r22295 - in /trunk/specific_analyses/relax_disp: disp_data.py optimisation.py parameters.py
Author: bugman Date: Tue Feb 25 09:13:32 2014 New Revision: 22295 URL: http://svn.gna.org/viewcvs/relax?rev=22295view=rev Log: Complete support for deselected spins has been added to the relaxation dispersion analysis. This fixes bug #21715 (https://gna.org/bugs/?21715), the failure of the relaxation dispersion auto-analysis when running a clustered analysis due to an IndexError during minimisation. Modified: trunk/specific_analyses/relax_disp/disp_data.py trunk/specific_analyses/relax_disp/optimisation.py trunk/specific_analyses/relax_disp/parameters.py Modified: trunk/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=22295r1=22294r2=22295view=diff == --- trunk/specific_analyses/relax_disp/disp_data.py (original) +++ trunk/specific_analyses/relax_disp/disp_data.py Tue Feb 25 09:13:32 2014 @@ -214,6 +214,19 @@ # Return the count. return count + + +def count_spins(spins=None): +Count the number of selected spins in the spin cluster. + +# Count the selected spins. +spin_num = 0 +for spin in spins: +if spin.select: +spin_num += 1 + +# Return the count. +return spin_num def cpmg_frq(spectrum_id=None, cpmg_frq=None): @@ -2698,7 +2711,10 @@ # The counts. exp_num = num_exp_types() -spin_num = len(spins) +spin_num = 0 +for spin in spins: +if spin.select: +spin_num += 1 # Initialise the data structures for the target function. fields_orig = fields @@ -2723,10 +2739,15 @@ # Assemble the data. data_flag = False -for si in range(spin_num): +si = 0 +for spin_index in range(len(spins)): +# Skip deselected spins. +if not spins[spin_index].select: +continue + # Alias the spin. -spin = spins[si] -spin_id = spin_ids[si] +spin = spins[spin_index] +spin_id = spin_ids[spin_index] # No data. shift = 0.0 @@ -2809,6 +2830,9 @@ else: theta[ei][si][mi][oi].append(atan(omega1 / Delta_omega)) +# Increment the spin index. +si += 1 + # No shift data for the spin cluster. if not data_flag: return None, None, None @@ -2874,7 +2898,7 @@ # The spin count. -spin_num = len(spins) +spin_num = count_spins(spins) # Initialise the data structure. r1 = -ones((spin_num, field_count), float64) @@ -2949,7 +2973,7 @@ # The counts. exp_num = num_exp_types() -spin_num = len(spins) +spin_num = count_spins(spins) # 1H MMQ flag. proton_mmq_flag = has_proton_mmq_cpmg() @@ -2990,10 +3014,15 @@ # Pack the R2eff/R1rho data. data_flag = False -for si in range(spin_num): +si = 0 +for spin_index in range(len(spins)): +# Skip deselected spins. +if not spins[spin_index].select: +continue + # Alias the spin. -spin = spins[si] -spin_id = spin_ids[si] +spin = spins[spin_index] +spin_id = spin_ids[spin_index] # Get the attached proton. proton = None @@ -3089,6 +3118,9 @@ # Store the time. relax_times[ei][mi] = relax_time + +# Increment the spin index. +si += 1 # No R2eff/R1rho data for the spin cluster. if not data_flag: Modified: trunk/specific_analyses/relax_disp/optimisation.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/optimisation.py?rev=22295r1=22294r2=22295view=diff == --- trunk/specific_analyses/relax_disp/optimisation.py (original) +++ trunk/specific_analyses/relax_disp/optimisation.py Tue Feb 25 09:13:32 2014 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2013 Edward d'Auvergne# +# Copyright (C) 2013-2014 Edward d'Auvergne # # # # This file is part of the program relax (http://www.nmr-relax.com). # # # @@ -35,7 +35,7 @@ from lib.errors import RelaxError from lib.text.sectioning import subsection from multi import Memo, Result_command, Slave_command -from specific_analyses.relax_disp.disp_data import has_disp_data, has_proton_mmq_cpmg, loop_exp, loop_exp_frq, loop_exp_frq_offset_point, loop_frq, loop_offset, pack_back_calc_r2eff, return_cpmg_frqs, return_index_from_disp_point, return_index_from_exp_type, return_index_from_frq, return_offset_data,
r22296 - in /branches/double_rotor: ./ test_suite/shared_data/dispersion/bug_21715_clustered_indexerror/ test_suite/system_t...
Author: bugman
Date: Tue Feb 25 09:20:26 2014
New Revision: 22296
URL: http://svn.gna.org/viewcvs/relax?rev=22296view=rev
Log:
Merged revisions 22289 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r22289 | bugman | 2014-02-24 16:33:08 +0100 (Mon, 24 Feb 2014) | 6 lines
Created the Relax_disp.test_bug_21715_clustered_indexerror system test.
This is to catch bug #21715 (https://gna.org/bugs/?21715), the failure of the
relaxation dispersion
auto-analysis when running a clustered analysis due to an IndexError during
minimisation.
Added:
branches/double_rotor/test_suite/shared_data/dispersion/bug_21715_clustered_indexerror/
- copied from r22289,
trunk/test_suite/shared_data/dispersion/bug_21715_clustered_indexerror/
Modified:
branches/double_rotor/ (props changed)
branches/double_rotor/test_suite/system_tests/relax_disp.py
Propchange: branches/double_rotor/
--
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Feb 25 09:20:26 2014
@@ -1,1 +1,1 @@
-/trunk:1-22288
+/trunk:1-22289
Modified: branches/double_rotor/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/test_suite/system_tests/relax_disp.py?rev=22296r1=22295r2=22296view=diff
==
--- branches/double_rotor/test_suite/system_tests/relax_disp.py (original)
+++ branches/double_rotor/test_suite/system_tests/relax_disp.py Tue Feb 25
09:20:26 2014
@@ -295,6 +295,23 @@
relax_disp.Relax_disp.opt_func_tol = 1e-5
relax_disp.Relax_disp.opt_max_iterations = 1000
relax_disp.Relax_disp(pipe_name=compare_128_FT_R2eff,
pipe_bundle=cpmg_disp_sod1d90a, results_dir=self.tmpdir, models=['R2eff'],
grid_inc=3, mc_sim_num=5, modsel='AIC', pre_run_dir=None, insignificance=1.0,
numeric_only=False, mc_sim_all_models=False, eliminate=True)
+
+
+def test_bug_21715_clustered_indexerror(self):
+Catch U{bug #21715https://gna.org/bugs/?21715}, the failure of a
clustered auto-analysis due to an IndexError.
+
+# Clear the data store.
+self.interpreter.reset()
+
+# Load the state.
+state = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21715_clustered_indexerror'+sep+'state.bz2'
+self.interpreter.state.load(state, force=True)
+
+# Execute the auto-analysis (fast).
