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bids_raw_data.cpp
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1//=============================================================================================================
34
35//=============================================================================================================
36// INCLUDES
37//=============================================================================================================
38
39#include "bids_raw_data.h"
40#include "bids_channel.h"
41#include "bids_dataset_description.h"
42#include "bids_const.h"
43#include "readers/bids_edf_reader.h"
44#include "readers/bids_brain_vision_reader.h"
45
46#include <fiff/fiff_constants.h>
47
48//=============================================================================================================
49// QT INCLUDES
50//=============================================================================================================
51
52#include <QDebug>
53#include <QFileInfo>
54#include <QDir>
55#include <QFile>
56#include <QJsonDocument>
57#include <QJsonObject>
58#include <cmath>
59
60//=============================================================================================================
61// USED NAMESPACES
62//=============================================================================================================
63
64using namespace BIDSLIB;
65using namespace FIFFLIB;
66using namespace Eigen;
67
68//=============================================================================================================
69// ANONYMOUS HELPERS — read side
70//=============================================================================================================
71
72namespace
73{
74
75//=========================================================================================================
76int bidsUnitToFiffUnit(const QString& sUnit)
77{
78 QString u = sUnit.toLower().trimmed();
79 if(u == "v" || u == "\u00B5v" || u == "uv" || u == "mv" || u == "nv")
80 return FIFF_UNIT_V;
81 if(u == "t" || u == "ft" || u == "pt")
82 return FIFF_UNIT_T;
83 return FIFF_UNIT_NONE;
84}
85
86//=========================================================================================================
87int bidsUnitToFiffUnitMul(const QString& sUnit)
88{
89 QString u = sUnit.toLower().trimmed();
90 if(u == "\u00B5v" || u == "uv" || u == "\u00B5s" || u == "us")
91 return FIFF_UNITM_MU;
92 if(u == "mv")
93 return FIFF_UNITM_M;
94 if(u == "nv")
95 return FIFF_UNITM_N;
96 if(u == "ft")
97 return FIFF_UNITM_F;
98 if(u == "pt")
99 return FIFF_UNITM_P;
100 return FIFF_UNITM_NONE;
101}
102
103//=========================================================================================================
104void applyChannelsTsv(FiffInfo& info, const QList<BidsChannel>& channels)
105{
106 if(channels.isEmpty())
107 return;
108
109 QMap<QString, int> bidsToFiff = bidsTypeToFiffKind();
110
111 QMap<QString, const BidsChannel*> channelMap;
112 for(const auto& ch : channels)
113 channelMap[ch.name] = &ch;
114
115 info.bads.clear();
116
117 for(int i = 0; i < info.chs.size(); ++i) {
118 FiffChInfo& fiffCh = info.chs[i];
119 auto it = channelMap.find(fiffCh.ch_name);
120 if(it == channelMap.end())
121 continue;
122 const BidsChannel* rec = it.value();
123
124 QString typeUpper = rec->type.toUpper();
125 if(bidsToFiff.contains(typeUpper))
126 fiffCh.kind = bidsToFiff[typeUpper];
127
128 if(!rec->units.isEmpty() && rec->units != "n/a") {
129 fiffCh.unit = bidsUnitToFiffUnit(rec->units);
130 fiffCh.unit_mul = bidsUnitToFiffUnitMul(rec->units);
131 }
132
133 if(rec->status.toLower() == "bad")
134 info.bads.append(fiffCh.ch_name);
135 }
136}
137
138//=========================================================================================================
139void applyElectrodePositions(FiffInfo& info,
140 const QList<BidsElectrode>& electrodes,
141 const QString& coordSystemName,
142 const QString& coordUnits)
143{
144 if(electrodes.isEmpty())
145 return;
146
147 QMap<QString, int> coordMap = bidsCoordToFiffFrame();
148 int coordFrame = FIFFV_COORD_UNKNOWN;
149 if(coordMap.contains(coordSystemName))
150 coordFrame = coordMap[coordSystemName];
151
152 float scaleFactor = 1.0f;
153 QString units = coordUnits.toLower();
154 if(units == "mm")
155 scaleFactor = 0.001f;
156 else if(units == "cm")
157 scaleFactor = 0.01f;
158
159 QSet<QString> chNames;
160 for(const auto& ch : info.chs)
161 chNames.insert(ch.ch_name);
162
163 info.dig.clear();
164 int ident = 1;
165 for(const auto& elec : electrodes) {
166 if(elec.x == "n/a" || elec.y == "n/a" || elec.z == "n/a")
167 continue;
168
169 FiffDigPoint dp;
170 dp.kind = chNames.contains(elec.name) ? FIFFV_POINT_EEG : FIFFV_POINT_EXTRA;
171 dp.ident = ident++;
172 dp.r[0] = elec.x.toFloat() * scaleFactor;
173 dp.r[1] = elec.y.toFloat() * scaleFactor;
174 dp.r[2] = elec.z.toFloat() * scaleFactor;
175 dp.coord_frame = coordFrame;
176
177 info.dig.append(dp);
178 }
179}
180
181//=========================================================================================================
182QJsonObject readJsonFile(const QString& sFilePath)
183{
184 QFile file(sFilePath);
185 if(!file.open(QIODevice::ReadOnly | QIODevice::Text))
186 return {};
187 QJsonParseError error;
188 QJsonDocument doc = QJsonDocument::fromJson(file.readAll(), &error);
189 file.close();
190 if(error.error != QJsonParseError::NoError)
191 return {};
192 return doc.object();
193}
194
195//=========================================================================================================
196bool writeJsonFile(const QString& sFilePath, const QJsonObject& json)
197{
198 QFile file(sFilePath);
199 if(!file.open(QIODevice::WriteOnly | QIODevice::Text))
200 return false;
201 file.write(QJsonDocument(json).toJson(QJsonDocument::Indented));
202 file.close();
203 return true;
204}
205
