def test_write_read_pipes(self):
"""Test the writing out, and re-reading of data pipes from the state file."""
# Create a data pipe.
self.interpreter.pipe.create('test', 'mf')
# Reset relax.
reset()
# The data pipe list.
pipe_types = deepcopy(VALID_TYPES)
pipe_types.pop(pipe_types.index("frame order"))
# Create a few data pipes.
for i in range(len(pipe_types)):
self.interpreter.pipe.create('test' + repr(i), pipe_types[i])
# Write the results.
self.interpreter.state.save(self.tmpfile)
# Reset relax.
reset()
# Re-read the results.
self.interpreter.state.load(self.tmpfile)
# Test the pipes.
for i in range(len(pipe_types)):
# Name.
name = 'test' + repr(i)
self.assert_(name in ds)
# Type.
pipe = get_pipe(name)
self.assertEqual(pipe.pipe_type, pipe_types[i])
def test_opt_sphere(self):
"""Check that the sphere diffusion tensor optimisation functions correctly."""
# Reset relax.
reset()
# The diffusion type (used by the script).
ds.diff_dir = 'sphere'
ds.diff_type = 'sphere'
# Execute the script.
self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'diff_tensor'+sep+'tensor_opt.py')
# Check the values.
self.assertAlmostEqual(cdp.chi2, 0.0)
self.assertEqual(cdp.diff_tensor.fixed, False)
self.assertEqual(cdp.diff_tensor.type, 'sphere')
self.assertAlmostEqual(cdp.diff_tensor.tm * 1e9, 1.0/(6.0*2e7) * 1e9)
self.assertEqual(cdp.diff_tensor.rotation[0, 0], 1.0)
self.assertEqual(cdp.diff_tensor.rotation[1, 1], 1.0)
self.assertEqual(cdp.diff_tensor.rotation[2, 2], 1.0)
self.assertEqual(cdp.diff_tensor.rotation[0, 1], 0.0)
self.assertEqual(cdp.diff_tensor.rotation[0, 2], 0.0)
self.assertEqual(cdp.diff_tensor.rotation[1, 2], 0.0)
self.assertEqual(cdp.diff_tensor.rotation[1, 0], 0.0)
self.assertEqual(cdp.diff_tensor.rotation[2, 0], 0.0)
self.assertEqual(cdp.diff_tensor.rotation[2, 1], 0.0)
def menu_close_all(self, event):
"""Close all analyses.
@param event: The wx event.
@type event: wx event
"""
# Notebook not created yet, so skip.
if not hasattr(self, 'notebook'):
return
# Execution lock.
if status.exec_lock.locked():
return
# Ask if this should be done.
msg = "Are you sure you would like to close all analyses? All data will be erased and the relax data store reset."
if status.show_gui and Question(msg, title="Close all analyses", size=(350, 150), default=False).ShowModal() == wx.ID_NO:
return
# Delete.
self.delete_all()
# Reset relax.
reset()
def tearDown(self):
"""Default tearDown operation - delete temp directories and files and reset relax."""
# Remove the temporary directory and variable (if there is a deletion failure, continue to allow the test suite to survive).
try:
deletion(obj=ds, name='tmpdir', dir=True)
except:
pass
try:
deletion(obj=self, name='tmpdir', dir=True)
except:
pass
# Remove temporary file and variable (if there is a deletion failure, continue to allow the test suite to survive).
try:
deletion(obj=ds, name='tmpfile', dir=False)
except:
pass
try:
deletion(obj=self, name='tmpfile', dir=False)
except:
pass
# Reset relax.
reset()
def tearDown(self):
"""Default tearDown operation - delete temp directories and files and reset relax."""
# Remove the temporary directory and variable (if there is a deletion failure, continue to allow the test suite to survive).
try:
deletion(obj=ds, name='tmpdir', dir=True)
except:
pass
try:
deletion(obj=self, name='tmpdir', dir=True)
except:
pass
# Remove temporary file and variable (if there is a deletion failure, continue to allow the test suite to survive).
try:
# Close the open file handles on the OS level.
close(ds.tmpfile_handle)
# Delete the temporary files.
deletion(obj=ds, name='tmpfile', dir=False)
except:
pass
try:
# Close the open file handles on the OS level.
close(self.tmpfile_handle)
# Delete the temporary files.
deletion(obj=self, name='tmpfile', dir=False)
except:
pass
# Reset relax.
reset()
def test_opt_ellipsoid(self):
"""Check that the ellipsoid diffusion tensor optimisation functions correctly."""
