further refactoring of disp3d by adding source space visulaization and revoked codecov

Author: chdinh

.github/workflows/pullrequest.yml

@@ -290,12 +290,6 @@ jobs:
       with:
         python-version: '3.7'
         architecture: 'x64'
-    - name: Install Codecov
-      if: matrix.os == 'ubuntu-latest'
-      run: |
-        curl -Os https://uploader.codecov.io/latest/linux/codecov
-        chmod +x codecov
-        echo "${pwd}" >> $GITHUB_PATH
     - name: Install Qt (Linux|MacOS)
       if: (matrix.os == 'ubuntu-20.04') || (matrix.os == 'macos-11')
       uses: jurplel/install-qt-action@v3
@@ -320,10 +314,14 @@ jobs:
     - name: Run tests (Linux)
       if: matrix.os == 'ubuntu-latest'
       env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         QTEST_FUNCTION_TIMEOUT: 900000
       run: |
         ./tools/test_all.bat verbose withCoverage
+    - name: Upload coverage to Codecov
+      if: matrix.os == 'ubuntu-latest'
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
     - name: Run tests (MacOS)
       if: matrix.os == 'macos-latest'
       env:

.github/workflows/testci.yml

@@ -199,10 +199,6 @@ jobs:
       with:
         python-version: '3.10'
         architecture: ${{ matrix.os == 'macos-26' && 'arm64' || 'x64' }}
-    - name: Install Codecov
-      if: matrix.os == 'ubuntu-24.04'
-      run: |
-        sudo pip install codecov
     - name: Install Qt (Linux|MacOS)
       if: (matrix.os == 'ubuntu-24.04') || (matrix.os == 'macos-26')
       uses: jurplel/install-qt-action@v3
@@ -237,10 +233,14 @@ jobs:
     - name: Run tests (Linux)
       if: matrix.os == 'ubuntu-24.04'
       env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         QTEST_FUNCTION_TIMEOUT: 900000
       run: |
         ./tools/test_all.bat verbose withCoverage
+    - name: Upload coverage to Codecov
+      if: matrix.os == 'ubuntu-24.04'
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
     - name: Run tests (MacOS)
       if: matrix.os == 'macos-26'
       env:

src/examples/CMakeLists.txt

@@ -12,7 +12,7 @@ add_subdirectory(ex_compute_forward)
 
 ## Examples requiring mne_disp3D (which needs Qt3D) - check if available
 find_package(Qt6 QUIET COMPONENTS 3DRender)
-if(Qt6_3DRender_FOUND)
+if(Qt63DRender_FOUND)
   add_subdirectory(ex_clustered_inverse_mne)
   add_subdirectory(ex_clustered_inverse_mne_raw)
   add_subdirectory(ex_clustered_inverse_pwl_rap_music_raw)

src/examples/ex_brain_view/CMakeLists.txt

@@ -26,6 +26,7 @@ set(SOURCES
     model/braintreemodel.cpp
     model/items/sensortreeitem.cpp
     model/items/dipoletreeitem.cpp
+    model/items/sourcespacetreeitem.cpp
 )
 
 if(${QT_VERSION_MAJOR} GREATER_EQUAL 6)

src/examples/ex_brain_view/app/mainwindow.cpp

@@ -299,6 +299,20 @@ void MainWindow::setupUI()
     dipoleLayout->addWidget(m_loadDipoleBtn);
     dipoleLayout->addWidget(m_showDipoleCheck);
 
+    // ===== Source Space Group =====
+    QGroupBox *srcSpaceGroup = new QGroupBox("Source Space");
+    QVBoxLayout *srcSpaceLayout = new QVBoxLayout(srcSpaceGroup);
+    srcSpaceLayout->setContentsMargins(10, 15, 10, 10);
+    srcSpaceLayout->setSpacing(8);
+
+    m_loadSrcSpaceBtn = new QPushButton("Load Source Space...");
+    m_showSrcSpaceCheck = new QCheckBox("Show Source Space");
+    m_showSrcSpaceCheck->setChecked(false);
+    m_showSrcSpaceCheck->setEnabled(false);
+
+    srcSpaceLayout->addWidget(m_loadSrcSpaceBtn);
+    srcSpaceLayout->addWidget(m_showSrcSpaceCheck);
+
     // ===== Sensor Group =====
     QGroupBox *sensorGroup = new QGroupBox("Sensors");
     QVBoxLayout *sensorLayout = new QVBoxLayout(sensorGroup);
@@ -335,6 +349,7 @@ void MainWindow::setupUI()
     sideLayout->addWidget(controlGroup);
     sideLayout->addWidget(stcGroup);
     sideLayout->addWidget(dipoleGroup);
+    sideLayout->addWidget(srcSpaceGroup);
     sideLayout->addWidget(sensorGroup);
     sideLayout->addStretch();
 
