From 31526ea31bad856ee66af85ebf53ee6000f32c15 Mon Sep 17 00:00:00 2001
From: Aaron Cuevas Lopez <aacuelo@teleco.upv.es>
Date: Wed, 4 Mar 2015 22:36:54 +0100
Subject: [PATCH] Move functions to own class
---
.../Processors/DataThreads/RHD2000Thread.cpp | 998 +++++++++---------
Source/Processors/DataThreads/RHD2000Thread.h | 57 +-
2 files changed, 539 insertions(+), 516 deletions(-)
diff --git a/Source/Processors/DataThreads/RHD2000Thread.cpp b/Source/Processors/DataThreads/RHD2000Thread.cpp
index c7564316b..7bc9ce5e0 100644
--- a/Source/Processors/DataThreads/RHD2000Thread.cpp
+++ b/Source/Processors/DataThreads/RHD2000Thread.cpp
@@ -124,11 +124,6 @@ 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.
- 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];
@@ -1601,499 +1596,6 @@ bool RHD2000Thread::updateBuffer()
}
-
-/***********************************/
-/* Below is code for impedance measurements */
-
-
-
-
-// Update electrode impedance measurement frequency, after checking that
-// 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)
-{
- int impedancePeriod;
- double lowerBandwidthLimit, upperBandwidthLimit;
- float actualImpedanceFreq;
-
- upperBandwidthLimit = actualUpperBandwidth / 1.5;
- lowerBandwidthLimit = actualLowerBandwidth * 1.5;
- if (dspEnabled)
- {
- if (actualDspCutoffFreq > actualLowerBandwidth)
- {
- lowerBandwidthLimit = actualDspCutoffFreq * 1.5;
- }
- }
-
- if (desiredImpedanceFreq > 0.0)
- {
- impedancePeriod = (boardSampleRate / desiredImpedanceFreq);
- if (impedancePeriod >= 4 && impedancePeriod <= 1024 &&
- desiredImpedanceFreq >= lowerBandwidthLimit &&
- desiredImpedanceFreq <= upperBandwidthLimit)
- {
- actualImpedanceFreq = boardSampleRate / impedancePeriod;
- impedanceFreqValid = true;
- }
- else
- {
- actualImpedanceFreq = 0.0;
- impedanceFreqValid = false;
- }
- }
- else
- {
- actualImpedanceFreq = 0.0;
- impedanceFreqValid = false;
- }
-
- return actualImpedanceFreq;
-}
-
-
-// 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 block, t, channel, stream, i, j;
- int indexAmp = 0;
- int indexAux = 0;
- int indexSupply = 0;
- int indexAdc = 0;
- int indexDig = 0;
- int numWordsWritten = 0;
-
- int bufferIndex;
- int16 tempQint16;
- uint16 tempQuint16;
- int32 tempQint32;
-
- bool triggerFound = false;
- const double AnalogTriggerThreshold = 1.65;
-
-
- 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)
- {
- // Amplifier waveform units = microvolts
- amplifierPreFilter[stream][channel][indexAmp] = 0.195 *
- (dataQueue.front().amplifierData[stream][channel][t] - 32768);
- }
- }
- ++indexAmp;
- }
- // We are done with this Rhd2000DataBlock object; remove it from dataQueue
- dataQueue.pop();
- }
-
- return 0;
-}
-
-#define PI 3.14159265359
-#define TWO_PI 6.28318530718
-#define DEGREES_TO_RADIANS 0.0174532925199
-#define RADIANS_TO_DEGREES 57.2957795132
-
-// 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)
-{
- 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)
- {
- startIndex += period;
- endIndex += period;
- }
-
- double iComponent, qComponent;
-
- // Measure real (iComponent) and imaginary (qComponent) amplitude of frequency component.
- amplitudeOfFreqComponent(iComponent, qComponent, amplifierPreFilter[stream][chipChannel],
- startIndex, endIndex, sampleRate, frequency);
- // Calculate magnitude and phase from real (I) and imaginary (Q) components.
- measuredMagnitude[stream][chipChannel][capIndex] =
- sqrt(iComponent * iComponent + qComponent * qComponent);
- measuredPhase[stream][chipChannel][capIndex] =
- 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)
-{
- int length = endIndex - startIndex + 1;
- const double k = TWO_PI * frequency / sampleRate; // precalculate for speed
-
- // Perform correlation with sine and cosine waveforms.
- double meanI = 0.0;
- double meanQ = 0.0;
- for (int t = startIndex; t <= endIndex; ++t)
- {
- meanI += data.at(t) * cos(k * t);
- meanQ += data.at(t) * -1.0 * sin(k * t);
- }
- meanI /= (double) length;
- meanQ /= (double) length;
-
- realComponent = 2.0 * meanI;
- imagComponent = 2.0 * meanQ;
-}
-
-
-
-// Given a measured complex impedance that is the result of an electrode impedance in parallel
-// 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)
-{
- // First, convert from polar coordinates to rectangular coordinates.
