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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//=========================================================================================================
54int bidsUnitToFiffUnit(const QString& sUnit)
55{
56 QString u = sUnit.toLower().trimmed();
57 if(u == "v" || u == "\u00B5v" || u == "uv" || u == "mv" || u == "nv")
58 return FIFF_UNIT_V;
59 if(u == "t" || u == "ft" || u == "pt")
60 return FIFF_UNIT_T;
61 return FIFF_UNIT_NONE;
62}
63
64//=========================================================================================================
65int bidsUnitToFiffUnitMul(const QString& sUnit)
66{
67 QString u = sUnit.toLower().trimmed();
68 if(u == "\u00B5v" || u == "uv" || u == "\u00B5s" || u == "us")
69 return FIFF_UNITM_MU;
70 if(u == "mv")
71 return FIFF_UNITM_M;
72 if(u == "nv")
73 return FIFF_UNITM_N;
74 if(u == "ft")
75 return FIFF_UNITM_F;
76 if(u == "pt")
77 return FIFF_UNITM_P;
78 return FIFF_UNITM_NONE;
79}
80
81//=========================================================================================================
82void applyChannelsTsv(FiffInfo& info, const QList<BidsChannel>& channels)
83{
84 if(channels.isEmpty())
85 return;
86
87 QMap<QString, int> bidsToFiff = bidsTypeToFiffKind();
88
89 QMap<QString, const BidsChannel*> channelMap;
90 for(const auto& ch : channels)
91 channelMap[ch.name] = &ch;
92
93 info.bads.clear();
94
95 for(int i = 0; i < info.chs.size(); ++i) {
96 FiffChInfo& fiffCh = info.chs[i];
97 auto it = channelMap.find(fiffCh.ch_name);
98 if(it == channelMap.end())
99 continue;
100 const BidsChannel* rec = it.value();
101
102 QString typeUpper = rec->type.toUpper();
103 if(bidsToFiff.contains(typeUpper))
104 fiffCh.kind = bidsToFiff[typeUpper];
105
106 if(!rec->units.isEmpty() && rec->units != "n/a") {
107 fiffCh.unit = bidsUnitToFiffUnit(rec->units);
108 fiffCh.unit_mul = bidsUnitToFiffUnitMul(rec->units);
109 }
110
111 if(rec->status.toLower() == "bad")
112 info.bads.append(fiffCh.ch_name);
113 }
114}
115
116//=========================================================================================================
117void applyElectrodePositions(FiffInfo& info,
118 const QList<BidsElectrode>& electrodes,
119 const QString& coordSystemName,
120 const QString& coordUnits)
121{
122 if(electrodes.isEmpty())
123 return;
124
125 QMap<QString, int> coordMap = bidsCoordToFiffFrame();
126 int coordFrame = FIFFV_COORD_UNKNOWN;
127 if(coordMap.contains(coordSystemName))
128 coordFrame = coordMap[coordSystemName];
129
130 float scaleFactor = 1.0f;
131 QString units = coordUnits.toLower();
132 if(units == "mm")
133 scaleFactor = 0.001f;
134 else if(units == "cm")
135 scaleFactor = 0.01f;
136
137 QSet<QString> chNames;
138 for(const auto& ch : info.chs)
139 chNames.insert(ch.ch_name);
140
141 info.dig.clear();
142 int ident = 1;
143 for(const auto& elec : electrodes) {
144 if(elec.x == "n/a" || elec.y == "n/a" || elec.z == "n/a")
145 continue;
146
147 FiffDigPoint dp;
148 dp.kind = chNames.contains(elec.name) ? FIFFV_POINT_EEG : FIFFV_POINT_EXTRA;
149 dp.ident = ident++;
150 dp.r[0] = elec.x.toFloat() * scaleFactor;
151 dp.r[1] = elec.y.toFloat() * scaleFactor;
152 dp.r[2] = elec.z.toFloat() * scaleFactor;
153 dp.coord_frame = coordFrame;
154
155 info.dig.append(dp);
156 }
157}
158
159//=========================================================================================================
160QJsonObject readJsonFile(const QString& sFilePath)
161{
162 QFile file(sFilePath);
163 if(!file.open(QIODevice::ReadOnly | QIODevice::Text))
164 return {};
165 QJsonParseError error;
166 QJsonDocument doc = QJsonDocument::fromJson(file.readAll(), &error);
167 file.close();
168 if(error.error != QJsonParseError::NoError)
169 return {};
170 return doc.object();
171}
172
173//=========================================================================================================
174bool writeJsonFile(const QString& sFilePath, const QJsonObject& json)
175{
176 QFile file(sFilePath);
177 if(!file.open(QIODevice::WriteOnly | QIODevice::Text))
178 return false;
179 file.write(QJsonDocument(json).toJson(QJsonDocument::Indented));
180 file.close();
181 return true;
182}
183
184//=========================================================================================================
185void readSidecarJson(const QString& sFilePath,
186 FiffInfo& info,
187 BidsRawData& data)
188{
189 QJsonObject json = readJsonFile(sFilePath);
190 if(json.isEmpty())
191 return;
192
193 // Apply to FiffInfo
194 double plf = json.value(QStringLiteral("PowerLineFrequency")).toDouble();
195 if(plf > 0.0)
196 info.linefreq = static_cast<float>(plf);
197
198 double sf = json.value(QStringLiteral("SamplingFrequency")).toDouble();
199 if(sf > 0.0 && std::abs(info.sfreq - static_cast<float>(sf)) > 0.5f)
200 qWarning() << "[BidsRawData::read] Sampling frequency mismatch: raw ="
201 << info.sfreq << "sidecar =" << sf;
202
203 // Store independent metadata fields on BidsRawData
204 data.ieegReference = json.value(QStringLiteral("iEEGReference")).toString();
205 data.taskDescription = json.value(QStringLiteral("TaskDescription")).toString();
206 data.manufacturer = json.value(QStringLiteral("Manufacturer")).toString();
