Author: tlinnet
Date: Thu Sep 11 21:31:38 2014
New Revision: 25755
URL: http://svn.gna.org/viewcvs/relax?rev=25755&view=rev
Log:
Added systemtest Relax_fit.test_curve_fitting_height_estimate_error() for the
manual and automated analysis of exponential fit.
This is to prepare for new methods in the auto analysis protocol.
Modified:
trunk/test_suite/system_tests/relax_fit.py
Modified: trunk/test_suite/system_tests/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_fit.py?rev=25755&r1=25754&r2=25755&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_fit.py (original)
+++ trunk/test_suite/system_tests/relax_fit.py Thu Sep 11 21:31:38 2014
@@ -25,9 +25,10 @@
from tempfile import mkdtemp
# relax module imports.
+from auto_analyses import relax_fit
from data_store import Relax_data_store; ds = Relax_data_store()
import dep_check
-from pipe_control.mol_res_spin import return_spin, spin_index_loop, spin_loop
+from pipe_control.mol_res_spin import count_spins, return_spin,
spin_index_loop, spin_loop
from pipe_control import pipes
from lib.errors import RelaxError
from status import Status; status = Status()
@@ -104,6 +105,39 @@
break
+ def check_curve_fitting_manual(self):
+ """Check the results of the curve-fitting."""
+
+ # Data.
+ relax_times = [0.0176, 0.0176, 0.0352, 0.0704, 0.0704, 0.1056,
0.1584, 0.1584, 0.1936, 0.1936]
+ chi2 = [2.916952651567855, 5.4916923952919632, 16.21182245065274,
4.3591263759462926, 9.8925377583244316, 6.0238341559877782]
+ rx = [8.0814894819820662, 8.6478971039559642, 9.5710638183013845,
10.716551838066295, 11.143793935455122, 12.82875370075309]
+ i0 = [1996050.9679875025, 2068490.9458927638, 1611556.5194095275,
1362887.2331948928, 1877670.5623875158, 897044.17382064369]
+
+ # Some checks.
+ self.assertEqual(cdp.curve_type, 'exp')
+ self.assertEqual(cdp.int_method, ds.int_type)
+ self.assertEqual(len(cdp.relax_times), 10)
+ cdp_relax_times = sorted(cdp.relax_times.values())
+ for i in range(10):
+ self.assertEqual(cdp_relax_times[i], relax_times[i])
+
+ # Check the errors.
+ for key in cdp.sigma_I:
+ self.assertAlmostEqual(cdp.sigma_I[key], 10578.039482421433, 6)
+ self.assertAlmostEqual(cdp.var_I[key], 111894919.29166669)
+
+ # Spin data check.
+ i = 0
+ for spin in spin_loop(skip_desel=True):
+ self.assertAlmostEqual(spin.chi2, chi2[i])
+ self.assertAlmostEqual(spin.rx, rx[i])
+ self.assertAlmostEqual(spin.i0/1e6, i0[i]/1e6)
+
+ # Increment the spin index.
+ i = i + 1
+
+
def test_bug_12670_12679(self):
"""Test the relaxation curve fitting, replicating U{bug
#12670<https://gna.org/bugs/?12670>} and U{bug
#12679<https://gna.org/bugs/?12679>}."""
@@ -180,6 +214,175 @@
# Check the curve-fitting results.
self.check_curve_fitting()
+
+
+ def test_curve_fitting_height_estimate_error(self):
+ """Test the relaxation curve fitting C modules and estimate error."""
+
+ # Reset
+ self.interpreter.reset()
+
+ # Create pipe.
+ pipe_name = 'base pipe'
+ pipe_bundle = 'relax_fit'
+ self.interpreter.pipe.create(pipe_name=pipe_name,
bundle=pipe_bundle, pipe_type='relax_fit')
+
+ # The intensity type.
+ ds.int_type = 'height'
+
+ # Create the data pipe and load the base data.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting'
+
+ # Create the spins
+ self.interpreter.spectrum.read_spins(file="T2_ncyc1_ave.list",
dir=data_path)
+
+ # Relaxation times (in seconds).
+ times = [
+ 0.0176,
+ 0.0176,
+ 0.0352,
+ 0.0704,
+ 0.0704,
+ 0.1056,
+ 0.1584,
+ 0.1584,
+ 0.1936,
+ 0.1936
+ ]
+
+ # Spectrum names.
+ names = [
+ 'T2_ncyc1_ave',
+ 'T2_ncyc1b_ave',
+ 'T2_ncyc2_ave',
+ 'T2_ncyc4_ave',
+ 'T2_ncyc4b_ave',
+ 'T2_ncyc6_ave',
+ 'T2_ncyc9_ave',
+ 'T2_ncyc9b_ave',
+ 'T2_ncyc11_ave',
+ 'T2_ncyc11b_ave'
+ ]
+
+
+ # Loop over Spectrum names.