+pre_run_dir = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21715_clustered_indexerror'+sep+'non_clustered'
+relax_disp.Relax_disp.opt_func_tol = 1e-5
+relax_disp.Relax_disp.opt_max_iterations = 1000
+relax_disp.Relax_disp(pipe_name='origin - relax_disp (Sun Feb 23
19:36:51 2014)', pipe_bundle='relax_disp (Sun Feb 23 19:36:51 2014)',
results_dir=self.tmpdir, models=['R2eff', 'No Rex'], grid_inc=11, mc_sim_num=2,
modsel='AIC', pre_run_dir=pre_run_dir, insignificance=1.0, numeric_only=True,
mc_sim_all_models=False, eliminate=True)
def test_curve_type_cpmg_fixed_time(self):
___
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r22297 - in /branches/double_rotor: ./ specific_analyses/relax_disp/ test_suite/unit_tests/_specific_analyses/_relax_disp/
Author: bugman Date: Tue Feb 25 09:22:19 2014 New Revision: 22297 URL: http://svn.gna.org/viewcvs/relax?rev=22297view=rev Log: Merged revisions 22291-22294 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r22291 | tlinnet | 2014-02-24 17:06:33 +0100 (Mon, 24 Feb 2014) | 5 lines Modified unit test to pass. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. Implemented as suggested in: https://mail.gna.org/public/relax-devel/2014-02/msg00142.html r22292 | tlinnet | 2014-02-24 17:06:35 +0100 (Mon, 24 Feb 2014) | 5 lines Expanded the loop_time function to optional take the offset and dispersion point as input for restricting looping. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. This is implemented as suggested in: https://mail.gna.org/public/relax-devel/2014-02/msg00143.html r22293 | tlinnet | 2014-02-24 17:06:36 +0100 (Mon, 24 Feb 2014) | 5 lines Added system test for loop_time. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. This system can be extended later for purposes to test the restriction of the looping. r22294 | tlinnet | 2014-02-24 18:28:11 +0100 (Mon, 24 Feb 2014) | 5 lines Replacing looping over time points from cdp.relax_time_list to loop_time(frq=frq). Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. loop_time has been modified to accept spectrometer frequency as input to restrict the looping. Modified: branches/double_rotor/ (props changed) branches/double_rotor/specific_analyses/relax_disp/api.py branches/double_rotor/specific_analyses/relax_disp/disp_data.py branches/double_rotor/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py Propchange: branches/double_rotor/ -- --- svnmerge-integrated (original) +++ svnmerge-integrated Tue Feb 25 09:22:19 2014 @@ -1,1 +1,1 @@ -/trunk:1-22289 +/trunk:1-22294 Modified: branches/double_rotor/specific_analyses/relax_disp/api.py URL: http://svn.gna.org/viewcvs/relax/branches/double_rotor/specific_analyses/relax_disp/api.py?rev=22297r1=22296r2=22297view=diff == --- branches/double_rotor/specific_analyses/relax_disp/api.py (original) +++ branches/double_rotor/specific_analyses/relax_disp/api.py Tue Feb 25 09:22:19 2014 @@ -149,7 +149,7 @@ values = [] errors = [] times = [] -for time in cdp.relax_time_list: +for time in loop_time(frq=frq): # The data. values.append(average_intensity(spin=spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time)) errors.append(average_intensity(spin=spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, error=True)) @@ -378,7 +378,7 @@ values = [] errors = [] times = [] -for time in cdp.relax_time_list: +for time in loop_time(frq=frq): values.append(average_intensity(spin=spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, sim_index=sim_index)) errors.append(average_intensity(spin=spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, error=True)) times.append(time) @@ -1373,7 +1373,7 @@ # Generate the data structure to return. errors = [] -for time in cdp.relax_time_list: +for time in loop_time(frq=frq): errors.append(average_intensity(spin=spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, error=True)) # All other models. @@ -1597,7 +1597,7 @@ # Loop over each time point. ti = 0 -for time in loop_time(): +for time in loop_time(frq=frq): # Get the intensity keys. int_keys = find_intensity_keys(exp_type=exp_type, frq=frq, point=point, time=time) Modified: branches/double_rotor/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/branches/double_rotor/specific_analyses/relax_disp/disp_data.py?rev=22297r1=22296r2=22297view=diff == --- branches/double_rotor/specific_analyses/relax_disp/disp_data.py (original) +++ branches/double_rotor/specific_analyses/relax_disp/disp_data.py Tue Feb 25 09:22:19 2014 @@ -1281,13 +1281,17 @@ yield id -def loop_time(exp_type=None, frq=None, return_indices=False): +def loop_time(exp_type=None, frq=None,
r22298 - in /branches/double_rotor: ./ specific_analyses/relax_disp/
Author: bugman Date: Tue Feb 25 09:23:31 2014 New Revision: 22298 URL: http://svn.gna.org/viewcvs/relax?rev=22298view=rev Log: Merged revisions 22295 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r22295 | bugman | 2014-02-25 09:13:32 +0100 (Tue, 25 Feb 2014) | 6 lines Complete support for deselected spins has been added to the relaxation dispersion analysis. This fixes bug #21715 (https://gna.org/bugs/?21715), the failure of the relaxation dispersion auto-analysis when running a clustered analysis due to an IndexError during minimisation. Modified: branches/double_rotor/ (props changed) branches/double_rotor/specific_analyses/relax_disp/disp_data.py branches/double_rotor/specific_analyses/relax_disp/optimisation.py branches/double_rotor/specific_analyses/relax_disp/parameters.py Propchange: branches/double_rotor/ -- --- svnmerge-integrated (original) +++ svnmerge-integrated Tue Feb 25 09:23:31 2014 @@ -1,1 +1,1 @@ -/trunk:1-22294 +/trunk:1-22297 Modified: branches/double_rotor/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/branches/double_rotor/specific_analyses/relax_disp/disp_data.py?rev=22298r1=22297r2=22298view=diff == --- branches/double_rotor/specific_analyses/relax_disp/disp_data.py (original) +++ branches/double_rotor/specific_analyses/relax_disp/disp_data.py Tue Feb 25 09:23:31 2014 @@ -214,6 +214,19 @@ # Return the count. return count + + +def count_spins(spins=None): +Count the number of selected spins in the spin cluster. + +# Count the selected spins. +spin_num = 0 +for spin in spins: +if spin.select: +spin_num += 1 + +# Return the count. +return spin_num def cpmg_frq(spectrum_id=None, cpmg_frq=None): @@ -2698,7 +2711,10 @@ # The counts. exp_num = num_exp_types() -spin_num = len(spins) +spin_num = 0 +for spin in spins: +if spin.select: +spin_num += 1 # Initialise the data structures for the target function. fields_orig = fields @@ -2723,10 +2739,15 @@ # Assemble the data. data_flag = False -for si in range(spin_num): +si = 0 +for spin_index in range(len(spins)): +# Skip deselected spins. +if not spins[spin_index].select: +continue + # Alias the spin. -spin = spins[si] -spin_id = spin_ids[si] +spin = spins[spin_index] +spin_id = spin_ids[spin_index] # No data. shift = 0.0 @@ -2809,6 +2830,9 @@ else: theta[ei][si][mi][oi].append(atan(omega1 / Delta_omega)) +# Increment the spin index. +si += 1 + # No shift data for the spin cluster. if not data_flag: return None, None, None @@ -2874,7 +2898,7 @@ # The spin count. -spin_num = len(spins) +spin_num = count_spins(spins) # Initialise the data structure. r1 = -ones((spin_num, field_count), float64) @@ -2949,7 +2973,7 @@ # The counts. exp_num = num_exp_types() -spin_num = len(spins) +spin_num = count_spins(spins) # 1H MMQ flag. proton_mmq_flag = has_proton_mmq_cpmg() @@ -2990,10 +3014,15 @@ # Pack the R2eff/R1rho data. data_flag = False -for si in range(spin_num): +si = 0 +for spin_index in range(len(spins)): +# Skip deselected spins. +if not spins[spin_index].select: +continue + # Alias the spin. -spin = spins[si] -spin_id = spin_ids[si] +spin = spins[spin_index] +spin_id = spin_ids[spin_index] # Get the attached proton. proton = None @@ -3089,6 +3118,9 @@ # Store the time. relax_times[ei][mi] = relax_time + +# Increment the spin index. +si += 1 # No R2eff/R1rho data for the spin cluster. if not data_flag: Modified: branches/double_rotor/specific_analyses/relax_disp/optimisation.py URL: http://svn.gna.org/viewcvs/relax/branches/double_rotor/specific_analyses/relax_disp/optimisation.py?rev=22298r1=22297r2=22298view=diff == --- branches/double_rotor/specific_analyses/relax_disp/optimisation.py (original) +++ branches/double_rotor/specific_analyses/relax_disp/optimisation.py Tue Feb 25 09:23:31 2014 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2013 Edward d'Auvergne# +# Copyright (C) 2013-2014 Edward d'Auvergne # #
