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Commit 92b54ed5 authored by Aaron Cuevas Lopez's avatar Aaron Cuevas Lopez
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Move record code on PSTH to recordengine system

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Builds/VisualStudio2013/open-ephys.sln
+ 2
− 2
View file @ 92b54ed5
Microsoft Visual Studio Solution File, Format Version 12.00 Microsoft Visual Studio Solution File, Format Version 12.00
# Visual Studio Express 2013 for Windows Desktop # Visual Studio 2013
VisualStudioVersion = 12.0.21005.1 VisualStudioVersion = 12.0.31101.0
MinimumVisualStudioVersion = 10.0.40219.1 MinimumVisualStudioVersion = 10.0.40219.1
Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "open-ephys", "open-ephys.vcxproj", "{9C924D66-7DEC-1AEF-B375-DB8666BFB909}" Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "open-ephys", "open-ephys.vcxproj", "{9C924D66-7DEC-1AEF-B375-DB8666BFB909}"
EndProject EndProject
......
Source/Processors/Editors/PeriStimulusTimeHistogramEditor.cpp
+ 3
− 3
View file @ 92b54ed5
...@@ -278,12 +278,12 @@ void PeriStimulusTimeHistogramEditor::buttonEvent(Button* button) ...@@ -278,12 +278,12 @@ void PeriStimulusTimeHistogramEditor::buttonEvent(Button* button)
PopupMenu m; PopupMenu m;
m.addItem(1,"TTL",true, processor->saveTTLs); /* m.addItem(1,"TTL",true, processor->saveTTLs);
m.addItem(2,"Network Events",true, processor->saveNetworkEvents); m.addItem(2,"Network Events",true, processor->saveNetworkEvents);
m.addItem(7,"Network Events [when recording is off]",true, processor->saveNetworkEventsWhenNotRecording); m.addItem(7,"Network Events [when recording is off]",true, processor->saveNetworkEventsWhenNotRecording);
m.addItem(3,"Eye Tracking",true, processor->saveEyeTracking); m.addItem(3,"Eye Tracking",true, processor->saveEyeTracking);*/
m.addItem(4,"Sorted Spikes: TS only ",true, processor->spikeSavingMode == 1); //m.addItem(4,"Sorted Spikes: TS only ",true, processor->spikeSavingMode == 1);
m.addItem(5,"Sorted Spikes: TS+waveform",true, processor->spikeSavingMode == 2); m.addItem(5,"Sorted Spikes: TS+waveform",true, processor->spikeSavingMode == 2);
m.addItem(6,"All Spikes: TS+waveform",true, processor->spikeSavingMode == 3); m.addItem(6,"All Spikes: TS+waveform",true, processor->spikeSavingMode == 3);
......
Source/Processors/PSTH/PeriStimulusTimeHistogramNode.cpp
+ 32
− 301
View file @ 92b54ed5
...@@ -37,7 +37,6 @@ PeriStimulusTimeHistogramNode::PeriStimulusTimeHistogramNode() ...@@ -37,7 +37,6 @@ PeriStimulusTimeHistogramNode::PeriStimulusTimeHistogramNode()
: GenericProcessor("PSTH"), displayBufferSize(5), redrawRequested(false) : GenericProcessor("PSTH"), displayBufferSize(5), redrawRequested(false)
{ {
trialCircularBuffer = nullptr; trialCircularBuffer = nullptr;
eventFile = nullptr;
isRecording = false; isRecording = false;
saveEyeTracking = saveTTLs = saveNetworkEvents = false; saveEyeTracking = saveTTLs = saveNetworkEvents = false;
saveNetworkEventsWhenNotRecording = false; saveNetworkEventsWhenNotRecording = false;
...@@ -120,6 +119,13 @@ void PeriStimulusTimeHistogramNode::updateSettings() ...@@ -120,6 +119,13 @@ void PeriStimulusTimeHistogramNode::updateSettings()
allocateTrialCircularBuffer(); allocateTrialCircularBuffer();
syncInternalDataStructuresWithSpikeSorter(); syncInternalDataStructuresWithSpikeSorter();
} }
electrodeChannels.clear();
for (int k = 0; k < eventChannels.size(); k++)
{
if ((eventChannels[k]->type == ELECTRODE_CHANNEL) &&
(static_cast<SpikeChannel*>(eventChannels[k]->extraData.get())->dataType == SpikeChannel::Sorted))