- double measuredR = impedanceMagnitude * cos(DEGREES_TO_RADIANS * impedancePhase);
- double measuredX = impedanceMagnitude * sin(DEGREES_TO_RADIANS * impedancePhase);
-
- double capTerm = TWO_PI * frequency * parasiticCapacitance;
- double xTerm = capTerm * (measuredR * measuredR + measuredX * measuredX);
- double denominator = capTerm * xTerm + 2 * capTerm * measuredX + 1;
- double trueR = measuredR / denominator;
- double trueX = (measuredX + xTerm) / denominator;
-
- // Now, convert from rectangular coordinates back to polar coordinates.
- impedanceMagnitude = sqrt(trueR * trueR + trueX * trueX);
- impedancePhase = RADIANS_TO_DEGREES * atan2(trueX, trueR);
-}
-
-// This is a purely empirical function to correct observed errors in the real component
-// of measured electrode impedances at sampling rates below 15 kS/s. At low sampling rates,
-// it is difficult to approximate a smooth sine wave with the on-chip voltage DAC and 10 kHz
-// 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)
-{
- // First, convert from polar coordinates to rectangular coordinates.
- double impedanceR = impedanceMagnitude * cos(DEGREES_TO_RADIANS * impedancePhase);
- double impedanceX = impedanceMagnitude * sin(DEGREES_TO_RADIANS * impedancePhase);
-
- // Emprically derived correction factor (i.e., no physical basis for this equation).
- impedanceR /= 10.0 * exp(-boardSampleRate / 2500.0) * cos(TWO_PI * boardSampleRate / 15000.0) + 1.0;
-
- // Now, convert from rectangular coordinates back to polar coordinates.
- impedanceMagnitude = sqrt(impedanceR * impedanceR + impedanceX * impedanceX);
- impedancePhase = RADIANS_TO_DEGREES * atan2(impedanceX, impedanceR);
-}
-
-void RHD2000Thread::runImpedanceTest(Array<int>& streams, Array<int>& channels, Array<float>& magnitudes, Array<float>& phases)
-{
- int commandSequenceLength, stream, channel, capRange;
- double cSeries;
- vector<int> commandList;
- 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)
- {
-
- if (evalBoard->isStreamEnabled(stream))
- {
- enabledStreams.add(stream);
- }
-
- if (chipId[stream] == CHIP_ID_RHD2164_B)
- {
- rhd2164ChipPresent = true;
- }
- }
-
- bool validImpedanceFreq;
- float actualImpedanceFreq = updateImpedanceFrequency(1000.0, validImpedanceFreq);
- if (!validImpedanceFreq)
- {
- return ;
- }
- // Create a command list for the AuxCmd1 slot.
- commandSequenceLength = chipRegisters.createCommandListZcheckDac(commandList, actualImpedanceFreq, 128.0);
- evalBoard->uploadCommandList(commandList, Rhd2000EvalBoard::AuxCmd1, 1);
- evalBoard->selectAuxCommandLength(Rhd2000EvalBoard::AuxCmd1,
- 0, commandSequenceLength - 1);
- if (fastTTLSettleEnabled)
- {
- evalBoard->enableExternalFastSettle(false);
- }
-
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortA,
- Rhd2000EvalBoard::AuxCmd1, 1);
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortB,
- Rhd2000EvalBoard::AuxCmd1, 1);
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortC,
- Rhd2000EvalBoard::AuxCmd1, 1);
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortD,
- Rhd2000EvalBoard::AuxCmd1, 1);
-
- // Select number of periods to measure impedance over
- int numPeriods = (0.020 * actualImpedanceFreq); // Test each channel for at least 20 msec...
- if (numPeriods < 5) numPeriods = 5; // ...but always measure across no fewer than 5 complete periods
- double period = boardSampleRate / actualImpedanceFreq;
- int numBlocks = ceil((numPeriods + 2.0) * period / 60.0); // + 2 periods to give time to settle initially
- if (numBlocks < 2) numBlocks = 2; // need first block for command to switch channels to take effect.
-
- actualDspCutoffFreq = chipRegisters.setDspCutoffFreq(desiredDspCutoffFreq);
- actualLowerBandwidth = chipRegisters.setLowerBandwidth(desiredLowerBandwidth);
- actualUpperBandwidth = chipRegisters.setUpperBandwidth(desiredUpperBandwidth);
- chipRegisters.enableDsp(dspEnabled);
- chipRegisters.enableZcheck(true);
- commandSequenceLength = chipRegisters.createCommandListRegisterConfig(commandList, false);
- // Upload version with no ADC calibration to AuxCmd3 RAM Bank 1.
