def hhC(Unit):
CNCT = TopCmds.GETPAR("P 44")
plH = TopCmds.GETPAR("PL" + Unit + " 44")
plC = TopCmds.GETPAR("PL" + Unit + " 45")
SP = "None"
SP = TopCmds.GETPAR2("SPNAM 44")
if SP == "" or SP == "None":
SP = "None"
return CNCT, plH, plC, SP
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 NH(Unit):
CNCT = TopCmds.GETPAR("P 46")
plH = TopCmds.GETPAR("SP" + Unit + " 46")
plN = TopCmds.GETPAR("PL" + Unit + " 47")
SP = "None"
SP = TopCmds.GETPAR2("SPNAM 46")
if SP == "" or SP == "None":
SP = "None"
return CNCT, plH, plN, SP
def name(input, SP):
Name = str("TAN_" + input[2] + "D_" + input[3] + "B.wave")
index = str(TopCmds.INPUT_DIALOG("TAN ramp Files", "", ["File = ","edWave =",],\
[Name,SP],["",""],["1","1"],["Accept","Close"], [spc,ret], 30))
File, SP = index
if SP.find("SPNAM ") >= 0:
TopCmds.PUTPAR(str(SP), str(File))
return File
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"], ['a','c'], 10)
return input
def CH(Unit):
CNCT = TopCmds.GETPAR("P 48")
plH = TopCmds.GETPAR("SP" + Unit + " 48")
plC = TopCmds.GETPAR("PL" + Unit + " 49")
SP = "None"
SP = TopCmds.GETPAR2("SPNAM 48")
if SP == "" or SP == "None":
SP = "None"
return CNCT, plH, plC, SP
def HC(Unit):
CNCT = TopCmds.GETPAR("P 15")
#plC=TopCmds.GETPAR("PL"+Unit+" 40")
#plH=TopCmds.GETPAR("PL"+Unit+" 41")
plC = TopCmds.GETPAR("SP" + Unit + " 40")
plH = TopCmds.GETPAR("SP" + Unit + " 41")
SPC = TopCmds.GETPAR2("SPNAM 40")
SPH = TopCmds.GETPAR2("SPNAM 41")
#TopCmds.MSG("CNCT: "+CNCT+"\n plH: "+plH+"\n plC: "+plC+"\n SPH: "+SPH+"\n SPC: "+SPC)
return CNCT, plH, plC, SPH, SPC
def dialog():
MAS = float(TopCmds.GETPAR("CNST 31"))
TauR = float(1000000 / MAS)
input = TopCmds.INPUT_DIALOG("R2T input", "", \
["Nominal RF ampl","MAS","R2T duration","RI,RO duration","steps","Ramp","I offset","S offset"],\
["85",str('%.0f' % MAS),"1.5",str( '%3.2f' % (TauR)),"1000","20","8.000","6.000"],\
["kHz"," Hz","ms","us","","+/- %","kHz","kHz"],\
["1","1","1","1","1","1","1","1"],\
["Accept","Close"], ['a','c'], 10)
return input
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(Scale, Delta, Beta):
MAS = float(TopCmds.GETPAR("CNST 31"))
TauR = float(1000000 / MAS)
input = TopCmds.INPUT_DIALOG("DREAM input", "", \
["Total Duration","RI,RO duration","Scale","Ramp","Adiabicity"],\
["1.0",str( '%3.2f' % TauR),str( '%3.1f' % Scale),str( '%3.1f' % Delta),str( '%3.1f' % Beta)],\
["ms","us","%","+/- %",""],\
["1","1","1","1","1","1","1"],\
["Accept","Close"], ['a','c'], 10)
return input
def dialog():
MAS = float(TopCmds.GETPAR("CNST 31"))
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"], ['a','c'], 10)
return Data
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 HN(Unit):
CNCT = TopCmds.GETPAR("P 25")
#plN=TopCmds.GETPAR("PL"+Unit+" 42")
#plH=TopCmds.GETPAR("PL"+Unit+" 43")
plH = TopCmds.GETPAR("SP" + Unit + " 42")
plN = TopCmds.GETPAR("SP" + Unit + " 43")
#TopCmds.MSG(TopCmds.GETPAR2("SPNAM 42"))
SPN = TopCmds.GETPAR2("SPNAM 42")
#TopCmds.MSG(TopCmds.GETPAR2("SPNAM 43"))
SPH = TopCmds.GETPAR2("SPNAM 43")
#TopCmds.MSG("CNCT: "+CNCT+"\n plH: "+plH+"\n plN: "+plN+"\n SPH: "+SPH+"\n SPN: "+SPN)
