Author: tlinnet
Date: Thu Sep 11 21:31:46 2014
New Revision: 25758
URL: http://svn.gna.org/viewcvs/relax?rev=25758&view=rev
Log:
Implemented a method to automatically find dublicates of spectrum in
exponential fit.
This is to ease the user intervention for error analysis, if this has been
forgotten.
Modified:
trunk/auto_analyses/relax_fit.py
Modified: trunk/auto_analyses/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/relax_fit.py?rev=25758&r1=25757&r2=25758&view=diff
==============================================================================
--- trunk/auto_analyses/relax_fit.py (original)
+++ trunk/auto_analyses/relax_fit.py Thu Sep 11 21:31:46 2014
@@ -24,8 +24,11 @@
# Python module imports.
from os import sep
+import sys
# relax module imports.
+from lib.text.sectioning import section
+from pipe_control.mol_res_spin import spin_loop
from pipe_control.pipes import cdp_name, has_pipe, switch
from prompt.interpreter import Interpreter
from status import Status; status = Status()
@@ -104,7 +107,7 @@
"""Set up and run the curve-fitting."""
# Peak intensity error analysis.
- self.interpreter.spectrum.error_analysis()
+ self.error_analysis()
# Set the relaxation curve type.
self.interpreter.relax_fit.select_model('exp')
@@ -147,6 +150,78 @@
self.interpreter.state.save(state=self.file_root+'.save',
dir=self.results_dir, force=True)
+ def error_analysis(self):
+ """Perform an error analysis of the peak intensities."""
+
+ # Printout.
+ section(file=sys.stdout, text="Error analysis", prespace=2)
+
+ # Check if intensity errors have already been calculated by the
user.
+ precalc = True
+ for spin in spin_loop(skip_desel=True):
+ # No structure.
+ if not hasattr(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 spin.peak_intensity_err:
+ precalc = False
+ break
+
+ # Skip.
+ if precalc:
+ print("Skipping the error analysis as it has already been
performed.")
+ return
+
+ # Check if there is replicates, and the user has not specified
them.
+ if not hasattr(cdp, 'replicates'):
+ # Has dublicates
+ has_dub = False
+
+ # Collect all times, and matching spectrum id.
+ all_times = []
+ all_id = []
+ for s_id, time in cdp.relax_times.iteritems():
+ all_times.append(time)
+ all_id.append(s_id)
+
+ # Get the dublicates.
+ dublicates = map(lambda val: (val, [i for i in
xrange(len(all_times)) if all_times[i] == val]), all_times)
+
+ # Loop over the list of the mapping of times and duplications.
+ list_dub_mapping = []
+ for i, dub in enumerate(dublicates):
+ # Get current spectum id.
+ cur_spectrum_id = all_id[i]
+
+ # Get the tuple of time and indexes of duplications.
+ time, list_index_occur = dub
+
+ # Collect mapping of index to id.
+ id_list = []
+ if len(list_index_occur) > 1:
+ # There exist dublications.
+ has_dub = True
+
+ for list_index in list_index_occur:
+ id_list.append(all_id[list_index])
+
+ # Store to list
+ list_dub_mapping.append((cur_spectrum_id, id_list))
+
+ # If there is dublication, then assign them.
+ if has_dub:
+ # Assign dublicates.
+ for spectrum_id, dub_pair in list_dub_mapping:
+ if len(dub_pair) > 0:
+
self.interpreter.spectrum.replicated(spectrum_ids=dub_pair)
+
+ # Run the error analysis.
+ self.interpreter.spectrum.error_analysis()
+
+
def check_vars(self):
"""Check that the user has set the variables correctly."""
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Re: r25758 - /trunk/auto_analyses/relax_fit.py