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FEAT: add skeleton for amico implementation#89

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matteofrigo wants to merge 31 commits into
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matteofrigo:amico
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FEAT: add skeleton for amico implementation#89
matteofrigo wants to merge 31 commits into
AthenaEPI:masterfrom
matteofrigo:amico

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@matteofrigo matteofrigo commented Apr 30, 2020

With this PR we add the skeleton for the implementation of AMICO. Let's open the discussion @Sara04 @rutgerfick .

dmipy.core.modeling_framework

For the MultiCompartmentAMICOModel and the MultiCompartmentAMICOSphericalMeanModel we have to do the following:

  • Implement _create_forward_model_matrix
  • Choose a strategy for the solver to use. The difficulty stands in keeping the syntax consistent with the other models
  • Update documentation of fit function
  • Complete the setup of the optimization before model fitting in the fit function, taking into account that the look-up table must be built or loaded.
  • Implement the fit_func method in the fit function
  • Preprocess the x0 as required by the solver
  • Implement the multi-tissue feature correctly

dmipy.core.fitted_modeling_framework

  • I added the fitted_distribution property to the FittedMultiCompartmentAMICOModel and FittedMultiCompartmentAMICOSphericalMeanModel classes. This is intended to return the distribution of each parameter obtained from the AMICO fitting.
  • The fitted_parameter property could be built on top of the fitted_distribution.

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