# Reset relax.
reset()
# The diffusion type (used by the script).
ds.diff_dir = 'ellipsoid'
ds.diff_type = 'ellipsoid'
# Execute the script.
self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'diff_tensor'+sep+'tensor_opt.py')
# Print out.
print(cdp.diff_tensor)
# The real data.
Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma, D, D_prime, R = self.get_ellipsoid()
# Check the values.
self.assertAlmostEqual(cdp.chi2, 0.0)
self.assertEqual(cdp.diff_tensor.fixed, False)
self.assertEqual(cdp.diff_tensor.type, 'ellipsoid')
# Check the ellipsoid.
self.check_ellipsoid(Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma, D, D_prime, R)
def test_write_read_pipes(self):
"""Test the writing out, and re-reading of data pipes from the state file."""
# Create a data pipe.
self.interpreter.pipe.create('test', 'mf')
# Reset relax.
reset()
# The data pipe list.
pipe_types = deepcopy(VALID_TYPES)
pipe_types.pop(pipe_types.index("frame order"))
# Create a few data pipes.
for i in range(len(pipe_types)):
self.interpreter.pipe.create('test' + repr(i), pipe_types[i])
# Write the results.
self.interpreter.state.save(self.tmpfile, compress_type=0, force=True)
# Reset relax.
reset()
# Re-read the results.
self.interpreter.state.load(self.tmpfile)
# Test the pipes.
for i in range(len(pipe_types)):
# Name.
name = 'test' + repr(i)
self.assert_(name in ds)
# Type.
pipe = get_pipe(name)
self.assertEqual(pipe.pipe_type, pipe_types[i])
def load_state(state=None, dir=None, verbosity=1, force=False):
"""Function for loading a saved program state.
@keyword state: The saved state file.
@type state: str
@keyword dir: The path of the state file.
@type dir: str
@keyword verbosity: The verbosity level.
@type verbosity: int
@keyword force: If True, the relax data store will be reset prior to state loading.
@type force: bool
"""
# Open the file for reading.
file = open_read_file(file_name=state, dir=dir, verbosity=verbosity)
# Reset.
if force:
reset()
# Make sure that the data store is empty.
if not ds.is_empty():
raise RelaxError("The relax data store is not empty.")
# Restore from the XML.
ds.from_xml(file)
# Signal a change in the current data pipe.
status.observers.pipe_alteration.notify()
# Signal the state loading
status.observers.state_load.notify()
def test_opt_sphere(self):
"""Check that the sphere diffusion tensor optimisation functions correctly."""
# Reset relax.
reset()
# The diffusion type (used by the script).
ds.diff_dir = 'sphere'
ds.diff_type = 'sphere'
# Execute the script.
self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'diff_tensor'+sep+'tensor_opt.py')
# Check the values.
self.assertAlmostEqual(cdp.chi2, 0.0)
self.assertEqual(cdp.diff_tensor.fixed, False)
self.assertEqual(cdp.diff_tensor.type, 'sphere')
self.assertAlmostEqual(cdp.diff_tensor.tm * 1e9, 1.0/(6.0*2e7) * 1e9)
self.assertEqual(cdp.diff_tensor.rotation[0, 0], 1.0)
self.assertEqual(cdp.diff_tensor.rotation[1, 1], 1.0)
self.assertEqual(cdp.diff_tensor.rotation[2, 2], 1.0)
self.assertEqual(cdp.diff_tensor.rotation[0, 1], 0.0)
self.assertEqual(cdp.diff_tensor.rotation[0, 2], 0.0)
self.assertEqual(cdp.diff_tensor.rotation[1, 2], 0.0)
self.assertEqual(cdp.diff_tensor.rotation[1, 0], 0.0)
self.assertEqual(cdp.diff_tensor.rotation[2, 0], 0.0)
self.assertEqual(cdp.diff_tensor.rotation[2, 1], 0.0)
def test_opt_ellipsoid(self):
"""Check that the ellipsoid diffusion tensor optimisation functions correctly."""
