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bids_raw_data.cpp
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1//=============================================================================================================
12
13//=============================================================================================================
14// INCLUDES
15//=============================================================================================================
16
17#include "bids_raw_data.h"
18#include "bids_channel.h"
19#include "bids_dataset_description.h"
20#include "bids_const.h"
21#include "readers/bids_edf_reader.h"
22#include "readers/bids_brain_vision_reader.h"
23
24#include <fiff/fiff_constants.h>
25
26//=============================================================================================================
27// QT INCLUDES
28//=============================================================================================================
29
30#include <QDebug>
31#include <QFileInfo>
32#include <QDir>
33#include <QFile>
34#include <QJsonDocument>
35#include <QJsonObject>
36#include <cmath>
37
38//=============================================================================================================
39// USED NAMESPACES
40//=============================================================================================================
41
42using namespace BIDSLIB;
43using namespace FIFFLIB;
44using namespace Eigen;
45
46//=============================================================================================================
47// ANONYMOUS HELPERS — read side
48//=============================================================================================================
49
50namespace
51{
52
53//=========================================================================================================
55struct BidsUnit
56{
57 const char16_t* bids;
58 int unit;
59 int mul;
60};
61const BidsUnit bidsUnits[] = {
62 {u"V", FIFF_UNIT_V, FIFF_UNITM_NONE},
63 {u"\u00B5V", FIFF_UNIT_V, FIFF_UNITM_MU},
64 {u"uV", FIFF_UNIT_V, FIFF_UNITM_MU},
65 {u"mV", FIFF_UNIT_V, FIFF_UNITM_M},
66 {u"nV", FIFF_UNIT_V, FIFF_UNITM_N},
67 {u"T", FIFF_UNIT_T, FIFF_UNITM_NONE},
68 {u"fT", FIFF_UNIT_T, FIFF_UNITM_F},
69 {u"pT", FIFF_UNIT_T, FIFF_UNITM_P},
70 {u"T/m", FIFF_UNIT_T_M, FIFF_UNITM_NONE},
71 {u"rad", FIFF_UNIT_RAD, FIFF_UNITM_NONE},
72 {u"S", FIFF_UNIT_MHO, FIFF_UNITM_NONE},
73 {u"oC", FIFF_UNIT_CEL, FIFF_UNITM_NONE},
74 {u"M", FIFF_UNIT_MOL, FIFF_UNITM_NONE},
75 {u"arbitrary", FIFF_UNIT_NONE, FIFF_UNITM_NONE},
76};
77
78//=========================================================================================================
80void bidsUnitToFiff(const QString& sUnit, int& unit, int& unitMul)
81{
82 const QString u = sUnit.trimmed();
83 for (const BidsUnit& e : bidsUnits) {
84 if (u == QStringView(e.bids)) {
85 unit = e.unit;
86 unitMul = e.mul;
87 return;
88 }
89 }
90}
91
92//=========================================================================================================
93void applyChannelsTsv(FiffInfo& info, const QList<BidsChannel>& channels)
94{
95 if (channels.isEmpty())
96 return;
97
98 QMap<QString, int> bidsToFiff = bidsTypeToFiffKind();
99
100 QMap<QString, const BidsChannel*> channelMap;
101 for (const auto& ch : channels)
102 channelMap[ch.name] = &ch;
103
104 info.bads.clear();
105
106 for (int i = 0; i < info.chs.size(); ++i) {
107 FiffChInfo& fiffCh = info.chs[i];
108 auto it = channelMap.find(fiffCh.ch_name);
109 if (it == channelMap.end())
110 continue;
111 const BidsChannel* rec = it.value();
112
113 QString typeUpper = rec->type.toUpper();
114 if (bidsToFiff.contains(typeUpper))
115 fiffCh.kind = bidsToFiff[typeUpper];
116
117 bidsUnitToFiff(rec->units, fiffCh.unit, fiffCh.unit_mul);
118
119 if (rec->status.toLower() == "bad")
120 info.bads.append(fiffCh.ch_name);
121 }
122}
123
124//=========================================================================================================
125void applyElectrodePositions(FiffInfo& info,
126 const QList<BidsElectrode>& electrodes,
127 const QString& coordSystemName,
128 const QString& coordUnits)
129{
130 if (electrodes.isEmpty())
131 return;
132
133 QMap<QString, int> coordMap = bidsCoordToFiffFrame();
134 int coordFrame = FIFFV_COORD_UNKNOWN;
135 if (coordMap.contains(coordSystemName))
136 coordFrame = coordMap[coordSystemName];
137
138 float scaleFactor = 1.0f;
139 QString units = coordUnits.toLower();
140 if (units == "mm")
141 scaleFactor = 0.001f;
142 else if (units == "cm")
143 scaleFactor = 0.01f;
144
145 // Ident = 1-based ordinal among electrode channels, the order buildElectrodeRecords() reads them back in
146 QMap<QString, int> chOrdinal;
147 for (const auto& ch : info.chs) {
148 if (ch.kind == FIFFV_EEG_CH || ch.kind == FIFFV_ECOG_CH || ch.kind == FIFFV_SEEG_CH || ch.kind == FIFFV_DBS_CH)
149 chOrdinal.insert(ch.ch_name, static_cast<int>(chOrdinal.size()) + 1);
150 }
151
152 info.dig.clear();
153 int extraIdent = static_cast<int>(chOrdinal.size()) + 1;
154 for (const auto& elec : electrodes) {
155 if (elec.x == "n/a" || elec.y == "n/a" || elec.z == "n/a")
156 continue;
157
158 FiffDigPoint dp;
159 dp.kind = chOrdinal.contains(elec.name) ? FIFFV_POINT_EEG : FIFFV_POINT_EXTRA;
160 dp.ident = chOrdinal.contains(elec.name) ? chOrdinal.value(elec.name) : extraIdent++;
161 dp.r[0] = elec.x.toFloat() * scaleFactor;
162 dp.r[1] = elec.y.toFloat() * scaleFactor;
163 dp.r[2] = elec.z.toFloat() * scaleFactor;
164 dp.coord_frame = coordFrame;
165
166 info.dig.append(dp);
167 }
168}
169
170//=========================================================================================================
171QJsonObject readJsonFile(const QString& sFilePath)
172{
173 QFile file(sFilePath);
174 if (!file.open(QIODevice::ReadOnly | QIODevice::Text))
175 return {};
176 QJsonParseError error;
177 QJsonDocument doc = QJsonDocument::fromJson(file.readAll(), &error);
178 file.close();
179 if (error.error != QJsonParseError::NoError)
180 return {};
181 return doc.object();
182}
183
184//=========================================================================================================