207 data.manufacturerModelName = json.value(QStringLiteral("ManufacturerModelName")).toString();
208 data.softwareVersions = json.value(QStringLiteral("SoftwareVersions")).toString();
209 data.recordingType = json.value(QStringLiteral("RecordingType")).toString();
210}
211
212//=============================================================================================================
213// ANONYMOUS HELPERS — write side
214//=============================================================================================================
215
216//=========================================================================================================
217QString fiffUnitToBidsString(int unit, int unitMul)
218{
219 if(unit == FIFF_UNIT_V) {
220 switch(unitMul) {
221 case FIFF_UNITM_MU: return QStringLiteral("\u00B5V");
222 case FIFF_UNITM_M: return QStringLiteral("mV");
223 case FIFF_UNITM_N: return QStringLiteral("nV");
224 default: return QStringLiteral("V");
225 }
226 }
227 if(unit == FIFF_UNIT_T) {
228 switch(unitMul) {
229 case FIFF_UNITM_F: return QStringLiteral("fT");
230 case FIFF_UNITM_P: return QStringLiteral("pT");
231 default: return QStringLiteral("T");
232 }
233 }
234 return QStringLiteral("n/a");
235}
236
237//=========================================================================================================
238QString channelTypeDescription(int kind)
239{
240 switch(kind) {
241 case FIFFV_EEG_CH: return QStringLiteral("ElectroEncephaloGram");
242 case FIFFV_ECOG_CH: return QStringLiteral("Electrocorticography");
243 case FIFFV_SEEG_CH: return QStringLiteral("StereoElectroEncephaloGram");
244 case FIFFV_DBS_CH: return QStringLiteral("DeepBrainStimulation");
245 case FIFFV_MEG_CH: return QStringLiteral("MagnetoEncephaloGram");
246 case FIFFV_STIM_CH: return QStringLiteral("Trigger");
247 case FIFFV_EOG_CH: return QStringLiteral("ElectroOculoGram");
248 case FIFFV_ECG_CH: return QStringLiteral("ElectroCardioGram");
249 case FIFFV_EMG_CH: return QStringLiteral("ElectroMyoGram");
250 case FIFFV_MISC_CH: return QStringLiteral("Miscellaneous");
251 case FIFFV_RESP_CH: return QStringLiteral("Respiration");
252 default: return QStringLiteral("n/a");
253 }
254}
255
256//=========================================================================================================
257QList<BidsChannel> buildChannelRecords(const FiffInfo& info)
258{
259 QList<BidsChannel> records;
260 QMap<int, QString> kindMap = fiffKindToBidsType();
261 QSet<QString> badsSet(info.bads.begin(), info.bads.end());
262
263 for(int i = 0; i < info.chs.size(); ++i) {
264 const FiffChInfo& ch = info.chs[i];
265
266 BidsChannel rec;
267 rec.name = ch.ch_name;
268 rec.type = kindMap.contains(ch.kind) ? kindMap[ch.kind] : QStringLiteral("MISC");
269 rec.units = fiffUnitToBidsString(ch.unit, ch.unit_mul);
270 rec.samplingFreq = QString::number(static_cast<double>(info.sfreq), 'g', 10);
271 rec.lowCutoff = (info.highpass > 0.0f)
272 ? QString::number(static_cast<double>(info.highpass), 'g', 10)
273 : QStringLiteral("n/a");
274 rec.highCutoff = (info.lowpass > 0.0f)
275 ? QString::number(static_cast<double>(info.lowpass), 'g', 10)
276 : QStringLiteral("n/a");
277 rec.notch = QStringLiteral("n/a");
278 rec.status = badsSet.contains(ch.ch_name) ? QStringLiteral("bad") : QStringLiteral("good");
279 rec.description = channelTypeDescription(ch.kind);
280
281 records.append(rec);
282 }
283 return records;
284}
285
286//=========================================================================================================
287QList<BidsElectrode> buildElectrodeRecords(const FiffInfo& info)
288{
289 QList<BidsElectrode> records;
290
291 QMap<int, const FiffDigPoint*> digByIdent;
292 for(const auto& dp : info.dig) {
293 if(dp.kind == FIFFV_POINT_EEG || dp.kind == FIFFV_POINT_EXTRA)
294 digByIdent[dp.ident] = &dp;
295 }
296
297 int digIdx = 0;
298
299 for(int i = 0; i < info.chs.size(); ++i) {
300 const FiffChInfo& ch = info.chs[i];
301
302 if(ch.kind == FIFFV_STIM_CH)
303 continue;
304 if(ch.kind != FIFFV_EEG_CH && ch.kind != FIFFV_ECOG_CH &&
305 ch.kind != FIFFV_SEEG_CH && ch.kind != FIFFV_DBS_CH)
306 continue;
307
308 BidsElectrode rec;
309 rec.name = ch.ch_name;
310
311 ++digIdx;
312 bool hasPosition = false;
313
314 if(digByIdent.contains(digIdx)) {
315 const FiffDigPoint* dp = digByIdent[digIdx];
316 if(std::isfinite(dp->r[0]) && std::isfinite(dp->r[1]) && std::isfinite(dp->r[2])) {
317 rec.x = QString::number(static_cast<double>(dp->r[0]), 'g', 8);
318 rec.y = QString::number(static_cast<double>(dp->r[1]), 'g', 8);
319 rec.z = QString::number(static_cast<double>(dp->r[2]), 'g', 8);
320 hasPosition = true;
321 }
322 }
323
324 if(!hasPosition) {
325 const Eigen::Vector3f& r0 = ch.chpos.r0;
326 if(r0.squaredNorm() > 0.0f && std::isfinite(r0[0])) {
327 rec.x = QString::number(static_cast<double>(r0[0]), 'g', 8);
328 rec.y = QString::number(static_cast<double>(r0[1]), 'g', 8);
329 rec.z = QString::number(static_cast<double>(r0[2]), 'g', 8);
330 } else {
331 rec.x = QStringLiteral("n/a");
332 rec.y = QStringLiteral("n/a");
333 rec.z = QStringLiteral("n/a");
334 }
335 }
336
337 rec.size = QStringLiteral("n/a");
338 rec.type = QStringLiteral("n/a");
339 rec.material = QStringLiteral("n/a");
340 rec.impedance = QStringLiteral("n/a");
341
342 records.append(rec);
