Re: r26975 - /trunk/pipe_control/spectrum.py -- December 06, 2014 - 16:01

Hi Troels,

Just to catch possible problems with integer ratio in Python 2, I
would suggest passing pint and pint_err through the float() builtin
function.  It probably will not happen very often, but this could
cause a lot of bugs when peak heights and errors are low integer
values.

Regards,

Edward


On 6 December 2014 at 14:45,  <tlinnet@xxxxxxxxxxxxx> wrote:
> Author: tlinnet
> Date: Sat Dec  6 14:45:16 2014
> New Revision: 26975
>
> URL: http://svn.gna.org/viewcvs/relax?rev=26975&view=rev
> Log:
> Added the pipe_control.spectrum.signal_noise_ratio() backend function, for 
> calculation of the signal to noise ratio per spin.
>
> Modified:
>     trunk/pipe_control/spectrum.py
>
> Modified: trunk/pipe_control/spectrum.py
> URL: 
> http://svn.gna.org/viewcvs/relax/trunk/pipe_control/spectrum.py?rev=26975&r1=26974&r2=26975&view=diff
> ==============================================================================
> --- trunk/pipe_control/spectrum.py      (original)
> +++ trunk/pipe_control/spectrum.py      Sat Dec  6 14:45:16 2014
> @@ -32,7 +32,7 @@
>
>  # relax module imports.
>  from lib.errors import RelaxError, RelaxImplementError, RelaxNoSpectraError
> -from lib.io import write_data
> +from lib.io import sort_filenames, write_data
>  from lib.text.sectioning import section
>  from lib.spectrum.peak_list import read_peak_list
>  from lib.statistics import std
> @@ -865,3 +865,73 @@
>
>      # Return the list.
>      return repl
> +
> +
> +def signal_noise_ratio(verbose=True):
> +    """Calculate the signal to noise ratio per spin.
> +
> +    @keyword verbose:       A flag which if True will print additional 
> information out.
> +    @type verbose:          bool
> +    """
> +
> +    # Tests.
> +    check_pipe()
> +    check_mol_res_spin_data()
> +
> +    # Test if spectra have been loaded.
> +    if not hasattr(cdp, 'spectrum_ids'):
> +        raise RelaxError("No spectra have been loaded.")
> +
> +    # Possible print.
> +    if verbose:
> +        print("\nThe following signal to noise ratios has been 
> calculated:\n")
> +
> +    # Set the spin specific signal to noise ratio.
> +    for spin, spin_id in spin_loop(return_id=True):
> +        # Skip deselected spins.
> +        if not spin.select:
> +            continue
> +
> +        # Skip spins missing intensity data.
> +        if not hasattr(spin, 'peak_intensity'):
> +            continue
> +
> +        # Test if error analysis has been performed.
> +        if not hasattr(spin, 'peak_intensity_err'):
> +            raise RelaxError("Intensity error analysis has not been 
> performed.  Please see spectrum.error_analysis().")
> +
> +        # If necessary, create the dictionary.
> +        if not hasattr(spin, 'sn_ratio'):
> +            spin.sn_ratio = {}
> +
> +        # Loop over the ID.
> +        ids = []
> +        for id in spin.peak_intensity:
> +            # Append the ID to the list.
> +            ids.append(id)
> +
> +            # Calculate the sn_ratio.
> +            pint = spin.peak_intensity[id]
> +            pint_err = spin.peak_intensity_err[id]
> +            sn_ratio = pint / pint_err
> +
> +            # Assign the sn_ratio.
> +            spin.sn_ratio[id] = sn_ratio
> +
> +        # Sort the ids alphanumeric.
> +        ids = sort_filenames(filenames=ids, rev=False)
> +
> +        # Collect the data under sorted ids.
> +        data_i = []
> +        for id in ids:
> +            # Get the values.
> +            pint = spin.peak_intensity[id]
> +            pint_err = spin.peak_intensity_err[id]
> +            sn_ratio = spin.sn_ratio[id]
> +
> +            # Store the data.
> +            data_i.append([id, repr(pint), repr(pint_err), repr(sn_ratio)])
> +
> +        if verbose:
> +            section(file=sys.stdout, text="Signal to noise ratio for spin 
> ID '%s'"%spin_id, prespace=1)
> +            write_data(out=sys.stdout, headings=["Spectrum ID", "Signal", 
> "Noise", "S/N"], data=data_i)
>
>
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