# Reset relax.
reset()
# The diffusion type (used by the script).
ds.diff_dir = 'ellipsoid'
ds.diff_type = 'ellipsoid'
# Execute the script.
self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'diff_tensor'+sep+'tensor_opt.py')
# Print out.
print(cdp.diff_tensor)
# The real data.
Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma, D, D_prime, R = self.get_ellipsoid()
# Check the values.
self.assertAlmostEqual(cdp.chi2, 0.0)
self.assertEqual(cdp.diff_tensor.fixed, False)
self.assertEqual(cdp.diff_tensor.type, 'ellipsoid')
# Check the ellipsoid.
self.check_ellipsoid(Dx, Dy, Dz, Diso, Da, Dr, alpha, beta, gamma, D, D_prime, R)
def menu_close_all(self, event):
"""Close all analyses.
@param event: The wx event.
@type event: wx event
"""
# Notebook not created yet, so skip.
if not hasattr(self, 'notebook'):
return
# Execution lock.
if status.exec_lock.locked():
return
# Ask if this should be done.
msg = "Are you sure you would like to close all analyses? All data will be erased and the relax data store reset."
if status.show_gui and Question(msg, title="Close all analyses", size=(350, 150), default=False).ShowModal() == wx.ID_NO:
return
# Delete.
self.delete_all()
# Reset relax.
reset()
def tearDown(self):
"""Reset the relax data storage object."""
# Delete the structural data object.
del self.data
# Reset relax.
reset()
def tearDown(self):
"""Reset the relax data storage object."""
# Reset relax.
reset()
# Delete the temporary files.
delete(self.tmpfile_sphere, fail=False)
delete(self.tmpfile_spheroid, fail=False)
delete(self.tmpfile_ellipsoid, fail=False)
def test_exists_mol_res_spin_data_no_pipe(self):
"""Determine if molecule-residue-spin data exists when no data pipe exists.
The function tested is pipe_control.mol_res_spin.exists_mol_res_spin_data().
"""
# Reset relax.
reset()
# This should fail.
self.assertRaises(RelaxNoPipeError, mol_res_spin.exists_mol_res_spin_data)
def test_count_spins_no_pipe(self):
"""Test that the counting of the number of spins raises an error when no pipe exists.
The function tested is pipe_control.mol_res_spin.count_spins().
"""
# Reset relax.
reset()
# Test for the error.
self.assertRaises(RelaxNoPipeError, mol_res_spin.count_spins)
def test_count_spins_no_pipe(self):
"""Test that the counting of the number of spins raises an error when no pipe exists.
The function tested is pipe_control.mol_res_spin.count_spins().
"""
# Reset relax.
reset()
# Test for the error.
self.assertRaises(RelaxNoPipeError, mol_res_spin.count_spins)
def test_display_fail_no_pipe(self):
"""Failure of the display of the diffusion tensor data structure when there is no data pipe.
The functions tested are both pipe_control.diffusion_tensor.display() and
prompt.diffusion_tensor.display().
"""
# Reset relax.
reset()
# Try to display the tensor data.
self.assertRaises(RelaxNoPipeError, self.diffusion_tensor_fns.display)
def test_exists_mol_res_spin_data_no_pipe(self):
"""Determine if molecule-residue-spin data exists when no data pipe exists.
The function tested is pipe_control.mol_res_spin.exists_mol_res_spin_data().
"""
# Reset relax.
reset()
# This should fail.
self.assertRaises(RelaxNoPipeError,
mol_res_spin.exists_mol_res_spin_data)
def test_delete_fail_no_pipe(self):
"""Failure of deletion of the diffusion tensor data structure when there is no data pipe.
The functions tested are both pipe_control.diffusion_tensor.delete() and
prompt.diffusion_tensor.delete().
"""
# Reset relax.
reset()
# Try to delete the tensor data.
self.assertRaises(RelaxNoPipeError, self.diffusion_tensor_fns.delete)
def test_display_fail_no_pipe(self):
"""Failure of the display of the alignment tensor data structure when there is no data pipe.
The functions tested are both pipe_control.align_tensor.display() and
prompt.align_tensor.display().
