From 3fbf2d31cba036b4922b4aeaa0d9edabfbdb9f7a Mon Sep 17 00:00:00 2001
From: Aaron Cuevas Lopez <aacuelo@teleco.upv.es>
Date: Fri, 29 Aug 2014 21:01:22 +0200
Subject: [PATCH] Add Spike Recording to OriginalRecording Engine
---
Source/Processors/OriginalRecording.cpp | 123 +++++++++++++++
Source/Processors/OriginalRecording.h | 6 +
Source/Processors/RecordEngine.cpp | 9 +-
Source/Processors/RecordEngine.h | 14 ++
Source/Processors/RecordNode.cpp | 28 ++++
Source/Processors/RecordNode.h | 12 ++
Source/Processors/SpikeDisplayNode.cpp | 191 ++----------------------
Source/Processors/SpikeDisplayNode.h | 26 ++--
8 files changed, 217 insertions(+), 192 deletions(-)
diff --git a/Source/Processors/OriginalRecording.cpp b/Source/Processors/OriginalRecording.cpp
index 3252146e2..d8455eeae 100644
--- a/Source/Processors/OriginalRecording.cpp
+++ b/Source/Processors/OriginalRecording.cpp
@@ -46,6 +46,10 @@ OriginalRecording::~OriginalRecording()
for (int i=0; i < fileArray.size(); i++)
{
if (fileArray[i] != nullptr) fclose(fileArray[i]);
+ }
+ for (int i=0; i < spikeFileArray.size(); i++)
+ {
+ if (spikeFileArray[i] != nullptr) fclose(spikeFileArray[i]);
}
delete continuousDataFloatBuffer;
delete continuousDataIntegerBuffer;
@@ -58,9 +62,15 @@ void OriginalRecording::addChannel(int index, Channel* chan)
fileArray.add(nullptr);
}
+void OriginalRecording::addSpikeElectrode(int index, SpikeRecordInfo* elec)
+{
+ spikeFileArray.add(nullptr);
+}
+
void OriginalRecording::resetChannels()
{
fileArray.clear();
+ spikeFileArray.clear();
}
void OriginalRecording::openFiles(File rootFolder, int recordingNumber)
@@ -74,6 +84,10 @@ void OriginalRecording::openFiles(File rootFolder, int recordingNumber)
openFile(rootFolder,getChannel(i));
}
}
+ for (int i = 0; i < spikeFileArray.size(); i++)
+ {
+ openSpikeFile(rootFolder,getSpikeElectrode(i));
+ }
blockIndex = 0;
}
@@ -129,6 +143,34 @@ void OriginalRecording::openFile(File rootFolder, Channel* ch)
}
+void OriginalRecording::openSpikeFile(File rootFolder, SpikeRecordInfo* elec)
+{
+
+ FILE* spFile;
+ String fullPath(rootFolder.getFullPathName() + rootFolder.separatorString);
+ fullPath += elec->name.removeCharacters(" ");
+ fullPath += ".spikes";
+
+ std::cout << "OPENING FILE: " << fullPath << std::endl;
+
+ File f = File(fullPath);
+
+ bool fileExists = f.exists();
+
+ diskWriteLock.enter();
+
+ spFile = fopen(fullPath.toUTF8(),"ab");
+
+ if (!fileExists)
+ {
+ String header = generateSpikeHeader(elec);
+ fwrite(header.toUTF8(), 1, header.getNumBytesAsUTF8(), spFile);
+ }
+ diskWriteLock.exit();
+ spikeFileArray.set(elec->recordIndex,spFile);
+
+}
+
String OriginalRecording::getFileName(Channel* ch)
{
String filename;
@@ -208,6 +250,39 @@ String OriginalRecording::generateHeader(Channel* ch)
}
+String OriginalRecording::generateSpikeHeader(SpikeRecordInfo* elec)
+{
+ String header = "header.format = 'Open Ephys Data Format'; \n";
+ header += "header.version = 0.2;";
+ header += "header.header_bytes = ";
+ header += String(HEADER_SIZE);
+ header += ";\n";
+
+ header += "header.description = 'Each record contains 1 uint8 eventType, 1 uint64 timestamp, 1 uint16 electrodeID, 1 uint16 numChannels (n), 1 uint16 numSamples (m), n*m uint16 samples, n uint16 channelGains, n uint16 thresholds, and 1 uint16 recordingNumber'; \n";
+
+ header += "header.date_created = '";
+ header += generateDateString();
+ header += "';\n";
+
+ header += "header.electrode = '";
+ header += elec->name;
+ header += "';\n";
+
+ header += "header.num_channels = ";
+ header += elec->numChannels;
+ header += ";\n";
+
+ header += "header.sampleRate = ";
