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nineML_classes.cpp
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nineML_classes.cpp
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/***************************************************************************
** **
** This file is part of SpineCreator, an easy to use, GUI for **
** describing spiking neural network models. **
** Copyright (C) 2013 Alex Cope, Paul Richmond **
** **
** 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 3 of the License, or **
** (at your option) any later version. **
** **
** This program is distributed in the hope that it will be useful, **
** but WITHOUT ANY WARRANTY; without even the implied warranty of **
** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the **
** GNU General Public License for more details. **
** **
** You should have received a copy of the GNU General Public License **
** along with this program. If not, see http://www.gnu.org/licenses/. **
** **
****************************************************************************
** Author: Alex Cope, Paul Richmond **
** Website/Contact: http://bimpa.group.shef.ac.uk/ **
****************************************************************************/
#include "nineML_classes.h"
#include "projections.h"
#include "nineml_layout_classes.h"
#include "genericinput.h"
#include "population.h"
//#include "stringify.h"
QString dim::toString() {
// do stuff
QString unit;
QString prefix;
unit = getUnitString();
prefix = getPrefixString();
unit = prefix+unit;
return unit;
}
void dim::fromString(QString in) {
// do stuff
if (in.size() == 0) return;
if (in.size() > 1 && in.startsWith("G"))
{scale = 9; in.remove(0,1);}
if (in.size() > 1 && in.startsWith("M"))
{scale = 6; in.remove(0,1);}
if (in.size() > 1 && in.startsWith("k"))
{scale = 3; in.remove(0,1);}
if (in.size() > 1 && in.startsWith("c") && in != "cd")
{scale = 2; in.remove(0,1);}
if (in.size() > 1 && in.startsWith("m") && in != "mol")
{scale = -3; in.remove(0,1);}
if (in.size() > 1 && in.startsWith("u"))
{scale = -6; in.remove(0,1);}
if (in.size() > 1 && in.startsWith("n"))
{scale = -9; in.remove(0,1);}
if (in.size() > 1 && in.startsWith("p"))
{scale = -12; in.remove(0,1);}
if (in.size() > 1 && in.startsWith("f"))
{scale = -15; in.remove(0,1);}
if (in == "V") {
m=1; l=2; t=-3; I=-1; Cd = 0; mol = 0; temp = 0;}
if (in == "Ohm") {
m=1; l=2; t=-3; I=-2; Cd = 0; mol = 0; temp = 0;}
if (in == "g") {
m=1; l=0; t=0; I=0; Cd = 0; mol = 0; temp = 0;}
if (in == "m") {
m=0; l=1; t=0; I=0; Cd = 0; mol = 0; temp = 0;}
if (in == "s") {
m=0; l=0; t=1; I=0; Cd = 0; mol = 0; temp = 0;}
if (in == "A") {
m=0; l=0; t=0; I=1; Cd = 0; mol = 0; temp = 0;}
if (in == "cd") {
m=0; l=0; t=0; I=0; Cd = 1; mol = 0; temp = 0;}
if (in == "mol") {
m=0; l=0; t=0; I=0; Cd = 0; mol = 1; temp = 0;}
if (in == "degC") {
m=0; l=0; t=0; I=0; Cd = 0; mol = 0; temp = 1;}
if (in == "S") {
m=-1; l=-2; t=3; I=2; Cd = 0; mol = 0; temp = 0;}
if (in == "F") {
m=-1; l=-2; t=4; I=2; Cd = 0; mol = 0; temp = 0;}
if (in == "Hz") {
m=0; l=0; t=-1; I=0; Cd = 0; mol = 0; temp = 0;}
if ((in == "?")||(in == "")) {
m=0; l=0; t=0; I=0; Cd = 0; mol = 0; temp = 0;}
}
void dim::setPrefix(QString p)
{
if (p == "")
scale = 0;
else if (p == "G")
scale = 9;
else if (p == "M")
scale = 6;
else if (p == "k")
scale = 3;
else if (p == "c")
scale = 2;
else if (p == "m")
scale = -3;
else if (p == "u")
scale = -6;
else if (p == "n")
scale = -9;
else if (p == "p")
scale = -12;
else if (p == "f")
scale = -15;
}
void dim::setUnit(QString u)
{
if (u == "V") {
m=1; l=2; t=-3; I=-1; Cd = 0; mol = 0; temp = 0;}
else if (u == "Ohm") {
