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Commit 0ce3effa authored by Aaron Cuevas Lopez's avatar Aaron Cuevas Lopez
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Adapt KWIK format to new hdf5 data types

parent 42e357bf
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Source/Plugins/KWIKFormat/RecordEngine/HDF5Recording.cpp
+ 2
− 2
View file @ 0ce3effa
......@@ -281,8 +281,8 @@ void HDF5Recording::writeSpike(int electrodeIndex, const SpikeEvent* spike)
void HDF5Recording::startAcquisition()
{
eventFile = new KWEFile();
eventFile->addEventType("TTL",HDF5FileBase::U8,"event_channels");
eventFile->addEventType("Messages",HDF5FileBase::STR,"Text");
eventFile->addEventType("TTL",HDF5FileBase::BaseDataType::U8,"event_channels");
eventFile->addEventType("Messages", HDF5FileBase::BaseDataType::DSTR, "Text");
spikesFile = new KWXFile();
}
......
Source/Plugins/KWIKFormat/RecordEngine/KWIKFormat.cpp
+ 38
− 37
View file @ 0ce3effa
......@@ -69,31 +69,31 @@ void KWDFile::startNewRecording(int recordingNumber, int nChannels, KWIKRecordin
String recordPath = String("/recordings/")+String(recordingNumber);
CHECK_ERROR(createGroup(recordPath));
CHECK_ERROR(setAttributeStr(info->name,recordPath,String("name")));
CHECK_ERROR(setAttribute(U64,&(info->start_time),recordPath,String("start_time")));
CHECK_ERROR(setAttribute(U32,&(info->start_sample),recordPath,String("start_sample")));
CHECK_ERROR(setAttribute(F32,&(info->sample_rate),recordPath,String("sample_rate")));
CHECK_ERROR(setAttribute(U32,&(info->bit_depth),recordPath,String("bit_depth")));
CHECK_ERROR(setAttribute(BaseDataType::U64, &(info->start_time), recordPath, String("start_time")));
CHECK_ERROR(setAttribute(BaseDataType::U32, &(info->start_sample), recordPath, String("start_sample")));
CHECK_ERROR(setAttribute(BaseDataType::F32, &(info->sample_rate), recordPath, String("sample_rate")));
CHECK_ERROR(setAttribute(BaseDataType::U32, &(info->bit_depth), recordPath, String("bit_depth")));
CHECK_ERROR(createGroup(recordPath+"/application_data"));
// CHECK_ERROR(setAttributeArray(F32,info->bitVolts.getRawDataPointer(),info->bitVolts.size(),recordPath+"/application_data",String("channel_bit_volts")));
bitVoltsSet = createDataSet(F32, info->bitVolts.size(), 0, recordPath + "/application_data/channel_bit_volts");
bitVoltsSet = createDataSet(BaseDataType::F32, info->bitVolts.size(), 0, recordPath + "/application_data/channel_bit_volts");
if (bitVoltsSet.get())
bitVoltsSet->writeDataBlock(info->bitVolts.size(), F32, info->bitVolts.getRawDataPointer());
bitVoltsSet->writeDataBlock(info->bitVolts.size(), BaseDataType::F32, info->bitVolts.getRawDataPointer());
else
std::cerr << "Error creating bitvolts data set" << std::endl;
CHECK_ERROR(setAttribute(U8,&mSample,recordPath+"/application_data",String("is_multiSampleRate_data")));
CHECK_ERROR(setAttribute(BaseDataType::U8, &mSample, recordPath + "/application_data", String("is_multiSampleRate_data")));
//CHECK_ERROR(setAttributeArray(F32,info->channelSampleRates.getRawDataPointer(),info->channelSampleRates.size(),recordPath+"/application_data",String("channel_sample_rates")));
sampleRateSet = createDataSet(F32, info->channelSampleRates.size(), 0, recordPath + "/application_data/channel_sample_rates");
sampleRateSet = createDataSet(BaseDataType::F32, info->channelSampleRates.size(), 0, recordPath + "/application_data/channel_sample_rates");
if (sampleRateSet.get())
sampleRateSet->writeDataBlock(info->channelSampleRates.size(), F32, info->channelSampleRates.getRawDataPointer());
sampleRateSet->writeDataBlock(info->channelSampleRates.size(), BaseDataType::F32, info->channelSampleRates.getRawDataPointer());
else
std::cerr << "Error creating sample rates data set" << std::endl;
recdata = createDataSet(I16,0,nChannels,CHUNK_XSIZE,recordPath+"/data");
recdata = createDataSet(BaseDataType::I16, 0, nChannels, CHUNK_XSIZE, recordPath + "/data");
if (!recdata.get())
std::cerr << "Error creating data set" << std::endl;