185bool writeJsonFile(const QString& sFilePath, const QJsonObject& json)
186{
187 QFile file(sFilePath);
188 if (!file.open(QIODevice::WriteOnly | QIODevice::Text))
189 return false;
190 file.write(QJsonDocument(json).toJson(QJsonDocument::Indented));
191 file.close();
192 return true;
193}
194
195//=========================================================================================================
196void readSidecarJson(const QString& sFilePath,
197 FiffInfo& info,
198 BidsRawData& data)
199{
200 QJsonObject json = readJsonFile(sFilePath);
201 if (json.isEmpty())
202 return;
203
204 // Apply to FiffInfo
205 double plf = json.value(QStringLiteral("PowerLineFrequency")).toDouble();
206 if (plf > 0.0)
207 info.linefreq = static_cast<float>(plf);
208
209 double sf = json.value(QStringLiteral("SamplingFrequency")).toDouble();
210 if (sf > 0.0 && std::abs(info.sfreq - static_cast<float>(sf)) > 0.5f)
211 qWarning() << "[BidsRawData::read] Sampling frequency mismatch: raw ="
212 << info.sfreq << "sidecar =" << sf;
213
214 // Store independent metadata fields on BidsRawData
215 data.ieegReference = json.value(QStringLiteral("iEEGReference")).toString();
216 data.taskDescription = json.value(QStringLiteral("TaskDescription")).toString();
217 data.manufacturer = json.value(QStringLiteral("Manufacturer")).toString();
218 data.manufacturerModelName = json.value(QStringLiteral("ManufacturerModelName")).toString();
219 data.softwareVersions = json.value(QStringLiteral("SoftwareVersions")).toString();
220 data.recordingType = json.value(QStringLiteral("RecordingType")).toString();
221}
222
223//=============================================================================================================
224// ANONYMOUS HELPERS — write side
225//=============================================================================================================
226
227//=========================================================================================================
228QString fiffUnitToBidsString(int unit, int unitMul)
229{
230 for (const BidsUnit& e : bidsUnits) {
231 if (e.unit == unit && e.mul == unitMul && e.unit != FIFF_UNIT_NONE)
232 return QString::fromUtf16(e.bids);
233 }
234 // A multiplier BIDS has no name for: the SI unit
235 for (const BidsUnit& e : bidsUnits) {
236 if (e.unit == unit && e.mul == FIFF_UNITM_NONE && e.unit != FIFF_UNIT_NONE)
237 return QString::fromUtf16(e.bids);
238 }
239 return QStringLiteral("n/a");
240}
241
242//=========================================================================================================
243QString channelTypeDescription(int kind)
244{
245 switch (kind) {
246 case FIFFV_EEG_CH:
247 return QStringLiteral("ElectroEncephaloGram");
248 case FIFFV_ECOG_CH:
249 return QStringLiteral("Electrocorticography");
250 case FIFFV_SEEG_CH:
251 return QStringLiteral("StereoElectroEncephaloGram");
252 case FIFFV_DBS_CH:
253 return QStringLiteral("DeepBrainStimulation");
254 case FIFFV_MEG_CH:
255 return QStringLiteral("MagnetoEncephaloGram");
256 case FIFFV_STIM_CH:
257 return QStringLiteral("Trigger");
258 case FIFFV_EOG_CH:
259 return QStringLiteral("ElectroOculoGram");
260 case FIFFV_ECG_CH:
261 return QStringLiteral("ElectroCardioGram");
262 case FIFFV_EMG_CH:
263 return QStringLiteral("ElectroMyoGram");
264 case FIFFV_MISC_CH:
265 return QStringLiteral("Miscellaneous");
266 case FIFFV_RESP_CH:
267 return QStringLiteral("Respiration");
268 default:
269 return QStringLiteral("n/a");
270 }
271}
272
273//=========================================================================================================
274QList<BidsChannel> buildChannelRecords(const FiffInfo& info)
275{
276 QList<BidsChannel> records;
277 QMap<int, QString> kindMap = fiffKindToBidsType();
278 QSet<QString> badsSet(info.bads.begin(), info.bads.end());
279
280 for (int i = 0; i < info.chs.size(); ++i) {
281 const FiffChInfo& ch = info.chs[i];
282
283 BidsChannel rec;
284 rec.name = ch.ch_name;
285 rec.type = kindMap.contains(ch.kind) ? kindMap[ch.kind] : QStringLiteral("MISC");
286 rec.units = fiffUnitToBidsString(ch.unit, ch.unit_mul);
287 rec.samplingFreq = QString::number(static_cast<double>(info.sfreq), 'g', 10);
288 rec.lowCutoff = (info.highpass > 0.0f)
289 ? QString::number(static_cast<double>(info.highpass), 'g', 10)
290 : QStringLiteral("n/a");
291 rec.highCutoff = (info.lowpass > 0.0f)
292 ? QString::number(static_cast<double>(info.lowpass), 'g', 10)
293 : QStringLiteral("n/a");
294 rec.notch = QStringLiteral("n/a");
295 rec.status = badsSet.contains(ch.ch_name) ? QStringLiteral("bad") : QStringLiteral("good");
296 rec.description = channelTypeDescription(ch.kind);
297
298 records.append(rec);
299 }
300 return records;
301}
302
303//=========================================================================================================
304QList<BidsElectrode> buildElectrodeRecords(const FiffInfo& info)
305{
306 QList<BidsElectrode> records;
307
308 QMap<int, const FiffDigPoint*> digByIdent;
309 for (const auto& dp : info.dig) {
310 if (dp.kind == FIFFV_POINT_EEG || dp.kind == FIFFV_POINT_EXTRA)
311 digByIdent[dp.ident] = &dp;
312 }
313
314 int digIdx = 0;
315
316 for (int i = 0; i < info.chs.size(); ++i) {
317 const FiffChInfo& ch = info.chs[i];
318
319 if (ch.kind == FIFFV_STIM_CH)
320 continue;
321 if (ch.kind != FIFFV_EEG_CH && ch.kind != FIFFV_ECOG_CH &&
322 ch.kind != FIFFV_SEEG_CH && ch.kind != FIFFV_DBS_CH)
323 continue;
324
325 BidsElectrode rec;
326 rec.name = ch.ch_name;
327
328 ++digIdx;
329 bool hasPosition = false;
330
331 if (digByIdent.contains(digIdx)) {
332 const FiffDigPoint* dp = digByIdent[digIdx];
333 if (std::isfinite(dp->r[0]) && std::isfinite(dp->r[1]) && std::isfinite(dp->r[2])) {
334 rec.x = QString::number(static_cast<double>(dp->r[0]), 'g', 8);
335 rec.y = QString::number(static_cast<double>(dp->r[1]), 'g', 8);
336 rec.z = QString::number(static_cast<double>(dp->r[2]), 'g', 8);
337 hasPosition = true;
338 }
339 }
340
341 if (!hasPosition) {
342 const Eigen::Vector3f& r0 = ch.chpos.r0;
343 if (r0.squaredNorm() > 0.0f && std::isfinite(r0[0])) {
344 rec.x = QString::number(static_cast<double>(r0[0]), 'g', 8);
