updates

Modules/Compatibility/Deprecated/include/itkAnalyzeImageIO.h

@@ -186,16 +186,16 @@ class ITK_EXPORT AnalyzeImageIO:public ImageIOBase
   void SwapBytesIfNecessary(void *buffer, SizeType numberOfPixels);
 
 /**
- * \author Hans J. Johnson
  * Performs byte swapping of the Analyze Image header if necessary.
+ * \author Hans J. Johnson
  * \param imageheader An Analyze 7.5 compliant image header.
  * \return void
  */
   void SwapHeaderBytesIfNecessary(struct dsr *const imageheader);
 
 /**
- * \author Hans J. Johnson
  * Defines the header object data type feilds according to Analyze v7.5 specifications
+ * \author Hans J. Johnson
  * \return nothing
  */
   void  DefineHeaderObjectDataType(void);
@@ -215,9 +215,9 @@ class ITK_EXPORT AnalyzeImageIO:public ImageIOBase
     unsigned int zsize;
   };
 /**
- * \author Kent Williams
  * Get values needed to re-orient image data to
  * Coronal scan order
+ * \author Kent Williams
  * \param dim - structure to fill in
  * \return nothing
  */
@@ -226,8 +226,8 @@ class ITK_EXPORT AnalyzeImageIO:public ImageIOBase
   ipl_dimensions m_OldDim, m_NewDim;
 #endif
 /**
- * \author Hans J. Johnson
  * Check the endedness of the header file.
+ * \author Hans J. Johnson
  * \param temphdr - a reference to the header structure
  * \return The endedness of the file
  */

Modules/Compatibility/Deprecated/test/itkTestDriverIncludeDeprecatedIOFactories.h

@@ -23,7 +23,10 @@
 #include "itkNiftiImageIOFactory.h"
 #include "itkGiplImageIOFactory.h"
 #include "itkJPEGImageIOFactory.h"
-#include "itkLSMImageIOFactory.h"
+#include "itk_tiff.h" // ITK_USE_SYSTEM_TIFF
+#ifndef ITK_USE_SYSTEM_TIFF
+#  include "itkLSMImageIOFactory.h"
+#endif // ITK_USE_SYSTEM_TIFF
 #include "itkMetaImageIOFactory.h"
 #include "itkPNGImageIOFactory.h"
 #include "itkNrrdImageIOFactory.h"
@@ -43,7 +46,9 @@ void ProcessArgumentsAndRegisterDeprecatedIOFactories(int *ac, ArgumentStringTyp
   itk::ObjectFactoryBase::RegisterFactory( itk::PNGImageIOFactory::New() );
   itk::ObjectFactoryBase::RegisterFactory( itk::VTKImageIOFactory::New() );
   itk::ObjectFactoryBase::RegisterFactory( itk::GiplImageIOFactory::New() );
+#ifndef ITK_USE_SYSTEM_TIFF
   itk::ObjectFactoryBase::RegisterFactory( itk::LSMImageIOFactory::New() );
+#endif // ITK_USE_SYSTEM_TIFF
   itk::ObjectFactoryBase::RegisterFactory( itk::NiftiImageIOFactory::New() );
   itk::ObjectFactoryBase::RegisterFactory( itk::JPEGImageIOFactory::New() );
   itk::ObjectFactoryBase::RegisterFactory( itk::TIFFImageIOFactory::New() );

Modules/Core/Common/include/itkImageToImageFilter.h

@@ -172,13 +172,15 @@ class ITK_EXPORT ImageToImageFilter:public ImageSource< TOutputImage >
    */
   itkSetMacro(CoordinateTolerance,double);
   itkGetMacro(CoordinateTolerance,double);
+
   /** get/set the direction tolerance
    *  This tolerance is used to make sure that all input
    *  images are oriented the same before performing the filter's
    *  transformations.
    */
   itkSetMacro(DirectionTolerance,double);
   itkGetMacro(DirectionTolerance,double);
+
 protected:
   ImageToImageFilter();
   ~ImageToImageFilter();

Modules/Core/Common/include/itkLogOutput.h

@@ -27,7 +27,7 @@
 namespace itk
 {
 /** \class LogOutput
- *  \brief Represents an output stream.
+ * \brief Represents an output stream.
  *
  *  \author Hee-Su Kim, Compute Science Dept. Kyungpook National University,
  *                      ISIS Center, Georgetown University.

