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[ENH] Flexible choice of cluster size #970

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merged 4 commits into from
Apr 30, 2024
Merged

[ENH] Flexible choice of cluster size #970

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2d8147a
[FIX] Segfault in forward computation
johaenns Mar 30, 2024
f21ff62
adapted fwdsettingsview for adaptive clustering
johaenns Apr 2, 2024
ab08536
[ENH] Flexible number of sources in clustering
johaenns Apr 2, 2024
5141bc7
[ENH] Finalized changes to allow variable cluster size
johaenns Apr 29, 2024
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32 changes: 25 additions & 7 deletions src/applications/mne_scan/plugins/rtfwd/rtfwd.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -91,6 +91,7 @@ RtFwd::RtFwd()
, m_bBusy(false)
, m_bDoRecomputation(false)
, m_bDoClustering(true)
, m_bNClusterChanged(true)
, m_bDoFwdComputation(false)
{
// set init values
Expand All @@ -105,6 +106,7 @@ RtFwd::RtFwd()
m_pFwdSettings->include_eeg = true;
m_pFwdSettings->accurate = true;
m_pFwdSettings->mindist = 5.0f/1000.0f;
m_pFwdSettings->ncluster = 200;

m_sAtlasDir = QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/subjects/sample/label";
}
Expand Down Expand Up @@ -320,6 +322,8 @@ void RtFwd::initPluginControlWidgets()
this, &RtFwd::onClusteringStatusChanged);
connect(pFwdSettingsView, &FwdSettingsView::atlasDirChanged,
this, &RtFwd::onAtlasDirChanged);
connect(pFwdSettingsView, &FwdSettingsView::clusterNumberChanged,
this, &RtFwd::onClusterNumberChanged);
connect(pFwdSettingsView, &FwdSettingsView::doForwardComputation,
this, &RtFwd::onDoForwardComputation);

Expand Down Expand Up @@ -390,6 +394,16 @@ void RtFwd::onAtlasDirChanged(const QString& sDirPath, const AnnotationSet::SPtr

//=============================================================================================================

void RtFwd::onClusterNumberChanged(int iNClusterNumber)
{
m_mutex.lock();
m_pFwdSettings->ncluster = iNClusterNumber;
m_bNClusterChanged = true;
m_mutex.unlock();
}

//=============================================================================================================

void RtFwd::run()
{
// Wait for fiff the info to arrive
Expand Down Expand Up @@ -425,6 +439,7 @@ void RtFwd::run()
bool bDoRecomputation = false; // indicate if we want to recompute
bool bDoClustering = false; // indicate if we want to cluster
bool bFwdReady = false; // only cluster if fwd is ready
bool bNClusterChanged = false; // Perform new clustering when cluster size changed
bool bHpiConnectected = false; // only update/recompute if hpi is connected
bool bDoFwdComputation = false; // compute forward if requested
bool bIsInit = false; // only recompute if initial fwd solulion is calculated
Expand Down Expand Up @@ -457,10 +472,9 @@ void RtFwd::run()
m_mutex.lock();
if(!m_bDoClustering) {
m_pRTFSOutput->measurementData()->setValue(pFwdSolution);
bFwdReady = false; // make sure to not cluster
emit statusInformationChanged(5); //finished
}
bFwdReady = true; // enable cluster
bFwdReady = true; // provide fwd for clustering if wanted
m_bDoFwdComputation = false; // don't call this again if not requested
bIsInit = true; // init computation finished -> recomputation possible
m_mutex.unlock();
Expand Down Expand Up @@ -500,7 +514,7 @@ void RtFwd::run()

if(!bDoClustering) {
m_pRTFSOutput->measurementData()->setValue(pFwdSolution);
bFwdReady = false;
//bFwdReady = false; // doesn't seem to be necessary? bDoClustering = false anyway
emit statusInformationChanged(5); //finished
}
}
Expand All @@ -509,18 +523,22 @@ void RtFwd::run()
// do clustering if requested and fwd is ready
m_mutex.lock();
bDoClustering = m_bDoClustering;
bNClusterChanged = m_bNClusterChanged;
m_mutex.unlock();

