Author: bugman
Date: Fri Apr 11 11:58:46 2014
New Revision: 22714
URL: http://svn.gna.org/viewcvs/relax?rev=22714&view=rev
Log:
Eliminated a lot of unused code from the pipe_control.align_tensor module.
This includes the functions data_names(), default_value(), map_bounds(),
map_labels(),
return_conversion_factor(), return_data_name() and return_units() as well as
the unused and very old
user function documentation __default_value_prompt_doc__,
__return_data_name_prompt_doc__ and
__set_prompt_doc__. These are all remnants from the origin of the module -
the copying of the
diffusion_tensor module. But they have never been used.
Modified:
trunk/pipe_control/align_tensor.py
Modified: trunk/pipe_control/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/align_tensor.py?rev=22714&r1=22713&r2=22714&view=diff
==============================================================================
--- trunk/pipe_control/align_tensor.py (original)
+++ trunk/pipe_control/align_tensor.py Fri Apr 11 11:58:46 2014
@@ -157,60 +157,6 @@
dp_to.align_ids.append(align_id)
-def data_names():
- """Function for returning a list of names of data structures associated
with the sequence."""
-
- names = [ 'align_params' ]
-
- return names
-
-
-def default_value(param):
- """Return the default values for the alignment tensor parameters.
-
- @param param: The name of the parameter.
- @type param: str
- @return: The default value, which for all parameters is set to
zero.
- @rtype: float
- """
-
- # Return 0.0.
- return 0.0
-
-# User function documentation.
-__default_value_prompt_doc__ = """
- Alignment tensor parameter default values
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- ________________________________________________________________________
- | | | |
- | Data type | Object name | Value |
- |________________________|____________________|________________________|
- | | | |
- | Axx | 'Axx' | 0.0 |
- | | | |
- | Ayy | 'Ayy' | 0.0 |
- | | | |
- | Azz | 'Azz' | 0.0 |
- | | | |
- | Axxyy | 'Axxyy' | 0.0 |
- | | | |
- | Axy | 'Axy' | 0.0 |
- | | | |
- | Axz | 'Axz' | 0.0 |
- | | | |
- | Ayz | 'Ayz' | 0.0 |
- | | | |
- | alpha | 'alpha' | 0.0 |
- | | | |
- | beta | 'beta' | 0.0 |
- | | | |
- | gamma | 'gamma' | 0.0 |
- |________________________|____________________|________________________|
-
-"""
-
-
def delete(tensor=None):
"""Function for deleting alignment tensor data.
@@ -943,92 +889,6 @@
tensor_obj.set(param='align_id', value=align_id)
-def map_bounds(param):
- """The function for creating bounds for the mapping function."""
-
- # {Axx, Ayy, Azz, Axxyy, Axy, Axz, Ayz}.
- if param in ['Axx', 'Ayy', 'Azz', 'Axxyy', 'Axy', 'Axz', 'Ayz']:
- return [-50, 50]
-
- # alpha.
- elif param == 'alpha':
- return [0, 2*pi]
-
- # beta.
- elif param == 'beta':
- return [0, pi]
-
- # gamma.
- elif param == 'gamma':
- return [0, 2*pi]
-
-
-def map_labels(index, params, bounds, swap, inc):
- """Function for creating labels, tick locations, and tick values for an
OpenDX map.
-
- @param index: The index (which isn't used here?!?).
- @type index: int
- @param params: The list of parameter names.
- @type params: list of str
- @param bounds: The bounds of the map.
- @type bounds: list of lists (of a float and bin)
- @param swap: An array for switching axes around.
- @type swap: list of int
- @param inc: The number of increments of one dimension in the map.
- @type inc: list of int
- """
-
- # Initialise.
- labels = "{"
- tick_locations = []
- tick_values = []
- n = len(params)
- axis_incs = 5
- loc_inc = inc / axis_incs
-
- # Increment over the model parameters.
- for i in range(n):
- # Parameter conversion factors.
- factor = return_conversion_factor(params[swap[i]])
-
- # Parameter units.
- units = return_units(params[swap[i]])
-
- # Labels.
- if units:
- labels = labels + "\"" + params[swap[i]] + " (" + units + ")\""
- else:
- labels = labels + "\"" + params[swap[i]] + "\""
-
- # Tick values.
- vals = bounds[swap[i], 0] / factor
- val_inc = (bounds[swap[i], 1] - bounds[swap[i], 0]) / (axis_incs *
factor)
-
- if i < n - 1:
- labels = labels + " "
- else:
- labels = labels + "}"
-
- # Tick locations.
- string = "{"
- val = 0.0
- for j in range(axis_incs + 1):
- string = string + " " + repr(val)
- val = val + loc_inc
- string = string + " }"
- tick_locations.append(string)
-
- # Tick values.
- string = "{"
- for j in range(axis_incs + 1):
- string = string + "\"" + "%.2f" % vals + "\" "
- vals = vals + val_inc
- string = string + "}"
- tick_values.append(string)
-
- return labels, tick_locations, tick_values
-
-
def matrix_angles(basis_set=0, tensors=None):
"""Function for calculating the 5D angles between the alignment tensors.
