Qt6 port and a bunch of compiler warning fixes

.github/workflows/build.yml

@@ -8,7 +8,7 @@ jobs:
     name: Validate Metadata
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Create Build Environment
       run: cd contrib/ci/ && podman build -t intanrhx_validate -f ./Dockerfile-debian-testing .
@@ -27,7 +27,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -40,7 +40,7 @@ jobs:
             ./contrib/ci/auto-build-deb.sh
 
     - name: Upload Debian package artifact
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name: Debian Package
         path: |
@@ -53,7 +53,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -66,7 +66,7 @@ jobs:
             ./contrib/ci/auto-build-deb.sh
 
     - name: Upload Ubuntu package artifact
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name: Ubuntu LTS Package
         path: |

Engine/API/Abstract/abstractrhxcontroller.cpp

@@ -62,7 +62,7 @@ AbstractRHXController::AbstractRHXController(ControllerType type_, AmplifierSamp
     pipeReadErrorCode(0)
 {
     usbBufferSize = MaxNumBlocksToRead * BytesPerWord * RHXDataBlock::dataBlockSizeInWords(type, maxNumDataStreams());
-    cout << "RHXController: Allocating " << usbBufferSize / 1.0e6 << " MBytes for USB buffer.\n";
+    std::cout << "RHXController: Allocating " << usbBufferSize / 1.0e6 << " MBytes for USB buffer." << std::endl;
     usbBuffer = nullptr;
     usbBuffer = new uint8_t [usbBufferSize];
     numDataStreams = 0;
@@ -665,14 +665,13 @@ unsigned int AbstractRHXController::fifoCapacityInWords()
 // Print a command list to the console in readable form.
 void AbstractRHXController::printCommandList(const vector<unsigned int> &commandList) const
 {
-    unsigned int i, cmd;
     int channel, reg, data, uFlag, mFlag, dFlag, hFlag;
 
     cout << '\n';
-    for (i = 0; i < commandList.size(); ++i) {
-        cmd = commandList[i];
+    for (uint i = 0; i < commandList.size(); ++i) {
+        auto cmd = commandList[i];
         if (type != ControllerStimRecord) {
-            if (cmd < 0 || cmd > 0xffff) {
+            if ((int)cmd < 0 || cmd > 0xffff) {
                 cout << "  command[" << i << "] = INVALID COMMAND: " << cmd << '\n';
             } else if ((cmd & 0xc000) == 0x0000) {
                 channel = (cmd & 0x3f00) >> 8;

Engine/API/Hardware/rhxcontroller.cpp

@@ -160,8 +160,8 @@ bool RHXController::uploadFPGABitfile(const string& filename)
     boardId = dev->GetWireOutValue(WireOutBoardId);
     boardVersion = dev->GetWireOutValue(WireOutBoardVersion);
 
-    cout << "Rhythm configuration file successfully loaded.  Rhythm version number: " <<
-            boardVersion << "\n\n";
+    std::cout << "Rhythm configuration file successfully loaded.  Rhythm version number: " <<
+        boardVersion << "\n" << std::endl;
 
     return true;
 }

Engine/API/Hardware/rhxregisters.cpp

@@ -1122,15 +1122,15 @@ unsigned int RHXRegisters::createRHXCommand(RHXCommandType commandType, unsigned
     } else {
         switch (commandType) {
         case RHXCommandConvert:
-            if ((arg1 < 0) || (arg1 > 63)) {
+            if (((int)arg1 < 0) || (arg1 > 63)) {
                 cerr << "Error in RHXRegisters::createRHXCommand: " <<
                         "Channel number out of range.\n";
                 return -1;
             }
             return 0x0000 + (arg1 << 8);  // 00cccccc0000000h; if the command is 'Convert',
                                           // arg1 is the channel number.
         case RHXCommandRegRead:
-            if ((arg1 < 0) || (arg1 > 63)) {
+            if (((int)arg1 < 0) || (arg1 > 63)) {
                 cerr << "Error in RHXRegisters::createRHXCommand: " <<
                         "Register address out of range.\n";
                 return -1;
@@ -1182,12 +1182,12 @@ unsigned int RHXRegisters::createRHXCommand(RHXCommandType commandType, unsigned
     } else {
         switch (commandType) {
         case RHXCommandRegWrite:
-            if ((arg1 < 0) || (arg1 > 63)) {
+            if (((int)arg1 < 0) || (arg1 > 63)) {
                 cerr << "Error in RHXRegisters::createRHXCommand: " <<
                         "Register address out of range.\n";
                 return -1;
             }
-            if ((arg2 < 0) || (arg2 > 255)) {
+            if (((int)arg2 < 0) || (arg2 > 255)) {
                 cerr << "Error in RHXRegisters::createRHXCommand: " <<
                         "Register data out of range.\n";
                 return -1;

