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NeuropixThread.cpp
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NeuropixThread.cpp
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/*
------------------------------------------------------------------
This file is part of the Open Ephys GUI
Copyright (C) 2017 Allen Institute for Brain Science and Open Ephys
------------------------------------------------------------------
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include "NeuropixThread.h"
#include "NeuropixEditor.h"
#include "Basestations/Basestation_v1.h"
#include "Basestations/Basestation_v3.h"
#include "Basestations/OneBox.h"
#include "Basestations/SimulatedBasestation.h"
#include "Probes/OneBoxADC.h"
#include "UI/NeuropixInterface.h"
#include <vector>
//Helpful for debugging when PXI system is connected but don't want to connect to real probes
#define FORCE_SIMULATION_MODE false
DataThread* NeuropixThread::createDataThread(SourceNode *sn, DeviceType type)
{
return new NeuropixThread(sn, type);
}
std::unique_ptr<GenericEditor> NeuropixThread::createEditor(SourceNode* sn)
{
std::unique_ptr<NeuropixEditor> ed = std::make_unique<NeuropixEditor>(sn, this);
editor = ed.get();
return ed;
}
void Initializer::run()
{
Neuropixels::scanBS();
Neuropixels::basestationID list[16];
int count = getDeviceList(&list[0], 16);
LOGC(" Found ", count, " device", count == 1 ? "." : "s.");
Array<int> slotIDs;
if (!FORCE_SIMULATION_MODE)
{
for (int i = 0; i < count; i++)
{
int slotID;
bool foundSlot = Neuropixels::tryGetSlotID(&list[i], &slotID);
Neuropixels::NP_ErrorCode ec = Neuropixels::getDeviceInfo(list[i].ID, &list[i]);
LOGD("Slot ID: ", slotID, "Platform ID : ", list[i].platformid);
if (foundSlot && list[i].platformid == Neuropixels::NPPlatform_PXI && type == PXI)
{
LOGC(" Opening device on slot ", slotID);
Basestation* bs = new Basestation_v3(neuropixThread, slotID);
if (bs->open()) //returns true if Basestation firmware >= 2.0
{
int insertionIndex = 0;
if (slotIDs.size() > 0)
{
insertionIndex = slotIDs.size();
LOGC(" Checking ", insertionIndex, ": ", slotIDs[insertionIndex - 1]);
while (insertionIndex > 0 && slotIDs[insertionIndex - 1] > slotID)
{
LOGC("Moving backward...");
insertionIndex--;
LOGC(" Checking ", insertionIndex, ": ", slotIDs[insertionIndex - 1]);
}
}
LOGC("Insertion index:", insertionIndex);
basestations.insert(insertionIndex, bs);
slotIDs.insert(insertionIndex, slotID);
LOGC(" Adding basestation");
}
else
{
LOGC(" Could not open basestation");
delete bs;
}
}
else if (list[i].platformid == Neuropixels::NPPlatform_USB && type == ONEBOX) {
Basestation* bs = new OneBox(neuropixThread, list[i].ID);
if (bs->open())
{
basestations.add(bs);
if (!bs->getProbeCount())
CoreServices::sendStatusMessage("OneBox found, no probes connected.");
}
else {
delete bs;
}
}
else {
LOGC(" Slot ", slotID, " did not match desired platform.");
}
}
if (basestations.size() == 0 && type == PXI) // no basestations with API version match
{
LOGD("Checking for V1 basestations...");
uint32_t availableslotmask;
std::vector<int> slotsToCheck;
np::scanPXI(&availableslotmask);
for (int slot = 0; slot < 32; slot++)
{
if ((availableslotmask >> slot) & 1)
{
LOGD(" Found V1 Basestation");
Basestation* bs = new Basestation_v1(neuropixThread, slot);
if (bs->open()) // detects # of probes; returns true if API version matches
{
api_v1.isActive = true;
api_v3.isActive = false;
basestations.add(bs);
}
else {
delete bs;
}
}
}
}
else
{
LOGD("Found ", basestations.size(), " V3 basestation", basestations.size() > 1 ? "s" : "");
