From e9dd581d8c4dceb7964dc2dae3408f19efd0d1b8 Mon Sep 17 00:00:00 2001
From: Aaron Cuevas Lopez <aacuelo@teleco.upv.es>
Date: Fri, 13 Jan 2017 04:12:26 +0100
Subject: [PATCH] Update Binary Recording plugin
---
.../Plugins/BinaryWriter/BinaryRecording.cpp | 144 +++++++++++-------
Source/Plugins/BinaryWriter/BinaryRecording.h | 15 +-
2 files changed, 99 insertions(+), 60 deletions(-)
diff --git a/Source/Plugins/BinaryWriter/BinaryRecording.cpp b/Source/Plugins/BinaryWriter/BinaryRecording.cpp
index d3abb257b..eeba19943 100644
--- a/Source/Plugins/BinaryWriter/BinaryRecording.cpp
+++ b/Source/Plugins/BinaryWriter/BinaryRecording.cpp
@@ -69,7 +69,7 @@ void BinaryRecording::openFiles(File rootFolder, int experimentNumber, int recor
openMessageFile(basepath, recordingNumber);
for (int i = 0; i < spikeFileArray.size(); i++)
{
- openSpikeFile(basepath, getSpikeElectrode(i), recordingNumber);
+ openSpikeFile(basepath, i, recordingNumber);
}
m_recordingNum = recordingNumber;
}
@@ -126,7 +126,7 @@ void BinaryRecording::writeData(int writeChannel, int realChannel, const float*
m_scaledBuffer.malloc(size);
m_intBuffer.malloc(size);
}
- double multFactor = 1 / (float(0x7fff) * getChannel(realChannel)->bitVolts);
+ double multFactor = 1 / (float(0x7fff) * getDataChannel(realChannel)->getBitVolts());
FloatVectorOperations::copyWithMultiply(m_scaledBuffer.getData(), buffer, multFactor, size);
AudioDataConverters::convertFloatToInt16LE(m_scaledBuffer.getData(), m_intBuffer.getData(), size);
@@ -135,7 +135,7 @@ void BinaryRecording::writeData(int writeChannel, int realChannel, const float*
//Code below is copied from OriginalRecording, so it's not as clean as newer one
-void BinaryRecording::addSpikeElectrode(int index, const SpikeRecordInfo* elec)
+void BinaryRecording::addSpikeElectrode(int index, const SpikeChannel* elec)
{
spikeFileArray.add(nullptr);
}
@@ -185,11 +185,11 @@ void BinaryRecording::openEventFile(String basepath, int recordingNumber)
}
-void BinaryRecording::openSpikeFile(String basePath, SpikeRecordInfo* elec, int recordingNumber)
+void BinaryRecording::openSpikeFile(String basePath, int spikeIndex, int recordingNumber)
{
-
+ const SpikeChannel* elec = getSpikeChannel(spikeIndex);
FILE* spFile;
- String fullPath = basePath + "_" + elec->name.removeCharacters(" ") + "_" + String(recordingNumber) + ".spikes";
+ String fullPath = basePath + "_" + elec->getName().removeCharacters(" ") + "_" + String(recordingNumber) + ".spikes";
std::cout << "OPENING FILE: " << fullPath << std::endl;
@@ -207,7 +207,7 @@ void BinaryRecording::openSpikeFile(String basePath, SpikeRecordInfo* elec, int
fwrite(header.toUTF8(), 1, header.getNumBytesAsUTF8(), spFile);
}
diskWriteLock.exit();
- spikeFileArray.set(elec->recordIndex, spFile);
+ spikeFileArray.set(spikeIndex, spFile);
}
@@ -263,7 +263,7 @@ String BinaryRecording::generateEventHeader()
header += "header.sampleRate = ";
// all channels need to have the same sample rate under the current scheme
- header += String(getChannel(0)->sampleRate);
+ header += String(getEventChannel(0)->getSampleRate());
header += ";\n";
header += "header.blockLength = ";
header += BLOCK_LENGTH;
@@ -283,7 +283,7 @@ String BinaryRecording::generateEventHeader()
}
-String BinaryRecording::generateSpikeHeader(SpikeRecordInfo* elec)
+String BinaryRecording::generateSpikeHeader(const SpikeChannel* elec)
{
String header = "header.format = 'Open Ephys Data Format'; \n";
header += "header.version = " + String(VERSION_STRING) + "; \n";
@@ -300,15 +300,15 @@ String BinaryRecording::generateSpikeHeader(SpikeRecordInfo* elec)
header += "';\n";
header += "header.electrode = '";
- header += elec->name;
+ header += elec->getName();
header += "';\n";
header += "header.num_channels = ";
- header += elec->numChannels;
+ header += elec->getNumChannels();
header += ";\n";
header += "header.sampleRate = ";
- header += String(elec->sampleRate);
+ header += String(elec->getSampleRate());
header += ";\n";
header = header.paddedRight(' ', HEADER_SIZE);
@@ -318,34 +318,41 @@ String BinaryRecording::generateSpikeHeader(SpikeRecordInfo* elec)
return header;
}
