Author: bugman
Date: Sun Feb 18 06:40:36 2007
New Revision: 3018
URL: http://svn.gna.org/viewcvs/relax?rev=3018&view=rev
Log:
Fix for bug #7979 (https://gna.org/bugs/?7979).
A large number of changes were required. Two private functions
'self.__update_sim_append()' and
'self.__update_sim_set()' have been added to the DiffTensorElement class.
These are used to
automatically update the Monte Carlo simulation parameter lists.
The name 'dependencies' is now properly spelt.
The unused Monte Carlo simulation code in the function
'self._update_object()' has been deleted.
The object DiffTensorSimList has been modifed to handle the two new private
functions.
Modified:
1.3/data/diff_tensor.py
1.3/generic_fns/diffusion_tensor.py
1.3/specific_fns/model_free.py
1.3/test_suite/unit_tests/data/test_diff_tensor.py
Modified: 1.3/data/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/diff_tensor.py?rev=3018&r1=3017&r2=3018&view=diff
==============================================================================
--- 1.3/data/diff_tensor.py (original)
+++ 1.3/data/diff_tensor.py Sun Feb 18 06:40:36 2007
@@ -151,6 +151,118 @@
self._update_object(param_name, target, update_if_set, depends,
category)
+ def __update_sim_append(self, param_name, index):
+ """Update the Monte Carlo simulation data lists when a simulation
value is appended.
+
+ @param param_name: The MC sim parameter name which is being
appended to.
+ @type param_name: str
+ @param index: The index of the Monte Carlo simulation which
was set.
+ @type index: int
+ """
+
+ # Loop over the targets.
+ for target, update_if_set, depends in
dependency_generator(self.type):
+ # Only update if the parameter name is within the
'update_if_set' list.
+ if not param_name in update_if_set:
+ continue
+
+ # Get the function for calculating the value.
+ fn = globals()['calc_'+target]
+
+ # Get all the dependencies if possible.
+ missing_dep = 0
+ deps = ()
+ for dep_name in depends:
+ # Modify the dependency name.
+ if dep_name != 'type':
+ dep_name = dep_name+'_sim'
+
+ # Test if the MC sim object exists.
+ if not hasattr(self, dep_name):
+ missing_dep = 1
+ break
+
+ # Get the MC dependency.
+ dep_obj = getattr(self, dep_name)
+
+ # The diffusion tensor type.
+ if dep_name == 'type':
+ deps = deps+(dep_obj,)
+ continue
+
+ # Test if the MC sim dependency is long enough.
+ if len(dep_obj) <= index:
+ missing_dep = 1
+ break
+
+ # Place the value corresponding to the index into the 'deps'
array.
+ deps = deps+(dep_obj[index],)
+
+ # Only update the MC simulation object if its dependencies exist.
+ if not missing_dep:
+ # Get the target object.
+ target_obj = getattr(self, target+'_sim')
+
+ # Calculate and set the value.
+ target_obj.append_untouchable_item(fn(*deps))
+
+
+ def __update_sim_set(self, param_name, index):
+ """Update the Monte Carlo simulation data lists when a simulation
value is set.
+
+ @param param_name: The MC sim parameter name which is being set.
+ @type param_name: str
+ @param index: The index of the Monte Carlo simulation which
was set.
+ @type index: int
+ """
+
+ # Loop over the targets.
+ for target, update_if_set, depends in
dependency_generator(self.type):
+ # Only update if the parameter name is within the
'update_if_set' list.
+ if not param_name in update_if_set:
+ continue
+
+ # Get the function for calculating the value.
+ fn = globals()['calc_'+target]
+
+ # Get all the dependencies if possible.
+ missing_dep = 0
+ deps = ()
+ for dep_name in depends:
+ # Modify the dependency name.
+ if dep_name != 'type':
+ dep_name = dep_name+'_sim'
+
+ # Test if the MC sim object exists.
+ if not hasattr(self, dep_name):
+ missing_dep = 1
+ break
+
+ # Get the MC dependency.
+ dep_obj = getattr(self, dep_name)
+
+ # The diffusion tensor type.
+ if dep_name == 'type':
+ deps = deps+(dep_obj,)
+ continue
+
+ # Test if the MC sim dependency is long enough.
