Merge branch 'testing' into development

Author: aacuevas

Builds/MacOSX/Plugins/EvntTrigAvg/EvntTrigAvg.xcodeproj/project.pbxproj

@@ -6,6 +6,13 @@
 	objectVersion = 48;
 	objects = {
 
+/* Begin PBXBuildFile section */
+		038C244D1FA389C4006EA927 /* EvntTrigAvg.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 038981DE1FA2F00200D25D7A /* EvntTrigAvg.cpp */; };
+		038C244E1FA389C4006EA927 /* EvntTrigAvgCanvas.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 038981E31FA2F00300D25D7A /* EvntTrigAvgCanvas.cpp */; };
+		038C244F1FA389C4006EA927 /* EvntTrigAvgEditor.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 038981E21FA2F00200D25D7A /* EvntTrigAvgEditor.cpp */; };
+		038C24501FA38A0F006EA927 /* OpenEphysLib.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 038981E11FA2F00200D25D7A /* OpenEphysLib.cpp */; };
+/* End PBXBuildFile section */
+
 /* Begin PBXFileReference section */
 		038981D31FA2EFB500D25D7A /* EvntTrigAvg.bundle */ = {isa = PBXFileReference; explicitFileType = wrapper.cfbundle; includeInIndex = 0; path = EvntTrigAvg.bundle; sourceTree = BUILT_PRODUCTS_DIR; };
 		038981D61FA2EFB500D25D7A /* Info.plist */ = {isa = PBXFileReference; lastKnownFileType = text.plist.xml; path = Info.plist; sourceTree = "<group>"; };
@@ -146,6 +153,10 @@
 			isa = PBXSourcesBuildPhase;
 			buildActionMask = 2147483647;
 			files = (
+				038C24501FA38A0F006EA927 /* OpenEphysLib.cpp in Sources */,
+				038C244D1FA389C4006EA927 /* EvntTrigAvg.cpp in Sources */,
+				038C244E1FA389C4006EA927 /* EvntTrigAvgCanvas.cpp in Sources */,
+				038C244F1FA389C4006EA927 /* EvntTrigAvgEditor.cpp in Sources */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};

Source/Plugins/BasicSpikeDisplay/SpikeDetector/SpikeDetector.cpp

@@ -101,8 +101,11 @@ void SpikeDetector::createSpikeChannels()
 
 void SpikeDetector::updateSettings()
 {
-    if (getNumInputs() > 0)
-        overflowBuffer.setSize (getNumInputs(), overflowBufferSize);
+	if (getNumInputs() > 0)
+	{
+		overflowBuffer.setSize(getNumInputs(), overflowBufferSize);
+		overflowBuffer.clear();
+	}
 
 }
 
@@ -516,7 +519,7 @@ float SpikeDetector::getNextSample (int& chan)
     }
     else
     {
-        if (sampleIndex < dataBuffer->getNumSamples())
+        if (sampleIndex < getNumSamples(chan))
             return *dataBuffer->getWritePointer (chan, sampleIndex);
         else
             return 0;

Source/Plugins/EvntTrigAvg/Makefile

@@ -0,0 +1,39 @@
+
+LIBNAME := $(notdir $(CURDIR))
+OBJDIR := $(OBJDIR)/$(LIBNAME)
+TARGET := $(LIBNAME).so
+
+
+SRC_DIR := ${shell find ./ -type d -print}
+VPATH := $(SOURCE_DIRS)
+
+SRC := $(foreach sdir,$(SRC_DIR),$(wildcard $(sdir)/*.cpp))
+OBJ := $(addprefix $(OBJDIR)/,$(notdir $(SRC:.cpp=.o)))
+
+BLDCMD := $(CXX) -shared -o $(OUTDIR)/$(TARGET) $(OBJ) $(LDFLAGS) $(RESOURCES) $(TARGET_ARCH)
+
+VPATH = $(SRC_DIR)
+
+.PHONY: objdir
+
+$(OUTDIR)/$(TARGET): objdir $(OBJ)
+	-@mkdir -p $(BINDIR)
+	-@mkdir -p $(LIBDIR)
+	-@mkdir -p $(OUTDIR)
+	@echo "Building $(TARGET)"
+	@$(BLDCMD)
+
+$(OBJDIR)/%.o : %.cpp
+	@echo "Compiling $<"
+	@$(CXX) $(CXXFLAGS) -o "$@" -c "$<"
+	
+	
+objdir:
+	-@mkdir -p $(OBJDIR)
+
+clean:
+	@echo "Cleaning $(LIBNAME)"
+	-@rm -rf $(OBJDIR)
+	-@rm -f $(OUTDIR)/$(TARGET)
+
+-include $(OBJ:%.o=%.d)

