Author: bugman
Date: Tue Sep 3 19:31:31 2013
New Revision: 20784
URL: http://svn.gna.org/viewcvs/relax?rev=20784&view=rev
Log:
Created the Relax_disp.test_tp02_data_to_tp02 GUI test.
This is based on the system test of the same name. This GUI test checks that
an off-resonance R1rho
analysis is functional in the GUI.
Modified:
branches/relax_disp/test_suite/gui_tests/relax_disp.py
Modified: branches/relax_disp/test_suite/gui_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/gui_tests/relax_disp.py?rev=20784&r1=20783&r2=20784&view=diff
==============================================================================
--- branches/relax_disp/test_suite/gui_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/gui_tests/relax_disp.py Tue Sep 3
19:31:31 2013
@@ -32,6 +32,8 @@
from gui.interpreter import Interpreter; interpreter = Interpreter()
from gui.string_conv import float_to_gui, str_to_gui
from gui.uf_objects import Uf_storage; uf_store = Uf_storage()
+from pipe_control.mol_res_spin import spin_loop
+from pipe_control.pipes import switch
from status import Status; status = Status()
from test_suite.gui_tests.base_classes import GuiTestCase
@@ -316,3 +318,186 @@
if status.relax_mode != 'gui' and wx.version() != '2.9.4.1 gtk2
(classic)':
self.assertEqual(self.app.gui.controller.mc_gauge_rx.GetValue(),
100)
self.assertEqual(self.app.gui.controller.main_gauge.GetValue(),
100)
+
+
+ def test_tp02_data_to_tp02(self):
+ """Test the GUI analysis with the relaxation dispersion 'TP02' model
fitting to the 'TP02' synthetic data."""
+
+ # The paths to the data files.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'r1rho_off_res_tp02'+sep
+
+ # Simulate the new analysis wizard, selecting the fixed time CPMG
experiment.
+ self.app.gui.analysis.menu_new(None)
+ page = self.app.gui.analysis.new_wizard.wizard.get_page(0)
+ page.select_disp(None)
+ self.app.gui.analysis.new_wizard.wizard._go_next(None)
+ page = self.app.gui.analysis.new_wizard.wizard.get_page(1)
+ page.uf_args['exp_type'].SetValue(str_to_gui('r1rho fixed'))
+ self.app.gui.analysis.new_wizard.wizard._go_next(None)
+ self.app.gui.analysis.new_wizard.wizard._go_next(None)
+
+ # Get the data.
+ analysis_type, analysis_name, pipe_name, pipe_bundle, uf_exec =
self.app.gui.analysis.new_wizard.get_data()
+
+ # Set up the analysis.
+ self.app.gui.analysis.new_analysis(analysis_type=analysis_type,
analysis_name=analysis_name, pipe_name=pipe_name, pipe_bundle=pipe_bundle,
uf_exec=uf_exec)
+
+ # Alias the analysis.
+ analysis = self.app.gui.analysis.get_page_from_name("Relaxation
dispersion")
+
+ # Change the results directory.
+ analysis.field_results_dir.SetValue(str_to_gui(ds.tmpdir))
+
+ # Create the sequence data.
+ self._execute_uf(uf_name='spin.create', res_name='Trp', res_num=1,
spin_name='N')
+ interpreter.flush()
+ self._execute_uf(uf_name='spin.create', res_name='Trp', res_num=2,
spin_name='N')
+ interpreter.flush()
+ self._execute_uf(uf_name='sequence.display')
+ interpreter.flush()
+
+ # Set up the nuclear isotopes.
+ analysis.spin_isotope()
+ uf_store['spin.isotope'].page.SetValue('spin_id', '')
+ uf_store['spin.isotope'].wizard._go_next()
+ interpreter.flush() # Required because of the asynchronous uf
call.
+
+ # Load the chemical shift data.
+ self._execute_uf(uf_name='chemical_shift.read',
file='ref_500MHz.list', dir=data_path)
+ interpreter.flush()
+
+ # Load the spectrum.
+ frq = [500, 800]
+ frq_label = ['500MHz', '800MHz']
+ error = 200000.0
+ for frq_index in range(len(frq)):
+ # Load the R1 data.
+ label = 'R1_%s' % frq_label[frq_index]
+ self._execute_uf(uf_name='relax_data.read', ri_id=label,
ri_type='R1', frq=frq[frq_index]*1e6, file='%s.out'%label, dir=data_path,
mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6, error_col=7)
+ interpreter.flush()
+
+ # Set up the peak intensity wizard for the reference spectrum.
+ analysis.peak_wizard_launch(None)
+ wizard = analysis.peak_wizard
+
+ # The reference spectrum ID.
+ id = str_to_gui('ref_%s' % frq_label[frq_index])
+
+ # Load the reference spectrum.
+ wizard.setup_page(page='read', file="%sref_%s.list" %
(data_path, frq_label[frq_index]), spectrum_id=id, int_method='height', dim=1)
+ wizard._go_next(None)
+
+ # The error type.
+ page = wizard.get_page(wizard.page_indices['err_type'])
+ page.selection = 'rmsd'
+ wizard._go_next(None)
+
+ # Baseplane RMSD.