}
}
if (basestations.size() == 0) // no basestations at all
{
bool response = true;
if (!FORCE_SIMULATION_MODE)
{
if (type == PXI)
{
response = AlertWindow::showOkCancelBox(AlertWindow::NoIcon,
"No basestations detected",
"No Neuropixels PXI basestations were detected. Do you want to run this plugin in simulation mode?",
"Yes", "No", 0, 0);
}
else if (type == ONEBOX)
{
response = AlertWindow::showOkCancelBox(AlertWindow::NoIcon,
"No OneBox detected",
"No OneBox was detected. Do you want to run this plugin in simulation mode?",
"Yes", "No", 0, 0);
}
}
if (response)
{
if (type == PXI)
{
basestations.add(new SimulatedBasestation(neuropixThread, type, 2));
basestations.getLast()->open(); // detects # of probes
}
else if (type == ONEBOX)
{
basestations.add(new SimulatedBasestation(neuropixThread, type, 16));
basestations.getLast()->open(); // detects # of probes
}
}
}
}
NeuropixThread::NeuropixThread(SourceNode* sn, DeviceType type_) :
DataThread(sn),
type(type_),
baseStationAvailable(false),
probesInitialized(false),
initializationComplete(false)
{
defaultSyncFrequencies.add(1);
defaultSyncFrequencies.add(10);
api_v1.isActive = false;
api_v3.isActive = true;
LOGC("Scanning for devices...");
LOGD("Setting debug level to 0");
Neuropixels::np_dbg_setlevel(0);
initializer = std::make_unique<Initializer>(this, basestations, type, api_v1, api_v3);
initializer->run();
bool foundSync = false;
int probeIndex = 0;
int streamIndex = 0;
for (auto probe : getProbes())
{
baseStationAvailable = true;
if (!foundSync)
{
probe->basestation->setSyncAsInput();
foundSync = true;
}
/* Generate names for probes based on order of appearance in chassis */
probe->customName.automatic = generateProbeName(probeIndex, ProbeNameConfig::AUTO_NAMING);
probe->displayName = probe->customName.automatic;
probe->streamIndex = streamIndex;
probe->customName.streamSpecific = generateProbeName(probeIndex, ProbeNameConfig::STREAM_INDICES);
if (probe->generatesLfpData())
streamIndex += 2;
else
streamIndex += 1;
probeIndex++;
}
updateStreamInfo();
}
String NeuropixThread::generateProbeName(int probeIndex, ProbeNameConfig::NamingScheme namingScheme)
{
StringArray probeNames = { "A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N",
"O" , "P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y", "Z" };
Array<Probe*> probes = getProbes();
Probe* probe = probes[probeIndex];
String name;
switch (namingScheme)
{
case ProbeNameConfig::AUTO_NAMING:
name = "Probe" + probeNames[probeIndex];
break;
case ProbeNameConfig::PROBE_SPECIFIC_NAMING:
name = probe->customName.probeSpecific;
break;
case ProbeNameConfig::PORT_SPECIFIC_NAMING:
name = probe->basestation->getCustomPortName(probe->headstage->port, probe->dock);
break;
case ProbeNameConfig::STREAM_INDICES:
name = String(probe->streamIndex);
if (probe->generatesLfpData())
name += "," + String(probe->streamIndex + 1);
break;
default:
name = "Probe" + probeNames[probeIndex];
}
return name;
}
void NeuropixThread::updateStreamInfo()
{
streamInfo.clear();
sourceBuffers.clear();
int probe_index = 0;
for (auto source : getDataSources() )
{
if (source->sourceType == DataSourceType::PROBE)
{
StreamInfo apInfo;
Probe* probe = (Probe*) source;
apInfo.num_channels = probe->sendSync ? probe->channel_count + 1 : probe->channel_count;
apInfo.sample_rate = probe->ap_sample_rate;
apInfo.probe = probe;
apInfo.probe_index = probe_index++;
if (probe->generatesLfpData())
apInfo.type = AP_BAND;
else
apInfo.type = BROAD_BAND;
apInfo.sendSyncAsContinuousChannel = probe->sendSync;
streamInfo.add(apInfo);
