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