206//=========================================================================================================
207void readSidecarJson(const QString& sFilePath,
208 FiffInfo& info,
209 BidsRawData& data)
210{
211 QJsonObject json = readJsonFile(sFilePath);
212 if(json.isEmpty())
213 return;
214
215 // Apply to FiffInfo
216 double plf = json.value(QStringLiteral("PowerLineFrequency")).toDouble();
217 if(plf > 0.0)
218 info.linefreq = static_cast<float>(plf);
219
220 double sf = json.value(QStringLiteral("SamplingFrequency")).toDouble();
221 if(sf > 0.0 && std::abs(info.sfreq - static_cast<float>(sf)) > 0.5f)
222 qWarning() << "[BidsRawData::read] Sampling frequency mismatch: raw ="
223 << info.sfreq << "sidecar =" << sf;
224
225 // Store independent metadata fields on BidsRawData
226 data.ieegReference = json.value(QStringLiteral("iEEGReference")).toString();
227 data.taskDescription = json.value(QStringLiteral("TaskDescription")).toString();
228 data.manufacturer = json.value(QStringLiteral("Manufacturer")).toString();
229 data.manufacturerModelName = json.value(QStringLiteral("ManufacturerModelName")).toString();
230 data.softwareVersions = json.value(QStringLiteral("SoftwareVersions")).toString();
231 data.recordingType = json.value(QStringLiteral("RecordingType")).toString();
232}
233
234//=============================================================================================================
235// ANONYMOUS HELPERS — write side
236//=============================================================================================================
237
238//=========================================================================================================
239QString fiffUnitToBidsString(int unit, int unitMul)
240{
241 if(unit == FIFF_UNIT_V) {
242 switch(unitMul) {
243 case FIFF_UNITM_MU: return QStringLiteral("\u00B5V");
244 case FIFF_UNITM_M: return QStringLiteral("mV");
245 case FIFF_UNITM_N: return QStringLiteral("nV");
246 default: return QStringLiteral("V");
247 }
248 }
249 if(unit == FIFF_UNIT_T) {
250 switch(unitMul) {
251 case FIFF_UNITM_F: return QStringLiteral("fT");
252 case FIFF_UNITM_P: return QStringLiteral("pT");
253 default: return QStringLiteral("T");
254 }
255 }
256 return QStringLiteral("n/a");
257}
258
259//=========================================================================================================
260QString channelTypeDescription(int kind)
261{
262 switch(kind) {
263 case FIFFV_EEG_CH: return QStringLiteral("ElectroEncephaloGram");
264 case FIFFV_ECOG_CH: return QStringLiteral("Electrocorticography");
265 case FIFFV_SEEG_CH: return QStringLiteral("StereoElectroEncephaloGram");
266 case FIFFV_DBS_CH: return QStringLiteral("DeepBrainStimulation");
267 case FIFFV_MEG_CH: return QStringLiteral("MagnetoEncephaloGram");
268 case FIFFV_STIM_CH: return QStringLiteral("Trigger");
269 case FIFFV_EOG_CH: return QStringLiteral("ElectroOculoGram");
270 case FIFFV_ECG_CH: return QStringLiteral("ElectroCardioGram");
271 case FIFFV_EMG_CH: return QStringLiteral("ElectroMyoGram");
272 case FIFFV_MISC_CH: return QStringLiteral("Miscellaneous");
273 case FIFFV_RESP_CH: return QStringLiteral("Respiration");
274 default: return QStringLiteral("n/a");
275 }
276}
277
278//=========================================================================================================
279QList<BidsChannel> buildChannelRecords(const FiffInfo& info)
280{
281 QList<BidsChannel> records;
282 QMap<int, QString> kindMap = fiffKindToBidsType();
283 QSet<QString> badsSet(info.bads.begin(), info.bads.end());
284
285 for(int i = 0; i < info.chs.size(); ++i) {
286 const FiffChInfo& ch = info.chs[i];
287
288 BidsChannel rec;
289 rec.name = ch.ch_name;
290 rec.type = kindMap.contains(ch.kind) ? kindMap[ch.kind] : QStringLiteral("MISC");
291 rec.units = fiffUnitToBidsString(ch.unit, ch.unit_mul);
292 rec.samplingFreq = QString::number(static_cast<double>(info.sfreq), 'g', 10);
293 rec.lowCutoff = (info.highpass > 0.0f)
294 ? QString::number(static_cast<double>(info.highpass), 'g', 10)
295 : QStringLiteral("n/a");
296 rec.highCutoff = (info.lowpass > 0.0f)
297 ? QString::number(static_cast<double>(info.lowpass), 'g', 10)
298 : QStringLiteral("n/a");
299 rec.notch = QStringLiteral("n/a");
300 rec.status = badsSet.contains(ch.ch_name) ? QStringLiteral("bad") : QStringLiteral("good");
301 rec.description = channelTypeDescription(ch.kind);
302
303 records.append(rec);
304 }
305 return records;
306}
307
308//=========================================================================================================
309QList<BidsElectrode> buildElectrodeRecords(const FiffInfo& info)
310{
311 QList<BidsElectrode> records;
312
313 QMap<int, const FiffDigPoint*> digByIdent;
314 for(const auto& dp : info.dig) {
315 if(dp.kind == FIFFV_POINT_EEG || dp.kind == FIFFV_POINT_EXTRA)
316 digByIdent[dp.ident] = &dp;
317 }
318
319 int digIdx = 0;
320
321 for(int i = 0; i < info.chs.size(); ++i) {
322 const FiffChInfo& ch = info.chs[i];
323
324 if(ch.kind == FIFFV_STIM_CH)
325 continue;
326 if(ch.kind != FIFFV_EEG_CH && ch.kind != FIFFV_ECOG_CH &&
327 ch.kind != FIFFV_SEEG_CH && ch.kind != FIFFV_DBS_CH)
328 continue;
329
330 BidsElectrode rec;
331 rec.name = ch.ch_name;
332
333 ++digIdx;
334 bool hasPosition = false;
335
336 if(digByIdent.contains(digIdx)) {
337 const FiffDigPoint* dp = digByIdent[digIdx];
338 if(std::isfinite(dp->r[0]) && std::isfinite(dp->r[1]) && std::isfinite(dp->r[2])) {
339 rec.x = QString::number(static_cast<double>(dp->r[0]), 'g', 8);
340 rec.y = QString::number(static_cast<double>(dp->r[1]), 'g', 8);
341 rec.z = QString::number(static_cast<double>(dp->r[2]), 'g', 8);
342 hasPosition = true;
343 }
344 }
345
346 if(!hasPosition) {
347 const Eigen::Vector3f& r0 = ch.chpos.r0;
348 if(r0.squaredNorm() > 0.0f && std::isfinite(r0[0])) {
349 rec.x = QString::number(static_cast<double>(r0[0]), 'g', 8);
350 rec.y = QString::number(static_cast<double>(r0[1]), 'g', 8);
