diff --git a/Source/Processors/DataThreads/RHD2000Thread.cpp b/Source/Processors/DataThreads/RHD2000Thread.cpp
index e62533202e839d75650bf9efbf0adcfa2571d89d..5a6194797519d6367308ecf464f5c2a50152a8b6 100644
--- a/Source/Processors/DataThreads/RHD2000Thread.cpp
+++ b/Source/Processors/DataThreads/RHD2000Thread.cpp
@@ -34,19 +34,21 @@
#define okLIB_NAME "./libokFrontPanel.so"
#define okLIB_EXTENSION "*.so"
#endif
-
+#define CHIP_ID_RHD2164_B 1000
// Allocates memory for a 3-D array of doubles.
-void allocateDoubleArray3D(std::vector<std::vector<std::vector<double> > > &array3D,
- int xSize, int ySize, int zSize)
+void allocateDoubleArray3D(std::vector<std::vector<std::vector<double> > >& array3D,
+ int xSize, int ySize, int zSize)
{
int i, j;
if (xSize == 0) return;
array3D.resize(xSize);
- for (i = 0; i < xSize; ++i) {
+ for (i = 0; i < xSize; ++i)
+ {
array3D[i].resize(ySize);
- for (j = 0; j < ySize; ++j) {
+ for (j = 0; j < ySize; ++j)
+ {
array3D[i][j].resize(zSize);
}
}
@@ -81,25 +83,25 @@ RHD2000Thread::RHD2000Thread(SourceNode* sn) : DataThread(sn),
// Returns 1 if successful, -1 if FrontPanel cannot be loaded, and -2 if XEM6010 can't be found.
File executable = File::getSpecialLocation(File::currentExecutableFile);
- #if defined(__APPLE__)
- const String executableDirectory =
- executable.getParentDirectory().getParentDirectory().getParentDirectory().getParentDirectory().getFullPathName();
- #else
- const String executableDirectory = executable.getParentDirectory().getFullPathName();
-
+#if defined(__APPLE__)
+ const String executableDirectory =
+ executable.getParentDirectory().getParentDirectory().getParentDirectory().getParentDirectory().getFullPathName();
+#else
+ const String executableDirectory = executable.getParentDirectory().getFullPathName();
+
+
+#endif
- #endif
-
std::cout << executableDirectory << std::endl;
-
+
String dirName = executableDirectory;
libraryFilePath = dirName;
libraryFilePath += File::separatorString;
libraryFilePath += okLIB_NAME;
-
+
dacStream = nullptr;
- dacChannels = nullptr;
+ dacChannels = nullptr;
dacThresholds = nullptr;
dacChannelsToUpdate = nullptr;
if (openBoard(libraryFilePath))
@@ -111,23 +113,23 @@ RHD2000Thread::RHD2000Thread(SourceNode* sn) : DataThread(sn),
// automatically find connected headstages
scanPorts(); // things would appear to run more smoothly if this were done after the editor has been created
- // to perform electrode impedance measurements at very low frequencies.
+ // to perform electrode impedance measurements at very low frequencies.
const int maxNumBlocks = 120;
int numStreams = 8;
allocateDoubleArray3D(amplifierPreFilter, numStreams, 32, SAMPLES_PER_DATA_BLOCK * maxNumBlocks);
// probably better to do this with a thread, but a timer works for now:
- // startTimer(10); // initialize the board in the background
- dacStream = new int[8];
- dacChannels = new int[8];
- dacThresholds = new float[8];
- dacChannelsToUpdate = new bool[8];
- for (int k = 0; k < 8; k++)
- {
+ // startTimer(10); // initialize the board in the background
+ dacStream = new int[8];
+ dacChannels = new int[8];
+ dacThresholds = new float[8];
+ dacChannelsToUpdate = new bool[8];
+ for (int k = 0; k < 8; k++)
+ {
dacChannelsToUpdate[k] = true;
dacStream[k] = 0;
setDACthreshold(k, 65534);
- }
+ }
evalBoard->getDacInformation(dacChannels,dacThresholds);
setDefaultChannelNamesAndType();
@@ -170,7 +172,7 @@ void RHD2000Thread::setDACthreshold(int dacOutput, float threshold)
dacChannelsToUpdate[dacOutput] = true;
dacOutputShouldChange = true;
-// evalBoard->setDacThresholdVoltage(dacOutput,threshold);
+ // evalBoard->setDacThresholdVoltage(dacOutput,threshold);
}
void RHD2000Thread::setDACchannel(int dacOutput, int stream, int channel)
@@ -202,17 +204,17 @@ bool RHD2000Thread::openBoard(String pathToLibrary)
}
else if (return_code == -1) // dynamic library not found
{
- bool response = AlertWindow::showOkCancelBox (AlertWindow::NoIcon,
- "Opal Kelly library not found.",
- "The Opal Kelly library file was not found in the directory of the executable. Would you like to browse for it?",
- "Yes", "No", 0, 0);
+ bool response = AlertWindow::showOkCancelBox(AlertWindow::NoIcon,
+ "Opal Kelly library not found.",
+ "The Opal Kelly library file was not found in the directory of the executable. Would you like to browse for it?",