if(bDoClustering && bFwdReady) {
if(bDoClustering && bFwdReady && bNClusterChanged) {
emit statusInformationChanged(3); // clustering
pClusteredFwd = MNEForwardSolution::SPtr(new MNEForwardSolution(pFwdSolution->cluster_forward_solution(*m_pAnnotationSet.data(), 200)));
pClusteredFwd = MNEForwardSolution::SPtr(new MNEForwardSolution(pFwdSolution->cluster_forward_solution(*m_pAnnotationSet.data(), m_pFwdSettings->ncluster)));
emit clusteringAvailable(pClusteredFwd->nsource);

m_pRTFSOutput->measurementData()->setValue(pClusteredFwd);

bFwdReady = false;
//bFwdReady = false; // fwd remains ready, allows for reclustering.
m_mutex.lock();
m_bNClusterChanged = false;
m_mutex.unlock();

emit statusInformationChanged(5); //finished
emit statusInformationChanged(6); //finished
}
}
}
Expand Down
10 changes: 10 additions & 0 deletions src/applications/mne_scan/plugins/rtfwd/rtfwd.h
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Original file line number Diff line number Diff line change
Expand Up @@ -190,6 +190,14 @@ class RTFWDSHARED_EXPORT RtFwd : public SCSHAREDLIB::AbstractAlgorithm
*/
void onClusteringStatusChanged(bool bDoRecomputation);

//=========================================================================================================
/**
* Call this function whenever the number of dipoles per cluster changed.
*
* @param[in] iNClusterNumber Number of dipoles per cluster.
*/
void onClusterNumberChanged(int iNClusterNumber);

//=========================================================================================================
/**
* Call this function whenever the atlas directory is set.
Expand All @@ -208,6 +216,8 @@ class RTFWDSHARED_EXPORT RtFwd : public SCSHAREDLIB::AbstractAlgorithm
bool m_bBusy; /**< Indicates if we have to update headposition.**/
bool m_bDoRecomputation; /**< If recomputation is activated.**/
bool m_bDoClustering; /**< If clustering is activated.**/
bool m_bNClusterChanged; /**< Perform new clustering when cluster size changed**/

bool m_bDoFwdComputation; /**< Do a forward computation. **/

QString m_sAtlasDir; /**< File to Atlas. */
Expand Down
29 changes: 28 additions & 1 deletion src/libraries/disp/viewers/formfiles/fwdsettingsview.ui
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<rect>
<x>0</x>
<y>0</y>
<width>333</width>
<width>362</width>
<height>939</height>
</rect>
</property>
Expand Down Expand Up @@ -221,6 +221,33 @@
</property>
</widget>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_2">
<item>
<widget class="QLabel" name="label_5">
<property name="text">
<string>Number of sources per cluster</string>
</property>
</widget>
</item>
<item>
<widget class="QSpinBox" name="m_spinBox_iNDipoleClustered">
<property name="baseSize">
<size>
<width>0</width>
<height>0</height>
</size>
</property>
<property name="minimum">
<number>5</number>
</property>
<property name="maximum">
<number>999</number>
</property>
</widget>
</item>
</layout>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout">
<item>
Expand Down
17 changes: 16 additions & 1 deletion src/libraries/disp/viewers/fwdsettingsview.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@
//=============================================================================================================

#include "fwdsettingsview.h"
#include "QtWidgets/qspinbox.h"
#include "ui_fwdsettingsview.h"

#include <fs/annotationset.h>
Expand Down Expand Up @@ -81,13 +82,15 @@ FwdSettingsView::FwdSettingsView(const QString& sSettingsPath,

// init
m_pUi->m_checkBox_bDoRecomputation->setChecked(false);
m_pUi->m_checkBox_bDoClustering->setChecked(false);
m_pUi->m_checkBox_bDoClustering->setChecked(true);
m_pUi->m_lineEdit_iNChan->setText(QString::number(0));
m_pUi->m_lineEdit_iNSourceSpace->setText(QString::number(0));
m_pUi->m_lineEdit_iNDipole->setText(QString::number(0));
m_pUi->m_lineEdit_sSourceOri->setText("fixed");
m_pUi->m_lineEdit_sCoordFrame->setText("Head Space");
m_pUi->m_lineEdit_iNDipoleClustered->setText("Not Clustered");
m_pUi->m_spinBox_iNDipoleClustered->setValue(200);
m_pUi->m_spinBox_iNDipoleClustered->setKeyboardTracking(false);