- evalBoard->uploadCommandList(commandList, Rhd2000EvalBoard::AuxCmd3, 3);
- evalBoard->selectAuxCommandLength(Rhd2000EvalBoard::AuxCmd3, 0, commandSequenceLength - 1);
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortA, Rhd2000EvalBoard::AuxCmd3, 3);
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortB, Rhd2000EvalBoard::AuxCmd3, 3);
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortC, Rhd2000EvalBoard::AuxCmd3, 3);
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortD, Rhd2000EvalBoard::AuxCmd3, 3);
-
- evalBoard->setContinuousRunMode(false);
- evalBoard->setMaxTimeStep(SAMPLES_PER_DATA_BLOCK * numBlocks);
-
- // Create matrices of doubles of size (numStreams x 32 x 3) to store complex amplitudes
- // of all amplifier channels (32 on each data stream) at three different Cseries values.
- std::vector<std::vector<std::vector<double>>> measuredMagnitude;
- std::vector<std::vector<std::vector<double>>> measuredPhase;
-
- measuredMagnitude.resize(evalBoard->getNumEnabledDataStreams());
- measuredPhase.resize(evalBoard->getNumEnabledDataStreams());
- for (int i = 0; i < evalBoard->getNumEnabledDataStreams(); ++i)
- {
- measuredMagnitude[i].resize(32);
- measuredPhase[i].resize(32);
- for (int j = 0; j < 32; ++j)
- {
- measuredMagnitude[i][j].resize(3);
- measuredPhase[i][j].resize(3);
- }
- }
-
-
-
- double distance, minDistance, current, Cseries;
- 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.
- 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.
- double relativeFreq = actualImpedanceFreq / boardSampleRate;
-
- int bestAmplitudeIndex;
-
- // 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)
- {
-
-
- 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)
- {
- cout << "running impedance on channel " << channel << endl;
-
- chipRegisters.setZcheckChannel(channel);
- commandSequenceLength =
- 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())
- {
-
- }
- queue<Rhd2000DataBlock> dataQueue;
- evalBoard->readDataBlocks(numBlocks, dataQueue);
- loadAmplifierData(dataQueue, numBlocks, numdataStreams);
- for (stream = 0; stream < numdataStreams; ++stream)
- {
- if (chipId[stream] != CHIP_ID_RHD2164_B)
- {
- measureComplexAmplitude(measuredMagnitude, measuredPhase,
- 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)
- {
- chipRegisters.setZcheckChannel(channel + 32); // address channels 32-63
- commandSequenceLength =
- 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())
- {
-
- }
- evalBoard->readDataBlocks(numBlocks, dataQueue);
- loadAmplifierData(dataQueue, numBlocks, numdataStreams);
-
- for (stream = 0; stream < evalBoard->getNumEnabledDataStreams(); ++stream)
- {
- if (chipId[stream] == CHIP_ID_RHD2164_B)
- {
- measureComplexAmplitude(measuredMagnitude, measuredPhase,
- capRange, stream, channel, numBlocks, boardSampleRate,
- actualImpedanceFreq, numPeriods);
- }
- }
- }
- }
- }
-
- streams.clear();
- channels.clear();
- magnitudes.clear();
- phases.clear();
-
- 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)
- {
- // Find the measured amplitude that is closest to bestAmplitude on a logarithmic scale
- distance = abs(log(measuredMagnitude[stream][channel][capRange] / bestAmplitude));
- 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;
- }
-
- // Calculate current amplitude produced by on-chip voltage DAC
- current = TWO_PI * actualImpedanceFreq * dacVoltageAmplitude * Cseries;
-
- // Calculate impedance magnitude from calculated current and measured voltage.
- impedanceMagnitude = 1.0e-6 * (measuredMagnitude[stream][channel][bestAmplitudeIndex] / current) *
- (18.0 * relativeFreq * relativeFreq + 1.0);
-
- // Calculate impedance phase, with small correction factor accounting for the
- // 3-command SPI pipeline delay.
- impedancePhase = measuredPhase[stream][channel][bestAmplitudeIndex] + (360.0 * (3.0 / period));
-
- // Factor out on-chip parasitic capacitance from impedance measurement.
- factorOutParallelCapacitance(impedanceMagnitude, impedancePhase, actualImpedanceFreq,
- parasiticCapacitance);
-
- // Perform empirical resistance correction to improve accuarcy at sample rates below
- // 15 kS/s.