+ "Yes", "No", 0, 0);
if (response)
{
// browse for file
FileChooser fc("Select the library file...",
- File::getCurrentWorkingDirectory(),
- okLIB_EXTENSION,
- true);
+ File::getCurrentWorkingDirectory(),
+ okLIB_EXTENSION,
+ true);
if (fc.browseForFileToOpen())
{
@@ -226,20 +228,25 @@ bool RHD2000Thread::openBoard(String pathToLibrary)
deviceFound = false;
}
- } else {
+ }
+ else
+ {
deviceFound = false;
}
- } else if (return_code == -2) // board could not be opened
+ }
+ else if (return_code == -2) // board could not be opened
{
- bool response = AlertWindow::showOkCancelBox (AlertWindow::NoIcon,
- "Acquisition board not found.",
- "An acquisition board could not be found. Please connect one now.",
- "OK", "Cancel", 0, 0);
-
+ bool response = AlertWindow::showOkCancelBox(AlertWindow::NoIcon,
+ "Acquisition board not found.",
+ "An acquisition board could not be found. Please connect one now.",
+ "OK", "Cancel", 0, 0);
+
if (response)
{
openBoard(libraryFilePath.getCharPointer()); // call recursively
- } else {
+ }
+ else
+ {
deviceFound = false;
}
@@ -251,24 +258,24 @@ bool RHD2000Thread::openBoard(String pathToLibrary)
bool RHD2000Thread::uploadBitfile(String bitfilename)
{
-
+
deviceFound = true;
-
+
if (!evalBoard->uploadFpgaBitfile(bitfilename.toStdString()))
{
std::cout << "Couldn't upload bitfile from " << bitfilename << std::endl;
-
- bool response = AlertWindow::showOkCancelBox (AlertWindow::NoIcon,
- "FPGA bitfile not found.",
- "The rhd2000.bit file was not found in the directory of the executable. Would you like to browse for it?",
- "Yes", "No", 0, 0);
+
+ bool response = AlertWindow::showOkCancelBox(AlertWindow::NoIcon,
+ "FPGA bitfile not found.",
+ "The rhd2000.bit file was not found in the directory of the executable. Would you like to browse for it?",
+ "Yes", "No", 0, 0);
if (response)
{
// browse for file
FileChooser fc("Select the FPGA bitfile...",
- File::getCurrentWorkingDirectory(),
- "*.bit",
- true);
+ File::getCurrentWorkingDirectory(),
+ "*.bit",
+ true);
if (fc.browseForFileToOpen())
{
@@ -282,12 +289,14 @@ bool RHD2000Thread::uploadBitfile(String bitfilename)
deviceFound = false;
}
- } else {
+ }
+ else
+ {
deviceFound = false;
}
}
-
+
return deviceFound;
}
@@ -298,12 +307,12 @@ void RHD2000Thread::initializeBoard()
File executable = File::getSpecialLocation(File::currentExecutableFile);
- #if defined(__APPLE__)
- const String executableDirectory =
- executable.getParentDirectory().getParentDirectory().getParentDirectory().getParentDirectory().getFullPathName();
- #else
- const String executableDirectory = executable.getParentDirectory().getFullPathName();
- #endif
+#if defined(__APPLE__)
+ const String executableDirectory =
+ executable.getParentDirectory().getParentDirectory().getParentDirectory().getParentDirectory().getFullPathName();
+#else
+ const String executableDirectory = executable.getParentDirectory().getFullPathName();
+#endif
bitfilename = executableDirectory;
bitfilename += File::separatorString;
@@ -354,7 +363,7 @@ void RHD2000Thread::initializeBoard()
Rhd2000DataBlock* dataBlock = new Rhd2000DataBlock(evalBoard->getNumEnabledDataStreams());
- // evalBoard->readDataBlock(dataBlock);
+ // evalBoard->readDataBlock(dataBlock);
// Now that ADC calibration has been performed, we switch to the command sequence
// that does not execute ADC calibration.
@@ -386,21 +395,44 @@ void RHD2000Thread::scanPorts()
int delay, stream, id;
//int numChannelsOnPort[4] = {0, 0, 0, 0};
-
+ Rhd2000EvalBoard::BoardDataSource initStreamPorts[8] =
+ {
+ Rhd2000EvalBoard::PortA1,
+ Rhd2000EvalBoard::PortA2,
+ Rhd2000EvalBoard::PortB1,
+ Rhd2000EvalBoard::PortB2,
+ Rhd2000EvalBoard::PortC1,
+ Rhd2000EvalBoard::PortC2,
+ Rhd2000EvalBoard::PortD1,
+ Rhd2000EvalBoard::PortD2
+ };
+
+ Rhd2000EvalBoard::BoardDataSource initStreamDdrPorts[8] =
+ {
+ Rhd2000EvalBoard::PortA1Ddr,
+ Rhd2000EvalBoard::PortA2Ddr,
+ Rhd2000EvalBoard::PortB1Ddr,
+ Rhd2000EvalBoard::PortB2Ddr,
+ Rhd2000EvalBoard::PortC1Ddr,
+ Rhd2000EvalBoard::PortC2Ddr,
+ Rhd2000EvalBoard::PortD1Ddr,
+ Rhd2000EvalBoard::PortD2Ddr
+ };
+
chipId.insertMultiple(0,-1,8);
setSampleRate(16, true); // set to 30 kHz temporarily
// Enable all data streams, and set sources to cover one or two chips
// on Ports A-D.