@@ -557,6 +572,20 @@ void MainWindow::setupConnections()
 
     connect(m_showDipoleCheck, &QCheckBox::toggled, [this](bool checked) { m_brainView->setDipoleVisible(checked); });
 
+    // Source Space
+    connect(m_loadSrcSpaceBtn, &QPushButton::clicked, [this]() {
+        QString path = QFileDialog::getOpenFileName(this, "Select Source Space / Forward Solution", "",
+            "Source Space Files (*-src.fif *-fwd.fif);;All FIF Files (*.fif)");
+        if (path.isEmpty()) return;
+        if (m_brainView->loadSourceSpace(path)) {
+            m_showSrcSpaceCheck->setEnabled(true);
+            m_showSrcSpaceCheck->setChecked(false);
+            m_brainView->setSourceSpaceVisible(false);
+        }
+    });
+
+    connect(m_showSrcSpaceCheck, &QCheckBox::toggled, [this](bool checked) { m_brainView->setSourceSpaceVisible(checked); });
+
     // Sync initial state
     m_brainView->setHemiVisible(0, m_lhCheck->isChecked());
     m_brainView->setHemiVisible(1, m_rhCheck->isChecked());
@@ -572,7 +601,8 @@ void MainWindow::loadInitialData(const QString &subjectPath,
                                   const QString &bemPath,
                                   const QString &transPath,
                                   const QString &stcPath,
-                                  const QString &digitizerPath)
+                                  const QString &digitizerPath,
+                                  const QString &srcSpacePath)
 {
     qDebug() << "Loading surfaces...";
 
@@ -604,6 +634,16 @@ void MainWindow::loadInitialData(const QString &subjectPath,
         m_brainView->loadTransformation(transPath);
     }
 
+    // Auto-load source space
+    if (!srcSpacePath.isEmpty() && QFile::exists(srcSpacePath)) {
+        qDebug() << "Auto-loading source space from:" << srcSpacePath;
+        if (m_brainView->loadSourceSpace(srcSpacePath)) {
+            m_showSrcSpaceCheck->setEnabled(true);
+            m_showSrcSpaceCheck->setChecked(false);
+            m_brainView->setSourceSpaceVisible(false);
+        }
+    }
+
     // Auto-load STC
     if (!stcPath.isEmpty() && QFile::exists(stcPath)) {
         qDebug() << "Auto-loading source estimate from:" << stcPath;

src/examples/ex_brain_view/app/mainwindow.h

@@ -97,7 +97,8 @@ class MainWindow : public QMainWindow
                          const QString &bemPath = QString(),
                          const QString &transPath = QString(),
                          const QString &stcPath = QString(),
-                         const QString &digitizerPath = QString());
+                         const QString &digitizerPath = QString(),
+                         const QString &srcSpacePath = QString());
 
 private:
     void setupUI();
@@ -159,6 +160,10 @@ class MainWindow : public QMainWindow
     // Control widgets - Dipoles
     QPushButton *m_loadDipoleBtn = nullptr;
     QCheckBox *m_showDipoleCheck = nullptr;
+
+    // Control widgets - Source Space
+    QPushButton *m_loadSrcSpaceBtn = nullptr;
+    QCheckBox *m_showSrcSpaceCheck = nullptr;
 };
 
 #endif // MAINWINDOW_H

src/examples/ex_brain_view/main.cpp

@@ -61,8 +61,9 @@ int main(int argc, char *argv[])
     QCommandLineOption transOption("trans", "Transformation file path", "path", "");
     QCommandLineOption stcOption("stc", "Source estimate file path", "path", "");
     QCommandLineOption digitizerOption("digitizer", "Digitizer/sensor file path", "path", "");
+    QCommandLineOption srcSpaceOption("srcSpace", "Source space / forward solution file path", "path", "");
 