+ wizard.setup_page(page='rmsd', spectrum_id=id, error=error)
+ wizard._go_next(None)
+
+ # Set the spectrometer frequency.
+ wizard.setup_page(page='spectrometer_frequency', id=id,
frq=frq[frq_index], units='MHz')
+ wizard._go_next(None)
+
+ # Set as the reference.
+ wizard.setup_page(page='relax_time', spectrum_id=id, time=0.1)
+ wizard._go_next(None)
+ wizard.setup_page(page='spin_lock_field', spectrum_id=id,
field=None)
+ wizard._go_next(None)
+ wizard.setup_page(page='spin_lock_offset', spectrum_id=id,
offset=110.0)
+ wizard._go_next(None) # Moving off the last page so the
wizard will terminate.
+
+ # The spectral data - spectrum ID, peak lists, offset frequency
(Hz).
+ data = []
+ spin_lock = [1000.0, 1500.0, 2000.0, 2500.0, 3000.0, 3500.0,
4000.0, 4500.0, 5000.0, 5500.0, 6000.0]
+ for spin_lock_index in range(len(spin_lock)):
+ data.append(["nu_%s_%s" % (spin_lock[spin_lock_index],
frq_label[frq_index]), "nu_%s_%s.list" % (spin_lock[spin_lock_index],
frq_label[frq_index]), spin_lock[spin_lock_index]])
+
+ # Loop over the spectral data, loading it and setting the
metadata.
+ for id, file, field in data:
+ # Set up the peak intensity wizard for the reference
spectrum.
+ analysis.peak_wizard_launch(None)
+ wizard = analysis.peak_wizard
+
+ # Load the peak intensities and set the errors.
+ wizard.setup_page(page='read', file=data_path+file,
spectrum_id=id, int_method='height')
+ wizard._go_next(None)
+
+ # The error type.
+ page = wizard.get_page(wizard.page_indices['err_type'])
+ page.selection = 'rmsd'
+ wizard._go_next(None)
+
+ # Set the errors.
+ wizard.setup_page(page='rmsd', spectrum_id=id, error=error)
+ wizard._go_next(None)
+
+ # Set the spectrometer frequency.
+ wizard.setup_page(page='spectrometer_frequency', id=id,
frq=frq[frq_index], units='MHz')
+ wizard._go_next(None)
+
+ # Set the relaxation times.
+ wizard.setup_page(page='relax_time', spectrum_id=id,
time=0.1)
+ wizard._go_next(None)
+
+ # Set the relaxation dispersion spin-lock field strength
(nu1).
+ wizard.setup_page(page='spin_lock_field', spectrum_id=id,
field=field)
+ wizard._go_next(None)
+
+ # Set the spin-lock offset.
+ wizard.setup_page(page='spin_lock_offset', spectrum_id=id,
offset=110.0)
+ wizard._go_next(None)
+
+ # Deselect all but the 'TP02' model.
+ for i in [1, 2, 3, 4, 6]:
+ analysis.model_field.select[i] = False
+ analysis.model_field.modify()
+
+ # Set the grid search size and number of MC sims.
+ analysis.grid_inc.SetValue(4)
+ analysis.mc_sim_num.SetValue(3)
+
+ # Optimisation speedups.
+ analysis.opt_func_tol = 1e-10
+ analysis.opt_max_iterations = 10000
+
+ # Execute relax.
+ analysis.execute(wx.CommandEvent(wx.wxEVT_COMMAND_BUTTON_CLICKED,
analysis.button_exec_relax.GetId()))
+
+ # Wait for execution to complete.
+ analysis.thread.join()
+
+ # Flush all wx events.
+ wx.Yield()
+
+ # Exceptions in the thread.
+ self.check_exceptions()
+
+ # Check the relax controller.
+ # FIXME: skipping the checks for certain wxPython bugs.
+ if status.relax_mode != 'gui' and wx.version() != '2.9.4.1 gtk2
(classic)':
+ self.assertEqual(self.app.gui.controller.mc_gauge_rx.GetValue(),
100)
+ self.assertEqual(self.app.gui.controller.main_gauge.GetValue(),
100)
+
+ # The original parameters.
+ r1rho_prime = [[10.0, 15.0], [12.0, 18.0]]
+ pA = 0.7654321
+ kex = 1234.56789
+ delta_omega = [7.0, 9.0]
+
+ # Switch to the 'TP02' model data pipe, then check for each spin.
+ switch('TP02')
+ spin_index = 0
+ for spin, spin_id in spin_loop(return_id=True):
+ # Printout.
+ print("\nSpin %s." % spin_id)
+
+ # Check the fitted parameters.
+ self.assertAlmostEqual(spin.r2[0]/10,
r1rho_prime[spin_index][0]/10, 4)
+ self.assertAlmostEqual(spin.r2[1]/10,
r1rho_prime[spin_index][1]/10, 4)
+ self.assertAlmostEqual(spin.dw, delta_omega[spin_index], 3)
+ self.assertAlmostEqual(spin.kex/1000.0, kex/1000.0, 3)
+
+ # Increment the spin index.
+ spin_index += 1
r20784 - /branches/relax_disp/test_suite/gui_tests/relax_disp.py