Add PortController, for both Port A and B, and add automatic port voltage discovery

- Moves the port voltage modifications, and checking the link state, to the new PortController class
- Add macros for checking the results of register read/writes to OnixDevice
- Ensures that the context is reset correctly so that devices stream data
- Automated port voltage discovery uses the same logic as OpenEphys.Onix1
- Changed the order of operations during stopAcquisition so that bad frames aren't read due to the context resetting
- Fixed an issue where PathParameters were being set with a value other than the default

Author: bparks13

Source/Devices/Neuropixels2e.cpp

@@ -1,8 +1,6 @@
 #include "Neuropixels2e.h"
 #include "DS90UB9x.h"
 
-#define ONI_OK(exp) {int res = exp; if (res != ONI_ESUCCESS){LOGD(oni_error_str(res));}} 
-
 Neuropixels2e::Neuropixels2e(String name, const oni_dev_idx_t deviceIdx_, const oni_ctx ctx_)
 	: OnixDevice(name, OnixDeviceType::NEUROPIXELS_2, deviceIdx_, ctx_)
 {}

Source/Devices/Neuropixels_1.cpp

@@ -46,8 +46,17 @@ void BackgroundUpdaterWithProgressWindow::run()
 	setProgress(-1);
 
 	// Parse ADC and Gain calibration files
-	File adcFile = File(device->getAdcPathParameter());
-	File gainFile = File(device->getGainPathParameter());
+	String adcPath = device->getAdcPathParameter();
+	String gainPath = device->getGainPathParameter();
+
+	if (adcPath == "None" || gainPath == "None")
+	{
+		result = -3;
+		return;
+	}
+
+	File adcFile = File(adcPath);
+	File gainFile = File(gainPath);
 
 	if (!adcFile.existsAsFile() || !gainFile.existsAsFile())
 	{
@@ -157,12 +166,14 @@ Neuropixels_1::Neuropixels_1(String name, OnixSource* s, const oni_dev_idx_t dev
 	//validExtensions.add("*_ADCCalibration.csv");
 
 	source->addPathParameter(Parameter::PROCESSOR_SCOPE, getAdcPathParameterName(), "ADC Calibration File", "Path to the ADC calibration file for this Neuropixels probe",
-		File::getSpecialLocation(File::userHomeDirectory).getFullPathName(), validExtensions, false, false, true);
+		"", validExtensions, false, false, true);
+	source->getParameter(getAdcPathParameterName())->setNextValue(File::getSpecialLocation(File::userHomeDirectory).getFullPathName());
 
 	//validExtensions.set(0, "*_gainCalValues.csv");
 
 	source->addPathParameter(Parameter::PROCESSOR_SCOPE, getGainPathParameterName(), "Gain Calibration File", "Path to the gain calibration file for this Neuropixels probe",
-		File::getSpecialLocation(File::userHomeDirectory).getFullPathName(), validExtensions, false, false, true);
+		"", validExtensions, false, false, true);
+	source->getParameter(getGainPathParameterName())->setNextValue(File::getSpecialLocation(File::userHomeDirectory).getFullPathName());
 }
 
 Neuropixels_1::~Neuropixels_1()
@@ -234,10 +245,6 @@ NeuropixelsReference Neuropixels_1::getReference(int index)
 
 int Neuropixels_1::enableDevice()
 {
-	int result = checkLinkState((oni_dev_idx_t)PortName::PortA);
-
-	if (result != 0) return result;
-
 	// Get Probe SN
 	uint32_t eepromOffset = 0;
 	uint32_t i2cAddr = 0x50;

Source/OnixDevice.cpp

@@ -28,15 +28,3 @@ OnixDevice::OnixDevice(String name_, OnixDeviceType type_, const oni_dev_idx_t d
 {
 	name = name_;
 }
-
-int OnixDevice::checkLinkState(oni_dev_idx_t port) const
-{
-	const oni_reg_addr_t linkStateRegister = 5;
-
-	oni_reg_val_t linkState;
-	int result = oni_read_reg(ctx, port, linkStateRegister, &linkState);
-
-	if (result != 0) { LOGE(oni_error_str(result)); return -1; }
-	else if ((linkState & (uint32_t)0x1) == 0) { LOGE("Unable to acquire communication lock."); return -1; }
-	else return result;
-}

