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CL_classes.cpp
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CL_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) 2013-2014 Alex Cope, Paul Richmond, Seb James **
** **
** 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 "CL_classes.h"
#include "NL_projection_and_synapse.h"
#include "CL_layout_classes.h"
#include "NL_genericinput.h"
#include "NL_population.h"
QString dim::toString()
{
QString unit;
QString prefix;
unit = getUnitString();
prefix = getPrefixString();
unit = prefix + unit;
return unit;
}
void dim::fromString(QString in)
{
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 Component::load(QDomDocument *doc)
{
QDomNode n = doc->documentElement().firstChild();
while (!n.isNull()) {
if (n.isComment()) {
n = n.nextSibling();
continue;
}
QDomElement e = n.toElement();
if (e.tagName() == "ComponentClass") {
this->name = e.attribute("name","");
this->islearning = !(e.attribute("islearning","").isEmpty());
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()) {
if (n2.isComment()) {
n2 = n2.nextSibling();
continue;
}
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()) {
if (n3.isComment()) {
// Ignore XML comments
n3 = n3.nextSibling();
continue;
}
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 if (e2.tagName() == "Annotation") {
// Any user-provided bits have to be stored.
QDomNode scNode;
QDomNodeList scAnns = e2.toElement().elementsByTagName("SpineCreator");
if (scAnns.length() == 1) { // There are SpineCreator-specific annotations
scNode = scAnns.at(0).cloneNode(); // Make a copy of the SpineCreator-specific annotations
e2.toElement().removeChild(scAnns.at(0)); // Remove the SpineCreator-specific annotations
// Now read the SpineCreator-specific parts that we just copied.
this->annotationTexts.clear();
// Find <Text key="something">Value</Text> nodes and populate annotationTexts
QDomNode sct = scNode.firstChild();
while (!sct.isNull()) {
if (sct.isElement()) {
QDomElement e = sct.toElement();
if (e.tagName() == "Text") {
QString key = e.attribute("key");
QString val = e.text();
this->annotationTexts[key] = val;
DBG() << "Added Text key=" << key << ", val=" << val << " to annotationTexts.";
}
}
sct = sct.nextSibling();
}
}
// Save any remaining non-SpineCreator specific annotations into this->annotations.
QTextStream temp(&this->annotation);
e2.save(temp,1);
} 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();
#ifdef _OUTPUT_A_MESSAGE_ABOUT_VALIDATION_
if (validated.size() > 1) {
QMessageBox msgBox;
QString message;
for (int i = 0; i < (int) validated.size(); ++i) {
message += validated[i] + "\n";
}
msgBox.setText(message);
msgBox.exec();
}
#endif
}
void Component::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);
if (this->islearning) {
CClass.setAttribute("islearning", true);
}
root.appendChild(CClass);
// Create component annotation element
QDomElement annot = doc->createElement("Annotation");
// Add non-SpineCreator annotations
QDomDocument userannot("Userannotations");
if (userannot.setContent(this->annotation, false)) {
QDomElement uaroot = userannot.documentElement();
QDomElement n = uaroot.firstChildElement();
while (!n.isNull()) {
QDomElement nxt = n.nextSiblingElement();
annot.appendChild (n);
n = nxt;
}
}
// Add SpineCreator-specific annotations
QDomElement spinecreator = doc->createElement("SpineCreator");
QMap<QString, QString>::const_iterator t = this->annotationTexts.constBegin();
while (t != this->annotationTexts.constEnd()) {
QDomElement txte = doc->createElement("Text");
txte.setAttribute("key", t.key());
QDomText text = doc->createTextNode(t.value());