tsData = createDataSet(I64, 0, nChannels, TIMESTAMP_CHUNK_SIZE, recordPath + "/application_data/timestamps");
tsData = createDataSet(BaseDataType::I64, 0, nChannels, TIMESTAMP_CHUNK_SIZE, recordPath + "/application_data/timestamps");
if (!tsData.get())
std::cerr << "Error creating timestamps data set" << std::endl;
......@@ -106,7 +106,7 @@ void KWDFile::stopRecording()
String path = String("/recordings/")+String(recordingNumber)+String("/data");
recdata->getRowXPositions(samples);
CHECK_ERROR(setAttributeArray(U32,samples.getRawDataPointer(),samples.size(),path,"valid_samples"));
CHECK_ERROR(setAttributeArray(BaseDataType::U32, samples.getRawDataPointer(), samples.size(), path, "valid_samples"));
//ScopedPointer does the deletion and destructors the closings
recdata = nullptr;
tsData = nullptr;
......@@ -116,13 +116,13 @@ int KWDFile::createFileStructure()
{
const uint16 ver = 2;
if (createGroup("/recordings")) return -1;
if (setAttribute(U16,(void*)&ver,"/","kwik_version")) return -1;
if (setAttribute(BaseDataType::U16, (void*)&ver, "/", "kwik_version")) return -1;
return 0;
}
void KWDFile::writeBlockData(int16* data, int nSamples)
{
CHECK_ERROR(recdata->writeDataBlock(nSamples,I16,data));
CHECK_ERROR(recdata->writeDataBlock(nSamples, BaseDataType::I16, data));
}
void KWDFile::writeRowData(int16* data, int nSamples)
......@@ -131,7 +131,7 @@ void KWDFile::writeRowData(int16* data, int nSamples)
{
curChan=0;
}
CHECK_ERROR(recdata->writeDataRow(curChan,nSamples,I16,data));
CHECK_ERROR(recdata->writeDataRow(curChan, nSamples, BaseDataType::I16, data));
curChan++;
}
......@@ -139,7 +139,7 @@ void KWDFile::writeRowData(int16* data, int nSamples, int channel)
{
if (channel >= 0 && channel < nChannels)
{
CHECK_ERROR(recdata->writeDataRow(channel, nSamples, I16, data));
CHECK_ERROR(recdata->writeDataRow(channel, nSamples, BaseDataType::I16, data));
curChan = channel;
}
}
......@@ -148,7 +148,7 @@ void KWDFile::writeTimestamps(int64* ts, int nTs, int channel)
{
if (channel >= 0 && channel < nChannels)
{
CHECK_ERROR(tsData->writeDataRow(channel, nTs, I64, ts));
CHECK_ERROR(tsData->writeDataRow(channel, nTs, BaseDataType::I64, ts));
}
}
......@@ -190,20 +190,21 @@ int KWEFile::createFileStructure()
if (createGroup(path)) return -1;
path += "/events";
if (createGroup(path)) return -1;
dSet = createDataSet(U64,0,EVENT_CHUNK_SIZE,path + "/time_samples");
dSet = createDataSet(BaseDataType::U64, 0, EVENT_CHUNK_SIZE, path + "/time_samples");
if (!dSet) return -1;
dSet = createDataSet(U16,0,EVENT_CHUNK_SIZE,path + "/recording");
dSet = createDataSet(BaseDataType::U16, 0, EVENT_CHUNK_SIZE, path + "/recording");
if (!dSet) return -1;
path += "/user_data";
if (createGroup(path)) return -1;
dSet = createDataSet(U8,0,EVENT_CHUNK_SIZE,path + "/eventID");
dSet = createDataSet(BaseDataType::U8, 0, EVENT_CHUNK_SIZE, path + "/eventID");
if (!dSet) return -1;
dSet = createDataSet(U8,0,EVENT_CHUNK_SIZE,path + "/nodeID");
dSet = createDataSet(BaseDataType::U8, 0, EVENT_CHUNK_SIZE, path + "/nodeID");
if (!dSet) return -1;
dSet = createDataSet(eventTypes[i],0,EVENT_CHUNK_SIZE,path + "/" + eventDataNames[i]);
if (!dSet) return -1;
}
if (setAttribute(U16,(void*)&ver,"/","kwik_version")) return -1;
if (setAttribute(BaseDataType::U16, (void*)&ver, "/", "kwik_version")) return -1;
return 0;
}
......@@ -214,10 +215,10 @@ void KWEFile::startNewRecording(int recordingNumber, KWIKRecordingInfo* info)
String recordPath = String("/recordings/")+String(recordingNumber);
CHECK_ERROR(createGroup(recordPath));
CHECK_ERROR(setAttributeStr(info->name,recordPath,String("name")));
CHECK_ERROR(setAttribute(U64,&(info->start_time),recordPath,String("start_time")));
CHECK_ERROR(setAttribute(BaseDataType::U64, &(info->start_time), recordPath, String("start_time")));
// CHECK_ERROR(setAttribute(U32,&(info->start_sample),recordPath,String("start_sample")));
CHECK_ERROR(setAttribute(F32,&(info->sample_rate),recordPath,String("sample_rate")));
CHECK_ERROR(setAttribute(U32,&(info->bit_depth),recordPath,String("bit_depth")));
