[WIP] Initial setup to add support for Neuropixels 1.0

Author: anjaldoshi

Source/Devices/Neuropixels_1.cpp

@@ -0,0 +1,63 @@
+/*
+	------------------------------------------------------------------
+
+	This file is part of the Open Ephys GUI
+	Copyright (C) 2020 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 "Neuropixels_1.h"
+#include <oni.h>
+#include <onix.h>
+
+Neuropixels_1::Neuropixels_1(String name)
+	: OnixDevice(name, NEUROPIXELS_1)
+{
+	StreamInfo apStream;
+	apStream.name = name + "-AP";
+	apStream.description = "Neuropixels 1.0 AP band data stream";
+	apStream.identifier = "onix-neuropixels1.data.ap";
+	apStream.numChannels = 384;
+	apStream.sampleRate = 30000.0f;
+	apStream.channelPrefix = "AP";
+	apStream.bitVolts = 0.195f;
+	apStream.channelType = ContinuousChannel::Type::ELECTRODE;
+	streams.add(apStream);
+
+	StreamInfo lfpStream;
+	lfpStream.name = name + "-LFP";
+	lfpStream.description = "Neuropixels 1.0 LFP band data stream";
+	lfpStream.identifier = "onix-neuropixels1.data.lfp";
+	lfpStream.numChannels = 384;
+	lfpStream.sampleRate = 2500.0f;
+	lfpStream.channelPrefix = "LFP";
+	lfpStream.bitVolts = 0.195f;
+	lfpStream.channelType = ContinuousChannel::Type::ELECTRODE;
+	streams.add(lfpStream);
+}
+
+
+Neuropixels_1::~Neuropixels_1()
+{
+
+}
+
+
+void Neuropixels_1::addFrame()
+{
+
+}

Source/Devices/Neuropixels_1.h

@@ -0,0 +1,69 @@
+/*
+	------------------------------------------------------------------
+
+	This file is part of the Open Ephys GUI
+	Copyright (C) 2020 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/>.
+
+*/
+
+#ifndef NEUROPIXELS1_H_DEFINED
+#define NEUROPIXELS1_H_DEFINED
+
+#include "../OnixDevice.h"
+
+#include <ctime>
+#include <chrono>
+
+enum NeuropixelsRegisters
+{
+	OP_MODE = 0x00,
+	REC_MOD = 0x01,
+	CAL_MOD = 0x02
+};
+
+/** 
+	
+	Streams data from an ONIX device
+
+*/
+class Neuropixels_1 : public OnixDevice
+{
+public:
+
+	/** Constructor */
+	Neuropixels_1(String name);
+
+	/** Destructor */
+	~Neuropixels_1();
+
+	DataBuffer* apBuffer = deviceBuffer;
+	DataBuffer* lfpBuffer;
+
+	void addFrame() override;
+
+private:
+
+	float samples[384 * MAX_SAMPLES_PER_BUFFER];
+	int64 sampleNumbers[MAX_SAMPLES_PER_BUFFER];
+    double timestamps[MAX_SAMPLES_PER_BUFFER];
+	uint64 event_codes[MAX_SAMPLES_PER_BUFFER];
+
+};
+
+
+#endif

Source/OnixDevice.cpp

@@ -23,59 +23,17 @@
 
 #include "OnixDevice.h"
 
-OnixDevice::OnixDevice(String name, int channels_, float sampleRate_, OnixDeviceType type_)
-	: Thread(name), numChannels(channels_), sampleRate(sampleRate_), type(type_)
+OnixDevice::OnixDevice(String name, OnixDeviceType type_)
+	: Thread(name), type(type_)
 {
-
+	
 }
 
 
 void OnixDevice::run()
 {
-
-	int64 sampleNumber = 0;
-	int64 uSecPerBuffer = samplesPerBuffer / sampleRate * 1e6;
-	eventCode = 0;
-
-	int64 start = Time::getHighResolutionTicks();
-	int64 bufferCount = 0;
-
 	while (!threadShouldExit())
 	{
 
-		bufferCount++;
-
-		// grab available data and add to buffer
-
-		/*for (int sample_num = 0; sample_num < samplesPerBuffer; sample_num++)
-		{
-
-			for (int i = 0; i < numChannels; i++)
-			{
-				samples[i + sample_num * numChannels] = (*data)[sampleNumber % availableSamples];
-			}
-
-			sampleNumbers[sample_num] = sampleNumber++;
-			timestamps[sample_num] = -1.0;
-			
-			if (sampleNumber % int(sampleRate) == 0)
-			{
-				if (eventCode == 0)
-					eventCode = 1;
-				else
-					eventCode = 0;
-			}
-
-			event_codes[sample_num] = eventCode;
-		}
-
-		buffer->addToBuffer(samples, sampleNumbers, timestamps, event_codes, samplesPerBuffer);
-
-		int64 uSecElapsed = int64(Time::highResolutionTicksToSeconds(Time::getHighResolutionTicks() - start) * 1e6);
-
-		if (uSecElapsed < (uSecPerBuffer * bufferCount))
-		{
-			std::this_thread::sleep_for(std::chrono::microseconds((uSecPerBuffer * bufferCount) - uSecElapsed));
-		}*/
 	}
 }

Source/OnixDevice.h

@@ -21,8 +21,8 @@
 
 */
 
-#ifndef SIMULATEDSOURCE_H_DEFINED
-#define SIMULATEDSOURCE_H_DEFINED
+#ifndef __OnixDevice_H__
+#define __OnixDevice_H__
 
 #include <DataThreadHeaders.h>
 
@@ -45,6 +45,17 @@ enum OnixDeviceType {
 	ADC
 };
 
+struct StreamInfo {
+	String name;
+	String description;
+	String identifier;
+	int numChannels;
+	float sampleRate;
+	String channelPrefix;
+	ContinuousChannel::Type channelType;
+	float bitVolts;
+};
+
 /** 
 	
 	Streams data from an ONIX device
@@ -55,35 +66,40 @@ class OnixDevice : public Thread
 public:
 
 	/** Constructor */
-	OnixDevice(String name, int channels, float sampleRate, OnixDeviceType type);
+	OnixDevice(String name, OnixDeviceType type);
 
 	/** Destructor */
 	~OnixDevice() { }
 
+	virtual void addFrame() = 0;
+
+	const String getName() { return name; }
+
+	OnixDeviceType type;
+
 	/** Holds incoming data */
-	DataBuffer* buffer;
+	DataBuffer* deviceBuffer;
+
+	Array<StreamInfo> streams;
 
 private:
 
 	/** Updates buffer during acquisition */
 	void run() override;
 
-	OnixDeviceType type;
-
 	std::vector<float>* data;
 	int availableSamples;
     int samplesPerBuffer;
 
-	int numChannels;
-	int packetSize;
-	float sampleRate;
 	int64 numSamples;
 	uint64 eventCode;
 
-	float samples[384 * MAX_SAMPLES_PER_BUFFER];
-	int64 sampleNumbers[MAX_SAMPLES_PER_BUFFER];
-    double timestamps[MAX_SAMPLES_PER_BUFFER];
-	uint64 event_codes[MAX_SAMPLES_PER_BUFFER];
+	String name;
+
+	// float samples[384 * MAX_SAMPLES_PER_BUFFER];
+	// int64 sampleNumbers[MAX_SAMPLES_PER_BUFFER];
+    // double timestamps[MAX_SAMPLES_PER_BUFFER];
+	// uint64 event_codes[MAX_SAMPLES_PER_BUFFER];
 
 };