351 rec.z = QString::number(static_cast<double>(r0[2]), 'g', 8);
352 } else {
353 rec.x = QStringLiteral("n/a");
354 rec.y = QStringLiteral("n/a");
355 rec.z = QStringLiteral("n/a");
356 }
357 }
358
359 rec.size = QStringLiteral("n/a");
360 rec.type = QStringLiteral("n/a");
361 rec.material = QStringLiteral("n/a");
362 rec.impedance = QStringLiteral("n/a");
363
364 records.append(rec);
365 }
366 return records;
367}
368
369//=========================================================================================================
370QJsonObject buildIeegSidecarJson(const BidsRawData& data,
371 const BIDSPath& bidsPath)
372{
373 QJsonObject json;
374 const FiffInfo& info = data.raw.info;
375
376 // Required
377 json[QStringLiteral("TaskName")] = bidsPath.task();
378 json[QStringLiteral("SamplingFrequency")] = static_cast<double>(info.sfreq);
379 json[QStringLiteral("PowerLineFrequency")] = static_cast<double>(info.linefreq);
380
381 // Reference
382 if(!data.ieegReference.isEmpty())
383 json[QStringLiteral("iEEGReference")] = data.ieegReference;
384 else
385 json[QStringLiteral("iEEGReference")] = QStringLiteral("n/a");
386
387 // Channel counts — computed from FiffInfo
388 int ecog = 0, seeg = 0, dbs = 0, eeg = 0, eog = 0, ecg = 0, emg = 0, misc = 0, trig = 0;
389 for(const auto& ch : info.chs) {
390 switch(ch.kind) {
391 case FIFFV_ECOG_CH: ++ecog; break;
392 case FIFFV_SEEG_CH: ++seeg; break;
393 case FIFFV_DBS_CH: ++dbs; break;
394 case FIFFV_EEG_CH: ++eeg; break;
395 case FIFFV_EOG_CH: ++eog; break;
396 case FIFFV_ECG_CH: ++ecg; break;
397 case FIFFV_EMG_CH: ++emg; break;
398 case FIFFV_MISC_CH: ++misc; break;
399 case FIFFV_STIM_CH: ++trig; break;
400 default: break;
401 }
402 }
403 json[QStringLiteral("ECOGChannelCount")] = ecog;
404 json[QStringLiteral("SEEGChannelCount")] = seeg;
405 if(dbs > 0) json[QStringLiteral("DBSChannelCount")] = dbs;
406 if(eeg > 0) json[QStringLiteral("EEGChannelCount")] = eeg;
407 if(eog > 0) json[QStringLiteral("EOGChannelCount")] = eog;
408 if(ecg > 0) json[QStringLiteral("ECGChannelCount")] = ecg;
409 if(emg > 0) json[QStringLiteral("EMGChannelCount")] = emg;
410 if(misc > 0) json[QStringLiteral("MiscChannelCount")] = misc;
411 if(trig > 0) json[QStringLiteral("TriggerChannelCount")] = trig;
412
413 // Recording metadata
414 if(!data.recordingType.isEmpty())
415 json[QStringLiteral("RecordingType")] = data.recordingType;
416 else
417 json[QStringLiteral("RecordingType")] = QStringLiteral("continuous");
418
419 if(info.sfreq > 0.0f && data.raw.last_samp >= data.raw.first_samp) {
420 double dur = static_cast<double>(data.raw.last_samp - data.raw.first_samp + 1)
421 / static_cast<double>(info.sfreq);
422 json[QStringLiteral("RecordingDuration")] = dur;
423 }
424
425 // Optional strings from BidsRawData
426 if(!data.taskDescription.isEmpty())
427 json[QStringLiteral("TaskDescription")] = data.taskDescription;
428 if(!data.manufacturer.isEmpty())
429 json[QStringLiteral("Manufacturer")] = data.manufacturer;
430 if(!data.manufacturerModelName.isEmpty())
431 json[QStringLiteral("ManufacturerModelName")] = data.manufacturerModelName;
432 if(!data.softwareVersions.isEmpty())
433 json[QStringLiteral("SoftwareVersions")] = data.softwareVersions;
434
435 return json;
436}
437
438//=========================================================================================================
439bool copyFile(const QString& src, const QString& dst, bool overwrite)
440{
441 if(!QFileInfo::exists(src)) {
442 qWarning() << "[BidsRawData::write] Source file does not exist:" << src;
443 return false;
444 }
445 if(QFileInfo::exists(dst)) {
446 if(!overwrite) {
447 qWarning() << "[BidsRawData::write] Target file already exists:" << dst;
448 return false;
449 }
450 QFile::remove(dst);
451 }
452 return QFile::copy(src, dst);
453}
454
455//=========================================================================================================
456bool copyBrainVisionFiles(const QString& srcVhdr, const BIDSPath& bidsPath, bool overwrite)
457{
458 QFileInfo srcInfo(srcVhdr);
459 QString srcDir = srcInfo.absolutePath();
460
461 QFile vhdrFile(srcVhdr);
462 if(!vhdrFile.open(QIODevice::ReadOnly | QIODevice::Text)) {
463 qWarning() << "[BidsRawData::write] Cannot open .vhdr file:" << srcVhdr;
464 return false;
465 }
466
467 QString dataFileName;
468 QString markerFileName;
469 QByteArray vhdrContent = vhdrFile.readAll();
470 vhdrFile.close();
471
472 for(const auto& line : vhdrContent.split('\n')) {
473 QString sLine = QString::fromUtf8(line).trimmed();
474 if(sLine.startsWith("DataFile=", Qt::CaseInsensitive))
475 dataFileName = sLine.mid(9).trimmed();
476 else if(sLine.startsWith("MarkerFile=", Qt::CaseInsensitive))
477 markerFileName = sLine.mid(11).trimmed();
478 }
479
480 QString dstDir = bidsPath.directory();
481 QString dstBase = bidsPath.basename();
482 dstBase = dstBase.left(dstBase.lastIndexOf('.'));
483
484 QString dstVhdr = bidsPath.filePath();
485 QString newDataFile = dstBase + QStringLiteral(".eeg");
486 QString newMarkerFile = dstBase + QStringLiteral(".vmrk");
487
488 QString vhdrStr = QString::fromUtf8(vhdrContent);
489 if(!dataFileName.isEmpty())
490 vhdrStr.replace("DataFile=" + dataFileName,
491 "DataFile=" + QFileInfo(newDataFile).fileName());
492 if(!markerFileName.isEmpty())
493 vhdrStr.replace("MarkerFile=" + markerFileName,
494 "MarkerFile=" + QFileInfo(newMarkerFile).fileName());
495
496 if(QFileInfo::exists(dstVhdr) && !overwrite) {
497 qWarning() << "[BidsRawData::write] Target file already exists:" << dstVhdr;
498 return false;
499 }
500 if(QFileInfo::exists(dstVhdr))
501 QFile::remove(dstVhdr);
502
503 QFile dstVhdrFile(dstVhdr);
504 if(!dstVhdrFile.open(QIODevice::WriteOnly | QIODevice::Text)) {
505 qWarning() << "[BidsRawData::write] Cannot write .vhdr file:" << dstVhdr;
506 return false;
507 }
508 dstVhdrFile.write(vhdrStr.toUtf8());
509 dstVhdrFile.close();
510
511 if(!dataFileName.isEmpty()) {