CHECK_ERROR(setAttribute(BaseDataType::F32, &(info->sample_rate), recordPath, String("sample_rate")));
CHECK_ERROR(setAttribute(BaseDataType::U32, &(info->bit_depth), recordPath, String("bit_depth")));
// CHECK_ERROR(createGroup(recordPath + "/raw"));
// CHECK_ERROR(createGroup(recordPath + "/raw/hdf5_paths"));
......@@ -264,10 +265,10 @@ void KWEFile::writeEvent(int type, uint8 id, uint8 processor, void* data, int64
std::cerr << "HDF5::writeEvent Invalid event type " << type << std::endl;
return;
}
CHECK_ERROR(timeStamps[type]->writeDataBlock(1,U64,&timestamp));
CHECK_ERROR(recordings[type]->writeDataBlock(1,I32,&recordingNumber));
CHECK_ERROR(eventID[type]->writeDataBlock(1,U8,&id));
CHECK_ERROR(nodeID[type]->writeDataBlock(1,U8,&processor));
CHECK_ERROR(timeStamps[type]->writeDataBlock(1, BaseDataType::U64, &timestamp));
CHECK_ERROR(recordings[type]->writeDataBlock(1, BaseDataType::I32, &recordingNumber));
CHECK_ERROR(eventID[type]->writeDataBlock(1, BaseDataType::U8, &id));
CHECK_ERROR(nodeID[type]->writeDataBlock(1, BaseDataType::U8, &processor));
CHECK_ERROR(eventData[type]->writeDataBlock(1,eventTypes[type],data));
}
......@@ -283,7 +284,7 @@ void KWEFile::writeEvent(int type, uint8 id, uint8 processor, void* data, int64
kwdIndex++;
}*/
void KWEFile::addEventType(String name, DataTypes type, String dataName)
void KWEFile::addEventType(String name, BaseDataType type, String dataName)
{
eventNames.add(name);
eventTypes.add(type);
......@@ -325,7 +326,7 @@ int KWXFile::createFileStructure()
{
const uint16 ver = 2;
if (createGroup("/channel_groups")) return -1;
if (setAttribute(U16,(void*)&ver,"/","kwik_version")) return -1;
if (setAttribute(BaseDataType::U16, (void*)&ver, "/", "kwik_version")) return -1;
for (int i=0; i < channelArray.size(); i++)
{
int res = createChannelGroup(i);
......@@ -346,11 +347,11 @@ int KWXFile::createChannelGroup(int index)
int nChannels = channelArray[index];
String path("/channel_groups/"+String(index));
CHECK_ERROR(createGroup(path));
dSet = createDataSet(I16,0,0,nChannels,SPIKE_CHUNK_XSIZE,SPIKE_CHUNK_YSIZE,path+"/waveforms_filtered");
dSet = createDataSet(BaseDataType::I16, 0, 0, nChannels, SPIKE_CHUNK_XSIZE, SPIKE_CHUNK_YSIZE, path + "/waveforms_filtered");
if (!dSet) return -1;
dSet = createDataSet(U64,0,SPIKE_CHUNK_XSIZE,path+"/time_samples");
dSet = createDataSet(BaseDataType::U64, 0, SPIKE_CHUNK_XSIZE, path + "/time_samples");
if (!dSet) return -1;
dSet = createDataSet(U16,0,SPIKE_CHUNK_XSIZE,path+"/recordings");
dSet = createDataSet(BaseDataType::U16, 0, SPIKE_CHUNK_XSIZE, path + "/recordings");
if (!dSet) return -1;
return 0;
}
......@@ -412,7 +413,7 @@ void KWXFile::writeSpike(int groupIndex, int nSamples, const float* data, Array<
}
}
CHECK_ERROR(spikeArray[groupIndex]->writeDataBlock(1,nSamples,I16,transformVector));
CHECK_ERROR(recordingArray[groupIndex]->writeDataBlock(1,I32,&recordingNumber));
CHECK_ERROR(timeStamps[groupIndex]->writeDataBlock(1,U64,&timestamp));
CHECK_ERROR(spikeArray[groupIndex]->writeDataBlock(1, nSamples, BaseDataType::I16, transformVector));
CHECK_ERROR(recordingArray[groupIndex]->writeDataBlock(1, BaseDataType::I32, &recordingNumber));
CHECK_ERROR(timeStamps[groupIndex]->writeDataBlock(1, BaseDataType::U64, &timestamp));
}
Source/Plugins/KWIKFormat/RecordEngine/KWIKFormat.h
+ 2
− 2
View file @ 0ce3effa
......@@ -80,7 +80,7 @@ public:
void stopRecording();
void writeEvent(int type, uint8 id, uint8 processor, void* data, int64 timestamp);
// void addKwdFile(String filename);
void addEventType(String name, DataTypes type, String dataName);
void addEventType(String name, BaseDataType type, String dataName);
String getFileName();
protected:
......@@ -95,7 +95,7 @@ private:
OwnedArray<HDF5RecordingData> nodeID;
OwnedArray<HDF5RecordingData> eventData;
Array<String> eventNames;
Array<DataTypes> eventTypes;
Array<BaseDataType> eventTypes;
Array<String> eventDataNames;
int kwdIndex;
......
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