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Update Neuropixels 2.0 Probes #128

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Merged
merged 2 commits into from
Jul 22, 2025
Merged

Update Neuropixels 2.0 Probes #128

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d5ed1fc
Add 2D arrays to correctly track both Neuropixels 2e probes
bparks13 Jul 18, 2025
6883d39
Remove unsigned integer offset in Neuropixels 2.0 probes
bparks13 Jul 21, 2025
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27 changes: 14 additions & 13 deletions Source/Devices/Neuropixels2e.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -30,14 +30,16 @@ Neuropixels2e::Neuropixels2e(std::string name, std::string hubName, const oni_de
INeuropixel(NeuropixelsV2eValues::numberOfSettings, NeuropixelsV2eValues::numberOfShanks)
{
probeSN.fill(0);
frameCount.fill(0);
sampleNumber.fill(0);

for (int i = 0; i < NeuropixelsV2eValues::numberOfSettings; i++)
{
defineMetadata(settings[i].get(), NeuropixelsV2eValues::numberOfShanks);
}

for (int i = 0; i < numFrames; i++)
eventCodes[i] = 0;
for (int i = 0; i < NumberOfProbes; i++)
eventCodes[i].fill(0);
}

Neuropixels2e::~Neuropixels2e()
Expand Down Expand Up @@ -495,8 +497,8 @@ uint64_t Neuropixels2e::getProbeSN(uint8_t probeSelect)

void Neuropixels2e::startAcquisition()
{
sampleNumber = 0;
frameCount = 0;
frameCount.fill(0);
sampleNumber.fill(0);
}

void Neuropixels2e::stopAcquisition()
Expand Down Expand Up @@ -535,8 +537,8 @@ void Neuropixels2e::processFrames()
uint16_t probeIndex = *(dataPtr + 4);
uint16_t* amplifierData = dataPtr + 9;

sampleNumbers[frameCount] = sampleNumber;
timestamps[frameCount] = deviceContext->convertTimestampToSeconds(frame->time);
sampleNumbers[probeIndex][frameCount[probeIndex]] = sampleNumber[probeIndex]++;
timestamps[probeIndex][frameCount[probeIndex]] = deviceContext->convertTimestampToSeconds(frame->time);

for (int i = 0; i < FramesPerSuperFrame; i++)
{
Expand All @@ -546,18 +548,17 @@ void Neuropixels2e::processFrames()
{
const size_t channelIndex = rawToChannel[j][i];

samples[channelIndex * numFrames + frameCount] =
(float)(*(amplifierData + adcIndices[j] + adcDataOffset)) * gainCorrection[probeIndex];
samples[probeIndex][channelIndex * numFrames + frameCount[probeIndex]] =
(float)(*(amplifierData + adcIndices[j] + adcDataOffset)) * gainCorrection[probeIndex] + DataMidpoint;
}
}

frameCount++;
sampleNumber++;
frameCount[probeIndex]++;

if (frameCount >= numFrames)
if (frameCount[probeIndex] >= numFrames)
{
amplifierBuffer[probeIndex]->addToBuffer(samples.data(), sampleNumbers, timestamps, eventCodes, numFrames);
frameCount = 0;
amplifierBuffer[probeIndex]->addToBuffer(samples[probeIndex].data(), sampleNumbers[probeIndex].data(), timestamps[probeIndex].data(), eventCodes[probeIndex].data(), numFrames);
frameCount[probeIndex] = 0;
}

oni_destroy_frame(frame);
Expand Down
15 changes: 9 additions & 6 deletions Source/Devices/Neuropixels2e.h
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,9 @@ namespace OnixSourcePlugin

static constexpr int NumberOfProbes = 2;

static constexpr uint16_t NumberOfAdcBins = 4096;
static constexpr float DataMidpoint = NumberOfAdcBins / 2;

DataBuffer* amplifierBuffer[NumberOfProbes];

std::array<uint64_t, NumberOfProbes> probeSN;
Expand Down Expand Up @@ -124,14 +127,14 @@ namespace OnixSourcePlugin
static const int numFrames = 10;
static const int numSamples = numberOfChannels * numFrames;

std::array<float, numSamples> samples;
std::array<std::array<float, numSamples>, NumberOfProbes> samples {};

int64 sampleNumbers[numFrames];
double timestamps[numFrames];
uint64 eventCodes[numFrames];
std::array<std::array<int64_t, numFrames>, NumberOfProbes> sampleNumbers {};
std::array<std::array<double, numFrames>, NumberOfProbes> timestamps {};
std::array<std::array<uint64_t, numFrames>, NumberOfProbes> eventCodes {};

int frameCount = 0;
int sampleNumber = 0;
std::array<int, NumberOfProbes> frameCount;
std::array<int64_t, NumberOfProbes> sampleNumber;

std::unique_ptr<I2CRegisterContext> serializer;
std::unique_ptr<I2CRegisterContext> deserializer;
Expand Down