-void BinaryRecording::writeEvent(int eventType, const MidiMessage& event, int64 timestamp)
+void BinaryRecording::writeEvent(int eventIndex, const MidiMessage& event)
+{
+ writeTTLEvent(eventIndex, event);
+ if (Event::getEventType(event) == EventChannel::TEXT)
+ {
+ TextEventPtr ev = TextEvent::deserializeFromMessage(event, getEventChannel(eventIndex));
+ if (ev == nullptr) return;
+ writeMessage(ev->getText(), ev->getSourceID(), ev->getChannel(), ev->getTimestamp());
+ }
+}
+
+void BinaryRecording::writeTimestampSyncText(uint16 sourceID, uint16 sourceIdx, uint64 timestamp, String text)
{
- if (isWritableEvent(eventType))
- writeTTLEvent(event, timestamp);
- if (eventType == GenericProcessor::MESSAGE)
- writeMessage(event, timestamp);
+ writeMessage(text, sourceID, 255, timestamp);
}
-void BinaryRecording::writeMessage(const MidiMessage& event, int64 timestamp)
+void BinaryRecording::writeMessage(String message, uint16 processorID, uint16 channel, uint64 timestamp)
{
if (messageFile == nullptr)
return;
- int msgLength = event.getRawDataSize() - 6;
- const char* dataptr = (const char*)event.getRawData() + 6;
+ int msgLength = message.getNumBytesAsUTF8();
String timestampText(timestamp);
diskWriteLock.enter();
fwrite(timestampText.toUTF8(), 1, timestampText.length(), messageFile);
fwrite(" ", 1, 1, messageFile);
- fwrite(dataptr, 1, msgLength, messageFile);
+ fwrite(message.toUTF8(), 1, msgLength, messageFile);
fwrite("\n", 1, 1, messageFile);
diskWriteLock.exit();
}
-void BinaryRecording::writeTTLEvent(const MidiMessage& event, int64 timestamp)
+void BinaryRecording::writeTTLEvent(int eventIndex, const MidiMessage& event)
{
// find file and write samples to disk
// std::cout << "Received event!" << std::endl;
@@ -353,56 +360,87 @@ void BinaryRecording::writeTTLEvent(const MidiMessage& event, int64 timestamp)
if (eventFile == nullptr)
return;
- const uint8* dataptr = event.getRawData();
-
+ uint8 data[16];
//With the new external recording thread, this field has no sense.
int16 samplePos = 0;
- diskWriteLock.enter();
+ EventPtr ev = Event::deserializeFromMessage(event, getEventChannel(eventIndex));
+ if (!ev) return;
+ *reinterpret_cast<uint64*>(data) = ev->getTimestamp();
+ *reinterpret_cast<int16*>(data + 8) = samplePos;
+ *(data + 10) = static_cast<uint8>(ev->getEventType());
+ *(data + 11) = static_cast<uint8>(ev->getSourceID());
+ *(data + 12) = (ev->getEventType() == EventChannel::TTL) ? (dynamic_cast<TTLEvent*>(ev.get())->getState() ? 1 : 0) : 0;
+ *(data + 13) = static_cast<uint8>(ev->getChannel());
+ *reinterpret_cast<uint16*>(data + 14) = static_cast<uint16>(m_recordingNum);
- fwrite(×tamp, // ptr
- 8, // size of each element
- 1, // count
- eventFile); // ptr to FILE object
- fwrite(&samplePos, // ptr
- 2, // size of each element
- 1, // count
- eventFile); // ptr to FILE object
+ diskWriteLock.enter();
- // write 1st four bytes of event (type, nodeId, eventId, eventChannel)
- fwrite(dataptr, 1, 4, eventFile);
- int16 recordingNumber = m_recordingNum;
- // write recording number
- fwrite(&recordingNumber, // ptr
- 2, // size of each element
- 1, // count
- eventFile); // ptr to FILE object
+ fwrite(&data, // ptr
+ sizeof(uint8), // size of each element
+ 16, // count
+ eventFile); // ptr to FILE object
diskWriteLock.exit();
}
-void BinaryRecording::writeSpike(int electrodeIndex, const SpikeObject& spike, int64 timestamp)
-{
- uint8_t spikeBuffer[MAX_SPIKE_BUFFER_LEN];
+void BinaryRecording::writeSpike(int electrodeIndex, const SpikeEvent* spike)
+{
if (spikeFileArray[electrodeIndex] == nullptr)
return;
- packSpike(&spike, spikeBuffer, MAX_SPIKE_BUFFER_LEN);
-
- int totalBytes = spike.nSamples * spike.nChannels * 2 + // account for samples
- spike.nChannels * 4 + // acount for gain
- spike.nChannels * 2 + // account for thresholds
- SPIKE_METADATA_SIZE; // 42, from SpikeObject.h
-
+ HeapBlock<char> spikeBuffer;
+ const SpikeChannel* channel = getSpikeChannel(electrodeIndex);
+
+ int totalSamples = channel->getTotalSamples() * channel->getNumChannels();
+ int numChannels = channel->getNumChannels();
+ int chanSamples = channel->getTotalSamples();
+