m=1; l=2; t=-3; I=-2; Cd = 0; mol = 0; temp = 0;}
else if (u == "g") {
m=1; l=0; t=0; I=0; Cd = 0; mol = 0; temp = 0;}
else if (u == "m") {
m=0; l=1; t=0; I=0; Cd = 0; mol = 0; temp = 0;}
else if (u == "s") {
m=0; l=0; t=1; I=0; Cd = 0; mol = 0; temp = 0;}
else if (u == "A") {
m=0; l=0; t=0; I=1; Cd = 0; mol = 0; temp = 0;}
else if (u == "cd") {
m=0; l=0; t=0; I=0; Cd = 1; mol = 0; temp = 0;}
else if (u == "mol") {
m=0; l=0; t=0; I=0; Cd = 0; mol = 1; temp = 0;}
else if (u == "degC") {
m=0; l=0; t=0; I=0; Cd = 0; mol = 0; temp = 1;}
else if (u == "S") {
m=-1; l=-2; t=3; I=2; Cd = 0; mol = 0; temp = 0;}
else if (u == "F") {
m=-1; l=-2; t=4; I=2; Cd = 0; mol = 0; temp = 0;}
else if (u == "Hz") {
m=0; l=0; t=-1; I=0; Cd = 0; mol = 0; temp = 0;}
else{
m=0; l=0; t=0; I=0; Cd = 0; mol = 0; temp = 0;}
}
QString dim::getPrefixString()
{
QString prefix;
if (scale==9)
prefix = "G";
else if (scale==6)
prefix = "M";
else if (scale==3)
prefix = "k";
else if (scale==2)
prefix = "c";
else if (scale==-3)
prefix = "m";
else if (scale==-6)
prefix = "u";
else if (scale==-9)
prefix = "n";
else if (scale==-12)
prefix = "p";
else if (scale==-15)
prefix = "f";
else
prefix = "";
return prefix;
}
QString dim::getUnitString()
{
QString unit;
if (m==1 && l==2 && t==-3 && I==-1 && Cd == 0 && mol == 0 && temp == 0)
unit = "V";
else if (m==1 && l==2 && t==-3 && I==-2 && Cd == 0 && mol == 0 && temp == 0)
unit = "Ohm";
else if (m==1 && l==0 && t==0 && I==0 && Cd == 0 && mol == 0 && temp == 0)
unit = "g";
else if (m==0 && l==1 && t==0 && I==0 && Cd == 0 && mol == 0 && temp == 0)
unit = "m";
else if (m==0 && l==0 && t==1 && I==0 && Cd == 0 && mol == 0 && temp == 0)
unit = "s";
else if (m==0 && l==0 && t==0 && I==1 && Cd == 0 && mol == 0 && temp == 0)
unit = "A";
else if (m==0 && l==0 && t==0 && I==0 && Cd == 1 && mol == 0 && temp == 0)
unit = "cd";
else if (m==0 && l==0 && t==0 && I==0 && Cd == 0 && mol == 1 && temp == 0)
unit = "mol";
else if (m==0 && l==0 && t==0 && I==0 && Cd == 0 && mol == 0 && temp == 1)
unit = "degC";
else if (m==-1 && l==-2 && t==3 && I==2 && Cd == 0 && mol == 0 && temp == 0)
unit = "S";
else if (m==-1 && l==-2 && t==4 && I==2 && Cd == 0 && mol == 0 && temp == 0)
unit = "F";
else if (m==0 && l==0 && t==-1 && I==0 && Cd == 0 && mol == 0 && temp == 0)
unit = "Hz";
// default for dimensionless
//if (m==0 && l==0 && t==0 && I==0 && Cd == 0 && mol == 0 && temp == 0)
else
unit = "?";
return unit;
}
Prefix dim::getPrefix()
{
if (scale==9)
return PREFIX_G;
else if (scale==6)
return PREFIX_M;
else if (scale==3)
return PREFIX_k;
else if (scale==2)
return PREFIX_c;
else if (scale==-3)
return PREFIX_m;
else if (scale==-6)
return PREFIX_u;
else if (scale==-9)
return PREFIX_n;
else if (scale==-12)
return PREFIX_p;
else if (scale==-15)
return PREFIX_f;
else
return PREFIX_NONE;
}
Unit dim::getUnit()
{
if (m==1 && l==2 && t==-3 && I==-1 && Cd == 0 && mol == 0 && temp == 0)
return UNIT_V;
else if (m==1 && l==2 && t==-3 && I==-2 && Cd == 0 && mol == 0 && temp == 0)
return UNIT_Ohm;
else if (m==1 && l==0 && t==0 && I==0 && Cd == 0 && mol == 0 && temp == 0)
return UNIT_g;
else if (m==0 && l==1 && t==0 && I==0 && Cd == 0 && mol == 0 && temp == 0)
return UNIT_m;
else if (m==0 && l==0 && t==1 && I==0 && Cd == 0 && mol == 0 && temp == 0)
return UNIT_s;
else if (m==0 && l==0 && t==0 && I==1 && Cd == 0 && mol == 0 && temp == 0)
return UNIT_A;
else if (m==0 && l==0 && t==0 && I==0 && Cd == 1 && mol == 0 && temp == 0)
return UNIT_cd;
else if (m==0 && l==0 && t==0 && I==0 && Cd == 0 && mol == 1 && temp == 0)
return UNIT_mol;
else if (m==0 && l==0 && t==0 && I==0 && Cd == 0 && mol == 0 && temp == 1)
return UNIT_degC;
