def test_pipe_bundle(self):
"""Test the pipe bundle concepts."""
# Execute the script.
self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'pipe_bundle.py')
# Checks.
self.assertEqual(pipes.cdp_name(), None)
self.assertEqual(pipes.has_bundle('test bundle 1'), True)
self.assertEqual(pipes.has_bundle('test bundle 2'), True)
self.assertEqual(pipes.has_bundle('test bundle 3'), False)
bundles = sorted(pipes.bundle_names())
self.assertEqual(bundles, ['test bundle 1', 'test bundle 2'])
for pipe, name in pipes.pipe_loop(name=True):
self.assert_(name in ['test pipe 1', 'test pipe 2', 'test pipe 3', 'test pipe 4', 'test pipe 5', 'test pipe 6'])
self.assert_(pipes.get_bundle(name) in ['test bundle 1', 'test bundle 2'])
def test_pipe_bundle(self):
"""Test the pipe bundle concepts."""
# Execute the script.
self.script_exec(status.install_path + sep + 'test_suite' + sep +
'system_tests' + sep + 'scripts' + sep +
'pipe_bundle.py')
# Checks.
self.assertEqual(pipes.cdp_name(), None)
self.assertEqual(pipes.has_bundle('test bundle 1'), True)
self.assertEqual(pipes.has_bundle('test bundle 2'), True)
self.assertEqual(pipes.has_bundle('test bundle 3'), False)
bundles = sorted(pipes.bundle_names())
self.assertEqual(bundles, ['test bundle 1', 'test bundle 2'])
for pipe, name in pipes.pipe_loop(name=True):
self.assert_(name in [
'test pipe 1', 'test pipe 2', 'test pipe 3', 'test pipe 4',
'test pipe 5', 'test pipe 6'
])
self.assert_(
pipes.get_bundle(name) in ['test bundle 1', 'test bundle 2'])
def pipe_deletion(self):
"""Remove analysis tabs for which the associated data pipe has been deleted."""
# Loop over the analyses, noting which no longer have an associated data pipe bundle.
del_list = []
for i in range(self._num_analyses):
if not pipes.has_bundle(ds.relax_gui.analyses[i].pipe_bundle):
del_list.append(i)
# Reverse the order of the list so the removal works correctly.
del_list.reverse()
# Delete the analyses.
for index in del_list:
self.delete_analysis(index)
def pipe_deletion(self):
"""Remove analysis tabs for which the associated data pipe has been deleted."""
# Loop over the analyses, noting which no longer have an associated data pipe bundle.
del_list = []
for i in range(self._num_analyses):
if not pipes.has_bundle(ds.relax_gui.analyses[i].pipe_bundle):
del_list.append(i)
# Reverse the order of the list so the removal works correctly.
del_list.reverse()
# Delete the analyses.
for index in del_list:
self.delete_analysis(index)
def __init__(self, parent, id=-1, pos=wx.Point(-1, -1), size=wx.Size(-1, -1), style=524288, name='scrolledpanel', gui=None, analysis_name=None, pipe_name=None, pipe_bundle=None, uf_exec=[], data_index=None):
"""Build the automatic R1 and R2 analysis GUI frame elements.
@param parent: The parent wx element.
@type parent: wx object
@keyword id: The unique ID number.
@type id: int
@keyword pos: The position.
@type pos: wx.Size object
@keyword size: The size.
@type size: wx.Size object
@keyword style: The style.
@type style: int
@keyword name: The name for the panel.
@type name: unicode
@keyword gui: The main GUI class.
@type gui: gui.relax_gui.Main instance
@keyword analysis_name: The name of the analysis (the name in the tab part of the notebook).
@type analysis_name: str
@keyword pipe_name: The name of the data pipe associated with this analysis.
@type pipe_name: str
@keyword pipe_bundle: The name of the data pipe bundle associated with this analysis.