- empiricalResistanceCorrection(impedanceMagnitude, impedancePhase,
- boardSampleRate);
-
- streams.add(enabledStreams[stream]);
- channels.add(channel);
- magnitudes.add(impedanceMagnitude);
- phases.add(impedancePhase);
-
- if (impedanceMagnitude > 1000000)
- cout << "stream " << stream << " channel " << 1+channel << " magnitude: " << String(impedanceMagnitude/1e6,2) << " mOhm , phase : " <<impedancePhase << endl;
- else
- cout << "stream " << stream << " channel " << 1+channel << " magnitude: " << String(impedanceMagnitude/1e3,2) << " kOhm , phase : " <<impedancePhase << endl;
-
- }
- }
- }
-
- evalBoard->setContinuousRunMode(false);
- evalBoard->setMaxTimeStep(0);
- evalBoard->flush();
-
- // Switch back to flatline
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortA, Rhd2000EvalBoard::AuxCmd1, 0);
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortB, Rhd2000EvalBoard::AuxCmd1, 0);
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortC, Rhd2000EvalBoard::AuxCmd1, 0);
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortD, Rhd2000EvalBoard::AuxCmd1, 0);
- evalBoard->selectAuxCommandLength(Rhd2000EvalBoard::AuxCmd1, 0, 1);
-
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortA, Rhd2000EvalBoard::AuxCmd3,
- fastSettleEnabled ? 2 : 1);
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortB, Rhd2000EvalBoard::AuxCmd3,
- fastSettleEnabled ? 2 : 1);
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortC, Rhd2000EvalBoard::AuxCmd3,
- fastSettleEnabled ? 2 : 1);
- evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortD, Rhd2000EvalBoard::AuxCmd3,
- fastSettleEnabled ? 2 : 1);
-
- if (fastTTLSettleEnabled)
- {
- evalBoard->enableExternalFastSettle(true);
- }
-}
-
int RHD2000Thread::getChannelFromHeadstage(int hs, int ch)
{
int channelCount = 0;
@@ -2237,4 +1739,504 @@ Rhd2000EvalBoard::BoardDataSource RHDHeadstage::getDataStream(int index)
bool RHDHeadstage::isPlugged()
{
return (numStreams > 0);
+}
+
+/***********************************/
+/* Below is code for impedance measurements */
+
+RHDImpedanceMeasure::RHDImpedanceMeasure(RHD2000Thread* b, ImpedanceData* d) : Thread(""), data(d), board(b)
+{
+ // 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);
+}
+
+
+
+
+// Update electrode impedance measurement frequency, after checking that
+// requested test frequency lies within acceptable ranges based on the
+// amplifier bandwidth and the sampling rate. See impedancefreqdialog.cpp
+// for more information.
+float RHDImpedanceMeasure::updateImpedanceFrequency(float desiredImpedanceFreq, bool& impedanceFreqValid)
+{
+ int impedancePeriod;
+ double lowerBandwidthLimit, upperBandwidthLimit;
+ float actualImpedanceFreq;
+
+ upperBandwidthLimit = board->actualUpperBandwidth / 1.5;
+ lowerBandwidthLimit = board->actualLowerBandwidth * 1.5;
+ if (board->dspEnabled)
+ {
+ if (board->actualDspCutoffFreq > board->actualLowerBandwidth)
+ {
+ lowerBandwidthLimit = board->actualDspCutoffFreq * 1.5;
+ }
+ }
+
+ if (desiredImpedanceFreq > 0.0)
+ {
+ impedancePeriod = (board->boardSampleRate / desiredImpedanceFreq);
+ if (impedancePeriod >= 4 && impedancePeriod <= 1024 &&
+ desiredImpedanceFreq >= lowerBandwidthLimit &&
+ desiredImpedanceFreq <= upperBandwidthLimit)
+ {
+ actualImpedanceFreq = board->boardSampleRate / impedancePeriod;
+ impedanceFreqValid = true;
+ }
+ else
+ {
+ actualImpedanceFreq = 0.0;
+ impedanceFreqValid = false;
+ }
+ }
+ else
+ {
+ actualImpedanceFreq = 0.0;
+ impedanceFreqValid = false;
+ }
+
+ return actualImpedanceFreq;
+}
+
+
+// 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 RHDImpedanceMeasure::loadAmplifierData(queue<Rhd2000DataBlock>& dataQueue,
+ int numBlocks, int numDataStreams)
+{
+
+ int block, t, channel, stream, i, j;
+ int indexAmp = 0;
+ int indexAux = 0;
+ int indexSupply = 0;
+ int indexAdc = 0;
+ int indexDig = 0;
+ int numWordsWritten = 0;
+
+ int bufferIndex;
+ int16 tempQint16;
+ uint16 tempQuint16;
+ int32 tempQint32;
+
+ bool triggerFound = false;
+ const double AnalogTriggerThreshold = 1.65;
+
+
+ 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)
+ {
+ // Amplifier waveform units = microvolts
+ amplifierPreFilter[stream][channel][indexAmp] = 0.195 *
+ (dataQueue.front().amplifierData[stream][channel][t] - 32768);
+ }
+ }
+ ++indexAmp;
+ }
+ // We are done with this Rhd2000DataBlock object; remove it from dataQueue
+ dataQueue.pop();
+ }
+
+ return 0;
+}
+
+#define PI 3.14159265359
+#define TWO_PI 6.28318530718
+#define DEGREES_TO_RADIANS 0.0174532925199
+#define RADIANS_TO_DEGREES 57.2957795132
+
+// 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 RHDImpedanceMeasure::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)
+ {
+ startIndex += period;
+ endIndex += period;
+ }
+
+ double iComponent, qComponent;
+
+ // Measure real (iComponent) and imaginary (qComponent) amplitude of frequency component.