else if (m==-1 && l==-2 && t==3 && I==2 && Cd == 0 && mol == 0 && temp == 0)
return UNIT_S;
else if (m==-1 && l==-2 && t==4 && I==2 && Cd == 0 && mol == 0 && temp == 0)
return UNIT_F;
else if (m==0 && l==0 && t==-1 && I==0 && Cd == 0 && mol == 0 && temp == 0)
return UNIT_Hz;
// default for dimensionless
//if (m==0 && l==0 && t==0 && I==0 && Cd == 0 && mol == 0 && temp == 0)
else
return UNIT_NONE;
}
void dim::reset()
{
m = 0;
l = 0;
t = 0;
I = 0;
Cd = 0;
mol = 0;
temp = 0;
scale = 1;
}
bool operator==(dim &dim1, dim &dim2)
{
return ((dim1.I==dim2.I)&&(dim1.l==dim2.l)&&(dim1.m==dim2.m)&&(dim1.mol==dim2.mol)&&(dim1.scale==dim2.scale)&&(dim1.t==dim2.t)&&(dim1.temp==dim2.temp));
}
dim::dim(QString str) {
m = 0;
l = 0;
t = 0;
I = 0;
Cd = 0;
mol = 0;
temp = 0;
scale = 1;
if (str != "")
this->fromString(str);
}
void NineMLComponent::load(QDomDocument *doc)
{
QDomNode n = doc->documentElement().firstChild();
while( !n.isNull() )
{
QDomElement e = n.toElement();
if( e.tagName() == "ComponentClass" )
{
this->name = e.attribute("name","");
if (this->name =="") {
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
settings.beginWriteArray("errors");
settings.setArrayIndex(num_errs + 1);
settings.setValue("errorText", "XML error: expected 'name' attribute'");
settings.endArray();
}
// default to unsorted if no type found
this->type = e.attribute("type", "");
QDomNode n2 = e.firstChild();
while( !n2.isNull() )
{
QDomElement e2 = n2.toElement();
if( e2.tagName() == "Parameter" )
{
Parameter *tempPar = new Parameter;
tempPar->readIn(e2);
this->ParameterList.push_back(tempPar);
}
else if( e2.tagName() == "Dynamics" )
{
this->initial_regime_name = e2.attribute("initial_regime");
QDomNode n3 = e2.firstChild();
while( !n3.isNull() )
{
QDomElement e3 = n3.toElement();
if( e3.tagName() == "Regime" )
{
Regime *tempRegime = new Regime;
tempRegime->readIn(e3);
this->RegimeList.push_back(tempRegime);
}
else if( e3.tagName() == "StateVariable" )
{
StateVariable *tempSV = new StateVariable;
tempSV->readIn(e3);
this->StateVariableList.push_back(tempSV);
}
else if( e3.tagName() == "Alias" )
{
Alias *tempAlias = new Alias;
tempAlias->readIn(e3);
this->AliasList.push_back(tempAlias);
} else {
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
settings.beginWriteArray("errors");
settings.setArrayIndex(num_errs + 1);
settings.setValue("errorText", "XML error: misplaced or unknown tag '" + e3.tagName() + "'");
settings.endArray();
}
n3 = n3.nextSibling();
}
}
else if( e2.tagName() == "AnalogSendPort" || e2.tagName() == "AnalogReceivePort" || e2.tagName() == "AnalogReducePort")
{
AnalogPort *tempAP = new AnalogPort;
tempAP->readIn(e2);
this->AnalogPortList.push_back(tempAP);
}
else if( e2.tagName() == "EventSendPort" || e2.tagName() == "EventReceivePort")
{
EventPort *tempEP = new EventPort;
tempEP->readIn(e2);
this->EventPortList.push_back(tempEP);
}
else if( e2.tagName() == "ImpulseSendPort" || e2.tagName() == "ImpulseReceivePort")
{
ImpulsePort *tempIP = new ImpulsePort;
tempIP->readIn(e2);
this->ImpulsePortList.push_back(tempIP);
} else {
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
settings.beginWriteArray("errors");
settings.setArrayIndex(num_errs + 1);
settings.setValue("errorText", "XML error: misplaced or unknown tag '" + e2.tagName() + "'");
settings.endArray();
}
n2 = n2.nextSibling();
}
} else {
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
settings.beginWriteArray("errors");
settings.setArrayIndex(num_errs + 1);
settings.setValue("errorText", "XML error: expected 'ComponentClass' tag'");
settings.endArray();
}
n = n.nextSibling();
}
// check for errors - no point validating if we have XML errors!