@type pipe_bundle: str
@keyword uf_exec: The list of user function on_execute methods returned from the new analysis wizard.
@type uf_exec: list of methods
@keyword data_index: The index of the analysis in the relax data store (set to None if no data currently exists).
@type data_index: None or int
"""
# Store the GUI main class.
self.gui = gui
# Init.
self.init_flag = True
# New data container.
if data_index == None:
# First create the data pipe if not already in existence.
if not has_pipe(pipe_name):
self.gui.interpreter.apply('pipe.create', pipe_name=pipe_name, pipe_type='relax_fit', bundle=pipe_bundle)
# Create the data pipe bundle if needed.
if not has_bundle(pipe_bundle):
self.gui.interpreter.apply('pipe.bundle', bundle=pipe_bundle, pipe=pipe_name)
# Generate a storage container in the relax data store, and alias it for easy access.
data_index = ds.relax_gui.analyses.add(self.label)
# Store the analysis and pipe names.
ds.relax_gui.analyses[data_index].analysis_name = analysis_name
ds.relax_gui.analyses[data_index].pipe_name = pipe_name
ds.relax_gui.analyses[data_index].pipe_bundle = pipe_bundle
# Initialise the variables.
ds.relax_gui.analyses[data_index].frq = ''
ds.relax_gui.analyses[data_index].grid_inc = None
ds.relax_gui.analyses[data_index].mc_sim_num = None
ds.relax_gui.analyses[data_index].save_dir = self.gui.launch_dir
# Alias the data.
self.data = ds.relax_gui.analyses[data_index]
self.data_index = data_index
# Register the method for updating the spin count for the completion of user functions.
self.observer_register()
# Execute the base class method to build the panel.
super(Auto_rx, self).__init__(parent, id=id, pos=pos, size=size, style=style, name=name)
def __init__(self,
parent,
id=-1,
pos=wx.Point(-1, -1),
size=wx.Size(-1, -1),
style=524288,
name='scrolledpanel',
gui=None,
analysis_name=None,
pipe_name=None,
pipe_bundle=None,
uf_exec=[],
data_index=None):
"""Build the automatic R1 and R2 analysis GUI frame elements.
@param parent: The parent wx element.
@type parent: wx object
@keyword id: The unique ID number.
@type id: int
@keyword pos: The position.
@type pos: wx.Size object
@keyword size: The size.
@type size: wx.Size object
@keyword style: The style.
@type style: int
@keyword name: The name for the panel.
@type name: unicode
@keyword gui: The main GUI class.
@type gui: gui.relax_gui.Main instance
@keyword analysis_name: The name of the analysis (the name in the tab part of the notebook).
@type analysis_name: str
@keyword pipe_name: The name of the data pipe associated with this analysis.
@type pipe_name: str
@keyword pipe_bundle: The name of the data pipe bundle associated with this analysis.
@type pipe_bundle: str
@keyword uf_exec: The list of user function on_execute methods returned from the new analysis wizard.
@type uf_exec: list of methods
@keyword data_index: The index of the analysis in the relax data store (set to None if no data currently exists).
@type data_index: None or int
"""
# Store the GUI main class.
self.gui = gui
# Init.
self.init_flag = True
# New data container.
if data_index == None:
# First create the data pipe if not already in existence.
if not has_pipe(pipe_name):
self.gui.interpreter.apply('pipe.create',
pipe_name=pipe_name,
pipe_type='relax_fit',
bundle=pipe_bundle)
# Create the data pipe bundle if needed.
if not has_bundle(pipe_bundle):
self.gui.interpreter.apply('pipe.bundle',
bundle=pipe_bundle,
pipe=pipe_name)
# Generate a storage container in the relax data store, and alias it for easy access.
data_index = ds.relax_gui.analyses.add(self.label)