"""
# Reset relax.
reset()
# Try to display the tensor data.
self.assertRaises(RelaxNoPipeError, self.align_tensor_fns.display, 'Pf1')
def tearDown(self):
"""Default tearDown operation - delete temp directories and files and reset relax."""
# Remove the temporary directory and variable.
deletion(obj=ds, name="tmpdir", dir=True)
deletion(obj=self, name="tmpdir", dir=True)
# Remove temporary file and variable.
deletion(obj=ds, name="tmpfile", dir=False)
deletion(obj=self, name="tmpfile", dir=False)
# Reset relax.
reset()
def test_delete_fail_no_pipe(self):
"""Failure of deletion of the alignment tensor data structure when there is no data pipe.
The functions tested are both pipe_control.align_tensor.delete() and
prompt.align_tensor.delete().
"""
# Reset relax.
reset()
# Try to delete the tensor data.
self.assertRaises(RelaxNoPipeError, self.align_tensor_fns.delete,
'Pf1')
def tearDown(self):
"""Default tearDown operation - delete temp directories and files and reset relax."""
# Remove the temporary directory and variable.
deletion(obj=ds, name='tmpdir', dir=True)
deletion(obj=self, name='tmpdir', dir=True)
# Remove temporary file and variable.
deletion(obj=ds, name='tmpfile', dir=False)
deletion(obj=self, name='tmpfile', dir=False)
# Reset relax.
reset()
def test_exists_mol_res_spin_data_no_data(self):
"""Determine if molecule-residue-spin data exists when no data exists.
The function tested is pipe_control.mol_res_spin.exists_mol_res_spin_data().
"""
# Reset relax.
reset()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# This should be False.
self.failIf(mol_res_spin.exists_mol_res_spin_data())
def test_exists_mol_res_spin_data_no_data(self):
"""Determine if molecule-residue-spin data exists when no data exists.
The function tested is pipe_control.mol_res_spin.exists_mol_res_spin_data().
"""
# Reset relax.
reset()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# This should be False.
self.failIf(mol_res_spin.exists_mol_res_spin_data())
def test_count_no_spins(self):
"""Test that the number of spins (zero) can be properly counted.
The function tested is pipe_control.mol_res_spin.count_spins().
"""
# Reset relax.
reset()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# Test the number of spins counted.
self.assertEqual(mol_res_spin.count_spins(), 0)
def test_count_no_spins(self):
"""Test that the number of spins (zero) can be properly counted.
The function tested is pipe_control.mol_res_spin.count_spins().
"""
# Reset relax.
reset()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# Test the number of spins counted.
self.assertEqual(mol_res_spin.count_spins(), 0)
def tearDown(self):
"""Reset the relax data storage object."""
# Reset relax.
reset()
# Close the open file handles on the OS level.
close(self.tmpfile_sphere_handle)
close(self.tmpfile_spheroid_handle)
close(self.tmpfile_ellipsoid_handle)
# Delete the temporary files.
delete(self.tmpfile_sphere, fail=False)
delete(self.tmpfile_spheroid, fail=False)
delete(self.tmpfile_ellipsoid, fail=False)
def test_residue_loop_no_pipe(self):
"""Test the proper operation of the residue loop when no data pipe is present.
The function tested is pipe_control.mol_res_spin.residue_loop().
"""
# Reset relax.
reset()
# Function for the problem of catching an error in a generator function.
def fail_test():
for residue in mol_res_spin.residue_loop():
pass
# Test for the no pipe error.
self.assertRaises(RelaxNoPipeError, fail_test)
def tearDown(self):
"""Default tearDown operation - delete temp directories and files and reset relax."""
# Flush all wx events prior to the clean up operations of this method. This prevents these events from occurring after the GUI elements have been deleted.
wx.Yield()
# Remove the temporary directory and variable.
deletion(obj=ds, name='tmpdir', dir=True)
deletion(obj=self, name='tmpdir', dir=True)
# Remove temporary file and variable.
deletion(obj=ds, name='tmpfile', dir=False)
deletion(obj=self, name='tmpfile', dir=False)
# Reset relax.
reset()
def test_spin_loop_no_pipe(self):
"""Test the proper operation of the spin loop when no data pipe is present.
The function tested is pipe_control.mol_res_spin.spin_loop().
