Ok, I now got it! I know how we can bludgeon the spectrum.read user
function to handle this. It's a simple trick, and also very simple
for the user. What we do is let the user set the int_col argument to
the Z_Ax column for the spectrum ID they will use. Then the backend
takes this column and multiplies it with the fixed column 6 to obtain
the real intensity (if it's not fixed, then we can work it out from
the position of the 'VOL' label in the VARS row). For this, we just
need to add a paragraph to the user function documentation saying how
NMRPipe seriesTab files are handled. It would also then be worth
adding this to the relax user manual. Do you know LaTeX?
As for reading everything in one go, have a look at the bruker.read
user function for inspiration
(http://www.nmr-relax.com/manual/bruker_read.html). We could create a
new user function for just this file format, maybe
spectrum.read_seriestab, which would read all of the data en masse.
Regards,
Edward
On 21 June 2013 20:52, Troels Emtekær Linnet <tlinnet@xxxxxxxxx> wrote:
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
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Reply to this item at:
<http://gna.org/support/?3043>
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Re: [sr #3043] Support for NMRPipe seriesTab format *.ser