+ header += String(elec->sampleRate);
+ header += ";\n";
+
+ header = header.paddedRight(' ', HEADER_SIZE);
+
+ //std::cout << header << std::endl;
+
+ return header;
+}
+
void OriginalRecording::writeEvent(MidiMessage& event, int samplePosition)
{
// find file and write samples to disk
@@ -399,6 +474,16 @@ void OriginalRecording::closeFiles()
}
}
}
+ for (int i = 0; i < spikeFileArray.size(); i++)
+ {
+ if (spikeFileArray[i] != nullptr)
+ {
+ diskWriteLock.enter();
+ fclose(spikeFileArray[i]);
+ spikeFileArray.set(i,nullptr);
+ diskWriteLock.exit();
+ }
+ }
if (eventFile != nullptr)
{
diskWriteLock.enter();
@@ -412,4 +497,42 @@ void OriginalRecording::closeFiles()
void OriginalRecording::updateTimeStamp(int64 timestamp)
{
this->timestamp = timestamp;
+}
+
+void OriginalRecording::writeSpike(const SpikeObject& spike, int electrodeIndex)
+{
+ uint8_t spikeBuffer[MAX_SPIKE_BUFFER_LEN];
+
+ 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 threshold and gain
+ 15; // 15 bytes in every SpikeObject
+
+
+ // format:
+ // 1 byte of event type (always = 4 for spikes)
+ // 8 bytes for 64-bit timestamp
+ // 2 bytes for 16-bit electrode ID
+ // 2 bytes for 16-bit number of channels (n)
+ // 2 bytes for 16-bit number of samples (m)
+ // 2*n*m bytes for 16-bit samples
+ // 2*n bytes for 16-bit gains
+ // 2*n bytes for 16-bit thresholds
+
+ // const MessageManagerLock mmLock;
+
+ diskWriteLock.enter();
+
+ fwrite(spikeBuffer, 1, totalBytes, spikeFileArray[electrodeIndex]);
+
+ fwrite(&recordingNumber, // ptr
+ 2, // size of each element
+ 1, // count
+ spikeFileArray[electrodeIndex]); // ptr to FILE object
+
+ diskWriteLock.exit();
}
\ No newline at end of file
diff --git a/Source/Processors/OriginalRecording.h b/Source/Processors/OriginalRecording.h
index 8755e0ca0..876278316 100644
--- a/Source/Processors/OriginalRecording.h
+++ b/Source/Processors/OriginalRecording.h
@@ -45,6 +45,8 @@ public:
void addChannel(int index, Channel* chan);
void resetChannels();
void updateTimeStamp(int64 timestamp);
+ void addSpikeElectrode(int index, SpikeRecordInfo* elec);
+ void writeSpike(const SpikeObject& spike, int electrodeIndex);
private:
String getFileName(Channel* ch);
@@ -54,6 +56,9 @@ private:
void writeTimestampAndSampleCount(FILE* file);
void writeRecordMarker(FILE* file);
+ void openSpikeFile(File rootFolder, SpikeRecordInfo* elec);
+ String generateSpikeHeader(SpikeRecordInfo* elec);
+
bool separateFiles;
int blockIndex;
int recordingNumber;
@@ -76,6 +81,7 @@ private:
FILE* eventFile;
Array<FILE*> fileArray;
+ Array<FILE*> spikeFileArray;
CriticalSection diskWriteLock;
JUCE_DECLARE_NON_COPYABLE_WITH_LEAK_DETECTOR(OriginalRecording);
diff --git a/Source/Processors/RecordEngine.cpp b/Source/Processors/RecordEngine.cpp
index c2d1cadbb..6450fb14a 100644
--- a/Source/Processors/RecordEngine.cpp
+++ b/Source/Processors/RecordEngine.cpp
@@ -43,4 +43,11 @@ String RecordEngine::generateDateString()
return getProcessorGraph()->getRecordNode()->generateDateString();
}
-void RecordEngine::updateTimeStamp(int64 timestamp) {}
\ No newline at end of file
+SpikeRecordInfo* RecordEngine::getSpikeElectrode(int index)
+{
+ return getProcessorGraph()->getRecordNode()->getSpikeElectrode(index);
+}
+
+void RecordEngine::updateTimeStamp(int64 timestamp) {}
+
+void RecordEngine::registerSpikeSource(GenericProcessor* processor) {}
\ No newline at end of file
diff --git a/Source/Processors/RecordEngine.h b/Source/Processors/RecordEngine.h
index 67abe072a..da5afdf15 100644
--- a/Source/Processors/RecordEngine.h
+++ b/Source/Processors/RecordEngine.h
@@ -27,6 +27,16 @@
#include "../../JuceLibraryCode/JuceHeader.h"