electrodeChannels.add(eventChannels[k]);
}
recordNode = getProcessorGraph()->getRecordNode(); recordNode = getProcessorGraph()->getRecordNode();
// diskWriteLock = recordNode->getLock(); // diskWriteLock = recordNode->getLock();
...@@ -136,6 +142,16 @@ bool PeriStimulusTimeHistogramNode::enable() ...@@ -136,6 +142,16 @@ bool PeriStimulusTimeHistogramNode::enable()
std::cout << "PeriStimulusTimeHistogramNode::enable()" << std::endl; std::cout << "PeriStimulusTimeHistogramNode::enable()" << std::endl;
PeriStimulusTimeHistogramEditor* editor = (PeriStimulusTimeHistogramEditor*) getEditor(); PeriStimulusTimeHistogramEditor* editor = (PeriStimulusTimeHistogramEditor*) getEditor();
editor->enable(); editor->enable();
recordNode->registerSpikeSource(this);
for (int i = 0; i < electrodeChannels.size(); i++)
{
SpikeRecordInfo *recElec = new SpikeRecordInfo();
recElec->name = electrodeChannels[i]->name;
recElec->numChannels = static_cast<SpikeChannel*>(electrodeChannels[i]->extraData.get())->numChannels;
recElec->sampleRate = settings.sampleRate;
electrodeChannels[i]->recordIndex = recordNode->addSpikeElectrode(recElec);
}
return true; return true;
...@@ -185,169 +201,6 @@ void PeriStimulusTimeHistogramNode::process(AudioSampleBuffer& buffer, MidiBuffe ...@@ -185,169 +201,6 @@ void PeriStimulusTimeHistogramNode::process(AudioSampleBuffer& buffer, MidiBuffe
void PeriStimulusTimeHistogramNode::dumpStartStopRecordEventToDisk(int64 ts, bool startRecord)
{
const ScopedLock myScopedLock(diskWriteLock);
#define SESSION 10
uint8 eventType = SESSION;
// write event type
fwrite(&eventType, 1,1, eventFile);
// write event size
int16 eventSize = 1 +2+ 8; // start/stop(1) + recordnumber (2) + timestamp (8)
fwrite(&eventSize, 2,1, eventFile);
// write event data
// 1. Start/stop
fwrite(&startRecord, 1,1, eventFile);
// 2. record number
fwrite(&recordingNumber, 2,1, eventFile);
// 3. the software timestamp
fwrite(&ts, 8,1, eventFile);
}
void PeriStimulusTimeHistogramNode::dumpNetworkEventToDisk(String S, int64 ts)
{
const ScopedLock myScopedLock(diskWriteLock);
uint8 eventType = NETWORK;
// write event type
fwrite(&eventType, 1,1, eventFile);
// write event size
int16 eventSize = S.getNumBytesAsUTF8() + 8; // string length + timestamp
fwrite(&eventSize, 2,1, eventFile);
// write event data
// 1. the network event string
fwrite(S.toUTF8(), S.getNumBytesAsUTF8(), 1, eventFile);
// 2. the software timestamp
fwrite(&ts, 8,1, eventFile);
}
void PeriStimulusTimeHistogramNode::dumpSpikeEventToDisk(SpikeObject *s, bool dumpWave)
{
const ScopedLock myScopedLock(diskWriteLock);
uint8 eventType = SPIKE;
// write event type
fwrite(&eventType, 1,1, eventFile);
int16 eventSize = 8+8+2+2+2+2+2 + s->nChannels*4; // ts, ts, sorted id, electrode ID, num channels, num data per channel + 4x gains
if (dumpWave)
eventSize += 2*(s->nSamples*s->nChannels); // uint16 per samples
// write event size
fwrite(&eventSize, 2,1, eventFile);
// write event data
// 1. software ts
fwrite(&s->timestamp_software, 8,1, eventFile);
// 2. hardware ts
fwrite(&s->timestamp, 8,1, eventFile);
// 3. sorted ID
fwrite(&s->sortedId, 2,1, eventFile);
// 4. electrod ID
fwrite(&s->electrodeID, 2,1, eventFile);
// 5. Channel in which threshold was detected
fwrite(&s->channel, 2,1, eventFile);
// 6. num channels
fwrite(&s->nChannels, 2,1, eventFile);
// 7. gains
fwrite(&s->gain, 4,s->nChannels, eventFile);
// 8. num data points per channel
fwrite(&s->nSamples, 2,1, eventFile);
if (dumpWave)
fwrite(&s->data, 2,s->nSamples*s->nChannels, eventFile);
}
void PeriStimulusTimeHistogramNode::dumpTTLeventToDisk(int channel, bool risingEdge, int64 ttl_timestamp_software, int64 ttl_timestamp_hardware, int samplePosition )
