Author: bugman
Date: Thu Apr 4 09:44:42 2013
New Revision: 19343
URL: http://svn.gna.org/viewcvs/relax?rev=19343&view=rev
Log:
Better management of the global relaxation dispersion data.
The user functions relax_disp.cpmg_frq, relax_disp.spin_lock_nu1, and
relax_disp.relax_time now
maintain data structures in the current data pipe of the unique frequencies,
fields, and times
(sorted) as well as the number of frequencies, fields, and times. This data
is used by the minimise
user function back end to set up the target function, and will be required by
many other parts of
the analysis.
Modified:
branches/relax_disp/specific_analyses/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp.py?rev=19343&r1=19342&r2=19343&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp.py Thu Apr 4 09:44:42
2013
@@ -31,7 +31,6 @@
# relax module imports.
from lib.errors import RelaxError, RelaxFuncSetupError, RelaxLenError,
RelaxNoModelError, RelaxNoSequenceError, RelaxNoSpectraError
-from lib.list import count_unique_elements
from lib.text.sectioning import subsection
from minfx.generic import generic_minimise
from pipe_control import pipes
@@ -352,15 +351,22 @@
if spectrum_id not in cdp.spectrum_ids:
raise RelaxNoSpectraError(spectrum_id)
- # Initialise the global CPMG frequency data structure if needed.
+ # Initialise the global CPMG frequency data structures if needed.
if not hasattr(cdp, 'cpmg_frqs'):
cdp.cpmg_frqs = {}
+ if not hasattr(cdp, 'cpmg_frqs_list'):
+ cdp.cpmg_frqs_list = []
# Add the frequency at the correct position, converting to a float
if needed.
cdp.cpmg_frqs[spectrum_id] = float(cpmg_frq)
+ # The unique curves for the R2eff fitting (CPMG).
+ if cdp.cpmg_frqs[spectrum_id] not in cdp.cpmg_frqs_list:
+ cdp.cpmg_frqs_list.append(cdp.cpmg_frqs[spectrum_id])
+ cdp.cpmg_frqs_list.sort()
+
# Update the exponential curve count.
- cdp.curve_count = count_unique_elements(cdp.cpmg_frqs.values())
+ cdp.curve_count = len(cdp.cpmg_frqs_list)
# Printout.
print("Setting the '%s' spectrum CPMG frequency %s Hz." %
(spectrum_id, cdp.cpmg_frqs[spectrum_id]))
@@ -779,12 +785,22 @@
if spectrum_id not in cdp.spectrum_ids:
raise RelaxNoSpectraError(spectrum_id)
- # Initialise the global relaxation time data structure if needed.
+ # Initialise the global relaxation time data structures if needed.
if not hasattr(cdp, 'relax_times'):
cdp.relax_times = {}
+ if not hasattr(cdp, 'relax_time_list'):
+ cdp.relax_time_list = []
# Add the time, converting to a float if needed.
cdp.relax_times[spectrum_id] = float(time)
+
+ # The unique time points.
+ if cdp.relax_times[spectrum_id] not in cdp.relax_time_list:
+ cdp.relax_time_list.append(cdp.relax_times[spectrum_id])
+ cdp.relax_time_list.sort()
+
+ # Update the exponential curve count.
+ cdp.num_time_pts = len(cdp.relax_time_list)
# Printout.
print("Setting the '%s' spectrum relaxation time period to %s s." %
(spectrum_id, cdp.relax_times[spectrum_id]))
@@ -849,15 +865,22 @@
if spectrum_id not in cdp.spectrum_ids:
raise RelaxNoSpectraError(spectrum_id)
- # Initialise the global nu1 data structure if needed.
+ # Initialise the global nu1 data structures if needed.
if not hasattr(cdp, 'spin_lock_nu1'):
cdp.spin_lock_nu1 = {}
+ if not hasattr(cdp, 'spin_lock_nu1_list'):
+ cdp.spin_lock_nu1_list = []
# Add the frequency, converting to a float if needed.
cdp.spin_lock_nu1[spectrum_id] = float(field)
+ # The unique curves for the R2eff fitting (R1rho).