+ amplitudeOfFreqComponent(iComponent, qComponent, amplifierPreFilter[stream][chipChannel],
+ startIndex, endIndex, sampleRate, frequency);
+ // Calculate magnitude and phase from real (I) and imaginary (Q) components.
+ measuredMagnitude[stream][chipChannel][capIndex] =
+ sqrt(iComponent * iComponent + qComponent * qComponent);
+ measuredPhase[stream][chipChannel][capIndex] =
+ 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 RHDImpedanceMeasure::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
+
+ // Perform correlation with sine and cosine waveforms.
+ double meanI = 0.0;
+ double meanQ = 0.0;
+ for (int t = startIndex; t <= endIndex; ++t)
+ {
+ meanI += data.at(t) * cos(k * t);
+ meanQ += data.at(t) * -1.0 * sin(k * t);
+ }
+ meanI /= (double)length;
+ meanQ /= (double)length;
+
+ realComponent = 2.0 * meanI;
+ imagComponent = 2.0 * meanQ;
+}
+
+
+
+// Given a measured complex impedance that is the result of an electrode impedance in parallel
+// 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 RHDImpedanceMeasure::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);
+ double measuredX = impedanceMagnitude * sin(DEGREES_TO_RADIANS * impedancePhase);
+
+ double capTerm = TWO_PI * frequency * parasiticCapacitance;
+ double xTerm = capTerm * (measuredR * measuredR + measuredX * measuredX);
+ double denominator = capTerm * xTerm + 2 * capTerm * measuredX + 1;
+ double trueR = measuredR / denominator;
+ double trueX = (measuredX + xTerm) / denominator;
+
+ // Now, convert from rectangular coordinates back to polar coordinates.
+ impedanceMagnitude = sqrt(trueR * trueR + trueX * trueX);
+ impedancePhase = RADIANS_TO_DEGREES * atan2(trueX, trueR);
+}
+
+// This is a purely empirical function to correct observed errors in the real component
+// of measured electrode impedances at sampling rates below 15 kS/s. At low sampling rates,
+// it is difficult to approximate a smooth sine wave with the on-chip voltage DAC and 10 kHz
+// 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 RHDImpedanceMeasure::empiricalResistanceCorrection(double& impedanceMagnitude, double& impedancePhase,
+ double boardSampleRate)
+{
+ // First, convert from polar coordinates to rectangular coordinates.
+ double impedanceR = impedanceMagnitude * cos(DEGREES_TO_RADIANS * impedancePhase);
+ double impedanceX = impedanceMagnitude * sin(DEGREES_TO_RADIANS * impedancePhase);
+
+ // Emprically derived correction factor (i.e., no physical basis for this equation).
+ impedanceR /= 10.0 * exp(-boardSampleRate / 2500.0) * cos(TWO_PI * boardSampleRate / 15000.0) + 1.0;
+
+ // Now, convert from rectangular coordinates back to polar coordinates.
+ impedanceMagnitude = sqrt(impedanceR * impedanceR + impedanceX * impedanceX);
+ impedancePhase = RADIANS_TO_DEGREES * atan2(impedanceX, impedanceR);
+}
+
+void RHDImpedanceMeasure::run()
+{
+ int commandSequenceLength, stream, channel, capRange;
+ double cSeries;
+ vector<int> commandList;
+ int triggerIndex; // dummy reference variable; not used
+ queue<Rhd2000DataBlock> bufferQueue; // dummy reference variable; not used
+ int numdataStreams = board->evalBoard->getNumEnabledDataStreams();
+
+ bool rhd2164ChipPresent = false;
+ Array<int> enabledStreams;
+ for (stream = 0; stream < MAX_NUM_DATA_STREAMS; ++stream)
+ {
+
+ if (board->evalBoard->isStreamEnabled(stream))
+ {
+ enabledStreams.add(stream);
+ }
+
+ if (board->chipId[stream] == CHIP_ID_RHD2164_B)
+ {
+ rhd2164ChipPresent = true;
+ }
+ }
+
+ bool validImpedanceFreq;
+ float actualImpedanceFreq = updateImpedanceFrequency(1000.0, validImpedanceFreq);
+ if (!validImpedanceFreq)
+ {
+ return;
+ }
+ // Create a command list for the AuxCmd1 slot.
