgH=1.
avgX=1.
if SPH != "None" and SPH != None:
avgH=IntShape.Integrate(SPH)/100.
if SPH == "None" or SPH == None:
avgH=1.
if SPX != "None" and SPX != None:
avgX=IntShape.Integrate(SPX)/100.
if SPX == "None" or SPX == None:
avgX=1.
MaxB1H = 1000000./4./p90H
MaxB1X = 1000000./4./p90X
HCPpw0=(p90H/avgH0)*(math.pow(10,((ampHCP0dB-ampHdB)/20.)))
XCPpw0=(p90X/avgX0)*(math.pow(10,((ampXCP0dB-ampXdB)/20.)))
HB1_0=1000000./HCPpw0/4.
XB1_0=1000000./XCPpw0/4.
HR0=HB1_0/MAS0
XR0=XB1_0/MAS0
### Choices for adjusting the match ###
value = TopCmds.SELECT(Dia[0],Dia[1],Dia[2])
if value == 0:
XB1=XB1_0
if HB1_0 > XB1_0 :
HB1=XB1_0+MAS
if HB1_0 <= XB1_0 :
HB1=XB1_0-MAS
HR=HB1/MAS
XR=XB1/MAS
elif value == 1:
HB1=HB1_0
if HB1_0 > XB1_0 :
XB1=HB1_0-MAS
if HB1_0 <= XB1_0 :
XB1=HB1_0+MAS
HR=HB1/MAS
XR=XB1/MAS
elif value == 2:
HB1=HR0*MAS
XB1=XR0*MAS
HR=HR0
XR=XR0
# If we are slowing down, keep CP levels similar to previous
if MAS0 < MAS:
if XB1 <= HB1:
while XB1 <= XB1_0 :
XR=XR+1
XB1=XR*MAS
HR=HR+1
if XB1 >> HB1:
while HB1 <= HB1_0 :
HR=HR+1
HB1=HR*MAS
XR=XR+1
XR=XR-1 #the above should always go one step too far
HR=HR-1
XB1=XR*MAS
HB1=HR*MAS
else:
TopCmds.EXIT()
# Don't allow feilds higher than max
while XB1 > MaxB1X :
HR=HR-1
XR=XR-1
HB1=HR*MAS
XB1=XR*MAS
while HB1 > MaxB1H :
HR=HR-1
XR=XR-1
HB1=HR*MAS
XB1=XR*MAS
adjust=20*(math.log10(HB1/HB1_0))
ampHCPdB = ampHCP0dB-adjust
adjust=20*(math.log10(avgH/avgH0)) #in case there is a Ramp change
ampHCPdB = ampHCP0dB-adjust
adjust=20*(math.log10(XB1/XB1_0))
ampXCPdB = ampXCP0dB-adjust
adjust=20*(math.log10(avgX/avgX0)) #in case there is a Ramp change
ampXCPdB = ampXCP0dB-adjust
return ampHCPdB, ampXCPdB
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 NCO(MAS0, MAS, units):
p90X = pul.GetPar('pC90', "")
ampX = pul.GetPar('aC', units)
ampXCP = pul.GetPar('aCnco', units)
SPX = pul.GetPar('sCnco', "")
avgX = 1.
p90Y = pul.GetPar('pN90', "")
ampY = pul.GetPar('aN', units)
ampYCP = pul.GetPar('aNnco', units)
SPY = pul.GetPar('sNnco', "")
avgY = 1.
CNCT = pul.GetPar('pNCO', "")
# Get the integration before possibly changing the shape.
if SPX != "None" and SPX != None and SPX != "Unused":
avgX = IntShape.Integrate(SPX) / 100.
if SPY == "None" or SPY == None and SPY != "Unused":
avgY = IntShape.Integrate(SPY) / 100.