+ if cdp.spin_lock_nu1[spectrum_id] not in cdp.spin_lock_nu1_list:
+ cdp.spin_lock_nu1_list.append(cdp.spin_lock_nu1[spectrum_id])
+ cdp.spin_lock_nu1_list.sort()
+
# Update the exponential curve count.
- cdp.curve_count = count_unique_elements(cdp.spin_lock_nu1.values())
+ cdp.curve_count = len(cdp.spin_lock_nu1_list)
# Printout.
print("Setting the '%s' spectrum spin-lock field strength to %s
kHz." % (spectrum_id, cdp.spin_lock_nu1[spectrum_id]/1000.0))
@@ -971,29 +994,11 @@
elif cdp.exp_type == 'r1rho':
raise RelaxError("The spin-lock field strengths have not
been set up.")
- # The unique curves for the R2eff fitting (CPMG).
- cpmg_frqs = []
- if cdp.exp_type == 'cpmg':
- for frq in cdp.cpmg_frqs.values():
- if frq not in cpmg_frqs:
- cpmg_frqs.append(frq)
- cpmg_frqs.sort()
-
- # The unique curves for the R2eff fitting (R1rho).
- spin_lock_nu1 = []
- if cdp.exp_type == 'r1rho':
- for field in cdp.spin_lock_nu1.values():
- if field not in spin_lock_nu1:
- spin_lock_nu1.append(field)
- spin_lock_nu1.sort()
-
- # The relaxation time points (sorted).
- relax_times = []
- for time in cdp.relax_times.values():
- if time not in relax_times:
- relax_times.append(time)
- relax_times.sort()
- num_time_pts = len(relax_times)
+ # Initialise some empty data pipe structures so that the target
function set up does not fail.
+ if not hasattr(cdp, 'cpmg_frqs_list'):
+ cdp.cpmg_frqs_list = []
+ if not hasattr(cdp, 'spin_lock_nu1_list'):
+ cdp.spin_lock_nu1_list = []
# Loop over the spin blocks.
for spins, spin_ids in self._block_loop():
@@ -1001,8 +1006,8 @@
spin_num = len(spins)
# Initialise the data structures for the target function.
- values = zeros((spin_num, cdp.curve_count, num_time_pts),
float64)
- errors = zeros((spin_num, cdp.curve_count, num_time_pts),
float64)
+ values = zeros((spin_num, cdp.curve_count, cdp.num_time_pts),
float64)
+ errors = zeros((spin_num, cdp.curve_count, cdp.num_time_pts),
float64)
# Pack the peak intensity data.
for spin_index in range(spin_num):
@@ -1016,10 +1021,10 @@
for key in keys:
# The indices.
if cdp.exp_type == 'cpmg':
- curve_index = cpmg_frqs.index(cdp.cpmg_frqs[key])
+ curve_index =
cdp.cpmg_frqs_list.index(cdp.cpmg_frqs[key])
elif cdp.exp_type == 'r1rho':
- curve_index =
spin_lock_nu1.index(cdp.spin_lock_nu1[key])
- time_index = relax_times.index(cdp.relax_times[key])
+ curve_index =
cdp.spin_lock_nu1_list.index(cdp.spin_lock_nu1[key])
+ time_index =
cdp.relax_time_list.index(cdp.relax_times[key])
# The values.
if sim_index == None:
@@ -1061,7 +1066,7 @@
print("Unconstrained grid search size: %s (constraints
may decrease this size).\n" % grid_size)
# Initialise the function to minimise.
- model = Dispersion(model=cdp.model,
num_params=self._param_num(spins=spins), num_times=num_time_pts,
curve_num=cdp.curve_count, values=values, errors=errors, cpmg_frqs=cpmg_frqs,
spin_lock_nu1=spin_lock_nu1, scaling_matrix=scaling_matrix)
+ model = Dispersion(model=cdp.model,
num_params=self._param_num(spins=spins), num_times=cdp.num_time_pts,
curve_num=cdp.curve_count, values=values, errors=errors,
relax_times=cdp.relax_time_list, cpmg_frqs=cdp.cpmg_frqs_list,
spin_lock_nu1=cdp.spin_lock_nu1_list, scaling_matrix=scaling_matrix)
# Setup the minimisation algorithm when constraints are present.
if constraints and not match('^[Gg]rid', min_algor):
r19343 - /branches/relax_disp/specific_analyses/relax_disp.py