+ if len(dep_obj) <= index:
+ missing_dep = 1
+ break
+
+ # Place the value corresponding to the index into the 'deps'
array.
+ deps = deps+(dep_obj[index],)
+
+ # Only update the MC simulation object if its dependencies exist.
+ if not missing_dep:
+ # Get the target object.
+ target_obj = getattr(self, target+'_sim')
+
+ # Calculate and set the value.
+ target_obj.set_untouchable_item(index, fn(*deps))
+
+
def _update_object(self, param_name, target, update_if_set, depends,
category):
"""Function for updating the target object, its error, and the MC
simulations.
@@ -166,7 +278,7 @@
@param update_if_set: If the parameter being set by the
__setattr__() function is not
within this list of parameters, don't waste time updating the
target.
- @param depends: An array of names objects that the target is
dependant upon.
+ @param depends: An array of names objects that the target is
dependent upon.
@type depends: array of str
@param category: The category of the object to update (one of
'val', 'err', or
'sim').
@@ -195,7 +307,7 @@
############
if category == 'val':
- # Get all the dependancies if possible.
+ # Get all the dependencies if possible.
missing_dep = 0
deps = ()
for dep_name in depends:
@@ -215,7 +327,7 @@
if Debug:
print "Deps: " + `deps`
- # Only update the object if its dependancies exist.
+ # Only update the object if its dependencies exist.
if not missing_dep:
# Calculate the value.
value = fn(*deps)
@@ -232,7 +344,7 @@
############
if category == 'err':
- # Get all the dependancies if possible.
+ # Get all the dependencies if possible.
missing_dep = 0
deps = ()
for dep_name in depends:
@@ -244,7 +356,7 @@
# Get the object and place it into the 'deps' tuple.
deps = deps+(getattr(self, dep_name+'_err'),)
- # Only update the error object if its dependancies exist.
+ # Only update the error object if its dependencies exist.
if not missing_dep:
# Calculate the value.
value = fn(*deps)
@@ -257,57 +369,49 @@
##############################
if category == 'sim':
- # Get all the dependancies if possible.
+ # Get all the dependencies if possible.
missing_dep = 0
deps = []
for dep_name in depends:
- # Test if the error object exists.
- if not hasattr(self, dep_name+'_sim'):
- missing_dep = 1
- break
-
- # Get the object and place it into the 'deps' array.
- deps.append(getattr(self, dep_name+'_sim'))
-
- # The number of simulations.
- if deps:
- num_sim = len(deps[0])
- else:
- num_sim = len(getattr(self, update_if_set[0]+'_sim'))
-
- # Only update the MC simulation object if its dependancies exist.
+ # Modify the dependency name.
+ if dep_name != 'type':
+ dep_name = dep_name+'_sim'
+
+ # Test if the MC sim object exists.
+ if not hasattr(self, dep_name):
+ missing_dep = 1
+ break
+
+ # Only create the MC simulation object if its dependencies exist.
if not missing_dep:
- # Initialise an empty array to store the MC simulation
object elements.
- sim_values = DiffTensorSimList(self)
-
- # Loop over the simulations.
- for i in xrange(num_sim):
- # Create a tuple of the dependancies.
- deps_tuple = ()
- for dep in deps:
- deps_tuple = deps_tuple+(dep[i],)
-
- # Calculate the value.
- sim_values.append(fn(*deps_tuple))
-
- # Set the attribute.
- self.__dict__[target+'_sim'] = sim_values
+ # Initialise an empty array to store the MC simulation
object elements (if it doesn't already exist).
+ if not target+'_sim' in self.__dict__:
+ self.__dict__[target+'_sim'] = DiffTensorSimList(target,
self)
class DiffTensorSimList(ListType):
"""Empty data container for Monte Carlo simulation diffusion tensor
data."""
- def __init__(self, diff_element):
- """Make the parent object accessible to this list object."""
-
- self.__diff_element = diff_element
+ def __init__(self, param_name, diff_element):
+ """Initialise the Monte Carlo simulation parameter list.
+
+ This function makes the parameter name and parent object accessible
to the functions of this
+ list object.