- evalBoard->setDataSource(0, Rhd2000EvalBoard::PortA1);
- evalBoard->setDataSource(1, Rhd2000EvalBoard::PortA2);
- evalBoard->setDataSource(2, Rhd2000EvalBoard::PortB1);
- evalBoard->setDataSource(3, Rhd2000EvalBoard::PortB2);
- evalBoard->setDataSource(4, Rhd2000EvalBoard::PortC1);
- evalBoard->setDataSource(5, Rhd2000EvalBoard::PortC2);
- evalBoard->setDataSource(6, Rhd2000EvalBoard::PortD1);
- evalBoard->setDataSource(7, Rhd2000EvalBoard::PortD2);
+ evalBoard->setDataSource(0, initStreamPorts[0]);
+ evalBoard->setDataSource(1, initStreamPorts[1]);
+ evalBoard->setDataSource(2, initStreamPorts[2]);
+ evalBoard->setDataSource(3, initStreamPorts[3]);
+ evalBoard->setDataSource(4, initStreamPorts[4]);
+ evalBoard->setDataSource(5, initStreamPorts[5]);
+ evalBoard->setDataSource(6, initStreamPorts[6]);
+ evalBoard->setDataSource(7, initStreamPorts[7]);
evalBoard->enableDataStream(0, true);
evalBoard->enableDataStream(1, true);
@@ -506,7 +538,18 @@ void RHD2000Thread::scanPorts()
if (chipId[stream] > 0)
{
//std::cout << "Enabling headstage on stream " << stream << std::endl;
- enableHeadstage(stream, true);
+ if (chipId[stream] == 4) //RHD2164
+ {
+ //We just add it like a second headstage, allowing only one RHD2164 per channel
+ //This would need to change
+ evalBoard->setDataSource(stream+1,initStreamDdrPorts[stream]);
+ enableHeadstage(stream,true);
+ enableHeadstage(stream+1,true);
+ chipId.set(stream+1,CHIP_ID_RHD2164_B);
+ stream++;
+ }
+ else
+ enableHeadstage(stream, true);
}
else
{
@@ -606,20 +649,20 @@ int RHD2000Thread::getNumADCchannels()
{
if (acquireAdcChannels)
return 8;
- else
+ else
return 0;
}
-void RHD2000Thread::getEventChannelNames(StringArray &Names)
+void RHD2000Thread::getEventChannelNames(StringArray& Names)
{
Names.clear();
- for (int k=0;k<8;k++)
+ for (int k=0; k<8; k++)
{
Names.add("TTL"+String(k+1));
}
}
-void RHD2000Thread::getChannelsInfo(StringArray &Names_, Array<channelType> &type_, Array<int> &stream_, Array<int> &originalChannelNumber_,Array<float> &gains_)
+void RHD2000Thread::getChannelsInfo(StringArray& Names_, Array<channelType>& type_, Array<int>& stream_, Array<int>& originalChannelNumber_,Array<float>& gains_)
{
Names_ = Names;
type_ = type;
@@ -635,11 +678,11 @@ void RHD2000Thread::updateChannelNames()
/* go over the old names and tests whether this particular channel name was changed.
if so, return the old name */
-bool RHD2000Thread::channelModified(channelType t, int str, int ch, String &oldName, float &oldGain, int &index)
+bool RHD2000Thread::channelModified(channelType t, int str, int ch, String& oldName, float& oldGain, int& index)
{
- for (int k=0;k<oldNames.size();k++)
+ for (int k=0; k<oldNames.size(); k++)
{
- if (oldType[k] == t && oldStream[k] == str && oldChannelNumber[k] == ch)
+ if (oldType[k] == t && oldStream[k] == str && oldChannelNumber[k] == ch)
{
oldName = oldNames[k];
oldGain = oldGains[k];
@@ -659,7 +702,8 @@ int RHD2000Thread::modifyChannelName(channelType t, int str, int ch, String newN
if (channelModified(t, str, ch, dummy, dummyFloat, index))
{
oldNames.set(index, newName);
- } else
+ }
+ else
{
oldNames.add(newName);
oldType.add(t);
@@ -668,9 +712,9 @@ int RHD2000Thread::modifyChannelName(channelType t, int str, int ch, String newN
oldGains.add(dummyFloat);
}
- for (int k=0;k<Names.size();k++)
+ for (int k=0; k<Names.size(); k++)
{
- if (type[k] == t && stream[k] == str && originalChannelNumber[k] == ch)
+ if (type[k] == t && stream[k] == str && originalChannelNumber[k] == ch)
{
Names.set(k,newName);
return k;
@@ -687,7 +731,8 @@ int RHD2000Thread::modifyChannelGain(channelType t, int str, int ch, float gain)
if (channelModified(t, str, ch, dummy, dummyFloat, index))
{
oldGains.set(index, gain);
- } else
+ }
+ else
{
oldNames.add(dummy);
oldType.add(t);
@@ -696,9 +741,9 @@ int RHD2000Thread::modifyChannelGain(channelType t, int str, int ch, float gain)
