diff --git a/Source/Processors/Editors/SpikeSorterEditor.cpp b/Source/Processors/Editors/SpikeSorterEditor.cpp
index fc286491a21271086d24fdf91c9cbd0b50208886..fc7340e4a73795bdd69d14d4ae94df87ab03aa23 100644
--- a/Source/Processors/Editors/SpikeSorterEditor.cpp
+++ b/Source/Processors/Editors/SpikeSorterEditor.cpp
@@ -431,6 +431,8 @@ void SpikeSorterEditor::buttonEvent(Button* button)
processor->addProbes(ProbeType,numProbes, nElectrodes,nChansPerElectrode, firstElectrodeOffset,interelectrodeDistance);
refreshElectrodeList();
+
+ getEditorViewport()->makeEditorVisible(this, true, true);
return;
diff --git a/Source/Processors/SpikeSortBoxes.cpp b/Source/Processors/SpikeSortBoxes.cpp
index 8c972882a6a5bc317930d5e19d2034154c8b51f7..d399221d3c44ee497f09df699ef418d0061d1990 100644
--- a/Source/Processors/SpikeSortBoxes.cpp
+++ b/Source/Processors/SpikeSortBoxes.cpp
@@ -1743,8 +1743,9 @@ float PCAjob::pythag(float a, float b) {
V (not V transpose) is output as the matrix V[nCols][nCols].
*/
int PCAjob::svdcmp(float **a, int nRows, int nCols, float *w, float **v) {
- int flag,i,its,j,jj,k,l,nm;
- float anorm,c,f,g,h,s,scale,x,y,z,*rv1;
+
+ int flag, i, its, j, jj, k, l, nm;
+ float anorm, c, f, g, h, s, scale, x, y, z, *rv1;
rv1 = new float[nCols];
if(rv1 == NULL) {
@@ -1753,14 +1754,14 @@ int PCAjob::svdcmp(float **a, int nRows, int nCols, float *w, float **v) {
}
g = scale = anorm = 0.0;
- for(i=0;i<nCols;i++) {
+ for(i = 0; i < nCols; i++) {
l = i+1;
rv1[i] = scale*g;
g = s = scale = 0.0;
if(i < nRows) {
- for(k=i;k<nRows;k++) scale += fabs(a[k][i]);
+ for(k = i; k < nRows; k++) scale += fabs(a[k][i]);
if(scale) {
- for(k=i;k<nRows;k++) {
+ for(k = i; k < nRows; k++) {
a[k][i] /= scale;
s += a[k][i] * a[k][i];
}
@@ -1768,20 +1769,21 @@ int PCAjob::svdcmp(float **a, int nRows, int nCols, float *w, float **v) {
g = -SIGN(sqrt(s),f);
h = f * g - s;
a[i][i] = f - g;
- for(j=l;j<nCols;j++) {
- for(s=0.0,k=i;k<nRows;k++) s += a[k][i] * a[k][j];
+ for(j = l; j < nCols; j++) {
+ for(s = 0.0, k = i; k < nRows; k++) s += a[k][i] * a[k][j];
f = s / h;
- for(k=i;k<nRows;k++) a[k][j] += f * a[k][i];
+ for(k = i; k < nRows; k++) a[k][j] += f * a[k][i];
}
- for(k=i;k<nRows;k++) a[k][i] *= scale;
+ for(k = i; k < nRows; k++) a[k][i] *= scale;
}
}
w[i] = scale * g;
g = s = scale = 0.0;
if(i < nRows && i != nCols-1) {
- for(k=l;k<nCols;k++) scale += fabs(a[i][k]);
+ for(k = l; k < nCols; k++) scale += fabs(a[i][k]);
if(scale) {
- for(k=l;k<nCols;k++) {
+ for(k = l; k < nCols; k++)
+ {
a[i][k] /= scale;
s += a[i][k] * a[i][k];
}
@@ -1939,8 +1941,8 @@ void PCAjob::computeCov()
{
// allocate and zero
cov = new float*[dim];
- float *mean = new float[dim];
- for (int k=0;k<dim;k++) {
+ float* mean = new float[dim];
+ for (int k = 0;k < dim; k++) {
cov[k] = new float[dim];
for (int j=0;j<dim;j++)
{
@@ -1981,6 +1983,13 @@ void PCAjob::computeCov()
}
delete mean;
+ // delete covariances
+ for (int k = 0; k < dim; k++)
+ delete cov[k];
+
+ delete(cov);
+ cov = nullptr;
+
}
std::vector<int> sort_indexes( std::vector<float> v)
@@ -1993,16 +2002,15 @@ std::vector<int> sort_indexes( std::vector<float> v)
idx[i] = i;
}
- //// NEED TO FIX THIS:::: -- Linux compiler doesn't understand syntax!