512 QString srcData = QDir(srcDir).absoluteFilePath(dataFileName);
513 QString dstData = dstDir + QFileInfo(newDataFile).fileName();
514 if(!copyFile(srcData, dstData, overwrite)) {
515 qWarning() << "[BidsRawData::write] Failed to copy data file:" << srcData;
516 return false;
517 }
518 }
519
520 if(!markerFileName.isEmpty()) {
521 QString srcMarker = QDir(srcDir).absoluteFilePath(markerFileName);
522 QString dstMarker = dstDir + QFileInfo(newMarkerFile).fileName();
523
524 if(QFileInfo::exists(srcMarker)) {
525 QFile markerFile(srcMarker);
526 if(markerFile.open(QIODevice::ReadOnly | QIODevice::Text)) {
527 QString markerContent = QString::fromUtf8(markerFile.readAll());
528 markerFile.close();
529
530 markerContent.replace("DataFile=" + dataFileName,
531 "DataFile=" + QFileInfo(newDataFile).fileName());
532
533 if(QFileInfo::exists(dstMarker)) {
534 if(!overwrite) {
535 qWarning() << "[BidsRawData::write] Target marker file already exists:" << dstMarker;
536 return false;
537 }
538 QFile::remove(dstMarker);
539 }
540
541 QFile dstMarkerFile(dstMarker);
542 if(dstMarkerFile.open(QIODevice::WriteOnly | QIODevice::Text)) {
543 dstMarkerFile.write(markerContent.toUtf8());
544 dstMarkerFile.close();
545 }
546 }
547 }
548 }
549
550 return true;
551}
552
553//=========================================================================================================
554bool copyRawDataFile(const QString& sourcePath, const BIDSPath& bidsPath, bool overwrite)
555{
556 if(sourcePath.isEmpty())
557 return true;
558
559 QString ext = bidsPath.extension().toLower();
560 if(ext == ".vhdr" || ext == ".ahdr")
561 return copyBrainVisionFiles(sourcePath, bidsPath, overwrite);
562
563 return copyFile(sourcePath, bidsPath.filePath(), overwrite);
564}
565
566} // anonymous namespace
567
568//=============================================================================================================
569// MEMBER METHODS
570//=============================================================================================================
571
572BidsRawData::BidsRawData(BidsRawData&& other) noexcept
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{
587 other.m_bIsValid = false;
588}
589
590//=============================================================================================================
591
592BidsRawData& BidsRawData::operator=(BidsRawData&& other) noexcept
593{
594 if(this != &other) {
595 raw = other.raw; // FiffRawData has only copy ctor
596 events = std::move(other.events);
597 eventIdMap = std::move(other.eventIdMap);
598 electrodes = std::move(other.electrodes);
599 coordinateSystem = std::move(other.coordinateSystem);
600 reader = std::move(other.reader);
601 ieegReference = std::move(other.ieegReference);
602 taskDescription = std::move(other.taskDescription);
603 manufacturer = std::move(other.manufacturer);
604 manufacturerModelName = std::move(other.manufacturerModelName);
605 softwareVersions = std::move(other.softwareVersions);
606 recordingType = std::move(other.recordingType);
607 m_bIsValid = other.m_bIsValid;
608 other.m_bIsValid = false;
609 }
610 return *this;
611}
612
613//=============================================================================================================
614
615void BidsRawData::clear()
616{
617 raw = FiffRawData();
618 events.clear();
619 eventIdMap.clear();
620 electrodes.clear();
621 reader.reset();
622
623 ieegReference.clear();
624 taskDescription.clear();
625 manufacturer.clear();
626 manufacturerModelName.clear();
627 softwareVersions.clear();
628 recordingType.clear();
629
630 coordinateSystem = BidsCoordinateSystem();
631
632 m_bIsValid = false;
633}
634
635//=============================================================================================================
636
637AbstractFormatReader::UPtr BidsRawData::createReader(const QString& sExtension)
638{
639 QString ext = sExtension.toLower();
640 if(ext == ".vhdr" || ext == ".ahdr")
641 return std::make_unique<BrainVisionReader>();
642 if(ext == ".edf" || ext == ".bdf")
643 return std::make_unique<EDFReader>();
644 return nullptr;
645}
646
647//=============================================================================================================
648// BidsRawData::read()
649//=============================================================================================================
650
651BidsRawData BidsRawData::read(const BIDSPath& bidsPath)
652{
653 BidsRawData result;
654
655 //=========================================================================================================
656 // Step 1 — Validate BIDSPath
657 //=========================================================================================================
658 if(bidsPath.root().isEmpty()) {
659 qWarning() << "[BidsRawData::read] BIDSPath root is not set";
660 return result;
661 }
662 if(bidsPath.subject().isEmpty()) {
663 qWarning() << "[BidsRawData::read] BIDSPath subject is not set";
664 return result;
665 }
666 if(bidsPath.extension().isEmpty()) {
667 qWarning() << "[BidsRawData::read] BIDSPath extension is not set";
668 return result;
669 }
670
671 //=========================================================================================================
672 // Step 2 — Resolve raw file path
673 //=========================================================================================================
674 QString rawFilePath = bidsPath.filePath();
675
676 if(!QFileInfo::exists(rawFilePath)) {
677 QString ext = bidsPath.extension();
678 if(ext.toLower() == ".edf") {
679 BIDSPath altPath(bidsPath);
680 altPath.setExtension(".EDF");
681 if(QFileInfo::exists(altPath.filePath()))
682 rawFilePath = altPath.filePath();
683 }
684 }
685
686 if(!QFileInfo::exists(rawFilePath)) {
687 qWarning() << "[BidsRawData::read] Raw data file not found:" << rawFilePath;
688 return result;
689 }
690
691 //=========================================================================================================