txte.appendChild(text);
spinecreator.appendChild(txte);
++t;
}
annot.appendChild(spinecreator);
// Append the component annotations onto the component class:
CClass.appendChild(annot);
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 (int i = 0; i < this->AnalogPortList.size(); ++i) {
AnalogPortList[i]->writeOut(doc, CClass);
}
for (int i = 0; i < this->EventPortList.size(); ++i) {
EventPortList[i]->writeOut(doc, CClass);
}
for (int i = 0; i < this->ImpulsePortList.size(); ++i) {
ImpulsePortList[i]->writeOut(doc, CClass);
}
for (int i = 0; i < this->ParameterList.size(); ++i) {
ParameterList[i]->writeOut(doc, CClass);
}
// dynamics
for (int i = 0; i < this->RegimeList.size(); ++i) {
RegimeList[i]->writeOut(doc, dynamics);
}
for (int i = 0; i < this->AliasList.size(); ++i) {
AliasList[i]->writeOut(doc, dynamics);
}
for (int i = 0; i < this->StateVariableList.size(); ++i) {
StateVariableList[i]->writeOut(doc, dynamics);
}
}
void ComponentRootInstance::write_node_xml(QXmlStreamWriter &xmlOut)
{
// definition
QString simpleName;
if (this->type == NineMLLayoutType) {
simpleName = (static_cast<NineMLLayoutData *> (this))->component->name.simplified();
}
if (this->type == NineMLComponentType) {
ComponentInstance * ptr = static_cast <ComponentInstance *> (this);
simpleName = ptr->component->name.simplified();
}
simpleName.replace (" ", "_");
xmlOut.writeAttribute("url", simpleName + ".xml");
// write the seed and minumum distance for the Layout
if (this->type == NineMLLayoutType) {
NineMLLayoutData * lay = static_cast<NineMLLayoutData *> (this);
xmlOut.writeAttribute("seed", QString::number(lay->seed));
xmlOut.writeAttribute("minimum_distance", QString::number(lay->minimumDistance));
}
if (this->type == NineMLComponentType) {
ComponentInstance * ptr = static_cast <ComponentInstance *> (this);
for (int i = 0; i < ptr->inputs.size(); ++i) {
if (ptr->inputs[i]->projInput == true) {
// add the special input for the synapse
if (ptr->component->type == "weight_update") {
// check we have ports
if (ptr->inputs[i]->srcPort.size() == 0 || ptr->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 '" + ptr->inputs[i]->srcCmpt->getXMLName() + "' and '" + ptr->inputs[i]->dstCmpt->getXMLName() + "'");
settings.endArray();
}
xmlOut.writeAttribute("input_src_port", ptr->inputs[i]->srcPort);
xmlOut.writeAttribute("input_dst_port", ptr->inputs[i]->dstPort);
}
// add the special input for the postsynapse
if (ptr->component->type == "postsynapse") {
// check we have ports
if (ptr->inputs[i]->srcPort.size() == 0 || ptr->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 '" + ptr->inputs[i]->srcCmpt->getXMLName() + "' and '" +ptr->inputs[i]->dstCmpt->getXMLName() + "'");
settings.endArray();
}
xmlOut.writeAttribute("input_src_port", ptr->inputs[i]->srcPort);
xmlOut.writeAttribute("input_dst_port", ptr->inputs[i]->dstPort);
}
}
}
if (ptr->component->type == "postsynapse") {
// search out the Synapse population and add the postsynapticMapping
for (int i = 0; i < (qSharedPointerDynamicCast<projection> (ptr->owner))->destination->neuronType->inputs.size(); ++i) {
if ((qSharedPointerDynamicCast<projection> (ptr->owner))->destination->neuronType->inputs[i]->srcCmpt == this && \
(qSharedPointerDynamicCast<projection> (ptr->owner))->destination->neuronType->inputs[i]->projInput == true) {
// check we have ports
if (qSharedPointerDynamicCast<projection> (ptr->owner)->destination->neuronType->inputs[i]->srcPort.size() == 0 || (qSharedPointerDynamicCast<projection> (ptr->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 '" + (qSharedPointerDynamicCast<projection> (ptr->owner))->destination->neuronType->inputs[i]->srcCmpt->getXMLName() + "' and '" + (qSharedPointerDynamicCast<projection> (ptr->owner))->destination->neuronType->inputs[i]->dstCmpt->getXMLName() + "'");
