Merge pull request #2484 from SCIInstitute/clean_warnings

Clean warnings

Author: akenmorris

Libs/Alignment/Procrustes3D.cpp

@@ -301,7 +301,7 @@ void Procrustes3D::AlignTwoShapes(SimilarityTransform3D& transform, ShapeType& s
   }
 
   // Rotation from SVD
-  vnl_svd<RealType> svd(shapeMat.transpose());
+  vnl_svd<RealType> svd(shapeMat.transpose().as_ref());
   newTransform.rotation = svd.V() * svd.U().transpose();
   transform.rotation = newTransform.rotation * transform.rotation;
 
@@ -459,7 +459,7 @@ void Procrustes3D::AlignSourceToTarget(SimilarityTransform3D& transform, ShapeTy
   }
 
   // Rotation from SVD
-  vnl_svd<RealType> svd(shapeMat.transpose());
+  vnl_svd<RealType> svd(shapeMat.transpose().as_ref());
   newTransform.rotation = svd.V() * svd.U().transpose();
   transform.rotation = newTransform.rotation;
 

Libs/Alignment/Transforms/itkKernelTransform2.cpp

@@ -396,7 +396,7 @@ ::ComputeK( void )
     // Compute the block diagonal element, i.e. kernel for pi->pi
     // Can ignore GMatrix, since p1 - p1 = 0
     this->ComputeReflexiveG( p1, G );
-    this->m_KMatrix.update( G, i * NDimensions, i * NDimensions );
+    this->m_KMatrix.update( G.as_ref(), i * NDimensions, i * NDimensions );
     p2++; j++;
 
     // Compute the upper (and copy into lower) triangular part of K
@@ -405,8 +405,8 @@ ::ComputeK( void )
       const InputVectorType s = p1.Value() - p2.Value();
       this->ComputeG( s, G );
       // write value in upper and lower triangle of matrix
-      this->m_KMatrix.update( G, i * NDimensions, j * NDimensions );
-      this->m_KMatrix.update( G, j * NDimensions, i * NDimensions );
+      this->m_KMatrix.update( G.as_ref(), i * NDimensions, j * NDimensions );
+      this->m_KMatrix.update( G.as_ref(), j * NDimensions, i * NDimensions );
       p2++; j++;
     }
     p1++; i++;
@@ -439,9 +439,9 @@ ::ComputeP( void )
     for( unsigned int j = 0; j < NDimensions; j++ )
     {
       temp = I * p[ j ];
-      this->m_PMatrix.update( temp, i * NDimensions, j * NDimensions );
+      this->m_PMatrix.update( temp.as_ref(), i * NDimensions, j * NDimensions );
     }
-    this->m_PMatrix.update( I, i * NDimensions, NDimensions * NDimensions );
+    this->m_PMatrix.update( I.as_ref(), i * NDimensions, NDimensions * NDimensions );
   }
 
 } // end ComputeP()

Libs/Mesh/PreviewMeshQC/FEVTKExport.cpp

@@ -105,7 +105,7 @@ bool FEVTKExport::ExportToStream(FEMesh &mesh, std::ostream &out)
     for (j = 0; j < m.Nodes();) {
       for (int k = 0; k < 9 && j + k < m.Nodes(); k++) {
         char buffer[1024];
-        sprintf(buffer, "%15.10lg ", nodeShellThickness[j + k]);
+        std::snprintf(buffer, sizeof(buffer), "%15.10lg ", nodeShellThickness[j + k]);
         out << buffer << "\n";
       }
       out << "\n";
@@ -124,7 +124,7 @@ bool FEVTKExport::ExportToStream(FEMesh &mesh, std::ostream &out)
       for (int k = 0; k < 9 && j + k < m.Nodes(); k++) {
         FENode& n = m.Node(j + k);
         char buffer[1024];
-        sprintf(buffer, "%15.10lg ", n.m_ndata);
+        std::snprintf(buffer, sizeof(buffer), "%15.10lg ", n.m_ndata);
         out << buffer << "\n";
       }
       out << "\n";

Libs/Optimize/Matrix/MixedEffectsShapeMatrix.h

@@ -199,6 +199,10 @@ class MixedEffectsShapeMatrix : public LegacyShapeMatrix {
     }
   }
 
+#if defined(__GNUC__) && !defined(__clang__)
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Walloc-size-larger-than="
+#endif
   void EstimateParameters() {
     //    std::cout << "Estimating params" << std::endl;
     //    std::cout << "Explanatory: " << m_Expl << std::endl;
@@ -210,6 +214,14 @@ class MixedEffectsShapeMatrix : public LegacyShapeMatrix {
     this->m_NumIndividuals = num_shapes / this->GetTimeptsPerIndividual();
     int nr = X.rows();  // number of points*3
 
