MAINT: add missing initilizations of bools.

Author: gabrielbmotta

src/applications/mne_scan/plugins/averaging/averaging.h

@@ -48,6 +48,7 @@
 #include <fiff/fiff_evoked_set.h>
 
 #include <thread>
+#include <atomic>
 
 //=============================================================================================================
 // QT INCLUDES

src/applications/mne_scan/plugins/babymeg/babymeg.cpp

@@ -88,6 +88,7 @@ BabyMEG::BabyMEG()
 , m_sFiffProjections(QCoreApplication::applicationDirPath() + "/../resources/mne_scan/plugins/babymeg/header.fif")
 , m_sFiffCompensators(QCoreApplication::applicationDirPath() + "/../resources/mne_scan/plugins/babymeg/compensator.fif")
 , m_sBadChannels(QCoreApplication::applicationDirPath() + "/../resources/mne_scan/plugins/babymeg/both.bad")
+, m_bProcessOutput(false)
 {
     m_pActionSqdCtrl = new QAction(QIcon(":/images/sqdctrl.png"), tr("Squid Control"),this);
 //    m_pActionSetupProject->setShortcut(tr("F12"));
@@ -107,7 +108,7 @@ BabyMEG::BabyMEG()
 
 BabyMEG::~BabyMEG()
 {
-    if(this->isRunning()) {
+    if(m_bProcessOutput) {
         stop();
     }
 
@@ -208,7 +209,8 @@ bool BabyMEG::start()
     initConnector();
 
     // Start thread
-    QThread::start();
+    m_bProcessOutput = true;
+    m_OutputProcessingThread = std::thread(&BabyMEG::run, this);
 
     return true;
 }
@@ -217,8 +219,11 @@ bool BabyMEG::start()
 
 bool BabyMEG::stop()
 {
-    requestInterruption();
-    wait(2000);
+    m_bProcessOutput = false;
+
+    if(m_OutputProcessingThread.joinable()){
+        m_OutputProcessingThread.join();
+    }
 
     // Clear all data in the buffer connected to displays and other plugins
     m_pRTMSABabyMEG->measurementData()->clear();
@@ -260,13 +265,13 @@ void BabyMEG::run()
 {
     MatrixXf matValue;
 
-    while(!isInterruptionRequested()) {
+    while(m_bProcessOutput) {
         //pop matrix
         if(m_pCircularBuffer->pop(matValue)) {
             //Create digital trigger information
             createDigTrig(matValue);
 
-            if(!isInterruptionRequested()) {
+            if(m_bProcessOutput) {
                 m_pRTMSABabyMEG->measurementData()->setValue(this->calibrate(matValue));
             }
         }
@@ -352,7 +357,7 @@ void BabyMEG::setFiffData(QByteArray data)
         IOUtils::swap_floatp(rawData.data()+i);
     }
 
-    if(this->isRunning()) {
+    if(m_bProcessOutput) {
         while(!m_pCircularBuffer->push(rawData)) {
             //Do nothing until the circular buffer is ready to accept new data again
         }

src/applications/mne_scan/plugins/babymeg/babymeg.h

@@ -50,6 +50,9 @@
 #include <scShared/Plugins/abstractsensor.h>
 #include <utils/generics/circularbuffer.h>
 
+#include <thread>
+#include <atomic>
+
 //=============================================================================================================
 // QT INCLUDES
 //=============================================================================================================
@@ -319,6 +322,8 @@ class BABYMEGSHARED_EXPORT BabyMEG : public SCSHAREDLIB::AbstractSensor
     QPointer<QAction>                       m_pActionSqdCtrl;               /**< show squid control. */
     QPointer<QAction>                       m_pActionUpdateFiffInfo;        /**< Update Fiff Info action. */
 
+    std::thread             m_OutputProcessingThread;
+    std::atomic_bool        m_bProcessOutput;
 signals:
     //=========================================================================================================
     /**

src/applications/mne_scan/plugins/brainamp/brainamp.cpp

@@ -84,6 +84,7 @@ BrainAMP::BrainAMP()
 , m_sRPA("2RD")
 , m_sNasion("0Z")
 , m_pCircularBuffer(QSharedPointer<CircularBuffer_Matrix_double>(new CircularBuffer_Matrix_double(8)))
+, m_bProcessOutput(false)
 {
     // Create record file option action bar item/button
     m_pActionSetupProject = new QAction(QIcon(":/images/database.png"), tr("Setup project"), this);

src/applications/mne_scan/plugins/brainamp/brainamp.h

@@ -47,6 +47,9 @@
 #include <scShared/Plugins/abstractsensor.h>
 #include <utils/generics/circularbuffer.h>
 
+#include <thread>
+#include <atomic>
+
 //=============================================================================================================
 // QT INCLUDES
 //=============================================================================================================
@@ -232,6 +235,9 @@ protected slots:
     QAction*                            m_pActionSetupStimulus;             /**< starts stimulus feature. */
 
     QMutex                              m_mutex;
+
+    std::thread             m_OutputProcessingThread;
+    std::atomic_bool        m_bProcessOutput;
 };
 } // NAMESPACE
 

src/applications/mne_scan/plugins/covariance/covariance.cpp

@@ -82,6 +82,7 @@ using namespace Eigen;
 Covariance::Covariance()
 : m_iEstimationSamples(2000)
 , m_pCircularBuffer(CircularBuffer_Matrix_double::SPtr::create(40))
+, m_bProcessOutput(false)
 {
 }
 

src/applications/mne_scan/plugins/covariance/covariance.h

@@ -46,6 +46,7 @@
 #include <utils/generics/circularbuffer.h>
 
 #include <thread>
+#include <atomic>
 
 //=============================================================================================================
 // EIGEN INCLUDES

src/applications/mne_scan/plugins/hpi/hpi.cpp

@@ -97,6 +97,7 @@ Hpi::Hpi()
 , m_bUseSSP(false)
 , m_bUseComp(false)
 , m_pCircularBuffer(CircularBuffer_Matrix_double::SPtr::create(40))
+, m_bProcessOutput(false)
 {
     connect(this, &Hpi::devHeadTransAvailable,
             this, &Hpi::onDevHeadTransAvailable, Qt::BlockingQueuedConnection);

src/applications/mne_scan/plugins/hpi/hpi.h

@@ -48,6 +48,7 @@
 #include <fiff/fiff_dig_point.h>
 
 #include <thread>
+#include <atomic>
 
 //=============================================================================================================
 // QT INCLUDES

src/applications/mne_scan/plugins/neuronalconnectivity/neuronalconnectivity.cpp

@@ -95,6 +95,7 @@ NeuronalConnectivity::NeuronalConnectivity()
 , m_pCircularBuffer(CircularBuffer<CONNECTIVITYLIB::Network>::SPtr::create(40))
 , m_pRtConnectivity(RtConnectivity::SPtr::create())
 , m_pActionShowYourWidget(Q_NULLPTR)
+, m_bProcessOutput(false)
 {
     AbstractMetric::m_bStorageModeIsActive = true;
     AbstractMetric::m_iNumberBinStart = 0;