Author: bugman
Date: Wed Jul 23 15:43:33 2014
New Revision: 24678
URL: http://svn.gna.org/viewcvs/relax?rev=24678&view=rev
Log:
The diffusion_tensor.init user function can now set initial tensor parameter
values of None.
This is to allow for the new grid search preset flag. Therefore allowing the
values to be None
allows for a grid search to be performed by default.
Modified:
branches/zooming_grid_search/pipe_control/diffusion_tensor.py
branches/zooming_grid_search/user_functions/diffusion_tensor.py
Modified: branches/zooming_grid_search/pipe_control/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/pipe_control/diffusion_tensor.py?rev=24678&r1=24677&r2=24678&view=diff
==============================================================================
--- branches/zooming_grid_search/pipe_control/diffusion_tensor.py
(original)
+++ branches/zooming_grid_search/pipe_control/diffusion_tensor.py Wed
Jul 23 15:43:33 2014
@@ -389,82 +389,84 @@
# The diffusion type.
cdp.diff_tensor.set_type('ellipsoid')
- # (tm, Da, Dr, alpha, beta, gamma).
- if param_types == 0:
- # Unpack the tuple.
- tm, Da, Dr, alpha, beta, gamma = params
-
- # Scaling.
- tm = tm * time_scale
- Da = Da * d_scale
-
- # Set the parameters.
- set(value=[tm, Da, Dr], param=['tm', 'Da', 'Dr'])
-
- # (Diso, Da, Dr, alpha, beta, gamma).
- elif param_types == 1:
- # Unpack the tuple.
- Diso, Da, Dr, alpha, beta, gamma = params
-
- # Scaling.
- Diso = Diso * d_scale
- Da = Da * d_scale
-
- # Set the parameters.
- set(value=[Diso, Da, Dr], param=['Diso', 'Da', 'Dr'])
-
- # (Dx, Dy, Dz, alpha, beta, gamma).
- elif param_types == 2:
- # Unpack the tuple.
- Dx, Dy, Dz, alpha, beta, gamma = params
-
- # Scaling.
- Dx = Dx * d_scale
- Dy = Dy * d_scale
- Dz = Dz * d_scale
-
- # Set the parameters.
- set(value=[Dx, Dy, Dz], param=['Dx', 'Dy', 'Dz'])
-
- # (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz).
- elif param_types == 3:
- # Unpack the tuple.
- Dxx, Dyy, Dzz, Dxy, Dxz, Dyz = params
-
- # Build the tensor.
- tensor = zeros((3, 3), float64)
- tensor[0, 0] = Dxx
- tensor[1, 1] = Dyy
- tensor[2, 2] = Dzz
- tensor[0, 1] = tensor[1, 0] = Dxy
- tensor[0, 2] = tensor[2, 0] = Dxz
- tensor[1, 2] = tensor[2, 1] = Dyz
-
- # Scaling.
- tensor = tensor * d_scale
-
- # Eigenvalues.
- Di, R, alpha, beta, gamma = tensor_eigen_system(tensor)
-
- # Set the parameters.
- set(value=[Di[0], Di[1], Di[2]], param=['Dx', 'Dy', 'Dz'])
-
- # Change the angular units.
- angle_units = 'rad'
-
- # Unknown parameter combination.
- else:
- raise RelaxUnknownParamCombError('param_types', param_types)
-
- # Convert the angles to radians.
- if angle_units == 'deg':
- print("Converting the angles from degrees to radian units.")
- alpha = (alpha / 360.0) * 2.0 * pi
- beta = (beta / 360.0) * 2.0 * pi
- gamma = (gamma / 360.0) * 2.0 * pi
-
- # Set the orientational parameters.
- set(value=[alpha, beta, gamma], param=['alpha', 'beta', 'gamma'])
+ # Set the parameter values.
+ if params[0] != None:
+ # (tm, Da, Dr, alpha, beta, gamma).
+ if param_types == 0:
+ # Unpack the tuple.
+ tm, Da, Dr, alpha, beta, gamma = params
+
+ # Scaling.
+ tm = tm * time_scale
+ Da = Da * d_scale
+
+ # Set the parameters.
+ set(value=[tm, Da, Dr], param=['tm', 'Da', 'Dr'])
+
+ # (Diso, Da, Dr, alpha, beta, gamma).
+ elif param_types == 1:
+ # Unpack the tuple.
+ Diso, Da, Dr, alpha, beta, gamma = params
+
+ # Scaling.
+ Diso = Diso * d_scale
+ Da = Da * d_scale
+
+ # Set the parameters.
+ set(value=[Diso, Da, Dr], param=['Diso', 'Da', 'Dr'])
+
+ # (Dx, Dy, Dz, alpha, beta, gamma).