Source/OnixDevice.h

@@ -37,6 +37,10 @@
 #include "I2CRegisterContext.h"
 #include "NeuropixComponents.h"
 
+#define ONI_OK(exp) {int res = exp; if (res != ONI_ESUCCESS){LOGD(oni_error_str(res));}}
+#define ONI_OK_RETURN_BOOL(exp) {int res = exp; if (res != ONI_ESUCCESS){LOGD(oni_error_str(res));return false;}}
+#define ONI_OK_RETURN_INT(exp, val) {int res = exp; if (res != ONI_ESUCCESS){LOGD(oni_error_str(res));return val;}}
+
 using namespace std::chrono;
 
 enum class PortName
@@ -109,8 +113,6 @@ class OnixDevice
 
 	Array<StreamInfo> streams;
 
-	int checkLinkState(oni_dev_idx_t port) const;
-
 	const int bufferSizeInSeconds = 10;
 
 protected:

Source/OnixSource.cpp

@@ -43,11 +43,6 @@ OnixSource::OnixSource(SourceNode* sn) :
 	initializeContext();
 
 	if (!contextInitialized) { LOGE("Failed to initialize context."); return; }
-
-	size_t block_size_sz = sizeof(block_read_size);
-
-	// set block read size
-	oni_set_opt(ctx, ONI_OPT_BLOCKREADSIZE, &block_read_size, block_size_sz);
 }
 
 DataThread* OnixSource::createDataThread(SourceNode* sn)
@@ -254,6 +249,9 @@ void OnixSource::initializeDevices(bool updateStreamInfo)
 		}
 	}
 
+	val = 1;
+	oni_set_opt(ctx, ONI_OPT_RESET, &val, sizeof(val));
+
 	oni_size_t frame_size = 0;
 	size_t frame_size_sz = sizeof(frame_size);
 	oni_get_opt(ctx, ONI_OPT_MAXREADFRAMESIZE, &frame_size, &frame_size_sz);
@@ -262,6 +260,10 @@ void OnixSource::initializeDevices(bool updateStreamInfo)
 	oni_get_opt(ctx, ONI_OPT_MAXWRITEFRAMESIZE, &frame_size, &frame_size_sz);
 	printf("Max. write frame size: %u bytes\n", frame_size);
 
+	// set block read size
+	size_t block_size_sz = sizeof(block_read_size);
+	oni_set_opt(ctx, ONI_OPT_BLOCKREADSIZE, &block_read_size, block_size_sz);
+
 	if (updateStreamInfo) CoreServices::updateSignalChain(editor);
 
 	LOGD("All devices initialized.");
@@ -292,28 +294,51 @@ void OnixSource::updateSourceBuffers()
 	}
 }
 
-bool OnixSource::setPortVoltage(oni_dev_idx_t port, int voltage) const
+void OnixSource::updateDiscoveryParameters(PortName port, DiscoveryParameters parameters)
 {
-	if (!contextInitialized) return false;
-
-	const oni_reg_addr_t voltageRegister = 3;
-
-	auto result = oni_write_reg(ctx, port, voltageRegister, 0);
-
-	sleep(500);
-
-	result = oni_write_reg(ctx, port, voltageRegister, voltage);
-
-	if (result != 0) { LOGE(oni_error_str(result)); return -1; }
+	switch (port)
+	{
+	case PortName::PortA:
+		portA.updateDiscoveryParameters(parameters);
+		break;
+	case PortName::PortB:
+		portB.updateDiscoveryParameters(parameters);
+		break;
+	default:
+		break;
+	}
+}
 
-	auto val = 1;
-	result = oni_set_opt(ctx, ONI_OPT_RESET, &val, sizeof(val));
+bool OnixSource::configurePortVoltage(PortName port, String voltage) const
+{
+	if (!contextInitialized) return false;
 