Source/Plugins/EvntTrigAvg/OpenEphysLib.cpp

@@ -37,7 +37,7 @@ using namespace Plugin;
 extern "C" EXPORT void getLibInfo(Plugin::LibraryInfo* info)
 {
 	info->apiVersion = PLUGIN_API_VER;
-	info->name = "EvntTrigAvg";
+	info->name = "Event Trig Avg";
 	info->libVersion = 1;
 	info->numPlugins = NUM_PLUGINS;
 }
@@ -48,7 +48,7 @@ extern "C" EXPORT int getPluginInfo(int index, Plugin::PluginInfo* info)
 	{
 	case 0:
 		info->type = Plugin::PLUGIN_TYPE_PROCESSOR;
-		info->processor.name = "EvntTrigAvg";
+		info->processor.name = "Event Trig Avg";
 		info->processor.type = Plugin::FilterProcessor;
 		info->processor.creator = &(Plugin::createProcessor<EvntTrigAvg>);
 		break;

Source/Plugins/SpikeSorter/SpikeSortBoxes.cpp

@@ -882,9 +882,10 @@ void SpikeSortBoxes::projectOnPrincipalComponents(SorterSpikePtr so)
         if ((spikeBufferIndex == bufferSize -1 && !bPCAcomputed && !bPCAJobSubmitted) || bRePCA)
         {
             bPCAJobSubmitted = true;
+	    bPCAcomputed = false;
             bRePCA = false;
             // submit a new job to compute the spike buffer.
-            PCAjob job(spikeBuffer,pc1,pc2, &pc1min, &pc2min, &pc1max, &pc2max, &bPCAjobFinished);
+            PCAJobPtr job = new PCAjob(spikeBuffer,pc1,pc2, pc1min, pc2min, pc1max, pc2max, bPCAjobFinished);
             computingThread->addPCAjob(job);
         }
     }
@@ -1706,15 +1707,13 @@ static double sqrarg;
 #define SQR(a) ((sqrarg = (a)) == 0.0 ? 0.0 : sqrarg * sqrarg)
 
 PCAjob::PCAjob(SorterSpikeArray& _spikes, float* _pc1, float* _pc2,
-               float* pc1Min, float* pc2Min, float* pc1Max, float* pc2Max, bool* _reportDone) : spikes(_spikes), reportDone(_reportDone)
+                std::atomic<float>& pc1Min,  std::atomic<float>& pc2Min,  std::atomic<float>&pc1Max,  std::atomic<float>& pc2Max, std::atomic<bool>& _reportDone) : spikes(_spikes),
+pc1min(pc1Min), pc2min(pc2Min), pc1max(pc1Max), pc2max(pc2Max), reportDone(_reportDone)
 {
     cov = nullptr;
     pc1 = _pc1;
     pc2 = _pc2;
-    pc1min = pc1Min;
-    pc2min = pc2Min;
-    pc1max = pc1Max;
-    pc2max = pc2Max;
+
     dim = spikes[0]->getChannel()->getNumChannels()*spikes[0]->getChannel()->getTotalSamples();
 
 };
@@ -2114,10 +2113,10 @@ void PCAjob::computeSVD()
     }
 
 
-    *pc1min = min1 - 1.5 * (max1-min1);
-    *pc2min = min2 - 1.5 * (max2-min2);
-    *pc1max = max1 + 1.5 * (max1-min1);
-    *pc2max = max2 + 1.5 * (max2-min2);
+    pc1min = min1 - 1.5 * (max1-min1);
+    pc2min = min2 - 1.5 * (max2-min2);
+    pc1max = max1 + 1.5 * (max1-min1);
+    pc2max = max2 + 1.5 * (max2-min2);
 