return CNCT, plH, plN, SPH, SPN
def name_confirm(Ttot, RIRO, Sc, Del, Bet):
Name = "DREAM_" + Del + "D_" + Bet + "B_" + Sc + "Sc_" + Ttot + "ms_" + RIRO + "us_ri.wave"
SP = "SPNAM 5"
Wave = str(TopCmds.INPUT_DIALOG("DREAM Files", "", ["C File = ","C Wave =",],\
[Name,SP],["",""],["1","1"],["Accept","Close"], ['a','c'], 30))
Files = Wave[27:len(Wave) - 3] #get rid of Java formatting
i = Files.find(",")
File = Files[0:i - 1]
SP = Files[i + 4:]
TopCmds.PUTPAR(SP, File)
return File, SP
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 SPC5_3(units):
p90C = float(TopCmds.GETPAR("P 1"))
ampC = float(TopCmds.GETPAR("PLdB 1"))
MaxB1 = 1000000. / 4. / p90C
C5B1 = 10.0 * MAS / 3.0
adjust = 20 * (math.log10(C5B1 / MaxB1))
Condition = ampC - adjust
if units == "W":
Condition = dBtoW(Condition)
TopCmds.PUTPAR("PL" + units + " 15", str('%3.2f' % Condition))
TopCmds.PUTPAR("L 5", str(10))
def name_confirm(input):
Name = str("R2T_" + input[1] + "MAS_" + input[6] + "I_" + input[7] +
"S.wave")
SP = str("SPNAM18")
Wave = str(TopCmds.INPUT_DIALOG("R2T Files", "", ["C File = ","C Wave =",],\
[Name,SP],["",""],["1","1"],["Accept","Close"], ['a','c'], 30))
Files = Wave[8:len(Wave) - 21] #get rid of Java formatting
i = Files.find(",")
File = Files[0:i - 1]
SP = Files[i + 3:]
TopCmds.PUTPAR(str(SP), str(File))
return File, SP
def C72(units):
p90C = float(TopCmds.GETPAR("P 1"))
ampC = float(TopCmds.GETPAR("PLdB 1"))
MaxB1 = 1000000. / 4. / p90C
C7B1 = 7.0 * MAS
adjust = 20 * (math.log10(C7B1 / MaxB1))
Condition = ampC - adjust
if units == "W":
Condition = dBtoW(Condition)
TopCmds.PUTPAR("PL" + units + " 17", str('%3.2f' % Condition))
TopCmds.PUTPAR("L 7", str(14))
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]
class O4:
OFFS=float(TopCmds.GETPAR("O4"))
BF=float(TopCmds.GETPAR("BF4"))
ref=float(TopCmds.GETPAR("SR"))
RF=BF*1000000.
RO=OFFS-ref
def ppm2offs(self,ppm):
frq=(O4.RF*ppm/1000000.)- O4.RO
return frq
def offs2ppm(self,frq):
ppm=(1000000./O4.RF)*(frq+O4.RO)
return ppm
def MAS(Home, Source, winfil, unit, qt):
MAS = 0
if winfil == 0: TopCmds.SET_SELECTED_WIN(Source)
if winfil == 1: TopCmds.RE(Source, "n")
MAS0 = Get.MAS(unit)
if winfil == 0: TopCmds.SET_SELECTED_WIN(Home)
if winfil == 1: TopCmds.RE(Home, "n")
MAS1 = Get.MAS(unit)
if MAS1 != MAS0:
Put.MAS(MAS0, "")
MAS = 1
return MAS
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 CC(units):
dfltSP = "square.100"
Title="CC DREAM Input"; SuTit="Carbon Carbon Adiabatic Mixing"
Label=["Carbon B1 Field","C Ramp","Contact Time",\
"H Decoupling"]
In =Title,SuTit,Label
Title="Adjusting the DREAM parameters:"; Label="1H","13C"
Out =Title,Label
Match, Delta, Devia = CMatch() #In Hz
Ramp=pul.GetPar('sCdrm',"")
GoRamp=TopCmds.SELECT("Ramp",\
"Would you like to use the ramp: "+Ramp+\
" \n Or make a new Tangent Ramp?",\
["Use Current","Make New"])
if GoRamp:
SP,Time=MakeRamp(Match,Delta,Devia,"13C")
else:
SP=Ramp; Time=pul.GetPar('pCdrm',"")
CalDREAM('pC90',Match,'aCdrm','aHdrmDC','pCdrm',SP,'sCdrm',dfltSP,units,In,Out)