"""
# Reset relax.
reset()
# Function for the problem of catching an error in a generator function.
def fail_test():
for spin in mol_res_spin.spin_loop():
pass
# Test for the no pipe error.
self.assertRaises(RelaxNoPipeError, fail_test)
def test_exists_mol_res_spin_data_single_spin_num(self):
"""Determine if molecule-residue-spin data exists (when a single spin is numbered).
The function tested is pipe_control.mol_res_spin.exists_mol_res_spin_data().
"""
# Reset relax.
reset()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
dp = pipes.get_pipe('orig')
# Number the first spin.
dp.mol[0].res[0].spin[0].num = 234
# This should be True.
self.failUnless(mol_res_spin.exists_mol_res_spin_data())
def test_exists_mol_res_spin_data_single_mol(self):
"""Determine if molecule-residue-spin data exists (with data for a single molecule).
The function tested is pipe_control.mol_res_spin.exists_mol_res_spin_data().
"""
# Reset relax.
reset()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
dp = pipes.get_pipe('orig')
# Name the first molecule.
dp.mol[0].name = 'TOM40'
# This should be True.
self.failUnless(mol_res_spin.exists_mol_res_spin_data())
def test_exists_mol_res_spin_data_single_mol(self):
"""Determine if molecule-residue-spin data exists (with data for a single molecule).
The function tested is pipe_control.mol_res_spin.exists_mol_res_spin_data().
"""
# Reset relax.
reset()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
dp = pipes.get_pipe('orig')
# Name the first molecule.
dp.mol[0].name = 'TOM40'
# This should be True.
self.failUnless(mol_res_spin.exists_mol_res_spin_data())
def test_exists_mol_res_spin_data_single_spin_num(self):
"""Determine if molecule-residue-spin data exists (when a single spin is numbered).
The function tested is pipe_control.mol_res_spin.exists_mol_res_spin_data().
"""
# Reset relax.
reset()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
dp = pipes.get_pipe('orig')
# Number the first spin.
dp.mol[0].res[0].spin[0].num = 234
# This should be True.
self.failUnless(mol_res_spin.exists_mol_res_spin_data())
def test_residue_loop_no_data(self):
"""Test the proper operation of the residue loop when no data is present.
The function tested is pipe_control.mol_res_spin.residue_loop().
"""
# Reset relax.
reset()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# Loop over the residues.
i = 0
for residue in mol_res_spin.residue_loop():
i = i + 1
# Test loop length.
self.assertEqual(i, 0)
def test_spin_loop_no_data(self):
"""Test the proper operation of the spin loop when no data is present.
The function tested is pipe_control.mol_res_spin.spin_loop().
"""
# Reset relax.
reset()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# Loop over the spins.
i = 0
for spin in mol_res_spin.spin_loop():
i = i + 1
# Test loop length.
self.assertEqual(i, 0)
def tearDown(self):
"""Default tearDown operation - delete temp directories and files and reset relax."""
# Flush all wx events prior to the clean up operations of this method. This prevents these events from occurring after the GUI elements have been deleted.
wx.Yield()
# Remove the temporary directory and variable.
deletion(obj=ds, name='tmpdir', dir=True)
deletion(obj=self, name='tmpdir', dir=True)
# Remove temporary file and variable.
deletion(obj=ds, name='tmpfile', dir=False)
deletion(obj=self, name='tmpfile', dir=False)
# Reset relax.
reset()
# Get the wx app.
self.app = wx.GetApp()
# Kill all windows.
self.clean_up_windows()
# Print out a list of all living windows to help ensure that custom Close() and Destroy() methods are cleaning up all objects.
print(
"\n\nList of all living GUI elements - this must only include the main GUI window and the relax controller:"
)
all_destroyed = True
for window in wx.GetTopLevelWindows():
# Printout.
print(" Window: %s" % window)
if isinstance(window, Wiz_window):
print(" Wizard title: %s" % window.title)
print(" Wizard pages: %s" % window._pages)
# Skip the main GUI window and the relax controller.
if isinstance(window, Main) or isinstance(window, Controller):
continue
# Failure of memory management.
all_destroyed = False
print("\n\n\n")
def test_test(self):
"""The throwing of RelaxNoPipeError when the pipe does not exist.
The function tested is pipe_control.pipes.check_pipe().