r22299 - /trunk/test_suite/system_tests/relax_disp.py
Author: bugman Date: Tue Feb 25 09:25:39 2014 New Revision: 22299 URL: http://svn.gna.org/viewcvs/relax?rev=22299view=rev Log: Fix for bug #21695 (https://gna.org/bugs/?21695). This is the failure of the relaxation dispersion system tests on a 64-bit MS Windows system due to lower precision of the platform. Two of the errors have already been found on a 64-bit Windows Vista virtual machine and fixed. The last test should now also pass. Modified: trunk/test_suite/system_tests/relax_disp.py Modified: trunk/test_suite/system_tests/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=22299r1=22298r2=22299view=diff == --- trunk/test_suite/system_tests/relax_disp.py (original) +++ trunk/test_suite/system_tests/relax_disp.py Tue Feb 25 09:25:39 2014 @@ -1787,12 +1787,12 @@ print(%-20s %20.15g\n % (chi2, spin.chi2)) # Checks for residue :9. -self.assertAlmostEqual(spin.r2[r20_key1], 8.334232330326190, 4) -self.assertAlmostEqual(spin.r2[r20_key2], 8.756773997879968, 4) -self.assertAlmostEqual(spin.r2[r20_key3], 10.219320492033058, 4) -self.assertAlmostEqual(spin.pA, 0.950310172115387, 4) -self.assertAlmostEqual(spin.dw, 4.356737157889636, 4) -self.assertAlmostEqual(spin.kex/1000, 433.176323890829849/1000, 4) +self.assertAlmostEqual(spin.r2[r20_key1], 8.334232330326190, 2) +self.assertAlmostEqual(spin.r2[r20_key2], 8.756773997879968, 2) +self.assertAlmostEqual(spin.r2[r20_key3], 10.219320492033058, 1) +self.assertAlmostEqual(spin.pA, 0.950310172115387, 3) +self.assertAlmostEqual(spin.dw, 4.356737157889636, 3) +self.assertAlmostEqual(spin.kex/1000, 433.176323890829849/1000, 3) self.assertAlmostEqual(spin.chi2, 17.37460582872912, 1) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r22300 - in /branches/double_rotor: ./ test_suite/system_tests/relax_disp.py
Author: bugman Date: Tue Feb 25 09:28:32 2014 New Revision: 22300 URL: http://svn.gna.org/viewcvs/relax?rev=22300view=rev Log: Merged revisions 22299 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r22299 | bugman | 2014-02-25 09:25:39 +0100 (Tue, 25 Feb 2014) | 7 lines Fix for bug #21695 (https://gna.org/bugs/?21695). This is the failure of the relaxation dispersion system tests on a 64-bit MS Windows system due to lower precision of the platform. Two of the errors have already been found on a 64-bit Windows Vista virtual machine and fixed. The last test should now also pass. Modified: branches/double_rotor/ (props changed) branches/double_rotor/test_suite/system_tests/relax_disp.py Propchange: branches/double_rotor/ -- --- svnmerge-integrated (original) +++ svnmerge-integrated Tue Feb 25 09:28:32 2014 @@ -1,1 +1,1 @@ -/trunk:1-22297 +/trunk:1-22299 Modified: branches/double_rotor/test_suite/system_tests/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/branches/double_rotor/test_suite/system_tests/relax_disp.py?rev=22300r1=22299r2=22300view=diff == --- branches/double_rotor/test_suite/system_tests/relax_disp.py (original) +++ branches/double_rotor/test_suite/system_tests/relax_disp.py Tue Feb 25 09:28:32 2014 @@ -1787,12 +1787,12 @@ print(%-20s %20.15g\n % (chi2, spin.chi2)) # Checks for residue :9. -self.assertAlmostEqual(spin.r2[r20_key1], 8.334232330326190, 4) -self.assertAlmostEqual(spin.r2[r20_key2], 8.756773997879968, 4) -self.assertAlmostEqual(spin.r2[r20_key3], 10.219320492033058, 4) -self.assertAlmostEqual(spin.pA, 0.950310172115387, 4) -self.assertAlmostEqual(spin.dw, 4.356737157889636, 4) -self.assertAlmostEqual(spin.kex/1000, 433.176323890829849/1000, 4) +self.assertAlmostEqual(spin.r2[r20_key1], 8.334232330326190, 2) +self.assertAlmostEqual(spin.r2[r20_key2], 8.756773997879968, 2) +self.assertAlmostEqual(spin.r2[r20_key3], 10.219320492033058, 1) +self.assertAlmostEqual(spin.pA, 0.950310172115387, 3) +self.assertAlmostEqual(spin.dw, 4.356737157889636, 3) +self.assertAlmostEqual(spin.kex/1000, 433.176323890829849/1000, 3) self.assertAlmostEqual(spin.chi2, 17.37460582872912, 1) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r22308 - /trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Author: tlinnet Date: Tue Feb 25 15:05:03 2014 New Revision: 22308 URL: http://svn.gna.org/viewcvs/relax?rev=22308view=rev Log: Re-ordered unit tests for test of get_curve_type() and has_exponential_exp_type(). Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. Modified: trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py Modified: trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py?rev=22308r1=22307r2=22308view=diff == --- trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py (original) +++ trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py Tue Feb 25 15:05:03 2014 @@ -88,15 +88,15 @@ print(times[exp_type]) self.assertEqual(len(times[exp_type]), 2) +# Check the return of get_curve_type function. +curve_type = get_curve_type() +print(curve_type) +self.assertEqual(curve_type, 'fixed time') + # Check the return of has_exponential_exp_type. exponential_exp_type = has_exponential_exp_type() print(exponential_exp_type) self.assertEqual(exponential_exp_type, False) - -# Check the return of get_curve_type function. -curve_type = get_curve_type() -print(curve_type) -self.assertEqual(curve_type, 'fixed time') def test_loop_exp_frq(self): ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r22305 - /trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Author: tlinnet Date: Tue Feb 25 15:04:56 2014 New Revision: 22305 URL: http://svn.gna.org/viewcvs/relax?rev=22305view=rev Log: Added test for return of get_curve_type(), to match 'fixed time'. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. Modified: trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py Modified: trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py?rev=22305r1=22304r2=22305view=diff == --- trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py (original) +++ trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py Tue Feb 25 15:04:56 2014 @@ -25,7 +25,7 @@ # relax module imports. from data_store import Relax_data_store; ds = Relax_data_store() from pipe_control import state -from specific_analyses.relax_disp.disp_data import count_relax_times, loop_exp_frq, loop_exp_frq_offset, loop_exp_frq_offset_point, loop_exp_frq_offset_point_time, loop_time +from specific_analyses.relax_disp.disp_data import count_relax_times, get_curve_type, loop_exp_frq, loop_exp_frq_offset, loop_exp_frq_offset_point, loop_exp_frq_offset_point_time, loop_time from status import Status; status = Status() from test_suite.unit_tests.base_classes import UnitTestCase @@ -80,6 +80,11 @@ self.assertEqual(frq, data[1][1]) # Test the time count self.assertEqual(count, 1) + +# Check the return of get_curve_type function. +curve_type = get_curve_type() +print(curve_type) +self.assertEqual(curve_type, 'fixed time') def test_loop_exp_frq(self): ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r22302 - /trunk/specific_analyses/relax_disp/disp_data.py
