Hi Edward.
Thank you for your suggestion.
I will keep this possibility in mind. :-)
I think I aim at exporting to a flat text files.
Here the value.write function actually fulfil my needs.
The loading and saving of state files is to slow for me, and I prefer to
also be able to inspect text files quickly. :-)
This seems to be a good way to handle the value.write files:
-----------------
# Importing this to prepare for python 3.x
#from __future__ import print_function
# Import other
import os, re
import itertools
import numpy as np
import matplotlib.pyplot as plt
# Loop through methods.
METHODS = ['XXX']
for METHOD in METHODS:
# Open pipe names file
pipes_r2eff_filename = 'pipes_r2eff_%s.txt'%(METHOD)
pipes_r2eff_file = open(pipes_r2eff_filename,'r')
pipes_r2eff_filelines = pipes_r2eff_file.readlines()
pipes_r2eff_file.close()
# Extract pipe names
setup_pipe_bundle = "%s"%pipes_r2eff_filelines[0].strip()
state_save_name = "%s.bz2"%pipes_r2eff_filelines[1].strip()
# Extract which to compare to
compare_ni_pipe_name_r2eff = pipes_r2eff_filelines[2].strip()
# Get index of file
with open(os.path.join('r2eff', compare_ni_pipe_name_r2eff), 'r') as f:
for line in f:
if line.startswith('# mol_name'):
fileindex = line.split()[1:]
# Remove not allowed letters
fileindex = [w.replace('(', '') for w in fileindex]
fileindex = [w.replace(')', '') for w in fileindex]
fileindex = [w.replace('.', '') for w in fileindex]
# Prepare to define what file exist of
fdtype="S20,i,S3,i,S5"
for item in fileindex[5:]:
fdtype += ",f8"
print fdtype
data = np.genfromtxt(fname=os.path.join('r2eff',
compare_ni_pipe_name_r2eff), dtype=fdtype, names=fileindex)
print(data.dtype)
print(data.dtype.names)
print data['%s'%fileindex[0]]
print data['%s'%fileindex[6]]
2014-02-14 14:21 GMT+01:00 Edward d'Auvergne <edw...@nmr-relax.com>:
> Hi,
>
> This is a difficult question as efficiency changes with any change to
> the pipe_control.mol_res_spin module, as well as the data set up and
> specific questions you have. You should browse the functions in that
> module to see what you have access to:
>
> $ grep "def " pipe_control/mol_res_spin.py
>
> You may even find that implementing your own custom function in that
> module would be the best. I think for your purposes though, that the
> spin_index_loop() function is what you need. This loops over the
> molecule, residue, and spin indices. From what I understand of your
> aims, you will have the same sequence data for all the data pipes you
> would like to compare. Is this correct? If this is the case, then
> the molecule, residue, and spin indices will be the same for all
> pipes. So you could use code in your script such as:
>
> # relax module imports.
> from pipe_control.mol_res_spin import spin_index_loop
> from pipe_control.pipes import get_pipe
>
> # Get the two pipes.
> dp1 = get_pipe('first pipe')
> dp2 = get_pipe('second pipe')
>
> # Loop over the sequence data.
> for mol_index, res_index, spin_index in spin_index_loop():
> # Alias the spins for the two pipes.
> spin1 = dp1.mol[mol_index].res[res_index].spin[spin_index]
> spin2 = dp2.mol[mol_index].res[res_index].spin[spin_index]
>
> # Sanity check.
> if spin1.x != spin2.x:
> raise RelaxError("X is not X?!?")
>
>
> That should be the absolute fastest implementation. But have a look
> at the code to get a better idea. As I know you are after the fastest
> possible solution to be able to scan lots of data, looking at the
> relax code would give you an idea of what the best solution is. You
> may find inefficiencies that can be fixed in the relax code too.
>
> Regards,
>
> Edward
>
>
>
> On 14 February 2014 12:50, Troels Emtekær Linnet <tlin...@nmr-relax.com>
> wrote:
> > Hi,
> >
> > I need an efficient way to compare spin.X values between pipes.
> > Here X could be:
> >
> > - spin.r2eff
> > - spin.chi2
> > - spin.kex
> > etc.
> >
> > I have tried implementing the following:
> >
> > for spin, mol_name, res_num, res_name, spin_id in
> spin_loop(full_info=True,
> > return_id=True, skip_desel=True):
> > cur_r2eff = spin.r2eff[index_str]
> >
> > The problem is that r2eff is a saved as a dictionary, with a current name
> > convention of:
> > sq_cpmg_599.%8f_0.000_100.000
> > sq_cpmg_599.%8f_0.000_133.333
> > sq_cpmg_599.%8f_0.000_133.%3f
> >
> > This naming convention is likely to change pattern.
> >
> > Do there exist a efficient way to compare data values between two pipes?
> >
> > I would need to compare one pipe to about 50 other pipes, where each
> > pipe contains about 80 spins recorded at 10-15 v_cpmg frequencies.
> >
> > The difference between pipe data would undergo standard statistics as RMS
> > etc.
> >
> > Best
> > Troels
> >
> > _______________________________________________
> > relax (http://www.nmr-relax.com)
> >
> > This is the relax-users mailing list
> > relax-users@gna.org
> >
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> > reminder, or change your subscription options,
> > visit the list information page at
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> >
>
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