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SC_logged_data.cpp
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SC_logged_data.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 **
** Website/Contact: http://bimpa.group.shef.ac.uk/ **
****************************************************************************/
// this file includes a class for accessing logs and communicating with the
// qcustomplot widget
#include "SC_logged_data.h"
#include <QXmlStreamReader>
logData::logData(QObject *parent) :
QObject(parent)
{
this->timeStep = 0.1;
}
void logData::deleteLogFile (void)
{
QDir dir;
dir.remove(this->logFileXMLname);
dir.remove(this->logFile.fileName());
}
double logData::getMax()
{
if (max != Q_INFINITY) {
return max;
}
// no max, must calculate
double tempMax = -Q_INFINITY;
QVector < double > rowData;
rowData.push_back(-Q_INFINITY);
int i = 0;
while (rowData.size() > 0) {
for (int j = 0; j < rowData.size(); ++j) {
if (rowData[j] > tempMax && rowData[j] < Q_INFINITY) {
tempMax = rowData[j];
}
}
//qDebug() << rowData[0] << rowData[1]<< rowData[2]<< rowData[3]<< rowData[4]<< rowData[5]<< rowData[6]<< rowData[7]<< rowData[8]<< rowData[9];}
rowData = getRow(i);
++i;
}
max = tempMax;
return max;
}
double logData::getMin()
{
if (min != Q_INFINITY) {
return min;
}
// no min, must calculate
double tempMin = Q_INFINITY;
QVector < double > rowData;
rowData.push_back(Q_INFINITY);
int i = 0;
while (rowData.size() > 0) {
for (int j = 0; j < rowData.size(); ++j) {
if (rowData[j] < tempMin) {
tempMin = rowData[j];
}
}
rowData = getRow(i);
++i;
}
min = tempMin;
return min;
}
QVector < double > logData::getRow(int rowNum)
{
QVector < double > rowData;
// is not analog return empty
//if (this->dataClass != ANALOGDATA)
// return rowData;
// get data
switch (dataFormat) {
case BINARY:
{
if (!calculateBinaryDataStride()) {
return rowData;
}
// stream data from file
QDataStream data(&logFile);
data.device()->seek(0);
// offset into file
data.skipRawData(binaryDataStride*rowNum);
// if we skip to the end of the file
if (data.atEnd()) {
return rowData;
}
// check that all are same type
dataType mainType;
mainType = columns[0].type;
for (int i = 0; i < columns.size(); ++i) {
if (columns[i].type != mainType) {
return rowData;
}
}
switch (columns[0].type) {
case TYPE_DOUBLE:
{
if (allLogged) {
rowData.resize(columns.size());
data.readRawData((char *) &rowData[0], sizeof(double)*rowData.size());
} else {
QVector < double > tempDbl;
tempDbl.resize(columns.size());
data.readRawData((char *) &tempDbl[0], sizeof(double)*tempDbl.size());
// a good first guess
vector <double> temp = rowData.toStdVector();
temp.resize(columns.back().index+1, Q_INFINITY);
rowData = QVector <double>::fromStdVector(temp);
for (int i = 0; i < columns.size(); ++i) {
if (static_cast<int>(columns[i].index) > rowData.size()) {
vector <double> temp = rowData.toStdVector();
temp.resize(columns[i].index+1, Q_INFINITY);
rowData = QVector <double>::fromStdVector(temp);
}
rowData[columns[i].index] = tempDbl[i];
}
}
return rowData;
}
break;
case TYPE_FLOAT:
{
QVector < float > tempFloat;
tempFloat.resize(columns.size());
data.setFloatingPointPrecision(QDataStream::SinglePrecision);
data.readRawData((char *) &tempFloat[0], sizeof(float)*tempFloat.size());
// a good first guess
vector <double> temp = rowData.toStdVector();
temp.resize(columns.back().index+1, Q_INFINITY);
rowData = QVector <double>::fromStdVector(temp);
for (int i = 0; i < columns.size(); ++i) {
if (static_cast<int>(columns[i].index) > rowData.size()) {
vector <double> temp = rowData.toStdVector();
temp.resize(columns[i].index+1, Q_INFINITY);
rowData = QVector <double>::fromStdVector(temp);
}
rowData[columns[i].index] = tempFloat[i];
}
return rowData;
}
break;
case TYPE_INT64:
{
// not supported currently
