Merge branch 'micro-manager:main' into pr

micro-manager · Sep 23, 2024 · 6aeac35 · 6aeac35
2 parents 9485c87 + 0d5608d
commit 6aeac35
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Showing 25 changed files with 571 additions and 131 deletions.
diff --git a/DeviceAdapters/MCL_MicroDrive/MicroDriveZStage.cpp b/DeviceAdapters/MCL_MicroDrive/MicroDriveZStage.cpp
@@ -370,7 +370,7 @@ int MCL_MicroDrive_ZStage::OnPositionMm(MM::PropertyBase* pProp, MM::ActionType
 		err = GetPositionMm(z);
 		if(err != MCL_SUCCESS)
 			return err;
-		err = BeginMovementThread(STANDARD_MOVE_TYPE, z);		
+		err = BeginMovementThread(STANDARD_MOVE_TYPE, pos);		
 		if (err != DEVICE_OK)
 			return err;
 	}

diff --git a/DeviceAdapters/NIDAQ/NIDigitalOutputPort.cpp b/DeviceAdapters/NIDAQ/NIDigitalOutputPort.cpp
@@ -98,6 +98,22 @@ int DigitalOutputPort::Initialize()
       supportsBlankingAndSequencing_ = true;
    GetHub()->StopDOBlankingAndSequence(portWidth_);
 
+   // Some cards lie about their portwidth, if blanking does not work, try 32 bits
+   // Workaround for possible DAQmx bug on USB-6341; see
+   // https://forums.ni.com/t5/Multifunction-DAQ/problem-with-correlated-DIO-on-USB-6341/td-p/3344066
+   if (!supportsBlankingAndSequencing_)
+   {
+      uInt32 oldPortWidth = portWidth_;
+      portWidth_ = 32;
+      if (GetHub()->StartDOBlankingAndOrSequence(tmpNiPort, portWidth_, true, false, 0, false, tmpTriggerTerminal) == DEVICE_OK)
+         supportsBlankingAndSequencing_ = true;
+      GetHub()->StopDOBlankingAndSequence(portWidth_);
+      if (!supportsBlankingAndSequencing_)
+      {
+         portWidth_ = oldPortWidth;
+      }
+   }
+
    CPropertyAction* pAct;
    if (supportsBlankingAndSequencing_)
    {

diff --git a/DeviceAdapters/Zaber/ConnectionManager.cpp b/DeviceAdapters/Zaber/ConnectionManager.cpp
@@ -1,17 +1,43 @@
 #include "ConnectionManager.h"
 
+#include <regex>
+#include <zaber/motion/exceptions/invalid_argument_exception.h>
+
 std::shared_ptr<zml::Connection> ConnectionManager::getConnection(std::string port)
-{	
+{
 	std::lock_guard<std::mutex> lockGuard(lock_);
 	if (connections_.count(port) > 0) {
 		if (auto connectionPtr = connections_.at(port).lock()) {
 			return connectionPtr;
 		}
 	}
 
-	auto connection = std::make_shared<zml::Connection>(zml::Connection::openSerialPort(port));
+	std::shared_ptr<zml::Connection> connection;
+	if (port.find("share://") == 0) {
+		// share://<host>:<port>/<connection>
+		std::regex parser("^share:\\/\\/([^:\\/]+)(:\\d+)?(\\/.*)?$", std::regex_constants::ECMAScript);
+		std::smatch partMatch;
+		if (!std::regex_match(port, partMatch, parser)) {
+			throw zmlbase::InvalidArgumentException("Invalid network share connection string: " + port);
+		}
+
+		std::string host = partMatch[1].str();
+		int sharePort = 11421;
+		std::string connectionName;
+		if (partMatch[2].matched) {
+			sharePort = std::stoi(partMatch[2].str().substr(1));
+		}
+		if (partMatch[3].matched) {
+			connectionName = partMatch[3].str().substr(1);
+		}
+
+		connection = std::make_shared<zml::Connection>(zml::Connection::openNetworkShare(host, sharePort, connectionName));
+	} else {
+		connection = std::make_shared<zml::Connection>(zml::Connection::openSerialPort(port));
+	}
+
 	auto id = connection->getInterfaceId();
-	connection->getDisconnected().subscribe([=](std::shared_ptr<zmlbase::MotionLibException>) {
+	connection->getDisconnected().subscribe([=, this](std::shared_ptr<zmlbase::MotionLibException>) {
 		removeConnection(port, id);
 	});
 	connections_[port] = connection;
@@ -22,18 +48,19 @@ std::shared_ptr<zml::Connection> ConnectionManager::getConnection(std::string po
 bool ConnectionManager::removeConnection(std::string port, int interfaceId)
 {
 	std::lock_guard<std::mutex> lockGuard(lock_);
-	if (connections_.count(port) == 0) {
+	auto it = connections_.find(port);
+	if (it == connections_.end()) {
 		return false;
-	} 
+	}
 