345 rec.y = QString::number(static_cast<double>(r0[1]), 'g', 8);
346 rec.z = QString::number(static_cast<double>(r0[2]), 'g', 8);
347 } else {
348 rec.x = QStringLiteral("n/a");
349 rec.y = QStringLiteral("n/a");
350 rec.z = QStringLiteral("n/a");
351 }
352 }
353
354 rec.size = QStringLiteral("n/a");
355 rec.type = QStringLiteral("n/a");
356 rec.material = QStringLiteral("n/a");
357 rec.impedance = QStringLiteral("n/a");
358
359 records.append(rec);
360 }
361 return records;
362}
363
364//=========================================================================================================
365QJsonObject buildIeegSidecarJson(const BidsRawData& data,
366 const BIDSPath& bidsPath)
367{
368 QJsonObject json;
369 const FiffInfo& info = data.raw.info;
370
371 // Required
372 json[QStringLiteral("TaskName")] = bidsPath.task();
373 json[QStringLiteral("SamplingFrequency")] = static_cast<double>(info.sfreq);
374 json[QStringLiteral("PowerLineFrequency")] = static_cast<double>(info.linefreq);
375
376 // Reference
377 if (!data.ieegReference.isEmpty())
378 json[QStringLiteral("iEEGReference")] = data.ieegReference;
379 else
380 json[QStringLiteral("iEEGReference")] = QStringLiteral("n/a");
381
382 // Channel counts — computed from FiffInfo
383 int ecog = 0, seeg = 0, dbs = 0, eeg = 0, eog = 0, ecg = 0, emg = 0, misc = 0, trig = 0;
384 for (const auto& ch : info.chs) {
385 switch (ch.kind) {
386 case FIFFV_ECOG_CH:
387 ++ecog;
388 break;
389 case FIFFV_SEEG_CH:
390 ++seeg;
391 break;
392 case FIFFV_DBS_CH:
393 ++dbs;
394 break;
395 case FIFFV_EEG_CH:
396 ++eeg;
397 break;
398 case FIFFV_EOG_CH:
399 ++eog;
400 break;
401 case FIFFV_ECG_CH:
402 ++ecg;
403 break;
404 case FIFFV_EMG_CH:
405 ++emg;
406 break;
407 case FIFFV_MISC_CH:
408 ++misc;
409 break;
410 case FIFFV_STIM_CH:
411 ++trig;
412 break;
413 default:
414 break;
415 }
416 }
417 json[QStringLiteral("ECOGChannelCount")] = ecog;
418 json[QStringLiteral("SEEGChannelCount")] = seeg;
419 if (dbs > 0)
420 json[QStringLiteral("DBSChannelCount")] = dbs;
421 if (eeg > 0)
422 json[QStringLiteral("EEGChannelCount")] = eeg;
423 if (eog > 0)
424 json[QStringLiteral("EOGChannelCount")] = eog;
425 if (ecg > 0)
426 json[QStringLiteral("ECGChannelCount")] = ecg;
427 if (emg > 0)
428 json[QStringLiteral("EMGChannelCount")] = emg;
429 if (misc > 0)
430 json[QStringLiteral("MiscChannelCount")] = misc;
431 if (trig > 0)
432 json[QStringLiteral("TriggerChannelCount")] = trig;
433
434 // Recording metadata
435 if (!data.recordingType.isEmpty())
436 json[QStringLiteral("RecordingType")] = data.recordingType;
437 else
438 json[QStringLiteral("RecordingType")] = QStringLiteral("continuous");
439
440 // mne-bids writes raw.times[-1]
441 if (info.sfreq > 0.0f && data.raw.last_samp >= data.raw.first_samp) {
442 double dur = static_cast<double>(data.raw.last_samp - data.raw.first_samp) / static_cast<double>(info.sfreq);
443 json[QStringLiteral("RecordingDuration")] = dur;
444 }
445
446 // Optional strings from BidsRawData
447 if (!data.taskDescription.isEmpty())
448 json[QStringLiteral("TaskDescription")] = data.taskDescription;
449 if (!data.manufacturer.isEmpty())
450 json[QStringLiteral("Manufacturer")] = data.manufacturer;
451 if (!data.manufacturerModelName.isEmpty())
452 json[QStringLiteral("ManufacturerModelName")] = data.manufacturerModelName;
453 if (!data.softwareVersions.isEmpty())
454 json[QStringLiteral("SoftwareVersions")] = data.softwareVersions;
455
456 return json;
457}
458
459//=========================================================================================================
460bool copyFile(const QString& src, const QString& dst, bool overwrite)
461{
462 if (!QFileInfo::exists(src)) {
463 qWarning() << "[BidsRawData::write] Source file does not exist:" << src;
464 return false;
465 }
466 if (QFileInfo::exists(dst)) {
467 if (!overwrite) {
468 qWarning() << "[BidsRawData::write] Target file already exists:" << dst;
469 return false;
470 }
471 QFile::remove(dst);
472 }
473 return QFile::copy(src, dst);
474}
475
476//=========================================================================================================
477bool copyBrainVisionFiles(const QString& srcVhdr, const BIDSPath& bidsPath, bool overwrite)
478{
479 QFileInfo srcInfo(srcVhdr);
480 QString srcDir = srcInfo.absolutePath();
481
482 QFile vhdrFile(srcVhdr);
483 if (!vhdrFile.open(QIODevice::ReadOnly | QIODevice::Text)) {
484 qWarning() << "[BidsRawData::write] Cannot open .vhdr file:" << srcVhdr;
485 return false;
486 }
487
488 QString dataFileName;
489 QString markerFileName;
490 QByteArray vhdrContent = vhdrFile.readAll();
491 vhdrFile.close();
492
493 for (const auto& line : vhdrContent.split('\n')) {
494 QString sLine = QString::fromUtf8(line).trimmed();
495 if (sLine.startsWith("DataFile=", Qt::CaseInsensitive))
496 dataFileName = sLine.mid(9).trimmed();
497 else if (sLine.startsWith("MarkerFile=", Qt::CaseInsensitive))
498 markerFileName = sLine.mid(11).trimmed();
499 }
500
501 QString dstDir = bidsPath.directory();
502 QString dstBase = bidsPath.basename();
503 dstBase = dstBase.left(dstBase.lastIndexOf('.'));
504
505 QString dstVhdr = bidsPath.filePath();
506 QString newDataFile = dstBase + QStringLiteral(".eeg");
507 QString newMarkerFile = dstBase + QStringLiteral(".vmrk");
508
509 QString vhdrStr = QString::fromUtf8(vhdrContent);
510 if (!dataFileName.isEmpty())
511 vhdrStr.replace("DataFile=" + dataFileName,
512 "DataFile=" + QFileInfo(newDataFile).fileName());
513 if (!markerFileName.isEmpty())
514 vhdrStr.replace("MarkerFile=" + markerFileName,
515 "MarkerFile=" + QFileInfo(newMarkerFile).fileName());
516
517 if (QFileInfo::exists(dstVhdr) && !overwrite) {
518 qWarning() << "[BidsRawData::write] Target file already exists:" << dstVhdr;
519 return false;
520 }
521 if (QFileInfo::exists(dstVhdr))
522 QFile::remove(dstVhdr);
523
524 QFile dstVhdrFile(dstVhdr);
525 if (!dstVhdrFile.open(QIODevice::WriteOnly | QIODevice::Text)) {
526 qWarning() << "[BidsRawData::write] Cannot write .vhdr file:" << dstVhdr;
527 return false;
528 }
529 dstVhdrFile.write(vhdrStr.toUtf8());
530 dstVhdrFile.close();
531
532 if (!dataFileName.isEmpty()) {