+ """
+
+ self.param_name = param_name
+ self.diff_element = diff_element
def __setitem__(self, index, value):
"""Set the value."""
+ # Set the value.
ListType.__setitem__(self, index, value)
+
+ # Then update the other lists.
+
self.diff_element._DiffTensorElement__update_sim_set(self.param_name, index)
def append(self, value):
@@ -315,3 +419,20 @@
# Append the value to the list.
self[len(self):len(self)] = [value]
+
+ # Update the other MC lists.
+
self.diff_element._DiffTensorElement__update_sim_append(self.param_name,
len(self)-1)
+
+
+ def append_untouchable_item(self, value):
+ """Append the value for an untouchable MC data structure."""
+
+ # Append the value to the list.
+ self[len(self):len(self)] = [value]
+
+
+ def set_untouchable_item(self, index, value):
+ """Set the value for an untouchable MC data structure."""
+
+ # Set the value.
+ ListType.__setitem__(self, index, value)
Modified: 1.3/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/diffusion_tensor.py?rev=3018&r1=3017&r2=3018&view=diff
==============================================================================
--- 1.3/generic_fns/diffusion_tensor.py (original)
+++ 1.3/generic_fns/diffusion_tensor.py Sun Feb 18 06:40:36 2007
@@ -382,6 +382,10 @@
# Return the tensor.
return rotation
+
+ # Raise an error.
+ else:
+ raise RelaxError, 'The diffusion tensor has not been specified'
def calc_tensor(rotation, tensor_diag):
Modified: 1.3/specific_fns/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free.py?rev=3018&r1=3017&r2=3018&view=diff
==============================================================================
--- 1.3/specific_fns/model_free.py (original)
+++ 1.3/specific_fns/model_free.py Sun Feb 18 06:40:36 2007
@@ -2783,7 +2783,7 @@
else:
# Create the data structure if it doesn't exist.
if not hasattr(self.relax.data.diff[self.run], 'tm_sim'):
- self.relax.data.diff[self.run].tm_sim =
DiffTensorSimList()
+ self.relax.data.diff[self.run].tm_sim =
DiffTensorSimList('tm', self.relax.data.diff[self.relax])
# Append the value.
self.relax.data.diff[self.run].tm_sim.append(tm)
@@ -2820,13 +2820,13 @@
else:
# Create the data structure if it doesn't exist.
if not hasattr(self.relax.data.diff[self.run], 'tm_sim'):
- self.relax.data.diff[self.run].tm_sim =
DiffTensorSimList()
+ self.relax.data.diff[self.run].tm_sim =
DiffTensorSimList('tm', self.relax.data.diff[self.relax])
if not hasattr(self.relax.data.diff[self.run], 'Da_sim'):
- self.relax.data.diff[self.run].Da_sim =
DiffTensorSimList()
+ self.relax.data.diff[self.run].Da_sim =
DiffTensorSimList('Da', self.relax.data.diff[self.relax])
if not hasattr(self.relax.data.diff[self.run], 'theta_sim'):
- self.relax.data.diff[self.run].theta_sim =
DiffTensorSimList()
+ self.relax.data.diff[self.run].theta_sim =
DiffTensorSimList('theta', self.relax.data.diff[self.relax])
if not hasattr(self.relax.data.diff[self.run], 'phi_sim'):
- self.relax.data.diff[self.run].phi_sim =
DiffTensorSimList()
+ self.relax.data.diff[self.run].phi_sim =
DiffTensorSimList('phi', self.relax.data.diff[self.relax])
# Append the value.
self.relax.data.diff[self.run].tm_sim.append(tm)
@@ -2870,17 +2870,17 @@
else:
# Create the data structure if it doesn't exist.
if not hasattr(self.relax.data.diff[self.run], 'tm_sim'):
- self.relax.data.diff[self.run].tm_sim =
DiffTensorSimList()
+ self.relax.data.diff[self.run].tm_sim =
DiffTensorSimList('tm', self.relax.data.diff[self.relax])
if not hasattr(self.relax.data.diff[self.run], 'Da_sim'):
- self.relax.data.diff[self.run].Da_sim =
DiffTensorSimList()
+ self.relax.data.diff[self.run].Da_sim =
DiffTensorSimList('Da', self.relax.data.diff[self.relax])
if not hasattr(self.relax.data.diff[self.run], 'Dr_sim'):
- self.relax.data.diff[self.run].Dr_sim =
DiffTensorSimList()
+ self.relax.data.diff[self.run].Dr_sim =
DiffTensorSimList('Dr', self.relax.data.diff[self.relax])
if not hasattr(self.relax.data.diff[self.run], 'alpha_sim'):
- self.relax.data.diff[self.run].alpha_sim =
DiffTensorSimList()
+ self.relax.data.diff[self.run].alpha_sim =
DiffTensorSimList('alpha', self.relax.data.diff[self.relax])
if not hasattr(self.relax.data.diff[self.run], 'beta_sim'):
- self.relax.data.diff[self.run].beta_sim =
DiffTensorSimList()
+ self.relax.data.diff[self.run].beta_sim =
DiffTensorSimList('beta', self.relax.data.diff[self.relax])
if not hasattr(self.relax.data.diff[self.run], 'gamma_sim'):
- self.relax.data.diff[self.run].gamma_sim =
DiffTensorSimList()
+ self.relax.data.diff[self.run].gamma_sim =
DiffTensorSimList('gamma', self.relax.data.diff[self.relax])
# Append the value.
self.relax.data.diff[self.run].tm_sim.append(tm)
Modified: 1.3/test_suite/unit_tests/data/test_diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/data/test_diff_tensor.py?rev=3018&r1=3017&r2=3018&view=diff
==============================================================================
--- 1.3/test_suite/unit_tests/data/test_diff_tensor.py (original)
+++ 1.3/test_suite/unit_tests/data/test_diff_tensor.py Sun Feb 18 06:40:36
2007
@@ -90,10 +90,10 @@
self.diff_data.type = 'spheroid'
# Set the MC sim diffusion parameter lists.
- self.diff_data.tm_sim = DiffTensorSimList(self.diff_data)
- self.diff_data.Da_sim = DiffTensorSimList(self.diff_data)
- self.diff_data.theta_sim = DiffTensorSimList(self.diff_data)
- self.diff_data.phi_sim = DiffTensorSimList(self.diff_data)
+ self.diff_data.tm_sim = DiffTensorSimList('tm', self.diff_data)
+ self.diff_data.Da_sim = DiffTensorSimList('Da', self.diff_data)
+ self.diff_data.theta_sim = DiffTensorSimList('theta', self.diff_data)
+ self.diff_data.phi_sim = DiffTensorSimList('phi', self.diff_data)
# Append the values.
self.diff_data.tm_sim.append(tm)
@@ -252,17 +252,16 @@
self.diff_data.type = 'spheroid'
# Set the MC sim diffusion parameter lists.
- self.diff_data.tm_sim = DiffTensorSimList(self.diff_data)
- self.diff_data.Da_sim = DiffTensorSimList(self.diff_data)
- self.diff_data.theta_sim = DiffTensorSimList(self.diff_data)
- self.diff_data.phi_sim = DiffTensorSimList(self.diff_data)
+ self.diff_data.tm_sim = DiffTensorSimList('tm', self.diff_data)
+ self.diff_data.Da_sim = DiffTensorSimList('Da', self.diff_data)
+ self.diff_data.theta_sim = DiffTensorSimList('theta', self.diff_data)
+ self.diff_data.phi_sim = DiffTensorSimList('phi', self.diff_data)
# Append the initial values.
self.diff_data.tm_sim.append(2e-9)
self.diff_data.Da_sim.append(1e5)
self.diff_data.theta_sim.append(0.0)
self.diff_data.phi_sim.append(2.0 * pi)
- print self.diff_data
# The new MC sim parameter values.
tm = 0.5e-9
@@ -277,7 +276,6 @@
self.diff_data.phi_sim[0] = phi
# Test the set values.
- print self.diff_data
self.assertEqual(self.diff_data.type, 'spheroid')
self.assertEqual(self.diff_data.tm_sim[0], tm)
self.assertEqual(self.diff_data.Da_sim[0], Da)
r3018 - in /1.3: data/ generic_fns/ specific_fns/ test_suite/unit_tests/data/