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/
>>> >
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