 	if (interfaceId != -1) {
-		if (auto connection = connections_.at(port).lock()) {
+		if (auto connection = it->second.lock()) {
 			if (connection->getInterfaceId() != interfaceId) {
 				return false;
 			}
 		}
 	}
 
-	connections_.erase(port);
+	connections_.erase(it);
 	return true;
-}
+}
diff --git a/DeviceAdapters/Zaber/FilterCubeTurret.cpp b/DeviceAdapters/Zaber/FilterCubeTurret.cpp
@@ -222,9 +222,7 @@ int FilterCubeTurret::PortGetSet(MM::PropertyBase* pProp, MM::ActionType eAct)
    {
       if (initialized_)
       {
-         // revert
-         pProp->Set(port_.c_str());
-         return ERR_PORT_CHANGE_FORBIDDEN;
+			resetConnection();
       }
 
       pProp->Get(port_);

diff --git a/DeviceAdapters/Zaber/FilterCubeTurret.h b/DeviceAdapters/Zaber/FilterCubeTurret.h
@@ -38,21 +38,21 @@ class FilterCubeTurret : public CStateDeviceBase<FilterCubeTurret>, public Zaber
 
    // Device API
    // ----------
-   int Initialize();
-   int Shutdown();
-   void GetName(char* name) const;
-   bool Busy();
+   int Initialize() override;
+   int Shutdown() override;
+   void GetName(char* name) const override;
+   bool Busy() override;
 
    // Stage API
    // ---------
-   unsigned long GetNumberOfPositions() const
+   unsigned long GetNumberOfPositions() const override
    {
       return numPositions_;
    }
 
    // Base class overrides
    // ----------------
-   virtual int GetPositionLabel(long pos, char* label) const;
+   int GetPositionLabel(long pos, char* label) const override;
 
    // Properties
    // ----------------

diff --git a/DeviceAdapters/Zaber/FilterWheel.cpp b/DeviceAdapters/Zaber/FilterWheel.cpp
@@ -217,9 +217,7 @@ int FilterWheel::PortGetSet(MM::PropertyBase* pProp, MM::ActionType eAct)
    {
       if (initialized_)
       {
-         // revert
-         pProp->Set(port_.c_str());
-         return ERR_PORT_CHANGE_FORBIDDEN;
+			resetConnection();
       }
 
       pProp->Get(port_);

diff --git a/DeviceAdapters/Zaber/FilterWheel.h b/DeviceAdapters/Zaber/FilterWheel.h
@@ -37,21 +37,21 @@ class FilterWheel : public CStateDeviceBase<FilterWheel>, public ZaberBase
 
    // Device API
    // ----------
-   int Initialize();
-   int Shutdown();
-   void GetName(char* name) const;
-   bool Busy();
+   int Initialize() override;
+   int Shutdown() override;
+   void GetName(char* name) const override;
+   bool Busy() override;
 
    // Stage API
    // ---------
-   unsigned long GetNumberOfPositions() const
+   unsigned long GetNumberOfPositions() const override
    {
       return numPositions_;
    }
 
    // Base class overrides
    // ----------------
-   virtual int GetPositionLabel(long pos, char* label) const;
+   int GetPositionLabel(long pos, char* label) const override;
 