#include "Channel.h"
#include "GenericProcessor.h"
+#include "Visualization\SpikeObject.h"
+
+struct SpikeRecordInfo
+{
+ String name;
+ int numChannels;
+ int sampleRate;
+
+ int recordIndex;
+};
class RecordNode;
@@ -41,12 +51,16 @@ public:
virtual void writeData(AudioSampleBuffer& buffer, int nSamples) =0;
virtual void writeEvent(MidiMessage& event, int samplePosition) =0;
virtual void addChannel(int index, Channel* chan) =0;
+ virtual void addSpikeElectrode(int index, SpikeRecordInfo* elec) =0;
+ virtual void writeSpike(const SpikeObject& spike, int electrodeIndex) =0;
virtual void registerProcessor(GenericProcessor* processor);
+ virtual void registerSpikeSource(GenericProcessor* processor);
virtual void resetChannels();
virtual void updateTimeStamp(int64 timestamp);
protected:
Channel* getChannel(int index);
+ SpikeRecordInfo* getSpikeElectrode(int index);
String generateDateString();
private:
diff --git a/Source/Processors/RecordNode.cpp b/Source/Processors/RecordNode.cpp
index ccaad9a34..cbbaac5bf 100755
--- a/Source/Processors/RecordNode.cpp
+++ b/Source/Processors/RecordNode.cpp
@@ -49,6 +49,8 @@ RecordNode::RecordNode()
recordingNumber = 0;
+ spikeElectrodeIndex = 0;
+
// 128 inputs, 0 outputs
setPlayConfigDetails(getNumInputs(),getNumOutputs(),44100.0,128);
@@ -106,9 +108,12 @@ void RecordNode::resetConnections()
//std::cout << "Resetting connections" << std::endl;
nextAvailableChannel = 0;
wasConnected = false;
+ spikeElectrodeIndex = 0;
channelPointers.clear();
eventChannelPointers.clear();
+ spikeElectrodePointers.clear();
+
EVERY_ENGINE->resetChannels();
}
@@ -436,4 +441,27 @@ Channel* RecordNode::getDataChannel(int index)
void RecordNode::registerRecordEngine(RecordEngine* engine)
{
engineArray.add(engine);
+}
+
+void RecordNode::registerSpikeSource(GenericProcessor* processor)
+{
+ EVERY_ENGINE->registerSpikeSource(processor);
+}
+
+int RecordNode::addSpikeElectrode(SpikeRecordInfo* elec)
+{
+ elec->recordIndex=spikeElectrodeIndex;
+ spikeElectrodePointers.add(elec);
+ EVERY_ENGINE->addSpikeElectrode(spikeElectrodeIndex,elec);
+ return spikeElectrodeIndex++;
+}
+
+void RecordNode::writeSpike(SpikeObject& spike, int electrodeIndex)
+{
+ EVERY_ENGINE->writeSpike(spike,electrodeIndex);
+}
+
+SpikeRecordInfo* RecordNode::getSpikeElectrode(int index)
+{
+ return spikeElectrodePointers[index];
}
\ No newline at end of file
diff --git a/Source/Processors/RecordNode.h b/Source/Processors/RecordNode.h
index f4a7cc70e..2291db99a 100755
--- a/Source/Processors/RecordNode.h
+++ b/Source/Processors/RecordNode.h
@@ -114,6 +114,14 @@ public:
void registerRecordEngine(RecordEngine* engine);
+ void registerSpikeSource(GenericProcessor* processor);
+
+ int addSpikeElectrode(SpikeRecordInfo* elec);
+
+ void writeSpike(SpikeObject& spike, int electrodeIndex);
+
+ SpikeRecordInfo* getSpikeElectrode(int index);
+
/** Signals when to create a new data directory when recording starts.*/
bool newDirectoryNeeded;
@@ -160,6 +168,10 @@ private:
/** Pointers to all event channels */
Array<Channel*> eventChannelPointers;
+ OwnedArray<SpikeRecordInfo> spikeElectrodePointers;
+
+ int spikeElectrodeIndex;;
+
/** Generates a default directory name, based on the current date and time */
String generateDirectoryName();
diff --git a/Source/Processors/SpikeDisplayNode.cpp b/Source/Processors/SpikeDisplayNode.cpp
index 6543f0292..c9d518db3 100755
--- a/Source/Processors/SpikeDisplayNode.cpp
+++ b/Source/Processors/SpikeDisplayNode.cpp
@@ -30,14 +30,9 @@
SpikeDisplayNode::SpikeDisplayNode()
- : GenericProcessor("Spike Viewer"), displayBufferSize(5), redrawRequested(false), isRecording(false),