oldGains.add(gain);
}
- for (int k=0;k<Names.size();k++)
+ for (int k=0; k<Names.size(); k++)
{
- if (type[k] == t && stream[k] == str && originalChannelNumber[k] == ch)
+ if (type[k] == t && stream[k] == str && originalChannelNumber[k] == ch)
{
gains.set(k,gain);
return k;
@@ -727,49 +772,57 @@ void RHD2000Thread::setDefaultChannelNamesAndType()
stream.clear();
gains.clear();
originalChannelNumber.clear();
- int aux_counter=1;
- int data_counter = 1;
- String oldName;
- int dummy;
- float oldGain;
- StringArray stream_prefix;
- stream_prefix.add("A1");stream_prefix.add("A2");
- stream_prefix.add("B1");stream_prefix.add("B2");
- stream_prefix.add("C1");stream_prefix.add("C2");
- stream_prefix.add("D1");stream_prefix.add("D2");
+ int aux_counter=1;
+ int data_counter = 1;
+ String oldName;
+ int dummy;
+ float oldGain;
+ StringArray stream_prefix;
+ stream_prefix.add("A1");
+ stream_prefix.add("A2");
+ stream_prefix.add("B1");
+ stream_prefix.add("B2");
+ stream_prefix.add("C1");
+ stream_prefix.add("C2");
+ stream_prefix.add("D1");
+ stream_prefix.add("D2");
for (int i = 0; i < MAX_NUM_DATA_STREAMS; i++)
{
if (numChannelsPerDataStream[i] > 0)
{
- for (int k=0;k<numChannelsPerDataStream[i];k++)
+ for (int k=0; k<numChannelsPerDataStream[i]; k++)
{
- if (channelModified(DATA_CHANNEL,i,k, oldName,oldGain,dummy)) {
+ if (channelModified(DATA_CHANNEL,i,k, oldName,oldGain,dummy))
+ {
Names.add(oldName);
gains.add(oldGain);
data_counter++;
- } else
+ }
+ else
{
if (numberingScheme == 1)
Names.add("CH"+String(data_counter++));
- else
+ else
Names.add("CH_"+stream_prefix[i]+"_"+String(1+k));
gains.add(getBitVolts());
}
-
+
type.add(DATA_CHANNEL);
stream.add(i);
originalChannelNumber.add(k);
-
+
}
- for (int k=0;k<3;k++)
+ for (int k=0; k<3; k++)
{
- if (channelModified(AUX_CHANNEL,i,numChannelsPerDataStream[i]+k, oldName,oldGain, dummy)) {
+ if (channelModified(AUX_CHANNEL,i,numChannelsPerDataStream[i]+k, oldName,oldGain, dummy))
+ {
Names.add(oldName);
gains.add(oldGain);
aux_counter++;
- } else
+ }
+ else
{
if (numberingScheme == 1)
Names.add("AUX"+String(aux_counter++));
@@ -782,27 +835,29 @@ void RHD2000Thread::setDefaultChannelNamesAndType()
type.add(AUX_CHANNEL);
stream.add(i);
originalChannelNumber.add(numChannelsPerDataStream[i]+k);
-
+
}
}
}
if (acquireAdcChannels)
{
- for (int k=0;k<8;k++)
+ for (int k=0; k<8; k++)
{
- if (channelModified(ADC_CHANNEL,MAX_NUM_DATA_STREAMS,k, oldName,oldGain,dummy)) {
+ if (channelModified(ADC_CHANNEL,MAX_NUM_DATA_STREAMS,k, oldName,oldGain,dummy))
+ {
Names.add(oldName);
gains.add(oldGain);
- } else
+ }
+ else
{
Names.add("ADC"+String(k+1));
gains.add(getBitVolts());
}
- type.add(ADC_CHANNEL);
- stream.add(MAX_NUM_DATA_STREAMS);
- originalChannelNumber.add(k);
-
+ type.add(ADC_CHANNEL);
+ stream.add(MAX_NUM_DATA_STREAMS);
+ originalChannelNumber.add(k);
+
}
}
@@ -871,7 +926,7 @@ void RHD2000Thread::setTTLoutputMode(bool state)
{
ttlMode = state;
dacOutputShouldChange = true;
-
+
}
void RHD2000Thread::setDAChpf(float cutoff, bool enabled)
@@ -892,13 +947,13 @@ int RHD2000Thread::setNoiseSlicerLevel(int level)
{
desiredNoiseSlicerLevel = level;
- if (deviceFound)
- evalBoard->setAudioNoiseSuppress(desiredNoiseSlicerLevel);
+ if (deviceFound)
+ evalBoard->setAudioNoiseSuppress(desiredNoiseSlicerLevel);
// Level has been checked once before this and then is checked again in setAudioNoiseSuppress.
// This may be overkill - maybe API should change so that the final function returns the value?
actualNoiseSlicerLevel = level;
-
+
return actualNoiseSlicerLevel;
}
@@ -1163,9 +1218,9 @@ void RHD2000Thread::updateRegisters()
evalBoard->selectAuxCommandLength(Rhd2000EvalBoard::AuxCmd3, 0,
commandSequenceLength - 1);
-
+
chipRegisters.setFastSettle(true);
-
+
commandSequenceLength = chipRegisters.createCommandListRegisterConfig(commandList, false);
// Upload version with fast settle enabled to AuxCmd3 RAM Bank 2.