+    // Guard against invalid m_NumIndividuals
+    if (m_NumIndividuals <= 0) {
+      return;
+    }
+
+    // Use local variable to help compiler understand value is positive
+    const size_t num_individuals = static_cast<size_t>(m_NumIndividuals);
+
     // set the sizes of random slope and intercept matrix
     m_SlopeRand.set_size(m_NumIndividuals, nr);      // num_groups X num_points*3
     m_InterceptRand.set_size(m_NumIndividuals, nr);  // num_groups X num_points*3
@@ -228,8 +240,8 @@ class MixedEffectsShapeMatrix : public LegacyShapeMatrix {
     identity_2.set_size(2, 2);
     identity_2.set_identity();
     vnl_matrix<double>*Ws = NULL, *Vs = NULL;
-    Ws = new vnl_matrix<double>[m_NumIndividuals];
-    Vs = new vnl_matrix<double>[m_NumIndividuals];
+    Ws = new vnl_matrix<double>[num_individuals];
+    Vs = new vnl_matrix<double>[num_individuals];
     for (int i = 0; i < m_NumIndividuals; i++) {
       Vs[i].set_size(m_TimeptsPerIndividual, m_TimeptsPerIndividual);
       Ws[i].set_size(m_TimeptsPerIndividual, m_TimeptsPerIndividual);
@@ -319,6 +331,9 @@ class MixedEffectsShapeMatrix : public LegacyShapeMatrix {
     // printf ("random: slopes %g %g, intercepts %g %g", m_SlopeRand(0,0), m_SlopeRand(1,0), m_InterceptRand(0,0),
     // m_InterceptRand(1,0));
   }
+#if defined(__GNUC__) && !defined(__clang__)
+#pragma GCC diagnostic pop
+#endif
 
   //
   void Initialize() {

Libs/Optimize/Utils/OptimizationVisualizer.cpp

@@ -125,8 +125,8 @@ void OptimizationVisualizer::IterationCallback(ParticleSystem* particleSystem) {
     windowToImageFilter->Update();
 
     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
-    char buffer[100];
-    int n = sprintf(buffer, "%s/screenshot_%08d.png", this->screenshotDirectory.c_str(), iteration);
+    char buffer[256];
+    std::snprintf(buffer, sizeof(buffer), "%s/screenshot_%08d.png", this->screenshotDirectory.c_str(), iteration);
     writer->SetFileName(buffer);
     writer->SetInputConnection(windowToImageFilter->GetOutputPort());
     writer->Write();

Libs/Optimize/Utils/ParticleGaussianModeWriter.txx

@@ -57,7 +57,7 @@ void ParticleGaussianModeWriter<VDimension>::Update() const {
   for (unsigned int d = 0; d < (unsigned int)DomainsPerShape; d++) {
     char fp[255];
     std::string fn = m_FileName;
-    ::sprintf(fp, "domain%d", d);
+    std::snprintf(fp, sizeof(fp), "domain%d", d);
     fn += fp;
 
     int rowsperdomain = num_dims / DomainsPerShape;
@@ -95,7 +95,7 @@ void ParticleGaussianModeWriter<VDimension>::Update() const {
         }
 
         char fp[255];
-        ::sprintf(fp, ".%d.%d.mode", s, modenum);
+        std::snprintf(fp, sizeof(fp), ".%d.%d.mode", s, modenum);
         std::string tmpstr = fn + fp;
 
         particles::write_particles_from_vector(tmpstr, modelist);

Studio/CMakeLists.txt

@@ -176,7 +176,7 @@ SET(STUDIO_UTILS_SRCS
   )
 
 SET(STUDIO_UTILS_MOC_HDRS
-  Utils/ImageLabel.h
+  # Utils/ImageLabel.h - doesn't have Q_OBJECT, no moc needed
   )
 
 SET(STUDIO_INTERFACE_SRCS
@@ -195,7 +195,7 @@ SET(STUDIO_INTERFACE_SRCS
   )
 SET(STUDIO_INTERFACE_MOC_HDRS
   Interface/CompareWidget.h
-  Interface/CustomSlider.h
+  # Interface/CustomSlider.h - doesn't have Q_OBJECT, no moc needed
   Interface/ExportImageDialog.h
   Interface/KeyboardShortcuts.h
   Interface/LogWindow.h

Studio/Interface/LogWindow.cpp

@@ -41,7 +41,7 @@ void LogWindow::add_message(MessageType message_type, QString message) {
   }
 
   QListWidgetItem* item = new QListWidgetItem(message, this->ui_->history_list_);
-  item->setTextColor(color);
+  item->setForeground(color);
   this->ui_->history_list_->addItem(item);
   this->ui_->history_list_->setCurrentItem(item);
 }

Studio/Interface/SplashScreen.cpp

@@ -127,7 +127,7 @@ void SplashScreen::resizeEvent(QResizeEvent* event) {
   QDialog::resizeEvent(event);
 
   QFontMetrics fm(this->ui_->title_->font());
-  int width = fm.width(this->ui_->title_->text());
+  int width = fm.horizontalAdvance(this->ui_->title_->text());
   this->ui_->title_->setMinimumWidth(width);
   this->resize(width * 2, width * 1.2);
 }

Studio/Optimize/OptimizeTool.ui

@@ -1148,7 +1148,7 @@ QWidget#optimize_panel {
                    </widget>
                   </item>
                   <item row="0" column="0">
-                   <spacer name="horizontalSpacer_13">
+                   <spacer name="horizontalSpacer_13a">
                     <property name="orientation">
                      <enum>Qt::Horizontal</enum>
                     </property>
@@ -1161,7 +1161,7 @@ QWidget#optimize_panel {
                    </spacer>
                   </item>
                   <item row="0" column="2">
-                   <spacer name="horizontalSpacer_14">
+                   <spacer name="horizontalSpacer_14a">
                     <property name="orientation">
                      <enum>Qt::Horizontal</enum>
                     </property>