Author: bugman
Date: Mon May 6 16:16:23 2013
New Revision: 19667
URL: http://svn.gna.org/viewcvs/relax?rev=19667&view=rev
Log:
Shifted the R2eff/R1rho value and error assembly into
specific_analyses.relax_disp.disp_data.
This is in the new return_r2eff_arrays() function. The code has also been
debugged and made
functional.
Modified:
branches/relax_disp/specific_analyses/relax_disp/__init__.py
branches/relax_disp/specific_analyses/relax_disp/disp_data.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=19667&r1=19666&r2=19667&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/__init__.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/__init__.py Mon May 6
16:16:23 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 exp_curve_index_from_key,
exp_curve_key_from_index, intensity_key, loop_all_data,
loop_dispersion_point, loop_exp_curve, loop_spectrometer, relax_time,
return_cpmg_frqs, return_key, return_spin_lock_nu1
+from specific_analyses.relax_disp.disp_data import exp_curve_index_from_key,
exp_curve_key_from_index, intensity_key, loop_all_data,
loop_dispersion_point, loop_exp_curve, loop_spectrometer, relax_time,
return_cpmg_frqs, return_key, 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
@@ -964,9 +964,9 @@
field_count = 1
fields = []
if hasattr(cdp, 'frq'):
- field_count = count_unique_elements(cdp.frq.values())
fields = unique_elements(cdp.frq.values())
fields.sort()
+ field_count = len(fields)
# The number of time points for the exponential curves (if present).
num_time_pts = 1
@@ -975,51 +975,8 @@
# Loop over the spin blocks.
for spins, spin_ids in self.model_loop():
- # The spin count.
- spin_num = len(spins)
-
- # Initialise the data structures for the target function.
- values = zeros((spin_num, field_count, cdp.dispersion_points),
float64)
- errors = zeros((spin_num, field_count, cdp.dispersion_points),
float64)
-
- # Pack the R2eff/R1rho data.
- data_flag = False
- for spin_index in range(spin_num):
- # Alias the spin.
- spin = spins[spin_index]
-
- # No data.
- if not hasattr(spin, 'r2eff'):
- continue
- data_flag = True
-
- # The keys.
- keys = list(spin.r2eff.keys())
-
- # Loop over the R2eff data.
- for key in keys:
- # The indices.
- disp_pt_index = 0
- if cdp.exp_type == 'cpmg':
- disp_pt_index =
cdp.cpmg_frqs_list.index(cdp.cpmg_frqs[key])
- elif cdp.exp_type == 'r1rho':
- disp_pt_index =
cdp.spin_lock_nu1_list.index(cdp.spin_lock_nu1[key])
- field_index = 0
- if hasattr(cdp, 'frqs'):
- field_index = fields.index(cdp.frqs[keys])
-
- # The values.
- if sim_index == None:
- values[spin_index, field_index, disp_pt_index] =
spin.r2eff[key]
- else:
- values[spin_index, field_index, disp_pt_index] =
spin.r2eff_sim[key][sim_index]
-
- # The errors.
- errors[spin_index, field_index, disp_pt_index] =
spin.r2eff_err[key]
-
- # No R2eff/R1rho data for the spin cluster.
- if not data_flag:
- raise RelaxError("No R2eff/R1rho data could be found for the
spin cluster %s." % spin_ids)
+ # The R2eff/R1rho data.
+ values, errors = return_r2eff_arrays(spins=spins,
spin_ids=spin_ids, fields=fields, field_count=field_count)
# Create the initial parameter vector.
param_vector = assemble_param_vector(spins=spins)
@@ -1052,7 +1009,7 @@
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=param_num(spins=spins), num_spins=spin_num, num_frq=field_count,
num_disp_points=cdp.dispersion_points, values=values, errors=errors,
cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
scaling_matrix=scaling_matrix)
+ model = Dispersion(model=cdp.model,
num_params=param_num(spins=spins), num_spins=len(spins), num_frq=field_count,
num_disp_points=cdp.dispersion_points, values=values, errors=errors,
cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
scaling_matrix=scaling_matrix)
# Grid search.
if search('^[Gg]rid', min_algor):
Modified: branches/relax_disp/specific_analyses/relax_disp/disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/disp_data.py?rev=19667&r1=19666&r2=19667&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/disp_data.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/disp_data.py Mon May 6
16:16:23 2013
@@ -22,6 +22,9 @@
# Module docstring.
"""Functions for handling relaxation dispersion data within the relax data
store."""