Author: tlinnet Date: Tue Feb 25 15:04:51 2014 New Revision: 22302 URL: http://svn.gna.org/viewcvs/relax?rev=22302view=rev Log: Made count_relax_times() take optional arguments as: exp_type, frq, offset, point. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. This is prepare for re-stricting the looping over time points in the function: loop_time() This is implemented as suggested in: http://www.mail-archive.com/relax-devel@gna.org/msg04993.html Modified: trunk/specific_analyses/relax_disp/disp_data.py Modified: trunk/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=22302r1=22301r2=22302view=diff == --- trunk/specific_analyses/relax_disp/disp_data.py (original) +++ trunk/specific_analyses/relax_disp/disp_data.py Tue Feb 25 15:04:51 2014 @@ -182,18 +182,26 @@ return cdp.spectrometer_frq_count -def count_relax_times(ei=None): +def count_relax_times(exp_type=None, frq=None, offset=None, point=None, ei=None): Count the number of relaxation times present. -@keyword ei:The experiment type index. -@type ei: str -@return:The relaxation time count for the given experiment. -@rtype: int +@keyword exp_type: The experiment type. +@type exp_type: str +@keyword frq: The spectrometer frequency in Hz. +@type frq: float +@keyword offset:The spin-lock or hard pulse offset value in ppm. +@type offset: None or float +@keyword point: The dispersion point data (either the spin-lock field strength in Hz or the nu_CPMG frequency in Hz). +@type point:float +@keyword ei:The experiment type index. +@type ei: str +@return:The relaxation time count for the given experiment. +@rtype: int # Loop over the times. count = 0 -for time in loop_time(): +for time in loop_time(exp_type=exp_type, frq=frq, offset=offset, point=point): # Find a matching experiment ID. found = False for id in cdp.exp_type.keys(): @@ -402,7 +410,7 @@ else: # Determine the curve type. curve_type = 'exponential' -if count_relax_times(cdp.exp_type_list.index(cdp.exp_type[id])) == 1: +if count_relax_times(ei = cdp.exp_type_list.index(cdp.exp_type[id])) == 1: curve_type = 'fixed time' # Return the type. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r22303 - /trunk/specific_analyses/relax_disp/disp_data.py
Author: tlinnet Date: Tue Feb 25 15:04:53 2014 New Revision: 22303 URL: http://svn.gna.org/viewcvs/relax?rev=22303view=rev Log: Modified to pass exp_typ, frq, offset or point to loop_time() where such information is available. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. Modified: trunk/specific_analyses/relax_disp/disp_data.py Modified: trunk/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=22303r1=22302r2=22303view=diff == --- trunk/specific_analyses/relax_disp/disp_data.py (original) +++ trunk/specific_analyses/relax_disp/disp_data.py Tue Feb 25 15:04:53 2014 @@ -894,7 +894,7 @@ # Then the dispersion points. for point, di in loop_point(exp_type=exp_type, frq=frq, offset=offset, return_indices=True): # Finally the relaxation times. -for time, ti in loop_time(frq=frq, return_indices=True): +for time, ti in loop_time(exp_type=exp_type, frq=frq, offset=offset, point=point, return_indices=True): # Yield the data. if return_indices: yield exp_type, frq, offset, point, time, ei, mi, oi, di, ti @@ -946,7 +946,7 @@ # Then the dispersion points. for point, di in loop_point(exp_type=exp_type, frq=frq, offset=0.0, return_indices=True): # Finally the relaxation times. -for time, ti in loop_time(return_indices=True): +for time, ti in loop_time(exp_type=exp_type, frq=frq, point=point, return_indices=True): # Yield all data. if return_indices: yield exp_type, frq, point, time, ei, mi, di, ti @@ -1062,7 +1062,7 @@ # Then the dispersion points. for point, di in loop_point(exp_type=exp_type, frq=frq, offset=0.0, return_indices=True): # Finally the relaxation times. -for time, ti in loop_time(return_indices=True): +for time, ti in loop_time(exp_type=exp_type, frq=frq, point=point, return_indices=True): # Yield all data. if return_indices: yield frq, point, time, mi, di, ti ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r22304 - /trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Author: tlinnet
Date: Tue Feb 25 15:04:55 2014
New Revision: 22304
URL: http://svn.gna.org/viewcvs/relax?rev=22304view=rev
Log:
Added unit test for count_relax_times.
Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis
with two fields at two delay times.
This follows the suggestion in:
http://www.mail-archive.com/relax-devel@gna.org/msg04993.html.
Modified:
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Modified:
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py?rev=22304r1=22303r2=22304view=diff
==
---
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
(original)
+++
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Tue Feb 25 15:04:55 2014
@@ -25,7 +25,7 @@
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
from pipe_control import state
-from specific_analyses.relax_disp.disp_data import loop_exp_frq,
loop_exp_frq_offset, loop_exp_frq_offset_point, loop_exp_frq_offset_point_time,
loop_time
+from specific_analyses.relax_disp.disp_data import count_relax_times,
loop_exp_frq, loop_exp_frq_offset, loop_exp_frq_offset_point,
loop_exp_frq_offset_point_time, loop_time
from status import Status; status = Status()
from test_suite.unit_tests.base_classes import UnitTestCase
@@ -38,6 +38,48 @@
# Create a dispersion data pipe.
ds.add(pipe_name='orig', pipe_type='relax_disp')
+
+
+def test_count_relax_times(self):
+Unit test of the count_relax_times() function.
+
+This uses the data of the saved state attached to U{bug
#21665https://gna.org/bugs/?21665}.
+
+
+# Load the state.
+statefile = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21665.bz2'
+state.load_state(statefile, force=True)
+
+# Original data (exp_type, frq).
+data = [
+['SQ CPMG', 499862140.0],
+['SQ CPMG', 599890858.6993]
+]
+
+# Original indices (ei, mi).
+indices = [
+[0, 0],
+[0, 1]
+]
+
+# Check the number of time counts.
+print(Checking the number of time counts.)
+for id in cdp.exp_type.keys():
+exp_type = cdp.exp_type[id]
+frq = cdp.spectrometer_frq[id]
+point = cdp.cpmg_frqs[id]
+count = count_relax_times(exp_type = exp_type, frq = frq, point =
point, ei = cdp.exp_type_list.index(cdp.exp_type[id]))
+print(id, exp_type, frq, point, count)
+
+# Test the data
+if id.split('A')[0] == 'Z_':
+self.assertEqual(exp_type, data[0][0])
+self.assertEqual(frq, data[0][1])
+elif id.split('B')[0] == 'Z_':
+self.assertEqual(exp_type, data[1][0])
+self.assertEqual(frq, data[1][1])
+# Test the time count
+self.assertEqual(count, 1)
def test_loop_exp_frq(self):
___
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r22306 - /trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Author: tlinnet Date: Tue Feb 25 15:04:58 2014 New Revision: 22306 URL: http://svn.gna.org/viewcvs/relax?rev=22306view=rev Log: Added check for return of has_exponential_exp_type to be False. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. Modified: trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py Modified: trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py?rev=22306r1=22305r2=22306view=diff == --- trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py (original) +++ trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py Tue Feb 25 15:04:58 2014 @@ -25,7 +25,7 @@ # relax module imports. from data_store import Relax_data_store; ds = Relax_data_store() from pipe_control import state -from specific_analyses.relax_disp.disp_data import count_relax_times, get_curve_type, loop_exp_frq, loop_exp_frq_offset, loop_exp_frq_offset_point, loop_exp_frq_offset_point_time, loop_time +from specific_analyses.relax_disp.disp_data import count_relax_times, get_curve_type, has_exponential_exp_type, loop_exp_frq, loop_exp_frq_offset, loop_exp_frq_offset_point, loop_exp_frq_offset_point_time, loop_time from status import Status; status = Status() from test_suite.unit_tests.base_classes import UnitTestCase @@ -80,6 +80,11 @@ self.assertEqual(frq, data[1][1]) # Test the time count self.assertEqual(count, 1) + +# Check the return of has_exponential_exp_type. +exponential_exp_type = has_exponential_exp_type() +print(exponential_exp_type) +self.assertEqual(exponential_exp_type, False) # Check the return of get_curve_type function. curve_type = get_curve_type() ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r22307 - /trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Author: tlinnet Date: Tue Feb 25 15:04:59 2014 New Revision: 22307 URL: http://svn.gna.org/viewcvs/relax?rev=22307view=rev Log: Added test for the return of get_times(). Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. Modified: trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py Modified: trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py?rev=22307r1=22306r2=22307view=diff == --- trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py (original) +++ trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py Tue Feb 25 15:04:59 2014 @@ -25,6 +25,7 @@ # relax module imports. from data_store import Relax_data_store; ds = Relax_data_store() from pipe_control import state +from specific_analyses.relax_disp.checks import get_times from specific_analyses.relax_disp.disp_data import count_relax_times, get_curve_type, has_exponential_exp_type, loop_exp_frq, loop_exp_frq_offset, loop_exp_frq_offset_point, loop_exp_frq_offset_point_time, loop_time from status import Status; status = Status() from test_suite.unit_tests.base_classes import UnitTestCase @@ -80,6 +81,12 @@ self.assertEqual(frq, data[1][1]) # Test the time count self.assertEqual(count, 1) + +# Check the return of get_times(). +times = get_times() +for exp_type in times: +print(times[exp_type]) +self.assertEqual(len(times[exp_type]), 2) # Check the return of has_exponential_exp_type. exponential_exp_type = has_exponential_exp_type() ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r22309 - /trunk/specific_analyses/relax_disp/disp_data.py