692 // Step 3 — Create and open the format reader
693 //=========================================================================================================
694 result.reader = createReader(bidsPath.extension());
695 if(!result.reader) {
696 qWarning() << "[BidsRawData::read] Unsupported file extension:" << bidsPath.extension();
697 return result;
698 }
699
700 if(!result.reader->open(rawFilePath)) {
701 qWarning() << "[BidsRawData::read] Failed to open raw file:" << rawFilePath;
702 return result;
703 }
704
705 //=========================================================================================================
706 // Step 4 — Build FiffRawData from the reader
707 //=========================================================================================================
708 result.raw = result.reader->toFiffRawData();
709
710 //=========================================================================================================
711 // Step 5 — Read and apply *_channels.tsv
712 //=========================================================================================================
713 BIDSPath channelsPath = bidsPath.channelsTsvPath();
714 if(QFileInfo::exists(channelsPath.filePath())) {
715 QList<BidsChannel> channels = BidsChannel::readTsv(channelsPath.filePath());
716 applyChannelsTsv(result.raw.info, channels);
717 }
718
719 //=========================================================================================================
720 // Step 6 — Read *_coordsystem.json (before electrodes, for scale/frame info)
721 //=========================================================================================================
722 BIDSPath coordsysPath = bidsPath.coordsystemJsonPath();
723 if(QFileInfo::exists(coordsysPath.filePath()))
724 result.coordinateSystem = BidsCoordinateSystem::readJson(coordsysPath.filePath());
725
726 //=========================================================================================================
727 // Step 7 — Read and apply *_electrodes.tsv
728 //=========================================================================================================
729 BIDSPath electrodesPath = bidsPath.electrodesTsvPath();
730 if(QFileInfo::exists(electrodesPath.filePath())) {
731 result.electrodes = BidsElectrode::readTsv(electrodesPath.filePath());
732 applyElectrodePositions(result.raw.info, result.electrodes,
733 result.coordinateSystem.system, result.coordinateSystem.units);
734 }
735
736 //=========================================================================================================
737 // Step 8 — Read *_events.tsv
738 //=========================================================================================================
739 BIDSPath eventsPath = bidsPath.eventsTsvPath();
740 if(QFileInfo::exists(eventsPath.filePath())) {
741 result.events = BidsEvent::readTsv(eventsPath.filePath());
742
743 // Compute sample from onset*sfreq if sample column was absent
744 float sfreq = result.raw.info.sfreq;
745 for(auto& ev : result.events) {
746 if(ev.sample == 0 && ev.onset > 0.0f && sfreq > 0)
747 ev.sample = static_cast<int>(ev.onset * sfreq);
748 }
749
750 // Build eventIdMap from trial_type → value
751 for(const auto& ev : result.events) {
752 if(!ev.trialType.isEmpty() && ev.trialType != "n/a")
753 result.eventIdMap.insert(ev.trialType, ev.value);
754 }
755 }
756
757 //=========================================================================================================
758 // Step 9 — Read sidecar *_{datatype}.json
759 //=========================================================================================================
760 BIDSPath sidecarPath = bidsPath.sidecarJsonPath();
761 if(QFileInfo::exists(sidecarPath.filePath()))
762 readSidecarJson(sidecarPath.filePath(), result.raw.info, result);
763
764 //=========================================================================================================
765 // Done
766 //=========================================================================================================
767 result.m_bIsValid = true;
768 return result;
769}
770
771//=============================================================================================================
772// BidsRawData::write()
773//=============================================================================================================
774
775BIDSPath BidsRawData::write(const BIDSPath& bidsPath,
776 const QString& sourcePath,
777 const WriteOptions& options) const
778{
779 BIDSPath result;
780
781 //=========================================================================================================
782 // Step 1 — Validate
783 //=========================================================================================================
784 if(bidsPath.root().isEmpty()) {
785 qWarning() << "[BidsRawData::write] BIDSPath root is not set";
786 return result;
787 }
788 if(bidsPath.subject().isEmpty()) {
789 qWarning() << "[BidsRawData::write] BIDSPath subject is not set";
790 return result;
791 }
792 if(bidsPath.task().isEmpty()) {
793 qWarning() << "[BidsRawData::write] BIDSPath task is not set";
794 return result;
795 }
796 if(bidsPath.datatype().isEmpty()) {
797 qWarning() << "[BidsRawData::write] BIDSPath datatype is not set";
798 return result;
799 }
800 if(raw.info.isEmpty()) {
801 qWarning() << "[BidsRawData::write] FiffRawData info is empty";
802 return result;
803 }
804
805 //=========================================================================================================
806 // Step 2 — Create directory structure
807 //=========================================================================================================
808 if(!bidsPath.mkdirs()) {
809 qWarning() << "[BidsRawData::write] Failed to create directory:" << bidsPath.directory();
810 return result;
811 }
812