return rowData;
}
break;
case TYPE_INT32:
{
QVector < int > tempInt;
tempInt.resize(columns.size());
data.readRawData((char *) &tempInt[0], sizeof(int)*tempInt.size());
// a good first guess
vector <double> temp = rowData.toStdVector();
temp.resize(columns.back().index+1, Q_INFINITY);
rowData = QVector <double>::fromStdVector(temp);
for (int i = 0; i < columns.size(); ++i) {
if (static_cast<int>(columns[i].index) > rowData.size()) {
vector <double> temp = rowData.toStdVector();
temp.resize(columns[i].index+1, Q_INFINITY);
rowData = QVector <double>::fromStdVector(temp);
}
rowData[columns[i].index] = tempInt[i];
}
return rowData;
}
break;
case TYPE_STRING:
return rowData;
} // end switch (columns[0].type)
break;
}
case CSVFormat:
case SSVFormat:
{
// read line by line
QTextStream data(&logFile);
data.device()->seek(0);
float desiredTimeMin = this->timeStep*rowNum-1.0-this->timeStep/2.0;
float desiredTimeMax = this->timeStep*rowNum+this->timeStep/2.0;
// read a line
while (!data.atEnd()) {
// get line
QString line = data.readLine();
// divide up
QStringList cols;
if (dataFormat == CSVFormat) {
line.remove(" ");
cols = line.split(",");
}
else if (dataFormat == SSVFormat) {
line = line.simplified();
cols = line.split(" ");
}
// parse
if (cols.size() != (int) columns.size()) {
qDebug() << "Col size incorrect on import";
rowData.clear();
return rowData;
}
// for each entry with the desired timerange, add the index to the list
if (cols[0].toDouble() > desiredTimeMin && cols[0].toDouble() < desiredTimeMax) {
rowData.push_back(cols[1].toInt());
}
}
}
default:
// do nothing in these cases.
break;
} // end switch (dataFormat)
return rowData;
}
bool logData::plotLine(QCustomPlot *plot, QMdiSubWindow* msw, int colNum, int update) {
// if no plot give up. FIXME - could get plot from msw. That's always where it comes from.
if (plot == NULL) {
DBG() << "No plot passed in, give up.";
return false;
}
// if out of range give up (should also catch no file)
if (colNum >= (int) columns.size()) {
DBG() << "Out of range/no file";
return false;
}
// Don't need this->plots anymore? Or used as temporary storage only?
this->plots.insert (plot, msw);
// clear existing data;
colData[colNum].clear();
// get data
switch (dataFormat) {
case BINARY:
{
if (!calculateBinaryDataStride()) {
return false;
}
int offset = calculateBinaryDataOffset(colNum);
if (offset == -1) {
return false;
}
// stream data from file
QDataStream data(&logFile);
data.device()->seek(0);
// offset into file
data.skipRawData(offset);
switch (columns[colNum].type) {
case TYPE_DOUBLE:
{
double tempDbl;
while (data.readRawData((char *) &tempDbl, sizeof(tempDbl)) != -1) {
// add to data
colData[colNum].push_back(tempDbl);
// skip to next row
data.skipRawData(binaryDataStride-sizeof(double));
if (data.atEnd())
break;
}
break;
}
case TYPE_FLOAT:
{
float tempFloat;
data.setFloatingPointPrecision(QDataStream::SinglePrecision);
while (data.readRawData((char *) &tempFloat, sizeof(tempFloat)) != -1) {
// add to data
colData[colNum].push_back((double) tempFloat);
// skip to next row
data.skipRawData(binaryDataStride-sizeof(float));
if (data.atEnd())
break;
}
break;
}
case TYPE_INT64:
{
// not supported currently
return false;
int tempInt;
while (data.readRawData((char *) &tempInt, sizeof(tempInt)) != -1) {
// add to data
colData[colNum].push_back((double) tempInt);
// skip to next row
data.skipRawData(binaryDataStride-sizeof(long int));
if (data.atEnd())
break;
}
break;
}
case TYPE_INT32:
{
int tempInt;
while (data.readRawData((char *) &tempInt, sizeof(tempInt)) != -1) {
// add to data
colData[colNum].push_back((double) tempInt);
// skip to next row
data.skipRawData(binaryDataStride-sizeof(int));
if (data.atEnd())
break;
}
break;
}
case TYPE_STRING:
return false;
break;
}
// what about default:?
