def processpre21(self):
mainPars = self.parFiles['acqus'].parameters
#
# Set pulseprogram info
#
pulseProgram = None
if self.parFiles.has_key('pulseprogram'):
pulseProgram = self.parFiles['pulseprogram']
ss = pulseProgram.get('name')
if ss:
self.pulProgName = ss
refs = {}
#
# Try get date out
#
dateInfo = self.parFiles['acqus'].infoStrings[0]
if dateInfo.count('T '):
dateString = dateInfo[:dateInfo.index('T ') + 1]
else:
dateString = dateInfo[:19].strip()
self.dateString = dateString
#
# Do quick check for 3D,4D to see if dimension order in filename matches
# the acqu2s/acqu3s, and switch their info content if necessary.
#
# TODO: THIS IS NOT FOOLPROOF! NUC1 for acqu2s, acqu3s not always set to
# nucleus used in that dimension! Is so for some setups, though (IE)
#
# TODO: ONLY works for 3Ds currently!
#
if (self.numDim == 3):
if not hasattr(self.parFiles['acqu3s'],'parameters'):
print " Illegal number of dimensions!! %s is not a 3d..." % self.fileDir
return
if not self.parFiles['acqu3s'].parameters.has_key('NUC1'):
#
# No acqu3s file... basically 3D recorded as 2D (or wrong experiment put in..)
# Assuming that L1, L2 give npts/2, getting as much info as possible from this...
#
print " Warning: no acqu3s file for Bruker 3D experiment."
pointsProduct = self.parFiles['acqu2s'].parameters['TD'].values[0]
npts1 = self.parFiles['acqus'].parameters['L'].values[1]
npts2 = self.parFiles['acqus'].parameters['L'].values[2]
if pointsProduct == (npts1 * npts2 * 4):
print " assuming L1,L2 give number of complex points."
# TODO: does it make sense to set this for acqu2/3?
self.parFiles['acqu3s'].parameters['TD'] = BrukerPar('TD')
self.parFiles['acqu3'].parameters['TD'] = BrukerPar('TD')
self.parFiles['acqu2s'].parameters['TD'].values[0] = npts1
self.parFiles['acqu2'].parameters['TD'].values[0] = self.parFiles['acqu'].parameters['L'].values[1]
self.parFiles['acqu3s'].parameters['TD'].addValues(1,[npts2])
self.parFiles['acqu3'].parameters['TD'].addValues(1,[self.parFiles['acqu'].parameters['L'].values[2]])
#
# Select appropriate increment per dimension
# Bit messy... this whole script has to be cleaned up
# TODO: very nasty to put tk stuff in here... have to:
# - Make whole def a class
"""
incrementList = []
for value in mainPars['IN'].values:
incrementList.append(value)
popup = IncrementSelect(guiParent,[2,3],incrementList)
for i in range(0,len(popup.increments)):
increment = popup.increments[i]
dim = i + 1
refs['inc'][dim] = mainPars['IN'].values.index(increment)
# TODO: nucleus!!!
popup.destroy()
"""
else:
print " cannot handle current case. Contact author."
elif (self.numDim > 3):
print " ERROR: %s had more than 3 dims for acqu<n>s file order (cannot handle this)!" % (self.fileDir)
#
# Set increment numbers found in pulse program
#
refs['inc'] = [-1]
if pulseProgram and self.numDim <= len(pulseProgram['increment']):
print " Warning: %s number of incremented delays found does not match number of dimensions!" % (self.fileDir)
for i in range(0,self.numDim-1):
if pulseProgram and len(pulseProgram['increment']) > i:
refs['inc'].append(int(pulseProgram['increment'][i]))
else:
refs['inc'].append(i)
#
# If AQSEQ == 1 and experiment is a 3D, then swap the first two indirect increments
# to correspond to the acqu files
#
if mainPars['AQSEQ'].values[0] == 1 and self.numDim == 3:
tempInc = refs['inc'][1]
refs['inc'][1] = refs['inc'][2]
refs['inc'][2] = tempInc
print " Warning: swapped increments for 3D based on AQSEQ setting %d!" % mainPars['AQSEQ'].values[0]