533 QString srcData = QDir(srcDir).absoluteFilePath(dataFileName);
534 QString dstData = dstDir + QFileInfo(newDataFile).fileName();
535 if (!copyFile(srcData, dstData, overwrite)) {
536 qWarning() << "[BidsRawData::write] Failed to copy data file:" << srcData;
537 return false;
538 }
539 }
540
541 if (!markerFileName.isEmpty()) {
542 QString srcMarker = QDir(srcDir).absoluteFilePath(markerFileName);
543 QString dstMarker = dstDir + QFileInfo(newMarkerFile).fileName();
544
545 if (QFileInfo::exists(srcMarker)) {
546 QFile markerFile(srcMarker);
547 if (markerFile.open(QIODevice::ReadOnly | QIODevice::Text)) {
548 QString markerContent = QString::fromUtf8(markerFile.readAll());
549 markerFile.close();
550
551 markerContent.replace("DataFile=" + dataFileName,
552 "DataFile=" + QFileInfo(newDataFile).fileName());
553
554 if (QFileInfo::exists(dstMarker)) {
555 if (!overwrite) {
556 qWarning() << "[BidsRawData::write] Target marker file already exists:" << dstMarker;
557 return false;
558 }
559 QFile::remove(dstMarker);
560 }
561
562 QFile dstMarkerFile(dstMarker);
563 if (dstMarkerFile.open(QIODevice::WriteOnly | QIODevice::Text)) {
564 dstMarkerFile.write(markerContent.toUtf8());
565 dstMarkerFile.close();
566 }
567 }
568 }
569 }
570
571 return true;
572}
573
574//=========================================================================================================
575bool copyRawDataFile(const QString& sourcePath, const BIDSPath& bidsPath, bool overwrite)
576{
577 if (sourcePath.isEmpty())
578 return true;
579
580 QString ext = bidsPath.extension().toLower();
581 if (ext == ".vhdr" || ext == ".ahdr")
582 return copyBrainVisionFiles(sourcePath, bidsPath, overwrite);
583
584 return copyFile(sourcePath, bidsPath.filePath(), overwrite);
585}
586
587} // anonymous namespace
588
589//=============================================================================================================
590// MEMBER METHODS
591//=============================================================================================================
592
593BidsRawData::BidsRawData(BidsRawData&& other) noexcept
594: raw(other.raw) // FiffRawData has only copy ctor
595, events(std::move(other.events))
596, eventIdMap(std::move(other.eventIdMap))
597, electrodes(std::move(other.electrodes))
598, coordinateSystem(std::move(other.coordinateSystem))
599, reader(std::move(other.reader))
600, ieegReference(std::move(other.ieegReference))
601, taskDescription(std::move(other.taskDescription))
602, manufacturer(std::move(other.manufacturer))
603, manufacturerModelName(std::move(other.manufacturerModelName))
604, softwareVersions(std::move(other.softwareVersions))
605, recordingType(std::move(other.recordingType))
606, m_bIsValid(other.m_bIsValid)
607{
608 other.m_bIsValid = false;
609}
610
611//=============================================================================================================
612
613BidsRawData& BidsRawData::operator=(BidsRawData&& other) noexcept
614{
615 if (this != &other) {
616 raw = other.raw; // FiffRawData has only copy ctor
617 events = std::move(other.events);
618 eventIdMap = std::move(other.eventIdMap);
619 electrodes = std::move(other.electrodes);
620 coordinateSystem = std::move(other.coordinateSystem);
621 reader = std::move(other.reader);
622 ieegReference = std::move(other.ieegReference);
623 taskDescription = std::move(other.taskDescription);
624 manufacturer = std::move(other.manufacturer);
625 manufacturerModelName = std::move(other.manufacturerModelName);
626 softwareVersions = std::move(other.softwareVersions);
627 recordingType = std::move(other.recordingType);
628 m_bIsValid = other.m_bIsValid;
629 other.m_bIsValid = false;
630 }
631 return *this;
632}
633
634//=============================================================================================================
635
636void BidsRawData::clear()
637{
638 raw = FiffRawData();
639 events.clear();
640 eventIdMap.clear();
641 electrodes.clear();
642 reader.reset();
643
644 ieegReference.clear();
645 taskDescription.clear();
646 manufacturer.clear();
647 manufacturerModelName.clear();
648 softwareVersions.clear();
649 recordingType.clear();
650
651 coordinateSystem = BidsCoordinateSystem();
652
653 m_bIsValid = false;
654}
655
656//=============================================================================================================
657
658AbstractFormatReader::UPtr BidsRawData::createReader(const QString& sExtension)
659{
660 QString ext = sExtension.toLower();
661 if (ext == ".vhdr" || ext == ".ahdr")
662 return std::make_unique<BrainVisionReader>();
663 if (ext == ".edf" || ext == ".bdf")
664 return std::make_unique<EDFReader>();
665 return nullptr;
666}
667
668//=============================================================================================================
669// BidsRawData::read()
670//=============================================================================================================
671
672BidsRawData BidsRawData::read(const BIDSPath& bidsPath)
673{
674 BidsRawData result;
675
676 //=========================================================================================================
677 // Step 1 — Validate BIDSPath
678 //=========================================================================================================
679 if (bidsPath.root().isEmpty()) {
680 qWarning() << "[BidsRawData::read] BIDSPath root is not set";
681 return result;
682 }
683 if (bidsPath.subject().isEmpty()) {
684 qWarning() << "[BidsRawData::read] BIDSPath subject is not set";
685 return result;
686 }
687 if (bidsPath.extension().isEmpty()) {
688 qWarning() << "[BidsRawData::read] BIDSPath extension is not set";
689 return result;
690 }
691
692 //=========================================================================================================
693 // Step 2 — Resolve raw file path
694 //=========================================================================================================
695 QString rawFilePath = bidsPath.filePath();
696
697 if (!QFileInfo::exists(rawFilePath)) {
698 QString ext = bidsPath.extension();
699 if (ext.toLower() == ".edf") {
700 BIDSPath altPath(bidsPath);
