Re: r25348 - /trunk/specific_analyses/relax_disp/data.py -- August 28, 2014 - 09:03

Hi Troels,

This should really be performed by the user and not automatically by
relax.  The current spectrum sub-setting you perform is no good.
Sometimes a user will have different settings for the same
spectrometer but for different offsets, for example they may change
the spectral width.  A good example is of HEHAHA experiments where you
only look at a spectrum with a single peak (you isolate each peak).
There is actually no sub-setting assumptions you can make
automatically here for the user that will be correct.  There are far
too many error analysis combinations that a user could come up with.
The best behaviour is to raise a RelaxError to tell the user that they
forgot to do something.  I would strongly prefer that this automatic
behaviour is not used, it's far to risky and will cause users to
perform something incorrectly without them ever knowing!

Cheers,

Edward





On 27 August 2014 20:06,  <tlinnet@xxxxxxxxxxxxx> wrote:
> Author: tlinnet
> Date: Wed Aug 27 20:06:24 2014
> New Revision: 25348
>
> URL: http://svn.gna.org/viewcvs/relax?rev=25348&view=rev
> Log:
> Added method to automatically perform error analysis on peak heights.
>
> task #7822(https://gna.org/task/index.php?7822): Implement user function to 
> estimate R2eff and associated errors for exponential curve fitting.
>
> Modified:
>     trunk/specific_analyses/relax_disp/data.py
>
> Modified: trunk/specific_analyses/relax_disp/data.py
> URL: 
> http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/data.py?rev=25348&r1=25347&r2=25348&view=diff
> ==============================================================================
> --- trunk/specific_analyses/relax_disp/data.py  (original)
> +++ trunk/specific_analyses/relax_disp/data.py  Wed Aug 27 20:06:24 2014
> @@ -68,13 +68,14 @@
>  from lib.physical_constants import g1H, return_gyromagnetic_ratio
>  from lib.sequence import read_spin_data, write_spin_data
>  from lib.software.grace import write_xy_data, write_xy_header, 
> script_grace2images
> +from lib.text.sectioning import section
>  from lib.warnings import RelaxWarning, RelaxNoSpinWarning
>  from pipe_control import pipes
>  from pipe_control.mol_res_spin import check_mol_res_spin_data, 
> exists_mol_res_spin_data, generate_spin_id_unique, generate_spin_string, 
> return_spin, spin_loop
>  from pipe_control.result_files import add_result_file
>  from pipe_control.selection import desel_spin
>  from pipe_control.sequence import return_attached_protons
> -from pipe_control.spectrum import add_spectrum_id
> +from pipe_control.spectrum import add_spectrum_id, error_analysis
>  from pipe_control.spectrometer import check_frequency, get_frequency
>  from pipe_control import value
>  import specific_analyses
> @@ -247,6 +248,50 @@
>
>      # Return the dic and list of keys
>      return [theta_spin_dic, Domega_spin_dic, w_eff_spin_dic, dic_key_list]
> +
> +
> +def check_intensity_errors(spin_id=None):
> +    """Check if intensity errors have already been calculated by the user.
> +
> +    @keyword spin_id:           The spin identification string.
> +    @type spin_id:              str
> +    """
> +
> +    # Check if intensity errors have already been calculated by the user.
> +    precalc = True
> +    for cur_spin, mol_name, resi, resn, cur_spin_id in 
> spin_loop(selection=spin_id, full_info=True, return_id=True, 
> skip_desel=True):
> +        # No structure.
> +        if not hasattr(cur_spin, 'peak_intensity_err'):
> +            precalc = False
> +            break
> +
> +        # Determine if a spectrum ID is missing from the list.
> +        for id in cdp.spectrum_ids:
> +            if id not in cur_spin.peak_intensity_err:
> +                precalc = False
> +                break
> +
> +    # If no error analysis of peak heights exists.
> +    if not precalc:
> +        # Printout.
> +        section(file=sys.stdout, text="Error analysis", prespace=2)
> +
> +        # Loop over the spectrometer frequencies.
> +        for frq in loop_frq():
> +            # Generate a list of spectrum IDs matching the frequency.
> +            ids = []
> +            for id in cdp.spectrum_ids:
> +                # Check that the spectrometer frequency matches.
> +                match_frq = True
> +                if frq != None and cdp.spectrometer_frq[id] != frq:
> +                    match_frq = False
> +
> +                # Add the ID.
> +                if match_frq:
> +                    ids.append(id)
> +
> +            # Run the error analysis on the subset.
> +            error_analysis(subset=ids)
>
>
>  def count_exp():
>
>
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