813 //=========================================================================================================
814 // Step 3 — Copy raw data file
815 //=========================================================================================================
816 if(options.copyData && !sourcePath.isEmpty()) {
817 if(!copyRawDataFile(sourcePath, bidsPath, options.overwrite)) {
818 qWarning() << "[BidsRawData::write] Failed to copy raw data file";
819 return result;
820 }
821 }
822
823 //=========================================================================================================
824 // Step 4 — Write *_channels.tsv
825 //=========================================================================================================
826 {
827 BIDSPath channelsPath = bidsPath.channelsTsvPath();
828 if(!options.overwrite && QFileInfo::exists(channelsPath.filePath())) {
829 qWarning() << "[BidsRawData::write] channels.tsv already exists:" << channelsPath.filePath();
830 return result;
831 }
832
833 QList<BidsChannel> channelRecords = buildChannelRecords(raw.info);
834 if(!BidsChannel::writeTsv(channelsPath.filePath(), channelRecords)) {
835 qWarning() << "[BidsRawData::write] Failed to write channels.tsv";
836 return result;
837 }
838 }
839
840 //=========================================================================================================
841 // Step 5 — Write *_electrodes.tsv + *_coordsystem.json
842 //=========================================================================================================
843 {
844 QList<BidsElectrode> electrodeRecords = buildElectrodeRecords(raw.info);
845
846 if(!electrodeRecords.isEmpty()) {
847 BIDSPath electrodesPath = bidsPath.electrodesTsvPath();
848 if(options.overwrite || !QFileInfo::exists(electrodesPath.filePath())) {
849 if(!BidsElectrode::writeTsv(electrodesPath.filePath(), electrodeRecords))
850 qWarning() << "[BidsRawData::write] Failed to write electrodes.tsv";
851 }
852
853 BIDSPath coordsysPath = bidsPath.coordsystemJsonPath();
854 if(options.overwrite || !QFileInfo::exists(coordsysPath.filePath())) {
855 // Build coordinate system, deriving defaults from FiffInfo if needed
856 BidsCoordinateSystem cs = coordinateSystem;
857 if(cs.system.isEmpty()) {
858 if(raw.info.dig.isEmpty()) {
859 cs.system = QStringLiteral("Other");
860 cs.units = QStringLiteral("n/a");
861 } else {
862 int coordFrame = raw.info.dig.first().coord_frame;
863 QMap<int, QString> frameMap = fiffFrameToBidsCoord();
864 cs.system = frameMap.contains(coordFrame)
865 ? frameMap[coordFrame]
866 : QStringLiteral("Other");
867 cs.units = QStringLiteral("m");
868 }
869 }
870 if(cs.description.isEmpty() && !raw.info.dig.isEmpty())
871 cs.description = QStringLiteral("Coordinate system derived from recording data");
872
873 if(!BidsCoordinateSystem::writeJson(coordsysPath.filePath(), cs))
874 qWarning() << "[BidsRawData::write] Failed to write coordsystem.json";
875 }
876 }
877 }
878
879 //=========================================================================================================
880 // Step 6 — Write *_events.tsv
881 //=========================================================================================================
882 if(!events.isEmpty()) {
883 BIDSPath eventsPath = bidsPath.eventsTsvPath();
884 if(!options.overwrite && QFileInfo::exists(eventsPath.filePath())) {
885 qWarning() << "[BidsRawData::write] events.tsv already exists:" << eventsPath.filePath();
886 return result;
887 }
888
889 QList<BidsEvent> eventsToWrite = events;
890
891 // Apply trial_type fallback from eventIdMap
892 QMap<int, QString> valueToType;
893 for(auto it = eventIdMap.constBegin(); it != eventIdMap.constEnd(); ++it)
894 valueToType[it.value()] = it.key();
895 for(auto& ev : eventsToWrite) {
896 if(ev.trialType.isEmpty() || ev.trialType == "n/a")
897 ev.trialType = valueToType.value(ev.value, QStringLiteral("n/a"));
898 }
899
900 if(!BidsEvent::writeTsv(eventsPath.filePath(), eventsToWrite))
901 qWarning() << "[BidsRawData::write] Failed to write events.tsv";
902 }
903
904 //=========================================================================================================
905 // Step 7 — Write *_{datatype}.json sidecar
906 //=========================================================================================================
907 {
908 BIDSPath sidecarPath = bidsPath.sidecarJsonPath();
909 if(!options.overwrite && QFileInfo::exists(sidecarPath.filePath())) {
910 qWarning() << "[BidsRawData::write] Sidecar JSON already exists:" << sidecarPath.filePath();
911 return result;
912 }
913
914 QJsonObject sidecarJson = buildIeegSidecarJson(*this, bidsPath);
915 if(!writeJsonFile(sidecarPath.filePath(), sidecarJson)) {
916 qWarning() << "[BidsRawData::write] Failed to write sidecar JSON";
917 return result;
918 }
919 }
920
921 //=========================================================================================================
922 // Step 8 — Write dataset_description.json (never overwrite)
923 //=========================================================================================================
924 {
925 QString descPath = bidsPath.root() + QDir::separator()
926 + QStringLiteral("dataset_description.json");
927
928 if(!QFileInfo::exists(descPath)) {
929 BidsDatasetDescription desc;
930 desc.name = options.datasetName.isEmpty()
931 ? QStringLiteral("[Unspecified]")
932 : options.datasetName;
933 desc.bidsVersion = QStringLiteral("1.9.0");
934 desc.datasetType = QStringLiteral("raw");
935
936 if(!BidsDatasetDescription::write(descPath, desc))
937 qWarning() << "[BidsRawData::write] Failed to write dataset_description.json";
938 }
939 }
940
941 //=========================================================================================================
942 // Done
943 //=========================================================================================================
944 result = bidsPath;
945 return result;
946}
fiff_constants.h
Fiff constants.