- // sort indexes based on comparing values in v
- // sort(
- // idx.begin(),
- // idx.end(),
- // [&v](size_t i1, size_t i2)
- // {
- // return v[i1] > v[i2];
- // }
- // );
+ //sort indexes based on comparing values in v
+ sort(
+ idx.begin(),
+ idx.end()//,
+ //[&v](size_t i1, size_t i2)
+ //{
+ // return v[i1] > v[i2];
+ //}
+ );
return idx;
}
@@ -2015,30 +2023,23 @@ void PCAjob::computeSVD()
sigvalues = new float[dim];
eigvec = new float*[dim];
- for (int k=0;k<dim;k++) {
+ for (int k = 0; k < dim; k++) {
eigvec[k] = new float[dim];
for (int j=0;j<dim;j++)
{
eigvec[k][j] = 0;
}
}
-
- svdcmp(cov, dim, dim, sigvalues,eigvec );
- // find the two largest eigen values
- for (int k=0;k<dim;k++)
- delete cov[k];
- delete(cov);
- cov=nullptr;
+ svdcmp(cov, dim, dim, sigvalues, eigvec);
+
- std::vector<float> sig;
- sig.resize(dim);
- for (int k=0;k<dim;k++)
- sig[k] = sigvalues[k];
-
+ std::vector<float> sig;
+ sig.resize(dim);
+ for (int k = 0; k < dim; k++)
+ sig[k] = sigvalues[k];
-
std::vector<int> sortind = sort_indexes(sig);
//
@@ -2076,7 +2077,7 @@ void PCAjob::computeSVD()
*pc2max = max2 + 1.5 * (max2-min2);
// clear memory
- for (int k=0;k<dim;k++)
+ for (int k = 0; k < dim; k++)
{
delete eigvec[k];
}
diff --git a/Source/Processors/SpikeSorter.cpp b/Source/Processors/SpikeSorter.cpp
index 12b317ed4df9408b435919f83f25f281b1b61461..7eb8cf1a08e7d63b89b551305706d2f3a0890f09 100644
--- a/Source/Processors/SpikeSorter.cpp
+++ b/Source/Processors/SpikeSorter.cpp
@@ -188,13 +188,19 @@ void SpikeSorter::updateSettings()
double ContinuousBufferLengthSec = 5;
channelBuffers = new ContinuousCircularBuffer(numChannels,SamplingRate,1, ContinuousBufferLengthSec);
- // instead, we pass things now in this new form:
- for (int k = 0; k < electrodes.size(); k++)
+ for (int i = 0; i < electrodes.size(); i++)
{
- String eventlog = "NewElectrode "+String(electrodes[k]->electrodeID) + " "+String(electrodes[k]->numChannels)+" ";
- for (int j=0;j<electrodes[k]->numChannels;j++)
- eventlog += String(electrodes[k]->channels[j])+ " "+electrodes[k]->name;
- //addNetworkEventToQueue(StringTS(eventlog));
+
+ Channel* ch = new Channel(this, i);
+ //ch->isEventChannel = true;
+ ch->eventType = SPIKE_BASE_CODE + electrodes[i]->numChannels;
+ ch->name = electrodes[i]->name;
+
+ eventChannels.add(ch);
+ // String eventlog = "NewElectrode "+String(electrodes[k]->electrodeID) + " "+String(electrodes[k]->numChannels)+" ";
+ // for (int j=0;j<electrodes[k]->numChannels;j++)
+ // eventlog += String(electrodes[k]->channels[j])+ " "+electrodes[k]->name;
+ // //addNetworkEventToQueue(StringTS(eventlog));
}
mut.exit();
@@ -319,14 +325,14 @@ void SpikeSorter::addNewUnit(int electrodeID, int newUnitID, uint8 r, uint8 g, u
{
String eventlog = "NewUnit "+String(electrodeID) + " "+String(newUnitID)+" "+String(r)+" "+String(g)+" "+String(b);
//addNetworkEventToQueue(StringTS(eventlog));
- updateSinks( electrodeID, newUnitID, r,g,b,true);
+ //updateSinks( electrodeID, newUnitID, r,g,b,true);
}
void SpikeSorter::removeUnit(int electrodeID, int unitID)
{
String eventlog = "RemoveUnit "+String(electrodeID) + " "+String(unitID);
//addNetworkEventToQueue(StringTS(eventlog));
- updateSinks( electrodeID, unitID, 0,0,0,false);
+ //updateSinks( electrodeID, unitID, 0,0,0,false);
}
@@ -335,7 +341,7 @@ void SpikeSorter::removeAllUnits(int electrodeID)
{
String eventlog = "RemoveAllUnits "+String(electrodeID);
//addNetworkEventToQueue(StringTS(eventlog));
- updateSinks( electrodeID,true);
