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CalcTMP Module and (pseudo) algo code
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‎src/Modules/Legacy/Forward/CalcTMP.cc‎

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/*
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For more information, please see: http://software.sci.utah.edu
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The MIT License
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Copyright (c) 2011 Scientific Computing and Imaging Institute,
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University of Utah.
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Permission is hereby granted, free of charge, to any person obtaining a
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copy of this software and associated documentation files (the "Software"),
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to deal in the Software without restriction, including without limitation
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the rights to use, copy, modify, merge, publish, distribute, sublicense,
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and/or sell copies of the Software, and to permit persons to whom the
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Software is furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included
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in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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DEALINGS IN THE SOFTWARE.
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*/
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//#include <Core/Datatypes/SparseRowMatrix.h>
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#include <Core/Datatypes/DenseMatrix.h>
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#include <Core/Datatypes/Matrix.h>
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#include <Core/Datatypes/Field.h>
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#include <Dataflow/Network/Ports/MatrixPort.h>
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#include <Dataflow/Network/Ports/FieldPort.h>
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#include <Dataflow/GuiInterface/GuiVar.h>
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#include <Dataflow/Network/Module.h>
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#include <Packages/BioPSE/Core/Algorithms/NumApproximation/CalcTMP.h>
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//#include <algorithm>
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namespace BioPSE {
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using namespace SCIRun;
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class CalcTMP : public Module, public CalcTMPAlgo {
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public:
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CalcTMP(GuiContext*);
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virtual ~CalcTMP() {}
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virtual void execute();
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private:
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//SCIRunAlgo::CalcTMPAlgo algo_;
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CalcTMPAlgo algo_;
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};
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DECLARE_MAKER(CalcTMP)
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CalcTMP::CalcTMP(GuiContext* ctx)
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: Module("CalcTMP", ctx, Source, "Forward", "BioPSE")
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{
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//algo_.set_progress_reporter(this);
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}
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void CalcTMP::execute()
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{
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//FieldHandle Field;
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MatrixHandle amplitudes;
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MatrixHandle deps;
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MatrixHandle depslopes;
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MatrixHandle platslopes;
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MatrixHandle reps;
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MatrixHandle repslopes;
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MatrixHandle rests;
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MatrixHandle TMPs;
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//if (!(get_input_handle("Mesh",Field,true))) return;
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get_input_handle("Amplitude", amplitudes, false);
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get_input_handle("Depolarization Time", deps, false);
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get_input_handle("Depolarization Slope", depslopes, false);
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get_input_handle("Plateau Slope", platslopes, false);
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get_input_handle("Repolarization Time", reps, false);
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get_input_handle("Repolarization Slope", repslopes, false);
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get_input_handle("Rest Potential", rests, false);
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if (inputs_changed_ || !oport_cached("TMPs") )
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{
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//algo_.set_bool("generate_basis",gui_use_basis_.get());
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//algo_.set_bool("force_symmetry",gui_force_symmetry_.get());
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//if(!(algo_.run(Field,Conductivity,SysMatrix))) return;
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algo_.calc_TMPs(amplitudes,
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deps,
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depslopes,
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platslopes,
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reps,
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repslopes,
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rests,
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500,
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TMPs);
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send_output_handle("TMPs", TMPs);
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}
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}
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} // End namespace BioPSE
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‎src/Modules/Legacy/Forward/CalcTMPAlgo.cc‎