"""
# The following should do nothing as the pipes exist.
pipes.check_pipe()
pipes.check_pipe('orig')
pipes.check_pipe('empty')
# Assert that a RelaxNoPipeError occurs when the pipe doesn't exist.
self.assertRaises(RelaxNoPipeError, pipes.check_pipe, 'x')
# Reset relax.
reset()
# Now none of the following pipes exist, hence errors should be thrown.
self.assertRaises(RelaxNoPipeError, pipes.check_pipe)
self.assertRaises(RelaxNoPipeError, pipes.check_pipe, 'orig')
self.assertRaises(RelaxNoPipeError, pipes.check_pipe, 'empty')
def test_load_and_reset(self):
"""The resetting of an unpickled and restored relax data storage singleton.
This tests the normal operation of the pipe_control.state.load() function.
"""
# Test the contents of the empty singleton.
self.assertEqual(list(ds.keys()), [])
self.assertEqual(pipes.cdp_name(), None)
self.assert_(not hasattr(ds, 'y'))
# Load the state.
self.state.load_state(state='basic_single_pipe', dir=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'saved_states')
# Reset relax.
reset()
# Test that there are no contents in the reset singleton.
self.assertEqual(list(ds.keys()), [])
self.assertEqual(pipes.cdp_name(), None)
self.assert_(not hasattr(ds, 'y'))
def test_back_calc_spheroid(self):
"""Check the back-calculation of relaxation data for the spherical diffusion tensor."""
# Reset relax.
reset()
# The diffusion type (used by the script).
ds.diff_dir = 'spheroid_prolate'
ds.diff_type = 'spheroid'
# Execute the script.
self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'diff_tensor'+sep+'ri_back_calc.py')
# Loop over all spins.
for i in range(len(cdp.mol[0].res)):
# Alias.
spin = cdp.mol[0].res[i].spin[0]
# Check the values.
for ri_id in cdp.ri_ids:
self.assertAlmostEqual(spin.ri_data_bc[ri_id], spin.ri_data[ri_id])
def test_opt_spheroid(self):
"""Check that the spheroid diffusion tensor optimisation functions correctly."""
# Reset relax.
reset()
# The diffusion type (used by the script).
ds.diff_dir = 'spheroid_prolate'
ds.diff_type = 'spheroid'
# Execute the script.
self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'diff_tensor'+sep+'tensor_opt.py')
# Check the values.
self.assertAlmostEqual(cdp.chi2, 0.0)
self.assertEqual(cdp.diff_tensor.fixed, False)
self.assertEqual(cdp.diff_tensor.type, 'spheroid')
self.assertAlmostEqual(cdp.diff_tensor.tm * 1e9, 1.0/(6.0*7e7/3.0) * 1e9)
self.assertAlmostEqual(cdp.diff_tensor.Da * 1e-7, 1.0)
self.assertAlmostEqual(cdp.diff_tensor.theta, 2.0)
self.assertAlmostEqual(cdp.diff_tensor.phi, pi-0.5)
def test_opt_spheroid(self):
"""Check that the spheroid diffusion tensor optimisation functions correctly."""
# Reset relax.
reset()
# The diffusion type (used by the script).
ds.diff_dir = 'spheroid_prolate'
ds.diff_type = 'spheroid'
# Execute the script.
self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'diff_tensor'+sep+'tensor_opt.py')
# Check the values.
self.assertAlmostEqual(cdp.chi2, 0.0)
self.assertEqual(cdp.diff_tensor.fixed, False)
self.assertEqual(cdp.diff_tensor.type, 'spheroid')
self.assertAlmostEqual(cdp.diff_tensor.tm * 1e9, 1.0/(6.0*7e7/3.0) * 1e9)
self.assertAlmostEqual(cdp.diff_tensor.Da * 1e-7, 1.0)
self.assertAlmostEqual(cdp.diff_tensor.theta, 2.0)
self.assertAlmostEqual(cdp.diff_tensor.phi, pi-0.5)
def test_test(self):
"""The throwing of RelaxNoPipeError when the pipe does not exist.
The function tested is pipe_control.pipes.check_pipe().