701 altPath.setExtension(".EDF");
702 if (QFileInfo::exists(altPath.filePath()))
703 rawFilePath = altPath.filePath();
704 }
705 }
706
707 if (!QFileInfo::exists(rawFilePath)) {
708 qWarning() << "[BidsRawData::read] Raw data file not found:" << rawFilePath;
709 return result;
710 }
711
712 //=========================================================================================================
713 // Step 3 — Create and open the format reader
714 //=========================================================================================================
715 result.reader = createReader(bidsPath.extension());
716 if (!result.reader) {
717 qWarning() << "[BidsRawData::read] Unsupported file extension:" << bidsPath.extension();
718 return result;
719 }
720
721 if (!result.reader->open(rawFilePath)) {
722 qWarning() << "[BidsRawData::read] Failed to open raw file:" << rawFilePath;
723 return result;
724 }
725
726 //=========================================================================================================
727 // Step 4 — Build FiffRawData from the reader
728 //=========================================================================================================
729 result.raw = result.reader->toFiffRawData();
730
731 //=========================================================================================================
732 // Step 5 — Read and apply *_channels.tsv
733 //=========================================================================================================
734 BIDSPath channelsPath = bidsPath.channelsTsvPath();
735 if (QFileInfo::exists(channelsPath.filePath())) {
736 QList<BidsChannel> channels = BidsChannel::readTsv(channelsPath.filePath());
737 applyChannelsTsv(result.raw.info, channels);
738 }
739
740 //=========================================================================================================
741 // Step 6 — Read *_coordsystem.json (before electrodes, for scale/frame info)
742 //=========================================================================================================
743 BIDSPath coordsysPath = bidsPath.coordsystemJsonPath();
744 if (QFileInfo::exists(coordsysPath.filePath()))
745 result.coordinateSystem = BidsCoordinateSystem::readJson(coordsysPath.filePath());
746
747 //=========================================================================================================
748 // Step 7 — Read and apply *_electrodes.tsv
749 //=========================================================================================================
750 BIDSPath electrodesPath = bidsPath.electrodesTsvPath();
751 if (QFileInfo::exists(electrodesPath.filePath())) {
752 result.electrodes = BidsElectrode::readTsv(electrodesPath.filePath());
753 applyElectrodePositions(result.raw.info, result.electrodes,
754 result.coordinateSystem.system, result.coordinateSystem.units);
755 }
756
757 //=========================================================================================================
758 // Step 8 — Read *_events.tsv
759 //=========================================================================================================
760 BIDSPath eventsPath = bidsPath.eventsTsvPath();
761 if (QFileInfo::exists(eventsPath.filePath())) {
762 result.events = BidsEvent::readTsv(eventsPath.filePath());
763
764 // Compute sample from onset*sfreq if sample column was absent
765 float sfreq = result.raw.info.sfreq;
766 for (auto& ev : result.events) {
767 if (ev.sample == 0 && ev.onset > 0.0f && sfreq > 0)
768 ev.sample = static_cast<int>(ev.onset * sfreq);
769 }
770
771 // Build eventIdMap from trial_type → value
772 for (const auto& ev : result.events) {
773 if (!ev.trialType.isEmpty() && ev.trialType != "n/a")
774 result.eventIdMap.insert(ev.trialType, ev.value);
775 }
776 }
777
778 //=========================================================================================================
779 // Step 9 — Read sidecar *_{datatype}.json
780 //=========================================================================================================
781 BIDSPath sidecarPath = bidsPath.sidecarJsonPath();
782 if (QFileInfo::exists(sidecarPath.filePath()))
783 readSidecarJson(sidecarPath.filePath(), result.raw.info, result);
784
785 //=========================================================================================================
786 // Done
787 //=========================================================================================================
788 result.m_bIsValid = true;
789 return result;
790}
791
792//=============================================================================================================
793// BidsRawData::write()
794//=============================================================================================================
795
796BIDSPath BidsRawData::write(const BIDSPath& bidsPath,
797 const QString& sourcePath,
798 const WriteOptions& options) const
799{
800 BIDSPath result;
801
802 //=========================================================================================================
803 // Step 1 — Validate
804 //=========================================================================================================
805 if (bidsPath.root().isEmpty()) {
806 qWarning() << "[BidsRawData::write] BIDSPath root is not set";
807 return result;
808 }
809 if (bidsPath.subject().isEmpty()) {
810 qWarning() << "[BidsRawData::write] BIDSPath subject is not set";
811 return result;
812 }
813 if (bidsPath.task().isEmpty()) {
814 qWarning() << "[BidsRawData::write] BIDSPath task is not set";
815 return result;
816 }
817 if (bidsPath.datatype().isEmpty()) {
818 qWarning() << "[BidsRawData::write] BIDSPath datatype is not set";
819 return result;
820 }
821 if (raw.info.isEmpty()) {
822 qWarning() << "[BidsRawData::write] FiffRawData info is empty";
823 return result;
824 }
825
826 //=========================================================================================================
827 // Step 2 — Create directory structure
828 //=========================================================================================================
829 if (!bidsPath.mkdirs()) {