- signalFilesShouldClose(false)
+ : GenericProcessor("Spike Viewer"), displayBufferSize(5), redrawRequested(false),
+ isRecording(false)
{
-
-
- spikeBuffer = new uint8_t[MAX_SPIKE_BUFFER_LEN]; // MAX_SPIKE_BUFFER_LEN defined in SpikeObject.h
-
- recordingNumber = -1;
}
@@ -60,7 +55,7 @@ void SpikeDisplayNode::updateSettings()
//std::cout << "Setting num inputs on SpikeDisplayNode to " << getNumInputs() << std::endl;
electrodes.clear();
-
+ getProcessorGraph()->getRecordNode()->registerSpikeSource(this);
for (int i = 0; i < eventChannels.size(); i++)
{
if ((eventChannels[i]->eventType < 999) && (eventChannels[i]->eventType > SPIKE_BASE_CODE))
@@ -77,14 +72,12 @@ void SpikeDisplayNode::updateSettings()
elec.displayThresholds.add(0);
elec.detectorThresholds.add(0);
}
-
+
electrodes.add(elec);
+
}
}
- recordNode = getProcessorGraph()->getRecordNode();
-// diskWriteLock = recordNode->getLock(); TODO: move spike writing to record engine
-
}
// void SpikeDisplayNode::updateVisualizer()
@@ -96,6 +89,16 @@ bool SpikeDisplayNode::enable()
{
std::cout << "SpikeDisplayNode::enable()" << std::endl;
SpikeDisplayEditor* editor = (SpikeDisplayEditor*) getEditor();
+ for (int i = 0; i < electrodes.size(); i ++)
+ {
+ Electrode& elec = electrodes.getReference(i);
+ SpikeRecordInfo *recElec = new SpikeRecordInfo();
+ recElec->name = elec.name;
+ recElec->numChannels = elec.numChannels;
+ recElec->sampleRate = settings.sampleRate;
+ elec.recordIndex = getProcessorGraph()->getRecordNode()->addSpikeElectrode(recElec);
+ }
+
editor->enable();
return true;
@@ -171,27 +174,11 @@ void SpikeDisplayNode::setParameter(int param, float val)
if (param == 0) // stop recording
{
isRecording = false;
- signalFilesShouldClose = true;
} else if (param == 1) // start recording
{
isRecording = true;
- dataDirectory = recordNode->getDataDirectory();
-
- if (dataDirectory.getFullPathName().length() == 0)
- {
- // temporary fix in case nothing is returned by the record node.
- dataDirectory = File::getSpecialLocation(File::userHomeDirectory);
- }
-
- baseDirectory = dataDirectory.getFullPathName();
-
- for (int i = 0; i < getNumElectrodes(); i++)
- {
- openFile(i);
- }
-
} else if (param == 2) // redraw
{
redrawRequested = true;
@@ -207,16 +194,6 @@ void SpikeDisplayNode::process(AudioSampleBuffer& buffer, MidiBuffer& events, in
checkForEvents(events); // automatically calls 'handleEvent
- if (signalFilesShouldClose)
- {
- for (int i = 0; i < getNumElectrodes(); i++)
- {
- closeFile(i);
- }
-
- signalFilesShouldClose = false;
- }
-
if (redrawRequested)
{
// update incoming thresholds
@@ -298,7 +275,7 @@ void SpikeDisplayNode::handleEvent(int eventType, MidiMessage& event, int sample
// save spike
if (isRecording)
{
- writeSpike(newSpike, electrodeNum);
+ getProcessorGraph()->getRecordNode()->writeSpike(newSpike,e.recordIndex);
}
}
@@ -327,139 +304,3 @@ bool SpikeDisplayNode::checkThreshold(int chan, float thresh, SpikeObject& s)
return false;
}
-
-void SpikeDisplayNode::openFile(int i)
-{
-
- String filename = baseDirectory;
- filename += File::separator;
- filename += getNameForElectrode(i).removeCharacters(" ");
- filename += ".spikes";
-
- std::cout << "OPENING FILE: " << filename << std::endl;
-
- File fileToUse = File(filename);
-
- diskWriteLock->enter();
- //const MessageManagerLock mmLock;
-
- Electrode& e = electrodes.getReference(i);
-
- FILE* file;
-
- if (!fileToUse.exists())
- {
- // open it and write header
-
- if (i == 0)
- {
- recordingNumber = 0;
- }
-
- file = fopen(filename.toUTF8(), "ab");
- String header = generateHeader(i);
- fwrite(header.toUTF8(), 1, header.getNumBytesAsUTF8(), file);