"""
# The following should do nothing as the pipes exist.
pipes.check_pipe()
pipes.check_pipe('orig')
pipes.check_pipe('empty')
# Assert that a RelaxNoPipeError occurs when the pipe doesn't exist.
self.assertRaises(RelaxNoPipeError, pipes.check_pipe, 'x')
# Reset relax.
reset()
# Now none of the following pipes exist, hence errors should be thrown.
self.assertRaises(RelaxNoPipeError, pipes.check_pipe)
self.assertRaises(RelaxNoPipeError, pipes.check_pipe, 'orig')
self.assertRaises(RelaxNoPipeError, pipes.check_pipe, 'empty')
def test_back_calc_spheroid(self):
"""Check the back-calculation of relaxation data for the spherical diffusion tensor."""
# Reset relax.
reset()
# The diffusion type (used by the script).
ds.diff_dir = 'spheroid_prolate'
ds.diff_type = 'spheroid'
# Execute the script.
self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'diff_tensor'+sep+'ri_back_calc.py')
# Loop over all spins.
for i in range(len(cdp.mol[0].res)):
# Alias.
spin = cdp.mol[0].res[i].spin[0]
# Check the values.
for ri_id in cdp.ri_ids:
self.assertAlmostEqual(spin.ri_data_bc[ri_id], spin.ri_data[ri_id])
def tearDown(self):
"""Default tearDown operation - delete temp directories and files and reset relax."""
# Flush all wx events prior to the clean up operations of this method. This prevents these events from occurring after the GUI elements have been deleted.
wx.Yield()
# Remove the temporary directory and variable.
deletion(obj=ds, name='tmpdir', dir=True)
deletion(obj=self, name='tmpdir', dir=True)
# Remove temporary file and variable.
deletion(obj=ds, name='tmpfile', dir=False)
deletion(obj=self, name='tmpfile', dir=False)
# Reset relax.
reset()
# Get the wx app.
self.app = wx.GetApp()
# Kill all windows.
self.clean_up_windows()
# Print out a list of all living windows to help ensure that custom Close() and Destroy() methods are cleaning up all objects.
print("\n\nList of all living GUI elements - this must only include the main GUI window and the relax controller:")
all_destroyed = True
for window in wx.GetTopLevelWindows():
# Printout.
print(" Window: %s" % window)
if isinstance(window, Wiz_window):
print(" Wizard title: %s" % window.title)
print(" Wizard pages: %s" % window._pages)
# Skip the main GUI window and the relax controller.
if isinstance(window, Main) or isinstance(window, Controller):
continue
# Failure of memory management.
all_destroyed = False
print("\n\n\n")
def test_load_and_reset(self):
"""The resetting of an unpickled and restored relax data storage singleton.
This tests the normal operation of the pipe_control.state.load() function.
"""
# Test the contents of the empty singleton.
self.assertEqual(list(ds.keys()), [])
self.assertEqual(pipes.cdp_name(), None)
self.assert_(not hasattr(ds, 'y'))
# Load the state.
self.state.load_state(state='basic_single_pipe',
dir=status.install_path + sep + 'test_suite' +
sep + 'shared_data' + sep + 'saved_states')
# Reset relax.
reset()
# Test that there are no contents in the reset singleton.
self.assertEqual(list(ds.keys()), [])
self.assertEqual(pipes.cdp_name(), None)
self.assert_(not hasattr(ds, 'y'))
def load_state(state=None, dir=None, verbosity=1, force=False):
"""Function for loading a saved program state.
@keyword state: The saved state file.
@type state: str
@keyword dir: The path of the state file.
@type dir: str
@keyword verbosity: The verbosity level.
@type verbosity: int
@keyword force: If True, the relax data store will be reset prior to state loading.
@type force: bool
"""
# Open the file for reading.
file = open_read_file(file_name=state, dir=dir, verbosity=verbosity)
# Reset.
if force:
reset()
# Make sure that the data store is empty.
if not ds.is_empty():
raise RelaxError("The relax data store is not empty.")
# Restore from the XML.
ds.from_xml(file)
# Update all of the required metadata structures.
for pipe, pipe_name in pipes.pipe_loop(name=True):
mol_res_spin.metadata_update(pipe=pipe_name)
interatomic.metadata_update(pipe=pipe_name)
# Signal a change in the current data pipe.
status.observers.pipe_alteration.notify()
# Signal the state loading
status.observers.state_load.notify()
def state_load(self, event=None, file_name=None):
"""Load the program state.