+ commandSequenceLength = board->chipRegisters.createCommandListZcheckDac(commandList, actualImpedanceFreq, 128.0);
+ board->evalBoard->uploadCommandList(commandList, Rhd2000EvalBoard::AuxCmd1, 1);
+ board->evalBoard->selectAuxCommandLength(Rhd2000EvalBoard::AuxCmd1,
+ 0, commandSequenceLength - 1);
+ if (board->fastTTLSettleEnabled)
+ {
+ board->evalBoard->enableExternalFastSettle(false);
+ }
+
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortA,
+ Rhd2000EvalBoard::AuxCmd1, 1);
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortB,
+ Rhd2000EvalBoard::AuxCmd1, 1);
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortC,
+ Rhd2000EvalBoard::AuxCmd1, 1);
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortD,
+ Rhd2000EvalBoard::AuxCmd1, 1);
+
+ // Select number of periods to measure impedance over
+ int numPeriods = (0.020 * actualImpedanceFreq); // Test each channel for at least 20 msec...
+ if (numPeriods < 5) numPeriods = 5; // ...but always measure across no fewer than 5 complete periods
+ double period = board->boardSampleRate / actualImpedanceFreq;
+ int numBlocks = ceil((numPeriods + 2.0) * period / 60.0); // + 2 periods to give time to settle initially
+ if (numBlocks < 2) numBlocks = 2; // need first block for command to switch channels to take effect.
+
+ board->actualDspCutoffFreq = board->chipRegisters.setDspCutoffFreq(board->desiredDspCutoffFreq);
+ board->actualLowerBandwidth = board->chipRegisters.setLowerBandwidth(board->desiredLowerBandwidth);
+ board->actualUpperBandwidth = board->chipRegisters.setUpperBandwidth(board->desiredUpperBandwidth);
+ board->chipRegisters.enableDsp(board->dspEnabled);
+ board->chipRegisters.enableZcheck(true);
+ commandSequenceLength = board->chipRegisters.createCommandListRegisterConfig(commandList, false);
+ // Upload version with no ADC calibration to AuxCmd3 RAM Bank 1.
+ board->evalBoard->uploadCommandList(commandList, Rhd2000EvalBoard::AuxCmd3, 3);
+ board->evalBoard->selectAuxCommandLength(Rhd2000EvalBoard::AuxCmd3, 0, commandSequenceLength - 1);
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortA, Rhd2000EvalBoard::AuxCmd3, 3);
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortB, Rhd2000EvalBoard::AuxCmd3, 3);
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortC, Rhd2000EvalBoard::AuxCmd3, 3);
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortD, Rhd2000EvalBoard::AuxCmd3, 3);
+
+ board->evalBoard->setContinuousRunMode(false);
+ board->evalBoard->setMaxTimeStep(SAMPLES_PER_DATA_BLOCK * numBlocks);
+
+ // Create matrices of doubles of size (numStreams x 32 x 3) to store complex amplitudes
+ // of all amplifier channels (32 on each data stream) at three different Cseries values.
+ std::vector<std::vector<std::vector<double>>> measuredMagnitude;
+ std::vector<std::vector<std::vector<double>>> measuredPhase;
+
+ measuredMagnitude.resize(board->evalBoard->getNumEnabledDataStreams());
+ measuredPhase.resize(board->evalBoard->getNumEnabledDataStreams());
+ for (int i = 0; i < board->evalBoard->getNumEnabledDataStreams(); ++i)
+ {
+ measuredMagnitude[i].resize(32);
+ measuredPhase[i].resize(32);
+ for (int j = 0; j < 32; ++j)
+ {
+ measuredMagnitude[i][j].resize(3);
+ measuredPhase[i][j].resize(3);
+ }
+ }
+
+
+
+ double distance, minDistance, current, Cseries;
+ 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.
+ 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.
+ double relativeFreq = actualImpedanceFreq / board->boardSampleRate;
+
+ int bestAmplitudeIndex;
+
+ // 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)
+ {
+
+
+ switch (capRange)
+ {
+ case 0:
+ board->chipRegisters.setZcheckScale(Rhd2000Registers::ZcheckCs100fF);
+ cSeries = 0.1e-12;
+ cout << "setting capacitance to 0.1pF" << endl;
+ break;
+ case 1:
+ board->chipRegisters.setZcheckScale(Rhd2000Registers::ZcheckCs1pF);
+ cSeries = 1.0e-12;
+ cout << "setting capacitance to 1pF" << endl;
+ break;
+ case 2:
+ board->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)
+ {
+ cout << "running impedance on channel " << channel << endl;
+
+ board->chipRegisters.setZcheckChannel(channel);
+ commandSequenceLength =
+ board->chipRegisters.createCommandListRegisterConfig(commandList, false);
+ // Upload version with no ADC calibration to AuxCmd3 RAM Bank 1.