     // clear memory
     for (int k = 0; k < dim; k++)
@@ -2129,7 +2128,7 @@ void PCAjob::computeSVD()
 
     // delete covariances
     for (int k = 0; k < dim; k++)
-        delete cov[k];
+        delete[] cov[k];
 
     delete[] cov;
     cov = nullptr;
@@ -2140,11 +2139,11 @@ void PCAjob::computeSVD()
 /**********************/
 
 
-void PCAcomputingThread::addPCAjob(PCAjob job)
+void PCAcomputingThread::addPCAjob(PCAJobPtr job)
 {
 	{
 		ScopedLock critical(lock);
-		jobs.push(job);
+		jobs.add(job);
 	}
 
     if (!isThreadRunning())
@@ -2158,19 +2157,19 @@ void PCAcomputingThread::run()
     while (jobs.size() > 0)
     {
 		lock.enter();
-        PCAjob J = jobs.front();
-        jobs.pop();
+        PCAJobPtr J = jobs.removeAndReturn(0);
+	if (J == nullptr) continue;
 		lock.exit();
         // compute PCA
         // 1. Compute Covariance matrix
         // 2. Apply SVD on covariance matrix
         // 3. Extract the two principal components corresponding to the largest singular values
 
-        J.computeCov();
-        J.computeSVD();
+        J->computeCov();
+        J->computeSVD();
 
         // 4. Report to the spike sorting electrode that PCA is finished
-        *(J.reportDone) = true;
+        J->reportDone = true;
     }
 }
 
@@ -2239,4 +2238,4 @@ const SpikeChannel* SorterSpikeContainer::getChannel() const
 int64 SorterSpikeContainer::getTimestamp() const
 {
 	return timestamp;
-}
+}

Source/Plugins/SpikeSorter/SpikeSortBoxes.h

@@ -28,6 +28,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include <algorithm>    // std::sort
 #include <list>
 #include <queue>
+#include <atomic>
 
 class SorterSpikeContainer : public ReferenceCountedObject
 {
@@ -176,26 +177,28 @@ class PCAjob
 public:
 PCAjob();
 };*/
-class PCAjob
+class PCAjob : public ReferenceCountedObject
 {
 public:
     PCAjob(SorterSpikeArray& _spikes, float* _pc1, float* _pc2,
-           float*, float*, float*, float*, bool* _reportDone);
+           std::atomic<float>&,  std::atomic<float>&,  std::atomic<float>&,  std::atomic<float>&, std::atomic<bool>& _reportDone);
     ~PCAjob();
     void computeCov();
     void computeSVD();
 
     float** cov;
     SorterSpikeArray spikes;
     float* pc1, *pc2;
-    float* pc1min, *pc2min, *pc1max, *pc2max;
-    bool* reportDone;
+    std::atomic<float>& pc1min, &pc2min, &pc1max, &pc2max;
+    std::atomic<bool>& reportDone;
 private:
     int svdcmp(float** a, int nRows, int nCols, float* w, float** v);
     float pythag(float a, float b);
     int dim;
 };
 
+typedef ReferenceCountedObjectPtr<PCAjob> PCAJobPtr;
+typedef ReferenceCountedArray<PCAjob, CriticalSection> PCAJobArray;
 
 class cPolygon
 {
@@ -213,10 +216,10 @@ class PCAcomputingThread : juce::Thread
 public:
     PCAcomputingThread();
     void run(); // computes PCA on waveforms
-    void addPCAjob(PCAjob job);
+    void addPCAjob(PCAJobPtr job);
 
 private:
-    std::queue<PCAjob> jobs;
+    PCAJobArray jobs;
 	CriticalSection lock;
 };
 
@@ -299,11 +302,12 @@ class SpikeSortBoxes
     std::vector<BoxUnit> boxUnits;
     std::vector<PCAUnit> pcaUnits;
     float* pc1, *pc2;
-    float pc1min, pc2min, pc1max, pc2max;
+    std::atomic<float> pc1min, pc2min, pc1max, pc2max;
     SorterSpikeArray spikeBuffer;
     int bufferSize,spikeBufferIndex;
     PCAcomputingThread* computingThread;
-    bool bPCAJobSubmitted,bPCAcomputed,bRePCA,bPCAjobFinished ;
+    bool bPCAJobSubmitted,bPCAcomputed,bRePCA;
+    std::atomic<bool> bPCAjobFinished ;
 
