Re: [sr #3043] Support for NMRPipe seriesTab format *.ser -- June 21, 2013 - 20:53

If -list list_of_files.txt contains:

../0/test.ft2

../1/test.ft2

../2/test.ft2

../3/test.ft2

Then this comes out.

----------------------

REMARK SeriesTab Input: ../../peaks.dat Output: allexp.ser

REMARK Mode: Summation Dimensions: 2

REMARK Input Region:    X +/- 0 X-ZF: 1

REMARK Analysis Region: X +/- 0

REMARK Input Region:    Y +/- 0 Y-ZF: 1

REMARK Analysis Region: Y +/- 0

VARS   INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS Z_A0 Z_A1 Z_A2 Z_A3

FORMAT %5d %9.3f %9.3f %8.3f %8.3f %+e %s %7.4f %7.4f %7.4f %7.4f

NULLVALUE -666

NULLSTRING *

    1   254.059   150.545    8.525  116.014 +1.660865e+05 A2N-H  1.0000  1.1887  1.1893  1.1876

    2   236.553    58.937    8.696  125.904 +8.106413e+05 A3N-H  1.0000  1.1940  1.1935  1.1954

    3   193.454    86.021    9.117  122.980 +4.835453e+05 A4N-H  1.0000  1.1958  1.1962  1.1941

    4   161.310   107.270    9.431  120.686 +2.538240e+05 A5N-H  1.0000  1.1919  1.1934  1.1924

    5   165.097    30.288    9.394  128.997 +4.701862e+05 A6N-H  1.0000  1.1965  1.1959  1.1970

    6   184.650    63.133    9.203  125.451 +4.951762e+05 A7N-H  1.0000  1.1937  1.1929  1.1910

    7   229.694    53.861    8.763  126.452 +4.193051e+05 A8N-H  1.0000  1.1936  1.1971  1.1939 

    8   277.092    99.897    8.300  121.482 +5.726205e+05 A9N-H  1.0000  1.1961  1.1976  1.1986

    9   243.719   183.928    8.626  112.410 +5.105667e+05 A10N-H  1.0000  1.1966  1.1961  1.1966

You would have to tell that the intensity is Col[6] X Col[line_nr+8]

Troels Emtekær Linnet

2013/6/21 Edward d'Auvergne <edward@xxxxxxxxxxxxx>

Hi,

This might be too difficult to incorporate into the current
spectrum.read user function.  I'm not 100% sure what you mean yet
though.  Would you be able to illustrate with examples?  Maybe this
could be considered after the single files can be successfully read.

Regards,

Edward

On 21 June 2013 20:21, Troels Emtekær Linnet <tlinnet@xxxxxxxxx> wrote:
> SeriesTab can be used for single files, if the keyword
>
> -list list_of_files.txt
> only contains one file.
>
> Then the intensity will be read from column 6.
> This is FINE for the GUI.
>
> But, if you provide it a list of several files, they will be compared, to 5
> digits.
> This is a nice feature, since you now have a matrix possibility.
>
> Say that you have a dispersion experiment and record 20 interleaved spectra.
> Then you change a parameter somewhere, and have 20 new files. And repeat.
> All this can be contained in one big file.
>
> So, you want to create a python file, which go through the list file, and
> takes Col[line_number +7] * Col[5]
> And then you have the name for the spectrum from the list file.
>
> Sooooo..... I would need this feature!
>
>
>
>
> Troels Emtekær Linnet
>
>
> 2013/6/21 Edward d'Auvergne <edward@xxxxxxxxxxxxx>
>>
>> Hi,
>>
>> For this one I would prefer not to apply the patch.  I think there are
>> already too many keyword arguments for the spectrum.read user function
>> and the GUI interface for it will be too crowded.  And as I mentioned
>> at:
>>
>> http://thread.gmane.org/gmane.science.nmr.relax.devel/3963/focus=4066
>>
>> we should be able to determine the scaling column from the *.ser file.
>>  What do you think?
>>
>> Regards,
>>
>> Edward
>>
>>
>>
>> On 21 June 2013 20:04, Troels E. Linnet
>> <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
>> > Follow-up Comment #26, sr #3043 (project relax):
>> >
>> > Intensity column keyword added for NMRPipe SeriesTab format.
>> >
>> > Progress sr #3043: (https://gna.org/support/index.php?3043) Support for
>> > NMRPipe seriesTab format *.ser
>> >
>> > Added the keyword "col_mult":
>> > """ The column which to multiply the peak intensity data (used by the
>> > SeriesTab intensity file format). """
>> > If the file 'allplanes.list' contains several paths to .ft2 files, the
>> > call
>> > to:
>> > seriesTab -in peaks.dat -out allplanes.ser -list allplanes.list
>> > will give a result file where the the total intensity will be given by
>> > column:
>> > VOL x Z_A0 etc.
>> >
>> > The result file contain the VARS keyword:
>> > INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS Z_A0 Z_A1 Z_A2 Z_A3
>> > Where Z_A0 Z_A1 Z_A2 Z_A3 matches allplanes.list
>> >
>> > An 'allplanes.list' is easily created by:
>> >> ls -v -d -1 /.ft2 > allplanes.list
>> >
>> >
>> > (file #18152)
>> >     _______________________________________________________
>> >
>> > Additional Item Attachment:
>> >
>> > File name: trunk_SeriesTab4_2             Size:1 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
>> > relax-devel@xxxxxxx
>> >
>> > 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
>
>