FIFFV_POINT_EXTRA
#define FIFFV_POINT_EXTRA
Definition fiff_constants.h:305
FIFFV_EOG_CH
#define FIFFV_EOG_CH
Definition fiff_constants.h:271
FIFFV_SEEG_CH
#define FIFFV_SEEG_CH
Definition fiff_constants.h:281
FIFFV_EEG_CH
#define FIFFV_EEG_CH
Definition fiff_constants.h:268
FIFF_UNIT_NONE
#define FIFF_UNIT_NONE
Definition fiff_constants.h:87
FIFFV_RESP_CH
#define FIFFV_RESP_CH
Definition fiff_constants.h:275
FIFFV_MISC_CH
#define FIFFV_MISC_CH
Definition fiff_constants.h:274
FIFF_UNIT_V
#define FIFF_UNIT_V
Definition fiff_constants.h:119
FIFFV_MEG_CH
#define FIFFV_MEG_CH
Definition fiff_constants.h:265
FIFF_UNITM_NONE
#define FIFF_UNITM_NONE
Definition fiff_constants.h:148
FIFFV_ECOG_CH
#define FIFFV_ECOG_CH
Definition fiff_constants.h:280
FIFF_UNITM_N
#define FIFF_UNITM_N
Definition fiff_constants.h:153
FIFF_UNITM_F
#define FIFF_UNITM_F
Definition fiff_constants.h:155
FIFFV_POINT_EEG
#define FIFFV_POINT_EEG
Definition fiff_constants.h:303
FIFF_UNITM_M
#define FIFF_UNITM_M
Definition fiff_constants.h:151
FIFFV_STIM_CH
#define FIFFV_STIM_CH
Definition fiff_constants.h:269
FIFF_UNITM_P
#define FIFF_UNITM_P
Definition fiff_constants.h:154
FIFFV_COORD_UNKNOWN
#define FIFFV_COORD_UNKNOWN
Definition fiff_constants.h:212
FIFF_UNIT_T
#define FIFF_UNIT_T
Definition fiff_constants.h:124
FIFFV_EMG_CH
#define FIFFV_EMG_CH
Definition fiff_constants.h:272
FIFFV_ECG_CH
#define FIFFV_ECG_CH
Definition fiff_constants.h:273
FIFFV_DBS_CH
#define FIFFV_DBS_CH
Definition fiff_constants.h:282
FIFF_UNITM_MU
#define FIFF_UNITM_MU
Definition fiff_constants.h:152
bids_brain_vision_reader.h
Contains the declaration of the BrainVisionReader class.
bids_edf_reader.h
Contains the declaration of the EDFReader class. Refactored from the mne_edf2fiff tool into a reusabl...
bids_const.h
BIDS constants, channel type mappings, and allowed values.
bids_raw_data.h
BidsRawData class declaration — central container for a BIDS raw dataset with integrated read/write c...
bids_dataset_description.h
BidsDatasetDescription struct — dataset_description.json I/O.
bids_channel.h
BidsChannel struct — channel metadata from *_channels.tsv.
BIDSLIB
BIDS dataset reading, writing, path construction, and sidecar metadata handling for iEEG/EEG/MEG.
Definition bids_channel.h:56
BIDSLIB::fiffKindToBidsType
QMap< int, QString > fiffKindToBidsType()
Definition bids_const.h:112
BIDSLIB::bidsCoordToFiffFrame
QMap< QString, int > bidsCoordToFiffFrame()
Definition bids_const.h:161
BIDSLIB::bidsTypeToFiffKind
QMap< QString, int > bidsTypeToFiffKind()
Definition bids_const.h:134
BIDSLIB::fiffFrameToBidsCoord
QMap< int, QString > fiffFrameToBidsCoord()
Definition bids_const.h:178
FIFFLIB
FIFF file I/O and data structures (raw, epochs, evoked, covariance, forward).
Definition connectivitysettings.h:71
BIDSLIB::BidsChannel
Channel metadata record corresponding to one row in *_channels.tsv.
Definition bids_channel.h:63
BIDSLIB::BidsChannel::readTsv
static QList< BidsChannel > readTsv(const QString &sFilePath)
Read a BIDS *_channels.tsv file.
Definition bids_channel.cpp:66
BIDSLIB::BidsChannel::writeTsv
static bool writeTsv(const QString &sFilePath, const QList< BidsChannel > &channels)
Write a BIDS *_channels.tsv file.
Definition bids_channel.cpp:93
BIDSLIB::BidsCoordinateSystem
Coordinate system metadata from *_coordsystem.json.
Definition bids_coordinate_system.h:64
BIDSLIB::BidsCoordinateSystem::writeJson
static bool writeJson(const QString &sFilePath, const BidsCoordinateSystem &cs)
Write a BIDS *_coordsystem.json file.