Engine/API/Synthetic/synthdatablockgenerator.cpp

@@ -228,7 +228,7 @@ SynthDataBlockGenerator::SynthDataBlockGenerator(ControllerType type_, double sa
 {
     int bufferSizeInWords = MaxNumBlocksToRead *
             RHXDataBlock::dataBlockSizeInWords(type, AbstractRHXController::maxNumDataStreams(type));
-    cout << "SynthDataBlockGenerator: Allocating " << BytesPerWord * bufferSizeInWords / 1.0e6 << " MBytes for synthetic USB data generator.\n";
+    std::cout << "SynthDataBlockGenerator: Allocating " << BytesPerWord * bufferSizeInWords / 1.0e6 << " MBytes for synthetic USB data generator." << std::endl;
     usbWords = nullptr;
     usbWords = new uint16_t [bufferSizeInWords];
     dataBlockPeriodInNsec = 1.0e9 * ((double)RHXDataBlock::samplesPerDataBlock(type)) / sampleRate;

Engine/Processing/DataFileReaders/fileperchannelmanager.cpp

@@ -30,6 +30,7 @@
 
 #include <QFileInfo>
 #include <iostream>
+#include <thread>
 #include "rhxglobals.h"
 #include "datafilereader.h"
 #include "fileperchannelmanager.h"
@@ -511,7 +512,7 @@ void FilePerChannelManager::updateEndOfData()
     // TODO - polish up to get the actual end of all data, not just assume from end of shortest amp file
     int tempTotalNumSamples = 0;
     for (int stream = 0; stream < info->numDataStreams; ++stream) {
-        for (int channel = 0; channel < amplifierFiles[stream].size(); ++channel) {
+        for (uint channel = 0; channel < amplifierFiles[stream].size(); ++channel) {
             if (amplifierWasSaved[stream][channel]) {
                 int64_t numAmpSamples = amplifierFiles[stream][channel]->fileSize() / 2;
                 if (numAmpSamples < tempTotalNumSamples || tempTotalNumSamples == 0) {

Engine/Processing/DataFileReaders/fileperchannelmanager.h

@@ -49,7 +49,7 @@ class FilePerChannelManager : public DataFileManager
                           DataFileReader* parent);
     ~FilePerChannelManager();
 
-    long readDataBlocksRaw(int numBlocks, uint8_t* buffer);
+    long readDataBlocksRaw(int numBlocks, uint8_t* buffer) override;
     int64_t getLastTimeStamp() override;
     int64_t jumpToTimeStamp(int64_t target) override;
     void loadDataFrame() override;

Engine/Processing/DataFileReaders/traditionalintanfilemanager.cpp

@@ -379,7 +379,7 @@ int64_t TraditionalIntanFileManager::blocksPresent()
 {
     // Should remain accurate even if data file continues growing
     int dataSizeBytes = 0;
-    for (int i = 0; i < consecutiveFiles.size(); i++) {
+    for (uint i = 0; i < consecutiveFiles.size(); i++) {
         dataSizeBytes += QFileInfo(consecutiveFiles[i].fileName).size() - info->headerSizeInBytes;
     }
     return dataSizeBytes / info->bytesPerDataBlock;

Engine/Processing/XPUInterfaces/gpuinterface.cpp

@@ -539,8 +539,12 @@ bool GPUInterface::createKernel(int devIndex)
     state->writeToLog("Completed clCreateContext()");
 
     state->writeToLog("About to call clCreateCommandQueue");
+    cl_queue_properties properties[] = {
+        CL_QUEUE_PROPERTIES,
+        0 // Terminates the list
+    };
     // Create command queue.
-    commandQueue = clCreateCommandQueue(context, id, 0, &ret);
+    commandQueue = clCreateCommandQueueWithProperties(context, id, properties, &ret);
     if (ret != CL_SUCCESS) {
         state->writeToLog("Failure creating OpenCL commandqueue. Ret: " + QString::number(ret));
         gpuErrorMessage("Error creating OpenCL commandqueue. Returned error code: " + QString::number(ret));