343 }
344 return records;
345}
346
347//=========================================================================================================
348QJsonObject buildIeegSidecarJson(const BidsRawData& data,
349 const BIDSPath& bidsPath)
350{
351 QJsonObject json;
352 const FiffInfo& info = data.raw.info;
353
354 // Required
355 json[QStringLiteral("TaskName")] = bidsPath.task();
356 json[QStringLiteral("SamplingFrequency")] = static_cast<double>(info.sfreq);
357 json[QStringLiteral("PowerLineFrequency")] = static_cast<double>(info.linefreq);
358
359 // Reference
360 if(!data.ieegReference.isEmpty())
361 json[QStringLiteral("iEEGReference")] = data.ieegReference;
362 else
363 json[QStringLiteral("iEEGReference")] = QStringLiteral("n/a");
364
365 // Channel counts — computed from FiffInfo
366 int ecog = 0, seeg = 0, dbs = 0, eeg = 0, eog = 0, ecg = 0, emg = 0, misc = 0, trig = 0;
367 for(const auto& ch : info.chs) {
368 switch(ch.kind) {
369 case FIFFV_ECOG_CH: ++ecog; break;
370 case FIFFV_SEEG_CH: ++seeg; break;
371 case FIFFV_DBS_CH: ++dbs; break;
372 case FIFFV_EEG_CH: ++eeg; break;
373 case FIFFV_EOG_CH: ++eog; break;
374 case FIFFV_ECG_CH: ++ecg; break;
375 case FIFFV_EMG_CH: ++emg; break;
376 case FIFFV_MISC_CH: ++misc; break;
377 case FIFFV_STIM_CH: ++trig; break;
378 default: break;
379 }
380 }
381 json[QStringLiteral("ECOGChannelCount")] = ecog;
382 json[QStringLiteral("SEEGChannelCount")] = seeg;
383 if(dbs > 0) json[QStringLiteral("DBSChannelCount")] = dbs;
384 if(eeg > 0) json[QStringLiteral("EEGChannelCount")] = eeg;
385 if(eog > 0) json[QStringLiteral("EOGChannelCount")] = eog;
386 if(ecg > 0) json[QStringLiteral("ECGChannelCount")] = ecg;
387 if(emg > 0) json[QStringLiteral("EMGChannelCount")] = emg;
388 if(misc > 0) json[QStringLiteral("MiscChannelCount")] = misc;
389 if(trig > 0) json[QStringLiteral("TriggerChannelCount")] = trig;
390
391 // Recording metadata
392 if(!data.recordingType.isEmpty())
393 json[QStringLiteral("RecordingType")] = data.recordingType;
394 else
395 json[QStringLiteral("RecordingType")] = QStringLiteral("continuous");
396
397 if(info.sfreq > 0.0f && data.raw.last_samp >= data.raw.first_samp) {
398 double dur = static_cast<double>(data.raw.last_samp - data.raw.first_samp + 1)
399 / static_cast<double>(info.sfreq);
400 json[QStringLiteral("RecordingDuration")] = dur;
401 }
402
403 // Optional strings from BidsRawData
404 if(!data.taskDescription.isEmpty())
405 json[QStringLiteral("TaskDescription")] = data.taskDescription;
406 if(!data.manufacturer.isEmpty())
407 json[QStringLiteral("Manufacturer")] = data.manufacturer;
408 if(!data.manufacturerModelName.isEmpty())
409 json[QStringLiteral("ManufacturerModelName")] = data.manufacturerModelName;
410 if(!data.softwareVersions.isEmpty())
411 json[QStringLiteral("SoftwareVersions")] = data.softwareVersions;
412
413 return json;
414}
415
416//=========================================================================================================
417bool copyFile(const QString& src, const QString& dst, bool overwrite)
418{
419 if(!QFileInfo::exists(src)) {
420 qWarning() << "[BidsRawData::write] Source file does not exist:" << src;
421 return false;
422 }
423 if(QFileInfo::exists(dst)) {
424 if(!overwrite) {
425 qWarning() << "[BidsRawData::write] Target file already exists:" << dst;
426 return false;
427 }
428 QFile::remove(dst);
429 }
430 return QFile::copy(src, dst);
431}
432
433//=========================================================================================================
434bool copyBrainVisionFiles(const QString& srcVhdr, const BIDSPath& bidsPath, bool overwrite)
435{
436 QFileInfo srcInfo(srcVhdr);
437 QString srcDir = srcInfo.absolutePath();
438
439 QFile vhdrFile(srcVhdr);
440 if(!vhdrFile.open(QIODevice::ReadOnly | QIODevice::Text)) {
441 qWarning() << "[BidsRawData::write] Cannot open .vhdr file:" << srcVhdr;
442 return false;
443 }
444
445 QString dataFileName;
446 QString markerFileName;
447 QByteArray vhdrContent = vhdrFile.readAll();
448 vhdrFile.close();
449
450 for(const auto& line : vhdrContent.split('\n')) {
451 QString sLine = QString::fromUtf8(line).trimmed();
452 if(sLine.startsWith("DataFile=", Qt::CaseInsensitive))
453 dataFileName = sLine.mid(9).trimmed();
454 else if(sLine.startsWith("MarkerFile=", Qt::CaseInsensitive))
455 markerFileName = sLine.mid(11).trimmed();
456 }
457
458 QString dstDir = bidsPath.directory();
459 QString dstBase = bidsPath.basename();
460 dstBase = dstBase.left(dstBase.lastIndexOf('.'));
461
462 QString dstVhdr = bidsPath.filePath();
463 QString newDataFile = dstBase + QStringLiteral(".eeg");
464 QString newMarkerFile = dstBase + QStringLiteral(".vmrk");
465
466 QString vhdrStr = QString::fromUtf8(vhdrContent);
467 if(!dataFileName.isEmpty())
468 vhdrStr.replace("DataFile=" + dataFileName,
469 "DataFile=" + QFileInfo(newDataFile).fileName());
470 if(!markerFileName.isEmpty())
471 vhdrStr.replace("MarkerFile=" + markerFileName,
472 "MarkerFile=" + QFileInfo(newMarkerFile).fileName());
473
474 if(QFileInfo::exists(dstVhdr) && !overwrite) {
475 qWarning() << "[BidsRawData::write] Target file already exists:" << dstVhdr;
476 return false;
477 }
478 if(QFileInfo::exists(dstVhdr))
479 QFile::remove(dstVhdr);
480
481 QFile dstVhdrFile(dstVhdr);
