Thanks, this is a similar problem to the one you hit yesterday, just in
another function. I'll discuss with Tim to see if we can put the "fix" in
somewhere a bit more central so it covers all the relevant functions.
Wayen
On Wed, 24 Nov 2010, Vitaliy Gorbatyuk wrote:
> Hello Wayne,
> I guess it was my mistake - now I can open the spectra. Perhaps I was using the
> Azara format for NMRPipe spectra. I noticed I keep forgeting to select the
> appropriate format. I appologize.
>
> Your fix for my import problem works. I was successful in importing NMRView
> shifts and peaks.
> Thanks!
>
> Though, I am not successful in using dataShifter (I guess it is the preferable
> method) for this purpose. I could not open the new project after the transfer.
> This is the error:
> >>> AttributeError: 'NoneType' object has no attribute 'expDimRef'
> File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/memops/editor/OpenProjectPopup.py", line
> 208, in apply
> self.callback(self.project)
> File "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisPopup.py",
> line 1553, in initProject
> Analysis.initProject(self, project)
> File "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/Analysis.py", line
> 294, in initProject
> self.initResonances()
> File "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/Analysis.py", line
> 1357, in initResonances
> AssignmentBasic.initResonance(resonance, doMerge=False)
> File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/AssignmentBasic.py",
> line 1146, in initResonance
> assignResonanceType(resonance, atomSets)
> File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/AssignmentBasic.py",
> line 2485, in assignResonanceType
> updateResonanceAnnotation(resonance)
> File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/AssignmentBasic.py",
> line 376, in updateResonanceAnnotation
> contrib.peakDim.setAnnotation( makePeakDimAnnotation(contrib.peakDim) )
> File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/AssignmentBasic.py",
> line 1323, in makePeakDimAnnotation
> makePeakAnnotation(peak)
> File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/PeakBasic.py", line
> 921, in makePeakAnnotation
> peakDimAnnos = [getPeakDimAtomTuple(pd) for pd in peak.sortedPeakDims()]
> File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/AssignmentBasic.py",
> line 1388, in getPeakDimAtomTuple
> myAtom = makeResonanceGuiName( resonance, fullName=False )
> File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/AssignmentBasic.py",
> line 1711, in makeResonanceGuiName
> return getResonanceName(resonance)
> File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/AssignmentBasic.py",
> line 1247, in getResonanceName
> name = name[:-1] + getAmbigProchiralLabel(resonance)
> File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/AssignmentBasic.py",
> line 702, in getAmbigProchiralLabel
> resonance2 = getOnebondResonance(resonance, isotopeCode='1H')
> File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/AssignmentBasic.py",
> line 625, in getOnebondResonance
> resonances = getBoundResonances(resonance)
> File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/AssignmentBasic.py",
> line 544, in getBoundResonances
> expDimRef1 = peakDim.dataDimRef.expDimRef
>
> Regards,
> Vitaliy
>
> > Date: Wed, 24 Nov 2010 20:43:18 +0000
> > From: [log in to unmask]
> > Subject: Re: problem with import
> > To: [log in to unmask]
> >
> > Hello,
> >
> > Not sure what that error is about but that file, ExternalParams.py, has
> > not been updated on the update server in v2.2 so I'm not sure why it would
> > be causing a problem, and even more specifically that problem. (And the
> > other fixes look pretty orthogonal to me.) Is this a bog-standard
> > spectrum you are tying to open? That error seems to be implying that
> > that spectrum has no dimensions (if I'm reading the code correctly).
> >
> > I can see that ExternalParams.py has been updated in our CVS repository,
> > though, so I'll ask Rasmus if he fixed something that should be on the
> > update server.
> >
> > Wayne
> >
> > On Wed, 24 Nov 2010, Vitaliy Gorbatyuk wrote:
> >
> > > Hi Wayne,
> > > I have also got blank the first e-mail but I can see its content in the
> jiscmail account.
> > > Weird...
> > > Anyhow, thank you for the response. I have done Analysis update and now I
> get the following
> > > traceback when I want to open a spectrum in a new project:
> > > Exception in Tkinter callback
> > > Traceback (most recent call last):
> > > File "/home/vitaliy/ccpnmr/python2.6/lib/python2.6/lib-tk/Tkinter.py",
> line 1410, in __call__
> > > return self.func(*args)
> > > File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/OpenSpectrum.py",
> line 361,
> > > in openSpectra
> > > shiftList)
> > > File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/OpenSpectrum.py",
> line 842,
> > > in openSpectrum
> > > extraData=extraData)
> > > File
> "/home/vitaliy/ccpnmr/ccpnmr2.2/python/ccp/format/spectra/params/ExternalParams.py",
> line
> > > 520, in createDataSource
> > > lastEdrs = expDims[-1].expDimRefs
> > > IndexError: list index out of range
> > >
> > > Regards,
> > > Vitaliy
> > >
> > >
> > > > Date: Wed, 24 Nov 2010 11:40:19 +0000
> > > > From: [log in to unmask]
> > > > Subject: Re: problem with import
> > > > To: [log in to unmask]
> > > >
> > > > Hello,
> > > >
> > > > The first email came out blank. But from the second email I think the
> > > > underlying problem is that the import did not set up the referencing for
> > > > the peak, and Analysis expects that to be set for peaks. I've changed it
> > > > now so that we set the referencing in that function if it is not set.
> > > >
> > > > Wayne
> > > >
> > > > On Wed, 24 Nov 2010, Vitaliy Gorbatyuk wrote:
> > > >
> > > > > Also, I imported files in nmrView format and got the similar error.
> Please see
> > > > > the attachment for details.
> > > > > Thank you,
> > > > > Vitaliy
> > > > >
> > > > >
> > >
> > >
>
>
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