} // end case BINARY
case CSVFormat:
case SSVFormat:
break;
default:
// oops, bad dataType
return false;
}
//
QVector < double > times;
for (int i = 0; i < colData[colNum].size(); ++i) {
times.push_back(((double) i)*timeStep);
}
if (update == -1) {
// add graph and setup data and name
DBG() << "plot->addGraph called";
plot->addGraph();
plot->graph(plot->graphCount()-1)->setData(times, colData[colNum]);
plot->graph(plot->graphCount()-1)->setName("Index " + QString::number(columns[colNum].index));
// add properties to graph so we know what it came from
plot->graph(plot->graphCount()-1)->setProperty("type", "linePlot");
plot->graph(plot->graphCount()-1)->setProperty("source", logFileXMLname);
plot->graph(plot->graphCount()-1)->setProperty("index", colNum);
// axis labels
plot->xAxis->setLabel("Time (ms)");
plot->yAxis->setLabel(columns[colNum].heading + " (" + columns[colNum].dims + ")");
// alternate colours
QPen pen;
pen.setColor((Qt::GlobalColor) (7+(plot->graphCount()-1)%11));
plot->graph(plot->graphCount()-1)->setPen(pen);
// fit all if not an update
plot->rescaleAxes();
} else {
DBG() << "plot->graph(update) called";
plot->graph(update)->setData(times, colData[colNum]);
}
plot->legend->setVisible(false); // fixme, make this an option
// title
QCPPlotTitle* t = (QCPPlotTitle*)0;
if (plot->plotLayout()->rowCount() == 1) {
plot->plotLayout()->insertRow(0); // inserts an empty row above the default axis rect
plot->plotLayout()->addElement(0, 0, new QCPPlotTitle(plot, this->logName));
t = (QCPPlotTitle*)plot->plotLayout()->element (0, 0);
} else {
// update title as it's empty
t = (QCPPlotTitle*)plot->plotLayout()->element (0, 0);
if (t->text().isEmpty()) {
t->setText (this->logName);
}
}
// Set font size based on text length here.
QFont f = t->font();
int len = this->logName.size();
int fs = 15; // original default for plots
if (len <= 24) {
fs = 15;
} else if (len > 24 && len <= 32) {
fs = 12;
} else if (len > 32 && len <= 43) {
fs = 10;
} else {
fs = 8;
}
if (f.pointSize() != fs) {
f.setPointSize(fs);
t->setFont(f);
}
// redraw
plot->replot();
// Ensure that when destroyed, the relevant plot will be removed. (no longer required)
//connect(plot, SIGNAL(destroyed()), this, SLOT(onPlotDestroyed()));
return true;
}
bool logData::plotRaster(QCustomPlot * plot, QMdiSubWindow* msw, QList < QVariant > indices, int update) {
// if no plot give up
if (plot == NULL) {
return false;
}
this->plots.insert (plot, msw);
// clear existing data;
colData[0].clear();
colData[1].clear();
// get data
for (int colNum = 0; colNum < 2; ++colNum) {
switch (dataFormat) {
case BINARY:
{
if (!calculateBinaryDataStride())
return false;
int offset = calculateBinaryDataOffset(colNum);
if (offset == -1)
return false;
// stream data from file
QDataStream data(&logFile);
data.device()->seek(0);
// offset into file
data.skipRawData(offset);
switch (columns[colNum].type) {
case TYPE_DOUBLE:
{
double tempDbl;
while (data.readRawData((char *) &tempDbl, sizeof(tempDbl)) != -1) {
// add to data
colData[colNum].push_back(tempDbl);
// skip to next row
data.skipRawData(binaryDataStride-sizeof(double));
if (data.atEnd())
break;
}
}
break;
case TYPE_FLOAT:
{
float tempFloat;
data.setFloatingPointPrecision(QDataStream::SinglePrecision);
while (data.readRawData((char *) &tempFloat, sizeof(tempFloat)) != -1) {
// add to data
colData[colNum].push_back((double) tempFloat);
// skip to next row
data.skipRawData(binaryDataStride-sizeof(float));
if (data.atEnd())