sourceBuffers.add(new DataBuffer(apInfo.num_channels, 460800)); // AP band buffer
probe->apBuffer = sourceBuffers.getLast();
if (probe->generatesLfpData())
{
StreamInfo lfpInfo;
lfpInfo.num_channels = probe->sendSync ? probe->channel_count + 1 : probe->channel_count;
lfpInfo.sample_rate = probe->lfp_sample_rate;
lfpInfo.type = LFP_BAND;
lfpInfo.probe = probe;
lfpInfo.sendSyncAsContinuousChannel = probe->sendSync;
sourceBuffers.add(new DataBuffer(lfpInfo.num_channels, 38400)); // LFP band buffer
probe->lfpBuffer = sourceBuffers.getLast();
streamInfo.add(lfpInfo);
}
LOGD("Probe (slot=", probe->basestation->slot, ", port=", probe->headstage->port, ") CH=", apInfo.num_channels, " SR=", apInfo.sample_rate, " Hz");
}
else {
if (true)
{
StreamInfo adcInfo;
adcInfo.num_channels = source->channel_count;
adcInfo.sample_rate = source->sample_rate;
adcInfo.type = ADC;
adcInfo.sendSyncAsContinuousChannel = false;
adcInfo.probe = nullptr;
adcInfo.adc = (OneBoxADC*)source;
sourceBuffers.add(new DataBuffer(adcInfo.num_channels, 10000)); // data buffer
source->apBuffer = sourceBuffers.getLast();
streamInfo.add(adcInfo);
}
}
}
}
NeuropixThread::~NeuropixThread()
{
closeConnection();
}
void NeuropixThread::updateProbeSettingsQueue(ProbeSettings settings)
{
probeSettingsUpdateQueue.add(settings);
}
void NeuropixThread::applyProbeSettingsQueue()
{
for (auto settings : probeSettingsUpdateQueue)
{
settings.probe->setStatus(SourceStatus::UPDATING);
}
for (auto settings: probeSettingsUpdateQueue)
{
if (settings.probe->basestation->isBusy())
settings.probe->basestation->waitForThreadToExit();
LOGC("Applying probe settings for ", settings.probe->name);
if (settings.probe != nullptr)
{
settings.probe->selectElectrodes();
settings.probe->setAllGains();
settings.probe->setAllReferences();
settings.probe->setApFilterState();
settings.probe->calibrate();
settings.probe->writeConfiguration();
settings.probe->setStatus(SourceStatus::CONNECTED);
LOGC("Wrote configuration");
}
}
probeSettingsUpdateQueue.clear();
}
void NeuropixThread::initialize(bool signalChainIsLoading)
{
editor->initialize(signalChainIsLoading);
}
void NeuropixThread::initializeBasestations(bool signalChainIsLoading)
{
// slower task, run in background thread
LOGD("NeuropixThread::initializeBasestations");
for (auto basestation : basestations)
{
basestation->initialize(signalChainIsLoading); // prepares probes for acquisition; may be slow
}
if (api_v1.isActive)
{
np::setParameter(np::NP_PARAM_BUFFERSIZE, MAXSTREAMBUFFERSIZE);
np::setParameter(np::NP_PARAM_BUFFERCOUNT, MAXSTREAMBUFFERCOUNT);
}
else {
Neuropixels::setParameter(Neuropixels::NP_PARAM_BUFFERSIZE, MAXSTREAMBUFFERSIZE);
Neuropixels::setParameter(Neuropixels::NP_PARAM_BUFFERCOUNT, MAXSTREAMBUFFERCOUNT);
}
initializationComplete = true;
}
Array<Basestation*> NeuropixThread::getBasestations()
{
Array<Basestation*> bs;
for (auto bs_ : basestations)
{
bs.add(bs_);
}
return bs;
}
Array<OneBox*> NeuropixThread::getOneBoxes()
{
Array<OneBox*> bs;
for (auto bs_ : basestations)
{
if (bs_->type == BasestationType::ONEBOX)
bs.add((OneBox*)bs_);
}
return bs;
}
Array<Basestation_v3*> NeuropixThread::getOptoBasestations()
{
Array<Basestation_v3*> bs;
for (auto bs_ : basestations)
{
if (bs_->type == BasestationType::OPTO)
bs.add((Basestation_v3*) bs_);
}
return bs;
}
Array<Probe*> NeuropixThread::getProbes()
{
Array<Probe*> probes;
for (auto bs : basestations)
{
for (auto probe : bs->getProbes())
{
probes.add(probe);
}
}
return probes;
}
String NeuropixThread::getProbeInfoString()
{
DynamicObject output;
