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 <tlinnet@xxxxxxxxx> 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 <edward@xxxxxxxxxxxxx>:
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 <tlinnet@xxxxxxxxx> 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 <edward@xxxxxxxxxxxxx>
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
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> 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)
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Re: [sr #3043] Support for NMRPipe seriesTab format *.ser