# Store the analysis and pipe names.
ds.relax_gui.analyses[data_index].analysis_name = analysis_name
ds.relax_gui.analyses[data_index].pipe_name = pipe_name
ds.relax_gui.analyses[data_index].pipe_bundle = pipe_bundle
# Initialise the variables.
ds.relax_gui.analyses[data_index].frq = ''
ds.relax_gui.analyses[data_index].grid_inc = None
ds.relax_gui.analyses[data_index].mc_sim_num = None
ds.relax_gui.analyses[
data_index].save_dir = self.gui.system_cwd_path
# Alias the data.
self.data = ds.relax_gui.analyses[data_index]
self.data_index = data_index
# Register the method for updating the spin count for the completion of user functions.
self.observer_register()
# Execute the base class method to build the panel.
super(Auto_rx, self).__init__(parent,
id=id,
pos=pos,
size=size,
style=style,
name=name)
def __init__(self, parent, id=-1, pos=wx.Point(-1, -1), size=wx.Size(-1, -1), style=524288, name='scrolledpanel', gui=None, analysis_name=None, pipe_name=None, pipe_bundle=None, uf_exec=[], data_index=None):
"""Build the automatic R1 and R2 analysis GUI frame elements.
@param parent: The parent wx element.
@type parent: wx object
@keyword id: The unique ID number.
@type id: int
@keyword pos: The position.
@type pos: wx.Size object
@keyword size: The size.
@type size: wx.Size object
@keyword style: The style.
@type style: int
@keyword name: The name for the panel.
@type name: unicode
@keyword gui: The main GUI class.
@type gui: gui.relax_gui.Main instance
@keyword analysis_name: The name of the analysis (the name in the tab part of the notebook).
@type analysis_name: str
@keyword pipe_name: The name of the data pipe associated with this analysis.
@type pipe_name: str
@keyword pipe_bundle: The name of the data pipe bundle associated with this analysis.
@type pipe_bundle: str
@keyword uf_exec: The list of user function on_execute methods returned from the new analysis wizard.
@type uf_exec: list of methods
@keyword data_index: The index of the analysis in the relax data store (set to None if no data currently exists).
@type data_index: None or int
"""
# Store the GUI main class.
self.gui = gui
# Init.
self.init_flag = True
# New data container.
if data_index == None:
# First create the data pipe if not already in existence.
if not has_pipe(pipe_name):
self.gui.interpreter.apply('pipe.create', pipe_name=pipe_name, pipe_type='relax_disp', bundle=pipe_bundle)
# Create the data pipe bundle if needed.
if not has_bundle(pipe_bundle):
self.gui.interpreter.apply('pipe.bundle', bundle=pipe_bundle, pipe=pipe_name)
# Generate a storage container in the relax data store, and alias it for easy access.
data_index = ds.relax_gui.analyses.add(self.label)
# Store the analysis and pipe names.
ds.relax_gui.analyses[data_index].analysis_name = analysis_name
ds.relax_gui.analyses[data_index].pipe_name = pipe_name
ds.relax_gui.analyses[data_index].pipe_bundle = pipe_bundle
# Initialise the variables.
ds.relax_gui.analyses[data_index].r1_fit = False
ds.relax_gui.analyses[data_index].numeric_only = False
ds.relax_gui.analyses[data_index].grid_inc = None
ds.relax_gui.analyses[data_index].mc_sim_num = None
ds.relax_gui.analyses[data_index].exp_mc_sim_num = None
ds.relax_gui.analyses[data_index].pre_run_dir = None
ds.relax_gui.analyses[data_index].mc_sim_all_models = False
ds.relax_gui.analyses[data_index].insignificance = 1.0
ds.relax_gui.analyses[data_index].save_dir = self.gui.launch_dir
# Set the default dispersion models based on the experiment type.
ds.relax_gui.analyses[data_index].disp_models = [
MODEL_R2EFF,
MODEL_NOREX,
MODEL_CR72,
MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_MP05,
MODEL_NS_R1RHO_2SITE
]
# Error checking.
if ds.relax_gui.analyses[data_index].pipe_bundle == None:
raise RelaxError("The pipe bundle must be supplied.")
