Merge pull request #162 from open-ephys-plugins/issue-138

Add depth and shank information to Neuropixels channels

Author: bparks13

Source/Devices/Neuropixels1e.cpp

@@ -135,6 +135,8 @@ int Neuropixels1e::configureDevice()
 
     LOGD ("Probe SN: ", probeMetadata.getProbeSerialNumber());
 
+    settings[0]->connected = probeMetadata.getProbeSerialNumber() != 0;
+
     return ONI_ESUCCESS;
 }
 

Source/Devices/Neuropixels1f.cpp

@@ -127,6 +127,8 @@ int Neuropixels1f::configureDevice()
 
     LOGD ("Probe SN: ", probeMetadata.getProbeSerialNumber());
 
+    settings[0]->connected = probeMetadata.getProbeSerialNumber() != 0;
+
     // Enable device streaming
     rc = deviceContext->writeRegister (deviceIdx, 0x8000, 1);
     if (rc != ONI_ESUCCESS)

Source/Devices/Neuropixels2e.cpp

@@ -316,18 +316,22 @@ int Neuropixels2e::configureDevice()
     LOGD ("Probe A SN: ", probeMetadata[0].getProbeSerialNumber());
     LOGD ("Probe B SN: ", probeMetadata[1].getProbeSerialNumber());
 
-    if (probeMetadata[0].getProbeSerialNumber() == 0 && probeMetadata[1].getProbeSerialNumber() == 0)
-    {
-        m_numProbes = 0;
-        throw error_str ("No probes were found connected at address " + std::to_string (getDeviceIdx()));
-    }
-    else if (probeMetadata[0].getProbeSerialNumber() != 0 && probeMetadata[1].getProbeSerialNumber() != 0)
+    m_numProbes = 0;
+
+    for(int i = 0; i < NumberOfProbes; i++)
     {
-        m_numProbes = 2;
+        if (probeMetadata[i].getProbeSerialNumber() != 0)
+        {
+            settings[i]->connected = true;
+            m_numProbes++;
+        }
+        else
+            settings[i]->connected = false;
     }
-    else
+
+    if (m_numProbes == 0)
     {
-        m_numProbes = 1;
+        throw error_str ("No probes were found connected at address " + std::to_string (getDeviceIdx()));
     }
 
     streamInfos.clear();
@@ -342,9 +346,9 @@ int Neuropixels2e::configureDevice()
 
 bool Neuropixels2e::updateSettings()
 {
-    for (int i = 0; i < 2; i++)
+    for (int i = 0; i < NumberOfProbes; i++)
     {
-        if (probeMetadata[i].getProbeSerialNumber() != 0)
+        if (settings[i]->connected)
         {
             if (! NeuropixelsProbeMetadata::validateProbeTypeAndPartNumber (settings[i]->probeType, probeMetadata[i]))
             {
@@ -416,7 +420,7 @@ bool Neuropixels2e::updateSettings()
 
     for (int i = 0; i < NumberOfProbes; i++)
     {
-        if (probeMetadata[i].getProbeSerialNumber() != 0)
+        if (settings[i]->connected)
         {
             selectProbe (serializer.get(), i == 0 ? ProbeASelected : ProbeBSelected);
             writeConfiguration (settings[i].get());
@@ -554,7 +558,7 @@ void Neuropixels2e::addSourceBuffers (OwnedArray<DataBuffer>& sourceBuffers)
     if (m_numProbes == 1)
     {
         sourceBuffers.add (new DataBuffer (streamInfos.getFirst().getNumChannels(), (int) streamInfos.getFirst().getSampleRate() * bufferSizeInSeconds));
-        auto bufferIndex = probeMetadata[0].getProbeSerialNumber() != 0 ? 0 : 1;
+        auto bufferIndex = settings[0]->connected ? 0 : 1;
         amplifierBuffer[bufferIndex] = sourceBuffers.getLast();
     }
     else

Source/NeuropixelsComponents.h

@@ -287,6 +287,7 @@ struct ProbeSettings
         lfpGainIndex = newSettings->lfpGainIndex;
         referenceIndex = newSettings->referenceIndex;
         apFilterState = newSettings->apFilterState;
+        connected = newSettings->connected;
 
         selectedBank = newSettings->selectedBank;
         selectedShank = newSettings->selectedShank;
@@ -344,6 +345,7 @@ struct ProbeSettings
     int lfpGainIndex = 0;
     int referenceIndex = 0;
     bool apFilterState = false;
+    bool connected = false;
 
