Author: tlinnet
Date: Mon Sep 1 23:25:37 2014
New Revision: 25520
URL: http://svn.gna.org/viewcvs/relax?rev=25520&view=rev
Log:
Further extended systemtest Relax_disp.test_task_model_par_est_tsmfk01() to
check the values.
Are getting close now.
task #7824(https://gna.org/task/index.php?7824): Model parameter ERROR
estimation from Jacobian and Co-variance matrix of dispersion models.
Modified:
branches/est_par_error/test_suite/system_tests/relax_disp.py
Modified: branches/est_par_error/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/est_par_error/test_suite/system_tests/relax_disp.py?rev=25520&r1=25519&r2=25520&view=diff
==============================================================================
--- branches/est_par_error/test_suite/system_tests/relax_disp.py
(original)
+++ branches/est_par_error/test_suite/system_tests/relax_disp.py Mon
Sep 1 23:25:37 2014
@@ -32,6 +32,7 @@
# relax module imports.
from auto_analyses import relax_disp
+from copy import deepcopy
from data_store import Relax_data_store; ds = Relax_data_store()
import dep_check
from lib.errors import RelaxError
@@ -40,11 +41,11 @@
from pipe_control.minimise import assemble_scaling_matrix
from specific_analyses.relax_disp.checks import check_missing_r1
from specific_analyses.relax_disp.estimate_r2eff import estimate_par_err,
estimate_r2eff
-from specific_analyses.relax_disp.data import average_intensity,
check_intensity_errors, generate_r20_key, get_curve_type,
has_exponential_exp_type, has_r1rho_exp_type, loop_exp_frq,
loop_exp_frq_offset_point, loop_exp_frq_offset_point_time, loop_time,
return_grace_file_name_ini, return_param_key_from_data, spin_ids_to_containers
+from specific_analyses.relax_disp.data import average_intensity,
check_intensity_errors, generate_r20_key, get_curve_type,
has_exponential_exp_type, has_r1rho_exp_type, loop_exp_frq,
loop_exp_frq_offset, loop_exp_frq_offset_point,
loop_exp_frq_offset_point_time, loop_time, return_grace_file_name_ini,
return_param_key_from_data, spin_ids_to_containers
from specific_analyses.relax_disp.data import INTERPOLATE_DISP,
INTERPOLATE_OFFSET, X_AXIS_DISP, X_AXIS_W_EFF, X_AXIS_THETA, Y_AXIS_R2_R1RHO,
Y_AXIS_R2_EFF
from specific_analyses.relax_disp.model import models_info, nesting_param
from specific_analyses.relax_disp.parameters import linear_constraints
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_LIST, EXP_TYPE_R1RHO,
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99,
MODEL_LIST_ANALYTIC_CPMG, MODEL_LIST_FULL, MODEL_LIST_NUMERIC_CPMG,
MODEL_LM63, MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_NOREX,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE,
MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_PARAMS, MODEL_R2EFF, MODEL_TP02,
MODEL_TAP03
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_LIST, EXP_TYPE_R1RHO,
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99,
MODEL_LIST_ANALYTIC_CPMG, MODEL_LIST_FULL, MODEL_LIST_NUMERIC_CPMG,
MODEL_LM63, MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_NOREX,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE,
MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_PARAMS, MODEL_R2EFF, MODEL_TP02,
MODEL_TAP03, PARAMS_R20
from status import Status; status = Status()
from test_suite.system_tests.base_classes import SystemTestCase
@@ -7372,21 +7373,94 @@
# Estimate model error.
estimate_par_err()
+ # Start dic.
+ my_dic = {}
+ spin_id_list = []
+
# Get the data.
for cur_spin, mol_name, resi, resn, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=True):
+ # Add key to dic.
+ my_dic[spin_id] = {}
+ # Store id, for ordering.
+ spin_id_list.append(spin_id)
+
+ # Get the parameters fitted in the model.