830 qWarning() << "[BidsRawData::write] Failed to create directory:" << bidsPath.directory();
831 return result;
832 }
833
834 //=========================================================================================================
835 // Step 3 — Copy raw data file
836 //=========================================================================================================
837 if (options.copyData && !sourcePath.isEmpty()) {
838 if (!copyRawDataFile(sourcePath, bidsPath, options.overwrite)) {
839 qWarning() << "[BidsRawData::write] Failed to copy raw data file";
840 return result;
841 }
842 }
843
844 //=========================================================================================================
845 // Step 4 — Write *_channels.tsv
846 //=========================================================================================================
847 {
848 BIDSPath channelsPath = bidsPath.channelsTsvPath();
849 if (!options.overwrite && QFileInfo::exists(channelsPath.filePath())) {
850 qWarning() << "[BidsRawData::write] channels.tsv already exists:" << channelsPath.filePath();
851 return result;
852 }
853
854 QList<BidsChannel> channelRecords = buildChannelRecords(raw.info);
855 if (!BidsChannel::writeTsv(channelsPath.filePath(), channelRecords)) {
856 qWarning() << "[BidsRawData::write] Failed to write channels.tsv";
857 return result;
858 }
859 }
860
861 //=========================================================================================================
862 // Step 5 — Write *_electrodes.tsv + *_coordsystem.json
863 //=========================================================================================================
864 {
865 QList<BidsElectrode> electrodeRecords = buildElectrodeRecords(raw.info);
866
867 if (!electrodeRecords.isEmpty()) {
868 BIDSPath electrodesPath = bidsPath.electrodesTsvPath();
869 if (options.overwrite || !QFileInfo::exists(electrodesPath.filePath())) {
870 if (!BidsElectrode::writeTsv(electrodesPath.filePath(), electrodeRecords))
871 qWarning() << "[BidsRawData::write] Failed to write electrodes.tsv";
872 }
873
874 BIDSPath coordsysPath = bidsPath.coordsystemJsonPath();
875 if (options.overwrite || !QFileInfo::exists(coordsysPath.filePath())) {
876 // Build coordinate system, deriving defaults from FiffInfo if needed
877 BidsCoordinateSystem cs = coordinateSystem;
878 if (cs.system.isEmpty()) {
879 if (raw.info.dig.isEmpty()) {
880 cs.system = QStringLiteral("Other");
881 cs.units = QStringLiteral("n/a");
882 } else {
883 int coordFrame = raw.info.dig.first().coord_frame;
884 QMap<int, QString> frameMap = fiffFrameToBidsCoord();
885 cs.system = frameMap.contains(coordFrame)
886 ? frameMap[coordFrame]
887 : QStringLiteral("Other");
888 cs.units = QStringLiteral("m");
889 }
890 }
891 if (cs.description.isEmpty() && !raw.info.dig.isEmpty())
892 cs.description = QStringLiteral("Coordinate system derived from recording data");
893
894 if (!BidsCoordinateSystem::writeJson(coordsysPath.filePath(), cs))
895 qWarning() << "[BidsRawData::write] Failed to write coordsystem.json";
896 }
897 }
898 }
899
900 //=========================================================================================================
901 // Step 6 — Write *_events.tsv
902 //=========================================================================================================
903 if (!events.isEmpty()) {
904 BIDSPath eventsPath = bidsPath.eventsTsvPath();
905 if (!options.overwrite && QFileInfo::exists(eventsPath.filePath())) {
906 qWarning() << "[BidsRawData::write] events.tsv already exists:" << eventsPath.filePath();
907 return result;
908 }
909
910 QList<BidsEvent> eventsToWrite = events;
911
912 // Apply trial_type fallback from eventIdMap
913 QMap<int, QString> valueToType;
914 for (auto it = eventIdMap.constBegin(); it != eventIdMap.constEnd(); ++it)
915 valueToType[it.value()] = it.key();
916 for (auto& ev : eventsToWrite) {
917 if (ev.trialType.isEmpty() || ev.trialType == "n/a")
918 ev.trialType = valueToType.value(ev.value, QStringLiteral("n/a"));
919 }
920
921 if (!BidsEvent::writeTsv(eventsPath.filePath(), eventsToWrite))
922 qWarning() << "[BidsRawData::write] Failed to write events.tsv";
923 }
924
925 //=========================================================================================================
926 // Step 7 — Write *_{datatype}.json sidecar
927 //=========================================================================================================
928 {
929 BIDSPath sidecarPath = bidsPath.sidecarJsonPath();
930 if (!options.overwrite && QFileInfo::exists(sidecarPath.filePath())) {
931 qWarning() << "[BidsRawData::write] Sidecar JSON already exists:" << sidecarPath.filePath();
932 return result;
933 }
934
935 QJsonObject sidecarJson = buildIeegSidecarJson(*this, bidsPath);
936 if (!writeJsonFile(sidecarPath.filePath(), sidecarJson)) {
937 qWarning() << "[BidsRawData::write] Failed to write sidecar JSON";
938 return result;
939 }
940 }
941
942 //=========================================================================================================
943 // Step 8 — Write dataset_description.json (never overwrite)
944 //=========================================================================================================
945 {
946 QString descPath = bidsPath.root() + QDir::separator() + QStringLiteral("dataset_description.json");
947
948 if (!QFileInfo::exists(descPath)) {
949 BidsDatasetDescription desc;
950 desc.name = options.datasetName.isEmpty()
951 ? QStringLiteral("[Unspecified]")
952 : options.datasetName;
953 desc.bidsVersion = QStringLiteral("1.9.0");
954 desc.datasetType = QStringLiteral("raw");
955
956 if (!BidsDatasetDescription::write(descPath, desc))
957 qWarning() << "[BidsRawData::write] Failed to write dataset_description.json";
958 }
959 }
960
961 //=========================================================================================================
962 // Done
963 //=========================================================================================================
964 result = bidsPath;
965 return result;
966}
bids_raw_data.h
Central container for a BIDS raw recording — the BIDS-side analogue of FIFFLIB::FiffRawData,...