    // Properties
    // ----------------

diff --git a/DeviceAdapters/Zaber/Illuminator.cpp b/DeviceAdapters/Zaber/Illuminator.cpp
@@ -373,9 +373,7 @@ int Illuminator::PortGetSet(MM::PropertyBase* pProp, MM::ActionType eAct)
    {
       if (initialized_)
       {
-         // revert
-         pProp->Set(port_.c_str());
-         return ERR_PORT_CHANGE_FORBIDDEN;
+			resetConnection();
       }
 
       pProp->Get(port_);

diff --git a/DeviceAdapters/Zaber/Illuminator.h b/DeviceAdapters/Zaber/Illuminator.h
@@ -37,15 +37,15 @@ class Illuminator : public CShutterBase<Illuminator>, public ZaberBase
 
 	// Device API
 	// ----------
-	int Initialize();
-	int Shutdown();
+	int Initialize() override;
+	int Shutdown() override;
 
-	void GetName(char* pszName) const;
-	bool Busy();
+	void GetName(char* pszName) const override;
+	bool Busy() override;
 
-	int SetOpen(bool open = true);
-	int GetOpen(bool& open);
-	int Fire(double deltaT);
+	int SetOpen(bool open = true) override;
+	int GetOpen(bool& open) override;
+	int Fire(double deltaT) override;
 
 	// Properties
 	// ----------------
@@ -66,7 +66,7 @@ class Illuminator : public CShutterBase<Illuminator>, public ZaberBase
 	bool *lampExists_;
 
 	// Enables the optimization of using the device-scope lamp on command.
-	bool canUseDeviceLampOnCommand_; 
+	bool canUseDeviceLampOnCommand_;
 
 	// Enables the optimization of only turning on individual axes that
 	// have nonzero flux when the shutter opens.
@@ -76,9 +76,9 @@ class Illuminator : public CShutterBase<Illuminator>, public ZaberBase
 	double* maxFlux_;
 
 	// These variables exist only to enable good UX in the absence of
-	// a device-scope lamp on command. The specific behavior these are 
+	// a device-scope lamp on command. The specific behavior these are
 	// for is when you are tuning presets, you leave the shutter open
-	// and adjust intensities. If you change a zero intensity to 
+	// and adjust intensities. If you change a zero intensity to
 	// nonzero, it must turn that axis on, only if the shutter is open.
 	bool *lampIsOn_;
 	bool isOpen_;

diff --git a/DeviceAdapters/Zaber/Makefile.am b/DeviceAdapters/Zaber/Makefile.am
@@ -2,6 +2,8 @@ AM_CXXFLAGS = $(MMDEVAPI_CXXFLAGS) $(ZML_CPPFLAGS)
 
 deviceadapter_LTLIBRARIES = libmmgr_dal_Zaber.la
 libmmgr_dal_Zaber_la_SOURCES = \
+	WdiAutofocus.cpp \
+	WdiAutofocus.h \
 	ObjectiveChanger.cpp \
 	ObjectiveChanger.h \
 	Illuminator.cpp \

diff --git a/DeviceAdapters/Zaber/ObjectiveChanger.cpp b/DeviceAdapters/Zaber/ObjectiveChanger.cpp
@@ -93,7 +93,7 @@ int ObjectiveChanger::Initialize()
 
 	this->LogMessage("ObjectiveChanger::Initialize\n", true);
 
-	auto ret = handleException([=]() {
+	auto ret = handleException([&]() {
 		ensureConnected();
 		if (!this->changer_.getFocusAxis().isHomed()) {
 			this->changer_.change(1);
@@ -232,9 +232,7 @@ int ObjectiveChanger::PortGetSet(MM::PropertyBase* pProp, MM::ActionType eAct)
 	{
 		if (initialized_)
 		{
-			// revert
-			pProp->Set(port_.c_str());
-			return ERR_PORT_CHANGE_FORBIDDEN;
+			resetConnection();
 		}
 
 		pProp->Get(port_);
@@ -350,7 +348,7 @@ int ObjectiveChanger::FocusOffsetGetSet(MM::PropertyBase* pProp, MM::ActionType
 }
 
 int ObjectiveChanger::setObjective(long objective, bool applyOffset) {
-	return handleException([=]() {
+	return handleException([&]() {
 		ensureConnected();
 		zmlbase::Measurement offset;
 		if (applyOffset) {

diff --git a/DeviceAdapters/Zaber/ObjectiveChanger.h b/DeviceAdapters/Zaber/ObjectiveChanger.h
@@ -38,25 +38,25 @@ class ObjectiveChanger : public CStateDeviceBase<ObjectiveChanger>, public Zaber
 