+
+# Python module imports.
+from numpy import float64, zeros
# relax module imports.
from lib.errors import RelaxError, RelaxNoSpectraError
@@ -313,6 +316,82 @@
return spin.intensities[key]
+def return_r2eff_arrays(spins=None, spin_ids=None, fields=None,
field_count=None, sim_index=None):
+ """Return numpy arrays of the R2eff/R1rho values and errors.
+
+ @keyword spins: The list of spin containers in the cluster.
+ @type spins: list of SpinContainer instances
+ @keyword spin_ids: The list of spin IDs for the cluster.
+ @type spin_ids: list of str
+ @keyword fields: The list of spectrometer field strengths.
+ @type fields: list of float
+ @keyword field_count: The number of spectrometer field strengths.
This may not be equal to the length of the fields list as the user may not
have set the field strength.
+ @type field_count: int
+ @keyword sim_index: The index of the simulation to return the data
of. This should be None if the normal data is required.
+ @type sim_index: None or int
+ @return: The numpy array structure of the R2eff/R1rho
values and the structure for the errors. For each structure, the first
dimension corresponds to the spins of a spin block, the second to the
spectrometer field strength, and the third is the dispersion points.
+ @rtype: numpy rank-3 float array, numpy rank-3 float
array
+ """
+
+ # The spin count.
+ spin_num = len(spins)
+
+ # Initialise the data structures for the target function.
+ values = zeros((spin_num, field_count, cdp.dispersion_points), float64)
+ errors = zeros((spin_num, field_count, cdp.dispersion_points), float64)
+
+ # Pack the R2eff/R1rho data.
+ data_flag = False
+ for spin_index in range(spin_num):
+ # Alias the spin.
+ spin = spins[spin_index]
+
+ # No data.
+ if not hasattr(spin, 'r2eff'):
+ continue
+ data_flag = True
+
+ # The keys.
+ keys = list(spin.r2eff.keys())
+
+ # Loop over the R2eff data.
+ for key in keys:
+ # Reference in the fixed time experiments.
+ if cdp.exp_type in FIXED_TIME_EXP:
+ if cdp.exp_type in CPMG_EXP and cdp.cpmg_frqs[key] == None:
+ continue
+ if cdp.exp_type in R1RHO_EXP and cdp.spin_lock_nu1[key] ==
None:
+ continue
+
+ # The indices.
+ disp_pt_index = 0
+ if cdp.exp_type in CPMG_EXP:
+ disp_pt_index = cdp.cpmg_frqs_list.index(cdp.cpmg_frqs[key])
+ elif cdp.exp_type in R1RHO_EXP:
+ disp_pt_index =
cdp.spin_lock_nu1_list.index(cdp.spin_lock_nu1[key])
+ if cdp.exp_type in FIXED_TIME_EXP:
+ disp_pt_index -= 1
+ field_index = 0
+ if hasattr(cdp, 'frq'):
+ field_index = fields.index(cdp.frq[key])
+
+ # The values.
+ if sim_index == None:
+ values[spin_index, field_index, disp_pt_index] =
spin.r2eff[key]
+ else:
+ values[spin_index, field_index, disp_pt_index] =
spin.r2eff_sim[key][sim_index]
+
+ # The errors.
+ errors[spin_index, field_index, disp_pt_index] =
spin.r2eff_err[key]
+
+ # No R2eff/R1rho data for the spin cluster.
+ if not data_flag:
+ raise RelaxError("No R2eff/R1rho data could be found for the spin
cluster %s." % spin_ids)
+
+ # Return the structures.
+ return values, errors
+
+
def return_key(frq=None, point=None, time=None):
"""Return the key corresponding to the spectrometer frequency,
dispersion point, and relaxation time.
r19667 - in /branches/relax_disp/specific_analyses/relax_disp: __init__.py disp_data.py