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
if (num_errs > 0)
return;
// no XML errors - so validate this!
QStringList validated = validateComponent();
if (validated.size() > 1) {
/* QMessageBox msgBox;
QString message;
for (uint i = 0; i < (uint) validated.size(); ++i) {
message += validated[i] + "\n";
}
msgBox.setText(message);
msgBox.exec();*/
}
}
void NineMLComponent::write(QDomDocument *doc)
{
// validate this (must be validated if is in memory)
QStringList validated = validateComponent();
// check for errors:
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
num_errs += settings.beginReadArray("warnings");
settings.endArray();
QString errors;
if (num_errs != 0) {
errors = errors + "<b>Errors found in current component:</b><br/><br/>";
// list errors
settings.beginReadArray("errors");
for (int j = 1; j < num_errs; ++j) {
settings.setArrayIndex(j);
errors = errors + settings.value("errorText", "").toString();
errors = errors + "<br/>";
}
settings.endArray();
settings.beginReadArray("warnings");
for (int j = 1; j < num_errs; ++j) {
settings.setArrayIndex(j);
errors = errors + settings.value("warnText", "").toString();
errors = errors + "<br/>";
}
settings.endArray();
// clear errors
settings.remove("errors");
settings.remove("warnings");
}
if (!errors.isEmpty()) {
// display errors
QMessageBox msgBox;
msgBox.setText("<P><b>" + this->name + ":Component validation failed</b></P>" + errors);
msgBox.setIcon(QMessageBox::Warning);
msgBox.setTextFormat(Qt::RichText);
msgBox.setModal(false);
msgBox.exec();
return;
}
// write out:
// create the root of the file:
QDomElement root = doc->createElement( "SpineML" );
QDomProcessingInstruction xmlDeclaration = doc->createProcessingInstruction("xml", "version=\"1.0\"");
doc->appendChild(xmlDeclaration);
doc->appendChild( root );
root.setAttribute("xmlns", "http://www.shef.ac.uk/SpineMLComponentLayer");
root.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance");
root.setAttribute("xsi:schemaLocation", "http://www.shef.ac.uk/SpineMLComponentLayer SpineMLComponentLayer.xsd");
QDomElement CClass = doc->createElement( "ComponentClass" );
CClass.setAttribute("name", this->name);
CClass.setAttribute("type", this->type);
root.appendChild(CClass);
QDomElement dynamics = doc->createElement( "Dynamics" );
if (this->initial_regime != NULL)
dynamics.setAttribute("initial_regime", this->initial_regime->name);
else
dynamics.setAttribute("initial_regime", "Error: No initial regime!");
CClass.appendChild(dynamics);
// declarations
for (unsigned int i = 0; i < this->AnalogPortList.size(); ++i) {
AnalogPortList[i]->writeOut(doc, CClass);
}
for (unsigned int i = 0; i < this->EventPortList.size(); ++i) {
EventPortList[i]->writeOut(doc, CClass);
}
for (unsigned int i = 0; i < this->ImpulsePortList.size(); ++i) {
ImpulsePortList[i]->writeOut(doc, CClass);
}
for (unsigned int i = 0; i < this->ParameterList.size(); ++i) {
ParameterList[i]->writeOut(doc, CClass);
}
// dynamics
for (unsigned int i = 0; i < this->RegimeList.size(); ++i) {
RegimeList[i]->writeOut(doc, dynamics);
}
for (unsigned int i = 0; i < this->AliasList.size(); ++i) {
AliasList[i]->writeOut(doc, dynamics);
}
for (unsigned int i = 0; i < this->StateVariableList.size(); ++i) {
StateVariableList[i]->writeOut(doc, dynamics);
}
}
void NineMLData::write_node_xml(QXmlStreamWriter &xmlOut) {
// definition
QString simpleName;
if (this->type == NineMLLayoutType) {
simpleName = ((NineMLLayoutData *) this)->component->name.simplified();
}