+ for i, sname in enumerate(names):
+ # Get the time.
+ time = times[i]
+
+ # Load the peak intensities.
+ self.interpreter.spectrum.read_intensities(file=sname+'.list',
dir=data_path, spectrum_id=sname, int_method=ds.int_type)
+
+ # Set the relaxation times.
+ self.interpreter.relax_fit.relax_time(time=time,
spectrum_id=sname)
+
+ # Collect all times, and matching spectrum id.
+ all_times = []
+ all_id = []
+ for s_id, time in cdp.relax_times.iteritems():
+ all_times.append(time)
+ all_id.append(s_id)
+
+ # Get the dublicates.
+ dublicates = map(lambda val: (val, [i for i in
xrange(len(all_times)) if all_times[i] == val]), all_times)
+
+ # Loop over the list of the mapping of times and duplications.
+ list_dub_mapping = []
+ for i, dub in enumerate(dublicates):
+ # Get current spectum id.
+ cur_spectrum_id = all_id[i]
+
+ # Get the tuple of time and indexes of duplications.
+ time, list_index_occur = dub
+
+ # Collect mapping of index to id.
+ id_list = []
+ if len(list_index_occur) > 1:
+ for list_index in list_index_occur:
+ id_list.append(all_id[list_index])
+
+ # Store to list
+ list_dub_mapping.append((cur_spectrum_id, id_list))
+
+ # Assign dublicates.
+ for spectrum_id, dub_pair in list_dub_mapping:
+ print spectrum_id, dub_pair
+ if len(dub_pair) > 0:
+ self.interpreter.spectrum.replicated(spectrum_ids=dub_pair)
+
+ # Test the number of replicates stored in cdp, is 4.
+ self.assertEqual(len(cdp.replicates), 4)
+
+ # Cannot test, since dictionary have no order.
+ #test_rep = [['T2_ncyc1_ave', 'T2_ncyc1b_ave'],
+ # ['T2_ncyc4_ave', 'T2_ncyc4b_ave'],
+ # ['T2_ncyc9b_ave', 'T2_ncyc9_ave'],
+ # ['T2_ncyc11_ave', 'T2_ncyc11b_ave']]
+
+ #for i, rep in enumerate(cdp.replicates):
+ # test_rep_i = test_rep[i]
+ # print(rep, test_rep_i)
+ # self.assertEqual(rep, test_rep_i)
+
+
self.interpreter.deselect.spin(':3,11,18,19,23,31,42,44,54,66,82,92,94,99,101,113,124,126,136,141,145,147,332,345,346,358,361')
+
+ GRID_INC = 11
+ MC_SIM = 3
+ results_dir = mkdtemp()
+ #min_method = 'simplex'
+ #min_method = 'BFGS'
+ min_method = 'newton'
+
+ # De select one more.
+ self.interpreter.deselect.spin(':512@ND2')
+
+ # Do automatic
+ if False:
+ relax_fit.Relax_fit(pipe_name=pipe_name,
pipe_bundle=pipe_bundle, file_root='R2', results_dir=results_dir,
grid_inc=GRID_INC, mc_sim_num=MC_SIM, view_plots=False)
+
+ else:
+ # Peak intensity error analysis.
+ self.interpreter.spectrum.error_analysis()
+
+ # Set the relaxation curve type.
+ self.interpreter.relax_fit.select_model('exp')
+
+ # Grid search.
+ self.interpreter.minimise.grid_search(inc=GRID_INC)
+
+ # Minimise.
+ self.interpreter.minimise.execute(min_method, scaling=False,
constraints=False)
+
+ # Monte Carlo simulations.
+ self.interpreter.monte_carlo.setup(number=MC_SIM)
+ self.interpreter.monte_carlo.create_data()
+ self.interpreter.monte_carlo.initial_values()
+ self.interpreter.minimise.execute(min_method, scaling=False,
constraints=False)
+ self.interpreter.monte_carlo.error_analysis()
+
+ # Test seq
+ tseq = [ [4, 'GLY', ':4@N'],
+ [5, 'SER', ':5@N'],
+ [6, 'MET', ':6@N'],
+ [7, 'ASP', ':7@N'],
+ [8, 'SER', ':8@N'],
+ [12, 'GLY', ':12@N']]
+
+ # Print spins
+ i = 0
+ for cur_spin, mol_name, resi, resn, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=True):
+ print(resi, resn, spin_id)
+ self.assertEqual(resi, tseq[i][0])
+ self.assertEqual(resn, tseq[i][1])
+ self.assertEqual(spin_id, tseq[i][2])
+
+ i += 1
+
+ # Test the number of spins.
+ self.assertEqual(count_spins(), 6)
+
+ # Check the curve-fitting results.
+ self.check_curve_fitting_manual()
def test_curve_fitting_volume(self):
r25755 - /trunk/test_suite/system_tests/relax_fit.py