# Alias the data.
self.data = ds.relax_gui.analyses[data_index]
self.data_index = data_index
# Register the method for updating the spin count for the completion of user functions.
self.observer_register()
# Execute the base class method to build the panel.
super(Auto_relax_disp, self).__init__(parent, id=id, pos=pos, size=size, style=style, name=name)
# Optimisation variables for speeding up the test suite.
self.opt_func_tol = 1e-25
self.opt_max_iterations = int(1e7)
# Update the isotope and cluster information.
self.update_clusters()
def __init__(self,
parent,
id=-1,
pos=wx.Point(-1, -1),
size=wx.Size(-1, -1),
style=524288,
name='scrolledpanel',
gui=None,
analysis_name=None,
pipe_name=None,
pipe_bundle=None,
uf_exec=[],
data_index=None):
"""Build the automatic model-free protocol GUI element.
@param parent: The parent wx element.
@type parent: wx object
@keyword id: The unique ID number.
@type id: int
@keyword pos: The position.
@type pos: wx.Size object
@keyword size: The size.
@type size: wx.Size object
@keyword style: The style.
@type style: int
@keyword name: The name for the panel.
@type name: unicode
@keyword gui: The main GUI class.
@type gui: gui.relax_gui.Main instance
@keyword analysis_name: The name of the analysis (the name in the tab part of the notebook).
@type analysis_name: str
@keyword pipe_name: The name of the original data pipe for this analysis.
@type pipe_name: str
@keyword pipe_bundle: The name of the data pipe bundle associated with this analysis.
@type pipe_bundle: str
@keyword uf_exec: The list of user function on_execute methods returned from the new analysis wizard.
@type uf_exec: list of methods
@keyword data_index: The index of the analysis in the relax data store (set to None if no data currently exists).
@type data_index: None or int
"""
# Store the GUI main class.
self.gui = gui
# Init.
self.init_flag = True
# New data container.
if data_index == None:
# First create the data pipe if not already in existence.
if not has_pipe(pipe_name):
self.gui.interpreter.apply('pipe.create',
pipe_name=pipe_name,
pipe_type='mf',
bundle=pipe_bundle)
# Create the data pipe bundle if needed.
if not has_bundle(pipe_bundle):
self.gui.interpreter.apply('pipe.bundle',
bundle=pipe_bundle,
pipe=pipe_name)
# Generate a storage container in the relax data store, and alias it for easy access.
data_index = ds.relax_gui.analyses.add('model-free')
# Store the analysis and pipe names.
ds.relax_gui.analyses[data_index].analysis_name = analysis_name
ds.relax_gui.analyses[data_index].pipe_name = pipe_name
ds.relax_gui.analyses[data_index].pipe_bundle = pipe_bundle
# Initialise the variables.
ds.relax_gui.analyses[data_index].grid_inc = None
ds.relax_gui.analyses[data_index].diff_tensor_grid_inc = {
'sphere': 11,
'prolate': 11,
'oblate': 11,
'ellipsoid': 6
}
ds.relax_gui.analyses[data_index].mc_sim_num = None
ds.relax_gui.analyses[
data_index].save_dir = self.gui.system_cwd_path
ds.relax_gui.analyses[data_index].local_tm_models = [
'tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8',
'tm9'
]
ds.relax_gui.analyses[data_index].mf_models = [
'm0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9'
]
ds.relax_gui.analyses[data_index].max_iter = 30
# Error checking.
if ds.relax_gui.analyses[data_index].pipe_bundle == None:
raise RelaxError("The pipe bundle must be supplied.")