if (this->type == NineMLComponentType) {
simpleName = ((NineMLComponentData *) this)->component->name.simplified();
}
simpleName.replace( " ", "_" );
// add version to components but not layouts (for now)
if (this->type == NineMLComponentType) {
NineMLComponentData * compData = (NineMLComponentData *) this;
xmlOut.writeAttribute("url", simpleName + compData->component->version.toFileString() + ".xml");
} else {
xmlOut.writeAttribute("url", simpleName + ".xml");
}
if (this->type == NineMLComponentType) {
for (uint i = 0; i < ((NineMLComponentData *) this)->inputs.size(); ++i) {
if (((NineMLComponentData *) this)->inputs[i]->projInput == true) {
// add the special input for the synapse
if (((NineMLComponentData *) this)->component->type == "weight_update") {
// check we have ports
if (((NineMLComponentData *) this)->inputs[i]->srcPort.size() == 0 || ((NineMLComponentData *) this)->inputs[i]->dstPort.size() == 0) {
QSettings settings;
int num_errs = settings.beginReadArray("warnings");
settings.endArray();
settings.beginWriteArray("warnings");
settings.setArrayIndex(num_errs + 1);
settings.setValue("warnText", "No matched ports between '" + ((NineMLComponentData *) this)->inputs[i]->src->getXMLName() + "' and '" + ((NineMLComponentData *) this)->inputs[i]->dst->getXMLName() + "'");
settings.endArray();
}
xmlOut.writeAttribute("input_src_port", ((NineMLComponentData *) this)->inputs[i]->srcPort);
xmlOut.writeAttribute("input_dst_port", ((NineMLComponentData *) this)->inputs[i]->dstPort);
}
// add the special input for the postsynapse
if (((NineMLComponentData *) this)->component->type == "postsynapse") {
// check we have ports
if (((NineMLComponentData *) this)->inputs[i]->srcPort.size() == 0 || ((NineMLComponentData *) this)->inputs[i]->dstPort.size() == 0) {
QSettings settings;
int num_errs = settings.beginReadArray("warnings");
settings.endArray();
settings.beginWriteArray("warnings");
settings.setArrayIndex(num_errs + 1);
settings.setValue("warnText", "No matched ports between '" + ((NineMLComponentData *) this)->inputs[i]->src->getXMLName() + "' and '" + ((NineMLComponentData *) this)->inputs[i]->dst->getXMLName() + "'");
settings.endArray();
}
xmlOut.writeAttribute("input_src_port", ((NineMLComponentData *) this)->inputs[i]->srcPort);
xmlOut.writeAttribute("input_dst_port", ((NineMLComponentData *) this)->inputs[i]->dstPort);
}
}
}
if (((NineMLComponentData *) this)->component->type == "postsynapse") {
// search out the Synapse population and add the postsynapticMapping
for (uint i = 0; i < ((projection *) ((NineMLComponentData *) this)->owner)->destination->neuronType->inputs.size(); ++i) {
if (((projection *) ((NineMLComponentData *) this)->owner)->destination->neuronType->inputs[i]->src == this && \
((projection *) ((NineMLComponentData *) this)->owner)->destination->neuronType->inputs[i]->projInput == true) {
// check we have ports
if (((projection *) ((NineMLComponentData *) this)->owner)->destination->neuronType->inputs[i]->srcPort.size() == 0 || ((projection *) ((NineMLComponentData *) this)->owner)->destination->neuronType->inputs[i]->dstPort.size() == 0) {
QSettings settings;
int num_errs = settings.beginReadArray("warnings");
settings.endArray();
settings.beginWriteArray("warnings");
settings.setArrayIndex(num_errs + 1);
settings.setValue("warnText", "No matched ports between '" + ((projection *) ((NineMLComponentData *) this)->owner)->destination->neuronType->inputs[i]->src->getXMLName() + "' and '" + ((projection *) ((NineMLComponentData *) this)->owner)->destination->neuronType->inputs[i]->dst->getXMLName() + "'");