 	// Device API
 	// ----------
-	int Initialize();
-	int Shutdown();
-	void GetName(char* name) const;
-	bool Busy();
+	int Initialize() override;
+	int Shutdown() override;
+	void GetName(char* name) const override;
+	bool Busy() override;
 
 	// Stage API
 	// ---------
-	unsigned long GetNumberOfPositions() const
+	unsigned long GetNumberOfPositions() const override
 	{
 		return numPositions_;
 	}
 
 	// Base class overrides
 	// ----------------
-	virtual int GetPositionLabel(long pos, char* label) const;
+	int GetPositionLabel(long pos, char* label) const override;
 
 	// ZaverBase class overrides
 	// ----------------
-	virtual void onNewConnection();
+	void onNewConnection() override;
 
 	// Properties
 	// ----------------
@@ -66,9 +66,9 @@ class ObjectiveChanger : public CStateDeviceBase<ObjectiveChanger>, public Zaber
 	int XLdaAddressGetSet(MM::PropertyBase* pProp, MM::ActionType eAct);
 	int PositionGetSet(MM::PropertyBase* pProp, MM::ActionType eAct);
 	int FocusOffsetGetSet(MM::PropertyBase* pProp, MM::ActionType eAct);
-
-	int setObjective(long objective, bool applyOffset);
 private:
+	int setObjective(long objective, bool applyOffset);
+
 	long xMorAddress_;
 	long xLdaAddress_;
 	long numPositions_;

diff --git a/DeviceAdapters/Zaber/Stage.cpp b/DeviceAdapters/Zaber/Stage.cpp
@@ -294,9 +294,7 @@ int Stage::OnPort (MM::PropertyBase* pProp, MM::ActionType eAct)
 	{
 		if (initialized_)
 		{
-			// revert
-			pProp->Set(port_.c_str());
-			return ERR_PORT_CHANGE_FORBIDDEN;
+			resetConnection();
 		}
 
 		pProp->Get(port_);

diff --git a/DeviceAdapters/Zaber/Stage.h b/DeviceAdapters/Zaber/Stage.h
@@ -36,28 +36,28 @@ class Stage : public CStageBase<Stage>, public ZaberBase
 
 	// Device API
 	// ----------
-	int Initialize();
-	int Shutdown();
-	void GetName(char* name) const;
-	bool Busy();
+	int Initialize() override;
+	int Shutdown() override;
+	void GetName(char* name) const override;
+	bool Busy() override;
 
 	// Stage API
 	// ---------
-	int GetPositionUm(double& pos);
-	int GetPositionSteps(long& steps);
-	int SetPositionUm(double pos);
-	int SetRelativePositionUm(double d);
-	int SetPositionSteps(long steps);
-	int SetRelativePositionSteps(long steps);
-	int Move(double velocity);
-	int Stop();
-	int Home();
-	int SetAdapterOriginUm(double d);
-	int SetOrigin();
-	int GetLimits(double& lower, double& upper);
+	int GetPositionUm(double& pos) override;
+	int GetPositionSteps(long& steps) override;
+	int SetPositionUm(double pos) override;
+	int SetRelativePositionUm(double d) override;
+	int SetPositionSteps(long steps) override;
+	int SetRelativePositionSteps(long steps); // not in the base class
+	int Move(double velocity) override;
+	int Stop() override;
+	int Home() override;
+	int SetAdapterOriginUm(double d) override;
+	int SetOrigin() override;
+	int GetLimits(double& lower, double& upper) override;
 
-	int IsStageSequenceable(bool& isSequenceable) const {isSequenceable = false; return DEVICE_OK;}
-	bool IsContinuousFocusDrive() const {return false;}
+	int IsStageSequenceable(bool& isSequenceable) const override { isSequenceable = false; return DEVICE_OK; }
+	bool IsContinuousFocusDrive() const override { return false; }
 
 	// action interface
 	// ----------------