# Alias the data.
self.data = ds.relax_gui.analyses[data_index]
self.data_index = data_index
# Backward compatibility.
if not hasattr(self.data, 'local_tm_models'):
self.data.local_tm_models = [
'tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8',
'tm9'
]
if not hasattr(self.data, 'mf_models'):
self.data.mf_models = [
'm0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9'
]
# Initialise the mode selection window.
self.mode_win = Protocol_mode_sel_window()
# Register the method for updating the spin count for the completion of user functions.
self.observer_register()
# Execute the base class method to build the panel.
super(Auto_model_free, self).__init__(parent,
id=id,
pos=pos,
size=size,
style=style,
name=name)
def __init__(self, parent, id=-1, pos=wx.Point(-1, -1), size=wx.Size(-1, -1), style=524288, name='scrolledpanel', gui=None, analysis_name=None, pipe_name=None, pipe_bundle=None, uf_exec=[], data_index=None):
"""Build the automatic R1 and R2 analysis GUI frame elements.
@param parent: The parent wx element.
@type parent: wx object
@keyword id: The unique ID number.
@type id: int
@keyword pos: The position.
@type pos: wx.Size object
@keyword size: The size.
@type size: wx.Size object
@keyword style: The style.
@type style: int
@keyword name: The name for the panel.
@type name: unicode
@keyword gui: The main GUI class.
@type gui: gui.relax_gui.Main instance
@keyword analysis_name: The name of the analysis (the name in the tab part of the notebook).
@type analysis_name: str
@keyword pipe_name: The name of the data pipe associated with this analysis.
@type pipe_name: str
@keyword pipe_bundle: The name of the data pipe bundle associated with this analysis.
@type pipe_bundle: str
@keyword uf_exec: The list of user function on_execute methods returned from the new analysis wizard.
@type uf_exec: list of methods
@keyword data_index: The index of the analysis in the relax data store (set to None if no data currently exists).
@type data_index: None or int
"""
# Store the GUI main class.
self.gui = gui
# Init.
self.init_flag = True
# New data container.
if data_index == None:
# First create the data pipe if not already in existence.
if not has_pipe(pipe_name):
self.gui.interpreter.apply('pipe.create', pipe_name=pipe_name, pipe_type='relax_disp', bundle=pipe_bundle)
# Create the data pipe bundle if needed.
if not has_bundle(pipe_bundle):
self.gui.interpreter.apply('pipe.bundle', bundle=pipe_bundle, pipe=pipe_name)
# Generate a storage container in the relax data store, and alias it for easy access.
data_index = ds.relax_gui.analyses.add(self.label)
# Store the analysis and pipe names.
ds.relax_gui.analyses[data_index].analysis_name = analysis_name
ds.relax_gui.analyses[data_index].pipe_name = pipe_name
ds.relax_gui.analyses[data_index].pipe_bundle = pipe_bundle
# Initialise the variables.
ds.relax_gui.analyses[data_index].r1_fit = False
ds.relax_gui.analyses[data_index].numeric_only = False
ds.relax_gui.analyses[data_index].grid_inc = None
ds.relax_gui.analyses[data_index].mc_sim_num = None
ds.relax_gui.analyses[data_index].exp_mc_sim_num = None
ds.relax_gui.analyses[data_index].pre_run_dir = None
ds.relax_gui.analyses[data_index].mc_sim_all_models = False
ds.relax_gui.analyses[data_index].insignificance = 1.0
ds.relax_gui.analyses[data_index].save_dir = self.gui.system_cwd_path
# Set the default dispersion models based on the experiment type.
ds.relax_gui.analyses[data_index].disp_models = [
MODEL_R2EFF,
MODEL_NOREX,
MODEL_CR72,
MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_MP05,
MODEL_NS_R1RHO_2SITE
]
# Error checking.
if ds.relax_gui.analyses[data_index].pipe_bundle == None:
raise RelaxError("The pipe bundle must be supplied.")