482 if(!dstVhdrFile.open(QIODevice::WriteOnly | QIODevice::Text)) {
483 qWarning() << "[BidsRawData::write] Cannot write .vhdr file:" << dstVhdr;
484 return false;
485 }
486 dstVhdrFile.write(vhdrStr.toUtf8());
487 dstVhdrFile.close();
488
489 if(!dataFileName.isEmpty()) {
490 QString srcData = QDir(srcDir).absoluteFilePath(dataFileName);
491 QString dstData = dstDir + QFileInfo(newDataFile).fileName();
492 if(!copyFile(srcData, dstData, overwrite)) {
493 qWarning() << "[BidsRawData::write] Failed to copy data file:" << srcData;
494 return false;
495 }
496 }
497
498 if(!markerFileName.isEmpty()) {
499 QString srcMarker = QDir(srcDir).absoluteFilePath(markerFileName);
500 QString dstMarker = dstDir + QFileInfo(newMarkerFile).fileName();
501
502 if(QFileInfo::exists(srcMarker)) {
503 QFile markerFile(srcMarker);
504 if(markerFile.open(QIODevice::ReadOnly | QIODevice::Text)) {
505 QString markerContent = QString::fromUtf8(markerFile.readAll());
506 markerFile.close();
507
508 markerContent.replace("DataFile=" + dataFileName,
509 "DataFile=" + QFileInfo(newDataFile).fileName());
510
511 if(QFileInfo::exists(dstMarker)) {
512 if(!overwrite) {
513 qWarning() << "[BidsRawData::write] Target marker file already exists:" << dstMarker;
514 return false;
515 }
516 QFile::remove(dstMarker);
517 }
518
519 QFile dstMarkerFile(dstMarker);
520 if(dstMarkerFile.open(QIODevice::WriteOnly | QIODevice::Text)) {
521 dstMarkerFile.write(markerContent.toUtf8());
522 dstMarkerFile.close();
523 }
524 }
525 }
526 }
527
528 return true;
529}
530
531//=========================================================================================================
532bool copyRawDataFile(const QString& sourcePath, const BIDSPath& bidsPath, bool overwrite)
533{
534 if(sourcePath.isEmpty())
535 return true;
536
537 QString ext = bidsPath.extension().toLower();
538 if(ext == ".vhdr" || ext == ".ahdr")
539 return copyBrainVisionFiles(sourcePath, bidsPath, overwrite);
540
541 return copyFile(sourcePath, bidsPath.filePath(), overwrite);
542}
543
544} // anonymous namespace
545
546//=============================================================================================================
547// MEMBER METHODS
548//=============================================================================================================
549
550BidsRawData::BidsRawData(BidsRawData&& other) noexcept
551 : raw(other.raw) // FiffRawData has only copy ctor
552 , events(std::move(other.events))
553 , eventIdMap(std::move(other.eventIdMap))
554 , electrodes(std::move(other.electrodes))
555 , coordinateSystem(std::move(other.coordinateSystem))
556 , reader(std::move(other.reader))
557 , ieegReference(std::move(other.ieegReference))
558 , taskDescription(std::move(other.taskDescription))
559 , manufacturer(std::move(other.manufacturer))
560 , manufacturerModelName(std::move(other.manufacturerModelName))
561 , softwareVersions(std::move(other.softwareVersions))
562 , recordingType(std::move(other.recordingType))
563 , m_bIsValid(other.m_bIsValid)
564{
565 other.m_bIsValid = false;
566}
567
568//=============================================================================================================
569
570BidsRawData& BidsRawData::operator=(BidsRawData&& other) noexcept
571{
572 if(this != &other) {
573 raw = other.raw; // FiffRawData has only copy ctor
574 events = std::move(other.events);
575 eventIdMap = std::move(other.eventIdMap);
576 electrodes = std::move(other.electrodes);
577 coordinateSystem = std::move(other.coordinateSystem);
578 reader = std::move(other.reader);
579 ieegReference = std::move(other.ieegReference);
580 taskDescription = std::move(other.taskDescription);
581 manufacturer = std::move(other.manufacturer);
582 manufacturerModelName = std::move(other.manufacturerModelName);
583 softwareVersions = std::move(other.softwareVersions);
584 recordingType = std::move(other.recordingType);
585 m_bIsValid = other.m_bIsValid;
586 other.m_bIsValid = false;
587 }
588 return *this;
589}
590
591//=============================================================================================================
592
593void BidsRawData::clear()
594{
595 raw = FiffRawData();
596 events.clear();
597 eventIdMap.clear();
598 electrodes.clear();
599 reader.reset();
600
601 ieegReference.clear();
602 taskDescription.clear();
603 manufacturer.clear();
604 manufacturerModelName.clear();
605 softwareVersions.clear();
606 recordingType.clear();
607
608 coordinateSystem = BidsCoordinateSystem();
609
610 m_bIsValid = false;
611}
612
613//=============================================================================================================
614
615AbstractFormatReader::UPtr BidsRawData::createReader(const QString& sExtension)
616{
617 QString ext = sExtension.toLower();
618 if(ext == ".vhdr" || ext == ".ahdr")
619 return std::make_unique<BrainVisionReader>();
620 if(ext == ".edf" || ext == ".bdf")
621 return std::make_unique<EDFReader>();
622 return nullptr;
623}
624
625//=============================================================================================================
626// BidsRawData::read()
627//=============================================================================================================
628