+ board->evalBoard->uploadCommandList(commandList, Rhd2000EvalBoard::AuxCmd3, 3);
+
+ board->evalBoard->run();
+ while (board->evalBoard->isRunning())
+ {
+
+ }
+ queue<Rhd2000DataBlock> dataQueue;
+ board->evalBoard->readDataBlocks(numBlocks, dataQueue);
+ loadAmplifierData(dataQueue, numBlocks, numdataStreams);
+ for (stream = 0; stream < numdataStreams; ++stream)
+ {
+ if (board->chipId[stream] != CHIP_ID_RHD2164_B)
+ {
+ measureComplexAmplitude(measuredMagnitude, measuredPhase,
+ capRange, stream, channel, numBlocks, board->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)
+ {
+ board->chipRegisters.setZcheckChannel(channel + 32); // address channels 32-63
+ commandSequenceLength =
+ board->chipRegisters.createCommandListRegisterConfig(commandList, false);
+ // Upload version with no ADC calibration to AuxCmd3 RAM Bank 1.
+ board->evalBoard->uploadCommandList(commandList, Rhd2000EvalBoard::AuxCmd3, 3);
+
+ board->evalBoard->run();
+ while (board->evalBoard->isRunning())
+ {
+
+ }
+ board->evalBoard->readDataBlocks(numBlocks, dataQueue);
+ loadAmplifierData(dataQueue, numBlocks, numdataStreams);
+
+ for (stream = 0; stream < board->evalBoard->getNumEnabledDataStreams(); ++stream)
+ {
+ if (board->chipId[stream] == CHIP_ID_RHD2164_B)
+ {
+ measureComplexAmplitude(measuredMagnitude, measuredPhase,
+ capRange, stream, channel, numBlocks, board->boardSampleRate,
+ actualImpedanceFreq, numPeriods);
+ }
+ }
+ }
+ }
+ }
+
+ data->streams.clear();
+ data->channels.clear();
+ data->magnitudes.clear();
+ data->phases.clear();
+
+ for (stream = 0; stream < board->evalBoard->getNumEnabledDataStreams(); ++stream)
+ {
+ for (channel = 0; channel < 32; ++channel)
+ {
+ if (1)
+ {
+ minDistance = 9.9e99; // ridiculously large number
+ 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)
+ {
+ 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;
+ }
+
+ // Calculate current amplitude produced by on-chip voltage DAC
+ current = TWO_PI * actualImpedanceFreq * dacVoltageAmplitude * Cseries;
+
+ // Calculate impedance magnitude from calculated current and measured voltage.
+ impedanceMagnitude = 1.0e-6 * (measuredMagnitude[stream][channel][bestAmplitudeIndex] / current) *
+ (18.0 * relativeFreq * relativeFreq + 1.0);
+
+ // Calculate impedance phase, with small correction factor accounting for the
+ // 3-command SPI pipeline delay.
+ impedancePhase = measuredPhase[stream][channel][bestAmplitudeIndex] + (360.0 * (3.0 / period));
+
+ // Factor out on-chip parasitic capacitance from impedance measurement.
+ factorOutParallelCapacitance(impedanceMagnitude, impedancePhase, actualImpedanceFreq,
+ parasiticCapacitance);
+
+ // Perform empirical resistance correction to improve accuarcy at sample rates below
+ // 15 kS/s.