+ //updateSinks( electrodeID,true);
}
RHD2000Thread* SpikeSorter::getRhythmAccess()
@@ -397,171 +403,13 @@ void SpikeSorter::assignDACtoChannel(int dacOutput, int channel)
}
}
-
-void SpikeSorter::updateSinks(int electrodeID, int unitID, uint8 r, uint8 g, uint8 b, bool addRemove)
-{
- // inform sinks about a new unit
- ProcessorGraph *gr = getProcessorGraph();
- Array<GenericProcessor*> p = gr->getListOfProcessors();
- // for (int k=0;k<p.size();k++)
- // {
- // if (p[k]->getName() == "PSTH")
- // {
- // PeriStimulusTimeHistogramNode *node = (PeriStimulusTimeHistogramNode*)p[k];
- // if (node->trialCircularBuffer != nullptr)
- // {
- // if (addRemove)
- // {
- // // add electrode
- // node->trialCircularBuffer->addNewUnit(electrodeID,unitID,r,g,b);
- // } else
- // {
- // // remove electrode
- // node->trialCircularBuffer->removeUnit(electrodeID,unitID);
- // }
- // ((PeriStimulusTimeHistogramEditor *) node->getEditor())->updateCanvas();
- // }
- // }
- // }
-}
-
-void SpikeSorter::updateSinks(int electrodeID, bool rem)
-{
- // inform sinks about a removal of all units
- ProcessorGraph *g = getProcessorGraph();
- Array<GenericProcessor*> p = g->getListOfProcessors();
- // for (int k=0;k<p.size();k++)
- // {
- // if (p[k]->getName() == "PSTH")
- // {
- // PeriStimulusTimeHistogramNode *node = (PeriStimulusTimeHistogramNode*)p[k];
- // if (node->trialCircularBuffer != nullptr)
- // {
- // if (rem)
- // {
- // node->trialCircularBuffer->removeAllUnits(electrodeID);
- // }
- // (((PeriStimulusTimeHistogramEditor *) node->getEditor()))->updateCanvas();
- // }
- // }
- // if (p[k]->getName() == "Spike Viewer")
- // {
- // SpikeDisplayNode* node = (SpikeDisplayNode*)p[k];
- // node->syncWithSpikeSorter();
- // }
- // }
-}
-
-void SpikeSorter::updateSinks(int electrodeID, int channelindex, int newchannel)
-{
- // inform sinks about a channel change
- ProcessorGraph *g = getProcessorGraph();
- Array<GenericProcessor*> p = g->getListOfProcessors();
- // for (int k=0;k<p.size();k++)
- // {
- // if (p[k]->getName() == "PSTH")
- // {
- // PeriStimulusTimeHistogramNode *node = (PeriStimulusTimeHistogramNode*)p[k];
- // if (node->trialCircularBuffer != nullptr)
- // {
- // node->trialCircularBuffer->channelChange(electrodeID, channelindex,newchannel);
- // }
- // }
- // if (p[k]->getName() == "Spike Viewer")
- // {
- // SpikeDisplayNode* node = (SpikeDisplayNode*)p[k];
- // node->syncWithSpikeSorter();
- // }
- // }
-}
-
-
-void SpikeSorter::updateSinks(Electrode* electrode)
-{
- // inform sinks about an electrode add
- ProcessorGraph *g = getProcessorGraph();
- Array<GenericProcessor*> p = g->getListOfProcessors();
- // for (int k=0;k<p.size();k++)
- // {
- // String s = p[k]->getName();
- // if (p[k]->getName() == "PSTH")
- // {
- // PeriStimulusTimeHistogramNode *node = (PeriStimulusTimeHistogramNode*)p[k];
- // if (node->trialCircularBuffer != nullptr)
- // {
- // // add electrode
- // node->trialCircularBuffer->addNewElectrode(electrode);
- // (((PeriStimulusTimeHistogramEditor *) node->getEditor()))->updateCanvas();
- // }
- // }
- // if (p[k]->getName() == "Spike Viewer")
- // {
- // SpikeDisplayNode* node = (SpikeDisplayNode*)p[k];
- // node->syncWithSpikeSorter();
- // }
- // }
-}
-
-void SpikeSorter::updateSinks(int electrodeID, String NewName)
-{
- // inform sinks about an electrode name change
- ProcessorGraph *g = getProcessorGraph();
- Array<GenericProcessor*> p = g->getListOfProcessors();
- // for (int k=0;k<p.size();k++)
- // {
- // String s = p[k]->getName();
