/* fwdmodel_custom.cc - A place for your own quick'n'dirty forward model implementations. Adrian Groves, FMRIB Image Analysis Group Copyright (C) 2008 University of Oxford */ /* Part of FSL - FMRIB's Software Library http://www.fmrib.ox.ac.uk/fsl fsl@fmrib.ox.ac.uk Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance Imaging of the Brain), Department of Clinical Neurology, Oxford University, Oxford, UK LICENCE FMRIB Software Library, Release 5.0 (c) 2012, The University of Oxford (the "Software") The Software remains the property of the University of Oxford ("the University"). 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Contact details are: innovation@isis.ox.ac.uk quoting reference DE/9564. */ /* fwdmodel_custom.h * Implementation for a custom forward model class * Template written by Adrian Groves, 2008 * FMRIB Centre, University of Oxford * * Last modified: $Date: 2009/01/23 12:58:53 $ $Author: adriang $ $Revision: 1.1 $ */ #include "fwdmodel_custom.h" // Constructor: CustomFwdModel::CustomFwdModel(ArgsType& args) { // Read any command-line arguments. These should probably be stored in // e.g. Mandatory option: // numRepeats = convertTo(args.Read("reps")); // An error will be thrown if there's no --reps=NNN option. // e.g. Optional option: // T1 = convertTo(args.ReadWithDefault("T1","1.6")) // e.g. a basis function: // string basisFile = args.Read("basis"); // error if --basis=??? option is missing // basis = read_vest(basisFile); // error if file is missing // e.g. a boolean option (present or absent); // wantFriesWithThat = args.ReadBool("chips"); // TODO: Read any commmand-line arguments and save them in the class's member variables. // Before you return, all of the implementation-specific variables in fwdmodel_custom.h // should have had values assigned to them. If you didn't add any variables then you // don't have to do anything here! return; } void CustomFwdModel::Evaluate(const ColumnVector& params, ColumnVector& result) const { assert(params.Nrows() == NumParams()); // TODO:This needs to equal the number of timepoints in your data. // If it varies, you need to be able to calculate it from the command-line options. // This may mean adding a (redundant) --data-length=NNN option above. const int dataLength = 10; // Example value if (result.Nrows() != dataLength) result.ReSize(dataLength); // TODO: Your model here! // A very simple forward model: fitting a quadratic equation, with inputs at 1..10 // Notice that NEWMAT vectors and matrices could from one, not zero! const double constantTerm = params(1); const double linearTerm = params(2); const double quadraticTerm = params(3); for (int i = 1; i <= dataLength; i++) { result(i) = constantTerm + i*linearTerm + i*i*quadraticTerm; } // Before you return, you should have assigned a predicted signal to "result". return; } int CustomFwdModel::NumParams() const { // TODO: How many parameters does your model need? return 3; // Example function } void CustomFwdModel::NameParams(vector& names) const { // TODO: Name your model parameters here. Should match NumParams() above! // Example function: names.push_back("Constant term"); names.push_back("Linear term"); names.push_back("Quadratic term"); } string CustomFwdModel::ModelVersion() const { return "$Id: fwdmodel_custom.cc,v 1.1 2009/01/23 12:58:53 adriang Exp $"; } void CustomFwdModel::HardcodedInitialDists(MVNDist& prior, MVNDist& posterior) const { Tracer_Plus tr("CustomFwdModel::HardcodedInitialDists"); // Pick a safe starting point for your model fits, if no other input is provided. // The default one just uses a N(0,1e12) prior, and starts with all parameters set to zeroes: assert(prior.means.Nrows() == NumParams()); prior.means = 0; prior.SetPrecisions(IdentityMatrix(NumParams()) * 1e-12); posterior = prior; // Ask Adrian for help if you want to modify this! // You can override prior at the command line with the --fwd-initial-prior=VESTFILE option, // and you can set initialization points using the --continue-from-mvn=MVNFILE option. } void CustomFwdModel::ModelUsage() { cout << "No model usage info available for --model=custom, yet." << endl; }