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"], ['a','c'],10)
return input
def make(Scale, input, name):
import math
ampl = [] # normalized to 0...100
ph = [] # normalized to 0...100
pi = 3.14159265
durat = 1000 * float(input[2])
RIRO = float(input[3])
steps = int(input[4])
Delta = float(input[5])
RIOsteps = int(steps * RIRO / durat)
Start = 100.0 - (Delta)
End = 100.0 + (Delta)
for i in range(steps):
if i < RIOsteps:
RF = 1.0 * i * Start / RIOsteps
if i >= RIOsteps:
RF = 1.0 * Start + (i - RIOsteps) * (End -
Start) / (steps -
(2 * RIOsteps))
if i > (steps - RIOsteps):
RF = 1.0 * End - (i - steps + RIOsteps) * End / RIOsteps
ampl.append(Scale * RF)
ph.append(0.0)
TopCmds.SAVE_SHAPE(name[0], "NoRotation", ampl, ph)
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 LoadFromData(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', "")
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"], ['a','c'], 10)
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 list():
Nucl = []
vers = Ver.get()
dataset = TopCmds.CURDATA()
if vers[1] == "2":
path = dataset[3] + '/data/' + dataset[4] + '/nmr/' + dataset[
0] + '/' + dataset[1]
if vers[1] == "3":
path = dataset[3] + '/' + dataset[0] + '/' + dataset[1]
acqu = path + '/acqu'
#TopCmds.MSG(acqu)
f = open(acqu, 'r')
text = f.readlines()
f.close
i = 0
for line in text:
lines = line.rstrip()
if lines.find('##$NUC') >= 0:
# MSG("I found something: " + lines)
j = lines.find('<')
k = lines.find('>')
if lines.find('off') <= 0:
Nucl.append(lines[j + 1:k])
return Nucl
def make(Name, Sc, Stps, Del, Be):
import math
ampl = [] # normalized to 0...100
ph = [] # normalized to 0...100
Scale = float(Sc)
steps = int(Stps)
Delta = float(Del)
Beta = float(Be)
pi = 3.14159265
k = (steps - 1) / 2.0
if Beta == 0.:
alpha = 0. #No division by Zero
else:
alpha = (2.0 / (steps - 1)) * math.atan(Delta / Beta)
absBeta = math.fabs(Beta)
for i in range(steps):
di = absBeta * math.tan(alpha * (float(i - k)))
di = di
ampl.append(Scale * (100. + di) / 100.)
ph.append(0.0)
TopCmds.SAVE_SHAPE(Name, "NoRotation", ampl, ph)
def Merger():
TopCmds.MSG("<html><p style='text-align: center;'><font size=14><font color=\'0000FF\'>"+\
"Merging Help</p></font><br>"+\
"\n\nMerge Parameters Between Experiments"+\
"Requirements: Previous Experiments\n"+\
"\n"+\
"Arguments:\n"+\
"-dB : interact with db instead of watts (TS3+)\n"+\
"-f : open and close files instead of switching windows\n"+\
"-EXPNO ##: grab from experiment number ## (default to n-1)\n"+\
"-qt : quiet all interaction- \n\n"+\
"By default, the pulse program name is used to determine parameter\n"+\
"To Specify Parameters input the elements separately or in a string.\n"+\
" Specify Hard pulses separately (hNCA H C)\n"+\
" H C N : Update hard pulses \n"+\
" HC HN NCO NCA NH CH hhC : Specified CP parameters\n"+\
" CX: PDSD/DARR \n"+\
" HDec: H-Dec\n"+\
" ph : Phasing \n"+\
"\nPath : "+str(root.UtilPath.getTopspinHome())+ "/exp/stan/nmr/py/BioPY/modules/\n"+\
"modules: Merge, MergeGet, MergePut\n"+\
"wrappers: MrMerger \n"+\
"\n"+\
"Failures: Incorrect dict keys\n"+\
"")