evalBoard->uploadCommandList(commandList, Rhd2000EvalBoard::AuxCmd3, 2);
@@ -1225,13 +1280,13 @@ bool RHD2000Thread::startAcquisition()
//std::cout << "Setting max timestep." << std::endl;
//evalBoard->setMaxTimeStep(100);
-
+
std::cout << "Starting acquisition." << std::endl;
if (1)
{
- // evalBoard->setContinuousRunMode(false);
- // evalBoard->setMaxTimeStep(0);
+ // evalBoard->setContinuousRunMode(false);
+ // evalBoard->setMaxTimeStep(0);
std::cout << "Flushing FIFO." << std::endl;
evalBoard->flush();
evalBoard->setContinuousRunMode(true);
@@ -1275,14 +1330,14 @@ bool RHD2000Thread::stopAcquisition()
evalBoard->setMaxTimeStep(0);
std::cout << "Flushing FIFO." << std::endl;
evalBoard->flush();
- // evalBoard->setContinuousRunMode(true);
- // evalBoard->run();
+ // evalBoard->setContinuousRunMode(true);
+ // evalBoard->run();
}
dataBuffer->clear();
- if(deviceFound)
+ if (deviceFound)
{
cout << "Number of 16-bit words in FIFO: " << evalBoard->numWordsInFifo() << endl;
@@ -1324,9 +1379,9 @@ bool RHD2000Thread::updateBuffer()
for (int chan = 0; chan < numChannelsPerDataStream[dataStream]; chan++)
{
-
- // std::cout << "reading sample stream " << streamNumber << " chan " << chan << " sample "<< samp << std::endl;
-
+
+ // std::cout << "reading sample stream " << streamNumber << " chan " << chan << " sample "<< samp << std::endl;
+
channel++;
int value = dataBlock->amplifierData[streamNumber][chan][samp];
@@ -1350,19 +1405,19 @@ bool RHD2000Thread::updateBuffer()
if (samp % 4 == 1) // every 4th sample should have auxiliary input data
{
- // std::cout << "reading sample stream " << streamNumber << " aux ADCs " << std::endl;
+ // std::cout << "reading sample stream " << streamNumber << " aux ADCs " << std::endl;
channel++;
thisSample[channel] = 0.0374 *
float(dataBlock->auxiliaryData[streamNumber][1][samp+0] - 45000.0f) ;
- // constant offset keeps the values visible in the LFP Viewer
+ // constant offset keeps the values visible in the LFP Viewer
auxBuffer[channel] = thisSample[channel];
channel++;
thisSample[channel] = 0.0374 *
float(dataBlock->auxiliaryData[streamNumber][1][samp+1] - 45000.0f) ;
- // constant offset keeps the values visible in the LFP Viewer
+ // constant offset keeps the values visible in the LFP Viewer
auxBuffer[channel] = thisSample[channel];
@@ -1370,7 +1425,7 @@ bool RHD2000Thread::updateBuffer()
channel++;
thisSample[channel] = 0.0374 *
float(dataBlock->auxiliaryData[streamNumber][1][samp+2] - 45000.0f) ;
- // constant offset keeps the values visible in the LFP Viewer
+ // constant offset keeps the values visible in the LFP Viewer
auxBuffer[channel] = thisSample[channel];
@@ -1419,7 +1474,7 @@ bool RHD2000Thread::updateBuffer()
if (dacOutputShouldChange)
{
- for (int k=0;k<8;k++)
+ for (int k=0; k<8; k++)
{
if (dacChannelsToUpdate[k])
{
@@ -1440,9 +1495,9 @@ bool RHD2000Thread::updateBuffer()
evalBoard->setTtlMode(ttlMode);
evalBoard->setFastSettleByTTL(fastTTLSettleEnabled);
- evalBoard->setFastSettleByTTLchannel(fastSettleTTLChannel);
+ evalBoard->setFastSettleByTTLchannel(fastSettleTTLChannel);
evalBoard->setDacHighpassFilter(desiredDAChpf);
- evalBoard->enableDacHighpassFilter(desiredDAChpfState);
+ evalBoard->enableDacHighpassFilter(desiredDAChpfState);
dacOutputShouldChange = false;
}
@@ -1455,7 +1510,7 @@ bool RHD2000Thread::updateBuffer()
/***********************************/
/* Below is code for impedance measurements */
-#define CHIP_ID_RHD2164_B 1000
+
@@ -1463,7 +1518,7 @@ bool RHD2000Thread::updateBuffer()
// requested test frequency lies within acceptable ranges based on the
// amplifier bandwidth and the sampling rate. See impedancefreqdialog.cpp
// for more information.
-float RHD2000Thread::updateImpedanceFrequency(float desiredImpedanceFreq, bool &impedanceFreqValid)
+float RHD2000Thread::updateImpedanceFrequency(float desiredImpedanceFreq, bool& impedanceFreqValid)
{
int impedancePeriod;
double lowerBandwidthLimit, upperBandwidthLimit;
@@ -1471,24 +1526,32 @@ float RHD2000Thread::updateImpedanceFrequency(float desiredImpedanceFreq, bool &
upperBandwidthLimit = actualUpperBandwidth / 1.5;
lowerBandwidthLimit = actualLowerBandwidth * 1.5;
- if (dspEnabled) {
- if (actualDspCutoffFreq > actualLowerBandwidth) {
+ if (dspEnabled)
+ {
+ if (actualDspCutoffFreq > actualLowerBandwidth)
+ {
lowerBandwidthLimit = actualDspCutoffFreq * 1.5;
}
}
- if (desiredImpedanceFreq > 0.0) {
+ if (desiredImpedanceFreq > 0.0)
+ {
impedancePeriod = (boardSampleRate / desiredImpedanceFreq);
if (impedancePeriod >= 4 && impedancePeriod <= 1024 &&
- desiredImpedanceFreq >= lowerBandwidthLimit &&
- desiredImpedanceFreq <= upperBandwidthLimit) {
+ desiredImpedanceFreq >= lowerBandwidthLimit &&
+ desiredImpedanceFreq <= upperBandwidthLimit)
+ {
actualImpedanceFreq = boardSampleRate / impedancePeriod;
impedanceFreqValid = true;
- } else {
+ }
+ else
+ {
actualImpedanceFreq = 0.0;
impedanceFreqValid = false;
}
- } else {
+ }
+ else
+ {
actualImpedanceFreq = 0.0;
impedanceFreqValid = false;
}
@@ -1500,10 +1563,10 @@ float RHD2000Thread::updateImpedanceFrequency(float desiredImpedanceFreq, bool &
// Reads numBlocks blocks of raw USB data stored in a queue of Rhd2000DataBlock
// objects, loads this data into this SignalProcessor object, scaling the raw
// data to generate waveforms with units of volts or microvolts.