@keyword event: The wx event.
@type event: wx event
@keyword file_name: The name of the file to load (for dialogless operation).
@type file_name: str
"""
# Execution lock.
if status.exec_lock.locked():
return
# Warning.
if not self.analysis.init_state or not ds.is_empty():
# The message.
msg = "Loading a saved relax state file will cause all unsaved data to be lost. Are you sure you would to open a save file?"
# The dialog.
if status.show_gui and Question(msg, default=True, size=(400, 150)).ShowModal() == wx.ID_NO:
return
# Open the dialog.
if not file_name:
dialog = RelaxFileDialog(parent=self, message='Select the relax save state file', defaultFile='state.bz2', wildcard='relax save files (*.bz2;*.gz)|*.bz2;*.gz|All files (*)|*', style=wx.FD_OPEN)
# Show the dialog and catch if no file has been selected.
if status.show_gui and dialog.ShowModal() != wx.ID_OK:
# Don't do anything.
return
# The file.
file_name = gui_to_str(dialog.get_file())
# Yield to allow the cursor to be changed.
wx.Yield()
# Change the cursor to waiting, and freeze the GUI.
wx.BeginBusyCursor()
self.Freeze()
# Make sure the GUI returns to normal if a failure occurs.
try:
# Delete the current tabs.
self.analysis.delete_all()
# Reset the relax data store.
reset()
# The new save file name.
self.save_file = file_name
# Load the relax state.
if protected_exec(state.load_state, file_name, verbosity=0):
# Update the core of the GUI to match the new data store.
self.sync_ds(upload=False)
# File loading failure.
else:
# Reset relax to clear any partially loaded data.
reset()
# Reinitialise the GUI data store structure.
self.init_data()
# Reset the cursor, and thaw the GUI.
finally:
self.Thaw()
# Turn off the busy cursor.
if wx.IsBusy():
wx.EndBusyCursor()
def run_test_suite(self, event=None, categories=['system', 'unit', 'gui']):
"""Execute the full test suite.
@keyword event: The wx event.
@type event: wx event
@keyword categories: The list of test categories to run, for example ['system', 'unit', 'gui'] for all tests.
@type categories: list of str
"""
# Ask if this should be done.
msg = "In running the test suite, relax will be reset and all data lost. Are you sure you would like to run the test suite?"
if Question(msg, parent=self, size=(400, 150), default=False).ShowModal() == wx.ID_NO:
return
# Set the test suite flag.
self.test_suite_flag = True
# Change the cursor to waiting.
wx.BeginBusyCursor()
# Set a new style to stay on top, refreshing to update the style (needed for Mac OS X and MS Windows).
orig_style = self.controller.GetWindowStyle()
self.controller.SetWindowStyle(orig_style | wx.STAY_ON_TOP)
self.controller.Refresh()
# Make the relax controller modal so that all other windows are deactivated (to stop users from clicking on things).
self.controller.MakeModal(True)
# Close all open windows.
if hasattr(self, 'spin_viewer'):
self.spin_viewer.Close()
if hasattr(self, 'pipe_editor'):
self.pipe_editor.Close()
if hasattr(self, 'results_viewer'):
self.results_viewer.Close()
if hasattr(self, 'relax_prompt'):
self.relax_prompt.Close()
# Reset relax.
reset()
# Show the relax controller.
self.show_controller(event)
# Yield
wx.GetApp().Yield(True)
# Prevent all new GUI elements from being shown.
status.show_gui = False
# Run the tests (with the import here to break a nasty circular import).
import test_suite.test_suite_runner
runner = test_suite.test_suite_runner.Test_suite_runner([], from_gui=True, categories=categories)
runner.run_all_tests()
# Reactive the GUI.
status.show_gui = True
# Turn off the busy cursor.
if wx.IsBusy():
wx.EndBusyCursor()
# Restore the controller.
self.controller.SetWindowStyle(orig_style)
self.controller.MakeModal(False)
self.controller.Refresh()
# Unset the test suite flag.
self.test_suite_flag = False
# Set the controller main gauge to 100%.
wx.CallAfter(self.controller.main_gauge.SetValue, 100)