@@ -1256,204 +1116,6 @@
cdp.align_tensors.reduction.append([index_full, index_red])
-def return_conversion_factor(param):
- """Function for returning the factor of conversion between different
parameter units.
-
- @param param: The parameter name.
- @type param: str
- @return: The conversion factor.
- @rtype: float
- """
-
- # Get the object name.
- object_name = return_data_name(param)
-
- # {Axx, Ayy, Azz, Axxyy, Axy, Axz, Ayz}.
- if object_name in ['Axx', 'Ayy', 'Azz', 'Axxyy', 'Axy', 'Axz', 'Ayz']:
- return 1.0
-
- # Angles.
- elif object_name in ['alpha', 'beta', 'gamma']:
- return (2.0*pi) / 360.0
-
- # No conversion factor.
- else:
- return 1.0
-
-
-def return_data_name(name):
- """Return the parameter name.
-
- @param name: The name of the parameter to return the name of.
- @type name: str
- @return: The parameter name.
- @rtype: str
- """
-
- # Enforce that the name must be a string.
- if not isinstance(name, str):
- raise RelaxStrError('name', name)
-
- # Sxx.
- if search('^[Ss]xx$', name):
- return 'Sxx'
-
- # Syy.
- if search('^[Ss]yy$', name):
- return 'Syy'
-
- # Szz.
- if search('^[Ss]zz$', name):
- return 'Szz'
-
- # Sxy.
- if search('^[Ss]xy$', name):
- return 'Sxy'
-
- # Sxz.
- if search('^[Ss]xz$', name):
- return 'Sxz'
-
- # Syz.
- if search('^[Ss]yz$', name):
- return 'Syz'
-
- # Sxx-yy.
- if search('^[Ss]xxyy$', name):
- return 'Sxxyy'
-
- # Axx.
- if search('^[Aa]xx$', name):
- return 'Axx'
-
- # Ayy.
- if search('^[Aa]yy$', name):
- return 'Ayy'
-
- # Azz.
- if search('^[Aa]zz$', name):
- return 'Azz'
-
- # Axy.
- if search('^[Aa]xy$', name):
- return 'Axy'
-
- # Axz.
- if search('^[Aa]xz$', name):
- return 'Axz'
-
- # Ayz.
- if search('^[Aa]yz$', name):
- return 'Ayz'
-
- # Axx-yy.
- if search('^[Aa]xxyy$', name):
- return 'Axxyy'
-
- # Pxx.
- if search('^[Pp]xx$', name):
- return 'Pxx'
-
- # Pyy.
- if search('^[Pp]yy$', name):
- return 'Pyy'
-
- # Pzz.
- if search('^[Pp]zz$', name):
- return 'Pzz'
-
- # Pxy.
- if search('^[Pp]xy$', name):
- return 'Pxy'
-
- # Pxz.
- if search('^[Pp]xz$', name):
- return 'Pxz'
-
- # Pyz.
- if search('^[Pp]yz$', name):
- return 'Pyz'
-
- # Pxx-yy.
- if search('^[Pp]xxyy$', name):
- return 'Pxxyy'
-
- # alpha.
- if search('^a$', name) or search('alpha', name):
- return 'alpha'
-
- # beta.
- if search('^b$', name) or search('beta', name):
- return 'beta'
-
- # gamma.
- if search('^g$', name) or search('gamma', name):
- return 'gamma'
-
- # No parameter?
- raise RelaxUnknownParamError(name)
-
-# User function documentation.
-__return_data_name_prompt_doc__ = """
- Alignment tensor parameter string matching patterns
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-
____________________________________________________________________________________________
- | |
| |
- | Data type | Object name
| Patterns |
-
|________________________________________________________|______________|__________________|
- | |
| |
- | The xx component of the Saupe order matrix - Sxx | 'Sxx'
| '^[Sa]xx$' |
- | |
| |
- | The yy component of the Saupe order matrix - Syy | 'Syy'
| '^[Sa]yy$' |
- | |
| |
- | The zz component of the Saupe order matrix - Szz | 'Szz'
| '^[Sa]zz$' |
- | |
| |
- | The xy component of the Saupe order matrix - Sxy | 'Sxy'
| '^[Sa]xy$' |
- | |
| |
- | The xz component of the Saupe order matrix - Sxz | 'Sxz'
| '^[Sa]xz$' |
- | |
| |
- | The yz component of the Saupe order matrix - Syz | 'Syz'
| '^[Sa]yz$' |
- | |
| |
- | The xx-yy component of the Saupe order matrix - Sxx-yy | 'Sxxyy'
| '^[Sa]xxyy$' |
- | |
| |
- | The xx component of the alignment tensor - Axx | 'Axx'
| '^[Aa]xx$' |
- | |
| |
- | The yy component of the alignment tensor - Ayy | 'Ayy'
| '^[Aa]yy$' |
- | |
| |
- | The zz component of the alignment tensor - Azz | 'Azz'
| '^[Aa]zz$' |
- | |
| |
- | The xy component of the alignment tensor - Axy | 'Axy'
| '^[Aa]xy$' |
- | |
| |
- | The xz component of the alignment tensor - Axz | 'Axz'