#Interact with user about MAS and power levels, likely not needed
params = TopCmds.INPUT_DIALOG("NCO CP MAS adjustment", "NCO", \
["Old MAS rate","New MAS rate","Old CO power ("+pul.pulDict['aCnco']+")",\
"Old 15N power ("+pul.pulDict['aNnco']+")","Contact Time ("+pul.pulDict['pNCO']+")",\
"CO-Ramp ("+pul.pulDict['sCnco']+")","N-Ramp ("+pul.pulDict['sNnco']+")"],\
[str(MAS0),str(MAS),str(ampXCP),str(ampYCP),str(CNCT),SPX,SPY],\
["Hz","Hz",units,units,"us","",""],\
["1","1","1","1","1","1","1"],\
["Accept","Close"], [spc,ret], 10)
if params == None: TopCmds.EXIT()
# Everything is written with dB, so we might have to convert
if units == "W":
params[2] = str(Setup.WtodB(float(params[2])))
params[3] = str(Setup.WtodB(float(params[3])))
ampX = Setup.WtodB(ampX)
ampY = Setup.WtodB(ampY)
pulses = p90X, ampX, p90Y, ampY, avgX, avgY
SelectorText="Adjust the NCO CP parameters:","Calculate New Power Level for:",\
["Carbon","Nitrogen","Both"]
ampXCP, ampYCP = FindMatch(params, pulses, SelectorText)
if units == "W":
ampXCP = Setup.dBtoW(ampXCP)
ampYCP = Setup.dBtoW(ampYCP)
value = TopCmds.SELECT("Adjusting the NCO CP parameters:",\
"This will set\n 13C power to: " + str('%3.2f' %ampXCP)+ " "+units+"\n \
15N power to: " +str('%3.2f' %ampYCP) + " "+units,["Update", "Keep Previous"])
if value != 1:
pul.SetPar('aCnco', ampXCP, units)
pul.SetPar('aNnco', ampYCP, units)
pul.SetPar('pNCO', CNCT, "")
pul.SetPar('sCnco', SPX, "")
pul.SetPar('sNnco', SPY, "")
def LoadFromData(Nuc,offs,units):
"""
Nuc : Nucleus for DREAM mixing
offs : dict key for Dream offset
units: dB or Watts
"""
p90H, p90C, p90N, ampH, ampC, ampN, MAS = Setup.ReadHPFromData(units)
#Define frequencies
Nucs=NUC.list()
i=0
for item in Nucs:
if item==Nuc:
if item =='13C':Frq=fq.fq(item,i+1)
if item =='15N':Frq=fq.fq(item,i+1)
if item =='1H' :Frq=fq.fq(item,i+1)
if item =='2H' :Frq=fq.fq(item,i+1)
i=i+1
FqUnit=pul.GetPar('uoffs',"")
FqMeth=pul.GetPar('oFrom',"")
#TopCmds.MSG(FqUnit + " "+FqMeth+" "+str(Frq.bf))
# Everything in absolute PPM
if FqMeth=="Carrier":
if FqUnit=="Hz" :OffsPPM=Frq.offs2ppm(pul.GetPar(offs,""))
if FqUnit=="ppm":OffsPPM=Frq.offsp-pul.GetPar(offs,"")
else:
if FqUnit=="Hz" :OffsPPM=Frq.offs2ppm(pul.GetPar(offs,"")-Frq.offs)
if FqUnit=="ppm":OffsPPM=pul.GetPar(offsp,"")
index = TopCmds.INPUT_DIALOG("Mr Setup Input", "Pulse Widths and Power", \
["1H 90 pw","1H ampl","13C 90 pw","13C ampl","15N 90 pw","15N ampl","DREAM Offset","MAS"],\
[str('%.2f' %p90H),str('%.2f' %ampH),str('%.2f' %p90C),str('%.2f' %ampC),\
str('%.2f' %p90N),str('%.2f' %ampN),str('%.2f' %Offsppm),str('%.2f' %MAS)],\
["us",units,"us",units,"us",units,"ppm"," Hz"],\
["1","1","1","1","1","1","1","1"],\
["Accept","Close"], [spc,ret], 10)
if index == None:TopCmds.EXIT()
p90H=float(index[0])
ampH=float(index[1])
p90C=float(index[2])
ampC=float(index[3])
p90N=float(index[4])
ampN=float(index[5])
MAS =float(index[7])
TauR= 1000000./MAS
Setup.PutPars(p90H,ampH,p90C,ampC,p90N,ampN,MAS,units)
if FqMeth=="Carrier":
if FqUnit=="Hz" :OffsPPM=Frq.offsp-float(index[6])
2ppm(pul.GetPar(offs,""))
if FqUnit=="ppm":OffsPPM=Frq.offsp-pul.GetPar(offs,"")
else:
if FqUnit=="Hz" :OffsPPM=Frq.offs2ppm(pul.GetPar(offs,"")-Frq.offs)
if FqUnit=="ppm":OffsPPM=pul.GetPar(offsp,"")
if FqMeth=="Zero" : Offsppm=
if FqMeth=="Carrier": Offsppm=Frq.offsp+float(index[6])
# Everything in the right units
if FqUnit=="Hz" :pul.Setpar(offs,Frq.ppm2offs(Offsppm,""),"")
if FqUnit=="ppm":pul.Setpar(offs,Offsppm,"")