settings.endArray();
}
xmlOut.writeAttribute("output_src_port", ((projection *) ((NineMLComponentData *) this)->owner)->destination->neuronType->inputs[i]->srcPort);
xmlOut.writeAttribute("output_dst_port", ((projection *) ((NineMLComponentData *) this)->owner)->destination->neuronType->inputs[i]->dstPort);
}
}
}
}
if (this->ParameterList.size()+this->StateVariableList.size() > 0) {
for (uint i = 0; i < this->ParameterList.size(); ++i) {
xmlOut.writeStartElement("Property");
xmlOut.writeAttribute("name",this->ParameterList[i]->name);
xmlOut.writeAttribute("dimension", this->ParameterList[i]->dims->toString());
if (this->ParameterList[i]->currType == FixedValue) {
xmlOut.writeEmptyElement("FixedValue");
xmlOut.writeAttribute("value", QString::number(this->ParameterList[i]->value[0]));
}
if (this->ParameterList[i]->currType == Statistical) {
switch (int(round(this->ParameterList[i]->value[0]))) {
case 0:
break;
case 1:
{
xmlOut.writeEmptyElement("UniformDistribution");
xmlOut.writeAttribute("minimum", QString::number(this->ParameterList[i]->value[1]));
xmlOut.writeAttribute("maximum", QString::number(this->ParameterList[i]->value[2]));
xmlOut.writeAttribute("seed", QString::number(this->ParameterList[i]->value[3]));
}
break;
case 2:
{
xmlOut.writeEmptyElement("NormalDistribution");
xmlOut.writeAttribute("mean", QString::number(this->ParameterList[i]->value[1]));
xmlOut.writeAttribute("variance", QString::number(this->ParameterList[i]->value[2]));
xmlOut.writeAttribute("seed", QString::number(this->ParameterList[i]->value[3]));
}
break;
}
}
if (this->ParameterList[i]->currType == ExplicitList) {
xmlOut.writeStartElement("ValueList");
for (uint ind = 0; ind < this->ParameterList[i]->value.size(); ++ind) {
xmlOut.writeEmptyElement("Value");
xmlOut.writeAttribute("index", QString::number(float(this->ParameterList[i]->indices[ind])));
xmlOut.writeAttribute("value", QString::number(float(this->ParameterList[i]->value[ind])));
}
xmlOut.writeEndElement(); // valueList
}
xmlOut.writeEndElement(); // property
}
for (uint i = 0; i < this->StateVariableList.size(); ++i) {
xmlOut.writeStartElement("Property");
xmlOut.writeAttribute("name",this->StateVariableList[i]->name);
xmlOut.writeAttribute("dimension", this->StateVariableList[i]->dims->toString());
if (this->StateVariableList[i]->currType == FixedValue) {
xmlOut.writeEmptyElement("FixedValue");
xmlOut.writeAttribute("value", QString::number(this->StateVariableList[i]->value[0]));
}
if (this->StateVariableList[i]->currType == Statistical) {
switch (int(round(this->StateVariableList[i]->value[0]))) {
case 0:
break;
case 1:
{
xmlOut.writeEmptyElement("UniformDistribution");
xmlOut.writeAttribute("minimum", QString::number(this->StateVariableList[i]->value[1]));
xmlOut.writeAttribute("maximum", QString::number(this->StateVariableList[i]->value[2]));
xmlOut.writeAttribute("seed", QString::number(this->StateVariableList[i]->value[3]));
}
break;
case 2:
{
xmlOut.writeEmptyElement("NormalDistribution");
xmlOut.writeAttribute("mean", QString::number(this->StateVariableList[i]->value[1]));
xmlOut.writeAttribute("variance", QString::number(this->StateVariableList[i]->value[2]));
xmlOut.writeAttribute("seed", QString::number(this->StateVariableList[i]->value[3]));
}
break;
}
}
if (this->StateVariableList[i]->currType == ExplicitList) {
xmlOut.writeStartElement("ValueList");
for (uint ind = 0; ind < this->StateVariableList[i]->value.size(); ++ind) {
