Author: bugman
Date: Thu Sep 5 12:28:20 2013
New Revision: 20833
URL: http://svn.gna.org/viewcvs/relax?rev=20833&view=rev
Log:
Fixes for the specific_analyses.relax_disp.api module for the
relax_disp.exp_type change.
This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530,
the thread about
supporting multiple data types such as SQ+MQ data simultaneously.
The loop_exp*() functions are now being used throughout the module. The
specific_analyses.relax_disp.checks.check_*() functions are also used to
simplify the code and fix
changes to cdp.exp_type. And some auxiliary functions from
specific_analyses.relax_disp.disp_data
are being used as well.
Modified:
branches/relax_disp/specific_analyses/relax_disp/api.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=20833&r1=20832&r2=20833&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Thu Sep 5
12:28:20 2013
@@ -37,16 +37,17 @@
# relax module imports.
from dep_check import C_module_exp_fn
from lib.dispersion.two_point import calc_two_point_r2eff,
calc_two_point_r2eff_err
-from lib.errors import RelaxError, RelaxFuncSetupError, RelaxLenError,
RelaxNoModelError, RelaxNoSequenceError, RelaxNoSpectraError
+from lib.errors import RelaxError, RelaxLenError, RelaxNoModelError,
RelaxNoSpectraError
from lib.list import count_unique_elements, unique_elements
from lib.mathematics import round_to_next_order
from lib.statistics import std
from lib.text.sectioning import subsection
from pipe_control import pipes, sequence
-from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
+from pipe_control.mol_res_spin import check_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_r1_data, return_r2eff_arrays,
return_spin_lock_nu1, return_value_from_frq_index, spin_ids_to_containers
+from specific_analyses.relax_disp.checks import check_c_modules,
check_disp_points, check_exp_type, check_exp_type_fixed_time,
check_model_type, check_pipe_type
+from specific_analyses.relax_disp.disp_data import average_intensity,
find_intensity_keys, get_curve_type, has_exponential_exp_type, loop_cluster,
loop_exp_frq_point, 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 EXP_TYPE_LIST_FIXED_TIME,
EXP_TYPE_LIST_VAR_TIME, 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_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TP02,
MODEL_TSMFK01
from target_functions.relax_disp import Dispersion
@@ -143,7 +144,7 @@
# Convert to a dictionary matching the R2eff data structure.
results = {}
- for frq, point in loop_frq_point():
+ for exp_type, frq, point in loop_exp_frq_point():
# The indices.
frq_index = return_index_from_frq(frq)
point_index = return_index_from_disp_point(point)
@@ -176,7 +177,7 @@
"""
# Check.
- if cdp.exp_type in EXP_TYPE_LIST_FIXED_TIME:
+ if not has_exponential_exp_type():
raise RelaxError("Back-calculation is not allowed for the fixed
time experiment types.")
# The key.
@@ -333,7 +334,7 @@
spin = spins[spin_index]
# Loop over each spectrometer frequency and dispersion
point.
- for frq, point in loop_frq_point():
+ for exp_type, frq, point in loop_exp_frq_point():
# Loop over the parameters.
for i in range(len(spin.params)):
# R2eff relaxation rate (from 1 to 40 s^-1).
@@ -446,15 +447,17 @@
continue
# Loop over each spectrometer frequency and dispersion point.
- for frq, point in loop_frq_point():
+ for exp_type, frq, point in loop_exp_frq_point():
# The parameter key.
param_key = return_param_key_from_data(frq=frq, point=point)
# The initial parameter vector.
param_vector = assemble_param_vector(spins=[spin],
key=param_key, sim_index=sim_index)
+ print param_vector
# Diagonal scaling.
scaling_matrix = assemble_scaling_matrix(spins=[spin],
key=param_key, scaling=scaling)
+ print scaling_matrix
if len(scaling_matrix):
param_vector = dot(inv(scaling_matrix), param_vector)
@@ -597,43 +600,37 @@
@type model: str
"""
- # Test if the current pipe exists.
+ # Data checks.
pipes.test()
-
- # Test if the pipe type is set to 'relax_disp'.
- function_type = cdp.pipe_type
- if function_type != 'relax_disp':
- raise
RelaxFuncSetupError(specific_setup.get_string(function_type))
-
- # Test if sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test if the experiment type is set.
- if not hasattr(cdp, 'exp_type'):
- raise RelaxError("The relaxation dispersion experiment type has
not been set.")
-
- # Test for the C-modules.
- if model == MODEL_R2EFF and cdp.exp_type in EXP_TYPE_LIST_VAR_TIME
and not C_module_exp_fn:
- raise RelaxError("The exponential curve-fitting C module cannot
be found.")