-	if (result != 0) { LOGE(oni_error_str(result)); return -1; }
+	switch (port)
+	{
+	case PortName::PortA:
+		if (voltage == "") return portA.configureVoltage(ctx);
+		else			   return portA.configureVoltage(ctx, voltage.getFloatValue());
+	case PortName::PortB:
+		if (voltage == "") return portB.configureVoltage(ctx);
+		else			   return portB.configureVoltage(ctx, voltage.getFloatValue());
+	default:
+		return false;
+	}
+}
 
-	sleep(200);
+bool OnixSource::setPortVoltage(PortName port, float voltage) const
+{
+	if (!contextInitialized) return false;
 
-	return result;
+	switch (port)
+	{
+	case PortName::PortA:
+		return portA.setVoltage(ctx, voltage);
+	case PortName::PortB:
+		return portB.setVoltage(ctx, voltage);
+	default:
+		return false;
+	}
 }
 
 void OnixSource::updateSettings(OwnedArray<ContinuousChannel>* continuousChannels,
@@ -464,6 +489,14 @@ bool OnixSource::startAcquisition()
 
 bool OnixSource::stopAcquisition()
 {
+	if (isThreadRunning())
+		signalThreadShouldExit();
+
+	if (frameReader->isThreadRunning())
+		frameReader->signalThreadShouldExit();
+
+	waitForThreadToExit(2000);
+
 	if (devicesFound)
 	{
 		oni_size_t reg = 0;
@@ -479,14 +512,6 @@ bool OnixSource::stopAcquisition()
 		oni_set_opt(ctx, ONI_OPT_BLOCKREADSIZE, &block_read_size, sizeof(block_read_size));
 	}
 
-	if (isThreadRunning())
-		signalThreadShouldExit();
-
-	if (frameReader->isThreadRunning())
-		frameReader->stopThread(1000);
-
-	waitForThreadToExit(2000);
-
 	for (auto source : sources)
 	{
 		if (!source->isEnabled()) continue;

Source/OnixSource.h

@@ -24,9 +24,6 @@
 #ifndef __OnixSource_H__
 #define __OnixSource_H__
 
-#include <stdio.h>
-#include <string.h>
-
 #include <oni.h>
 #include <onix.h>
 
@@ -36,6 +33,7 @@
 #include "OnixSourceEditor.h"
 #include "Devices/DeviceList.h"
 #include "FrameReader.h"
+#include "PortController.h"
 
 /**
 
@@ -55,8 +53,8 @@ class OnixSource : public DataThread
 	{
 		if (ctx != NULL && contextInitialized)
 		{
-			int result = setPortVoltage((oni_dev_idx_t)PortName::PortA, 0);
-			if (result != 0) LOGE("Error setting port voltage to zero.");
+			portA.setVoltage(ctx, 0.0f);
+			portB.setVoltage(ctx, 0.0f);
 			oni_destroy_ctx(ctx);
 		}
 	}
@@ -82,7 +80,13 @@ class OnixSource : public DataThread
 	/** Stops data transfer.*/
 	bool stopAcquisition();
 
-	bool setPortVoltage(oni_dev_idx_t port, int voltage) const;
+	void updateDiscoveryParameters(PortName port, DiscoveryParameters parameters);
+
+	/** Takes a string from the editor. Can be an empty string to allow for automated discovery */
+	bool configurePortVoltage(PortName port, String voltage) const;
+
+	/** Sets the port voltage */
+	bool setPortVoltage(PortName port, float voltage) const;
 
 	void initializeContext();
 
@@ -116,6 +120,9 @@ class OnixSource : public DataThread
 	/** The ONI context object */
 	oni_ctx ctx;
 
+	PortController portA = PortController(PortName::PortA);
+	PortController portB = PortController(PortName::PortB);
+
 	const oni_size_t block_read_size = 2048;
 
 	bool contextInitialized = false;

