Package specific_analyses :: Package relax_disp :: Module parameters
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Module parameters

source code

Functions relating to the parameters of the relaxation dispersion models.

Functions [hide private]
numpy float array
assemble_param_vector(spins=None, key=None, sim_index=None)
Assemble the dispersion relaxation dispersion curve fitting parameter vector.
source code
 
copy(pipe_from=None, pipe_to=None)
Copy dispersion parameters from one data pipe to another.
source code
 
disassemble_param_vector(param_vector=None, key=None, spins=None, sim_index=None)
Disassemble the relaxation dispersion parameter vector.
source code
 
get_param_names(spins=None, full=False)
Generate a list of dispersion parameter names for the given spins.
source code
float
get_value(key=None, spins=None, sim_index=None, param_name=None, spin_index=None, r20_key=None)
Return the value for the given parameter.
source code
numpy rank-2 NxM array, numpy rank-1 N array
linear_constraints(spins=None, scaling_matrix=None)
Set up the relaxation dispersion curve fitting linear constraint matrices A and b.
source code
str, int, int, str
loop_parameters(spins=None)
Generator function for looping of the model parameters of the cluster.
source code
 
param_conversion(key=None, spins=None, sim_index=None)
Calculate the non-model parameter values from the current parameter values.
source code
str, int, int
param_index_to_param_info(index=None, spins=None)
Convert the given parameter array index to parameter identifying information.
source code
int
param_num(spins=None)
Determine the number of parameters in the model.
source code
 
r1_setup()
Modify the current spin parameter list to either include or exclude the R1 parameter.
source code
 
set_value(value=None, key=None, spins=None, sim_index=None, param_name=None, spin_index=None, r20_key=None)
Set a specific parameter value.
source code
Variables [hide private]
  __package__ = 'specific_analyses.relax_disp'

Imports: deepcopy, array, float64, median, zeros, sys, MODEL_LIST_MMQ, MODEL_M61B, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, PARAMS_R1, PARAMS_R20, PARAMS_CHEM_SHIFT_DIFF, PARAMS_CHEM_SHIFT_DIFF_MMQ, PARAMS_SPIN, RelaxError, RelaxNoSequenceError, subsection, pipes, exists_mol_res_spin_data, return_spin, spin_loop, check_pipe, count_spins, generate_r20_key, has_exponential_exp_type, is_r1_optimised, loop_cluster, loop_exp_frq


Function Details [hide private]

assemble_param_vector(spins=None, key=None, sim_index=None)

source code 

Assemble the dispersion relaxation dispersion curve fitting parameter vector.

Parameters:
  • spins (list of SpinContainer instances) - The list of spin data containers for the block.
  • key (str or None) - The key for the R2eff and I0 parameters.
  • sim_index (int) - The optional MC simulation index.
Returns: numpy float array
An array of the parameter values of the dispersion relaxation model.

copy(pipe_from=None, pipe_to=None)

source code 

Copy dispersion parameters from one data pipe to another.

For spin clusters, the median of previous values is taken to avoid extreme outliers.

Parameters:
  • pipe_from (str) - The data pipe to copy the value from. This defaults to the current data pipe.
  • pipe_to (str) - The data pipe to copy the value to. This defaults to the current data pipe.

disassemble_param_vector(param_vector=None, key=None, spins=None, sim_index=None)

source code 

Disassemble the relaxation dispersion parameter vector.

Parameters:
  • param_vector (numpy array) - The parameter vector.
  • key (str or None) - The key for the R2eff and I0 parameters.
  • spins (list of SpinContainer instances) - The list of spin data containers for the block.
  • sim_index (int) - The optional MC simulation index.

get_param_names(spins=None, full=False)

source code 

Generate a list of dispersion parameter names for the given spins.

Parameters:
  • spins (list of SpinContainer instances) - The list of spin data containers for the block.
  • full (bool) - A flag which if True will add the R2 key to the parameter names.

get_value(key=None, spins=None, sim_index=None, param_name=None, spin_index=None, r20_key=None)

source code 

Return the value for the given parameter.

Parameters:
  • key (str or None) - The key for the R2eff and I0 parameters.
  • spins (list of SpinContainer instances) - The list of spin data containers for the block.
  • sim_index (int) - The optional MC simulation index.
  • param_name (str) - The parameter name.
  • spin_index (int) - The spin index (for the cluster).
  • r20_key (str) - The unique R20 parameter key.
Returns: float
The parameter value.

linear_constraints(spins=None, scaling_matrix=None)

source code 

Set up the relaxation dispersion curve fitting linear constraint matrices A and b.