-int RHD2000Thread::loadAmplifierData(queue<Rhd2000DataBlock> &dataQueue,
- int numBlocks, int numDataStreams)
+int RHD2000Thread::loadAmplifierData(queue<Rhd2000DataBlock>& dataQueue,
+ int numBlocks, int numDataStreams)
{
-
+
int block, t, channel, stream, i, j;
int indexAmp = 0;
int indexAux = 0;
@@ -1520,17 +1583,21 @@ int RHD2000Thread::loadAmplifierData(queue<Rhd2000DataBlock> &dataQueue,
bool triggerFound = false;
const double AnalogTriggerThreshold = 1.65;
-
- for (block = 0; block < numBlocks; ++block) {
+
+ for (block = 0; block < numBlocks; ++block)
+ {
// Load and scale RHD2000 amplifier waveforms
// (sampled at amplifier sampling rate)
- for (t = 0; t < SAMPLES_PER_DATA_BLOCK; ++t) {
- for (channel = 0; channel < 32; ++channel) {
- for (stream = 0; stream < numDataStreams; ++stream) {
+ for (t = 0; t < SAMPLES_PER_DATA_BLOCK; ++t)
+ {
+ for (channel = 0; channel < 32; ++channel)
+ {
+ for (stream = 0; stream < numDataStreams; ++stream)
+ {
// Amplifier waveform units = microvolts
amplifierPreFilter[stream][channel][indexAmp] = 0.195 *
- (dataQueue.front().amplifierData[stream][channel][t] - 32768);
+ (dataQueue.front().amplifierData[stream][channel][t] - 32768);
}
}
++indexAmp;
@@ -1539,7 +1606,7 @@ int RHD2000Thread::loadAmplifierData(queue<Rhd2000DataBlock> &dataQueue,
dataQueue.pop();
}
- return 0;
+ return 0;
}
#define PI 3.14159265359
@@ -1549,17 +1616,18 @@ int RHD2000Thread::loadAmplifierData(queue<Rhd2000DataBlock> &dataQueue,
// Return the magnitude and phase (in degrees) of a selected frequency component (in Hz)
// for a selected amplifier channel on the selected USB data stream.
-void RHD2000Thread::measureComplexAmplitude(std::vector<std::vector<std::vector<double>>> &measuredMagnitude,
- std::vector<std::vector<std::vector<double>>> &measuredPhase,
- int capIndex, int stream, int chipChannel, int numBlocks,
- double sampleRate, double frequency, int numPeriods)
+void RHD2000Thread::measureComplexAmplitude(std::vector<std::vector<std::vector<double>>>& measuredMagnitude,
+ std::vector<std::vector<std::vector<double>>>& measuredPhase,
+ int capIndex, int stream, int chipChannel, int numBlocks,
+ double sampleRate, double frequency, int numPeriods)
{
int period = (sampleRate / frequency);
int startIndex = 0;
int endIndex = startIndex + numPeriods * period - 1;
// Move the measurement window to the end of the waveform to ignore start-up transient.
- while (endIndex < SAMPLES_PER_DATA_BLOCK * numBlocks - period) {
+ while (endIndex < SAMPLES_PER_DATA_BLOCK * numBlocks - period)
+ {
startIndex += period;
endIndex += period;
}
@@ -1571,16 +1639,16 @@ void RHD2000Thread::measureComplexAmplitude(std::vector<std::vector<std::vector<
startIndex, endIndex, sampleRate, frequency);
// Calculate magnitude and phase from real (I) and imaginary (Q) components.
measuredMagnitude[stream][chipChannel][capIndex] =
- sqrt(iComponent * iComponent + qComponent * qComponent);
+ sqrt(iComponent * iComponent + qComponent * qComponent);
measuredPhase[stream][chipChannel][capIndex] =
- RADIANS_TO_DEGREES *atan2(qComponent, iComponent);
+ RADIANS_TO_DEGREES *atan2(qComponent, iComponent);
}
// Returns the real and imaginary amplitudes of a selected frequency component in the vector
// data, between a start index and end index.
-void RHD2000Thread::amplitudeOfFreqComponent(double &realComponent, double &imagComponent,
- const std::vector<double> &data, int startIndex,
- int endIndex, double sampleRate, double frequency)
+void RHD2000Thread::amplitudeOfFreqComponent(double& realComponent, double& imagComponent,
+ const std::vector<double>& data, int startIndex,
+ int endIndex, double sampleRate, double frequency)
{
int length = endIndex - startIndex + 1;
const double k = TWO_PI * frequency / sampleRate; // precalculate for speed
@@ -1588,7 +1656,8 @@ void RHD2000Thread::amplitudeOfFreqComponent(double &realComponent, double &imag
// Perform correlation with sine and cosine waveforms.
double meanI = 0.0;
double meanQ = 0.0;
- for (int t = startIndex; t <= endIndex; ++t) {
+ for (int t = startIndex; t <= endIndex; ++t)
+ {
meanI += data.at(t) * cos(k * t);
meanQ += data.at(t) * -1.0 * sin(k * t);
}
@@ -1605,8 +1674,8 @@ void RHD2000Thread::amplitudeOfFreqComponent(double &realComponent, double &imag
// with a parasitic capacitance (i.e., due to the amplifier input capacitance and other
// capacitances associated with the chip bondpads), this function factors out the effect of the
// parasitic capacitance to return the acutal electrode impedance.
-void RHD2000Thread::factorOutParallelCapacitance(double &impedanceMagnitude, double &impedancePhase,
- double frequency, double parasiticCapacitance)
+void RHD2000Thread::factorOutParallelCapacitance(double& impedanceMagnitude, double& impedancePhase,
+ double frequency, double parasiticCapacitance)
{
// First, convert from polar coordinates to rectangular coordinates.
double measuredR = impedanceMagnitude * cos(DEGREES_TO_RADIANS * impedancePhase);
@@ -1629,8 +1698,8 @@ void RHD2000Thread::factorOutParallelCapacitance(double &impedanceMagnitude, dou
// 2-pole lowpass filter. This function attempts to somewhat correct for this, but a better
// solution is to always run impedance measurements at 20 kS/s, where they seem to be most
// accurate.