#
# TODO: Check if acqu<n>s info corresponds to reported nucleus order - reset values if so.
#
#
# Make a list of reference values for accessing acqus file
#
self.setupBrukerRefList()
nullValue = 'off'
self.getSpecRefs(mainPars,nullValue)
#
# Now set the fid and freq info from the file
#
for i in range(0,self.numDim):
#
# Handling depends on which dim (complex points or not)
#
if i == 0:
acqusPars = mainPars
acquPars = self.parFiles['acqu'].parameters
complexFactor = 2.0
#
# Acquisition dimension always complex
#
#
# Spectral width in Hz per dimension and associated increment
#swText = '(from acqus file)'
#incText = '(calculated from SW_h, assuming complex)'
#
swh = float(acqusPars['SW_h'].values[0])
valuePerPoint = 1 / swh
else:
#
# Try to get info on acquisition mode for dimension...
#
#currentAcqusFile = self.parFiles['acqu' + str(i+1) + 's']
acqusPars = self.parFiles['acqu' + str(i+1) + 's'].parameters
acquPars = self.parFiles['acqu' + str(i+1)].parameters
if acqusPars.has_key('FnMODE'):
(fnMode,complexFactor) = self.fnModeDict[acqusPars['FnMODE'].values[0]]
self.fnModes[i-1] = fnMode
else:
complexFactor = 2.0
#
# Increment (based on values read in from pulseprogram!). Multiplied by 2: assuming complex.
#incText = "(using IN%s in acqus file)" % brukerrefs['inc'][i]
#
#
# TODO: will this cause problems if the acqu2/3s files not switched yet?
# Keep in mind!!
#
valuePerPoint = complexFactor * float(mainPars['IN'].values[refs['inc'][i]])
# set nucleus
#nucleus = mainPars['NUC1'].values[0]
nucleus = self.convertNucleusCode(acqusPars['NUC1'].values[0])
self.nuc[i] = nucleus
# Number of COMPLEX points per dimension.
# set values into parameter arrays
numPoints = int(acquPars['TD'].values[0]) / 2
numPointsValid = int(acqusPars['TD'].values[0]) / 2
self.npts[i] = numPoints
self.numPointsValid[i] = numPointsValid
self.sw[i] = swhz = numPoints * valuePerPoint
self.isComplex[i] = (complexFactor != 1.0)
self.sf[i] = sf = float(acqusPars['SFO1'].values[0])
self.baseFreq[i] = baseFreq = float(acqusPars['BF1'].values[0])
# set approx referencing (starting value. Formula from Bruker manual)
self.refpt[i] = 1.0
self.refppm[i] = 1.0e6 * (sf / baseFreq - 1.0) + 0.5 * swhz / baseFreq
#
# Now set the values for the FID
#
if numPointsValid > numPoints:
print " ERROR: %s has greater number of valid points than actual ones" % (self.fileDir)
self.fidDimRefs[i] = FidDimReference(numPoints,numPointsValid,
valuePerPoint,nucleus)
#
# And for the Freq
#
(numPoints,numPointsOrig,valuePerPoint) = self.getFreqDimInfo(valuePerPoint,numPointsValid)
self.freqDimRefs[i] = FreqDimReference(numPoints,numPointsOrig,
valuePerPoint,nucleus)
def process(self):
#
# Only one file...
#
mainPars = self.parFiles['procpar'].parameters
if mainPars.has_key('nt'):
self.numScans = returnInt(mainPars['nt'].values[0])
else:
print "No num scans for %s" % (self.fileDir)
self.numScans = 0
#
# Get frequencies for nuclei (TODO: REFLIST IN settings?)
#
self.refList = [['sfrq', 'tof', 'tn'], ['dfrq', 'dof', 'dn'],
['dfrq2', 'dof2', 'dn2'], ['dfrq3', 'dof3', 'dn3'],
['dfrq4', 'dof4', 'dn4']]
nullValue = ''
self.getSpecRefs(mainPars, nullValue, specTypeRef='console')
refsNp = ['np', 'ni', 'ni2', 'ni3']
refsSw = ['sw', 'sw1', 'sw2', 'sw3']
self.fidDimRefs = []
self.freqDimRefs = []
for i in range(0, self.numDim):
if i == 0:
#
# Different handling for acquisition dimension!
# TODO: if data is NOT COMPLEX, take out factor 2!
# In CCPN data model, npoints is number of COMPLEX points!
#
numPoints = mainPars[refsNp[i]].values[0] / 2
else:
#
# Data always complex in indirect? Assuming so...
# Note that ni, ni2, ... HAS A DIFFERENT DEFINITION than np!!! Is number of COMPLEX points!
#
numPoints = mainPars[refsNp[i]].values[0]
#
# TODO: this is assumed for Varian
#
numPointsValid = numPoints
#
# Set sw and increment
# TODO: If data is NOT COMPLEX, divide valppoint by 2!
# (one half of spectrum is redundant)
#
swh = mainPars[refsSw[i]].values[0]
valuePerPoint = 1 / swh
#
# Set FID info
#
self.fidDimRefs.append(
FidDimReference(numPoints, numPointsValid, valuePerPoint,
None))
#
# Set freq domain info
# PROBLEM with acquisition time: Rasmus uses valppoint * (npointsvalid-1)
# But this doesn't correspond to value from Varian (is valppoint * npointsvalid)
# WHY? Contact Varian. Have to VERY SPECIFICALLY define these parameters!!!
# How does this work for Bruker?
#
(numPoints, numPointsOrig,
valuePerPoint) = self.getFreqDimInfo(valuePerPoint,
numPointsValid)
self.freqDimRefs.append(
FreqDimReference(numPoints, numPointsOrig, valuePerPoint,
None))
#
# Try to get phasing info (often not correct...)
#
refsPhase = 2 * ['']
refsPhase[0] = ['rp', 'rp1', 'rp2', 'rp3']
refsPhase[1] = ['lp', 'lp1', 'lp2', 'lp3']
for po in range(0, 2):
if mainPars.has_key(refsPhase[po][i]):
self.freqDimRefs[-1].phase[po] = mainPars[refsPhase[po]
[i]].values[0]
else:
print " ERROR: %s has no phase for %d (dim %d)" % (
self.fileDir, po, i)
def processv21(self):
"""process function for TOPSPIN versions >= 2.1
"""
# Tolerance for letting SW_h override SW * sf
swhzTolerance = 0.001
mainPars = self.parFiles['acqus'].parameters
# get date string
match = self.patt[self.format + "Date"].match(self.parFiles['acqus'].infoStrings[0])
if match:
self.dateString = match.group()
else:
self.dateString = ""
self.specRefs = specRefs = {}
# default specType
specType = None
#get pulProgName:
if mainPars.has_key('PULPROG'):
self.pulProgName = mainPars['PULPROG'].values[0]
# convert data one dimension at a time
for ii in range(self.numDim):
# set up file names
if ii == 0:
acquname = 'acqu'
else:
acquname = 'acqu' + str(ii+1)
acquPars = self.parFiles[acquname].parameters
acqusPars = self.parFiles[acquname + 's'].parameters
# set complexFactor (complex/real handling).
# NB assumes acq dim is alwasy complex
if acqusPars.has_key('FnMODE') and ii != 0:
(fnMode,complexFactor) = self.fnModeDict[acqusPars['FnMODE'].values[0]]
self.fnModes[ii-1] = fnMode
else:
complexFactor = 2.0
# set
self.isComplex[ii] = (complexFactor != 1.0)
npts = int(acquPars['TD'].values[0])
if npts != 1:
# npts == 1 is default for unused/projection dimensions. Keep as ia.
npts = int(npts/complexFactor)
self.npts[ii] = npts
numPointsValid = int(acqusPars['TD'].values[0])/complexFactor
self.numPointsValid[ii] = numPointsValid
nucleus = self.convertNucleusCode(acqusPars['NUC1'].values[0])
self.nuc[ii] = nucleus
self.sf[ii] = sf = float(acqusPars['SFO1'].values[0])
self.baseFreq[ii] = baseFreq = float(acqusPars['BF1'].values[0])
swppm = float(acqusPars['SW'].values[0])
swhz = swppm * sf
if acqusPars.has_key('SW_h'):
# NB SW seems more reliable than SW_h.
# Use SW_h only for greater precision where the values fit.
val = float(acqusPars['SW_h'].values[0])
if abs(val/swhz - 1.0) < swhzTolerance:
swhz = val
self.sw[ii] = swhz
if numPointsValid > npts:
print (" WARNING: %s dim %s has greater number of valid points than actual ones"
% (self.fileDir, ii))
# set approx referencing (starting value. Formula from Bruker manual)
self.refpt[ii] = 1.0
self.refppm[ii] = 1.0e6 * (sf / baseFreq - 1.0) + 0.5 * swhz / baseFreq
# set self.specRefs for FormatConverter purposes
self.specRefs[nucleus] = SpectrometerReference(sf, baseFreq)
#if ii != 0:
# from ccp.general.Constants import chemShiftRefRatios
# refRatio = chemShiftRefRatios.get(nucleus)
# if refRatio is not None:
# bf2 = self.baseFreq[0] * refRatio
# xx = 1.0e6*(sf/bf2 -1.0)
# print '###1', baseFreq, bf2, xx, xx + 0.5*swhz/bf2 - self.refppm[ii]
#
#print ('###2', ii, acquname, sf, baseFreq, swhz, swppm, self.refppm[ii],
# 1.0e6 * (sf / baseFreq - 1.0), 0.5 * swhz / baseFreq)
# set self.fidDimRefs - for FormatCOnverter use
timePerPoint = complexFactor / (2.0 * swhz)
self.fidDimRefs[ii] = FidDimReference(npts, numPointsValid,
timePerPoint, nucleus)