break;
}
}
break;
case TYPE_INT64:
{
// not supported currently
return false;
int tempInt;
while (data.readRawData((char *) &tempInt, sizeof(tempInt)) != -1) {
// add to data
colData[colNum].push_back((double) tempInt);
// skip to next row
data.skipRawData(binaryDataStride-sizeof(long int));
if (data.atEnd())
break;
}
}
break;
case TYPE_INT32:
{
int tempInt;
while (data.readRawData((char *) &tempInt, sizeof(tempInt)) != -1) {
// add to data
colData[colNum].push_back((double) tempInt);
// skip to next row
data.skipRawData(binaryDataStride-sizeof(int));
if (data.atEnd())
break;
}
}
break;
case TYPE_STRING:
return false;
}
}
break;
case CSVFormat:
case SSVFormat:
{
// read line by line
QTextStream data(&logFile);
data.device()->seek(0);
// read a line
while (!data.atEnd()) {
// get line
QString line = data.readLine();
// divide up
QStringList cols;
if (dataFormat == CSVFormat) {
line.remove(" ");
cols = line.split(",");
}
else if (dataFormat == SSVFormat) {
line = line.simplified();
cols = line.split(" ");
}
// parse
if (cols.size() != (int) columns.size()) {
qDebug() << "Col size incorrect on import";
return false;
}
for (int i = 0; i < indices.size(); ++i) {
if (cols[1].toInt() == indices[i].toInt()) {
colData[0].push_back(cols[0].toDouble());
colData[1].push_back(cols[1].toDouble());
}
}
}
}
break;
default:
// oops, bad dataType
qDebug() << "Bad dataType";
return false;
}
}
if (colData.size() != 2 && colData.size() != 3) {
qDebug() << "Not 2 cols (spike log) or 3 cols (impulse log)";
return false;
}
// add graph and setup data and name, or update existing
DBG() << "plot-> functions to be called";
if (update == -1) {
plot->addGraph();
plot->graph(plot->graphCount()-1)->setData(colData[0], colData[1]);
plot->graph(plot->graphCount()-1)->setScatterStyle(QCPScatterStyle(QCPScatterStyle::ssDisc, 1));
plot->graph(plot->graphCount()-1)->setLineStyle(QCPGraph::lsNone);
// add properties to graph so we know what it came from
plot->graph(plot->graphCount()-1)->setProperty("type", "rasterPlot");
plot->graph(plot->graphCount()-1)->setProperty("source", logFileXMLname);
QVariant var(indices);
plot->graph(plot->graphCount()-1)->setProperty("indices", var);
// axis labels
plot->xAxis->setLabel("Time (ms)");
plot->yAxis->setLabel("Index");
// alternate colours
QPen pen;
pen.setColor((Qt::GlobalColor) (7+(plot->graphCount()-1)%11));
plot->graph(plot->graphCount()-1)->setPen(pen);
plot->xAxis->setRange(0, endTime);
plot->yAxis->setRange(-0.5, eventIndices.size()-0.5);
plot->yAxis->setTickStep(1.0);
} else {
plot->graph(update)->setData(colData[0], colData[1]);
}
// title
if (plot->plotLayout()->rowCount() == 1) {
plot->plotLayout()->insertRow(0); // inserts an empty row above the default axis rect
plot->plotLayout()->addElement(0, 0, new QCPPlotTitle(plot, this->logName));
} else {
QCPPlotTitle* t = (QCPPlotTitle*)plot->plotLayout()->element (0, 0);
if (t->text().isEmpty()) {
t->setText (this->logName);
}
}
// redraw
plot->replot();
connect(plot, SIGNAL(destroyed()), this, SLOT(onPlotDestroyed()));
return true;
}
bool logData::calculateBinaryDataStride()
{
binaryDataStride = 0;
for (int i = 0; i < (int) columns.size(); ++i) {
switch (columns[i].type) {
case TYPE_DOUBLE:
binaryDataStride += sizeof(double);
break;
case TYPE_FLOAT:
binaryDataStride += sizeof(float);
break;
case TYPE_INT64:
binaryDataStride += sizeof(long int);
break;
case TYPE_INT32:
binaryDataStride += sizeof(int);
break;
case TYPE_STRING:
binaryDataStride = 0;