{
const ScopedLock myScopedLock(diskWriteLock);
uint8 eventType = TTL;
// write event type
fwrite(&eventType, 1,1, eventFile);
// write event size
int16 eventSize = 1 + 2 + 8 + 8; // rising/falling(1) + software ts (8) + hardware ts (8)
fwrite(&eventSize, 2,1, eventFile);
// write event data
// 1. rising/falling edge
fwrite(&risingEdge, 1, 1, eventFile);
// 2. channel
fwrite(&channel, 2,1,eventFile);
// 2. software ts
fwrite(&ttl_timestamp_software, 8,1, eventFile);
// 3. hardware ts
fwrite(&ttl_timestamp_hardware, 8,1, eventFile);
}
/*
void PeriStimulusTimeHistogramNode::dumpEyeTrackingEventToDisk(EyePosition pos)
{
diskWriteLock->enter();
uint8 eventType = EYE_POSITION;
// write event type
fwrite(&eventType, 1,1, eventFile);
// write event size
int16 eventSize = 8 + 8 + 8 + 8 + 8 +8 +8; // x,y,xc,yc,pupil,timestamp
fwrite(&eventSize, 2,1, eventFile);
// write event data
// 1. eye x position
fwrite(&pos.x, 8,1, eventFile);
// 2. eye y position
fwrite(&pos.y, 8,1, eventFile);
// 3. calibrated eye x position
fwrite(&pos.xc, 8,1, eventFile);
// 4. calibrated eye y position
fwrite(&pos.yc, 8,1, eventFile);
// 5. eye pupil
fwrite(&pos.pupil, 8,1, eventFile);
// 6. software timestamp
fwrite(&pos.software_timestamp, 8,1, eventFile);
// 7. hardware timestamp
fwrite(&pos.hardware_timestamp, 8,1, eventFile);
diskWriteLock->exit();
}
*/
void PeriStimulusTimeHistogramNode::dumpTimestampEventToDisk(int64 softwareTS,int64 hardwareTS)
{
const ScopedLock myScopedLock(diskWriteLock);
uint8 eventType = TIMESTAMP;
// write event type
fwrite(&eventType, 1,1, eventFile);
// write event size
int16 eventSize = 8 + 8; // software ts (8) + hardware ts (8)
fwrite(&eventSize, 2,1, eventFile);
// write event data
// 1. software ts
fwrite(&softwareTS, 8,1, eventFile);
// 2. hardware ts
fwrite(&hardwareTS, 8,1, eventFile);
}
void PeriStimulusTimeHistogramNode::syncInternalDataStructuresWithSpikeSorter() void PeriStimulusTimeHistogramNode::syncInternalDataStructuresWithSpikeSorter()
{ {
Array<Electrode*> electrodes; Array<Electrode*> electrodes;
...@@ -401,13 +254,13 @@ void PeriStimulusTimeHistogramNode::handleNetworkMessage(StringTS s) ...@@ -401,13 +254,13 @@ void PeriStimulusTimeHistogramNode::handleNetworkMessage(StringTS s)
ed->updateCanvas(); ed->updateCanvas();
} }
if (isRecording && saveNetworkEvents) /* if (isRecording && saveNetworkEvents)
{ {
dumpNetworkEventToDisk(s.getString(),s.timestamp); dumpNetworkEventToDisk(s.getString(),s.timestamp);
} else if (!isRecording && saveNetworkEvents && saveNetworkEventsWhenNotRecording) } else if (!isRecording && saveNetworkEvents && saveNetworkEventsWhenNotRecording)
{ {
networkEventsHistory.push(s); networkEventsHistory.push(s);
} }*/
} }
void PeriStimulusTimeHistogramNode::handleEvent(int eventType, MidiMessage& event, int samplePosition) void PeriStimulusTimeHistogramNode::handleEvent(int eventType, MidiMessage& event, int samplePosition)
...@@ -446,7 +299,7 @@ void PeriStimulusTimeHistogramNode::handleEvent(int eventType, MidiMessage& even ...@@ -446,7 +299,7 @@ void PeriStimulusTimeHistogramNode::handleEvent(int eventType, MidiMessage& even
memcpy(&hardware_timestamp, dataptr + 4, 8); // remember to skip first four bytes memcpy(&hardware_timestamp, dataptr + 4, 8); // remember to skip first four bytes
memcpy(&software_timestamp, dataptr + 12, 8); // remember to skip first four bytes memcpy(&software_timestamp, dataptr + 12, 8); // remember to skip first four bytes
if (isRecording) /* if (isRecording)
{ {
if (syncCounter == 0) if (syncCounter == 0)