+ params = cur_spin.params
+ my_dic[spin_id]['params'] = params
+ my_dic[spin_id]['params_err'] = []
+
# Generate spin string.
spin_string = generate_spin_string(spin=cur_spin,
mol_name=mol_name, res_num=resi, res_name=resn)
- for exp_type, frq, offset, point, ei, mi, oi, di in
loop_exp_frq_offset_point(return_indices=True):
- # Generate the param_key.
- param_key = return_param_key_from_data(exp_type=exp_type,
frq=frq, offset=offset, point=point)
+ param_key_list = []
+ for exp_type, frq, offset, ei, mi, oi, in
loop_exp_frq_offset(return_indices=True):
+ # Get the parameter key.
param_key = generate_r20_key(exp_type=exp_type, frq=frq)
+
+ # Add key to dic.
+ my_dic[spin_id][param_key] = {}
+ param_key_list.append(param_key)
+
+ # Loop over params.
+ for i, param in enumerate(params):
+ # Set the param error name
+ param_err = param + '_err'
+ my_dic[spin_id]['params_err'].append(param_err)
+
+ # If param in PARAMS_R20, values are stored in with
parameter key.
+ if param in PARAMS_R20:
+ # Get the error.
+ param_err_val = deepcopy(getattr(cur_spin,
param_err)[param_key])
+ my_dic[spin_id][param_key][param_err] = param_err_val
+
+ else:
+ # Get the error.
+ param_err_val = deepcopy(getattr(cur_spin,
param_err))
+ my_dic[spin_id][param_key][param_err] = param_err_val
+
+ my_dic[spin_id]['param_key_list'] = param_key_list
# After Monte-Carlo.
resultsfile_mc = 'final_results_mc'
- #self.interpreter.pipe.create(pipe_name='mc pipe',
pipe_type='relax_disp')
- #self.interpreter.results.read(file=resultsfile_mc, dir=data_path)
-
+ self.interpreter.pipe.create(pipe_name='mc pipe',
pipe_type='relax_disp')
+ self.interpreter.results.read(file=resultsfile_mc, dir=data_path)
+
+ # Get the data.
+ for cur_spin, mol_name, resi, resn, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=True):
+ # Get the parameters fitted in the model.
+ params = cur_spin.params
+
+ for exp_type, frq, offset, ei, mi, oi, in
loop_exp_frq_offset(return_indices=True):
+ # Get the parameter key.
+ param_key = generate_r20_key(exp_type=exp_type, frq=frq)
+
+ # Loop over params.
+ for i, param in enumerate(params):
+ # Set the param error name
+ param_err = param + '_err'
+
+ # If param in PARAMS_R20, values are stored in with
parameter key.
+ if param in PARAMS_R20:
+ # Get the error.
+ param_err_val = deepcopy(getattr(cur_spin,
param_err)[param_key])
+ my_dic[spin_id][param_key][param_err+'MC'] =
param_err_val
+
+ else:
+ # Get the error.
+ param_err_val = deepcopy(getattr(cur_spin,
param_err))
+ my_dic[spin_id][param_key][param_err+'MC'] =
param_err_val
+
+
+ # Loop over parameters to print.
+ for spin_id in spin_id_list:
+ param_key_list = my_dic[spin_id]['param_key_list']
+ for param_key in param_key_list:
+ params_err = my_dic[spin_id]['params_err']
+ # Loop over params.
+ for i, param_err in enumerate(params_err):
+ param_err_val = my_dic[spin_id][param_key][param_err]
+ param_err_val_mc =
my_dic[spin_id][param_key][param_err+'MC']
+ print("param: %s, with err: %3.8f, compared to MC:
%3.8f" % (param_err, param_err_val, param_err_val_mc) )
def test_tp02_data_to_ns_r1rho_2site(self, model=None):
r25520 - /branches/est_par_error/test_suite/system_tests/relax_disp.py