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Allow individual Neuropixels 2.0 probes to be enabled #116

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Allow individual Neuropixels 2.0 probes to be enabled #116

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164 changes: 145 additions & 19 deletions Source/Devices/Neuropixels2e.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@ Neuropixels2e::Neuropixels2e(std::string name, std::string hubName, const oni_de
INeuropixel(NeuropixelsV2eValues::numberOfSettings, NeuropixelsV2eValues::numberOfShanks)
{
probeSN.fill(0);
probeEnabled.fill(true);

for (int i = 0; i < NeuropixelsV2eValues::numberOfSettings; i++)
{
Expand All @@ -40,6 +41,18 @@ Neuropixels2e::Neuropixels2e(std::string name, std::string hubName, const oni_de
eventCodes[i] = 0;
}

Neuropixels2e::~Neuropixels2e()
{
if (serializer != nullptr)
{
selectProbe(ProbeSelected::NoProbe);
serializer->WriteByte((uint32_t)DS90UB9x::DS90UB9xSerializerI2CRegister::GPIO10, DefaultGPO10Config);
}

if (deviceContext != nullptr && deviceContext->isInitialized())
deviceContext->setOption(ONIX_OPT_PASSTHROUGH, 0);
}

void Neuropixels2e::createDataStream(int n)
{
StreamInfo apStream = StreamInfo(
Expand All @@ -63,6 +76,64 @@ int Neuropixels2e::getNumProbes() const
return m_numProbes;
}

std::string Neuropixels2e::getName(int index)
{
switch (index)
{
case 0: return "Probe0";
case 1: return "Probe1";
default: return "UNKNOWN";
}

return "";
}

std::string Neuropixels2e::getName(ProbeSelected probe)
{
switch (probe)
{
case ProbeSelected::ProbeA: return getName(0);
case ProbeSelected::ProbeB: return getName(1);
default: return "UNKNOWN";
}

return "";
}

bool Neuropixels2e::isEnabled() const
{
return std::any_of(probeEnabled.cbegin(), probeEnabled.cend(), [](bool en) { return en; });
}

bool Neuropixels2e::setProbeEnabled(int index, bool status)
{
try
{
probeEnabled[index] = status;
return true;
}
catch (const std::out_of_range& ex) // filter for out of range
{
LOGE("Invalid index given setting probe enable status.");
}

return false;
}

bool Neuropixels2e::getProbeEnabled(int index)
{
try
{
return probeEnabled[index];
}
catch (const std::out_of_range& ex) // filter for out of range
{
LOGE("Invalid index given getting probe enable status.");
}

return false;
}

void Neuropixels2e::selectElectrodesInRange(std::vector<int>& selection, int startIndex, int numberOfElectrodes)
{
for (int i = startIndex; i < startIndex + numberOfElectrodes; i++)
Expand Down Expand Up @@ -235,22 +306,34 @@ OnixDeviceType Neuropixels2e::getDeviceType()
int Neuropixels2e::configureDevice()
{
if (deviceContext == nullptr || !deviceContext->isInitialized())
throw error_str("Device context is not initialized properly for " + getName());
throw error_str("Device context is not initialized properly for " + OnixDevice::getName());

int rc = deviceContext->writeRegister(deviceIdx, DS90UB9x::ENABLE, isEnabled() ? 1 : 0);
int rc = deviceContext->writeRegister(deviceIdx, DS90UB9x::ENABLE, isEnabled() ? 1u : 0u);
if (rc != ONI_ESUCCESS)
throw error_str("Unable to enable " + getName());
throw error_str("Unable to enable passthrough device.");

if (!isEnabled())
return ONI_ESUCCESS;

configureSerDes();
setProbeSupply(true);
rc = serializer->set933I2cRate(400e3);
if (rc != ONI_ESUCCESS)
throw error_str("Unable to set I2C rate for " + getName());
probeSN[0] = getProbeSN(ProbeASelected);
probeSN[1] = getProbeSN(ProbeBSelected);
throw error_str("Unable to set I2C rate for " + OnixDevice::getName());

probeSN[0] = getProbeSN(ProbeSelected::ProbeA);
if (probeSN[0] != 0)
{
LOGD("Probe A SN: ", probeSN[0]);
}

probeSN[1] = getProbeSN(ProbeSelected::ProbeB);
if (probeSN[1] != 0)
{
LOGD("Probe B SN: ", probeSN[1]);
}

setProbeSupply(false);
LOGD("Probe A SN: ", probeSN[0]);
LOGD("Probe B SN: ", probeSN[1]);

