/***************************************************************************                          lsmtopology.cpp  -  description                             -------------------    begin                : Wed Mar 30 2005    copyright            : (C) 2005 by Rudiger Koch    email                : rkoch@amygdala.org ***************************************************************************//*************************************************************************** *                                                                         * *   This program is free software; you can redistribute it and/or modify  * *   it under the terms of the GNU General Public License as published by  * *   the Free Software Foundation; either version 2 of the License, or     * *   (at your option) any later version.                                   * *                                                                         * ***************************************************************************/#include "lsmtopology.h"#include "spikeinput.h"#include "factory.h"#include "physicalproperties.h"#include "neuronproperties.h"#include "neuron.h"#include "spikingneuron.h"#include "inputneuron.h"#include "nconnector.h"#include "synapse.h"#include "synapseproperties.h"#include "utilities.h"#include "logging.h"#include <stdexcept>#include <cstdlib>namespace Amygdala {using namespace std;LSMTopology::LSMTopology(string name) :     Topology(name),    X(0), Y(0), Z(0),    lastInX(0), lastInY(0), lastInZ(0), lastInSide(0),    lastOutX(0), lastOutY(0), lastOutZ(0){}LSMTopology::~LSMTopology(){}Topology * LSMTopology::MakeInput(SpikeInput * sInput, unsigned int iNeurons){    if( X==0 || Y==0 || Z==0) throw runtime_error("No cube defined yet. Call MakeCube before attempting to create Input");    //TFactory * lsmInput = dynamic_cast<TFactory*> (Factory::GetRegistry().GetFactory("LSMTopology::Input"));    //if(!lsmInput) throw runtime_error("No LSMTopology::Input factory registered");    TopologyFactory<LSMTopology::Input> lsmInput;    Input* in = lsmInput("LSM Input");    input.push_back(in);        // Move the code that used to be in Input::MakeInput() to here since more than one Input    // object is now allowed.  Since we have to keep track of where input neurons have been added    // previously, it will be easier to do that here.    //in->MakeInput(sInput, X, Y, Z, iNeurons);    LOGGER(3, "Making Inputs");    unsigned int neuronCounter = 1;    unsigned int inputLocs = 2*X*Z + 2*Y*Z;    unsigned int totInputs = 0;        for (unsigned int i=0; i<input.size(); ++i) {        totInputs += input[i]->size();    }    totInputs += iNeurons;    if(totInputs > inputLocs)             throw runtime_error("Insufficient space for InputNeurons. Consider making the cube larger");        if (lastInSide == 0) {        int y=-1;        // distribute the InputNeurons alongside at the X-Z side of the cube (y == -1)        for(int x=lastInX; x < X; x++){            for(int z=lastInZ; z < Z; z++){                InputNeuron * inNrn = in->MakeInputNeuron(x, y, z);                sInput->AddNeuron(inNrn);                lastInZ = z;                if(++neuronCounter > iNeurons) return in;            }            lastInZ = 0;               lastInX = x;        }        lastInX = 0;        lastInZ = 0;        lastInSide = 1;    }        if (lastInSide == 1) {        int y=Y;        // distribute the InputNeurons alongside at the X-Z side of the cube (y == Y)        for(int x=lastInX; x < X; x++){            for(int z=lastInZ; z < Z; z++){                InputNeuron * inNrn = in->MakeInputNeuron(x, y, z);                sInput->AddNeuron(inNrn);                lastInZ = z;                if(++neuronCounter > iNeurons) return in;            }               lastInZ = 0;            lastInX = x;        }        lastInX = 0;        lastInZ = 0;        lastInSide = 2;    }        if (lastInSide == 2) {        // if there are still more input neurons        // distribute them alongside at the X-Y side of the cube (z == -1)        int z=-1;        for(int x=lastInX; x < X; x++){            for(int y=lastInY; y < Y; y++){                InputNeuron * inNrn = in->MakeInputNeuron(x, y, z);                sInput->AddNeuron(inNrn);                lastInY = y;                if(++neuronCounter > iNeurons) return in;            }               lastInY = 0;            lastInX = x;        }        lastInX = 0;        lastInSide = 3;    }        if (lastInSide == 3) {        // if there are still more input neurons        // distribute them alongside at the X-Y side of the cube (z == Z)        int z=Z;        for(int x=lastInX; x < X; x++){            for(int y=lastInY; y < Y; y++){                InputNeuron * inNrn = in->MakeInputNeuron(x, y, z);                sInput->AddNeuron(inNrn);                lastInY = y;                if(++neuronCounter > iNeurons) return in;            }               lastInY = 0;            lastInX = x;        }        lastInX = 0;        lastInSide = 4;    }        return in;}Topology * LSMTopology::MakeReadout(const string & nType, unsigned int oNeurons){    if( X==0 || Y==0 || Z==0) throw runtime_error("No cube defined yet. Call MakeCube before attempting to create Output");    TFactory * lsmOutput = dynamic_cast<TFactory*> (Factory::GetRegistry().GetFactory("LSMTopology::Output"));    if(!lsmOutput) throw runtime_error("No LSMTopology::Output factory registered");    Output* out = dynamic_cast<Output*> (lsmOutput->MakeTopology("LSM Output"));    output.push_back(out);        // Move the code that used to be in Output::MakeReadout() to here since more than one Output    // object is now allowed.  Since we have to keep track of where neurons have been added    // previously, it will be easier to do that here.    //out->MakeReadout(nType, X, Y, oNeurons);    LOGGER(3, "Making Outputs");    unsigned int neuronCounter = 1;    NFactory * nf =  dynamic_cast<NFactory*> (Factory::GetRegistry().GetFactory(nType));    if (nf == NULL) throw runtime_error("No neuron type " + nType + " registered!");    NeuronProperties * nProps = nf->MakeNeuronProperties(true);    PhysicalProperties * pProps = nProps->GetPhysicalProps();    // distribute the OutputNeurons alongside at the Y-Z side of the cube starting at X+1, 0, 0    for (int z=lastOutZ; true; z++){        for (int y = lastOutY; y < Y; y++){            pProps->SetPosition(X + 1, y, z);            Neuron * n = nf->MakeNeuron(Network::GetNetworkRef()->GetNewNeuronId(), nProps, out);            OutputManager::AddNeuronToGroup(n, OUTPUTGROUP);            LOGGER(4, "Output neuron at " << X+1 << ", " << y << ", " << z);            lastOutY++;            if(++neuronCounter > oNeurons) return out;        }        lastOutY=0;        lastOutZ++;    }        return out;}Topology * LSMTopology::MakeReadout(NFactory* nf, NeuronProperties* np, unsigned int oNeurons){    if( X==0 || Y==0 || Z==0) throw runtime_error("No cube defined yet. Call MakeCube before attempting to create Output");    TFactory * lsmOutput = dynamic_cast<TFactory*> (Factory::GetRegistry().GetFactory("LSMTopology::Output"));    if(!lsmOutput) throw runtime_error("No LSMTopology::Output factory registered");    Output* out = dynamic_cast<Output*> (lsmOutput->MakeTopology("LSM Output"));    output.push_back(out);        // Move the code that used to be in Output::MakeReadout() to here since more than one Output    // object is now allowed.  Since we have to keep track of where neurons have been added    // previously, it will be easier to do that here.    //out->MakeReadout(nType, X, Y, oNeurons);    LOGGER(3, "Making Outputs");    unsigned int neuronCounter = 1;    /*NFactory * nf =  dynamic_cast<NFactory*> (Factory::GetRegistry().GetFactory(nType));    if (nf == NULL) throw runtime_error("No neuron type " + nType + " registered!");*/    //NeuronProperties * nProps = nf->MakeNeuronProperties(true);    PhysicalProperties * pProps = np->GetPhysicalProps();    // distribute the OutputNeurons alongside at the Y-Z side of the cube starting at X+1, 0, 0    for (int z=lastOutZ; true; z++){        for (int y = lastOutY; y < Y; y++){            pProps->SetPosition(X + 1, y, z);            Neuron * n = nf->MakeNeuron(Network::GetNetworkRef()->GetNewNeuronId(), np, out);            OutputManager::AddNeuronToGroup(n, OUTPUTGROUP);            LOGGER(4, "Output neuron at " << X+1 << ", " << y << ", " << z);            lastOutY++;            if(++neuronCounter > oNeurons) return out;        }        lastOutY=0;        lastOutZ++;    }        return out;}void LSMTopology::MakeCube(const string & nType, unsigned int lx, unsigned int ly, unsigned int lz){    X=lx; Y=ly; Z=lz;    LOGGER(1, "Making Cube of size " << X << ", " << Y << ", " << Z);        NFactory * nf =  dynamic_cast<NFactory*> (Factory::GetRegistry().GetFactory(nType));    if (nf == NULL) throw runtime_error("No neuron type " + nType + " registered!");        NeuronProperties * nProps = nf->MakeNeuronProperties(true);    PhysicalProperties * pProps = nProps->GetPhysicalProps();        for (int x = 0; x < X; x++){