+ check_pipe_type()
+ check_mol_res_spin_data()
+ check_exp_type()
+ if model == MODEL_R2EFF:
+ check_c_modules()
+
+ # The curve type.
+ curve_type = get_curve_type()
# R2eff/R1rho model.
if model == MODEL_R2EFF:
print("R2eff/R1rho value and error determination.")
- params = ['r2eff', 'i0']
+ if curve_type == 'exponential':
+ params = ['r2eff', 'i0']
+ else:
+ params = ['r2eff']
# The model for no chemical exchange relaxation.
elif model == MODEL_NOREX:
print("The model for no chemical exchange relaxation.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2')
# LM63 model.
elif model == MODEL_LM63:
print("The Luz and Meiboom (1963) 2-site fast exchange model.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2')
params += ['phi_ex', 'kex']
@@ -641,7 +638,7 @@
elif model == MODEL_LM63_3SITE:
print("The Luz and Meiboom (1963) 3-site fast exchange model.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2')
params += ['phi_ex_B', 'phi_ex_C', 'kB', 'kC']
@@ -649,9 +646,9 @@
elif model == MODEL_CR72_FULL:
print("The full Carver and Richards (1972) 2-site model for all
time scales.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2a')
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2b')
params += ['pA', 'dw', 'kex']
@@ -659,7 +656,7 @@
elif model == MODEL_CR72:
print("The reduced Carver and Richards (1972) 2-site model for
all time scales, whereby the simplification R20A = R20B is assumed.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2')
params += ['pA', 'dw', 'kex']
@@ -667,7 +664,7 @@
elif model == MODEL_IT99:
print("The Ishima and Torchia (1999) CPMG 2-site model for all
time scales with pA >> pB.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2')
params += ['phi_ex', 'padw2', 'tex']
@@ -675,7 +672,7 @@
elif model == MODEL_TSMFK01:
print("The Tollinger, Kay et al. (2001) 2-site very-slow
exchange model, range of microsecond to second time scale.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2a')
params += ['dw', 'kA']
@@ -683,9 +680,9 @@
elif model == MODEL_NS_CPMG_2SITE_3D_FULL:
print("The full numerical solution for the 2-site
Bloch-McConnell equations for CPMG data using 3D magnetisation vectors.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2a')
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2b')
params += ['pA', 'dw', 'kex']
@@ -693,7 +690,7 @@
elif model == MODEL_NS_CPMG_2SITE_3D:
print("The reduced numerical solution for the 2-site
Bloch-McConnell equations for CPMG data using 3D magnetisation vectors,
whereby the simplification R20A = R20B is assumed.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2')
params += ['pA', 'dw', 'kex']
@@ -701,7 +698,7 @@
elif model == MODEL_NS_CPMG_2SITE_EXPANDED:
print("The numerical solution for the 2-site Bloch-McConnell
equations for CPMG data expanded using Maple by Nikolai Skrynnikov.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2')
params += ['pA', 'dw', 'kex']
@@ -709,9 +706,9 @@
elif model == MODEL_NS_CPMG_2SITE_STAR_FULL:
print("The full numerical solution for the 2-site
Bloch-McConnell equations for CPMG data using complex conjugate matrices.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2a')
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2b')
params += ['pA', 'dw', 'kex']
@@ -719,7 +716,7 @@
elif model == MODEL_NS_CPMG_2SITE_STAR:
print("The numerical reduced solution for the 2-site
Bloch-McConnell equations for CPMG data using complex conjugate matrices,
whereby the simplification R20A = R20B is assumed.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2')
params += ['pA', 'dw', 'kex']
@@ -727,7 +724,7 @@
elif model == MODEL_M61:
print("The Meiboom (1961) 2-site fast exchange model for
R1rho-type experiments.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2')
params += ['phi_ex', 'kex']
@@ -735,7 +732,7 @@
elif model == MODEL_M61B:
print("The Meiboom (1961) on-resonance 2-site model with skewed
populations (pA >> pB) for R1rho-type experiments.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2')
params += ['pA', 'dw', 'kex']
@@ -743,7 +740,7 @@
elif model == MODEL_DPL94:
print("The Davis, Perlman and London (1994) 2-site fast exchange
model for R1rho-type experiments.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2')
params += ['phi_ex', 'kex']
@@ -751,7 +748,7 @@
elif model == MODEL_TP02:
print("The Trott and Palmer (2002) off-resonance 2-site model
for R1rho-type experiments.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2')
params += ['pA', 'dw', 'kex']
@@ -759,7 +756,7 @@
elif model == MODEL_NS_R1RHO_2SITE:
print("The reduced numerical solution for the 2-site
Bloch-McConnell equations for R1rho data using 3D magnetisation vectors,
whereby the simplification R20A = R20B is assumed.")
params = []
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
params.append('r2')
params += ['pA', 'dw', 'kex']
@@ -794,8 +791,8 @@
continue
# Loop over each spectrometer frequency and dispersion point.
- for frq, point in loop_frq_point():
- yield spin, frq, point
+ for exp_type, frq, point in loop_exp_frq_point():
+ yield spin, exp_type, frq, point
# All other models (the base data is the R2eff/R1rho values).
else:
@@ -824,31 +821,13 @@
@type sim_index: None
"""
- # Test if the current pipe exists.