     std::vector<Bank> selectedBank;
     std::vector<int> selectedShank;
@@ -562,4 +564,67 @@ static class NeuropixelsV1
         return baseConfigs;
     }
 };
+
+static class NeuropixelsHelpers
+{
+public:
+    /** Set all channel metadata, starting with the last (most recently added) channel and working backwards over all selected electrodes */
+    static void setChannelMetadata (OwnedArray<ContinuousChannel>* continuousChannels, const std::vector<std::unique_ptr<ProbeSettings>>& probeSettings)
+    {
+        ContinuousChannel** channels = continuousChannels->end();
+        channels--;
+
+        for (auto it = probeSettings.rbegin(); it != probeSettings.rend(); it++)
+        {
+            ProbeSettings* probeSetting = it->get();
+
+            if (! probeSetting->connected)
+                continue;
+
+            for (int i = probeSetting->numberOfChannels - 1; i >= 0; i--)
+            {
+                auto channel = *channels--;
+
+                int globalIndex = probeSetting->selectedElectrode[i];
+                int shankIndex = probeSetting->electrodeMetadata[globalIndex].shank;
+
+                float xpos = probeSetting->electrodeMetadata[globalIndex].xpos;
+                float ypos = probeSetting->electrodeMetadata[globalIndex].ypos;
+
+                // NB: Depth must be a unique value for compatibility with legacy LFP viewer channel sorting algorithm
+                float depth = ypos + (float)shankIndex * 10000.0f + xpos * 0.001f;
+
+                channel->position.x = xpos;
+                channel->position.y = depth;
+
+                channel->group.name = "Shank " + String (shankIndex + 1);
+                channel->group.number = shankIndex;
+
+                // NB: Add real Y position as a metadata descriptor
+                MetadataDescriptor yposDescriptor (MetadataDescriptor::MetadataType::FLOAT,
+                                                   1,
+                                                   "ypos",
+                                                   "Channel y-position (relative to shank tip)",
+                                                   "channel.ypos");
+
+                MetadataValue yposValue (MetadataDescriptor::MetadataType::FLOAT, 1);
+                yposValue.setValue (ypos);
+
+                channel->addMetadata (yposDescriptor, yposValue);
+
+                // NB: Add electrode index as metadata
+                MetadataDescriptor selectedElectrodeDescriptor (MetadataDescriptor::MetadataType::UINT16,
+                                                                1,
+                                                                "electrode_index",
+                                                                "Electrode index for this channel",
+                                                                "neuropixels.electrode_index");
+
+                MetadataValue selectedElectrodeValue (MetadataDescriptor::MetadataType::UINT16, 1);
+                selectedElectrodeValue.setValue ((uint16) globalIndex);
+
+                channel->addMetadata (selectedElectrodeDescriptor, selectedElectrodeValue);
+            }
+        }
+    }
+};
 } // namespace OnixSourcePlugin

Source/OnixSource.cpp

@@ -836,6 +836,8 @@ void OnixSource::updateSettings (OwnedArray<ContinuousChannel>* continuousChanne
                 deviceInfos->add (device);
 
                 addIndividualStreams (source->streamInfos, dataStreams, deviceInfos, continuousChannels);
+
+                NeuropixelsHelpers::setChannelMetadata (continuousChannels, std::static_pointer_cast<Neuropixels1f> (source)->settings);
             }
             else if (type == OnixDeviceType::BNO || type == OnixDeviceType::POLLEDBNO)
             {
@@ -885,6 +887,8 @@ void OnixSource::updateSettings (OwnedArray<ContinuousChannel>* continuousChanne
                 deviceInfos->add (device);
 
                 addIndividualStreams (source->streamInfos, dataStreams, deviceInfos, continuousChannels);
+
+                NeuropixelsHelpers::setChannelMetadata (continuousChannels, std::static_pointer_cast<Neuropixels2e> (source)->settings);
             }
             else if (type == OnixDeviceType::MEMORYMONITOR)
             {
@@ -979,6 +983,8 @@ void OnixSource::updateSettings (OwnedArray<ContinuousChannel>* continuousChanne
                 deviceInfos->add (device);
 
                 addIndividualStreams (source->streamInfos, dataStreams, deviceInfos, continuousChannels);
+
+                NeuropixelsHelpers::setChannelMetadata (continuousChannels, std::static_pointer_cast<Neuropixels1e> (source)->settings);
             }
             else if (type == OnixDeviceType::OUTPUTCLOCK)
             {

Source/UI/NeuropixelsV1Interface.cpp

@@ -925,6 +925,8 @@ void NeuropixelsV1Interface::selectElectrodes (std::vector<int> electrodes)
 {
     std::static_pointer_cast<Neuropixels1> (device)->settings[0]->selectElectrodes (electrodes);
 
+    CoreServices::updateSignalChain (editor);
+
     repaint();
 }
 

Source/UI/NeuropixelsV2eProbeInterface.cpp

@@ -682,6 +682,8 @@ void NeuropixelsV2eProbeInterface::selectElectrodes (std::vector<int> electrodes
 {
     std::static_pointer_cast<Neuropixels2e> (device)->settings[probeIndex]->selectElectrodes (electrodes);
 
+    CoreServices::updateSignalChain (editor);
+
     repaint();
 }