Author: bugman
Date: Tue Jun 23 16:45:44 2009
New Revision: 9137
URL: http://svn.gna.org/viewcvs/relax?rev=9137&view=rev
Log:
Updated the init() and set() method to allow alignment tensor errors to be
input.
Modified:
branches/frame_order/generic_fns/align_tensor.py
Modified: branches/frame_order/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order/generic_fns/align_tensor.py?rev=9137&r1=9136&r2=9137&view=diff
==============================================================================
--- branches/frame_order/generic_fns/align_tensor.py (original)
+++ branches/frame_order/generic_fns/align_tensor.py Tue Jun 23 16:45:44 2009
@@ -425,23 +425,23 @@
return data
-def init(tensor=None, params=None, scale=1.0, angle_units='deg',
param_types=0, errors=0):
+def init(tensor=None, params=None, scale=1.0, angle_units='deg',
param_types=0, errors=False):
"""Function for initialising the alignment tensor.
- @param tensor: The alignment tensor identification string.
+ @keyword tensor: The alignment tensor identification string.
@type tensor: str
- @param params: The alignment tensor parameters.
+ @keyword params: The alignment tensor parameters.
@type params: float
- @param scale: The alignment tensor eigenvalue scaling value.
+ @keyword scale: The alignment tensor eigenvalue scaling value.
@type scale: float
- @param angle_units: The units for the angle parameters (either 'deg'
or 'rad').
+ @keyword angle_units: The units for the angle parameters (either 'deg'
or 'rad').
@type angle_units: str
- @param param_types: The type of parameters supplied. The flag
values correspond to, 0:
+ @keyword param_types: The type of parameters supplied. The flag
values correspond to, 0:
{Axx, Ayy, Axy, Axz, Ayz}, and 1: {Azz, Axx-yy,
Axy, Axz, Ayz}.
@type param_types: int
- @param errors: A flag which determines if the alignment tensor
data or its errors are
+ @keyword errors: A flag which determines if the alignment tensor
data or its errors are
being input.
- @type errors: bin
+ @type errors: bool
"""
# Test if the current data pipe exists.
@@ -451,7 +451,7 @@
cdp = pipes.get_pipe()
# Test if alignment tensor data already exists.
- if align_data_exists(tensor):
+ if not errors and align_data_exists(tensor):
raise RelaxTensorError, 'alignment'
# Check the validity of the angle_units argument.
@@ -477,7 +477,7 @@
Syz = Syz * scale
# Set the parameters.
- set(tensor=cdp.align_tensors[-1], value=[Sxx, Syy, Sxy, Sxz, Syz],
param=['Sxx', 'Syy', 'Sxy', 'Sxz', 'Syz'])
+ set(tensor=cdp.align_tensors[-1], value=[Sxx, Syy, Sxy, Sxz, Syz],
param=['Sxx', 'Syy', 'Sxy', 'Sxz', 'Syz'], errors=errors)
# {Szz, Sxx-yy, Sxy, Sxz, Syz}.
elif param_types == 1:
@@ -1081,7 +1081,7 @@
return 'deg'
-def set(tensor=None, value=None, param=None):
+def set(tensor=None, value=None, param=None, errors=False):
"""Set the tensor.
@keyword tensor: The alignment tensor object.
@@ -1090,6 +1090,9 @@
@type value: list of float
@keyword param: The list of parameter names.
@type param: list of str
+ @keyword errors: A flag which determines if the alignment tensor data
or its errors are being
+ input.
+ @type errors: bool
"""
# Alias the current data pipe.
@@ -1217,11 +1220,18 @@
Syz = geo_values[geo_params.index('Syz')]
# Set the internal parameter values.
- tensor.Axx = 2.0/3.0 * Sxx
- tensor.Ayy = 2.0/3.0 * Syy
- tensor.Axy = 2.0/3.0 * Sxy
- tensor.Axz = 2.0/3.0 * Sxz
- tensor.Ayz = 2.0/3.0 * Syz
+ if errors:
+ tensor.Axx_err = 2.0/3.0 * Sxx
+ tensor.Ayy_err = 2.0/3.0 * Syy
+ tensor.Axy_err = 2.0/3.0 * Sxy
+ tensor.Axz_err = 2.0/3.0 * Sxz
+ tensor.Ayz_err = 2.0/3.0 * Syz
+ else:
+ tensor.Axx = 2.0/3.0 * Sxx
+ tensor.Ayy = 2.0/3.0 * Syy
+ tensor.Axy = 2.0/3.0 * Sxy
+ tensor.Axz = 2.0/3.0 * Sxz
+ tensor.Ayz = 2.0/3.0 * Syz
# The geometric parameter set {Szz, Sxxyy, Sxy, Sxz, Syz}.
elif geo_params.count('Szz') == 1 and geo_params.count('Sxxyy') == 1
and geo_params.count('Sxy') == 1 and geo_params.count('Sxz') == 1 and
geo_params.count('Syz') == 1:
@@ -1233,11 +1243,18 @@
Syz = geo_values[geo_params.index('Syz')]