-
- }
- else
- {
- // append it
- if (i == 0)
- {
- recordingNumber++;
- }
-
- file = fopen(filename.toUTF8(), "ab");
- }
-
- diskWriteLock->exit();
-
- e.file = file;
-}
-
-void SpikeDisplayNode::closeFile(int i)
-{
-
- Electrode& e = electrodes.getReference(i);
-
- std::cout << "CLOSING FILE for " << e.name << std::endl;
-
- diskWriteLock->enter();
-
- if (e.file != NULL)
- {
- fclose(e.file);
- }
-
- diskWriteLock->exit();
-
-}
-
-void SpikeDisplayNode::writeSpike(const SpikeObject& s, int i)
-{
-
- packSpike(&s, spikeBuffer, MAX_SPIKE_BUFFER_LEN);
-
- int totalBytes = s.nSamples * s.nChannels * 2 + // account for samples
- s.nChannels * 4 + // acount for threshold and gain
- 15; // 15 bytes in every SpikeObject
-
-
- // format:
- // 1 byte of event type (always = 4 for spikes)
- // 8 bytes for 64-bit timestamp
- // 2 bytes for 16-bit electrode ID
- // 2 bytes for 16-bit number of channels (n)
- // 2 bytes for 16-bit number of samples (m)
- // 2*n*m bytes for 16-bit samples
- // 2*n bytes for 16-bit gains
- // 2*n bytes for 16-bit thresholds
-
- // const MessageManagerLock mmLock;
-
- diskWriteLock->enter();
-
- fwrite(spikeBuffer, 1, totalBytes, electrodes[i].file);
-
- fwrite(&recordingNumber, // ptr
- 2, // size of each element
- 1, // count
- electrodes[i].file); // ptr to FILE object
-
- diskWriteLock->exit();
-
-
-}
-
-String SpikeDisplayNode::generateHeader(int electrodeNum)
-{
- String header = "header.format = 'Open Ephys Data Format'; \n";
- header += "header.version = 0.2;";
- header += "header.header_bytes = ";
- header += String(HEADER_SIZE);
- header += ";\n";
-
- header += "header.description = 'Each record contains 1 uint8 eventType, 1 uint64 timestamp, 1 uint16 electrodeID, 1 uint16 numChannels (n), 1 uint16 numSamples (m), n*m uint16 samples, n uint16 channelGains, n uint16 thresholds, and 1 uint16 recordingNumber'; \n";
-
- header += "header.date_created = '";
- header += recordNode->generateDateString();
- header += "';\n";
-
- header += "header.electrode = '";
- header += electrodes[electrodeNum].name;
- header += "';\n";
-
- header += "header.num_channels = ";
- header += electrodes[electrodeNum].numChannels;
- header += ";\n";
-
- header += "header.sampleRate = ";
- header += String(settings.sampleRate);
- header += ";\n";
-
- header = header.paddedRight(' ', HEADER_SIZE);
-
- //std::cout << header << std::endl;
-
- return header;
-}
\ No newline at end of file
diff --git a/Source/Processors/SpikeDisplayNode.h b/Source/Processors/SpikeDisplayNode.h
index b6909c2f6..3fa0c364b 100755
--- a/Source/Processors/SpikeDisplayNode.h
+++ b/Source/Processors/SpikeDisplayNode.h
@@ -95,7 +95,7 @@ private:
SpikePlot* spikePlot;
- FILE* file;
+ int recordIndex;
};
@@ -104,24 +104,18 @@ private:
int displayBufferSize;
bool redrawRequested;
- // methods for recording:
- void openFile(int index);
- void closeFile(int index);
- void writeSpike(const SpikeObject& s, int index);
- String generateHeader(int index);
-
// members for recording
bool isRecording;
- bool signalFilesShouldClose;
- RecordNode* recordNode;
- String baseDirectory;
- File dataDirectory;
- uint8_t* spikeBuffer;
- SpikeObject currentSpike;
-
- uint16 recordingNumber;
+ // bool signalFilesShouldClose;
+ // RecordNode* recordNode;
+ // String baseDirectory;
+ // File dataDirectory;
+ // uint8_t* spikeBuffer;
+ // SpikeObject currentSpike;
+
+ // uint16 recordingNumber;
- CriticalSection* diskWriteLock;
+// CriticalSection* diskWriteLock;
JUCE_DECLARE_NON_COPYABLE_WITH_LEAK_DETECTOR(SpikeDisplayNode);
--
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