return false;
}
}
return true;
}
int logData::calculateBinaryDataOffset(int colNum) {
int tempInt = 0;
for (int i = 0; i < colNum; ++i) {
switch (columns[i].type) {
case TYPE_DOUBLE:
tempInt += sizeof(double);
break;
case TYPE_FLOAT:
tempInt += sizeof(float);
break;
case TYPE_INT64:
tempInt += sizeof(long int);
break;
case TYPE_INT32:
tempInt += sizeof(int);
break;
case TYPE_STRING:
return -1;
}
}
return tempInt;
}
bool logData::setupFromXML() {
// no log specified
if (logFileXMLname.isEmpty()) {
qDebug() << "XML filename not set";
return false;
}
// open XML for reading
QFile xmlfile( logFileXMLname );
if( !xmlfile.open( QIODevice::ReadOnly ) ) {
// could not open
qDebug() << "Couldn't open XML file";
return false;}
// setup XML reader
QXmlStreamReader * reader = new QXmlStreamReader;
reader->setDevice( &xmlfile );
// clear up
columns.clear();
eventIndices.clear();
allLogged = false;
min = Q_INFINITY;
max = Q_INFINITY;
// temp config data
QString logFileName;
// parse XML
while (reader->readNextStartElement()) {
if (reader->name() == "LogReport") {
while (reader->readNextStartElement()) {
if (reader->name() == "AnalogLog") {
dataClass = ANALOGDATA;
while (reader->readNextStartElement()) {
if (reader->name() == "LogFile") {
// store logfile name
logFileName = reader->readElementText();
} else if (reader->name() == "LogFileType") {
QString tempStr = reader->readElementText();
if (tempStr == "binary") {
dataFormat = BINARY;
} else if (tempStr == "csv") {
dataFormat = CSVFormat;
} else if (tempStr == "ssv") {
dataFormat = SSVFormat;
} else {
// invalid file format
qDebug() << "Invalid file format";
delete reader;
return false;
}
} else if (reader->name() == "LogEndTime") {
QString tempStr = reader->readElementText();
endTime = tempStr.toDouble();
} else if (reader->name() == "LogCol") {
column newCol;
if (reader->attributes().hasAttribute("index")) {
newCol.index = reader->attributes().value("index").toString().toInt();
} else {
// required attribute
qDebug() << "Index attr missing";
delete reader;
return false;
}
if (reader->attributes().hasAttribute("heading")) {
newCol.heading = reader->attributes().value("heading").toString();
} else {
// required attribute
qDebug() << "Heading attr missing";
delete reader;
return false;
}
if (reader->attributes().hasAttribute("dims")) {
newCol.dims = reader->attributes().value("dims").toString();
} else {
// required attribute
qDebug() << "Dims attr missing";
delete reader;
return false;
}
if (reader->attributes().hasAttribute("type")) {
QString tempStr = reader->attributes().value("type").toString();
if (tempStr == "double") {
newCol.type = TYPE_DOUBLE;
} else if (tempStr == "float") {
newCol.type = TYPE_FLOAT;
} else if (tempStr == "int") {
newCol.type = TYPE_INT32;
} else if (tempStr == "longint") {
newCol.type = TYPE_INT64;
} else if (tempStr == "string") {
newCol.type = TYPE_STRING;
} else {
// invalid data type
qDebug() << "Wrong data type label";
delete reader;
return false;
}
} else {
// required attribute
qDebug() << "Type attr missing";
delete reader;
return false;
}
// as unclosed
reader->readNextStartElement();
// add column
columns.push_back(newCol);
} else if (reader->name() == "LogAll") {
allLogged = true;
column newCol;
int size;
if (reader->attributes().hasAttribute("size")) {
size = reader->attributes().value("size").toString().toInt();
} else {
// required attribute
qDebug() << "Size attr missing";
delete reader;
return false;
}
if (reader->attributes().hasAttribute("headings")) {