# Set the internal parameter values.
- tensor.Axx = 2.0/3.0 * -0.5*(Szz-Sxxyy)
- tensor.Ayy = 2.0/3.0 * -0.5*(Szz+Sxxyy)
- tensor.Axy = 2.0/3.0 * Sxy
- tensor.Axz = 2.0/3.0 * Sxz
- tensor.Ayz = 2.0/3.0 * Syz
+ if errors:
+ tensor.Axx_err = 2.0/3.0 * -0.5*(Szz-Sxxyy)
+ tensor.Ayy_err = 2.0/3.0 * -0.5*(Szz+Sxxyy)
+ tensor.Axy_err = 2.0/3.0 * Sxy
+ tensor.Axz_err = 2.0/3.0 * Sxz
+ tensor.Ayz_err = 2.0/3.0 * Syz
+ else:
+ tensor.Axx = 2.0/3.0 * -0.5*(Szz-Sxxyy)
+ tensor.Ayy = 2.0/3.0 * -0.5*(Szz+Sxxyy)
+ tensor.Axy = 2.0/3.0 * Sxy
+ tensor.Axz = 2.0/3.0 * Sxz
+ tensor.Ayz = 2.0/3.0 * Syz
# The geometric parameter set {Axx, Ayy, Axy, Axz, Ayz}.
elif geo_params.count('Axx') == 1 and geo_params.count('Ayy') == 1
and geo_params.count('Axy') == 1 and geo_params.count('Axz') == 1 and
geo_params.count('Ayz') == 1:
@@ -1249,11 +1266,18 @@
Ayz = geo_values[geo_params.index('Ayz')]
# Set the internal parameter values.
- tensor.Axx = Axx
- tensor.Ayy = Ayy
- tensor.Axy = Axy
- tensor.Axz = Axz
- tensor.Ayz = Ayz
+ if errors:
+ tensor.Axx_err = Axx
+ tensor.Ayy_err = Ayy
+ tensor.Axy_err = Axy
+ tensor.Axz_err = Axz
+ tensor.Ayz_err = Ayz
+ else:
+ tensor.Axx = Axx
+ tensor.Ayy = Ayy
+ tensor.Axy = Axy
+ tensor.Axz = Axz
+ tensor.Ayz = Ayz
# The geometric parameter set {Azz, Axxyy, Axy, Axz, Ayz}.
elif geo_params.count('Azz') == 1 and geo_params.count('Axxyy') == 1
and geo_params.count('Axy') == 1 and geo_params.count('Axz') == 1 and
geo_params.count('Ayz') == 1:
@@ -1265,11 +1289,18 @@
Ayz = geo_values[geo_params.index('Ayz')]
# Set the internal parameter values.
- tensor.Axx = -0.5*(Azz-Axxyy)
- tensor.Ayy = -0.5*(Azz+Axxyy)
- tensor.Axy = Axy
- tensor.Axz = Axz
- tensor.Ayz = Ayz
+ if errors:
+ tensor.Axx_err = -0.5*(Azz-Axxyy)
+ tensor.Ayy_err = -0.5*(Azz+Axxyy)
+ tensor.Axy_err = Axy
+ tensor.Axz_err = Axz
+ tensor.Ayz_err = Ayz
+ else:
+ tensor.Axx = -0.5*(Azz-Axxyy)
+ tensor.Ayy = -0.5*(Azz+Axxyy)
+ tensor.Axy = Axy
+ tensor.Axz = Axz
+ tensor.Ayz = Ayz
# The geometric parameter set {Pxx, Pyy, Pxy, Pxz, Pyz}.
elif geo_params.count('Pxx') == 1 and geo_params.count('Pyy') == 1
and geo_params.count('Pxy') == 1 and geo_params.count('Pxz') == 1 and
geo_params.count('Pyz') == 1:
@@ -1281,11 +1312,18 @@
Pyz = geo_values[geo_params.index('Pyz')]
# Set the internal parameter values.
- tensor.Axx = Pxx - 1.0/3.0
- tensor.Ayy = Pyy - 1.0/3.0
- tensor.Axy = Pxy
- tensor.Axz = Pxz
- tensor.Ayz = Pyz
+ if errors:
+ tensor.Axx_err = Pxx - 1.0/3.0
+ tensor.Ayy_err = Pyy - 1.0/3.0
+ tensor.Axy_err = Pxy
+ tensor.Axz_err = Pxz
+ tensor.Ayz_err = Pyz
+ else:
+ tensor.Axx = Pxx - 1.0/3.0
+ tensor.Ayy = Pyy - 1.0/3.0
+ tensor.Axy = Pxy
+ tensor.Axz = Pxz
+ tensor.Ayz = Pyz
# The geometric parameter set {Pzz, Pxxyy, Pxy, Pxz, Pyz}.
elif geo_params.count('Pzz') == 1 and geo_params.count('Pxxyy') == 1
and geo_params.count('Pxy') == 1 and geo_params.count('Pxz') == 1 and
geo_params.count('Pyz') == 1:
@@ -1297,11 +1335,18 @@
Pyz = geo_values[geo_params.index('Pyz')]
# Set the internal parameter values.
- tensor.Axx = -0.5*(Pzz-Pxxyy) - 1.0/3.0
- tensor.Ayy = -0.5*(Pzz+Pxxyy) - 1.0/3.0
- tensor.Axy = Pxy
- tensor.Axz = Pxz
- tensor.Ayz = Pyz
+ if errors:
+ tensor.Axx_err = -0.5*(Pzz-Pxxyy) - 1.0/3.0
+ tensor.Ayy_err = -0.5*(Pzz+Pxxyy) - 1.0/3.0
+ tensor.Axy_err = Pxy
+ tensor.Axz_err = Pxz
+ tensor.Ayz_err = Pyz
+ else:
+ tensor.Axx = -0.5*(Pzz-Pxxyy) - 1.0/3.0
+ tensor.Ayy = -0.5*(Pzz+Pxxyy) - 1.0/3.0
+ tensor.Axy = Pxy
+ tensor.Axz = Pxz
+ tensor.Ayz = Pyz
# Unknown parameter combination.
else:
r9137 - /branches/frame_order/generic_fns/align_tensor.py