Hi Ed,
Ok... That clarifies things...
I first wanted to use the
"test_suite/shared_data/peak_lists/generic.txt" file for the reason that
it includes everything, both intensities and relaxation times. However,
this would mean developing something completely different to what is
made for the reading of the other formats (Sparky, XEasy, nmrview).
Moreover, as you proposed using
"test_suite/shared_data/peak_lists/generic_intensity.txt" and maybe also
"test_suite/shared_data/peak_lists/generic_delays.txt" would be much
easier and simple using the current code...
Thus, that is what I will implement...
Regards,
Séb :)
Edward d'Auvergne wrote:
> Hi,
>
> Sorry, I should have mentioned this earlier. It might have cleared
> things up for you Seb with the generic peak intensity code. So, now
> things are a bit different in relax when handling spectral data. I
> have made a clear separation between the peak intensity reading code -
> in generic_fns.spectrum - and the specific analyses such as relaxation
> curve-fitting, steady-state NOE analysis, or any new analyses which in
> the future might use peak intensities. This introduces much more
> flexibility into relax, but makes it a bit more complicated to read in
> the data. For peak intensities, there are 2 parts required - loading
> the intensities from file and setting the intensity errors. So for
> example in the NOE sample script, this is done with the lines:
>
> # Load the reference spectrum and saturated spectrum peak intensities.
> spectrum.read_intensities(file='ref.list', spectrum_id='ref_ave')
> spectrum.read_intensities(file='sat.list', spectrum_id='sat_ave')
>
> # Set the errors.
> spectrum.baseplane_rmsd(error=3600, spectrum_id='ref_ave')
> spectrum.baseplane_rmsd(error=3000, spectrum_id='sat_ave')
>
> # Peak intensity error analysis.
> spectrum.error_analysis()
>
>
> The last user function, spectrum.error_analysis() is very important as
> it determines the spin specific peak intensity errors. Reading the
> docstring of this user function, through for example:
>
> relax> help(spectrum.error_analysis)
>
> is highly recommended. The last part for peak intensities in this
> script is to associated the spectrum_ids to the experiment. This
> allows multiple reference and saturated spectra to be analysed
> simultaneously. The important part of the script is:
>
> # Set the spectrum types.
> noe.spectrum_type('ref', 'ref_ave')
> noe.spectrum_type('sat', 'sat_ave')
>
>
> The rest of the script is the same. As for the relaxation
> curve-fitting sample script, this is a little more elaborate. First
> of all, we load the peak intensities and simultaneously set the time
> associated with each point. The lines are:
>
> # Spectrum names.
> names = [
> 'T2_ncyc1_ave',
> 'T2_ncyc1b_ave',
> 'T2_ncyc2_ave',
> 'T2_ncyc4_ave',
> 'T2_ncyc4b_ave',
> 'T2_ncyc6_ave',
> 'T2_ncyc9_ave',
> 'T2_ncyc9b_ave',
> 'T2_ncyc11_ave',
> 'T2_ncyc11b_ave'
> ]
>
> # Relaxation times (in seconds).
> times = [
> 0.0176,
> 0.0176,
> 0.0352,
> 0.0704,
> 0.0704,
> 0.1056,
> 0.1584,
> 0.1584,
> 0.1936,
> 0.1936
> ]
>
> # Loop over the spectra.
> for i in xrange(len(names)):
> # Load the peak intensities.
> spectrum.read_intensities(file=names[i]+'.list', dir=data_path,
> spectrum_id=names[i], int_method='height')
>
> # Set the relaxation times.
> relax_fit.relax_time(time=times[i], spectrum_id=names[i])
>
>
> Here the 'names' list contain the spectrum ids, which also correspond
> to the base name of the Sparky *.list files read by the
> spectrum.read_intensities() user function. The order of the times in
> the 'times' list match the spectrum ids list. Each spectrum is
> associated with its time through the relax_fit.relax_time() user
> function. The next part of the script is:
>
> # Specify the duplicated spectra.
> spectrum.replicated(spectrum_ids=['T2_ncyc1_ave', 'T2_ncyc1b_ave'])
> spectrum.replicated(spectrum_ids=['T2_ncyc4_ave', 'T2_ncyc4b_ave'])
> spectrum.replicated(spectrum_ids=['T2_ncyc9_ave', 'T2_ncyc9b_ave'])
> spectrum.replicated(spectrum_ids=['T2_ncyc11_ave', 'T2_ncyc11b_ave'])
>
> # Peak intensity error analysis.
> spectrum.error_analysis()
>
>
> Here, a different type of error analysis is performed as we have
> duplicate spectra. Again see the spectrum.error_analysis() docstring
> for full details. But instead of using the baseplane RMSD measure,
> the errors are taken from duplicate spectra as specified by the
> spectrum.replicated() user function. From here, the script is the
> same as before. I hope this description clarifies how peak
> intensities are now handled.
>
> Regards,
>
> Edward
>
>
> P.S. Note, this is in the 1.3 development line and that the user
> function names or the way peak intensities are handles may change if
> improvements are found and implemented.
>
> P.P.S. Seb, for the system test of the generic peak intensity file,
> setting the relaxation times should not be done. I would instead use
> the test_suite/shared_data/peak_lists/generic_intensity.txt file for
> this test. If you would like to use the times in the
> test_suite/shared_data/peak_lists/generic_delays.txt file, I would
> recommend creating a new system test in the
> test_suite/system_tests/relax_fit.py file. This will require a new
> user function to be written, something like relax_fit.read_times().
> And finally, the file test_suite/shared_data/peak_lists/generic.txt is
> no longer necessary.
>
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