Allright, I agree. I have put it on the wish list, so I dont forget. Regarding File format: That looks to me as a nmrDraw peak list files.
http://spin.niddk.nih.gov/NMRPipe/doc2new/ http://eurocarbdb-nmr.googlecode.com/svn/trunk/api/ccpnmr2.0/python/ccp/format/nmrDraw/peaksIO.py http://nmr.uthscsa.edu/~ahinck/html/soft_packs/nmrpipe/nlinLS.html Troels Emtekær Linnet 2013/8/2 Edward d'Auvergne <[email protected]>: > Hi, > > I would factor in a few solid days. The longest part is the creation > of system or GUI tests. Also, in this case, you will need to learn > how to create a user function definition and then fill out the > backend. It should be very doable though. I suggest that it would be > best to get the NMRPipe seriesTab support up and running first. Then > maybe look at the dispersion models that you still need. So I suggest > waiting until a little later. Once you are an accepted developer with > full commit access, you can add all the polish you like to get relax > to do what ever you wish. Through the feedback on your patches, you > are learning how the relax development works and are learning a lot of > the relax APIs and code layout. And this helps a lot when you have > full commit access, as then I don't need to point out issues as often. > You can convert as many of your scripts as you like into user > functions and instantly have them available in the GUI. And, for > that. we should discuss branches in the subversion repository for > implementing it, as you will have to do this part, at least, via svn > and svnmerge.py commands. On a similar note, can you identify if the > nlin_600.tab file in > https://gna.org/support/download.php?file_id=18262 is a seriesTab > file? > > Cheers, > > Edward > > > > On 2 August 2013 18:13, Troels Emtekær Linnet <[email protected]> wrote: >> I was thinking... >> >> On 10/10 scale, how long time would it take to make a GUI user function. >> >> nmrpipe -> create NMRPipe-format Peak Table from SPARKY assigment. >> >> Input: A SPARKY output file with X and Y in PPM >> Input frqX, frqY from OBS MHz >> Input sizeX, sizeY from DATA SIZE >> Input origX, origY from ORIG Hz >> Input swX, swY from SW Hz >> >> ------------------------------------------------------------------- >> [tlinnet@tomat ft2_data]$ showhdr test.ft2 >> FILE: test.ft2 DIM: 2 QUAD: Real 2DMODE: States >> BYTES: 527360 PRED: 527360 MIN: 0 MAX: 0 VALID: 0 >> ORDER: 2 1 PIPE: 0 PLANES: 1 513x256x1 Not Transposed >> >> X-Axis Y-Axis >> >> DATA SIZE: 513 256 >> APOD SIZE: 160 128 >> SW Hz: 2504.882812 1400.020996 >> OBS MHz: 499.862000 50.655998 >> ORIG Hz: 2996.960938 5300.190918 >> DOMAIN: Freq Freq >> MODE: Real Real >> NAME: H1 N15 >> -------------------------------------------------------- >> >> This is in perl: >> $stepX=$swX/$frqX/$sizeX; >> $highX=($origX+$swX)/$frqX; >> $stepY=$swY/$frqY/$sizeY; >> $highY=($origY+$swY)/$frqY; >> $i=1; >> print "VARS INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS\n"; >> print "FORMAT %5d %9.3f %9.3f %8.3f %8.3f %+e %s\n\n"; >> >> open IN, "$sparkyList" or die "Cannot open $sparkyList for read"; >> while (<IN>){ >> @process = split (/\s+/, $_); >> if ($process[0] eq ""){splice (@process, 0, 1)}; >> if ($process[0] ne "Assignment" && $process[0] ne ""){ >> $ptsX=($highX-$process[2])/$stepX; >> $ptsY=($highY-$process[1])/$stepY; >> printf "%5d %9.3f %9.3f %8.3f %8.3f %+e >> %s\n",$i,$ptsX,$ptsY,$process[2],$process[1],700000,$process[0]; >> $i++; >> }; >> }; >> close (IN); >> >> Best >> Troels Emtekær Linnet >> >> >> 2013/8/2 Edward d'Auvergne <[email protected]>: >>> Hi, >>> >>> Ok, then we keep it as the Sparky format. When a user encounters a >>> non-Sparky format, we can deal with it then. >>> >>> Cheers, >>> >>> Edward >>> >>> >>> >>> On 2 August 2013 17:50, Troels Emtekær Linnet <[email protected]> wrote: >>>> Hi Edward. >>>> >>>> When you generate NMRPipe series tab file, you need to have >>>> a file with the spectral points. >>>> >>>> See example here: >>>> http://wiki.nmr-relax.com/NMRPipe_seriesTab >>>> >>>> VARS INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS >>>> FORMAT %5d %9.3f %9.3f %8.3f %8.3f %+e %s >>>> >>>> 1 246.658 18.268 9.932 128.374 +7.000000e+05 W62NE1-W62HE1 >>>> 2 321.698 30.994 9.419 127.066 +7.000000e+05 L10N-L10HN >>>> 3 320.089 55.737 9.430 124.523 +7.000000e+05 V6N-V6HN >>>> >>>> It is the X_AXIS and Y_AXIS spectral points that is essential to make >>>> the summation correct. >>>> And it will just snap the assignment in the last column, without any >>>> check (As far as I know.) >>>> >>>> If you use SPARKY to export your file, you should get the assignment >>>> as seen above. >>>> And you get the Y_AXIS X_PPM Y_PPM. >>>> You can calculate X_AXIS Y_AXIS, if you extract information from use >>>> of nmrpipe "head" on the .ft2 file >>>> >>>> But here comes the trouble. Different NMR program can export in SPARKY >>>> like format, but always a little >>>> different. So, until now, I keep it in SPARKY format. >>>> >>>> Best >>>> Troels Emtekær Linnet >>>> >>>> >>>> 2013/8/2 Edward d'Auvergne <[email protected]> >>>>> >>>>> Hi Troels, >>>>> >>>>> I'm getting through you patches and have applied the first two. These >>>>> are ok. I have an issue with >>>>> 0003-The-ID-of-spins-in-seriesTab_multi.ser-was-not-forma.patch though >>>>> (git hash f49b4f096773cb2f7ecb70293122e03b0b40e889). It says that you >>>>> are changing the seriesTab_multi.ser file's 'ASS' column format to >>>>> that of Sparky. Why is this so? Is there an NMRPipe seriesTab format >>>>> which is different from Sparky? If so, we should support that. >>>>> >>>>> Cheers, >>>>> >>>>> Edward >>>>> >>>>> >>>>> On 2 August 2013 17:29, Troels E. Linnet >>>>> <[email protected]> wrote: >>>>> > Follow-up Comment #53, sr #3043 (project relax): >>>>> > >>>>> > Multi colums import now supported. >>>>> > >>>>> > Note, I made it possible to autogenerate spectrum ID's, if >>>>> > spectrum_id='auto' for the function: >>>>> > >>>>> > spectrum.read_intensities(file="seriesTab_multi.ser", >>>>> > dir=status.install_path >>>>> > + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', >>>>> > spectrum_id='auto', >>>>> > int_method='point sum') >>>>> > >>>>> > (file #18619) >>>>> > _______________________________________________________ >>>>> > >>>>> > Additional Item Attachment: >>>>> > >>>>> > File name: stab.patch.tar.gz Size:4 KB >>>>> > >>>>> > >>>>> > _______________________________________________________ >>>>> > >>>>> > Reply to this item at: >>>>> > >>>>> > <http://gna.org/support/?3043> >>>>> > >>>>> > _______________________________________________ >>>>> > Message sent via/by Gna! >>>>> > http://gna.org/ >>>>> > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