output.setProperty(Identifier("plugin"),
var("Neuropix-PXI"));
output.setProperty(Identifier("version"),
var(PLUGIN_VERSION));
Array<var> probes;
for (auto probe : getProbes())
{
DynamicObject::Ptr p = new DynamicObject();
p->setProperty(Identifier("name"), probe->displayName);
p->setProperty(Identifier("type"), probe->probeMetadata.name);
p->setProperty(Identifier("slot"), probe->basestation->slot);
p->setProperty(Identifier("port"), probe->headstage->port);
p->setProperty(Identifier("dock"), probe->dock);
p->setProperty(Identifier("part_number"), probe->info.part_number);
p->setProperty(Identifier("serial_number"), String(probe->info.serial_number));
p->setProperty(Identifier("is_calibrated"), probe->isCalibrated);
probes.add(p.get());
}
output.setProperty(Identifier("probes"), probes);
MemoryOutputStream f;
output.writeAsJSON(f, 0, true, 4);
return f.toString();
}
Array<DataSource*> NeuropixThread::getDataSources()
{
Array<DataSource*> sources;
for (auto bs : basestations)
{
for (auto probe : bs->getProbes())
{
sources.add(probe);
}
for (auto additionalSource : bs->getAdditionalDataSources())
{
sources.add(additionalSource);
}
}
return sources;
}
String NeuropixThread::getApiVersion()
{
if (api_v1.isActive)
return api_v1.info.version;
else
return api_v3.info.version;
}
void NeuropixThread::setMainSync(int slotIndex)
{
if (foundInputSource() && slotIndex > -1)
basestations[slotIndex]->setSyncAsInput();
}
void NeuropixThread::setSyncOutput(int slotIndex)
{
if (basestations.size() && slotIndex > -1)
basestations[slotIndex]->setSyncAsOutput(0);
}
Array<int> NeuropixThread::getSyncFrequencies()
{
if (foundInputSource())
return basestations[0]->getSyncFrequencies();
else
return defaultSyncFrequencies;
}
void NeuropixThread::setSyncFrequency(int slotIndex, int freqIndex)
{
if (foundInputSource() && slotIndex > -1)
basestations[slotIndex]->setSyncAsOutput(freqIndex);
}
void NeuropixThread::closeConnection()
{
}
/** Returns true if the data source is connected, false otherwise.*/
bool NeuropixThread::foundInputSource()
{
return baseStationAvailable;
}
XmlElement NeuropixThread::getInfoXml()
{
XmlElement neuropix_info("NEUROPIX-PXI");
XmlElement* api_info = new XmlElement("API");
if (api_v1.isActive)
api_info->setAttribute("version", api_v1.info.version);
else
api_info->setAttribute("version", api_v3.info.version);
neuropix_info.addChildElement(api_info);
for (int i = 0; i < basestations.size(); i++)
{
XmlElement* basestation_info = new XmlElement("BASESTATION");
basestation_info->setAttribute("index", i + 1);
basestation_info->setAttribute("slot", int(basestations[i]->slot));
basestation_info->setAttribute("firmware_version", basestations[i]->info.boot_version);
basestation_info->setAttribute("bsc_firmware_version", basestations[i]->basestationConnectBoard->info.boot_version);
basestation_info->setAttribute("bsc_part_number", basestations[i]->basestationConnectBoard->info.part_number);
basestation_info->setAttribute("bsc_serial_number", String(basestations[i]->basestationConnectBoard->info.serial_number));
for (auto probe : basestations[i]->getProbes())
{
XmlElement* probe_info = new XmlElement("PROBE");
probe_info->setAttribute("port", probe->headstage->port);
probe_info->setAttribute("port", probe->dock);
probe_info->setAttribute("probe_serial_number", String(probe->info.serial_number));
probe_info->setAttribute("hs_serial_number", String(probe->headstage->info.serial_number));
probe_info->setAttribute("hs_part_number", probe->info.part_number);
probe_info->setAttribute("hs_version", probe->headstage->info.version);