Author: tlinnet Date: Tue Feb 25 15:05:04 2014 New Revision: 22309 URL: http://svn.gna.org/viewcvs/relax?rev=22309view=rev Log: Added the extraction of exp_type and frq from cdp, to be sent into count_relax_times. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. Modified: trunk/specific_analyses/relax_disp/disp_data.py Modified: trunk/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=22309r1=22308r2=22309view=diff == --- trunk/specific_analyses/relax_disp/disp_data.py (original) +++ trunk/specific_analyses/relax_disp/disp_data.py Tue Feb 25 15:05:04 2014 @@ -410,7 +410,9 @@ else: # Determine the curve type. curve_type = 'exponential' -if count_relax_times(ei = cdp.exp_type_list.index(cdp.exp_type[id])) == 1: +exp_type = cdp.exp_type[id] +frq = cdp.spectrometer_frq[id] +if count_relax_times(exp_type = exp_type, frq = frq, ei = cdp.exp_type_list.index(cdp.exp_type[id])) == 1: curve_type = 'fixed time' # Return the type. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r22310 - /trunk/specific_analyses/relax_disp/checks.py
Author: tlinnet Date: Tue Feb 25 15:05:06 2014 New Revision: 22310 URL: http://svn.gna.org/viewcvs/relax?rev=22310view=rev Log: Modified check_exp_type_fixed_time to loop over id's and use count_relax_times for each id. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. Modified: trunk/specific_analyses/relax_disp/checks.py Modified: trunk/specific_analyses/relax_disp/checks.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/checks.py?rev=22310r1=22309r2=22310view=diff == --- trunk/specific_analyses/relax_disp/checks.py (original) +++ trunk/specific_analyses/relax_disp/checks.py Tue Feb 25 15:05:06 2014 @@ -103,12 +103,13 @@ @raises RelaxError: If exponential curves are present. -# Get the times. -times = get_times() - -# Loop over all experiment types. -for exp_type in times: -if len(times[exp_type]) 1: +# Loop over the id's. +for id in cdp.exp_type.keys(): +# Get the exp_type and frq. +exp_type = cdp.exp_type[id] +frq = cdp.spectrometer_frq[id] + +if specific_analyses.relax_disp.disp_data.count_relax_times(exp_type = exp_type, frq = frq, ei = cdp.exp_type_list.index(cdp.exp_type[id])) 1: raise RelaxError(The experiment '%s' is not of the fixed relaxation time period data type. % exp_type) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r22301 - in /trunk/specific_analyses/relax_disp: api.py disp_data.py
Author: tlinnet Date: Tue Feb 25 15:04:49 2014 New Revision: 22301 URL: http://svn.gna.org/viewcvs/relax?rev=22301view=rev Log: Added exp_type, frq, offset, point to the loop_time() function. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. Implemented as suggested in: http://www.mail-archive.com/relax-devel@gna.org/msg04993.html In all these cases, that information is available, so it should be used. If one are analysing a combination of data types simultaneously (SQ CPMG, DQ CPMG, R1rho), one will not have the same relaxation time for each. For different spin-lock or 180 degree pulse offsets and even different dispersion points, the time may also be different. Modified: trunk/specific_analyses/relax_disp/api.py trunk/specific_analyses/relax_disp/disp_data.py Modified: trunk/specific_analyses/relax_disp/api.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/api.py?rev=22301r1=22300r2=22301view=diff == --- trunk/specific_analyses/relax_disp/api.py (original) +++ trunk/specific_analyses/relax_disp/api.py Tue Feb 25 15:04:49 2014 @@ -149,7 +149,7 @@ values = [] errors = [] times = [] -for time in loop_time(frq=frq): +for time in loop_time(exp_type=exp_type, frq=frq, offset=offset, point=point): # The data. values.append(average_intensity(spin=spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time)) errors.append(average_intensity(spin=spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, error=True)) @@ -378,7 +378,7 @@ values = [] errors = [] times = [] -for time in loop_time(frq=frq): +for time in loop_time(exp_type=exp_type, frq=frq, offset=offset, point=point): values.append(average_intensity(spin=spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, sim_index=sim_index)) errors.append(average_intensity(spin=spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, error=True)) times.append(time) @@ -1373,7 +1373,7 @@ # Generate the data structure to return. errors = [] -for time in loop_time(frq=frq): +for time in loop_time(exp_type=exp_type, frq=frq, offset=offset, point=point): errors.append(average_intensity(spin=spin, exp_type=exp_type, frq=frq, offset=offset, point=point, time=time, error=True)) # All other models. @@ -1597,7 +1597,7 @@ # Loop over each time point. ti = 0 -for time in loop_time(frq=frq): +for time in loop_time(exp_type=exp_type, frq=frq, offset=offset, point=point): # Get the intensity keys. int_keys = find_intensity_keys(exp_type=exp_type, frq=frq, point=point, time=time) Modified: trunk/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=22301r1=22300r2=22301view=diff == --- trunk/specific_analyses/relax_disp/disp_data.py (original) +++ trunk/specific_analyses/relax_disp/disp_data.py Tue Feb 25 15:04:49 2014 @@ -1943,7 +1943,7 @@ set_labels.append(Spin %s % id) # Loop over the relaxation time periods. -for time in loop_time(frq=frq): +for time in loop_time(exp_type=exp_type, frq=frq, offset=offset, point=point): # The key. keys = find_intensity_keys(exp_type=exp_type, frq=frq, point=point, time=time) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r22311 - /trunk/docs/latex/fetch_docstrings.py
Author: bugman
Date: Tue Feb 25 15:42:27 2014
New Revision: 22311
URL: http://svn.gna.org/viewcvs/relax?rev=22311view=rev
Log:
The fetch_docstrings.py script now creates a new LaTeX listing language for
relax log messages.
This is in the script_definitions() method which creates the
script_definition.tex file. The idea
is to avoid colouring relax/Python keywords such as 'as', 'from', etc. in the
log messages.
Modified:
trunk/docs/latex/fetch_docstrings.py
Modified: trunk/docs/latex/fetch_docstrings.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/fetch_docstrings.py?rev=22311r1=22310r2=22311view=diff
==
--- trunk/docs/latex/fetch_docstrings.py (original)
+++ trunk/docs/latex/fetch_docstrings.py Tue Feb 25 15:42:27 2014
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2005-2013 Edward d'Auvergne #
+# Copyright (C) 2005-2014 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -795,47 +795,52 @@
'def',
]
-# The relax language.
-file.write(\lstdefinelanguage{relax}{\n)
-
-# Allow the user function '.' character to be part of the keywords.
-file.write(alsoletter={.|},\n)
-
-# Output the first set of Python keywords.
-file.write(morekeywords={)
-for name in py_keywords:
-file.write(%s, % name)
-file.write(},\n)
-
-# Output the second set of Python keywords.
-file.write(morekeywords=[2]{)
-for name in py_keywords2:
-file.write(%s, % name)
-file.write(},\n)
-
-# Output the third set of Python keywords.
-file.write(morekeywords=[3]{)
-for name in py_keywords3:
-file.write(%s, % name)
-file.write(},\n)
-
-# Output the relax prompt.
-file.write(morekeywords=[4]{relax,relax|},\n)
-
-# Output the relax user functions as keywords.
-file.write(morekeywords=[5]{)
-for name in uf_names:
-file.write(%s, % name)
-file.write(},\n)
-
-# The rest of the definition.
-file.write(moreprocnamekeys={def,class},\n)
-file.write(sensitive=true,\n)
-file.write(morecomment=[l]{\#},\n)
-file.write(morestring=[b]',\n)
-file.write(morestring=[b]\,\n)
-file.write(morestring=[b]\\\,\n)
-file.write(}\n)
+# Loop over the relax definitions.