{ {
...@@ -459,7 +312,7 @@ void PeriStimulusTimeHistogramNode::handleEvent(int eventType, MidiMessage& even ...@@ -459,7 +312,7 @@ void PeriStimulusTimeHistogramNode::handleEvent(int eventType, MidiMessage& even
syncCounter++; syncCounter++;
if (syncCounter > 10) if (syncCounter > 10)
syncCounter = 0; syncCounter = 0;
} }*/
} }
if (eventType == TTL) if (eventType == TTL)
...@@ -476,8 +329,7 @@ void PeriStimulusTimeHistogramNode::handleEvent(int eventType, MidiMessage& even ...@@ -476,8 +329,7 @@ void PeriStimulusTimeHistogramNode::handleEvent(int eventType, MidiMessage& even
//memcpy(&ttl_timestamp_hardware, dataptr+12, 8); //memcpy(&ttl_timestamp_hardware, dataptr+12, 8);
if (ttl_raise) if (ttl_raise)
trialCircularBuffer->addTTLevent(channel,ttl_timestamp_software,ttl_timestamp_hardware, ttl_raise, true); trialCircularBuffer->addTTLevent(channel,ttl_timestamp_software,ttl_timestamp_hardware, ttl_raise, true);
if (isRecording && saveTTLs)
dumpTTLeventToDisk(channel,ttl_raise,ttl_timestamp_software,ttl_timestamp_hardware,samplePosition );
} }
if (eventType == SPIKE) if (eventType == SPIKE)
...@@ -494,12 +346,15 @@ void PeriStimulusTimeHistogramNode::handleEvent(int eventType, MidiMessage& even ...@@ -494,12 +346,15 @@ void PeriStimulusTimeHistogramNode::handleEvent(int eventType, MidiMessage& even
} }
if (isRecording) if (isRecording)
{ {
if (spikeSavingMode == 1 && newSpike.sortedId > 0) if (spikeSavingMode == 1 && newSpike.sortedId > 0)
dumpSpikeEventToDisk(&newSpike, false); recordNode->writeSpike(newSpike, electrodeChannels[newSpike.source]->recordIndex);
//dumpSpikeEventToDisk(&newSpike, false);
else if (spikeSavingMode == 2 && newSpike.sortedId > 0) else if (spikeSavingMode == 2 && newSpike.sortedId > 0)
dumpSpikeEventToDisk(&newSpike, true); recordNode->writeSpike(newSpike, electrodeChannels[newSpike.source]->recordIndex);
//dumpSpikeEventToDisk(&newSpike, true);
else if (spikeSavingMode == 3) else if (spikeSavingMode == 3)
dumpSpikeEventToDisk(&newSpike, true); recordNode->writeSpike(newSpike, electrodeChannels[newSpike.source]->recordIndex);
//dumpSpikeEventToDisk(&newSpike, true);
} }
} }
} }
...@@ -507,136 +362,12 @@ void PeriStimulusTimeHistogramNode::handleEvent(int eventType, MidiMessage& even ...@@ -507,136 +362,12 @@ void PeriStimulusTimeHistogramNode::handleEvent(int eventType, MidiMessage& even
} }
String PeriStimulusTimeHistogramNode::generateHeader()
{
String header = "header.format = 'Open Ephys Data Format'; \n";
header += "header.version = 0.32;";
header += "header.header_bytes = ";
header += String(HEADER_SIZE);
header += ";\n";
header += "header.description = 'each record is size-varying. First is the record size (16-bit), followed by record type (uint8), followed by the actual data (which vary, depending on the type) '; \n";
header += "header.date_created = '";
header += recordNode->generateDateString();
header += "';\n";
header += "header.channel = '";
header += "events";
header += "';\n";
header += "header.channelType = 'Event';\n";
header += "header.sampleRate = ";
// all channels need to have the same sample rate under the current scheme
header += String(getSampleRate());
header += ";\n";
header += "header.blockLength = ";
header += BLOCK_LENGTH;
header += ";\n";
header += "header.bufferSize = ";
header += getAudioComponent()->getBufferSize();
header += ";\n";
header += "header.bitVolts = ";
if (recordNode->channels.size() > 0)
{
header += String(recordNode->channels[0]->bitVolts);
}
else
{
header += String(getDefaultBitVolts());
}
header += ";\n";
Time t;
header += "header.ticksPerSec = ";
header += String(t.getHighResolutionTicksPerSecond());