629BidsRawData BidsRawData::read(const BIDSPath& bidsPath)
630{
631 BidsRawData result;
632
633 //=========================================================================================================
634 // Step 1 — Validate BIDSPath
635 //=========================================================================================================
636 if(bidsPath.root().isEmpty()) {
637 qWarning() << "[BidsRawData::read] BIDSPath root is not set";
638 return result;
639 }
640 if(bidsPath.subject().isEmpty()) {
641 qWarning() << "[BidsRawData::read] BIDSPath subject is not set";
642 return result;
643 }
644 if(bidsPath.extension().isEmpty()) {
645 qWarning() << "[BidsRawData::read] BIDSPath extension is not set";
646 return result;
647 }
648
649 //=========================================================================================================
650 // Step 2 — Resolve raw file path
651 //=========================================================================================================
652 QString rawFilePath = bidsPath.filePath();
653
654 if(!QFileInfo::exists(rawFilePath)) {
655 QString ext = bidsPath.extension();
656 if(ext.toLower() == ".edf") {
657 BIDSPath altPath(bidsPath);
658 altPath.setExtension(".EDF");
659 if(QFileInfo::exists(altPath.filePath()))
660 rawFilePath = altPath.filePath();
661 }
662 }
663
664 if(!QFileInfo::exists(rawFilePath)) {
665 qWarning() << "[BidsRawData::read] Raw data file not found:" << rawFilePath;
666 return result;
667 }
668
669 //=========================================================================================================
670 // Step 3 — Create and open the format reader
671 //=========================================================================================================
672 result.reader = createReader(bidsPath.extension());
673 if(!result.reader) {
674 qWarning() << "[BidsRawData::read] Unsupported file extension:" << bidsPath.extension();
675 return result;
676 }
677
678 if(!result.reader->open(rawFilePath)) {
679 qWarning() << "[BidsRawData::read] Failed to open raw file:" << rawFilePath;
680 return result;
681 }
682
683 //=========================================================================================================
684 // Step 4 — Build FiffRawData from the reader
685 //=========================================================================================================
686 result.raw = result.reader->toFiffRawData();
687
688 //=========================================================================================================
689 // Step 5 — Read and apply *_channels.tsv
690 //=========================================================================================================
691 BIDSPath channelsPath = bidsPath.channelsTsvPath();
692 if(QFileInfo::exists(channelsPath.filePath())) {
693 QList<BidsChannel> channels = BidsChannel::readTsv(channelsPath.filePath());
694 applyChannelsTsv(result.raw.info, channels);
695 }
696
697 //=========================================================================================================
698 // Step 6 — Read *_coordsystem.json (before electrodes, for scale/frame info)
699 //=========================================================================================================
700 BIDSPath coordsysPath = bidsPath.coordsystemJsonPath();
701 if(QFileInfo::exists(coordsysPath.filePath()))
702 result.coordinateSystem = BidsCoordinateSystem::readJson(coordsysPath.filePath());
703
704 //=========================================================================================================
705 // Step 7 — Read and apply *_electrodes.tsv
706 //=========================================================================================================
707 BIDSPath electrodesPath = bidsPath.electrodesTsvPath();
708 if(QFileInfo::exists(electrodesPath.filePath())) {
709 result.electrodes = BidsElectrode::readTsv(electrodesPath.filePath());
710 applyElectrodePositions(result.raw.info, result.electrodes,
711 result.coordinateSystem.system, result.coordinateSystem.units);
712 }
713
714 //=========================================================================================================
715 // Step 8 — Read *_events.tsv
716 //=========================================================================================================
717 BIDSPath eventsPath = bidsPath.eventsTsvPath();
718 if(QFileInfo::exists(eventsPath.filePath())) {
719 result.events = BidsEvent::readTsv(eventsPath.filePath());
720
721 // Compute sample from onset*sfreq if sample column was absent
722 float sfreq = result.raw.info.sfreq;
723 for(auto& ev : result.events) {
724 if(ev.sample == 0 && ev.onset > 0.0f && sfreq > 0)
725 ev.sample = static_cast<int>(ev.onset * sfreq);
726 }
727
728 // Build eventIdMap from trial_type → value
729 for(const auto& ev : result.events) {
730 if(!ev.trialType.isEmpty() && ev.trialType != "n/a")
731 result.eventIdMap.insert(ev.trialType, ev.value);
732 }
733 }
734
735 //=========================================================================================================
736 // Step 9 — Read sidecar *_{datatype}.json
737 //=========================================================================================================
738 BIDSPath sidecarPath = bidsPath.sidecarJsonPath();
