fiff_annotations.cpp

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//=============================================================================================================
 
//=============================================================================================================
// INCLUDES
//=============================================================================================================
 
#include "fiff_annotations.h"
 
//=============================================================================================================
// QT INCLUDES
//=============================================================================================================
 
#include <QFile>
#include <QJsonDocument>
#include <QJsonObject>
#include <QJsonArray>
#include <QTextStream>
#include <QDebug>
#include <QFileInfo>
 
//=============================================================================================================
// USED NAMESPACES
//=============================================================================================================
 
using namespace FIFFLIB;
 
//=============================================================================================================
// DEFINE MEMBER METHODS
//=============================================================================================================
 
FiffAnnotations::FiffAnnotations()
{
}
 
//=============================================================================================================
 
int FiffAnnotations::size() const
{
    return m_annotations.size();
}
 
//=============================================================================================================
 
bool FiffAnnotations::isEmpty() const
{
    return m_annotations.isEmpty();
}
 
//=============================================================================================================
 
const FiffAnnotation& FiffAnnotations::operator[](int index) const
{
    return m_annotations[index];
}
 
//=============================================================================================================
 
FiffAnnotation& FiffAnnotations::operator[](int index)
{
    return m_annotations[index];
}
 
//=============================================================================================================
 
void FiffAnnotations::append(const FiffAnnotation& annotation)
{
    m_annotations.append(annotation);
}
 
//=============================================================================================================
 
void FiffAnnotations::append(double onset, double duration, const QString& description,
                             const QStringList& channelNames, const QString& comment)
{
    FiffAnnotation a;
    a.onset = onset;
    a.duration = duration;
    a.description = description;
    a.channelNames = channelNames;
    a.comment = comment;
    m_annotations.append(a);
}
 
//=============================================================================================================
 
void FiffAnnotations::remove(int index)
{
    m_annotations.remove(index);
}
 
//=============================================================================================================
 
void FiffAnnotations::clear()
{
    m_annotations.clear();
}
 
//=============================================================================================================
 
const QVector<FiffAnnotation>& FiffAnnotations::toVector() const
{
    return m_annotations;
}
 
//=============================================================================================================
 
int FiffAnnotations::onsetToSample(int index, double sfreq, int firstSample) const
{
    return static_cast<int>(m_annotations[index].onset * sfreq) + firstSample;
}
 
//=============================================================================================================
 
int FiffAnnotations::endToSample(int index, double sfreq, int firstSample) const
{
    const FiffAnnotation& a = m_annotations[index];
    return static_cast<int>((a.onset + a.duration) * sfreq) + firstSample;
}
 
//=============================================================================================================
 
FiffAnnotations FiffAnnotations::select(const QString& descriptionFilter) const
{
    FiffAnnotations result;
    for (const FiffAnnotation& a : m_annotations) {
        if (a.description.startsWith(descriptionFilter)) {
            result.append(a);
        }
    }
    return result;
}
 
//=============================================================================================================
 
FiffAnnotations FiffAnnotations::selectByChannel(const QString& channelName) const
{
    FiffAnnotations result;
    for (const FiffAnnotation& a : m_annotations) {
        if (a.channelNames.isEmpty() || a.channelNames.contains(channelName)) {
            result.append(a);
        }
    }
    return result;
}
 
//=============================================================================================================
 
FiffAnnotations FiffAnnotations::crop(double tmin, double tmax) const
{
    FiffAnnotations result;
    for (const FiffAnnotation& a : m_annotations) {
        double aEnd = a.onset + a.duration;
 
        // Check overlap: annotation interval [onset, aEnd] vs window [tmin, tmax]
        if (a.onset > tmax || aEnd < tmin) {
            continue;
        }
 
        FiffAnnotation clipped = a;
        if (clipped.onset < tmin) {
            double shift = tmin - clipped.onset;
            clipped.onset = tmin;
            clipped.duration -= shift;
        }
        double clippedEnd = clipped.onset + clipped.duration;
        if (clippedEnd > tmax) {
            clipped.duration = tmax - clipped.onset;
        }
        result.append(clipped);
    }
    return result;
}
 
//=============================================================================================================
 
FiffAnnotations FiffAnnotations::readJson(const QString& path)
{
    FiffAnnotations annot;
 
    QFile file(path);
    if (!file.open(QIODevice::ReadOnly | QIODevice::Text)) {
        qWarning() << "[FiffAnnotations::readJson] Cannot open file:" << path;
        return annot;
    }
 
    QByteArray data = file.readAll();
    file.close();
 
    QJsonParseError parseError;
    QJsonDocument doc = QJsonDocument::fromJson(data, &parseError);
    if (parseError.error != QJsonParseError::NoError) {
        qWarning() << "[FiffAnnotations::readJson] JSON parse error:" << parseError.errorString();
        return annot;
    }
 