+ # Data checks.
pipes.test()
-
- # Test if sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test if the model has been set.
- if not hasattr(cdp, 'exp_type'):
- raise RelaxError("The relaxation dispersion experiment type has
not been specified.")
-
- # Test if the model has been set.
- if not hasattr(cdp, 'model_type'):
- raise RelaxError("The relaxation dispersion model has not been
specified.")
-
- # Test if the curve count exists.
- if not hasattr(cdp, 'dispersion_points'):
- if cdp.exp_type == 'cpmg':
- raise RelaxError("The CPMG frequencies have not been set
up.")
- elif cdp.exp_type == 'r1rho':
- raise RelaxError("The spin-lock field strengths have not
been set up.")
-
- # Only allow the fixed relaxation time period data types.
- if cdp.exp_type not in EXP_TYPE_LIST_FIXED_TIME:
- raise RelaxError("The experiment '%s' is not of the fixed
relaxation time period data type, the R2eff/R1rho values cannot be directly
calculated." % cdp.exp_type)
+ check_mol_res_spin_data()
+ check_exp_type()
+ check_model_type()
+ check_disp_points()
+ check_exp_type_fixed_time()
# Printouts.
print("Calculating the R2eff/R1rho values for fixed relaxation time
period data.")
@@ -869,7 +848,7 @@
spin.r2eff_err = {}
# Loop over all the data.
- for frq, point, time in loop_frq_point_time():
+ for exp_type, frq, point, time in loop_exp_frq_point_time():
# The three keys.
ref_keys = find_intensity_keys(frq=frq, point=None,
time=time)
int_keys = find_intensity_keys(frq=frq, point=point,
time=time)
@@ -1077,24 +1056,11 @@
@type inc: array of int
"""
- # Test if sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test if the model has been set.
- if not hasattr(cdp, 'exp_type'):
- raise RelaxError("The relaxation dispersion experiment type has
not been specified.")
-
- # Test if the model has been set.
- if not hasattr(cdp, 'model_type'):
- raise RelaxError("The relaxation dispersion model has not been
specified.")
-
- # Test if the curve count exists.
- if not hasattr(cdp, 'dispersion_points'):
- if cdp.exp_type == 'cpmg':
- raise RelaxError("The CPMG frequencies have not been set
up.")
- elif cdp.exp_type == 'r1rho':
- raise RelaxError("The spin-lock field strengths have not
been set up.")
+ # Data checks.
+ check_mol_res_spin_data()
+ check_exp_type()
+ check_model_type()
+ check_disp_points()
# Initialise some empty data pipe structures so that the target
function set up does not fail.
if not hasattr(cdp, 'cpmg_frqs_list'):
@@ -1105,8 +1071,8 @@
# Special exponential curve-fitting for the 'R2eff' model.
if cdp.model_type == 'R2eff':
# Sanity checks.
- if cdp.exp_type in EXP_TYPE_LIST_FIXED_TIME:
- raise RelaxError("The R2eff model with the fixed time period
CPMG experiment cannot be optimised.")
+ if not has_exponential_exp_type():
+ raise RelaxError("The R2eff model with the fixed time period
dispersion experiments cannot be optimised.")
# Optimisation.
self._minimise_r2eff(min_algor=min_algor,
min_options=min_options, func_tol=func_tol, grad_tol=grad_tol,
max_iterations=max_iterations, constraints=constraints, scaling=scaling,
verbosity=verbosity, sim_index=sim_index, lower=lower, upper=upper, inc=inc)
@@ -1269,7 +1235,7 @@
spin.r2eff_bc = {}
# Loop over the R2eff data.
- for frq, point in loop_frq_point():
+ for exp_type, frq, point in loop_exp_frq_point():
# The indices.
disp_pt_index = return_index_from_disp_point(point)
frq_index = return_index_from_frq(frq)
@@ -1372,8 +1338,7 @@
"""
# Test the sequence data exists.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
+ check_mol_res_spin_data()
# Loop over spin data.
for spin in spin_loop():
r20833 - /branches/relax_disp/specific_analyses/relax_disp/api.py