739 if(QFileInfo::exists(sidecarPath.filePath()))
740 readSidecarJson(sidecarPath.filePath(), result.raw.info, result);
741
742 //=========================================================================================================
743 // Done
744 //=========================================================================================================
745 result.m_bIsValid = true;
746 return result;
747}
748
749//=============================================================================================================
750// BidsRawData::write()
751//=============================================================================================================
752
753BIDSPath BidsRawData::write(const BIDSPath& bidsPath,
754 const QString& sourcePath,
755 const WriteOptions& options) const
756{
757 BIDSPath result;
758
759 //=========================================================================================================
760 // Step 1 — Validate
761 //=========================================================================================================
762 if(bidsPath.root().isEmpty()) {
763 qWarning() << "[BidsRawData::write] BIDSPath root is not set";
764 return result;
765 }
766 if(bidsPath.subject().isEmpty()) {
767 qWarning() << "[BidsRawData::write] BIDSPath subject is not set";
768 return result;
769 }
770 if(bidsPath.task().isEmpty()) {
771 qWarning() << "[BidsRawData::write] BIDSPath task is not set";
772 return result;
773 }
774 if(bidsPath.datatype().isEmpty()) {
775 qWarning() << "[BidsRawData::write] BIDSPath datatype is not set";
776 return result;
777 }
778 if(raw.info.isEmpty()) {
779 qWarning() << "[BidsRawData::write] FiffRawData info is empty";
780 return result;
781 }
782
783 //=========================================================================================================
784 // Step 2 — Create directory structure
785 //=========================================================================================================
786 if(!bidsPath.mkdirs()) {
787 qWarning() << "[BidsRawData::write] Failed to create directory:" << bidsPath.directory();
788 return result;
789 }
790
791 //=========================================================================================================
792 // Step 3 — Copy raw data file
793 //=========================================================================================================
794 if(options.copyData && !sourcePath.isEmpty()) {
795 if(!copyRawDataFile(sourcePath, bidsPath, options.overwrite)) {
796 qWarning() << "[BidsRawData::write] Failed to copy raw data file";
797 return result;
798 }
799 }
800
801 //=========================================================================================================
802 // Step 4 — Write *_channels.tsv
803 //=========================================================================================================
804 {
805 BIDSPath channelsPath = bidsPath.channelsTsvPath();
806 if(!options.overwrite && QFileInfo::exists(channelsPath.filePath())) {
807 qWarning() << "[BidsRawData::write] channels.tsv already exists:" << channelsPath.filePath();
808 return result;
809 }
810
811 QList<BidsChannel> channelRecords = buildChannelRecords(raw.info);
812 if(!BidsChannel::writeTsv(channelsPath.filePath(), channelRecords)) {
813 qWarning() << "[BidsRawData::write] Failed to write channels.tsv";
814 return result;
815 }
816 }
817
818 //=========================================================================================================
819 // Step 5 — Write *_electrodes.tsv + *_coordsystem.json
820 //=========================================================================================================
821 {
822 QList<BidsElectrode> electrodeRecords = buildElectrodeRecords(raw.info);
823
824 if(!electrodeRecords.isEmpty()) {
825 BIDSPath electrodesPath = bidsPath.electrodesTsvPath();
826 if(options.overwrite || !QFileInfo::exists(electrodesPath.filePath())) {
827 if(!BidsElectrode::writeTsv(electrodesPath.filePath(), electrodeRecords))
828 qWarning() << "[BidsRawData::write] Failed to write electrodes.tsv";
829 }
830
831 BIDSPath coordsysPath = bidsPath.coordsystemJsonPath();
832 if(options.overwrite || !QFileInfo::exists(coordsysPath.filePath())) {
833 // Build coordinate system, deriving defaults from FiffInfo if needed
834 BidsCoordinateSystem cs = coordinateSystem;
835 if(cs.system.isEmpty()) {
836 if(raw.info.dig.isEmpty()) {
837 cs.system = QStringLiteral("Other");
838 cs.units = QStringLiteral("n/a");
839 } else {
840 int coordFrame = raw.info.dig.first().coord_frame;
841 QMap<int, QString> frameMap = fiffFrameToBidsCoord();
842 cs.system = frameMap.contains(coordFrame)
843 ? frameMap[coordFrame]
844 : QStringLiteral("Other");
845 cs.units = QStringLiteral("m");
846 }
847 }
848 if(cs.description.isEmpty() && !raw.info.dig.isEmpty())
849 cs.description = QStringLiteral("Coordinate system derived from recording data");
850
851 if(!BidsCoordinateSystem::writeJson(coordsysPath.filePath(), cs))
852 qWarning() << "[BidsRawData::write] Failed to write coordsystem.json";
853 }
854 }
855 }
856
857 //=========================================================================================================
858 // Step 6 — Write *_events.tsv