Standard notation

The different constraints used within different models are:

   0 <= R1 <= 200
   0 <= R2 <= 200
   0 <= R2A <= 200
   0 <= R2B <= 200
   pC <= pB <= pA <= 1
   pA >= 0.85 (the skewed condition, pA >> pB)
   pB >= 0
   pC >= 0
   phi_ex >= 0
   phi_ex_B >= 0
   phi_ex_C >= 0
   padw2 >= 0
   dw >= 0
   0 <= kex <= 2e6
   0 <= kB <= 2e6
   0 <= kC <= 2e6
   0 <= k_AB <= 100
   tex >= 0

Matrix notation

In the notation A.x >= b, where A is a matrix of coefficients, x is an array of parameter values, and b is a vector of scalars, these inequality constraints are:

   | 1  0  0 |     |    R1    |      |    0    |
   |         |     |          |      |         |
   |-1  0  0 |     |    R1    |      |  -200   |
   |         |     |          |      |         |
   | 1  0  0 |     |    R2    |      |    0    |
   |         |     |          |      |         |
   |-1  0  0 |     |    R2    |      |  -200   |
   |         |     |          |      |         |
   | 1  0  0 |     |   R2A    |      |    0    |
   |         |     |          |      |         |
   |-1  0  0 |     |   R2A    |      |  -200   |
   |         |     |          |      |         |
   | 1  0  0 |     |   R2B    |      |    0    |
   |         |     |          |      |         |
   |-1  0  0 |     |   R2B    |      |  -200   |
   |         |     |          |      |         |
   | 1  0  0 |     |    pA    |      |   0.5   |
   |         |     |          |      |         |
   |-1  0  0 |     |    pA    |      |   -1    |
   |         |     |          |      |         |
   | 1  0  0 |     |    pA    |      |   0.85  |
   |         |     |          |      |         |
   | 1  0  0 |     |    pB    |      |    0    |
   |         |     |          |      |         |
   | 1  0  0 |     |  phi_ex  |      |    0    |
   |         |     |          |      |         |
   | 1  0  0 |  .  | phi_ex_B |  >=  |    0    |
   |         |     |          |      |         |
   | 1  0  0 |     | phi_ex_C |      |    0    |
   |         |     |          |      |         |
   | 1  0  0 |     |  padw2   |      |    0    |
   |         |     |          |      |         |
   | 1  0  0 |     |    dw    |      |    0    |
   |         |     |          |      |         |
   | 1  0  0 |     |   kex    |      |    0    |
   |         |     |          |      |         |
   |-1  0  0 |     |   kex    |      |  -2e6   |
   |         |     |          |      |         |
   | 1  0  0 |     |    kB    |      |    0    |
   |         |     |          |      |         |
   |-1  0  0 |     |    kB    |      |  -2e6   |
   |         |     |          |      |         |
   | 1  0  0 |     |    kC    |      |    0    |
   |         |     |          |      |         |
   |-1  0  0 |     |    kC    |      |  -2e6   |
   |         |     |          |      |         |
   | 1  0  0 |     |   k_AB   |      |    0    |
   |         |     |          |      |         |
   |-1  0  0 |     |   k_AB   |      |   100   |
   |         |     |          |      |         |
   | 1  0  0 |     |   tex    |      |    0    |
Parameters:
  • spins (list of SpinContainer instances) - The list of spin data containers for the block.
  • scaling_matrix (numpy diagonal matrix) - The diagonal, square scaling matrix.
Returns: numpy rank-2 NxM array, numpy rank-1 N array
The matrices A and b.

loop_parameters(spins=None)

source code 

Generator function for looping of the model parameters of the cluster.

Parameters:
  • spins (list of SpinContainer instances) - The list of spin data containers for the block.
Returns: str, int, int, str
The parameter name, the parameter index (for the parameter vector), the spin index (for the cluster), and the R20 parameter key (for R20, R20A, and R20B parameters stored as dictionaries).

param_conversion(key=None, spins=None, sim_index=None)

source code 

Calculate the non-model parameter values from the current parameter values.

Parameters:
  • key (str or None) - The key for the R2eff and I0 parameters.
  • spins (list of SpinContainer instances) - The list of spin data containers for the block.
  • sim_index (int) - The optional MC simulation index.

param_index_to_param_info(index=None, spins=None)

source code 

Convert the given parameter array index to parameter identifying information.

The parameter index will be converted to the parameter name, the relevant spin index in the cluster, and relevant exponential curve key.

Parameters:
  • index (int) - The index of the parameter array.
  • spins (list of SpinContainer instances) - The list of spin data containers for the block.
Returns: str, int, int
The parameter name, the spin index (for the cluster), and the frequency index (for parameters with different values per spectrometer field strength).

param_num(spins=None)

source code 

Determine the number of parameters in the model.

Parameters:
  • spins (list of SpinContainer instances) - The list of spin data containers for the block.
Returns: int
The number of model parameters.

set_value(value=None, key=None, spins=None, sim_index=None, param_name=None, spin_index=None, r20_key=None)

source code 

Set a specific parameter value.

Parameters:
  • value (float) - The parameter value to set.
  • key (str or None) - The key for the R2eff and I0 parameters.
  • spins (list of SpinContainer instances) - The list of spin data containers for the block.
  • sim_index (int) - The optional MC simulation index.
  • param_name (str) - The parameter name.
  • spin_index (int) - The spin index (for the cluster).
  • r20_key (str) - The unique R20 parameter key.