+ empiricalResistanceCorrection(impedanceMagnitude, impedancePhase,
+ board->boardSampleRate);
+
+ data->streams.add(enabledStreams[stream]);
+ data->channels.add(channel);
+ data->magnitudes.add(impedanceMagnitude);
+ data->phases.add(impedancePhase);
+
+ if (impedanceMagnitude > 1000000)
+ cout << "stream " << stream << " channel " << 1 + channel << " magnitude: " << String(impedanceMagnitude / 1e6, 2) << " mOhm , phase : " << impedancePhase << endl;
+ else
+ cout << "stream " << stream << " channel " << 1 + channel << " magnitude: " << String(impedanceMagnitude / 1e3, 2) << " kOhm , phase : " << impedancePhase << endl;
+
+ }
+ }
+ }
+
+ board->evalBoard->setContinuousRunMode(false);
+ board->evalBoard->setMaxTimeStep(0);
+ board->evalBoard->flush();
+
+ // Switch back to flatline
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortA, Rhd2000EvalBoard::AuxCmd1, 0);
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortB, Rhd2000EvalBoard::AuxCmd1, 0);
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortC, Rhd2000EvalBoard::AuxCmd1, 0);
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortD, Rhd2000EvalBoard::AuxCmd1, 0);
+ board->evalBoard->selectAuxCommandLength(Rhd2000EvalBoard::AuxCmd1, 0, 1);
+
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortA, Rhd2000EvalBoard::AuxCmd3,
+ board->fastSettleEnabled ? 2 : 1);
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortB, Rhd2000EvalBoard::AuxCmd3,
+ board->fastSettleEnabled ? 2 : 1);
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortC, Rhd2000EvalBoard::AuxCmd3,
+ board->fastSettleEnabled ? 2 : 1);
+ board->evalBoard->selectAuxCommandBank(Rhd2000EvalBoard::PortD, Rhd2000EvalBoard::AuxCmd3,
+ board->fastSettleEnabled ? 2 : 1);
+
+ if (board->fastTTLSettleEnabled)
+ {
+ board->evalBoard->enableExternalFastSettle(true);
+ }
}
\ No newline at end of file
diff --git a/Source/Processors/DataThreads/RHD2000Thread.h b/Source/Processors/DataThreads/RHD2000Thread.h
index 8ca1a68b5..3cba97cd8 100644
--- a/Source/Processors/DataThreads/RHD2000Thread.h
+++ b/Source/Processors/DataThreads/RHD2000Thread.h
@@ -44,6 +44,16 @@
class SourceNode;
class RHDHeadstage;
+class RHDImpedanceMeasure;
+
+struct ImpedanceData
+{
+ Array<int> streams;
+ Array<int> channels;
+ Array<float> magnitudes;
+ Array<float> phases;
+};
+
/**
Communicates with the RHD2000 Evaluation Board from Intan Technologies
@@ -53,8 +63,8 @@ class RHDHeadstage;
*/
class RHD2000Thread : public DataThread, public Timer
-
{
+ friend class RHDImpedanceMeasure;
public:
RHD2000Thread(SourceNode* sn);
~RHD2000Thread();
@@ -83,22 +93,11 @@ public:
void setDSPOffset(bool state);
int setNoiseSlicerLevel(int level);
- void runImpedanceTest(Array<int>& stream, Array<int>& channel, Array<float>& magnitude, Array<float>& phase);
void setFastTTLSettle(bool state, int channel);
void setTTLoutputMode(bool state);
void setDAChpf(float cutoff, bool enabled);
void scanPorts();
- float updateImpedanceFrequency(float desiredImpedanceFreq, bool& impedanceFreqValid);
- int loadAmplifierData(queue<Rhd2000DataBlock>& dataQueue,
- int numBlocks, int numDataStreams);
- void 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 amplitudeOfFreqComponent(double& realComponent, double& imagComponent,
- const std::vector<double>& data, int startIndex,
- int endIndex, double sampleRate, double frequency);
int getNumEventChannels();
void enableAdcs(bool);
@@ -136,12 +135,7 @@ private:
Rhd2000Registers chipRegisters;
Rhd2000DataBlock* dataBlock;
- std::vector<std::vector<std::vector<double>>> amplifierPreFilter;
- void factorOutParallelCapacitance(double& impedanceMagnitude, double& impedancePhase,
- double frequency, double parasiticCapacitance);
- void empiricalResistanceCorrection(double& impedanceMagnitude, double& impedancePhase,
- double boardSampleRate);
- int numChannels;
+ int numChannels;
bool deviceFound;
float thisSample[256];
@@ -227,4 +221,31 @@ private:
JUCE_DECLARE_NON_COPYABLE_WITH_LEAK_DETECTOR(RHDHeadstage);
};
+class RHDImpedanceMeasure : public Thread
+{
+public:
+ RHDImpedanceMeasure(RHD2000Thread* b, ImpedanceData* d);
+ void run();
+private:
+ void 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 amplitudeOfFreqComponent(double& realComponent, double& imagComponent,
+ const std::vector<double>& data, int startIndex,
+ int endIndex, double sampleRate, double frequency);
+ float updateImpedanceFrequency(float desiredImpedanceFreq, bool& impedanceFreqValid);
+ void factorOutParallelCapacitance(double& impedanceMagnitude, double& impedancePhase,
+ double frequency, double parasiticCapacitance);
+ void empiricalResistanceCorrection(double& impedanceMagnitude, double& impedancePhase,
+ double boardSampleRate);
+ int loadAmplifierData(queue<Rhd2000DataBlock>& dataQueue,
+ int numBlocks, int numDataStreams);
+
+ std::vector<std::vector<std::vector<double>>> amplifierPreFilter;
+
+ ImpedanceData* data;
+ RHD2000Thread* board;
+};
+
#endif // __RHD2000THREAD_H_2C4CBD67__
--
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