+ int totalBytes = totalSamples * 2 + // account for samples
+ numChannels * 4 + // acount for gain
+ numChannels * 2 + // account for thresholds
+ 42; // 42, from SpikeObject.h
+ spikeBuffer.malloc(totalBytes);
+ *(spikeBuffer.getData()) = static_cast<char>(channel->getChannelType());
+ *reinterpret_cast<uint64*>(spikeBuffer.getData() + 1) = spike->getTimestamp();
+ *reinterpret_cast<uint64*>(spikeBuffer.getData() + 9) = 0; //Legacy unused value
+ *reinterpret_cast<uint16*>(spikeBuffer.getData() + 17) = spike->getSourceID();
+ *reinterpret_cast<uint16*>(spikeBuffer.getData() + 19) = numChannels;
+ *reinterpret_cast<uint16*>(spikeBuffer.getData() + 21) = chanSamples;
+ *reinterpret_cast<uint16*>(spikeBuffer.getData() + 23) = spike->getSortedID();
+ *reinterpret_cast<uint16*>(spikeBuffer.getData() + 25) = electrodeIndex; //Legacy value
+ *reinterpret_cast<uint16*>(spikeBuffer.getData() + 27) = 0; //Legacy unused value
+ zeromem(spikeBuffer.getData() + 29, 3 * sizeof(uint8));
+ zeromem(spikeBuffer.getData() + 32, 2 * sizeof(float));
+ *reinterpret_cast<uint16*>(spikeBuffer.getData() + 40) = channel->getSampleRate();
+
+ int ptrIdx = 0;
+ for (int i = 0; i < numChannels; i++)
+ {
+ float scaleFactor = 1 / (float(0x7fff) * channel->getChannelBitVolts(i));
+ FloatVectorOperations::copyWithMultiply(m_scaledBuffer + ptrIdx, spike->getDataPointer(i), scaleFactor, chanSamples);
+ ptrIdx += chanSamples;
+ }
+ AudioDataConverters::convertFloatToInt16LE(m_scaledBuffer, (spikeBuffer.getData() + 42), totalSamples);
+ ptrIdx = totalSamples * 2 + 42;
+ for (int i = 0; i < numChannels; i++)
+ {
+ *reinterpret_cast<float*>(spikeBuffer.getData() + ptrIdx) = channel->getGain();
+ ptrIdx += sizeof(float);
+ }
+ for (int i = 0; i < numChannels; i++)
+ {
+ *reinterpret_cast<int16*>(spikeBuffer.getData() + ptrIdx) = spike->getThreshold(i);
+ ptrIdx += sizeof(int16);
+ }
diskWriteLock.enter();
fwrite(spikeBuffer, 1, totalBytes, spikeFileArray[electrodeIndex]);
- int16 recordingNumber = m_recordingNum;
- fwrite(&recordingNumber, // ptr
+ fwrite(&m_recordingNum, // ptr
2, // size of each element
1, // count
spikeFileArray[electrodeIndex]); // ptr to FILE object
diff --git a/Source/Plugins/BinaryWriter/BinaryRecording.h b/Source/Plugins/BinaryWriter/BinaryRecording.h
index 30a9f942f..579485272 100644
--- a/Source/Plugins/BinaryWriter/BinaryRecording.h
+++ b/Source/Plugins/BinaryWriter/BinaryRecording.h
@@ -47,23 +47,24 @@ namespace BinaryRecordingEngine
void openFiles(File rootFolder, int experimentNumber, int recordingNumber) override;
void closeFiles() override;
void writeData(int writeChannel, int realChannel, const float* buffer, int size) override;
- void writeEvent(int eventType, const MidiMessage& event, int64 timestamp) override;
+ void writeEvent(int eventType, const MidiMessage& event) override;
void resetChannels() override;
- void addSpikeElectrode(int index, const SpikeRecordInfo* elec) override;
- void writeSpike(int electrodeIndex, const SpikeObject& spike, int64 timestamp) override;
+ void addSpikeElectrode(int index, const SpikeChannel* elec) override;
+ void writeSpike(int electrodeIndex, const SpikeEvent* spike) override;
+ void writeTimestampSyncText(uint16 sourceID, uint16 sourceIdx, uint64 timestamp, String text);
static RecordEngineManager* getEngineManager();
private:
- void openSpikeFile(String basepath, SpikeRecordInfo* elec, int recordingNumber);
- String generateSpikeHeader(SpikeRecordInfo* elec);
+ void openSpikeFile(String basepath, int spikeIndex, int recordingNumber);
+ String generateSpikeHeader(const SpikeChannel* elec);
String generateEventHeader();
void openMessageFile(String basepath, int recordingNumber);
void openEventFile(String basepath, int recordingNumber);
- void writeTTLEvent(const MidiMessage& event, int64 timestamp);
- void writeMessage(const MidiMessage& event, int64 timestamp);
+ void writeTTLEvent(int eventIndex, const MidiMessage& event);
+ void writeMessage(String message, uint16 processorID, uint16 channel, uint64 timestamp);
HeapBlock<float> m_scaledBuffer;
HeapBlock<int16> m_intBuffer;
--
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