+ elif param_types == 2:
+ # Unpack the tuple.
+ Dx, Dy, Dz, alpha, beta, gamma = params
+
+ # Scaling.
+ Dx = Dx * d_scale
+ Dy = Dy * d_scale
+ Dz = Dz * d_scale
+
+ # Set the parameters.
+ set(value=[Dx, Dy, Dz], param=['Dx', 'Dy', 'Dz'])
+
+ # (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz).
+ elif param_types == 3:
+ # Unpack the tuple.
+ Dxx, Dyy, Dzz, Dxy, Dxz, Dyz = params
+
+ # Build the tensor.
+ tensor = zeros((3, 3), float64)
+ tensor[0, 0] = Dxx
+ tensor[1, 1] = Dyy
+ tensor[2, 2] = Dzz
+ tensor[0, 1] = tensor[1, 0] = Dxy
+ tensor[0, 2] = tensor[2, 0] = Dxz
+ tensor[1, 2] = tensor[2, 1] = Dyz
+
+ # Scaling.
+ tensor = tensor * d_scale
+
+ # Eigenvalues.
+ Di, R, alpha, beta, gamma = tensor_eigen_system(tensor)
+
+ # Set the parameters.
+ set(value=[Di[0], Di[1], Di[2]], param=['Dx', 'Dy', 'Dz'])
+
+ # Change the angular units.
+ angle_units = 'rad'
+
+ # Unknown parameter combination.
+ else:
+ raise RelaxUnknownParamCombError('param_types', param_types)
+
+ # Convert the angles to radians.
+ if angle_units == 'deg':
+ print("Converting the angles from degrees to radian units.")
+ alpha = (alpha / 360.0) * 2.0 * pi
+ beta = (beta / 360.0) * 2.0 * pi
+ gamma = (gamma / 360.0) * 2.0 * pi
+
+ # Set the orientational parameters.
+ set(value=[alpha, beta, gamma], param=['alpha', 'beta', 'gamma'])
def fold_angles(sim_index=None):
@@ -664,7 +666,7 @@
cdp.diff_tensor.set_fixed(fixed)
# Spherical diffusion.
- if isinstance(params, float):
+ if isinstance(params, float) or params == None:
num_params = 1
sphere(params, time_scale, param_types)
@@ -1216,25 +1218,27 @@
# The diffusion type.
cdp.diff_tensor.set_type('sphere')
- # tm.
- if param_types == 0:
- # Scaling.
- tm = params * time_scale
-
- # Set the parameters.
- set(value=[tm], param=['tm'])
-
- # Diso
- elif param_types == 1:
- # Scaling.
- Diso = params * d_scale
-
- # Set the parameters.
- set(value=[Diso], param=['Diso'])
-
- # Unknown parameter combination.
- else:
- raise RelaxUnknownParamCombError('param_types', param_types)
+ # Set the parameter values.
+ if params != None:
+ # tm.
+ if param_types == 0:
+ # Scaling.
+ tm = params * time_scale
+
+ # Set the parameters.
+ set(value=[tm], param=['tm'])
+
+ # Diso
+ elif param_types == 1:
+ # Scaling.
+ Diso = params * d_scale
+
+ # Set the parameters.
+ set(value=[Diso], param=['Diso'])
+
+ # Unknown parameter combination.
+ else:
+ raise RelaxUnknownParamCombError('param_types', param_types)
def spheroid(params=None, time_scale=None, d_scale=None, angle_units=None,
param_types=None, spheroid_type=None):
@@ -1266,80 +1270,86 @@
raise RelaxError("The 'spheroid_type' argument " +
repr(spheroid_type) + " should be 'oblate', 'prolate', or None.")
cdp.diff_tensor.set(param='spheroid_type', value=spheroid_type)
- # (tm, Da, theta, phi).
- if param_types == 0:
- # Unpack the tuple.
- tm, Da, theta, phi = params
-
- # Scaling.
- tm = tm * time_scale
- Da = Da * d_scale
-
- # Set the parameters.
- set(value=[tm, Da], param=['tm', 'Da'])
-
- # (Diso, Da, theta, phi).
- elif param_types == 1:
- # Unpack the tuple.
- Diso, Da, theta, phi = params
-
- # Scaling.
- Diso = Diso * d_scale
- Da = Da * d_scale
-
- # Set the parameters.
- set(value=[Diso, Da], param=['Diso', 'Da'])
-
- # (tm, Dratio, theta, phi).
- elif param_types == 2:
- # Unpack the tuple.
- tm, Dratio, theta, phi = params
-
- # Scaling.