+for lang in ['relax', 'relax_log']:
+# The relax language.
+file.write(\lstdefinelanguage{%s}{\n % lang)
+
+# Allow the user function '.' character to be part of the keywords.
+file.write(alsoletter={.|},\n)
+
+# Output the first set of Python keywords.
+if lang == 'relax':
+file.write(morekeywords={)
+for name in py_keywords:
+file.write(%s, % name)
+file.write(},\n)
+
+# Output the second set of Python keywords.
+if lang == 'relax':
+file.write(morekeywords=[2]{)
+for name in py_keywords2:
+file.write(%s, % name)
+file.write(},\n)
+
+# Output the third set of Python keywords.
+if lang == 'relax':
+file.write(morekeywords=[3]{)
+for name in py_keywords3:
+file.write(%s, % name)
+file.write(},\n)
+
+# Output the relax prompt.
+file.write(morekeywords=[4]{relax,relax|},\n)
+
+# Output the relax user functions as keywords.
+file.write(morekeywords=[5]{)
+for name in uf_names:
+file.write(%s, % name)
+file.write(},\n)
+
+# The rest of the definition.
+file.write(moreprocnamekeys={def,class},\n)
+file.write(sensitive=true,\n)
+file.write(morecomment=[l]{\#},\n)
+file.write(morestring=[b]',\n)
+file.write(morestring=[b]\,\n)
+file.write(morestring=[b]\\\,\n)
+file.write(}\n)
# Close the file.
file.close()
___
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r22314 - /trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Author: tlinnet
Date: Tue Feb 25 16:39:35 2014
New Revision: 22314
URL: http://svn.gna.org/viewcvs/relax?rev=22314view=rev
Log:
Moved the unit test get_curve_type() to its own test.
Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis
with two fields at two delay times.
Modified:
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Modified:
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py?rev=22314r1=22313r2=22314view=diff
==
---
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
(original)
+++
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Tue Feb 25 16:39:35 2014
@@ -81,6 +81,17 @@
self.assertEqual(frq, data[1][1])
# Test the time count
self.assertEqual(count, 1)
+
+
+def test_get_curve_type(self):
+Unit test of the get_curve_type() function.
+
+This uses the data of the saved state attached to U{bug
#21665https://gna.org/bugs/?21665}.
+
+
+# Load the state.
+statefile = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21665.bz2'
+state.load_state(statefile, force=True)
# Check the return of get_curve_type function.
curve_type = get_curve_type()
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r22313 - /trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Author: tlinnet
Date: Tue Feb 25 16:39:33 2014
New Revision: 22313
URL: http://svn.gna.org/viewcvs/relax?rev=22313view=rev
Log:
Moved the unit test of has_exponential_exp_type() to its own test.
Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis
with two fields at two delay times.
Modified:
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Modified:
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py?rev=22313r1=22312r2=22313view=diff
==
---
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
(original)
+++
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Tue Feb 25 16:39:33 2014
@@ -87,11 +87,6 @@
print(curve_type)
self.assertEqual(curve_type, 'fixed time')
-# Check the return of has_exponential_exp_type.
-exponential_exp_type = has_exponential_exp_type()
-print(exponential_exp_type)
-self.assertEqual(exponential_exp_type, False)
-
def test_get_times(self):
Unit test of the get_times() function.
@@ -108,6 +103,22 @@
for exp_type in times:
print(times[exp_type])
self.assertEqual(len(times[exp_type]), 2)
+
+
+def test_has_exponential_exp_type(self):
+Unit test of the has_exponential_exp_type() function.
+
+This uses the data of the saved state attached to U{bug
#21665https://gna.org/bugs/?21665}.
+
+
+# Load the state.
+statefile = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21665.bz2'
+state.load_state(statefile, force=True)
+
+# Check the return of has_exponential_exp_type.
+exponential_exp_type = has_exponential_exp_type()
+print(exponential_exp_type)
+self.assertEqual(exponential_exp_type, False)
def test_loop_exp_frq(self):
___
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r22312 - /trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Author: tlinnet
Date: Tue Feb 25 16:39:32 2014
New Revision: 22312
URL: http://svn.gna.org/viewcvs/relax?rev=22312view=rev
Log:
Moved the unit test get_times() to its own test.
Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis
with two fields at two delay times.
Modified:
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Modified:
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py?rev=22312r1=22311r2=22312view=diff
==
---
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
(original)
+++
trunk/test_suite/unit_tests/_specific_analyses/_relax_disp/test_disp_data.py
Tue Feb 25 16:39:32 2014
@@ -82,21 +82,32 @@
# Test the time count
self.assertEqual(count, 1)
+# Check the return of get_curve_type function.
+curve_type = get_curve_type()
+print(curve_type)
+self.assertEqual(curve_type, 'fixed time')
+
+# Check the return of has_exponential_exp_type.
+exponential_exp_type = has_exponential_exp_type()
+print(exponential_exp_type)
+self.assertEqual(exponential_exp_type, False)
+
+
+def test_get_times(self):
+Unit test of the get_times() function.
+
+This uses the data of the saved state attached to U{bug
#21665https://gna.org/bugs/?21665}.
+
+
+# Load the state.
+statefile = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21665.bz2'
+state.load_state(statefile, force=True)
+
# Check the return of get_times().
times = get_times()
for exp_type in times:
print(times[exp_type])
self.assertEqual(len(times[exp_type]), 2)
-
-# Check the return of get_curve_type function.
-curve_type = get_curve_type()
-print(curve_type)
-self.assertEqual(curve_type, 'fixed time')
-
-# Check the return of has_exponential_exp_type.
-exponential_exp_type = has_exponential_exp_type()
-print(exponential_exp_type)
-self.assertEqual(exponential_exp_type, False)
def test_loop_exp_frq(self):
___
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r22315 - /trunk/test_suite/shared_data/dispersion/bug_21344.bz2
Author: tlinnet Date: Tue Feb 25 16:58:36 2014 New Revision: 22315 URL: http://svn.gna.org/viewcvs/relax?rev=22315view=rev Log: Added save state for bug 21344. Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of in sparse acquired R1rho dataset with missing combinations of time and spin-lock field strengths. Added: trunk/test_suite/shared_data/dispersion/bug_21344.bz2 [This mail would be too long, it was shortened to contain the URLs only.] Added: trunk/test_suite/shared_data/dispersion/bug_21344.bz2 URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/bug_21344.bz2?rev=22315view=auto ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r22316 - in /branches/double_rotor: ./ docs/latex/ specific_analyses/relax_disp/ test_suite/shared_data/dispersion/ test_sui...