header += ";\n";
header = header.paddedRight(' ', HEADER_SIZE);
return header;
}
void PeriStimulusTimeHistogramNode::openFile(String filename)
{
std::cout << "OPENING FILE: " << filename << std::endl;
File f = File(filename);
bool fileExists = f.exists();
const ScopedLock myScopedLock(diskWriteLock);
eventFile = fopen(filename.toUTF8(), "ab");
if (!fileExists)
{
// create and write header
std::cout << "Writing header." << std::endl;
String header = generateHeader();
int headerSize = header.getNumBytesAsUTF8();
std::cout << "File ID: " << eventFile << ", number of bytes: " << headerSize << std::endl;
fwrite(header.toUTF8(), header.getNumBytesAsUTF8(), 1, eventFile);
std::cout << "Wrote header." << std::endl;
}
else
{
std::cout << "File already exists, just opening." << std::endl;
}
}
void PeriStimulusTimeHistogramNode::startRecording() void PeriStimulusTimeHistogramNode::startRecording()
{ {
if (!isRecording) isRecording = true;
{
File dataDirectory = recordNode->getDataDirectory();
if (dataDirectory.getFullPathName().length() == 0)
{
// temporary fix in case nothing is returned by the record node.
dataDirectory = File::getSpecialLocation(File::userHomeDirectory);
}
String baseDirectory = dataDirectory.getFullPathName();
String eventChannelFilename = baseDirectory + dataDirectory.separatorString + "all_channels.events";
openFile(eventChannelFilename);
// dump network events that arrived when we weren't recording
if (saveNetworkEventsWhenNotRecording)
{
while (networkEventsHistory.size() > 0)
{
StringTS s = networkEventsHistory.front();
dumpNetworkEventToDisk(s.getString(),s.timestamp);
networkEventsHistory.pop();
}
}
// recordingNumber = recordNode->getRecordingNumber();
Time t;
dumpStartStopRecordEventToDisk(t.getHighResolutionTicks(), true);
isRecording = true;
}
} }
void PeriStimulusTimeHistogramNode::stopRecording() void PeriStimulusTimeHistogramNode::stopRecording()
{ {
if (isRecording) isRecording = false;
{ }
// close files, etc. \ No newline at end of file
const ScopedLock myScopedLock(diskWriteLock);
std::cout << "CLOSING EVENT FILE: " << std::endl;
if (eventFile != nullptr)
fclose(eventFile);
isRecording = false;
}
}
Source/Processors/PSTH/PeriStimulusTimeHistogramNode.h
+ 2
− 12
View file @ 92b54ed5
...@@ -90,17 +90,6 @@ public: ...@@ -90,17 +90,6 @@ public:
void handleNetworkMessage(StringTS s); void handleNetworkMessage(StringTS s);
private: private:
FILE* eventFile;
String generateHeader();
void openFile(String filename);
void dumpNetworkEventToDisk(String S, int64 ts);
void dumpSpikeEventToDisk(SpikeObject *s, bool dumpWave);
void dumpTimestampEventToDisk(int64 softwareTS,int64 hardwareTS);
void dumpTTLeventToDisk(int channel,bool risingEdge, int64 ttl_timestamp_software, int64 ttl_timestamp_hardware, int samplePosition );
void dumpStartStopRecordEventToDisk(int64 ts, bool startRecord);
// void dumpEyeTrackingEventToDisk(EyePosition pos);
bool isRecording; bool isRecording;
int displayBufferSize; int displayBufferSize;
bool redrawRequested; bool redrawRequested;
...@@ -109,8 +98,9 @@ private: ...@@ -109,8 +98,9 @@ private:
std::queue<StringTS> networkEventsHistory; std::queue<StringTS> networkEventsHistory;
RecordNode* recordNode; RecordNode* recordNode;
uint16 recordingNumber; // uint16 recordingNumber;
CriticalSection diskWriteLock; CriticalSection diskWriteLock;
Array<Channel*> electrodeChannels;
JUCE_DECLARE_NON_COPYABLE_WITH_LEAK_DETECTOR(PeriStimulusTimeHistogramNode); JUCE_DECLARE_NON_COPYABLE_WITH_LEAK_DETECTOR(PeriStimulusTimeHistogramNode);
......
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