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Hi, thanks for that, now working fine and saved me having to return to xeasy! Jo Wayne Boucher wrote: > Hello, > > Right, that definitely implied it was an edge of spectrum effect, and > indeed it was. For those who want to read the gory details, see below. > Otherwise just update. (But let me know if you see anything odd.) > > So for those who want to know, the problem was that in dimensions with > number of points (say) 256, then for peak positions between 1 and 257 (but > < 257) we want numAliasing to be 0 and the peak position to be as stated. > For peak positions above 257 (until 513) we want numAliasing to be 1 and > the peak position to be as stated - 256. Well, to get the intensity > (before interpolation) for a peak, we look to the nearest grid point and > get the spectrum value there. Only for points between 256.5 and 257 (but > < 257) the nearest position is 257, which is outside the grid, so the code > was getting an error because it was not correcting for this. It is now > wrapping around to point 1 instead. > > Two things worth noting. This wrap-around to 1 only makes sense if > numPoints = numPointsOrig (so you haven't thrown any data out when you > processed the spectrum). Otherwise in fact we wouldn't really have the > data for the real position 257. There's not a heck of a lot we can do > about that. But basically, beware of edge-of-spectrum peaks in these > circumstances. > > And also, the bug above was only be noticed in the third dimension because > the way the code was calculating where in the file on disk to get the > information, it was happily doing something for the other dimensions but > just going to the wrong point (so not good!). It failed for the third > dimension because it was asking for information beyond the end of the > file. So I've now added some more error checking in the code to make sure > that shouldn't happen again either. (But it won't in this particular > circumstance in any case because of the other fix.) > > Wayne > > On Fri, 29 Feb 2008, Jolyon Claridge wrote: > > >> Hi, >> >> the "number points" reads 512 x 128 x 256 so the spectrum is less than >> 257 in the third dimension. >> As far as I can tell the spectrum is drawing ok. >> >> cheers, >> Jo >> >> >> Wayne Boucher wrote: >> >>> Hello, >>> >>> I assume the spectrum is drawing ok (so no such error when producing the >>> contours, even when you are zoomed out). >>> >>> Is your spectrum less than 258 x 52 x 257 in size in at least one of those >>> dimensions? (If you don't know you can check what Analysis thinks the >>> size is in Experiment -> Edit Spectra -> File Details, in the "Number >>> Points" column.) >>> >>> (So this question will help determine whether this is more likely an error >>> in the Python or in the C. My guess is the former and I'll see if I can >>> find anything obvious.) >>> >>> Wayne >>> >>> On Wed, 27 Feb 2008, Jo Claridge wrote: >>> >>> >>> >>>> Hi, >>>> >>>> I got the following error when using predict from shifts with an HNCO spectrum: >>>> >>>> Exception in Tkinter callback >>>> Traceback (most recent call last): >>>> File "/usr/local/software/ccpnmr/python2.4/lib/python2.4/lib-tk/Tkinter.py", line 1345, in >>>> __call__ >>>> return self.func(*args) >>>> File "/usr/local/software/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/EditPeakListsPopup.py", >>>> line 540, in synthesiseFromShifts >>>> progressBar=progressBar) >>>> File "/usr/local/software/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/PeakBasic.py", line 2416, >>>> in makePeakListFromShifts >>>> peak = pickPeak(peakList, position, unit=shiftList.unit) >>>> File "/usr/local/software/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/PeakBasic.py", line 1353, >>>> in pickPeak >>>> setupPeak(peak, doFit=doFit) >>>> File "/usr/local/software/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/PeakBasic.py", line 1546, >>>> in setupPeak >>>> setupPeakFit(peak) >>>> File "/usr/local/software/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/PeakBasic.py", line 1579, >>>> in setupPeakFit >>>> center = peak.cPeak.fitCenter(fitMethod, spectrum.block_file, dimDone) >>>> Peak.error: could not get point: 258 52 257 >>>> >>>> cheers, >>>> Jo >>>> >>>> >>>> >>> . >>> >>> >>> > > . > >