859 //=========================================================================================================
860 if(!events.isEmpty()) {
861 BIDSPath eventsPath = bidsPath.eventsTsvPath();
862 if(!options.overwrite && QFileInfo::exists(eventsPath.filePath())) {
863 qWarning() << "[BidsRawData::write] events.tsv already exists:" << eventsPath.filePath();
864 return result;
865 }
866
867 QList<BidsEvent> eventsToWrite = events;
868
869 // Apply trial_type fallback from eventIdMap
870 QMap<int, QString> valueToType;
871 for(auto it = eventIdMap.constBegin(); it != eventIdMap.constEnd(); ++it)
872 valueToType[it.value()] = it.key();
873 for(auto& ev : eventsToWrite) {
874 if(ev.trialType.isEmpty() || ev.trialType == "n/a")
875 ev.trialType = valueToType.value(ev.value, QStringLiteral("n/a"));
876 }
877
878 if(!BidsEvent::writeTsv(eventsPath.filePath(), eventsToWrite))
879 qWarning() << "[BidsRawData::write] Failed to write events.tsv";
880 }
881
882 //=========================================================================================================
883 // Step 7 — Write *_{datatype}.json sidecar
884 //=========================================================================================================
885 {
886 BIDSPath sidecarPath = bidsPath.sidecarJsonPath();
887 if(!options.overwrite && QFileInfo::exists(sidecarPath.filePath())) {
888 qWarning() << "[BidsRawData::write] Sidecar JSON already exists:" << sidecarPath.filePath();
889 return result;
890 }
891
892 QJsonObject sidecarJson = buildIeegSidecarJson(*this, bidsPath);
893 if(!writeJsonFile(sidecarPath.filePath(), sidecarJson)) {
894 qWarning() << "[BidsRawData::write] Failed to write sidecar JSON";
895 return result;
896 }
897 }
898
899 //=========================================================================================================
900 // Step 8 — Write dataset_description.json (never overwrite)
901 //=========================================================================================================
902 {
903 QString descPath = bidsPath.root() + QDir::separator()
904 + QStringLiteral("dataset_description.json");
905
906 if(!QFileInfo::exists(descPath)) {
907 BidsDatasetDescription desc;
908 desc.name = options.datasetName.isEmpty()
909 ? QStringLiteral("[Unspecified]")
910 : options.datasetName;
911 desc.bidsVersion = QStringLiteral("1.9.0");
912 desc.datasetType = QStringLiteral("raw");
913
914 if(!BidsDatasetDescription::write(descPath, desc))
915 qWarning() << "[BidsRawData::write] Failed to write dataset_description.json";
916 }
917 }
918
919 //=========================================================================================================
920 // Done
921 //=========================================================================================================
922 result = bidsPath;
923 return result;
924}
bids_edf_reader.h
BIDSLIB::AbstractFormatReader implementation for European Data Format (EDF / EDF+) files.
bids_brain_vision_reader.h
BIDSLIB::AbstractFormatReader implementation for the BrainVision .vhdr / .vmrk / ....
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_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.
fiff_constants.h
Symbolic FIFF tag, block, value, unit and channel-type constants shared across FIFFLIB.
FIFFV_POINT_EXTRA
#define FIFFV_POINT_EXTRA
Definition fiff_constants.h:304
FIFFV_EOG_CH
#define FIFFV_EOG_CH
Definition fiff_constants.h:270
FIFFV_SEEG_CH
#define FIFFV_SEEG_CH
Definition fiff_constants.h:280
FIFFV_EEG_CH
#define FIFFV_EEG_CH
Definition fiff_constants.h:267
FIFF_UNIT_NONE
#define FIFF_UNIT_NONE
Definition fiff_constants.h:86
FIFFV_RESP_CH
#define FIFFV_RESP_CH
Definition fiff_constants.h:274
FIFFV_MISC_CH
#define FIFFV_MISC_CH
Definition fiff_constants.h:273
FIFF_UNIT_V
#define FIFF_UNIT_V
Definition fiff_constants.h:118
FIFFV_MEG_CH
#define FIFFV_MEG_CH
Definition fiff_constants.h:264
FIFF_UNITM_NONE
#define FIFF_UNITM_NONE
Definition fiff_constants.h:147
FIFFV_ECOG_CH
#define FIFFV_ECOG_CH
Definition fiff_constants.h:279
FIFF_UNITM_N
#define FIFF_UNITM_N
Definition fiff_constants.h:152
FIFF_UNITM_F
#define FIFF_UNITM_F
Definition fiff_constants.h:154
FIFFV_POINT_EEG
#define FIFFV_POINT_EEG
Definition fiff_constants.h:302
FIFF_UNITM_M
#define FIFF_UNITM_M
Definition fiff_constants.h:150
FIFFV_STIM_CH
#define FIFFV_STIM_CH
Definition fiff_constants.h:268
FIFF_UNITM_P
#define FIFF_UNITM_P
Definition fiff_constants.h:153
FIFFV_COORD_UNKNOWN
#define FIFFV_COORD_UNKNOWN
Definition fiff_constants.h:211
FIFF_UNIT_T
#define FIFF_UNIT_T
Definition fiff_constants.h:123
FIFFV_EMG_CH
#define FIFFV_EMG_CH
Definition fiff_constants.h:271
FIFFV_ECG_CH
#define FIFFV_ECG_CH
Definition fiff_constants.h:272
FIFFV_DBS_CH
#define FIFFV_DBS_CH
Definition fiff_constants.h:281
FIFF_UNITM_MU
#define FIFF_UNITM_MU
Definition fiff_constants.h:151
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:108
BIDSLIB::bidsCoordToFiffFrame
QMap< QString, int > bidsCoordToFiffFrame()
Definition bids_const.h:157
BIDSLIB::bidsTypeToFiffKind
QMap< QString, int > bidsTypeToFiffKind()
Definition bids_const.h:130
BIDSLIB::fiffFrameToBidsCoord
QMap< int, QString > fiffFrameToBidsCoord()
Definition bids_const.h:174
FIFFLIB
FIFF file I/O, in-memory data structures and high-level readers/writers.