    QJsonObject root = doc.object();
    QJsonArray arr = root.value("annotations").toArray();
 
    for (int i = 0; i < arr.size(); ++i) {
        QJsonObject obj = arr[i].toObject();
        FiffAnnotation a;
        a.onset = obj.value("onset").toDouble(0.0);
        a.duration = obj.value("duration").toDouble(0.0);
        a.description = obj.value("description").toString();
 
        QJsonArray chArr = obj.value("channel_names").toArray();
        for (int j = 0; j < chArr.size(); ++j) {
            a.channelNames.append(chArr[j].toString());
        }
 
        a.comment = obj.value("comment").toString();
        a.extras = obj.value("extras").toObject().toVariantMap();
 
        annot.append(a);
    }
 
    return annot;
}
 
//=============================================================================================================
 
bool FiffAnnotations::writeJson(const QString& path, const FiffAnnotations& annot)
{
    QJsonArray arr;
    for (const FiffAnnotation& a : annot.toVector()) {
        QJsonObject obj;
        obj["onset"] = a.onset;
        obj["duration"] = a.duration;
        obj["description"] = a.description;
 
        QJsonArray chArr;
        for (const QString& ch : a.channelNames) {
            chArr.append(ch);
        }
        obj["channel_names"] = chArr;
        obj["comment"] = a.comment;
        obj["extras"] = QJsonObject::fromVariantMap(a.extras);
        arr.append(obj);
    }
 
    QJsonObject root;
    root["annotations"] = arr;
    QJsonDocument doc(root);
 
    QFile file(path);
    if (!file.open(QIODevice::WriteOnly | QIODevice::Text)) {
        qWarning() << "[FiffAnnotations::writeJson] Cannot open file for writing:" << path;
        return false;
    }
    file.write(doc.toJson(QJsonDocument::Indented));
    file.close();
    return true;
}
 
//=============================================================================================================
 
FiffAnnotations FiffAnnotations::readCsv(const QString& path)
{
    FiffAnnotations annot;
 
    QFile file(path);
    if (!file.open(QIODevice::ReadOnly | QIODevice::Text)) {
        qWarning() << "[FiffAnnotations::readCsv] Cannot open file:" << path;
        return annot;
    }
 
    QTextStream in(&file);
    // Skip header line
    if (!in.atEnd()) {
        in.readLine();
    }
 
    while (!in.atEnd()) {
        QString line = in.readLine().trimmed();
        if (line.isEmpty()) {
            continue;
        }
 
        // Parse: onset,duration,description
        // Description may contain commas, so split only the first two commas
        int firstComma = line.indexOf(',');
        if (firstComma < 0) continue;
        int secondComma = line.indexOf(',', firstComma + 1);
        if (secondComma < 0) continue;
 
        bool onsetOk = false, durationOk = false;
        double onset = line.left(firstComma).toDouble(&onsetOk);
        double duration = line.mid(firstComma + 1, secondComma - firstComma - 1).toDouble(&durationOk);
        QString description = line.mid(secondComma + 1);
 
        if (!onsetOk || !durationOk) {
            continue;
        }
 
        annot.append(onset, duration, description);
    }
 
    file.close();
    return annot;
}
 
//=============================================================================================================
 
bool FiffAnnotations::writeCsv(const QString& path, const FiffAnnotations& annot)
{
    QFile file(path);
    if (!file.open(QIODevice::WriteOnly | QIODevice::Text)) {
        qWarning() << "[FiffAnnotations::writeCsv] Cannot open file for writing:" << path;
        return false;
    }
 
    QTextStream out(&file);
    out << "onset,duration,description\n";
 
    for (const FiffAnnotation& a : annot.toVector()) {
        out << a.onset << "," << a.duration << "," << a.description << "\n";
    }
 
    file.close();
    return true;
}
 
//=============================================================================================================
 
FiffAnnotations FiffAnnotations::read(const QString& path)
{
    QString ext = QFileInfo(path).suffix().toLower();
 
    if (ext == "json") {
        return readJson(path);
    } else if (ext == "csv") {
        return readCsv(path);
    }
 
    // Unknown extension: try JSON first, then CSV
    FiffAnnotations annot = readJson(path);
    if (!annot.isEmpty()) {
        return annot;
    }
    return readCsv(path);
}
 
//=============================================================================================================
 
bool FiffAnnotations::write(const QString& path, const FiffAnnotations& annot)
{
    QString ext = QFileInfo(path).suffix().toLower();
 
    if (ext == "csv") {
        return writeCsv(path, annot);
    }
    // Default to JSON
    return writeJson(path, annot);
}