Definition bids_coordinate_system.cpp:92
BIDSLIB::BidsCoordinateSystem::readJson
static BidsCoordinateSystem readJson(const QString &sFilePath)
Read a BIDS *_coordsystem.json file.
Definition bids_coordinate_system.cpp:60
BIDSLIB::BidsDatasetDescription
Dataset-level metadata from dataset_description.json.
Definition bids_dataset_description.h:65
BIDSLIB::BidsDatasetDescription::write
static bool write(const QString &sFilePath, const BidsDatasetDescription &desc)
Write a dataset_description.json file.
Definition bids_dataset_description.cpp:91
BIDSLIB::BidsElectrode
Electrode position record corresponding to one row in *_electrodes.tsv.
Definition bids_electrode.h:63
BIDSLIB::BidsElectrode::writeTsv
static bool writeTsv(const QString &sFilePath, const QList< BidsElectrode > &electrodes)
Write a BIDS *_electrodes.tsv file.
Definition bids_electrode.cpp:92
BIDSLIB::BidsElectrode::readTsv
static QList< BidsElectrode > readTsv(const QString &sFilePath)
Read a BIDS *_electrodes.tsv file.
Definition bids_electrode.cpp:66
BIDSLIB::BidsEvent::readTsv
static QList< BidsEvent > readTsv(const QString &sFilePath)
Read a BIDS *_events.tsv file.
Definition bids_event.cpp:52
BIDSLIB::BidsEvent::writeTsv
static bool writeTsv(const QString &sFilePath, const QList< BidsEvent > &events)
Write a BIDS *_events.tsv file.
Definition bids_event.cpp:99
BIDSLIB::BIDSPath
BIDS-compliant path and filename construction.
Definition bids_path.h:92
BIDSLIB::BIDSPath::subject
QString subject() const
Definition bids_path.cpp:133
BIDSLIB::BIDSPath::filePath
QString filePath() const
Definition bids_path.cpp:210
BIDSLIB::BIDSPath::electrodesTsvPath
BIDSPath electrodesTsvPath() const
Definition bids_path.cpp:236
BIDSLIB::BIDSPath::root
QString root() const
Definition bids_path.cpp:132
BIDSLIB::BIDSPath::channelsTsvPath
BIDSPath channelsTsvPath() const
Definition bids_path.cpp:229
BIDSLIB::BIDSPath::directory
QString directory() const
Definition bids_path.cpp:192
BIDSLIB::BIDSPath::extension
QString extension() const
Definition bids_path.cpp:145
BIDSLIB::BIDSPath::basename
QString basename() const
Definition bids_path.cpp:151
BIDSLIB::BIDSPath::coordsystemJsonPath
BIDSPath coordsystemJsonPath() const
Definition bids_path.cpp:249
BIDSLIB::BIDSPath::task
QString task() const
Definition bids_path.cpp:135
BIDSLIB::BIDSPath::eventsTsvPath
BIDSPath eventsTsvPath() const
Definition bids_path.cpp:262
BIDSLIB::BIDSPath::setExtension
void setExtension(const QString &sExtension)
Definition bids_path.cpp:126
BIDSLIB::BIDSPath::mkdirs
bool mkdirs() const
Definition bids_path.cpp:284
BIDSLIB::BIDSPath::datatype
QString datatype() const
Definition bids_path.cpp:143
BIDSLIB::BIDSPath::sidecarJsonPath
BIDSPath sidecarJsonPath() const
Definition bids_path.cpp:269
BIDSLIB::BidsRawData
Central container for a BIDS raw dataset, bundling electrophysiological data with all associated side...
Definition bids_raw_data.h:99
BIDSLIB::BidsRawData::clear
void clear()
Clears all data members and resets to invalid state.
Definition bids_raw_data.cpp:615
BIDSLIB::BidsRawData::read
static BidsRawData read(const BIDSPath &bidsPath)
Read a BIDS dataset from disk.
Definition bids_raw_data.cpp:651
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:637
BIDSLIB::BidsRawData::raw
FIFFLIB::FiffRawData raw
Definition bids_raw_data.h:228
BIDSLIB::BidsRawData::reader
AbstractFormatReader::UPtr reader
Definition bids_raw_data.h:233
BIDSLIB::BidsRawData::eventIdMap
QMap< QString, int > eventIdMap
Definition bids_raw_data.h:230
BIDSLIB::BidsRawData::electrodes
QList< BidsElectrode > electrodes
Definition bids_raw_data.h:231
BIDSLIB::BidsRawData::operator=
BidsRawData & operator=(BidsRawData &&other) noexcept
Definition bids_raw_data.cpp:592
BIDSLIB::BidsRawData::events
QList< BidsEvent > events
Definition bids_raw_data.h:229
BIDSLIB::BidsRawData::coordinateSystem
BidsCoordinateSystem coordinateSystem
Definition bids_raw_data.h:232
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:775
BIDSLIB::BidsRawData::WriteOptions
Options controlling how write() operates.
Definition bids_raw_data.h:109
BIDSLIB::AbstractFormatReader::UPtr
std::unique_ptr< AbstractFormatReader > UPtr
Definition bids_abstract_format_reader.h:77
FIFFLIB::FiffChInfo
Channel info descriptor.
Definition fiff_ch_info.h:76
FIFFLIB::FiffChPos::r0
Eigen::Vector3f r0
Definition fiff_ch_pos.h:115
FIFFLIB::FiffDigPoint
Digitization point description.
Definition fiff_dig_point.h:70
FIFFLIB::FiffInfo
FIFF measurement file information.
Definition fiff_info.h:86
FIFFLIB::FiffInfo::dig
QList< FiffDigPoint > dig
Definition fiff_info.h:273
FIFFLIB::FiffInfoBase::chs
QList< FiffChInfo > chs
Definition fiff_info_base.h:252
FIFFLIB::FiffRawData
FIFF raw measurement data.
Definition fiff_raw_data.h:81
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