-    parser.addOptions({subjectPathOption, subjectOption, hemiOption, bemOption, transOption, stcOption, digitizerOption});
+    parser.addOptions({subjectPathOption, subjectOption, hemiOption, bemOption, transOption, stcOption, digitizerOption, srcSpaceOption});
     parser.process(app);
 
     MainWindow mainWindow;
@@ -72,7 +73,8 @@ int main(int argc, char *argv[])
         parser.value(bemOption),
         parser.value(transOption),
         parser.value(stcOption),
-        parser.value(digitizerOption)
+        parser.value(digitizerOption),
+        parser.value(srcSpaceOption)
     );
     mainWindow.show();
 

src/examples/ex_brain_view/model/braintreemodel.cpp

@@ -3,7 +3,9 @@
 #include "bemtreeitem.h"
 #include "sensortreeitem.h"
 #include "dipoletreeitem.h"
+#include "sourcespacetreeitem.h"
 #include <inverse/dipoleFit/ecd_set.h>
+#include <mne/mne_hemisphere.h>
 
 BrainTreeModel::BrainTreeModel(QObject *parent)
     : QStandardItemModel(parent)
@@ -133,3 +135,43 @@ void BrainTreeModel::addDipoles(const INVERSELIB::ECDSet &set)
     item->setCheckState(Qt::Checked);
     this->appendRow(item);
 }
+
+//=============================================================================================================
+
+void BrainTreeModel::addSourceSpace(const MNELIB::MNESourceSpace &srcSpace)
+{
+    QStandardItem* parentItem = new QStandardItem("Source Space");
+    parentItem->setCheckable(true);
+    parentItem->setCheckState(Qt::Checked);
+
+    // Color: LH = bright cyan, RH = bright magenta
+    QColor lhColor(0, 230, 180);    // Vibrant cyan-green for left hemisphere
+    QColor rhColor(230, 80, 230);   // Vibrant magenta for right hemisphere
+
+    for (int h = 0; h < srcSpace.size(); ++h) {
+        const MNELIB::MNEHemisphere &hemi = srcSpace[h];
+        QColor color = (h == 0) ? lhColor : rhColor;
+        QString hemiLabel = (h == 0) ? "LH" : "RH";
+
+        // Collect all source point positions for this hemisphere
+        QVector<QVector3D> positions;
+        positions.reserve(hemi.vertno.size());
+        for (int i = 0; i < hemi.vertno.size(); ++i) {
+            int vIdx = hemi.vertno(i);
+            if (vIdx < 0 || vIdx >= hemi.rr.rows()) continue;
+            positions.append(QVector3D(hemi.rr(vIdx, 0), hemi.rr(vIdx, 1), hemi.rr(vIdx, 2)));
+        }
+
+        // One item per hemisphere with all positions batched
+        parentItem->appendRow(new SourceSpaceTreeItem(hemiLabel, positions, color, 0.00025f));
+        qDebug() << "BrainTreeModel: Source space" << hemiLabel
+                 << "- points:" << positions.size()
+                 << "coord_frame:" << hemi.coord_frame;
+        if (!positions.isEmpty()) {
+            qDebug() << "  First point:" << positions.first()
+                     << "  Last point:" << positions.last();
+        }
+    }
+
+    this->appendRow(parentItem);
+}

src/examples/ex_brain_view/model/braintreemodel.h

@@ -5,6 +5,7 @@
 #include <fs/surface.h>
 #include <fs/annotation.h>
 #include <mne/mne_bem_surface.h>
+#include <mne/mne_sourcespace.h>
 
 namespace INVERSELIB {
 class ECDSet;
@@ -35,6 +36,9 @@ class BrainTreeModel : public QStandardItemModel
     void addSensors(const QString &type, const QList<QStandardItem*> &items);
     void addDipoles(const INVERSELIB::ECDSet &set);
 
+    // Add source space points
+    void addSourceSpace(const MNELIB::MNESourceSpace &srcSpace);
+
 private:
    // Helpers to find specific items
    QStandardItem* getSubjectItem(const QString &subject);

src/examples/ex_brain_view/model/items/abstracttreeitem.h

@@ -22,7 +22,8 @@ class AbstractTreeItem : public QStandardItem
         SurfaceItem,
         BemItem,
         SensorItem,
-        DipoleItem
+        DipoleItem,
+        SourceSpaceItem
     };
 
     explicit AbstractTreeItem(const QString &text = "", int type = AbstractItem);