Author: bugman Date: Tue Feb 25 17:45:38 2014 New Revision: 22316 URL: http://svn.gna.org/viewcvs/relax?rev=22316view=rev Log: Merged revisions 22301-22315 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r22301 | tlinnet | 2014-02-25 15:04:49 +0100 (Tue, 25 Feb 2014) | 9 lines Added exp_type, frq, offset, point to the loop_time() function. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. Implemented as suggested in: http://www.mail-archive.com/relax-devel@gna.org/msg04993.html In all these cases, that information is available, so it should be used. If one are analysing a combination of data types simultaneously (SQ CPMG, DQ CPMG, R1rho), one will not have the same relaxation time for each. For different spin-lock or 180 degree pulse offsets and even different dispersion points, the time may also be different. r22302 | tlinnet | 2014-02-25 15:04:51 +0100 (Tue, 25 Feb 2014) | 6 lines Made count_relax_times() take optional arguments as: exp_type, frq, offset, point. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. This is prepare for re-stricting the looping over time points in the function: loop_time() This is implemented as suggested in: http://www.mail-archive.com/relax-devel@gna.org/msg04993.html r22303 | tlinnet | 2014-02-25 15:04:53 +0100 (Tue, 25 Feb 2014) | 3 lines Modified to pass exp_typ, frq, offset or point to loop_time() where such information is available. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. r22304 | tlinnet | 2014-02-25 15:04:55 +0100 (Tue, 25 Feb 2014) | 5 lines Added unit test for count_relax_times. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. This follows the suggestion in: http://www.mail-archive.com/relax-devel@gna.org/msg04993.html. r22305 | tlinnet | 2014-02-25 15:04:56 +0100 (Tue, 25 Feb 2014) | 3 lines Added test for return of get_curve_type(), to match 'fixed time'. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. r22306 | tlinnet | 2014-02-25 15:04:58 +0100 (Tue, 25 Feb 2014) | 3 lines Added check for return of has_exponential_exp_type to be False. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. r22307 | tlinnet | 2014-02-25 15:04:59 +0100 (Tue, 25 Feb 2014) | 3 lines Added test for the return of get_times(). Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. r22308 | tlinnet | 2014-02-25 15:05:03 +0100 (Tue, 25 Feb 2014) | 3 lines Re-ordered unit tests for test of get_curve_type() and has_exponential_exp_type(). Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. r22309 | tlinnet | 2014-02-25 15:05:04 +0100 (Tue, 25 Feb 2014) | 3 lines Added the extraction of exp_type and frq from cdp, to be sent into count_relax_times. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. r22310 | tlinnet | 2014-02-25 15:05:06 +0100 (Tue, 25 Feb 2014) | 3 lines Modified check_exp_type_fixed_time to loop over id's and use count_relax_times for each id. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. r22311 | bugman | 2014-02-25 15:42:27 +0100 (Tue, 25 Feb 2014) | 6 lines The fetch_docstrings.py script now creates a new LaTeX listing language for relax log messages. This is in the script_definitions() method which creates the script_definition.tex file. The idea is to avoid colouring relax/Python keywords such as 'as', 'from', etc. in the log messages. r22312 | tlinnet | 2014-02-25 16:39:32 +0100 (Tue, 25 Feb 2014) | 3 lines Moved the unit test get_times() to its own test. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. r22313 | tlinnet | 2014-02-25 16:39:33 +0100 (Tue, 25 Feb 2014) | 3 lines Moved the unit test of has_exponential_exp_type() to its own test. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. r22314 | tlinnet | 2014-02-25 16:39:35 +0100 (Tue, 25 Feb 2014) | 3 lines Moved the unit test get_curve_type() to its own test. Regarding bug #21665, (https://gna.org/bugs/?21665) - Running a CPMG analysis with two fields at two delay times. r22315 |
r22317 - /trunk/docs/latex/dispersion.tex
Author: bugman
Date: Tue Feb 25 17:54:57 2014
New Revision: 22317
URL: http://svn.gna.org/viewcvs/relax?rev=22317view=rev
Log:
Completed the tutorial for using the dispersion analysis in the GUI.
This is for the relaxation dispersion chapter of the manual.
Modified:
trunk/docs/latex/dispersion.tex
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=22317r1=22316r2=22317view=diff
==
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Tue Feb 25 17:54:57 2014
@@ -2598,10 +2598,6 @@
\example{\$ relax --help}
-In this example, Gary Thompson's multiprocessor framework (see
section~\ref{sect: Relaxation dispersion using OpenMPI} on page~\pageref{sect:
Relaxation dispersion using OpenMPI}) will be used with OpenMPI on a single
four-core, hyper-threaded computer with the command:
-
-\example{\$ mpirun -np 8 /data/relax/relax-trunk/relax --multi='mpi4py' --log
$\sim$/tmp/dispersion/log\_non\_clustered --gui}
-
% Two analyses.
%~~
@@ -2614,6 +2610,13 @@
This will use model selection to determine if any statistically
significant relaxation dispersion is present by comparing to the `No Rex'
dispersion model.
\item The second analysis will consists of clustering spins with similar
kinetics and thermodynamics parameters (exchange rates and populations
respectively) and optimising these clusters using a common set of exchange
parameters.
\end{itemize}
+
+In this example, Gary Thompson's multiprocessor framework (see
section~\ref{sect: Relaxation dispersion using OpenMPI} on page~\pageref{sect:
Relaxation dispersion using OpenMPI}) will be used with OpenMPI on a single
four-core, hyper-threaded computer with the command:
+
+\example{\$ mpirun -np 8 /data/relax/relax-trunk/relax --multi='mpi4py' --log
$\sim$/tmp/dispersion/log\_non\_clustered --gui}
+
+A different command will be used for the clustered analysis to store the log
messages in a separate file.
+The logs will be used in the end to compare the two analysis types.
% Initialisation of the data pipe.
@@ -2975,7 +2978,7 @@
Change the frequency to 800.0 MHz and continue for the next set of matching
spectrum IDs.
Finally click on \guibutton{Next} to move to the next wizard page.
If you have not used the exact values from the files, the relax controller
window will appear with the warning:
-\begin{lstlisting}[numbers=none]
+\begin{lstlisting}[language=relax_log,numbers=none]
relax spectrometer.frequency(id='500_reference', frq=500.0, units='MHz')
RelaxWarning: The precise spectrometer frequency should be suppled, a value
such as 5 or 5e8 for a 500 MHz machine is not acceptable. Please see
the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in the
Bruker acqus file.
\end{lstlisting}
@@ -3138,7 +3141,7 @@
Firstly, to see which models have been chosen for the spin systems and which
have no statistically significant dispersion, find the \file{model.out} file
and double click on it.
You should see the following:
-\begin{lstlisting}[basicstyle=\scriptsize,numbers=none]
+\begin{lstlisting}[basicstyle=\ttfamily \scriptsize,numbers=none]
# Parameter description: The dispersion model.
#
# mol_nameres_numres_namespin_numspin_namevalue
error
@@ -3255,7 +3258,7 @@
To improve the appearance of this plot, please refer to the Grace software
documentation.
-% comparing models.
+% Comparing models.
%~~
\subsection{Dispersion GUI mode -- comparing models}
@@ -3283,10 +3286,17 @@
\subsection{Dispersion GUI mode -- the clustered analysis}
+Before this second analysis will be performed, the relax state will be saved
in the file \file{state.bz2} and the program closed.
+Then to store the details of the second analysis, relax will be restarted with
the command:
+
+\example{\$ mpirun -np 8 /data/relax/relax-trunk/relax --multi='mpi4py' --log
$\sim$/tmp/dispersion/log\_clustered --gui}
+
+When the GUI has started, load the \file{state.bz2} file.
+
For the clustered analysis, we will focus on one group of spins -- those from
residues 59 to 67.
These can be seen to have very similar dynamics:
-\begin{lstlisting}[basicstyle=\scriptsize,numbers=none]
+\begin{lstlisting}[basicstyle=\ttfamily \scriptsize,numbers=none]
# Parameter description: The population for state A.
#
# mol_name res_num res_name spin_num spin_name value
error
@@ -3303,7 +3313,7 @@
[snip]
\end{lstlisting}
-\begin{lstlisting}[basicstyle=\scriptsize,numbers=none]
+\begin{lstlisting}[basicstyle=\ttfamily \scriptsize,numbers=none]
# Parameter description: The exchange rate.
#
# mol_name res_num res_name spin_num spin_name value
error
@@ -3323,7 +,7 @@
All other spins will be
r22319 - /trunk/docs/latex/dispersion.tex
Author: bugman
Date: Tue Feb 25 18:55:25 2014
New Revision: 22319
URL: http://svn.gna.org/viewcvs/relax?rev=22319view=rev
Log:
Fixes for some incorrectly reported results in the dispersion GUI tutorial in
the manual.
The non-clustered results had been incorrectly copied from the log messages.
Modified:
trunk/docs/latex/dispersion.tex
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=22319r1=22318r2=22319view=diff
==
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Tue Feb 25 18:55:25 2014
@@ -3434,70 +3434,70 @@
\begin{lstlisting}[basicstyle=\ttfamily \tiny,language=relax_log,numbers=none]
The spin cluster [':59@N'].