Definition connectivitysettings.h:66
BIDSLIB::BidsChannel
Channel metadata record corresponding to one row in *_channels.tsv.
Definition bids_channel.h:55
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:69
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:59
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:67
BIDSLIB::BidsElectrode::writeTsv
static bool writeTsv(const QString &sFilePath, const QList< BidsElectrode > &electrodes)
Write a BIDS *_electrodes.tsv file.
Definition bids_electrode.cpp:72
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:93
BIDSLIB::BIDSPath::subject
QString subject() const
Definition bids_path.cpp:111
BIDSLIB::BIDSPath::filePath
QString filePath() const
Definition bids_path.cpp:188
BIDSLIB::BIDSPath::electrodesTsvPath
BIDSPath electrodesTsvPath() const
Definition bids_path.cpp:214
BIDSLIB::BIDSPath::root
QString root() const
Definition bids_path.cpp:110
BIDSLIB::BIDSPath::channelsTsvPath
BIDSPath channelsTsvPath() const
Definition bids_path.cpp:207
BIDSLIB::BIDSPath::directory
QString directory() const
Definition bids_path.cpp:170
BIDSLIB::BIDSPath::extension
QString extension() const
Definition bids_path.cpp:123
BIDSLIB::BIDSPath::basename
QString basename() const
Definition bids_path.cpp:129
BIDSLIB::BIDSPath::coordsystemJsonPath
BIDSPath coordsystemJsonPath() const
Definition bids_path.cpp:227
BIDSLIB::BIDSPath::task
QString task() const
Definition bids_path.cpp:113
BIDSLIB::BIDSPath::eventsTsvPath
BIDSPath eventsTsvPath() const
Definition bids_path.cpp:240
BIDSLIB::BIDSPath::setExtension
void setExtension(const QString &sExtension)
Definition bids_path.cpp:104
BIDSLIB::BIDSPath::mkdirs
bool mkdirs() const
Definition bids_path.cpp:262
BIDSLIB::BIDSPath::datatype
QString datatype() const
Definition bids_path.cpp:121
BIDSLIB::BIDSPath::sidecarJsonPath
BIDSPath sidecarJsonPath() const
Definition bids_path.cpp:247
BIDSLIB::BidsRawData
Central container for a BIDS raw dataset, bundling electrophysiological data with all associated side...
Definition bids_raw_data.h:98
BIDSLIB::BidsRawData::clear
void clear()
Clears all data members and resets to invalid state.
Definition bids_raw_data.cpp:593
BIDSLIB::BidsRawData::read
static BidsRawData read(const BIDSPath &bidsPath)
Read a BIDS dataset from disk.
Definition bids_raw_data.cpp:629
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:615
BIDSLIB::BidsRawData::raw
FIFFLIB::FiffRawData raw
Definition bids_raw_data.h:227
BIDSLIB::BidsRawData::reader
AbstractFormatReader::UPtr reader
Definition bids_raw_data.h:232
BIDSLIB::BidsRawData::eventIdMap
QMap< QString, int > eventIdMap
Definition bids_raw_data.h:229
BIDSLIB::BidsRawData::electrodes
QList< BidsElectrode > electrodes
Definition bids_raw_data.h:230
BIDSLIB::BidsRawData::operator=
BidsRawData & operator=(BidsRawData &&other) noexcept
Definition bids_raw_data.cpp:570
BIDSLIB::BidsRawData::events
QList< BidsEvent > events
Definition bids_raw_data.h:228
BIDSLIB::BidsRawData::coordinateSystem
BidsCoordinateSystem coordinateSystem
Definition bids_raw_data.h:231
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:753
BIDSLIB::BidsRawData::WriteOptions
Options controlling how write() operates.
Definition bids_raw_data.h:108
BIDSLIB::AbstractFormatReader::UPtr
std::unique_ptr< AbstractFormatReader > UPtr
Definition bids_abstract_format_reader.h:72
FIFFLIB::FiffChInfo
Per-channel FIFF descriptor: identifiers, kind, calibration, coil type, channel-frame coil position a...
Definition fiff_ch_info.h:76
FIFFLIB::FiffChPos::r0
Eigen::Vector3f r0
Definition fiff_ch_pos.h:110
FIFFLIB::FiffDigPoint
One digitizer point: kind (cardinal/HPI/EEG/extra), ident, 3D position in FIFFV_COORD_HEAD.
Definition fiff_dig_point.h:68
FIFFLIB::FiffInfo
Full FIFF measurement info: per-channel descriptors, sampling and filter setup, projectors,...
Definition fiff_info.h:88
FIFFLIB::FiffInfo::dig
QList< FiffDigPoint > dig
Definition fiff_info.h:275
FIFFLIB::FiffInfoBase::chs
QList< FiffChInfo > chs
Definition fiff_info_base.h:250
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