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/*
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For more information, please see: http://software.sci.utah.edu
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The MIT License
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Copyright (c) 2011 Scientific Computing and Imaging Institute,
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University of Utah.
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Permission is hereby granted, free of charge, to any person obtaining a
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copy of this software and associated documentation files (the "Software"),
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to deal in the Software without restriction, including without limitation
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the rights to use, copy, modify, merge, publish, distribute, sublicense,
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and/or sell copies of the Software, and to permit persons to whom the
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Software is furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included
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in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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DEALINGS IN THE SOFTWARE.
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*/
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/*
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* CalcTMP.cc: class to calcuate transmenbrane potential
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* using algorithm from ECGSim.
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*
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* Written by:
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* Michael Steffen
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* Scientific Computing and Imaging Institute
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* May 2011
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*/
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#include <Packages/BioPSE/Core/Algorithms/NumApproximation/CalcTMP.h>
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#include <Core/Datatypes/MatrixTypeConverter.h>
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namespace BioPSE {
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using namespace SCIRun;
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bool CalcTMPAlgo::calc_single_TMP(
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const double amplitude,
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const double dep,
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const double depslope,
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const double platslope,
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const double rep,
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const double repslope,
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const double rest,
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DenseMatrix& TMP_values)
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{
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/*
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Inputs: tdep: Depolarization Time
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trep: Repolarization Time
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depslope: Depolarization Slope
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platslope: Plateau Slope
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repslope: Repolarization Slope
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res:
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amplitude: Amplitude
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Output: Dense Matrix (1xsize of matrix) containing the transmembrane potential
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*/
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size_type nrows = TMP_values.nrows();
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size_type ncols = TMP_values.ncols();
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if(nrows != 1){
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error("CalcTMPAlgo: TMP_values size incorrect");
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return false;
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}
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if(ncols <= 0){
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error("CalcTMPAlgo: TMP_values size incorrect");
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return false;
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}
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double tdep = -dep;
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double trep = -rep;
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double maxAmpl = 1e-6;
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for(index_type t = 0; t < ncols; ++t)
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{
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double vali = 1.0 / (1.0 + exp(-depslope * tdep)) *
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(1.0 / (1.0 + exp(platslope * trep))) *
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(1.0 / (1.0 + exp(repslope * trep)));
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TMP_values.put(0,t,vali);
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if(vali > maxAmpl)
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{
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maxAmpl = vali;
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}
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tdep += 1.0;
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trep += 1.0;
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}
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double ampl = (amplitude - rest) / maxAmpl;
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for(index_type t = 0; t < ncols; ++t)
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{
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TMP_values.put(0,t,TMP_values.get(0,t)*ampl + rest);
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}
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return true;
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}
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bool CalcTMPAlgo::calc_all_TMPs(
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const DenseMatrix& amplitudes,
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const DenseMatrix& deps,
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const DenseMatrix& depslopes,
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const DenseMatrix& platslopes,
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const DenseMatrix& reps,
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const DenseMatrix& repslopes,
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const DenseMatrix& rests,
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DenseMatrix& TMP_values)
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{
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if(amplitudes.ncols() != 1 ||
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deps.ncols() != 1 ||
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depslopes.ncols() != 1 ||
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platslopes.ncols() != 1 ||
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reps.ncols() != 1 ||
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repslopes.ncols() != 1 ||
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rests.ncols() != 1)
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{
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error("CalcTMPAlgo: All inputs must be of size 1 x nodes");
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return false;
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}
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size_type nnodes = amplitudes.nrows();
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if(nnodes <= 0){
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error("CalcTMPAlgo: Size of inputs must be > 0");
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return false;
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}
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if(deps.nrows() != nnodes ||
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depslopes.nrows() != nnodes ||
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platslopes.nrows() != nnodes ||
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reps.nrows() != nnodes ||
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repslopes.nrows() != nnodes ||
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rests.nrows() != nnodes)
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{
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error("CalcTMPAlgo: All inputs sizes must match");
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return false;
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}
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if(TMP_values.nrows() != nnodes)
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{
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error("CalcTMPAlgo: MP_values size does not match number of nodes");
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return false;
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}
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if(TMP_values.ncols() <= 0)
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{
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error("CalcTMPAlgo: Number of columns in TMP_values must be greater than 0 for output");
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return false;
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}
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DenseMatrix mat(1, TMP_values.ncols());
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for(index_type node = 0; node < nnodes; ++node)
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{
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if (!calc_single_TMP(amplitudes.get(node,0),
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deps.get(node,0),
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depslopes.get(node,0),
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platslopes.get(node,0),
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reps.get(node,0),
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repslopes.get(node,0),
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rests.get(node,0),
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mat))
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{
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return false;
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}
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for(index_type t = 0; t < TMP_values.ncols(); ++t)
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{
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TMP_values.put(node, t, mat.get(0, t));
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}
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}
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return true;
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}
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bool CalcTMPAlgo::calc_TMPs(MatrixHandle amplitudes,
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MatrixHandle deps,
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MatrixHandle depslopes,
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MatrixHandle platslopes,
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MatrixHandle reps,
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MatrixHandle repslopes,
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MatrixHandle rests,
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unsigned int nsamples,
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MatrixHandle& output)
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{
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if(matrix_is::sparse(amplitudes) ||
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matrix_is::sparse(deps) ||
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matrix_is::sparse(depslopes) ||
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matrix_is::sparse(platslopes) ||
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matrix_is::sparse(reps) ||
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matrix_is::sparse(repslopes) ||
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matrix_is::sparse(rests))
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{
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error("CalcTMPAlgo: Sparse matrices not supported.");
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return false;
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}
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output = new DenseMatrix(amplitudes->nrows(), nsamples);
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if(!calc_all_TMPs(*(amplitudes->dense()),
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*(deps->dense()),
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*(depslopes->dense()),
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*(platslopes->dense()),
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*(reps->dense()),
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*(repslopes->dense()),
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*(rests->dense()),
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*(output->dense())))
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{
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return false;
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}
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return true;
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}
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} // end namespace BioPSE

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