- // if (p[k]->getName() == "PSTH")
- // {
- // PeriStimulusTimeHistogramNode *node = (PeriStimulusTimeHistogramNode*)p[k];
- // if (node->trialCircularBuffer != nullptr)
- // {
- // // add electrode
- // node->trialCircularBuffer->updateElectrodeName(electrodeID, NewName);
- // (((PeriStimulusTimeHistogramEditor *) node->getEditor()))->updateCanvas();
- // }
- // }
- // if (p[k]->getName() == "Spike Viewer")
- // {
- // SpikeDisplayNode* node = (SpikeDisplayNode*)p[k];
- // node->syncWithSpikeSorter();
- // }
- // }
-}
-
-
-void SpikeSorter::updateSinks(int electrodeID)
-{
- // inform sinks about an electrode removal
- ProcessorGraph *g = getProcessorGraph();
- Array<GenericProcessor*> p = g->getListOfProcessors();
- // for (int k=0;k<p.size();k++)
- // {
- // String s = p[k]->getName();
- // if (p[k]->getName() == "PSTH")
- // {
- // PeriStimulusTimeHistogramNode *node = (PeriStimulusTimeHistogramNode*)p[k];
- // if (node->trialCircularBuffer != nullptr)
- // {
- // // remove electrode
- // node->trialCircularBuffer->removeElectrode(electrodeID);
- // ((PeriStimulusTimeHistogramEditor *) node->getEditor())->updateCanvas();
- // }
- // }
- // if (p[k]->getName() == "Spike Viewer")
- // {
- // SpikeDisplayNode* node = (SpikeDisplayNode*)p[k];
- // node->syncWithSpikeSorter();
- // }
- // }
-}
-
void SpikeSorter::addElectrode(Electrode* newElectrode)
{
mut.enter();
resetElectrode(newElectrode);
electrodes.add(newElectrode);
// inform PSTH sink, if it exists, about this new electrode.
- updateSinks(newElectrode);
+ //updateSinks(newElectrode);
mut.exit();
}
@@ -605,7 +453,7 @@ bool SpikeSorter::addElectrode(int nChans, String name, double Depth)
resetElectrode(newElectrode);
electrodes.add(newElectrode);
- updateSinks(newElectrode);
+ //updateSinks(newElectrode);
setCurrentElectrodeIndex(electrodes.size()-1);
mut.exit();
return true;
@@ -654,7 +502,7 @@ bool SpikeSorter::removeElectrode(int index)
int idToRemove = electrodes[index]->electrodeID;
electrodes.remove(index);
- updateSinks(idToRemove);
+ //(idToRemove);
if (electrodes.size() > 0)
currentElectrode = electrodes.size()-1;
@@ -669,7 +517,7 @@ void SpikeSorter::setElectrodeName(int index, String newName)
{
mut.enter();
electrodes[index-1]->name = newName;
- updateSinks(electrodes[index-1]->electrodeID, newName);
+ //updateSinks(electrodes[index-1]->electrodeID, newName);
mut.exit();
}
@@ -685,7 +533,7 @@ void SpikeSorter::setChannel(int electrodeIndex, int channelNum, int newChannel)
String eventlog = "ChanelElectrodeChannel " + String(electrodes[electrodeIndex]->electrodeID) + " " + String(channelNum) + " " + String(newChannel);
//addNetworkEventToQueue(StringTS(eventlog));
- updateSinks(electrodes[electrodeIndex]->electrodeID, channelNum,newChannel);
+ //updateSinks(electrodes[electrodeIndex]->electrodeID, channelNum,newChannel);
*(electrodes[electrodeIndex]->channels+channelNum) = newChannel;
mut.exit();
diff --git a/Source/Processors/SpikeSorter.h b/Source/Processors/SpikeSorter.h
index 3df7bddc4edd1ad6c744948e66a2b7ab2185074b..82136225e4c17963071dd4a8f89c6f84d5d0697c 100644
--- a/Source/Processors/SpikeSorter.h
+++ b/Source/Processors/SpikeSorter.h
@@ -238,19 +238,6 @@ public:
/** returns a channel's detection threshold */
double getChannelThreshold(int electrodeNum, int channelNum);
-
- /** sync PSTH : inform of a new electrode added */
- void updateSinks(Electrode* newElectrode);
- /** sync PSTH : inform of an electrode removal */
- void updateSinks(int electrodeID);
- /** sync PSTH : inform of a channel swap */
