Author: bugman
Date: Tue Aug 27 14:49:36 2013
New Revision: 20699
URL: http://svn.gna.org/viewcvs/relax?rev=20699&view=rev
Log:
The dispersion specific code is now assembling the R1 data and passing it to
the target function.
The new specific_analyses.relax_disp.disp_data.return_r1_data() function
creates a data structure
holding all the R1 data. This is used in the off-resonance R1rho experiments.
Modified:
branches/relax_disp/specific_analyses/relax_disp/api.py
branches/relax_disp/specific_analyses/relax_disp/disp_data.py
Modified: branches/relax_disp/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/api.py?rev=20699&r1=20698&r2=20699&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Tue Aug 27
14:49:36 2013
@@ -46,7 +46,7 @@
from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
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_cluster, 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_offset_data,
return_param_key_from_data, return_r2eff_arrays, return_spin_lock_nu1,
return_value_from_frq_index, spin_ids_to_containers
+from specific_analyses.relax_disp.disp_data import average_intensity,
find_intensity_keys, loop_cluster, 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_offset_data,
return_param_key_from_data, return_r1_data, return_r2eff_arrays,
return_spin_lock_nu1, return_value_from_frq_index, spin_ids_to_containers
from specific_analyses.relax_disp.parameters import assemble_param_vector,
assemble_scaling_matrix, disassemble_param_vector, linear_constraints,
loop_parameters, param_conversion, param_index_to_param_info, param_num
from specific_analyses.relax_disp.variables import CPMG_EXP, FIXED_TIME_EXP,
MODEL_LIST_FULL, MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL,
MODEL_DPL94, MODEL_IT99, MODEL_M61, MODEL_M61B, MODEL_NOREX,
MODEL_NS_2SITE_3D, MODEL_NS_2SITE_3D_FULL, MODEL_NS_2SITE_EXPANDED,
MODEL_NS_2SITE_STAR, MODEL_NS_2SITE_STAR_FULL, MODEL_R2EFF, MODEL_TP02,
MODEL_TSMFK01, R1RHO_EXP, VAR_TIME_EXP
from target_functions.relax_disp import Dispersion
@@ -129,11 +129,14 @@
# Initialise the data structures for the target function.
values, errors, missing, frqs = return_r2eff_arrays(spins=[spin],
spin_ids=[spin_id], fields=fields, field_count=field_count)
- # The offset data.
- chemical_shifts, offsets, tilt_angles =
return_offset_data(spins=[spin], spin_ids=[spin_id], fields=fields,
field_count=field_count)
+ # The offset and R1 data for R1rho off-resonance models.
+ chemical_shifts, offsets, tilt_angles, r1 = None, None, None, None
+ if spin.model in [MODEL_DPL94, MODEL_TP02]:
+ chemical_shifts, offsets, tilt_angles =
return_offset_data(spins=[spin], spin_ids=[spin_id], fields=fields,
field_count=field_count)
+ r1 = return_r1_data(spins=[spin], spin_ids=[spin_id],
fields=fields, field_count=field_count)
# Initialise the relaxation dispersion fit functions.
- model = Dispersion(model=spin.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, frqs=frqs, cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
chemical_shifts=chemical_shifts, spin_lock_offsets=offsets,
tilt_angles=tilt_angles, relax_time=cdp.relax_time_list[0],
scaling_matrix=scaling_matrix)
+ model = Dispersion(model=spin.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, frqs=frqs, cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
chemical_shifts=chemical_shifts, spin_lock_offsets=offsets,
tilt_angles=tilt_angles, r1=r1, relax_time=cdp.relax_time_list[0],
scaling_matrix=scaling_matrix)
# Make a single function call. This will cause back calculation and
the data will be stored in the class instance.
model.func(param_vector)
@@ -1165,8 +1168,11 @@
# The R2eff/R1rho data.
values, errors, missing, frqs = return_r2eff_arrays(spins=spins,
spin_ids=spin_ids, fields=fields, field_count=field_count,
sim_index=sim_index)
- # The offset data.
- chemical_shifts, offsets, tilt_angles =
return_offset_data(spins=spins, spin_ids=spin_ids, fields=fields,
field_count=field_count)
+ # The offset and R1 data for R1rho off-resonance models.
+ chemical_shifts, offsets, tilt_angles, r1 = None, None, None,
None
+ if spins[0].model in [MODEL_DPL94, MODEL_TP02]:
+ chemical_shifts, offsets, tilt_angles =
return_offset_data(spins=spins, spin_ids=spin_ids, fields=fields,
field_count=field_count)
+ r1 = return_r1_data(spins=spins, spin_ids=spin_ids,
fields=fields, field_count=field_count, sim_index=sim_index)
# Create the initial parameter vector.
param_vector = assemble_param_vector(spins=spins)
@@ -1199,7 +1205,7 @@
print("Unconstrained grid search size: %s (constraints
may decrease this size).\n" % grid_size)
# Initialise the function to minimise.
- model = Dispersion(model=spins[0].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,
missing=missing, frqs=frqs, cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
chemical_shifts=chemical_shifts, spin_lock_offsets=offsets,
tilt_angles=tilt_angles, relax_time=cdp.relax_time_list[0],
scaling_matrix=scaling_matrix)
+ model = Dispersion(model=spins[0].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,
missing=missing, frqs=frqs, cpmg_frqs=return_cpmg_frqs(ref_flag=False),
spin_lock_nu1=return_spin_lock_nu1(ref_flag=False),
chemical_shifts=chemical_shifts, spin_lock_offsets=offsets,
tilt_angles=tilt_angles, r1=r1, relax_time=cdp.relax_time_list[0],
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=20699&r1=20698&r2=20699&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/disp_data.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/disp_data.py Tue Aug 27
14:49:36 2013
@@ -912,6 +912,51 @@
return "%s_%s" % (frq/1e6, point)
+def return_r1_data(spins=None, spin_ids=None, fields=None, field_count=None,
sim_index=None):
+ """Return the R1 data structures for off-resonance R1rho experiments.
+
+ @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 R1
data of. This should be None if the normal data is required.
+ @type sim_index: None or int
+ @return: The R1 relaxation data.
+ @rtype: numpy rank-2 float array
+ """
+
+ # The spin count.
+ spin_num = len(spins)
+
+ # Initialise the data structure.
+ r1 = zeros((spin_num, field_count), float64)
+
+ # Loop over the Rx IDs.
+ for ri_id in cdp.ri_ids:
+ # Only use R1 data.
+ if cdp.ri_type[ri_id] != 'R1':
+ continue
+
+ # The frequency.
+ frq = cdp.spectrometer_frq[ri_id]
+ frq_index = return_index_from_frq(frq)
+
+ # Spin loop.
+ for spin_index in range(spin_num):
+ # Store the data.
+ if sim_index != None:
+ r1[spin_index, frq_index] =
spins[spin_index].ri_data_sim[ri_id][sim_index]
+ else:
+ r1[spin_index, frq_index] = spins[spin_index].ri_data[ri_id]
+
+ # Return the data.
+ return r1
+
+
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.
r20699 - in /branches/relax_disp/specific_analyses/relax_disp: api.py disp_data.py