Add activity view for Quad Base probes

open-ephys-plugins · Jul 3, 2024 · 48df0c5 · 48df0c5
1 parent b8b09c7
commit 48df0c5
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Showing 3 changed files with 32 additions and 9 deletions.
diff --git a/Source/Probes/Neuropixels_QuadBase.cpp b/Source/Probes/Neuropixels_QuadBase.cpp
@@ -111,7 +111,7 @@ bool Neuropixels_QuadBase::open()
     lfp_timestamp = 0;
     eventCode = 0;
 
-    apView = new ActivityView (384, 3000);
+    apView = new ActivityView (384 * 4, 3000);
 
     return errorCode == Neuropixels::SUCCESS;
 }
@@ -324,6 +324,9 @@ void Neuropixels_QuadBase::writeConfiguration()
 
 void Neuropixels_QuadBase::startAcquisition()
 {
+
+    apView->reset();
+
     if (acquisitionThreads.size() == 0)
     {
         for (int shank = 0; shank < 4; shank++)
@@ -336,12 +339,11 @@ void Neuropixels_QuadBase::startAcquisition()
                                        dock,
                                        shank,
                                        quadBaseBuffers[shank],
-                                       this));
+                                       this,
+                                       apView));
         }
     }
 
-    apView->reset();
-
     for (int shank = 0; shank < 4; shank++)
     {
         jassert (quadBaseBuffers[shank]->getNumSamples() == 0);
@@ -366,13 +368,15 @@ AcquisitionThread::AcquisitionThread (
     int dock_,
     int shank_,
     DataBuffer* buffer_,
-    Probe* probe_) : Thread ("AcquisitionThread" + String (shank)),
+    Probe* probe_,
+    ActivityView* apView_) : Thread ("AcquisitionThread" + String (shank)),
                      slot (slot_),
                      port (port_),
                      dock (dock_),
                      shank (shank_),
                      buffer (buffer_),
                      probe (probe_),
+                     apView(apView_),
                      ap_sample_rate (30000.0f),
                      ap_timestamp (0),
                      last_npx_timestamp (0),
@@ -392,7 +396,6 @@ AcquisitionThread::AcquisitionThread (
 
 void AcquisitionThread::run()
 {
-    //apView->reset();
 
     ap_timestamp = 0;
     last_npx_timestamp = 0;
@@ -451,7 +454,7 @@ void AcquisitionThread::run()
                     apSamples[packetNum + count * j] =
                         float (data[packetNum * shank_channel_count + j]) / 4096.0f / 100.0f * 1000000.0f; // convert to microvolts
 
-                    //probe->apView->addSample(apSamples[j + packetNum * SKIP], j);
+                    apView->addSample (apSamples[packetNum + count * j], j + shank * 384);
                 }
 
                 if (sendSync)

diff --git a/Source/Probes/Neuropixels_QuadBase.h b/Source/Probes/Neuropixels_QuadBase.h
@@ -31,12 +31,14 @@
 class AcquisitionThread : public Thread
 {
 public:
+
     AcquisitionThread (int slot,
                        int port,
                        int dock,
                        int shank,
                        DataBuffer* buffer,
-                       Probe* probe);
+                       Probe* probe,
+                       ActivityView* apView);
 
     /** Acquires data from the probe */
     void run() override; // acquire data
@@ -77,6 +79,7 @@ class AcquisitionThread : public Thread
     DataBuffer* buffer;
     Probe* probe;
     bool invertSyncLine = false;
+    ActivityView* apView;
 };
 
 /**
@@ -88,6 +91,7 @@ class AcquisitionThread : public Thread
 class Neuropixels_QuadBase : public Probe
 {
 public:
+
     /** Constructor */
     Neuropixels_QuadBase (Basestation*,
                           Headstage*,

diff --git a/Source/UI/ProbeBrowser.cpp b/Source/UI/ProbeBrowser.cpp
@@ -28,7 +28,20 @@ ProbeBrowser::ProbeBrowser (NeuropixInterface* parent_) : parent (parent_)
     cursorType = MouseCursor::NormalCursor;
 
     activityToView = ActivityToView::APVIEW;
-    maxPeakToPeakAmplitude = 250.0f;
+
+    ProbeType probeType = parent->probe->type;
+
+    if (probeType == ProbeType::QUAD_BASE ||
+        probeType == ProbeType::NP2_1 ||
+        probeType == ProbeType::NP2_4)
+    {
+        maxPeakToPeakAmplitude = 1000.0f;
+    }
+    else
+    {
+        maxPeakToPeakAmplitude = 250.0f;
+    }
+
 
     isOverZoomRegion = false;
     isOverUpperBorder = false;
@@ -1015,6 +1028,9 @@ void ProbeBrowser::timerCallback()
         if (parent->electrodeMetadata[i].status == ElectrodeStatus::CONNECTED)
         {
             int channelNumber = parent->electrodeMetadata[i].channel;
+
+            if (parent->probe->type == ProbeType::QUAD_BASE)
+                channelNumber += parent->electrodeMetadata[i].shank * 384;
 
             parent->electrodeMetadata.getReference (i).colour =
                 ColourScheme::getColourForNormalizedValue (peakToPeakValues[channelNumber] / maxPeakToPeakAmplitude);