Engine/Processing/XPUInterfaces/xpucontroller.cpp

@@ -32,9 +32,9 @@
 
 XPUController::XPUController(SystemState *state_, bool useOpenCL_, QObject *parent) :
     QObject(parent),
+    useOpenCL(useOpenCL_),
     state(state_),
-    usedXPUIndex(-1),
-    useOpenCL(useOpenCL_)
+    usedXPUIndex(-1)
 {
     state->writeToLog("Entered XPUController ctor");
     connect(state, SIGNAL(stateChanged()), this, SLOT(updateFromState()));
@@ -126,7 +126,11 @@ void XPUController::updateFromState()
     if (state->usedXPUIndex() != usedXPUIndex) {
         activeInterface->cleanupMemory();
         usedXPUIndex = state->usedXPUIndex();
-        activeInterface = (usedXPUIndex == 0) ? activeInterface = cpuInterface : activeInterface = gpuInterface;
+        if (usedXPUIndex == 0) {
+            activeInterface = cpuInterface;
+        } else {
+            activeInterface = gpuInterface;
+        }
         activeInterface->setupMemory();
     }
     activeInterface->updateFromState();

Engine/Processing/commandparser.cpp

@@ -33,8 +33,8 @@
 
 CommandParser::CommandParser(SystemState* state_, ControllerInterface *controllerInterface_, QObject *parent) :
     QObject(parent),
-    controllerInterface(controllerInterface_),
     controlWindow(nullptr),
+    controllerInterface(controllerInterface_),
     state(state_)
 {
     // These connections allow for interactions with communicators that may live in another thread
@@ -871,6 +871,8 @@ QString CommandParser::validateStimParams(StimParameters *stimParams) const
         if (stimParams->pulseTrainPeriod->getValue() < stimDuration)
             return "PulseTrainPeriodMicroseconds cannot be less than total pulse duration (sum of all phases used for this Shape)";
 
+        break;
+
     case BoardDacSignal:
         // PulseTrainPeriod cannot be less than stimDuration (which depends on Shape)
         // Biphasic: stimDuration = FirstPhaseDuration + SecondPhaseDuration
@@ -888,11 +890,15 @@ QString CommandParser::validateStimParams(StimParameters *stimParams) const
         if (stimParams->pulseTrainPeriod->getValue() < stimDuration)
             return "PulseTrainPeriodMicroseconds cannot be less than total pulse duration (sum of all phases used for this Shape)";
 
+        break;
+
     case BoardDigitalOutSignal:
         // PulseTrainPeriod cannot be less than FirstPhaseDuration
         if (stimParams->pulseTrainPeriod->getValue() < stimParams->firstPhaseDuration->getValue())
             return "PulseTrainPeriodMicroseconds cannot be less than pulse duration (FirstPhaseDurationMicroseconds)";
 
+        break;
+
     default:
         break;
     }

Engine/Processing/controllerinterface.cpp

@@ -299,8 +299,7 @@ int ControllerInterface::scanPorts(vector<ChipType> &chipType, vector<int> &port
                                                         state->lastDetectedChip->getValue(),
                                                         state->lastDetectedNumStreams->getValue());
 
-    for (int i = 0; i < chipType.size(); i++) {
-        qDebug() << "Here... i: " << i << " chip type: " << (int) chipType[i];
+    for (uint i = 0; i < chipType.size(); i++) {
         if (chipType[i] != NoChip) {
             state->lastDetectedChip->setValue((int) chipType[i]);
             break;