probe_info->setAttribute("flex_part_number", probe->flex->info.part_number);
probe_info->setAttribute("flex_version", probe->flex->info.version);
basestation_info->addChildElement(probe_info);
}
neuropix_info.addChildElement(basestation_info);
}
return neuropix_info;
}
String NeuropixThread::getInfoString()
{
String infoString;
infoString += "API Version: ";
if (api_v1.isActive)
infoString += api_v1.info.version;
else
infoString += api_v3.info.version;
infoString += "\n";
infoString += "\n";
infoString += "\n";
for (int i = 0; i < basestations.size(); i++)
{
infoString += "Basestation ";
infoString += String(i + 1);
infoString += "\n";
infoString += " Firmware version: ";
infoString += basestations[i]->info.boot_version;
infoString += "\n";
infoString += " BSC firmware version: ";
infoString += basestations[i]->basestationConnectBoard->info.boot_version;
infoString += "\n";
infoString += " BSC part number: ";
infoString += basestations[i]->basestationConnectBoard->info.part_number;
infoString += "\n";
infoString += " BSC serial number: ";
infoString += String(basestations[i]->basestationConnectBoard->info.serial_number);
infoString += "\n";
infoString += "\n";
for (auto probe : basestations[i]->getProbes())
{
infoString += " Port ";
infoString += String(probe->headstage->port);
infoString += "\n";
infoString += "\n";
infoString += " Probe serial number: ";
infoString += String(probe->info.serial_number);
infoString += "\n";
infoString += "\n";
infoString += " Headstage serial number: ";
infoString += String(probe->headstage->info.serial_number);
infoString += "\n";
infoString += " Headstage part number: ";
infoString += probe->headstage->info.part_number;
infoString += "\n";
infoString += " Headstage version: ";
infoString += probe->headstage->info.version;
infoString += "\n";
infoString += "\n";
infoString += " Flex part number: ";
infoString += probe->flex->info.part_number;
infoString += "\n";
infoString += " Flex version: ";
infoString += probe->flex->info.version;
infoString += "\n";
infoString += "\n";
infoString += "\n";
}
infoString += "\n";
infoString += "\n";
}
return infoString;
}
/** Initializes data transfer.*/
bool NeuropixThread::startAcquisition()
{
startTimer(100);
return true;
}
void NeuropixThread::timerCallback()
{
LOGD("Timer callback.");
if (editor->uiLoader->isThreadRunning())
{
LOGD("Waiting for Neuropixels settings thread to exit.");
editor->uiLoader->waitForThreadToExit(20000);
LOGD("Neuropixels settings thread finished.");
}
for (int i = 0; i < basestations.size(); i++)
{
basestations[i]->startAcquisition();
}
startThread();
stopTimer();
}
void NeuropixThread::setDirectoryForSlot(int slotIndex, File directory)
{
LOGD("Thread setting directory for slot ", slotIndex, " to ", directory.getFileName());
if (slotIndex < basestations.size())
{
basestations[slotIndex]->setSavingDirectory(directory);
}
}
File NeuropixThread::getDirectoryForSlot(int slotIndex)
{
if (slotIndex < basestations.size())
{
return basestations[slotIndex]->getSavingDirectory();
}
else {
return File::getCurrentWorkingDirectory();
}
}
void NeuropixThread::setNamingSchemeForSlot(int slot, ProbeNameConfig::NamingScheme namingScheme)
{
for (auto bs : getBasestations())
if (bs->slot == slot)
bs->setNamingScheme(namingScheme);
}
ProbeNameConfig::NamingScheme NeuropixThread::getNamingSchemeForSlot(int slot)
{
for (auto bs : getBasestations())
if (bs->slot == slot)
return bs->getNamingScheme();
}
/** Stops data transfer.*/
bool NeuropixThread::stopAcquisition()
{
LOGC("Stopping Neuropixels thread.");