# set self.freqDimRefs - for FormatConverter use
# for setting up future procesasing.
# For actual processing data read procs (etc.) file
(nPoints,nPointsOrig,valuePerPoint) = self.getFreqDimInfo(timePerPoint,
numPointsValid)
self.freqDimRefs[ii] = FreqDimReference(nPoints, nPointsOrig,
timePerPoint, nucleus)
def process(self):
mainPars = self.parFiles['acqus'].parameters
pulseProgram = None
if self.parFiles.has_key('pulseprogram'):
pulseProgram = self.parFiles['pulseprogram']
refs = {}
self.numScans = returnInt(mainPars['NS'].values[0])
#
# Try get date out
#
dateInfo = self.parFiles['acqus'].infoStrings[0]
if dateInfo.count('T '):
dateString = dateInfo[:dateInfo.index('T ') + 1]
else:
dateString = ""
self.dateString = dateString
#
# Do quick check for 3D,4D to see if dimension order in filename matches
# the acqu2s/acqu3s, and switch their info content if necessary.
#
# TODO: THIS IS NOT FOOLPROOF! NUC1 for acqu2s, acqu3s not always set to
# nucleus used in that dimension! Is so for some setups, though (IE)
#
# TODO: ONLY works for 3Ds currently!
#
if (self.numDim == 3):
if not hasattr(self.parFiles['acqu3s'], 'parameters'):
print " Illegal number of dimensions!! %s is not a 3d..." % self.fileDir
return
if not self.parFiles['acqu3s'].parameters.has_key('NUC1'):
#
# No acqu3s file... basically 3D recorded as 2D (or wrong experiment put in..)
# Assuming that L1, L2 give npts/2, getting as much info as possible from this...
#
print " Warning: no acqu3s file for Bruker 3D experiment."
pointsProduct = self.parFiles['acqu2s'].parameters[
'TD'].values[0]
npts1 = self.parFiles['acqus'].parameters['L'].values[1]
npts2 = self.parFiles['acqus'].parameters['L'].values[2]
if pointsProduct == (npts1 * npts2 * 4):
print " assuming L1,L2 give number of complex points."
# TODO: does it make sense to set this for acqu2/3?
self.parFiles['acqu3s'].parameters['TD'] = BrukerPar('TD')
self.parFiles['acqu3'].parameters['TD'] = BrukerPar('TD')
self.parFiles['acqu2s'].parameters['TD'].values[0] = npts1
self.parFiles['acqu2'].parameters['TD'].values[
0] = self.parFiles['acqu'].parameters['L'].values[1]
self.parFiles['acqu3s'].parameters['TD'].addValues(
1, [npts2])
self.parFiles['acqu3'].parameters['TD'].addValues(
1, [self.parFiles['acqu'].parameters['L'].values[2]])
#
# Select appropriate increment per dimension
# Bit messy... this whole script has to be cleaned up
# TODO: very nasty to put tk stuff in here... have to:
# - Make whole def a class
"""
incrementList = []
for value in mainPars['IN'].values:
incrementList.append(value)
popup = IncrementSelect(guiParent,[2,3],incrementList)
for i in range(0,len(popup.increments)):
increment = popup.increments[i]
dim = i + 1
refs['inc'][dim] = mainPars['IN'].values.index(increment)
# TODO: nucleus!!!
popup.destroy()
"""
else:
print " cannot handle current case. Contact author."