xmlOut.writeEmptyElement("Value");
xmlOut.writeAttribute("index", QString::number(float(this->StateVariableList[i]->indices[ind])));
xmlOut.writeAttribute("value", QString::number(float(this->StateVariableList[i]->value[ind])));
}
xmlOut.writeEndElement(); // valueList
}
xmlOut.writeEndElement(); // property
}
}
// if it is not a layout, add the inputs
if (this->type == NineMLComponentType) {
bool inputsTag = false;
for (uint i = 0; i < ((NineMLComponentData *) this)->inputs.size(); ++i) {
if (((NineMLComponentData *) this)->inputs[i]->projInput == false) {
inputsTag = true;
}
}
if (inputsTag) {
// inputs
for (uint i = 0; i < ((NineMLComponentData *) this)->inputs.size(); ++i) {
if (((NineMLComponentData *) this)->inputs[i]->projInput == false) {
// check we have ports
if (((NineMLComponentData *) this)->inputs[i]->srcPort.size() == 0 || ((NineMLComponentData *) this)->inputs[i]->dstPort.size() == 0) {
QSettings settings;
int num_errs = settings.beginReadArray("warnings");
settings.endArray();
settings.beginWriteArray("warnings");
settings.setArrayIndex(num_errs + 1);
settings.setValue("warnText", "No matched ports between '" + ((NineMLComponentData *) this)->inputs[i]->src->getXMLName() + "' and '" + ((NineMLComponentData *) this)->inputs[i]->dst->getXMLName() + "'");
settings.endArray();
}
xmlOut.writeStartElement("LL:Input");
xmlOut.writeAttribute("src", ((NineMLComponentData *) this)->inputs[i]->src->getXMLName());
xmlOut.writeAttribute("src_port", ((NineMLComponentData *) this)->inputs[i]->srcPort);
xmlOut.writeAttribute("dst_port", ((NineMLComponentData *) this)->inputs[i]->dstPort);
if (((NineMLComponentData *) this)->inputs[i]->connectionType->type == Kernel) {
((kernel_connection *) ((NineMLComponentData *) this)->inputs[i]->connectionType)->src = (population *) ((NineMLComponentData *) this)->inputs[i]->source;
((kernel_connection *) ((NineMLComponentData *) this)->inputs[i]->connectionType)->dst = (population *) ((NineMLComponentData *) this)->inputs[i]->destination;
}
if (((NineMLComponentData *) this)->inputs[i]->connectionType->type == DistanceBased) {
((distanceBased_connection *) ((NineMLComponentData *) this)->inputs[i]->connectionType)->src = (population *) ((NineMLComponentData *) this)->inputs[i]->source;
((distanceBased_connection *) ((NineMLComponentData *) this)->inputs[i]->connectionType)->dst = (population *) ((NineMLComponentData *) this)->inputs[i]->destination;
}
((NineMLComponentData *) this)->inputs[i]->connectionType->write_node_xml(xmlOut);
xmlOut.writeEndElement(); // input
}
}
}
}
}
void Parameter::readIn(QDomElement e)
{
this->name = e.attribute("name","");
if (this->name == "") {
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
settings.beginWriteArray("errors");
settings.setArrayIndex(num_errs + 1);
settings.setValue("errorText", "XML error: missing Parameter attribute 'name'");
settings.endArray();
}
// we need dims in here too eventually
//delete dims;
this->dims->fromString(e.attribute("dimension",""));
}
void Parameter::writeOut(QDomDocument * doc, QDomElement &parent)
{
QDomElement parameter = doc->createElement( "Parameter" );
parameter.setAttribute("name", this->name);
parameter.setAttribute("dimension", this->dims->toString());
parent.appendChild(parameter);
}
QString Parameter::getName()
{
return name;
}
void Parameter::setName(QString name)
{
this->name = name;
emit nameChanged();
}
void StateAssignment::readIn(QDomElement e) {
// we need to handle the statevariable stuff here... how?