| '^[Aa]xz$' |
- | |
| |
- | The yz component of the alignment tensor - Ayz | 'Ayz'
| '^[Aa]yz$' |
- | |
| |
- | The xx-yy component of the alignment tensor - Axx-yy | 'Axxyy'
| '^[Aa]xxyy$' |
- | |
| |
- | The xx component of the probability matrix - Pxx | 'Pxx'
| '^[Pa]xx$' |
- | |
| |
- | The yy component of the probability matrix - Pyy | 'Pyy'
| '^[Pa]yy$' |
- | |
| |
- | The zz component of the probability matrix - Pzz | 'Pzz'
| '^[Pa]zz$' |
- | |
| |
- | The xy component of the probability matrix - Pxy | 'Pxy'
| '^[Pa]xy$' |
- | |
| |
- | The xz component of the probability matrix - Pxz | 'Pxz'
| '^[Pa]xz$' |
- | |
| |
- | The yz component of the probability matrix - Pyz | 'Pyz'
| '^[Pa]yz$' |
- | |
| |
- | The xx-yy component of the probability matrix - Pxx-yy | 'Pxxyy'
| '^[Pa]xxyy$' |
- | |
| |
- | The first Euler angle of the alignment tensor - alpha | 'alpha'
| '^a$' or 'alpha' |
- | |
| |
- | The second Euler angle of the alignment tensor - beta | 'beta'
| '^b$' or 'beta' |
- | |
| |
- | The third Euler angle of the alignment tensor - gamma | 'gamma'
| '^g$' or 'gamma' |
-
|________________________________________________________|______________|__________________|
-"""
-
-
def return_tensor(index, skip_fixed=True):
"""Return the tensor container for the given index, skipping fixed
tensors if required.
@@ -1483,27 +1145,6 @@
# Return False if the container was not found.
return False
-
-
-def return_units(param):
- """Function for returning a string representing the parameters units.
-
- @param param: The parameter name.
- @type param: str
- @return: The string representation of the units.
- @rtype: str
- """
-
- # Get the object name.
- object_name = return_data_name(param)
-
- # {Axx, Ayy, Azz, Axxyy, Axy, Axz, Ayz}.
- if object_name in ['Axx', 'Ayy', 'Azz', 'Axxyy', 'Axy', 'Axz', 'Ayz']:
- return 'Hz'
-
- # Angles.
- elif object_name in ['alpha', 'beta', 'gamma']:
- return 'deg'
def set(tensor=None, value=None, param=None, errors=False):
@@ -1528,16 +1169,13 @@
# Loop over the parameters.
for i in range(len(param)):
- # Get the object name.
- param[i] = return_data_name(param[i])
-
# Unknown parameter.
if param[i] == None:
raise RelaxUnknownParamError("alignment tensor", 'None')
# Default value.
if value[i] == None:
- value[i] = default_value(object_names[i])
+ value[i] = 0.0
# Geometric parameter.
if param[i] in ['Sxx', 'Syy', 'Szz', 'Sxxyy', 'Sxy', 'Sxz', 'Syz',
'Axx', 'Ayy', 'Azz', 'Axxyy', 'Axy', 'Axz', 'Ayz', 'Pxx', 'Pyy', 'Pzz',
'Pxxyy', 'Pxy', 'Pxz', 'Pyz']:
@@ -1912,35 +1550,6 @@
if orient_params:
fold_angles()
-# User function documentation.
-__set_prompt_doc__ = """
- Alignment tensor set details
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- If the alignment tensor has not been setup, use the more powerful
function
- 'alignment_tensor.init' to initialise the tensor parameters.
-
- The alignment tensor parameters can only be set when the data pipe
corresponds to model-free
- analysis. The units of the parameters are:
-
- Unitless for Sxx, Syy, Szz, Sxxyy, Sxy, Sxz, Syz.
- Unitless for Axx, Ayy, Azz, Axxyy, Axy, Axz, Ayz.
- Unitless for Pxx, Pyy, Pzz, Pxxyy, Pxy, Pxz, Pyz.
- Radians for all angles (alpha, beta, gamma).
-
- If a single geometric parameter is supplied, it must be one of Bxx, Byy,
Bxy, Bxz, Byz, where B
- is one of S, A, or P. For the parameters Bzz and Bxxyy, it is not
possible to determine how to
- use the currently set values together with the supplied value to
calculate the new internal
- parameters. When supplying multiple geometric parameters, the set must
belong to one of
-
- {Sxx, Syy, Sxy, Sxz, Syz},
- {Szz, Sxxyy, Sxy, Sxz, Syz}.
- {Axx, Ayy, Axy, Axz, Ayz},
- {Azz, Axxyy, Axy, Axz, Ayz}.
- {Pxx, Pyy, Pxy, Pxz, Pyz},
- {Pzz, Pxxyy, Pxy, Pxz, Pyz}.
-"""
-
def set_align_id(tensor=None, align_id=None):
"""Set the align ID string for the given tensor.
r22714 - /trunk/pipe_control/align_tensor.py