// load init annotation set
QString t_sAtlasDir = QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/subjects/sample/label";
Expand Down Expand Up @@ -115,6 +118,8 @@ FwdSettingsView::FwdSettingsView(const QString& sSettingsPath,
this, &FwdSettingsView::onClusteringStatusChanged);
connect(m_pUi->m_qPushButton_ComputeForward, &QPushButton::clicked,
this, &FwdSettingsView::doForwardComputation);
connect(m_pUi->m_spinBox_iNDipoleClustered, QOverload<int>::of(&QSpinBox::valueChanged),
this, &FwdSettingsView::clusterNumberChanged);

// load settings
loadSettings();
Expand Down Expand Up @@ -203,6 +208,9 @@ void FwdSettingsView::setRecomputationStatus(int iStatus)
} else if (iStatus == 4) {
m_pUi->m_label_recomputationFeedback->setText("Not Computed");
m_pUi->m_label_recomputationFeedback->setStyleSheet("QLabel { background-color : red;}");
} else if (iStatus == 5) {
m_pUi->m_label_recomputationFeedback->setText("Not Clustered");
m_pUi->m_label_recomputationFeedback->setStyleSheet("QLabel { background-color : yellow;}");
} else {
m_pUi->m_label_recomputationFeedback->setText("Finished");
m_pUi->m_label_recomputationFeedback->setStyleSheet("QLabel { background-color : green;}");
Expand Down Expand Up @@ -255,6 +263,13 @@ bool FwdSettingsView::getClusteringStatusChanged()

//=============================================================================================================

int FwdSettingsView::getClusterNumber()
{
return m_pUi->m_spinBox_iNDipoleClustered->value();
}

//=============================================================================================================

void FwdSettingsView::onClusteringStatusChanged(bool bChecked)
{
if(!m_bAnnotaionsLoaded) {
Expand Down
16 changes: 16 additions & 0 deletions src/libraries/disp/viewers/fwdsettingsview.h
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Original file line number Diff line number Diff line change
Expand Up @@ -120,6 +120,14 @@ class DISPSHARED_EXPORT FwdSettingsView : public AbstractView
*/
bool getClusteringStatusChanged();

//=========================================================================================================
/**
* Get status of cluster size spin box.
*
* @return Desired number of sources in clustered source space.
*/
int getClusterNumber();

//=========================================================================================================
/**
* Shows atlas selection dialog
Expand Down Expand Up @@ -235,6 +243,14 @@ class DISPSHARED_EXPORT FwdSettingsView : public AbstractView
*/
void doForwardComputation();

//=========================================================================================================
/**
* Emit this signal whenever a forward computation is supposed to be triggered.
*
* @param[in] iNCluster Number of desired sources in the clustered source space.
*/
void clusterNumberChanged(int iNCluster);

};

//=============================================================================================================
Expand Down
5 changes: 0 additions & 5 deletions src/libraries/fwd/computeFwd/compute_fwd.cpp
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Expand Up @@ -1867,11 +1867,6 @@ void ComputeFwd::initFwd()
m_listEegChs = QList<FiffChInfo>();
m_listCompChs = QList<FiffChInfo>();

if(!m_pSettings->compute_grad) {
m_meg_forward_grad = Q_NULLPTR;
m_eeg_forward_grad = Q_NULLPTR;
}

int iNMeg = 0;
int iNEeg = 0;
int iNComp = 0;
Expand Down
1 change: 1 addition & 0 deletions src/libraries/fwd/computeFwd/compute_fwd_settings.h
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Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,7 @@ class FWDSHARED_EXPORT ComputeFwdSettings
bool do_all;
QStringList labels; /**< Compute the solution only for these labels. */
int nlabel;
int ncluster; /**< Number of sources desired in clustered solution. */

QString eeg_model_file; /**< File of EEG sphere model specifications. */
QString eeg_model_name; /**< Name of the EEG model to use. */
Expand Down
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