bids_channel.h
Reader/writer for the BIDS _channels.tsv sidecar — one record per recorded channel.
bids_const.h
Centralised BIDS vocabulary: datatype / suffix / extension whitelists, FIFF↔BIDS channel-type and coo...
bids_dataset_description.h
Reader/writer for dataset_description.json — the REQUIRED root sidecar of every BIDS dataset.
bids_edf_reader.h
BIDSLIB::AbstractFormatReader implementation for European Data Format (EDF / EDF+) and BioSemi BDF fi...
bids_brain_vision_reader.h
BIDSLIB::AbstractFormatReader implementation for the BrainVision .vhdr / .vmrk / ....
fiff_constants.h
Symbolic FIFF tag, block, value, unit and channel-type constants shared across FIFFLIB.
FIFF_UNIT_T_M
constexpr auto FIFF_UNIT_T_M
Definition fiff_constants.h:130
FIFFV_POINT_EXTRA
constexpr auto FIFFV_POINT_EXTRA
Definition fiff_constants.h:320
FIFFV_ECG_CH
constexpr auto FIFFV_ECG_CH
Definition fiff_constants.h:270
FIFFV_EEG_CH
#define FIFFV_EEG_CH
Definition fiff_constants.h:265
FIFF_UNIT_CEL
constexpr auto FIFF_UNIT_CEL
Definition fiff_constants.h:123
FIFFV_DBS_CH
constexpr auto FIFFV_DBS_CH
Definition fiff_constants.h:287
FIFF_UNITM_F
constexpr auto FIFF_UNITM_F
Definition fiff_constants.h:152
FIFFV_MISC_CH
constexpr auto FIFFV_MISC_CH
Definition fiff_constants.h:271
FIFF_UNITM_NONE
constexpr auto FIFF_UNITM_NONE
Definition fiff_constants.h:145
FIFFV_SEEG_CH
constexpr auto FIFFV_SEEG_CH
Definition fiff_constants.h:286
FIFFV_POINT_EEG
constexpr auto FIFFV_POINT_EEG
Definition fiff_constants.h:318
FIFFV_MEG_CH
#define FIFFV_MEG_CH
Definition fiff_constants.h:262
FIFFV_ECOG_CH
constexpr auto FIFFV_ECOG_CH
Definition fiff_constants.h:285
FIFFV_STIM_CH
constexpr auto FIFFV_STIM_CH
Definition fiff_constants.h:266
FIFF_UNIT_RAD
constexpr auto FIFF_UNIT_RAD
Definition fiff_constants.h:99
FIFF_UNIT_T
constexpr auto FIFF_UNIT_T
Definition fiff_constants.h:121
FIFFV_COORD_UNKNOWN
constexpr auto FIFFV_COORD_UNKNOWN
Definition fiff_constants.h:209
FIFF_UNIT_MHO
constexpr auto FIFF_UNIT_MHO
Definition fiff_constants.h:119
FIFF_UNITM_MU
constexpr auto FIFF_UNITM_MU
Definition fiff_constants.h:149
FIFFV_EMG_CH
constexpr auto FIFFV_EMG_CH
Definition fiff_constants.h:269
FIFF_UNIT_MOL
constexpr auto FIFF_UNIT_MOL
Definition fiff_constants.h:94
FIFF_UNIT_V
constexpr auto FIFF_UNIT_V
Definition fiff_constants.h:116
FIFF_UNITM_P
constexpr auto FIFF_UNITM_P
Definition fiff_constants.h:151
FIFF_UNITM_M
constexpr auto FIFF_UNITM_M
Definition fiff_constants.h:148
FIFF_UNIT_NONE
constexpr auto FIFF_UNIT_NONE
Definition fiff_constants.h:84
FIFFV_EOG_CH
constexpr auto FIFFV_EOG_CH
Definition fiff_constants.h:268
FIFFV_RESP_CH
constexpr auto FIFFV_RESP_CH
Definition fiff_constants.h:272
FIFF_UNITM_N
constexpr auto FIFF_UNITM_N
Definition fiff_constants.h:150
BIDSLIB
BIDS dataset reading, writing, path construction, and sidecar metadata handling for iEEG/EEG/MEG.
Definition bids_channel.h:48
BIDSLIB::fiffKindToBidsType
QMap< int, QString > fiffKindToBidsType()
Definition bids_const.h:126
BIDSLIB::bidsCoordToFiffFrame
QMap< QString, int > bidsCoordToFiffFrame()
Definition bids_const.h:179
BIDSLIB::bidsTypeToFiffKind
QMap< QString, int > bidsTypeToFiffKind()
Definition bids_const.h:150
BIDSLIB::fiffFrameToBidsCoord
QMap< int, QString > fiffFrameToBidsCoord()
Definition bids_const.h:198
FIFFLIB
FIFF file I/O, in-memory data structures and high-level readers/writers.
Definition connectivitysettings.h:69
BIDSLIB::BidsChannel
Channel metadata record corresponding to one row in *_channels.tsv.
Definition bids_channel.h:57
BIDSLIB::BidsChannel::readTsv
static QList< BidsChannel > readTsv(const QString &sFilePath)
Read a BIDS *_channels.tsv file.
Definition bids_channel.cpp:44
BIDSLIB::BidsChannel::writeTsv
static bool writeTsv(const QString &sFilePath, const QList< BidsChannel > &channels)
Write a BIDS *_channels.tsv file.
Definition bids_channel.cpp:71
BIDSLIB::BidsCoordinateSystem
Coordinate system metadata from *_coordsystem.json.
Definition bids_coordinate_system.h:71
BIDSLIB::BidsCoordinateSystem::writeJson
static bool writeJson(const QString &sFilePath, const BidsCoordinateSystem &cs)
Write a BIDS *_coordsystem.json file.
Definition bids_coordinate_system.cpp:106
BIDSLIB::BidsCoordinateSystem::readJson
static BidsCoordinateSystem readJson(const QString &sFilePath)
Read a BIDS *_coordsystem.json file.