settings.endArray();
}
xmlOut.writeAttribute("output_src_port", (qSharedPointerDynamicCast<projection> (ptr->owner))->destination->neuronType->inputs[i]->srcPort);
xmlOut.writeAttribute("output_dst_port", (qSharedPointerDynamicCast<projection> (ptr->owner))->destination->neuronType->inputs[i]->dstPort);
}
}
} // if component type is postsynapse
}
// Have now finished writing attributes into the PostSynapse/WeightUpdate
// Add Annotations element:
if (!this->annotation.isEmpty()) {
// old annotations
this->annotation.replace("\n", "");
this->annotation.replace("<LL:Annotation>", "");
this->annotation.replace("</LL:Annotation>", "");
if (!this->annotation.isEmpty()) {
xmlOut.writeStartElement("LL:Annotation");
QXmlStreamReader reader(this->annotation);
while (!reader.atEnd()) {
if (reader.tokenType() != QXmlStreamReader::StartDocument
&& reader.tokenType() != QXmlStreamReader::EndDocument) {
xmlOut.writeCurrentToken(reader);
}
reader.readNext();
}
xmlOut.writeEndElement(); // "LL:Annotation"
}
}
// Add any parameter or state variable properties that exist
if (this->ParameterList.size()+this->StateVariableList.size() > 0) {
// Output parameter properties
for (int 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) {
// Write out the explicit list either to XML or to binary by calling a built in function
this->ParameterList[i]->writeExplicitListNodeData(xmlOut);
}
xmlOut.writeEndElement(); // property
} // done with parameter properties
// Output state variable properties
for (int 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) {
this->StateVariableList[i]->writeExplicitListNodeData(xmlOut);
}
xmlOut.writeEndElement(); // property
} // Done with state variable properties
} // else there are no properties
// if it is not a layout, add the inputs
if (this->type == NineMLComponentType) {
ComponentInstance * ptr = static_cast <ComponentInstance *> (this);
bool inputsTag = false;
for (int i = 0; i < ptr->inputs.size(); ++i) {
if (ptr->inputs[i]->projInput == false) {
inputsTag = true;
}
}
if (inputsTag) {
// inputs
for (int i = 0; i < ptr->inputs.size(); ++i) {
if (ptr->inputs[i]->projInput == false) {
// check we have ports
if (ptr->inputs[i]->srcPort.size() == 0 || ptr->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 '" + ptr->inputs[i]->srcCmpt->getXMLName() + "' and '" + ptr->inputs[i]->dstCmpt->getXMLName() + "'");
settings.endArray();
}
xmlOut.writeStartElement("LL:Input");
xmlOut.writeAttribute("src", ptr->inputs[i]->srcCmpt->getXMLName());
xmlOut.writeAttribute("src_port", ptr->inputs[i]->srcPort);
xmlOut.writeAttribute("dst_port", ptr->inputs[i]->dstPort);
// write annotations
ptr->inputs[i]->write_model_meta_xml (&xmlOut);
if (ptr->inputs[i]->conn->type == Python) {
((pythonscript_connection *) ptr->inputs[i]->conn)->srcPop = qSharedPointerDynamicCast <population> (ptr->inputs[i]->source);
((pythonscript_connection *) ptr->inputs[i]->conn)->dstPop = qSharedPointerDynamicCast <population> (ptr->inputs[i]->destination);
} else if (ptr->inputs[i]->conn->type == CSV) {
((csv_connection *) ptr->inputs[i]->conn)->srcPop = qSharedPointerDynamicCast <population> (ptr->inputs[i]->source);
((csv_connection *) ptr->inputs[i]->conn)->dstPop = qSharedPointerDynamicCast <population> (ptr->inputs[i]->destination);
}
ptr->inputs[i]->conn->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()) {
if (n.isComment()) {
n = n.nextSibling();
continue;
}
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);