elif (self.numDim > 3):
print " ERROR: %s had more than 3 dims for acqu<n>s file order (cannot handle this)!" % (
self.fileDir)
#
# Set increment numbers found in pulse program
#
refs['inc'] = [-1]
if pulseProgram and self.numDim <= len(pulseProgram['increment']):
print " Warning: %s number of incremented delays found does not match number of dimensions!" % (
self.fileDir)
for i in range(0, self.numDim - 1):
if pulseProgram and len(pulseProgram['increment']) > i:
refs['inc'].append(int(pulseProgram['increment'][i]))
else:
refs['inc'].append(i)
#
# If AQSEQ == 1 and experiment is a 3D, then swap the first two indirect increments
# to correspond to the acqu files
#
if mainPars['AQSEQ'].values[0] == 1 and self.numDim == 3:
tempInc = refs['inc'][1]
refs['inc'][1] = refs['inc'][2]
refs['inc'][2] = tempInc
print " Warning: swapped increments for 3D based on AQSEQ setting %d!" % mainPars[
'AQSEQ'].values[0]
#
# TODO: Check if acqu<n>s info corresponds to reported nucleus order - reset values if so.
#
#
# Make a list of reference values for accessing acqus file
#
self.setupBrukerRefList()
nullValue = 'off'
self.getSpecRefs(mainPars, nullValue)
#
# Now set the fid and freq info from the file
#
self.fidDimRefs = []
self.freqDimRefs = []
for i in range(0, self.numDim):
#
# Handling depends on which dim (complex points or not)
#
if i == 0:
#
# Acquisition dimension always complex
#
#
# Number of COMPLEX points per dimension.
#
numPoints = int(
self.parFiles['acqu'].parameters['TD'].values[0]) / 2
numPointsValid = int(mainPars['TD'].values[0]) / 2
#
# Spectral width in Hz per dimension and associated increment
#swText = '(from acqus file)'
#incText = '(calculated from SW_h, assuming complex)'
#
swh = float(mainPars['SW_h'].values[0])
valuePerPoint = 1 / swh
#
# Keep nucleus info
#
nucleus = mainPars['NUC1'].values[0]
else:
#
# Try to get info on acquisition mode for dimension...
#
currentAcqusFile = self.parFiles['acqu' + str(i + 1) + 's']
if currentAcqusFile.parameters.has_key('FnMODE'):
(fnMode, complexFactor) = self.fnModeDict[
currentAcqusFile.parameters['FnMODE'].values[0]]
self.fnModes[i - 1] = fnMode
else:
complexFactor = 2.0
#
# Number of COMPLEX points per dimension.
#
numPoints = int(self.parFiles['acqu' + str(i + 1)].
parameters['TD'].values[0]) / complexFactor
numPointsValid = int(currentAcqusFile.parameters['TD'].
values[0]) / complexFactor
#
# Increment (based on values read in from pulseprogram!). Multiplied by 2: assuming complex.
#incText = "(using IN%s in acqus file)" % brukerrefs['inc'][i]
#
#
# TODO: will this cause problems if the acqu2/3s files not switched yet?
# Keep in mind!!
#
valuePerPoint = complexFactor * float(
mainPars['IN'].values[refs['inc'][i]])
#print
#print "COMPARE"
#print " ", valuePerPoint, refs['inc'][i]
#print " ", 1 / currentAcqusFile.parameters['SW_h'].values[0]
#print
# swh not calculated here? If it is, use that?
#
# Now set the values for the FID
#
if numPointsValid > numPoints:
print " ERROR: %s has greater number of valid points than actual ones" % (
self.fileDir)
self.fidDimRefs.append(
FidDimReference(numPoints, numPointsValid, valuePerPoint,
nucleus))
#
# And for the Freq
#
(numPoints, numPointsOrig,
valuePerPoint) = self.getFreqDimInfo(valuePerPoint,
numPointsValid)
self.freqDimRefs.append(
FreqDimReference(numPoints, numPointsOrig, valuePerPoint,
nucleus))
#
# Phase is automatically set to 0.0 each
# TODO: Could in principle access Bruker procpars for this
#
#
# Special additions
#
if mainPars.has_key('AQ_mod'):
acqModeCode = mainPars['AQ_mod'].values[0]
self.acqMode = 'QSIM'
if acqModeCode == 3:
self.acqMode = 'DQD'
for par in ('DECIM', 'DSPFVS'):
if mainPars.has_key(par):
self.acqModeValues[par] = mainPars[par].values[0]
elif acqModeCode == 1:
pass
else:
print "ERROR: Bruker AQ_mod %d not recognized. Using QSIM." % acqModeCode
#
# Reset specType if DQD data (must be DMX or higher)
#
if mainPars.has_key('DECIM'):
for nucleus in self.specRefs.keys():
self.specRefs[nucleus].setSpecType('DMX')