if (isThreadRunning())
{
signalThreadShouldExit();
}
for (int i = 0; i < basestations.size(); i++)
{
basestations[i]->stopAcquisition();
}
return true;
}
void NeuropixThread::updateSettings(OwnedArray<ContinuousChannel>* continuousChannels,
OwnedArray<EventChannel>* eventChannels,
OwnedArray<SpikeChannel>* spikeChannels,
OwnedArray<DataStream>* dataStreams,
OwnedArray<DeviceInfo>* devices,
OwnedArray<ConfigurationObject>* configurationObjects)
{
if (sourceStreams.size() == 0) // initialize data streams
{
String lastName;
for (auto info : streamInfo)
{
String streamName, description, identifier;
if (info.type == stream_type::ADC)
{
streamName = "OneBox-ADC";
description = "OneBox ADC data stream";
identifier = "onebox.adc";
}
else if (info.type == stream_type::AP_BAND)
{
lastName = generateProbeName(info.probe_index, info.probe->namingScheme);
if (info.probe->namingScheme != ProbeNameConfig::STREAM_INDICES)
streamName = lastName + "-AP";
else
streamName = String(info.probe->streamIndex);
description = "Neuropixels AP band data stream";
identifier = "neuropixels.data.ap";
}
else if (info.type == stream_type::BROAD_BAND)
{
streamName = generateProbeName(info.probe_index, info.probe->namingScheme);
description = "Neuropixels data stream";
identifier = "neuropixels.data";
}
else if (info.type == stream_type::LFP_BAND)
{
if (info.probe->namingScheme != ProbeNameConfig::STREAM_INDICES)
streamName = lastName + "-LFP";
else
streamName = String(info.probe->streamIndex + 1);
description = "Neuropixels LFP band data stream";
identifier = "neuropixels.data.lfp";
}
DataStream::Settings settings
{
streamName,
"description",
"identifier",
info.sample_rate
};
sourceStreams.add(new DataStream(settings));
}
}
dataStreams->clear();
eventChannels->clear();
continuousChannels->clear();
spikeChannels->clear();
devices->clear();
configurationObjects->clear();
int probeIdx = 0;
for (int i = 0; i < sourceStreams.size(); i++)
{
DataStream* currentStream = sourceStreams[i];
String streamName;
StreamInfo info = streamInfo[i];
if (info.type == stream_type::AP_BAND)
{
Probe* p = getProbes()[probeIdx];
p->updateNamingScheme(p->namingScheme); // update displayName
streamName = generateProbeName(probeIdx, p->namingScheme);
if (p->namingScheme != ProbeNameConfig::STREAM_INDICES)
streamName += "-AP";
else
streamName = String(p->streamIndex);
}
else if (info.type == stream_type::LFP_BAND)
{
Probe* p = getProbes()[probeIdx];
p->updateNamingScheme(p->namingScheme); // update displayName
streamName = generateProbeName(probeIdx, p->namingScheme);
if (p->namingScheme != ProbeNameConfig::STREAM_INDICES)
streamName += "-LFP";
else
streamName = String(p->streamIndex + 1);
probeIdx++;
}
else if (info.type == stream_type::BROAD_BAND)
{
Probe* p = getProbes()[probeIdx];
p->updateNamingScheme(p->namingScheme); // update displayName
streamName = generateProbeName(probeIdx, p->namingScheme);
probeIdx++;
}
else {
streamName = currentStream->getName();
}
currentStream->setName(streamName);
ContinuousChannel::Type type;
String description, identifier;
if (info.type == stream_type::ADC)
{
type = ContinuousChannel::Type::ADC;
description = "OneBox ADC channel";
identifier = "neuropixels.adc";
}
else
{
type = ContinuousChannel::Type::ELECTRODE;
description = "Neuropixels electrode";
identifier = "neuropixels.electrode";
}
currentStream->clearChannels();
for (int ch = 0; ch < info.num_channels; ch++)
{
float bitVolts;
if (info.type == stream_type::ADC) {
bitVolts = info.adc->getChannelGain(ch);
}
else {
bitVolts = 0.1950000f;
}
String name;