newCol.heading = reader->attributes().value("headings").toString();
} else {
// required attribute
qDebug() << "Headings attr missing";
delete reader;
return false;
}
if (reader->attributes().hasAttribute("dims")) {
newCol.dims = reader->attributes().value("dims").toString();
} else {
// required attribute
qDebug() << "Dims attr missing";
delete reader;
return false;
}
if (reader->attributes().hasAttribute("type")) {
QString tempStr = reader->attributes().value("type").toString();
if (tempStr == "double") {
newCol.type = TYPE_DOUBLE;
} else if (tempStr == "float") {
newCol.type = TYPE_FLOAT;
} else if (tempStr == "int") {
newCol.type = TYPE_INT32;
} else if (tempStr == "longint") {
newCol.type = TYPE_INT64;
} else if (tempStr == "string") {
newCol.type = TYPE_STRING;
} else {
// invalid data type
qDebug() << "Wrong data type name";
delete reader;
return false;
}
} else {
// required attribute
qDebug() << "Type attr missing";
delete reader;
return false;
}
// as unclosed
reader->readNextStartElement();
// add columns
vector <column> temp = columns.toStdVector();
temp.resize(size, newCol);
columns = QVector<column>::fromStdVector(temp);
// setup indices
for (int i = 0; i < columns.size(); ++i)
columns[i].index = i;
} else if (reader->name() == "TimeStep") {
if (reader->attributes().hasAttribute("dt")) {
timeStep = reader->attributes().value("dt").toString().toDouble();
} else {
// required attribute
qDebug() << "Timestep attr missing";
delete reader;
return false;
}
} else {
// XML tag not recognised
qDebug() << "Unknown tag name " << reader->name();
delete reader;
return false;
}
}
} else if (reader->name() == "EventLog") {
dataClass = EVENTDATA;
while (reader->readNextStartElement()) {
if (reader->name() == "LogFile") {
// store logfile name
logFileName = reader->readElementText();
} else if (reader->name() == "LogFileType") {
QString tempStr = reader->readElementText();
if (tempStr == "binary") {
dataFormat = BINARY;
} else if (tempStr == "csv") {
dataFormat = CSVFormat;
} else if (tempStr == "ssv") {
dataFormat = SSVFormat;
} else {
// invalid file format
qDebug() << "File format unkown";
delete reader;
return false;
}
} else if (reader->name() == "LogEndTime") {
QString tempStr = reader->readElementText();
endTime = tempStr.toDouble();
} else if (reader->name() == "LogCol") {
column newCol;
// event port logs don't use the index
newCol.index = -1;
if (reader->attributes().hasAttribute("heading")) {
newCol.heading = reader->attributes().value("heading").toString();
} else {
// required attribute
qDebug() << "Heading attr missing";
delete reader;
return false;
}
if (reader->attributes().hasAttribute("dims")) {
newCol.dims = reader->attributes().value("dims").toString();
} else {
// required attribute
qDebug() << "Dims attr missing";
delete reader;
return false;
}
if (reader->attributes().hasAttribute("type")) {
QString tempStr = reader->attributes().value("type").toString();
if (tempStr == "double") {
newCol.type = TYPE_DOUBLE;
} else if (tempStr == "float") {
newCol.type = TYPE_FLOAT;
} else if (tempStr == "int") {
newCol.type = TYPE_INT32;
} else if (tempStr == "longint") {
newCol.type = TYPE_INT64;
} else if (tempStr == "string") {
newCol.type = TYPE_STRING;
} else {
// invalid data type
qDebug() << "Data type unknown";
delete reader;
return false;
}
} else {
// required attribute
qDebug() << "Type attr missing";
delete reader;
return false;
}
// as unclosed
reader->readNextStartElement();