-void RHD2000Thread::empiricalResistanceCorrection(double &impedanceMagnitude, double &impedancePhase,
- double boardSampleRate)
+void RHD2000Thread::empiricalResistanceCorrection(double& impedanceMagnitude, double& impedancePhase,
+ double boardSampleRate)
{
// First, convert from polar coordinates to rectangular coordinates.
double impedanceR = impedanceMagnitude * cos(DEGREES_TO_RADIANS * impedancePhase);
@@ -1644,7 +1713,7 @@ void RHD2000Thread::empiricalResistanceCorrection(double &impedanceMagnitude, do
impedancePhase = RADIANS_TO_DEGREES * atan2(impedanceX, impedanceR);
}
-void RHD2000Thread::runImpedanceTest(Array<int> &streams, Array<int> &channels, Array<float> &magnitudes, Array<float> &phases)
+void RHD2000Thread::runImpedanceTest(Array<int>& streams, Array<int>& channels, Array<float>& magnitudes, Array<float>& phases)
{
int commandSequenceLength, stream, channel, capRange;
double cSeries;
@@ -1652,17 +1721,19 @@ void RHD2000Thread::runImpedanceTest(Array<int> &streams, Array<int> &channels,
int triggerIndex; // dummy reference variable; not used
queue<Rhd2000DataBlock> bufferQueue; // dummy reference variable; not used
int numdataStreams = evalBoard->getNumEnabledDataStreams();
-
+
bool rhd2164ChipPresent = false;
Array<int> enabledStreams;
- for (stream = 0; stream < MAX_NUM_DATA_STREAMS; ++stream) {
-
+ for (stream = 0; stream < MAX_NUM_DATA_STREAMS; ++stream)
+ {
+
if (evalBoard->isStreamEnabled(stream))
{
enabledStreams.add(stream);
}
- if (chipId[stream] == CHIP_ID_RHD2164_B) {
+ if (chipId[stream] == CHIP_ID_RHD2164_B)
+ {
rhd2164ChipPresent = true;
}
}
@@ -1724,10 +1795,12 @@ void RHD2000Thread::runImpedanceTest(Array<int> &streams, Array<int> &channels,
measuredMagnitude.resize(evalBoard->getNumEnabledDataStreams());
measuredPhase.resize(evalBoard->getNumEnabledDataStreams());
- for (int i = 0; i < evalBoard->getNumEnabledDataStreams(); ++i) {
+ for (int i = 0; i < evalBoard->getNumEnabledDataStreams(); ++i)
+ {
measuredMagnitude[i].resize(32);
measuredPhase[i].resize(32);
- for (int j = 0; j < 32; ++j) {
+ for (int j = 0; j < 32; ++j)
+ {
measuredMagnitude[i][j].resize(3);
measuredPhase[i][j].resize(3);
}
@@ -1739,10 +1812,10 @@ void RHD2000Thread::runImpedanceTest(Array<int> &streams, Array<int> &channels,
double impedanceMagnitude, impedancePhase;
const double bestAmplitude = 250.0; // we favor voltage readings that are closest to 250 uV: not too large,
- // and not too small.
+ // and not too small.
const double dacVoltageAmplitude = 128 * (1.225 / 256); // this assumes the DAC amplitude was set to 128
const double parasiticCapacitance = 14.0e-12; // 14 pF: an estimate of on-chip parasitic capacitance,
- // including 10 pF of amplifier input capacitance.
+ // including 10 pF of amplifier input capacitance.
double relativeFreq = actualImpedanceFreq / boardSampleRate;
int bestAmplitudeIndex;
@@ -1750,75 +1823,83 @@ void RHD2000Thread::runImpedanceTest(Array<int> &streams, Array<int> &channels,
// We execute three complete electrode impedance measurements: one each with
// Cseries set to 0.1 pF, 1 pF, and 10 pF. Then we select the best measurement
// for each channel so that we achieve a wide impedance measurement range.
- for (capRange = 0; capRange < 3; ++ capRange)
+ for (capRange = 0; capRange < 3; ++ capRange)
{
-
- switch (capRange) {
- case 0:
- chipRegisters.setZcheckScale(Rhd2000Registers::ZcheckCs100fF);
- cSeries = 0.1e-12;
- cout << "setting capacitance to 0.1pF" << endl;
- break;
- case 1:
- chipRegisters.setZcheckScale(Rhd2000Registers::ZcheckCs1pF);
- cSeries = 1.0e-12;
- cout << "setting capacitance to 1pF" << endl;
- break;
- case 2:
- chipRegisters.setZcheckScale(Rhd2000Registers::ZcheckCs10pF);
- cSeries = 10.0e-12;
- cout << "setting capacitance to 10pF" << endl;
- break;
+
+ switch (capRange)
+ {
+ case 0:
+ chipRegisters.setZcheckScale(Rhd2000Registers::ZcheckCs100fF);
+ cSeries = 0.1e-12;
+ cout << "setting capacitance to 0.1pF" << endl;
+ break;
+ case 1:
+ chipRegisters.setZcheckScale(Rhd2000Registers::ZcheckCs1pF);
+ cSeries = 1.0e-12;
+ cout << "setting capacitance to 1pF" << endl;
+ break;
+ case 2:
+ chipRegisters.setZcheckScale(Rhd2000Registers::ZcheckCs10pF);
+ cSeries = 10.0e-12;
+ cout << "setting capacitance to 10pF" << endl;
+ break;
}
// Check all 32 channels across all active data streams.
