Author: bugman
Date: Thu May 16 19:26:25 2013
New Revision: 19694
URL: http://svn.gna.org/viewcvs/relax?rev=19694&view=rev
Log:
A number of fixes to partly enable Monte Carlo simulations for the non
'R2eff' dispersion models.
Modified:
branches/relax_disp/specific_analyses/relax_disp/__init__.py
branches/relax_disp/specific_analyses/relax_disp/parameters.py
Modified: branches/relax_disp/specific_analyses/relax_disp/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/__init__.py?rev=19694&r1=19693&r2=19694&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/__init__.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/__init__.py Thu May 16
19:26:25 2013
@@ -55,7 +55,7 @@
from pipe_control.result_files import add_result_file
from specific_analyses.api_base import API_base
from specific_analyses.api_common import API_common
-from specific_analyses.relax_disp.disp_data import average_intensity,
find_intensity_keys, loop_frq, loop_frq_point, loop_frq_point_key,
loop_frq_point_time, loop_point, loop_time, relax_time, return_cpmg_frqs,
return_key_from_disp_point_index, return_param_key_from_data,
return_r2eff_arrays, return_spin_lock_nu1
+from specific_analyses.relax_disp.disp_data import average_intensity,
find_intensity_keys, loop_frq, loop_frq_point, loop_frq_point_key,
loop_frq_point_time, loop_point, loop_time, relax_time, return_cpmg_frqs,
return_index_from_disp_point, return_index_from_frq,
return_key_from_disp_point_index, return_param_key_from_data,
return_r2eff_arrays, return_spin_lock_nu1
from specific_analyses.relax_disp.parameters import assemble_param_vector,
assemble_scaling_matrix, disassemble_param_vector, linear_constraints,
param_index_to_param_info, param_num
from specific_analyses.relax_disp.variables import CPMG_EXP, FIXED_TIME_EXP,
MODEL_R2EFF, MODEL_LM63, MODEL_CR72, R1RHO_EXP, VAR_TIME_EXP
from target_functions.relax_disp import Dispersion
@@ -102,13 +102,15 @@
self.PARAMS.add_min_data(min_stats_global=False, min_stats_spin=True)
- def _back_calc_r2eff(self, spin=None):
+ def _back_calc_r2eff(self, spin=None, spin_id=None):
"""Back-calculation of R2eff/R1rho values for the given spin.
- @keyword spin: The specific spin data container.
- @type spin: SpinContainer instance
- @return: The back-calculated R2eff/R1rho value for the given
spin.
- @rtype: numpy rank-1 float array
+ @keyword spin: The specific spin data container.
+ @type spin: SpinContainer instance
+ @keyword spin_id: The spin ID string for the spin container.
+ @type spin_id: str
+ @return: The back-calculated R2eff/R1rho value for the
given spin.
+ @rtype: numpy rank-1 float array
"""
# Create the initial parameter vector.
@@ -126,9 +128,7 @@
field_count = len(fields)
# Initialise the data structures for the target function.
- values = zeros((1, field_count, cdp.dispersion_points), float64)
- errors = ones((1, field_count, cdp.dispersion_points), float64)
- missing = zeros((1, field_count, cdp.dispersion_points), float64)
+ values, errors, missing = return_r2eff_arrays(spins=[spin],
spin_ids=[spin_id], fields=fields, field_count=field_count)
# Initialise the relaxation dispersion fit functions.
model = Dispersion(model=cdp.model,
num_params=param_num(spins=[spin]), num_spins=1, num_frq=field_count,
num_disp_points=cdp.dispersion_points, values=values, errors=errors,
missing=missing, cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
scaling_matrix=scaling_matrix)
@@ -138,10 +138,20 @@
# Convert to a dictionary matching the R2eff data structure.
results = {}
- for frq_index in range(field_count):
- for point_index in range(cdp.dispersion_points):
- key = return_key_from_disp_point_index(frq_index=frq_index,
disp_point_index=point_index)
- results[key] = model.back_calc[0, frq_index, point_index]
+ for frq, point in loop_frq_point():
+ # The indices.
+ frq_index = return_index_from_frq(frq)
+ point_index = return_index_from_disp_point(point)
+
+ # The parameter key.
+ param_key = return_param_key_from_data(frq=frq, point=point)
+
+ # Skip missing data.
+ if missing[0, frq_index, point_index]:
+ continue
+
+ # Store the result.
+ results[param_key] = model.back_calc[0, frq_index, point_index]
# Return the back calculated R2eff values.
return results
@@ -738,8 +748,8 @@
For the R2eff model, the base data is the peak intensity data
defining a single exponential curve. For all other models, the base data is
the R2eff/R1rho values for individual spins.
- @return: For the R2eff model, a tuple of the spin container and
the exponential curve identifying key (the CPMG frequency or R1rho spin-lock
field strength). For all other models, just the spin containers from the
spin loop.
- @rtype: tuple of SpinContainer instance and float or
SpinContainer instance
+ @return: For the R2eff model, a tuple of the spin container and
the exponential curve identifying key (the CPMG frequency or R1rho spin-lock
field strength). For all other models, the spin container and ID from the
spin loop.
+ @rtype: (tuple of SpinContainer instance and float) or
(SpinContainer instance and str)
"""
# The R2eff model data (the base data is peak intensities).
@@ -761,7 +771,7 @@
# All other models (the base data is the R2eff/R1rho values).
else:
# Loop over the sequence.
- for spin in spin_loop():
+ for spin, spin_id in spin_loop(return_id=True):
# Skip deselected spins.
if not spin.select:
continue
@@ -770,8 +780,8 @@
if not hasattr(spin, 'r2eff'):
continue
- # Yield the spin container.
- yield spin
+ # Yield the spin container and ID.
+ yield spin, spin_id
def calculate(self, spin_id=None, verbosity=1, sim_index=None):
@@ -901,10 +911,10 @@
# All other models (with R2eff/R1rho base data).
else:
# Unpack the data.
- spin = data_id
+ spin, spin_id = data_id
# Back calculate the R2eff/R1rho data.
- values = self._back_calc_r2eff(spin=spin)
+ values = self._back_calc_r2eff(spin=spin, spin_id=spin_id)
# Return the MC data.
return values
@@ -1239,7 +1249,7 @@
# All other models.
else:
# Unpack the data.
- spin = data_id
+ spin, spin_id = data_id
# The errors.
return spin.r2eff_err
@@ -1347,7 +1357,7 @@
# All other models (with R2eff/R1rho base data).
else:
# Unpack the data.
- spin = data_id
+ spin, spin_id = data_id
# Pack the data.
spin.r2eff_sim = sim_data
Modified: branches/relax_disp/specific_analyses/relax_disp/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/parameters.py?rev=19694&r1=19693&r2=19694&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Thu May 16
19:26:25 2013
@@ -511,7 +511,7 @@
# All other parameters.
else:
- param_name = names[index-num+2]
+ param_name = names[index-2]
# Return the data.
return param_name, spin_index
r19694 - in /branches/relax_disp/specific_analyses/relax_disp: __init__.py parameters.py