Measurements Module

The purpose for this module is to generate synthetic measurements for a given EIT protocol with the possibility to add noise to simulate real measurements.

Main Function

measurements.GenMeasurements(name1, value1, name2, value2...)
Description:

Function to generate synthetic measurements from a head model and some provided conductivities (see arguments below). The default current is 0.02mA but can be specified with an argument. Please ensure an injection pattern data file is available for the function to run properly. For help with this please see ‘help OrderedModelClass.patterns’.

Parameters:

  • synth_cond – (essential) the conductivities of the tissues in the head model

  • model – path to the head model

  • sinks_path – path the file with the injection patterns

  • sinks – the injection pattern data in a 2D array

  • current – injection current

  • top – path to the top of the ROMEG data tree

  • num_samples – number of conductivity samples

  • sample_num – array of sample numbers to generate (e.g 10:20)

  • mu_min – (essential for num_sample) array of the minimum conductivity values

  • mu_max – (essential for num_sample) array of the maximum conductivity values

  • noise – how much noise do you want to include?

  • ROM – would you like these to be calculated using ROM?

  • use_sinks – tell this function that ROM used ‘use_sinks’

  • anis_tan – array of tissue numbers to tag with tangential conductivity

  • anis_rad – array of tissue numbers to tag with radial conductivity.

  • angles – true if model contains theta values (default: false)

  • ratio – The ratio between tan and rad conds, e.g, 5 means tan is 5 times rad. A value of 1 will give an isotropic conductivity.

  • new_sinks – (boolean) use a new set of sinks called new_sinks.mat

  • redo – Redo the measurements using existing prep.mat file

  • RB_path – path for the RBModel if NOT in $ROMEG_DATA

  • debug – (boolean) turn debug mode on

  • Cluster – should these measurements be made on the cluster?

  • pre_stiff – are the stiffness matrices already in the model.mat file?

Examples

Basic isotropic measurements with no noise:

GenMeasurements(‘model’,model,’num_samples’,num_samples,’mu_min’,mu_min,… ‘mu_max’,mu_max,’noise’,0)

Skull anisotropic measurements with noise and a ratio of tangential to radial conductivities where the angles are already in the head_model.mat file:

GenMeasurements(‘model’,model,’num_samples’,num_samples,’mu_min’,mu_min,… ‘mu_max’,mu_max,’anis_tan’,2,’anis_rad’,3,’angles’,true,’ratio’,3,’noise’,0.82e-6)

Classes

class measurements.MeasurementClass

Bases: core.OrderedModelClass

Method Summary
saveData(num)

Data = obj;

% Clean up Data.p = []; Data.t = []; Data.f = []; Data.Ind_E = [];