- void updateSinks(int electrodeID, int channelindex, int newchannel);
- /** sync PSTH: inform of a new unit added / removed */
- void updateSinks(int electrodeID, int unitID, uint8 r, uint8 g, uint8 b, bool addRemove);
- /** sync PSTH: inform of a name change*/
- void updateSinks(int electrodeID, String NewName);
- /** sync PSTH: remove all units*/
- void updateSinks(int electrodeID, bool b);
/** used to generate messages over the network and to inform PSTH sink */
void addNewUnit(int electrodeID, int newUnitID, uint8 r, uint8 g, uint8 b);
diff --git a/Source/Processors/Visualization/SpikeDisplayCanvas.cpp b/Source/Processors/Visualization/SpikeDisplayCanvas.cpp
index 7145dca563b4775c91d34def9e2cfcc2d91a21f0..67db2c80ca9c6f5740705461a04ce4d9134fa496 100755
--- a/Source/Processors/Visualization/SpikeDisplayCanvas.cpp
+++ b/Source/Processors/Visualization/SpikeDisplayCanvas.cpp
@@ -486,12 +486,14 @@ float SpikeDisplay::getRangeForWaveAxis(int plotNum, int axisNum)
void SpikeDisplay::setThresholdForWaveAxis(int plotNum, int axisNum, float range)
{
- return spikePlots[plotNum]->setDisplayThresholdForChannel(axisNum, range);
+ if (spikePlots.size() > plotNum)
+ return spikePlots[plotNum]->setDisplayThresholdForChannel(axisNum, range);
}
void SpikeDisplay::setRangeForWaveAxis(int plotNum, int axisNum, float range)
{
- return spikePlots[plotNum]->setRangeForChannel(axisNum, range);
+ if (spikePlots.size() > plotNum)
+ return spikePlots[plotNum]->setRangeForChannel(axisNum, range);
}
// ----------------------------------------------------------------
diff --git a/Source/Processors/Visualization/SpikeSorterCanvas.cpp b/Source/Processors/Visualization/SpikeSorterCanvas.cpp
index cccddfbff3f9edca6eae7e2cce022ab2dc70219a..170f41189b2c4af5a86e0e85eed5ac063076f1aa 100644
--- a/Source/Processors/Visualization/SpikeSorterCanvas.cpp
+++ b/Source/Processors/Visualization/SpikeSorterCanvas.cpp
@@ -108,14 +108,14 @@ void SpikeSorterCanvas::beginAnimation()
{
std::cout << "SpikeSorterCanvas beginning animation." << std::endl;
- //startCallbacks();
+ startCallbacks();
}
void SpikeSorterCanvas::endAnimation()
{
std::cout << "SpikeSorterCanvas ending animation." << std::endl;
- // stopCallbacks();
+ stopCallbacks();
}
void SpikeSorterCanvas::update()
@@ -380,7 +380,7 @@ void SpikeSorterCanvas::buttonClicked(Button* button)
// generate new IDs
processor->getActiveElectrode()->spikeSort->generateNewIDs();
electrode->spikePlot->updateUnitsFromProcessor();
- processor->updateSinks(electrode->electrodeID,false);
+ //processor->updateSinks(electrode->electrodeID,false);
} else if (button == deleteAllUnits)
{
// delete unit
@@ -1853,20 +1853,20 @@ void PCAProjectionAxes::drawProjectedSpike(SpikeObject s)
void PCAProjectionAxes::redraw(bool subsample)
{
-// Graphics g(projectionImage);
-//
-// // recompute image
-// int w = getWidth();
-// int h = getHeight();
-// projectionImage.clear(juce::Rectangle<int>(0, 0, projectionImage.getWidth(), projectionImage.getHeight()),
-// Colours::black);
-//
-// int dk = (subsample) ? 5 : 1;
-//
-// for (int k=0;k<bufferSize;k+=dk)
-// {
-// drawProjectedSpike(spikeBuffer[k]);
-// }
+ Graphics g(projectionImage);
+
+ // recompute image
+ int w = getWidth();
+ int h = getHeight();
+ projectionImage.clear(juce::Rectangle<int>(0, 0, projectionImage.getWidth(), projectionImage.getHeight()),
+ Colours::black);
+
+ int dk = (subsample) ? 5 : 1;
+
+ for (int k=0;k<bufferSize;k+=dk)
+ {
+ drawProjectedSpike(spikeBuffer[k]);
+ }
}