Engine/Processing/datastreamfifo.cpp

@@ -45,19 +45,19 @@ DataStreamFifo::DataStreamFifo(int bufferSize_, int maxReadLength_) :
 {
     int bufferSizeWithExtra = bufferSize + maxReadLength;
     memoryNeededGB = sizeof(uint16_t) * bufferSizeWithExtra / (1024.0 * 1024.0 * 1024.0);
-    cout << "DataStreamFifo: Allocating " << 2 * bufferSizeWithExtra / 1.0e6 << " MBytes for FIFO buffer." << '\n';
+    std::cout << "DataStreamFifo: Allocating " << 2 * bufferSizeWithExtra / 1.0e6 << " MBytes for FIFO buffer." << std::endl;
     buffer = nullptr;
 
     memoryAllocated = true;
     try {
         buffer = new uint16_t [bufferSizeWithExtra];
     } catch (std::bad_alloc&) {
         memoryAllocated = false;
-        cerr << "Error: DataStreamFifo constructor could not allocate " << memoryNeededGB << " GB of memory." << '\n';
+        std::cerr << "Error: DataStreamFifo constructor could not allocate " << memoryNeededGB << " GB of memory." << std::endl;
     }
 
     if (!buffer) {
-        cerr << "Error: DataStreamFifo constructor could not allocate " << 2 * bufferSizeWithExtra << " bytes of memory." << '\n';
+        std::cerr << "Error: DataStreamFifo constructor could not allocate " << 2 * bufferSizeWithExtra << " bytes of memory." << std::endl;
     }
     resetBuffer();
 }

Engine/Processing/softwarereferenceprocessor.cpp

@@ -342,7 +342,7 @@ void SoftwareReferenceProcessor::readReferenceSamples(vector<StreamChannelPair>
 {
     const uint16_t* pRead;
 
-    for (int i = 0; i < addresses.size(); ++i) {
+    for (uint i = 0; i < addresses.size(); ++i) {
         pRead = start;
         pRead += 6; // Skip header and timestamp.
         pRead += misoWordSize * (numDataStreams * 3);  // Skip auxiliary channels.

Engine/Processing/stateitem.h

@@ -142,7 +142,7 @@ class StateFilenameItem : public StateItem
     bool isValid() const { return !path.isEmpty() && !baseFilename.isEmpty(); }
     QString getFullFilename() const { return isValid() ? path + "/" + baseFilename : ""; }
 
-    QString getValidValues() const { return "Path: [path/to/file], BaseFilename: [filename.rhx]"; }
+    QString getValidValues() const override { return "Path: [path/to/file], BaseFilename: [filename.rhx]"; }
 
 private:
     QString path;

Engine/Processing/waveformfifo.cpp

@@ -35,12 +35,12 @@
 #include "waveformfifo.h"
 
 WaveformFifo::WaveformFifo(SignalSources *signalSources_, int bufferSizeInDataBlocks_, int memorySizeInDataBlocks_, int maxWriteSizeInDataBlocks_, SystemState* state_) :
+    state(state_),
     signalSources(signalSources_),
     bufferSizeInDataBlocks(bufferSizeInDataBlocks_),
     memorySizeInDataBlocks(memorySizeInDataBlocks_),
     maxWriteSizeInDataBlocks(maxWriteSizeInDataBlocks_),
-    numReaders(NumberOfReaders),
-    state(state_)
+    numReaders(NumberOfReaders)
 {
     if (numReaders < 1) {
         cerr << "WaveformFifo constructor: numReaders must be one or greater." << '\n';
@@ -64,7 +64,7 @@ WaveformFifo::WaveformFifo(SignalSources *signalSources_, int bufferSizeInDataBl
     bufferAllocateSize = bufferSize + maxWriteSizeInSamples;
     bufferAllocateSizeInBlocks = bufferSizeInDataBlocks + maxWriteSizeInDataBlocks;
 
-    usedWordsNewData = new Semaphore [numReaders];
+    usedWordsNewData = new Semaphore[numReaders];
     bufferReadIndex.resize(numReaders);
     bufferMemoryIndex.resize(numReaders);
     numWordsToBeRead.resize(numReaders);

Engine/Processing/waveformfifo.h

@@ -36,7 +36,6 @@
 #include <map>
 #include <vector>
 #include <mutex>
-#include "rhxglobals.h"
 #include "semaphore.h"
 #include "minmax.h"
 #include "signalsources.h"
@@ -76,7 +75,7 @@ const uint8_t SpikeIdLikelyArtifact = 0x80u;
 class WaveformFifo
 {
 public:
-    enum Reader {
+    enum Reader : uint {
         ReaderDisplay = 0,
         ReaderDisk,
         ReaderAudio,