# Data pipe
Num_params_(k)Num_data_sets_(n)Chi2 Criterion
-No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
31 1886.140161890.14016
-CR72 - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 32.15110 42.15110
-NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014)5
31 32.61624 42.61624
+No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
30 1577.422861581.42286
+CR72 - relax_disp (Mon Feb 17 18:00:16 2014) 5
30 31.48415 41.48415
+NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014)5
30 31.84758 41.84758
The model from the data pipe 'CR72 - relax_disp (Mon Feb 17 18:00:16 2014)'
has been selected.
The spin cluster [':60@N'].
-# Data pipeNum_params_(k)
Num_data_sets_(n)Chi2 Criterion
-No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2 31
3240.493123244.49312
+# Data pipe Num_params_(k)
Num_data_sets_(n)Chi2 Criterion
+No Rex - relax_disp (Mon Feb 17 18:00:16 2014)2 30
2647.974492651.97449
The model from the data pipe 'No Rex - relax_disp (Mon Feb 17 18:00:16 2014)'
has been selected.
The spin cluster [':61@N'].
# Data pipe
Num_params_(k)Num_data_sets_(n)Chi2 Criterion
-No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
31 17285.6621717289.66217
-CR72 - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 95.95234 105.95234
-NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014)5
31 92.56628 102.56628
+No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
30 15019.2438215023.24382
+CR72 - relax_disp (Mon Feb 17 18:00:16 2014) 5
30 77.50622 87.50622
+NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014)5
30 74.73334 84.73334
The model from the data pipe 'NS CPMG 2-site expanded - relax_disp (Mon Feb 17
18:00:16 2014)' has been selected.
The spin cluster [':62@N'].
# Data pipe
Num_params_(k)Num_data_sets_(n)Chi2 Criterion
-No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
31 851.74421855.74421
-NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014)5
31 31.48142 41.48142
+No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
30 722.91592726.91592
+NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014)5
30 30.11618 40.11618
The model from the data pipe 'NS CPMG 2-site expanded - relax_disp (Mon Feb 17
18:00:16 2014)' has been selected.
The spin cluster [':63@N'].
# Data pipe
Num_params_(k)Num_data_sets_(n)Chi2 Criterion
-No Rex - relax_disp (Mon Feb 17 18:00:16 2014) 2
31 6452.876236456.87623
-CR72 - relax_disp (Mon Feb 17 18:00:16 2014) 5
31 61.70881 71.70881
-NS CPMG 2-site expanded - relax_disp (Mon Feb 17 18:00:16 2014)5
31 63.14294
r22320 - /trunk/docs/latex/dispersion.tex
Author: bugman
Date: Tue Feb 25 21:58:40 2014
New Revision: 22320
URL: http://svn.gna.org/viewcvs/relax?rev=22320view=rev
Log:
More incorrect value fixes for the dispersion GUI tutorial in the manual.
The pA and kex values were also somehow incorrect.
Modified:
trunk/docs/latex/dispersion.tex
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=22320r1=22319r2=22320view=diff
==
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Tue Feb 25 21:58:40 2014
@@ -3336,15 +3336,15 @@
#
# mol_name res_num res_name spin_num spin_name value
error
[snip]
-None59 GLY None N 0.991889219955985
0.0450783237839957
+None59 GLY None N 0.991169677577733
0.0254974551085798
None60 GLY None N None None
-None61 GLY None N 0.988921118720546
0.000172502417409869
-None62 GLY None N 0.890931457907137
0.144215844986902
-None63 GLY None N 0.99156311187483
0.00115458534680375
-None64 GLY None N 0.983421376088971
0.00136664677079204
-None65 GLY None N 0.993825345814723
0.00190588775997763
-None66 GLY None N 0.996758947832568
0.0446859094999393
-None67 GLY None N 0.987205570324475
0.000218557328139047
+None61 GLY None N 0.989169345780449
0.000173707304433962
+None62 GLY None N 0.892612114003636
0.156741312688688
+None63 GLY None N 0.991579380015928
0.00101555844987099
+None64 GLY None N 0.983519617639107
0.00141882200997569
+None65 GLY None N 0.993831316342131
0.00840481515172743
+None66 GLY None N 0.996816227018878
0.00495523034494496
+None67 GLY None N 0.987206586948786
0.000217099775069814
[snip]
\end{lstlisting}
@@ -3353,15 +3353,15 @@
#
# mol_name res_num res_name spin_num spin_name value
error
[snip]
-None59 GLY None N 1809.98484500718
220.217062176079
+None59 GLY None N 1856.39029180567
258.796681611922
None60 GLY None N None None
-None61 GLY None N 1721.40918090412
77.6195110540786
-None62 GLY None N 1561.11252768657
234.177688850931
-None63 GLY None N 1444.52431393838
116.228169825369
-None64 GLY None N 1920.62433476407
92.6644161872285
-None65 GLY None N 1310.87783806055
162.660315854685
-None66 GLY None N 1227.3688268331
261.646351662978
-None67 GLY None N 1768.87422361068
75.8203628883989
+None61 GLY None N 1706.42820099893
79.5779060629935
+None62 GLY None N 1560.77926730839
246.876174669559
+None63 GLY None N 1448.69535431372
121.940593279104
+None64 GLY None N 1922.2405164604
96.0557804598977
+None65 GLY None N 1333.8423680145
168.000554346898
+None66 GLY None N 1243.45993122534
238.215664971556
+None67 GLY None N 1753.32557147779
78.2028166128168
[snip]
\end{lstlisting}
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r22321 - /trunk/test_suite/system_tests/relax_disp.py
Author: tlinnet
Date: Wed Feb 26 08:36:29 2014
New Revision: 22321
URL: http://svn.gna.org/viewcvs/relax?rev=22321view=rev
Log:
Added system test for bug 21344.
Regarding bug #21344, (https://gna.org/bugs/index.php?21344) - Handling of in
sparse acquired R1rho dataset with missing combinations of time and spin-lock
field strengths.
This test will fail with:
No intensity data could be found corresponding to the spectrometer frequency of
799.7773991 MHz, dispersion point of 431.0 and relaxation time of 0.14 s.
Data for a dispersion point of 431.0 and time 0.14 does not exist, and so some
of the looping in collecting data for calculation must be wrong.
This behaviour and probably its solution is related to bug 21665, Running a
CPMG analysis with two fields at two delay times
(https://gna.org/bugs/index.php?21665).
Modified:
trunk/test_suite/system_tests/relax_disp.py
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=22321r1=22320r2=22321view=diff
==
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Wed Feb 26 08:36:29 2014
@@ -265,6 +265,22 @@
relax_disp.Relax_disp.opt_func_tol = 1e-5
relax_disp.Relax_disp.opt_max_iterations = 1000
relax_disp.Relax_disp(pipe_name=origin - relax_disp (Thu Jan 2
13:46:44 2014), pipe_bundle=relax_disp (Thu Jan 2 13:46:44 2014),
results_dir=self.tmpdir, models=['R2eff', 'No Rex', 'CR72', 'NS CPMG 2-site
expanded'], grid_inc=3, mc_sim_num=5, modsel='AIC', pre_run_dir=None,
insignificance=1.0, numeric_only=False, mc_sim_all_models=False, eliminate=True)
+
+
+def test_bug_21344_cpmg_two_fields_two_delaytimes_fail_relax_disp(self):
+U{Bug #21665https://gna.org/bugs/?21344} catch, the failure of an
analysis of a sparse acquired R1rho dataset with missing combinations of time
and spin-lock field strengths using auto_analysis.
+
+# Clear the data store.
+self.interpreter.reset()
+
+# Load the state.
+state = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21344.bz2'
+self.interpreter.state.load(state, force=True)
+
+# Execute the auto-analysis (fast).
+relax_disp.Relax_disp.opt_func_tol = 1e-5
+relax_disp.Relax_disp.opt_max_iterations = 1000
+relax_disp.Relax_disp(pipe_name='base pipe', pipe_bundle='relax_disp',
results_dir=self.tmpdir, models=['R2eff'], grid_inc=3, mc_sim_num=5,
modsel='AIC', pre_run_dir=None, insignificance=1.0, numeric_only=False,
mc_sim_all_models=False, eliminate=True)
def test_bug_21665_cpmg_two_fields_two_delaytimes_fail_calc(self):
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