# Alias the data.
self.data = ds.relax_gui.analyses[data_index]
self.data_index = data_index
# Register the method for updating the spin count for the completion of user functions.
self.observer_register()
# Execute the base class method to build the panel.
super(Auto_relax_disp, self).__init__(parent, id=id, pos=pos, size=size, style=style, name=name)
# Optimisation variables for speeding up the test suite.
self.opt_func_tol = 1e-25
self.opt_max_iterations = int(1e7)
# Update the isotope and cluster information.
self.update_clusters()
def __init__(self, parent, id=-1, pos=wx.Point(-1, -1), size=wx.Size(-1, -1), style=524288, name='scrolledpanel', gui=None, analysis_name=None, pipe_name=None, pipe_bundle=None, uf_exec=[], data_index=None):
"""Build the automatic model-free protocol GUI element.
@param parent: The parent wx element.
@type parent: wx object
@keyword id: The unique ID number.
@type id: int
@keyword pos: The position.
@type pos: wx.Size object
@keyword size: The size.
@type size: wx.Size object
@keyword style: The style.
@type style: int
@keyword name: The name for the panel.
@type name: unicode
@keyword gui: The main GUI class.
@type gui: gui.relax_gui.Main instance
@keyword analysis_name: The name of the analysis (the name in the tab part of the notebook).
@type analysis_name: str
@keyword pipe_name: The name of the original data pipe for this analysis.
@type pipe_name: str
@keyword pipe_bundle: The name of the data pipe bundle associated with this analysis.
@type pipe_bundle: str
@keyword uf_exec: The list of user function on_execute methods returned from the new analysis wizard.
@type uf_exec: list of methods
@keyword data_index: The index of the analysis in the relax data store (set to None if no data currently exists).
@type data_index: None or int
"""
# Store the GUI main class.
self.gui = gui
# Init.
self.init_flag = True
# New data container.
if data_index == None:
# First create the data pipe if not already in existence.
if not has_pipe(pipe_name):
self.gui.interpreter.apply('pipe.create', pipe_name=pipe_name, pipe_type='mf', bundle=pipe_bundle)
# Create the data pipe bundle if needed.
if not has_bundle(pipe_bundle):
self.gui.interpreter.apply('pipe.bundle', bundle=pipe_bundle, pipe=pipe_name)
# Generate a storage container in the relax data store, and alias it for easy access.
data_index = ds.relax_gui.analyses.add('model-free')
# Store the analysis and pipe names.
ds.relax_gui.analyses[data_index].analysis_name = analysis_name
ds.relax_gui.analyses[data_index].pipe_name = pipe_name
ds.relax_gui.analyses[data_index].pipe_bundle = pipe_bundle
# Initialise the variables.
ds.relax_gui.analyses[data_index].grid_inc = None
ds.relax_gui.analyses[data_index].diff_tensor_grid_inc = {'sphere': 11, 'prolate': 11, 'oblate': 11, 'ellipsoid': 6}
ds.relax_gui.analyses[data_index].mc_sim_num = None
ds.relax_gui.analyses[data_index].save_dir = self.gui.system_cwd_path
ds.relax_gui.analyses[data_index].local_tm_models = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9']
ds.relax_gui.analyses[data_index].mf_models = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
ds.relax_gui.analyses[data_index].max_iter = 30
# Error checking.
if ds.relax_gui.analyses[data_index].pipe_bundle == None:
raise RelaxError("The pipe bundle must be supplied.")
# Alias the data.
self.data = ds.relax_gui.analyses[data_index]
self.data_index = data_index
# Backward compatibility.
if not hasattr(self.data, 'local_tm_models'):
self.data.local_tm_models = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9']
if not hasattr(self.data, 'mf_models'):
self.data.mf_models = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
# Initialise the mode selection window.
self.mode_win = Protocol_mode_sel_window()
# Register the method for updating the spin count for the completion of user functions.
self.observer_register()
# Execute the base class method to build the panel.
super(Auto_model_free, self).__init__(parent, id=id, pos=pos, size=size, style=style, name=name)