- tm = tm * time_scale
-
- # Set the parameters.
- set(value=[tm, Dratio], param=['tm', 'Dratio'])
-
- # (Dpar, Dper, theta, phi).
- elif param_types == 3:
- # Unpack the tuple.
- Dpar, Dper, theta, phi = params
-
- # Scaling.
- Dpar = Dpar * d_scale
- Dper = Dper * d_scale
-
- # Set the parameters.
- set(value=[Dpar, Dper], param=['Dpar', 'Dper'])
-
- # (Diso, Dratio, theta, phi).
- elif param_types == 4:
- # Unpack the tuple.
- Diso, Dratio, theta, phi = params
-
- # Scaling.
- Diso = Diso * d_scale
-
- # Set the parameters.
- set(value=[Diso, Dratio], param=['Diso', 'Dratio'])
-
- # Unknown parameter combination.
- else:
- raise RelaxUnknownParamCombError('param_types', param_types)
-
- # Convert the angles to radians.
- if angle_units == 'deg':
- print("Converting the angles from degrees to radian units.")
- theta = (theta / 360.0) * 2.0 * pi
- phi = (phi / 360.0) * 2.0 * pi
-
- # Set the orientational parameters.
- set(value=[theta, phi], param=['theta', 'phi'])
+ # Set the parameter values.
+ if params[0] != None:
+ # (tm, Da, theta, phi).
+ if param_types == 0:
+ # Unpack the tuple.
+ tm, Da, theta, phi = params
+
+ # Scaling.
+ tm = tm * time_scale
+ Da = Da * d_scale
+
+ # Set the parameters.
+ set(value=[tm, Da], param=['tm', 'Da'])
+
+ # (Diso, Da, theta, phi).
+ elif param_types == 1:
+ # Unpack the tuple.
+ Diso, Da, theta, phi = params
+
+ # Scaling.
+ Diso = Diso * d_scale
+ Da = Da * d_scale
+
+ # Set the parameters.
+ set(value=[Diso, Da], param=['Diso', 'Da'])
+
+ # (tm, Dratio, theta, phi).
+ elif param_types == 2:
+ # Unpack the tuple.
+ tm, Dratio, theta, phi = params
+
+ # Scaling.
+ tm = tm * time_scale
+
+ # Set the parameters.
+ set(value=[tm, Dratio], param=['tm', 'Dratio'])
+
+ # (Dpar, Dper, theta, phi).
+ elif param_types == 3:
+ # Unpack the tuple.
+ Dpar, Dper, theta, phi = params
+
+ # Scaling.
+ Dpar = Dpar * d_scale
+ Dper = Dper * d_scale
+
+ # Set the parameters.
+ set(value=[Dpar, Dper], param=['Dpar', 'Dper'])
+
+ # (Diso, Dratio, theta, phi).
+ elif param_types == 4:
+ # Unpack the tuple.
+ Diso, Dratio, theta, phi = params
+
+ # Scaling.
+ Diso = Diso * d_scale
+
+ # Set the parameters.
+ set(value=[Diso, Dratio], param=['Diso', 'Dratio'])
+
+ # Unknown parameter combination.
+ else:
+ raise RelaxUnknownParamCombError('param_types', param_types)
+
+ # Convert the angles to radians.
+ if angle_units == 'deg':
+ print("Converting the angles from degrees to radian units.")
+ theta = (theta / 360.0) * 2.0 * pi
+ phi = (phi / 360.0) * 2.0 * pi
+
+ # Set the orientational parameters.
+ set(value=[theta, phi], param=['theta', 'phi'])
def test_params(num_params):
"""Function for testing the validity of the input parameters."""
+
+ # No parameters were set.
+ if not hasattr(cdp.diff_tensor, 'tm'):
+ return
# An allowable error to account for machine precision, optimisation
quality, etc.
error = 1e-4
Modified: branches/zooming_grid_search/user_functions/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/user_functions/diffusion_tensor.py?rev=24678&r1=24677&r2=24678&view=diff
==============================================================================
--- branches/zooming_grid_search/user_functions/diffusion_tensor.py
(original)
+++ branches/zooming_grid_search/user_functions/diffusion_tensor.py Wed
Jul 23 15:43:33 2014
@@ -118,7 +118,8 @@
py_type = "num_or_num_tuple",
dim = [4, 6],
desc_short = "diffusion tensor parameters",
- desc = "The diffusion tensor data."
+ desc = "The diffusion tensor data.",
+ can_be_none = True
)
uf.add_keyarg(
name = "time_scale",
r24678 - in /branches/zooming_grid_search: pipe_control/diffusion_tensor.py user_functions/diffusion_tensor.py