 
 };

Source/Plugins/SpikeSorter/SpikeSorter.cpp

@@ -172,9 +172,13 @@ void SpikeSorter::updateSettings()
 {
 
     mut.enter();
+	sorterReady = false;
     int numChannels = getNumInputs();
-    if (numChannels > 0)
-        overflowBuffer.setSize(getNumInputs(), overflowBufferSize);
+	if (numChannels > 0)
+	{
+		overflowBuffer.setSize(getNumInputs(), overflowBufferSize);
+		overflowBuffer.clear();
+	}
 
     if (channelBuffers != nullptr)
         delete channelBuffers;
@@ -191,7 +195,13 @@ void SpikeSorter::updateSettings()
 		Array<const DataChannel*> chans;
 		for (int c = 0; c < nChans; c++)
 		{
-			chans.add(getDataChannel(elec->channels[c]));
+			const DataChannel* ch = getDataChannel(elec->channels[c]);
+			if (!ch)
+			{
+				//not enough channels for the electrodes
+				return;
+			}
+			chans.add(ch);
 		}
 
 		SpikeChannel* spk = new SpikeChannel(SpikeChannel::typeFromNumChannels(nChans), this, chans);
@@ -200,7 +210,7 @@ void SpikeSorter::updateSettings()
 
         spikeChannelArray.add(spk);
     }
-
+	sorterReady = true;
     mut.exit();
 }
 
@@ -212,9 +222,6 @@ Electrode::~Electrode()
     delete[] voltageScale;
     delete[] channels;
     delete[] runningStats;
-
-	delete spikeSort;
-
 }
 
 Electrode::Electrode(int ID, UniqueIDgenerator* uniqueIDgenerator_, PCAcomputingThread* pth, String _name, int _numChannels, int* _channels, float default_threshold, int pre, int post, float samplingRate , int sourceId, int subIdx)
@@ -459,6 +466,7 @@ bool SpikeSorter::addElectrode(int nChans, String name, double Depth)
         eventlog += String(chans[k])+ " " + name;
 
     //addNetworkEventToQueue(StringTS(eventlog));
+    delete[] chans;
 
     resetElectrode(newElectrode);
     electrodes.add(newElectrode);
@@ -647,6 +655,12 @@ bool SpikeSorter::enable()
 {
 
     useOverflowBuffer.clear();
+	if (!sorterReady)
+	{
+		CoreServices::sendStatusMessage("Not enough channels for the configured electrodes");
+		std::cout << "SpikeSorter: Not enough channels for the configured electrodes" << std::endl;
+		return false;
+	}
 
     for (int i = 0; i < electrodes.size(); i++)
         useOverflowBuffer.add(false);
@@ -1036,7 +1050,7 @@ float SpikeSorter::getNextSample(int& chan)
         //  useOverflowBuffer = false;
         // std::cout << "  sample index " << sampleIndex << "from regular buffer" << std::endl;
 
-        if (sampleIndex < dataBuffer->getNumSamples())
+        if (sampleIndex < getNumSamples(chan))
             return (*dataBuffer->getReadPointer(chan, sampleIndex));
         else
             return 0;
@@ -1112,7 +1126,7 @@ void SpikeSorter::addProbes(String probeType,int numProbes, int nElectrodesPerPr
         increaseUniqueProbeID(probeType);
     }
 }
-Array<Electrode*> SpikeSorter::getElectrodes()
+const OwnedArray<Electrode>& SpikeSorter::getElectrodes()
 {
     return electrodes;
 }
@@ -1292,6 +1306,9 @@ void SpikeSorter::loadCustomParametersFromXml()
                             newElectrode->thresholds[k] = thres[k];
                             newElectrode->isActive[k] = isActive[k];
                         }
+			delete[] channels;
+			delete[] thres;
+			delete[] isActive;
 
                         newElectrode->advancerID = advancerID;
                         newElectrode->depthOffsetMM = depthOffsetMM;