Definition bids_coordinate_system.cpp:39
BIDSLIB::BidsDatasetDescription
Dataset-level metadata from dataset_description.json.
Definition bids_dataset_description.h:61
BIDSLIB::BidsDatasetDescription::write
static bool write(const QString &sFilePath, const BidsDatasetDescription &desc)
Write a dataset_description.json file.
Definition bids_dataset_description.cpp:69
BIDSLIB::BidsElectrode
Electrode position record corresponding to one row in *_electrodes.tsv.
Definition bids_electrode.h:69
BIDSLIB::BidsElectrode::writeTsv
static bool writeTsv(const QString &sFilePath, const QList< BidsElectrode > &electrodes)
Write a BIDS *_electrodes.tsv file.
Definition bids_electrode.cpp:74
BIDSLIB::BidsElectrode::readTsv
static QList< BidsElectrode > readTsv(const QString &sFilePath)
Read a BIDS *_electrodes.tsv file.
Definition bids_electrode.cpp:46
BIDSLIB::BidsEvent::readTsv
static QList< BidsEvent > readTsv(const QString &sFilePath)
Read a BIDS *_events.tsv file.
Definition bids_event.cpp:30
BIDSLIB::BidsEvent::writeTsv
static bool writeTsv(const QString &sFilePath, const QList< BidsEvent > &events)
Write a BIDS *_events.tsv file.
Definition bids_event.cpp:77
BIDSLIB::BIDSPath
BIDS-compliant path and filename construction.
Definition bids_path.h:74
BIDSLIB::BIDSPath::subject
QString subject() const
Definition bids_path.cpp:158
BIDSLIB::BIDSPath::filePath
QString filePath() const
Definition bids_path.cpp:274
BIDSLIB::BIDSPath::electrodesTsvPath
BIDSPath electrodesTsvPath() const
Definition bids_path.cpp:300
BIDSLIB::BIDSPath::root
QString root() const
Definition bids_path.cpp:154
BIDSLIB::BIDSPath::channelsTsvPath
BIDSPath channelsTsvPath() const
Definition bids_path.cpp:293
BIDSLIB::BIDSPath::directory
QString directory() const
Definition bids_path.cpp:256
BIDSLIB::BIDSPath::extension
QString extension() const
Definition bids_path.cpp:206
BIDSLIB::BIDSPath::basename
QString basename() const
Definition bids_path.cpp:215
BIDSLIB::BIDSPath::coordsystemJsonPath
BIDSPath coordsystemJsonPath() const
Definition bids_path.cpp:313
BIDSLIB::BIDSPath::task
QString task() const
Definition bids_path.cpp:166
BIDSLIB::BIDSPath::eventsTsvPath
BIDSPath eventsTsvPath() const
Definition bids_path.cpp:326
BIDSLIB::BIDSPath::setExtension
void setExtension(const QString &sExtension)
Definition bids_path.cpp:145
BIDSLIB::BIDSPath::mkdirs
bool mkdirs() const
Definition bids_path.cpp:348
BIDSLIB::BIDSPath::datatype
QString datatype() const
Definition bids_path.cpp:198
BIDSLIB::BIDSPath::sidecarJsonPath
BIDSPath sidecarJsonPath() const
Definition bids_path.cpp:333
BIDSLIB::BidsRawData
Central container for a BIDS raw dataset, bundling electrophysiological data with all associated side...
Definition bids_raw_data.h:88
BIDSLIB::BidsRawData::clear
void clear()
Clears all data members and resets to invalid state.
Definition bids_raw_data.cpp:636
BIDSLIB::BidsRawData::read
static BidsRawData read(const BIDSPath &bidsPath)
Read a BIDS dataset from disk.
Definition bids_raw_data.cpp:672
BIDSLIB::BidsRawData::createReader
static AbstractFormatReader::UPtr createReader(const QString &sExtension)
Create the appropriate format reader for a given file extension.
Definition bids_raw_data.cpp:658
BIDSLIB::BidsRawData::raw
FIFFLIB::FiffRawData raw
Definition bids_raw_data.h:232
BIDSLIB::BidsRawData::reader
AbstractFormatReader::UPtr reader
Definition bids_raw_data.h:237
BIDSLIB::BidsRawData::eventIdMap
QMap< QString, int > eventIdMap
Definition bids_raw_data.h:234
BIDSLIB::BidsRawData::electrodes
QList< BidsElectrode > electrodes
Definition bids_raw_data.h:235
BIDSLIB::BidsRawData::operator=
BidsRawData & operator=(BidsRawData &&other) noexcept
Definition bids_raw_data.cpp:613
BIDSLIB::BidsRawData::events
QList< BidsEvent > events
Definition bids_raw_data.h:233
BIDSLIB::BidsRawData::coordinateSystem
BidsCoordinateSystem coordinateSystem
Definition bids_raw_data.h:236
BIDSLIB::BidsRawData::write
BIDSPath write(const BIDSPath &bidsPath, const QString &sourcePath, const WriteOptions &options) const
Write this dataset to a BIDS-compliant directory.
Definition bids_raw_data.cpp:796
BIDSLIB::BidsRawData::WriteOptions
Options controlling how write() operates.
Definition bids_raw_data.h:98
BIDSLIB::AbstractFormatReader::UPtr
std::unique_ptr< AbstractFormatReader > UPtr
Definition bids_abstract_format_reader.h:74
FIFFLIB::FiffChInfo
Per-channel FIFF descriptor: identifiers, kind, calibration, coil type, channel-frame coil position a...
Definition fiff_ch_info.h:78
FIFFLIB::FiffChPos::r0
Eigen::Vector3f r0
Definition fiff_ch_pos.h:126
FIFFLIB::FiffDigPoint
One digitizer point: kind (cardinal/HPI/EEG/extra), ident, 3D position in FIFFV_COORD_HEAD.
Definition fiff_dig_point.h:70
FIFFLIB::FiffInfo
Full FIFF measurement info: per-channel descriptors, sampling and filter setup, projectors,...
Definition fiff_info.h:90
FIFFLIB::FiffInfo::dig
QList< FiffDigPoint > dig
Definition fiff_info.h:290
FIFFLIB::FiffInfoBase::chs
QList< FiffChInfo > chs
Definition fiff_info_base.h:297
FIFFLIB::FiffRawData
Continuous FIFF raw recording: FiffInfo plus a random-access directory of FIFF_DATA_BUFFER tags.
Definition fiff_raw_data.h:83
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