if (probeSN[0] == 0 && probeSN[1] == 0)
{
Expand Down Expand Up @@ -280,7 +363,7 @@ bool Neuropixels2e::updateSettings()
{
for (int i = 0; i < 2; i++)
{
if (probeSN[i] != 0)
if (probeSN[i] != 0 && probeEnabled[i])
{
if (gainCorrectionFilePath[i] == "None" || gainCorrectionFilePath[i] == "")
{
Expand Down Expand Up @@ -344,20 +427,59 @@ bool Neuropixels2e::updateSettings()
{
if (probeSN[i] != 0)
{
selectProbe(i == 0 ? ProbeASelected : ProbeBSelected);
writeConfiguration(settings[i].get());
configureProbeStreaming();
auto probeSelected = i == 0 ? ProbeSelected::ProbeA: ProbeSelected::ProbeB;

if (probeEnabled[i])
{
writeConfiguration(probeSelected, settings[i].get());
if (!configureProbeStreaming(probeSelected))
return false;
}
else
{
if (!disableProbeStreaming(probeSelected))
return false;
}
}
}

selectProbe(NoProbeSelected);
selectProbe(ProbeSelected::NoProbe);
//IMPORTANT! BNO polling thread must be started after this

return true;
}

void Neuropixels2e::configureProbeStreaming()
bool Neuropixels2e::disableProbeStreaming(ProbeSelected probeSelect)
{
if (probeControl == nullptr)
{
Onix1::showWarningMessageBoxAsync(
"Probe Stream",
"Unable to disable " + getName(probeSelect) + " streaming."
);
return false;
}

selectProbe(probeSelect);

probeControl->WriteByte(OP_MODE, 1 << 7);

return true;
}

bool Neuropixels2e::configureProbeStreaming(ProbeSelected probeSelect)
{
if (probeControl == nullptr)
{
Onix1::showWarningMessageBoxAsync(
"Probe Stream Configuration",
"Unable to configure " + getName(probeSelect) + " streaming."
);
return false;
}

selectProbe(probeSelect);

// Write super sync bits into ASIC
probeControl->WriteByte(SUPERSYNC11, 0b00011000);
probeControl->WriteByte(SUPERSYNC10, 0b01100001);
Expand All @@ -378,6 +500,8 @@ void Neuropixels2e::configureProbeStreaming()
// Set global ADC settings
// TODO: Undocumented
probeControl->WriteByte(ADC_CONFIG, 0b00001000);

return true;
}

void Neuropixels2e::configureSerDes()
Expand Down Expand Up @@ -427,20 +551,20 @@ void Neuropixels2e::setProbeSupply(bool en)
{
auto gpo10Config = en ? DefaultGPO10Config | GPO10SupplyMask : DefaultGPO10Config;

selectProbe(NoProbeSelected);
selectProbe(ProbeSelected::NoProbe);
serializer->WriteByte((uint32_t)(DS90UB9x::DS90UB9xSerializerI2CRegister::GPIO10), gpo10Config);
Thread::sleep(20);
}

void Neuropixels2e::selectProbe(uint8_t probeSelect)
void Neuropixels2e::selectProbe(ProbeSelected probeSelect)
{
if (serializer == nullptr)
{
LOGE("Serializer is not initialized for Neuropixels 2.0");
return;
}

serializer->WriteByte((uint32_t)(DS90UB9x::DS90UB9xSerializerI2CRegister::GPIO32), probeSelect);
serializer->WriteByte((uint32_t)(DS90UB9x::DS90UB9xSerializerI2CRegister::GPIO32), (uint8_t)probeSelect);
Thread::sleep(20);
}

Expand All @@ -453,7 +577,7 @@ void Neuropixels2e::resetProbes()
serializer->WriteByte((uint32_t)(DS90UB9x::DS90UB9xSerializerI2CRegister::GPIO10), gpo10Config);
}

uint64_t Neuropixels2e::getProbeSN(uint8_t probeSelect)
uint64_t Neuropixels2e::getProbeSN(ProbeSelected probeSelect)
{
if (flex == nullptr)
{
Expand Down Expand Up @@ -561,8 +685,10 @@ void Neuropixels2e::processFrames()
}
}

void Neuropixels2e::writeConfiguration(ProbeSettings<numberOfChannels, numberOfElectrodes>* settings)
void Neuropixels2e::writeConfiguration(ProbeSelected probeSelect, ProbeSettings<numberOfChannels, numberOfElectrodes>* settings)
{
selectProbe(probeSelect);

auto baseBits = makeBaseBits(getReference(settings->referenceIndex));
writeShiftRegister(SR_CHAIN5, baseBits[0]);
writeShiftRegister(SR_CHAIN6, baseBits[1]);
Expand Down
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