- for (channel = 0; channel < 32; ++channel)
+ for (channel = 0; channel < 32; ++channel)
{
cout << "running impedance on channel " << channel << endl;
chipRegisters.setZcheckChannel(channel);
commandSequenceLength =
- chipRegisters.createCommandListRegisterConfig(commandList, false);
+ chipRegisters.createCommandListRegisterConfig(commandList, false);
// Upload version with no ADC calibration to AuxCmd3 RAM Bank 1.
evalBoard->uploadCommandList(commandList, Rhd2000EvalBoard::AuxCmd3, 3);
evalBoard->run();
- while (evalBoard->isRunning() ) {
-
+ while (evalBoard->isRunning())
+ {
+
}
queue<Rhd2000DataBlock> dataQueue;
evalBoard->readDataBlocks(numBlocks, dataQueue);
loadAmplifierData(dataQueue, numBlocks, numdataStreams);
- for (stream = 0; stream < numdataStreams; ++stream) {
- if (chipId[stream] != CHIP_ID_RHD2164_B) {
+ for (stream = 0; stream < numdataStreams; ++stream)
+ {
+ if (chipId[stream] != CHIP_ID_RHD2164_B)
+ {
measureComplexAmplitude(measuredMagnitude, measuredPhase,
- capRange, stream, channel, numBlocks, boardSampleRate,
- actualImpedanceFreq, numPeriods);
- }
+ capRange, stream, channel, numBlocks, boardSampleRate,
+ actualImpedanceFreq, numPeriods);
+ }
}
// If an RHD2164 chip is plugged in, we have to set the Zcheck select register to channels 32-63
// and repeat the previous steps.
- if (rhd2164ChipPresent) {
+ if (rhd2164ChipPresent)
+ {
chipRegisters.setZcheckChannel(channel + 32); // address channels 32-63
commandSequenceLength =
- chipRegisters.createCommandListRegisterConfig(commandList, false);
+ chipRegisters.createCommandListRegisterConfig(commandList, false);
// Upload version with no ADC calibration to AuxCmd3 RAM Bank 1.
evalBoard->uploadCommandList(commandList, Rhd2000EvalBoard::AuxCmd3, 3);
evalBoard->run();
- while (evalBoard->isRunning() ) {
-
+ while (evalBoard->isRunning())
+ {
+
}
evalBoard->readDataBlocks(numBlocks, dataQueue);
loadAmplifierData(dataQueue, numBlocks, numdataStreams);
- for (stream = 0; stream < evalBoard->getNumEnabledDataStreams(); ++stream) {
- if (chipId[stream] == CHIP_ID_RHD2164_B) {
+ for (stream = 0; stream < evalBoard->getNumEnabledDataStreams(); ++stream)
+ {
+ if (chipId[stream] == CHIP_ID_RHD2164_B)
+ {
measureComplexAmplitude(measuredMagnitude, measuredPhase,
- capRange, stream, channel, numBlocks, boardSampleRate,
- actualImpedanceFreq, numPeriods);
+ capRange, stream, channel, numBlocks, boardSampleRate,
+ actualImpedanceFreq, numPeriods);
}
}
}
@@ -1830,28 +1911,34 @@ void RHD2000Thread::runImpedanceTest(Array<int> &streams, Array<int> &channels,
magnitudes.clear();
phases.clear();
- for (stream = 0; stream < evalBoard->getNumEnabledDataStreams(); ++stream) {
- for (channel = 0; channel < 32; ++channel) {
- if (1) {
+ for (stream = 0; stream < evalBoard->getNumEnabledDataStreams(); ++stream)
+ {
+ for (channel = 0; channel < 32; ++channel)
+ {
+ if (1)
+ {
minDistance = 9.9e99; // ridiculously large number
- for (capRange = 0; capRange < 3; ++capRange) {
+ for (capRange = 0; capRange < 3; ++capRange)
+ {
// Find the measured amplitude that is closest to bestAmplitude on a logarithmic scale
distance = abs(log(measuredMagnitude[stream][channel][capRange] / bestAmplitude));
- if (distance < minDistance) {
+ if (distance < minDistance)
+ {
bestAmplitudeIndex = capRange;
minDistance = distance;
}
}
- switch (bestAmplitudeIndex) {
- case 0:
- Cseries = 0.1e-12;
- break;
- case 1:
- Cseries = 1.0e-12;
- break;
- case 2:
- Cseries = 10.0e-12;
- break;
+ switch (bestAmplitudeIndex)
+ {
+ case 0:
+ Cseries = 0.1e-12;
+ break;
+ case 1:
+ Cseries = 1.0e-12;
+ break;
+ case 2:
+ Cseries = 10.0e-12;
+ break;
}
// Calculate current amplitude produced by on-chip voltage DAC
@@ -1859,7 +1946,7 @@ void RHD2000Thread::runImpedanceTest(Array<int> &streams, Array<int> &channels,
// Calculate impedance magnitude from calculated current and measured voltage.
impedanceMagnitude = 1.0e-6 * (measuredMagnitude[stream][channel][bestAmplitudeIndex] / current) *
- (18.0 * relativeFreq * relativeFreq + 1.0);
+ (18.0 * relativeFreq * relativeFreq + 1.0);
// Calculate impedance phase, with small correction factor accounting for the
// 3-command SPI pipeline delay.
@@ -1881,9 +1968,9 @@ void RHD2000Thread::runImpedanceTest(Array<int> &streams, Array<int> &channels,
if (impedanceMagnitude > 1000000)
cout << "stream " << stream << " channel " << 1+channel << " magnitude: " << String(impedanceMagnitude/1e6,2) << " mOhm , phase : " <<impedancePhase << endl;
- else
+ else
cout << "stream " << stream << " channel " << 1+channel << " magnitude: " << String(impedanceMagnitude/1e3,2) << " kOhm , phase : " <<impedancePhase << endl;
-
+
}
}
}