this->name = e.attribute("variable","");
if (this->name == "") {
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
settings.beginWriteArray("errors");
settings.setArrayIndex(num_errs + 1);
settings.setValue("errorText", "XML error: missing StateAssignment attribute 'variable'");
settings.endArray();
}
QDomNode n = e.firstChild();
QDomElement e2 = n.toElement();
if( e2.tagName() == "MathInline" )
{
this->maths = new MathInLine;
this->maths->readIn(e2);
} else {
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
settings.beginWriteArray("errors");
settings.setArrayIndex(num_errs + 1);
settings.setValue("errorText", "XML error: missing StateAssignment 'MathInLine' tag'");
settings.endArray();
}
}
void StateAssignment::writeOut(QDomDocument * doc, QDomElement &parent)
{
QDomElement StateAssignment = doc->createElement( "StateAssignment" );
StateAssignment.setAttribute("variable", this->name);
parent.appendChild(StateAssignment);
this->maths->writeOut(doc, StateAssignment);
}
void OnEvent::readIn(QDomElement e) {
this->target_regime_name = e.attribute("target_regime","");
if (this->target_regime_name == "") {
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
settings.beginWriteArray("errors");
settings.setArrayIndex(num_errs + 1);
settings.setValue("errorText", "XML error: missing OnEvent 'target_regime' attribute'");
settings.endArray();
}
this->src_port_name = e.attribute("src_port","");
if (this->target_regime_name == "") {
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
settings.beginWriteArray("errors");
settings.setArrayIndex(num_errs + 1);
settings.setValue("errorText", "XML error: missing OnEvent 'src_port' attribute'");
settings.endArray();
}
QDomNode n = e.firstChild();
while( !n.isNull() )
{
QDomElement e2 = n.toElement();
if( e2.tagName() == "StateAssignment" )
{
StateAssignment *tempSA = new StateAssignment;
tempSA->readIn(e2);
this->StateAssignList.push_back(tempSA);
}
else if( e2.tagName() == "EventOut" )
{
EventOut *tempEO = new EventOut;
tempEO->readIn(e2);
this->eventOutList.push_back(tempEO);
}
else if( e2.tagName() == "ImpulseOut" )
{
ImpulseOut *tempIO = new ImpulseOut;
tempIO->readIn(e2);
this->impulseOutList.push_back(tempIO);
} else {
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
settings.beginWriteArray("errors");
settings.setArrayIndex(num_errs + 1);
settings.setValue("errorText", "XML error: misplaced or unknown tag - '" + e2.tagName() + "'");
settings.endArray();
}
n = n.nextSibling();
}
}
void OnEvent::writeOut(QDomDocument * doc, QDomElement &parent)
{
QDomElement OnEvent = doc->createElement( "OnEvent" );
parent.appendChild(OnEvent);
if (target_regime != NULL)
OnEvent.setAttribute("target_regime", this->target_regime->name);
else
OnEvent.setAttribute("target_regime", "Error: No Synapse Regime!");
if (src_port != NULL)
OnEvent.setAttribute("src_port", this->src_port->getName());
else
OnEvent.setAttribute("src_port", "Error: No Source Event Port!");
for (unsigned int i = 0; i < this->StateAssignList.size(); ++i) {
this->StateAssignList[i]->writeOut(doc, OnEvent);
}
for (unsigned int i = 0; i < this->eventOutList.size(); ++i) {
this->eventOutList[i]->writeOut(doc, OnEvent);
}
for (unsigned int i = 0; i < this->impulseOutList.size(); ++i) {
this->impulseOutList[i]->writeOut(doc, OnEvent);
}
}
void OnImpulse::readIn(QDomElement e) {
this->target_regime_name = e.attribute("target_regime","");
if (this->target_regime_name == "") {
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
settings.beginWriteArray("errors");
settings.setArrayIndex(num_errs + 1);
settings.setValue("errorText", "XML error: missing OnImpulse 'target_regime' attribute'");
settings.endArray();
}
this->src_port_name = e.attribute("src_port","");
if (this->target_regime_name == "") {
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
settings.beginWriteArray("errors");
settings.setArrayIndex(num_errs + 1);
settings.setValue("errorText", "XML error: missing OnImpulse 'src_port' attribute'");
settings.endArray();
}
QDomNode n = e.firstChild();
while( !n.isNull() )
{
QDomElement e2 = n.toElement();
if( e2.tagName() == "StateAssignment" )
{
StateAssignment *tempSA = new StateAssignment;
tempSA->readIn(e2);
this->StateAssignList.push_back(tempSA);
}
else if( e2.tagName() == "EventOut" )
{
EventOut *tempEO = new EventOut;
tempEO->readIn(e2);
this->eventOutList.push_back(tempEO);
}
else if( e2.tagName() == "ImpulseOut" )
{
ImpulseOut *tempIO = new ImpulseOut;
tempIO->readIn(e2);
this->impulseOutList.push_back(tempIO);
} else {
QSettings settings;
int num_errs = settings.beginReadArray("errors");
settings.endArray();
settings.beginWriteArray("errors");
settings.setArrayIndex(num_errs + 1);
settings.setValue("errorText", "XML error: misplaced or unknown tag - '" + e2.tagName() + "'");
settings.endArray();
}
n = n.nextSibling();
}
}
void OnImpulse::writeOut(QDomDocument * doc, QDomElement &parent)
{
QDomElement OnImpulse = doc->createElement( "OnImpulse" );
parent.appendChild(OnImpulse);