Source/OnixSourceEditor.cpp

@@ -45,6 +45,9 @@ OnixSourceEditor::OnixSourceEditor(GenericProcessor* parentNode, OnixSource* oni
 	headstageComboBoxA->setItemEnabled(1, false);
 	headstageComboBoxA->addSeparator();
 	// TODO: Add list of available devices here
+	headstageComboBoxA->addItem("Neuropixels 1.0f", 2);
+
+	headstageComboBoxA->setSelectedId(1, dontSendNotification);
 	addAndMakeVisible(headstageComboBoxA.get());
 
 	passthroughEditorA = std::make_unique<ToggleParameterEditor>(onixSource->getParameter("passthroughA"));
@@ -75,6 +78,9 @@ OnixSourceEditor::OnixSourceEditor(GenericProcessor* parentNode, OnixSource* oni
 	headstageComboBoxB->setItemEnabled(1, false);
 	headstageComboBoxB->addSeparator();
 	// TODO: Add list of available devices here
+	headstageComboBoxB->addItem("Neuropixels 1.0f", 2);
+
+	headstageComboBoxB->setSelectedId(1, dontSendNotification);
 	addAndMakeVisible(headstageComboBoxB.get());
 
 	passthroughEditorB = std::make_unique<ToggleParameterEditor>(onixSource->getParameter("passthroughB"));
@@ -116,9 +122,26 @@ void OnixSourceEditor::buttonClicked(Button* b)
 	{
 		if (connectButton->getToggleState() == true)
 		{
-			int result = thread->setPortVoltage((oni_dev_idx_t)PortName::PortA, (int)(portVoltageValueA->getText().getFloatValue() * 10));
-
-			if (result != 0) { CoreServices::sendStatusMessage("Unable to set port voltage to " + portVoltageValueA->getText() + " for Port A."); return; }
+			// NB: Configure port voltages, using either the automated voltage discovery algorithm, or the explicit voltage value given
+			if (headstageComboBoxA->getSelectedItemIndex() > 0)
+			{
+				if (!thread->configurePortVoltage(PortName::PortA, portVoltageValueA->getText()))
+				{
+					CoreServices::sendStatusMessage("Unable to set port voltage for Port A.");
+					connectButton->setToggleState(false, true);
+					return;
+				}
+			}
+			
+			if (headstageComboBoxB->getSelectedItemIndex() > 0)
+			{
+				if (!thread->configurePortVoltage(PortName::PortB, portVoltageValueB->getText()))
+				{
+					CoreServices::sendStatusMessage("Unable to set port voltage for Port B.");
+					connectButton->setToggleState(false, true);
+					return;
+				}
+			}
 
 			thread->initializeDevices(true);
 			canvas->refreshTabs();
@@ -128,15 +151,22 @@ void OnixSourceEditor::buttonClicked(Button* b)
 			if (!thread->foundInputSource())
 			{
 				CoreServices::sendStatusMessage("No Onix hardware found.");
-				connectButton->setToggleState(false, NotificationType::dontSendNotification);
-				connectButton->setLabel("CONNECT");
+				connectButton->setToggleState(false, true);
 			}
 		}
 		else
 		{
-			int result = thread->setPortVoltage((oni_dev_idx_t)PortName::PortA, 0);
+			if (!thread->setPortVoltage(PortName::PortA, 0))
+			{
+				CoreServices::sendStatusMessage("Unable to set port voltage to 0 for Port A.");
+				return;
+			}
 
-			if (result != 0) { CoreServices::sendStatusMessage("Unable to set port voltage to 0 for Port A."); return; }
+			if (!thread->setPortVoltage(PortName::PortB, 0))
+			{
+				CoreServices::sendStatusMessage("Unable to set port voltage to 0 for Port B.");
+				return;
+			}
 
 			canvas->removeTabs();
 			thread->disconnectDevices(true);
@@ -150,6 +180,16 @@ void OnixSourceEditor::comboBoxChanged(ComboBox* cb)
 	if (cb == headstageComboBoxA.get())
 	{
 		// TODO: Call canvas to remove / add tabs as needed depending on what is chosen
+		String headstage = headstageComboBoxA->getText();
+
+		thread->updateDiscoveryParameters(PortName::PortA, PortController::getHeadstageDiscoveryParameters(headstage));
+	}
+	else if (cb == headstageComboBoxB.get())
+	{
+		// TODO: Call canvas to remove / add tabs as needed depending on what is chosen
+		String headstage = headstageComboBoxB->getText();
+
+		thread->updateDiscoveryParameters(PortName::PortB, PortController::getHeadstageDiscoveryParameters(headstage));
 	}
 }