Modules/Core/Common/include/itkMetaDataObject.h

@@ -86,52 +86,51 @@ class ITK_EXPORT MetaDataObject:public MetaDataObjectBase
   itkTypeMacro(MetaDataObject, MetaDataObjectBase);
 
   /**
-   * \author Hans J. Johnson
    * Default constructor with no initialization.
+   * \author Hans J. Johnson
    */
   MetaDataObject(void);
-  /** \author Hans J. Johnson
+  /**
    * Default virtual Destructor
+   * \author Hans J. Johnson
    */
   virtual ~MetaDataObject(void);
   /**
-   * \author Hans J. Johnson
    * Initializer constructor that sets m_MetaDataObjectValue to InitializerValue
+   * \author Hans J. Johnson
    */
   MetaDataObject(const MetaDataObjectType InitializerValue);
   /**
-   * \author Hans J. Johnson
    * Copy constructor that sets m_MetaDataObjectValue to TemplateObject.m_MetaDataObjectValue
+   * \author Hans J. Johnson
    */
   MetaDataObject(const MetaDataObject< MetaDataObjectType > & TemplateObject);
   /**
-   * \author Hans J. Johnson
-   *
    * The definition of this function is necessary to fulfill
    * the interface of the MetaDataObjectBase
+   * \author Hans J. Johnson
    * \return A pointer to a const char array containing the unique type name.
    */
   virtual const char * GetMetaDataObjectTypeName(void) const;
 
   /**
-   * \author Hans J. Johnson
-   *
    * The definition of this function is necessary to fulfill
    * the interface of the MetaDataObjectBase
+   * \author Hans J. Johnson
    * \return A constant reference to a std::type_info object
    */
   virtual const std::type_info & GetMetaDataObjectTypeInfo(void) const;
 
   /**
-   * \author Hans J. Johnson
    * Function to return the stored value of type MetaDataObjectType.
+   * \author Hans J. Johnson
    * \return a constant reference to a MetaDataObjectType
    */
   const MetaDataObjectType & GetMetaDataObjectValue(void) const;
 
   /**
-   * \author Hans J. Johnson
    * Function to set the stored value of type MetaDataObjectType.
+   * \author Hans J. Johnson
    * \param NewValue A constant reference to at MetaDataObjectType.
    */
   void SetMetaDataObjectValue(const MetaDataObjectType & NewValue);
@@ -143,12 +142,13 @@ class ITK_EXPORT MetaDataObject:public MetaDataObjectBase
   virtual void Print(std::ostream & os) const;
 
 private:
-  //This is made private to force the use of the
+  // This is made private to force the use of the
   // MetaDataObject<MetaDataObjectType>::New() operator!
   //void * operator new(SizeValueType nothing) {};//purposefully not implemented
+
   /**
-   * \author Hans J. Johnson
    * A variable to store this derived type.
+   * \author Hans J. Johnson
    */
   MetaDataObjectType m_MetaDataObjectValue;
 };

Modules/Core/Common/include/itkMultipleLogOutput.h

@@ -26,14 +26,14 @@
 namespace itk
 {
 /** \class MultipleLogOutput
- *  \brief Allows writing simultaneously to multiple streams. Note that the
- *         class derives from std::streambuf and contains a
- *         std::set<> of LogOutput.
+ * \brief Allows writing simultaneously to multiple streams. Note that the
+ *        class derives from std::streambuf and contains a
+ *        std::set<> of LogOutput.
  *
  * \author Hee-Su Kim, Compute Science Dept. Kyungpook National University,
  *                     ISIS Center, Georgetown University.
  *
- *  \ingroup OSSystemObjects LoggingObjects
+ * \ingroup OSSystemObjects LoggingObjects
  * \ingroup ITKCommon
  */
 

Modules/Core/Common/include/itkOctreeNode.h

@@ -30,13 +30,15 @@ class OctreeBase;
  * \class OctreeNode
  * \brief A data structure representing a node in an Octree.
  *
- * OctreeNode data structure,  OctreeNodes have two states: 1) They are a Colored node and the
- * m_Branch is a sentinal value indicating the color, or 2) they are a branch node, and m_Branch
- * is a dynamically allocated array of 8 pointers to OctreeNodes.  In the second state, the 8 child
- * OctreeNodes are instantiated by the parent node.
+ * OctreeNode is the basic building block of an octree. It is rarely used by
+ * itself, and commonly used by the Octree class.
+ *
+ * OctreeNodes have two states: 1) They are a Colored node and the m_Branch is
+ * a sentinal value indicating the color, or 2) they are a branch node, and
+ * m_Branch is a dynamically allocated array of 8 pointers to OctreeNodes. In
+ * the second state, the 8 child OctreeNodes are instantiated by the parent node.
+ *
  * \author Hans J. Johnson
- * This class is the basic building block of an octree.  It is rarely used by itself, and commonly
- * used by the Octree class.
  * \todo FIXME copy & paste documentation in all methods.
  * \ingroup ITKCommon
  */
@@ -49,6 +51,7 @@ class ITKCommon_EXPORT OctreeNode
    * with values of 0.
    */
   OctreeNode(void);
+
   /**
    * Default destructor
    */
@@ -64,8 +67,9 @@ class ITKCommon_EXPORT OctreeNode
   OctreeNode & GetChild(const enum LeafIdentifier ChildID) const;
 
   OctreeNode & GetChild(const enum LeafIdentifier ChildID);
+  /** @}
+  */
 
-  /** @} */
   /**
    * Determines the color value of the specified Child for this OctreeNode
    * \pre Must determine that the specified node is colored (Use IsNodeColored()

Modules/Core/Transform/include/itkBSplineTransform.h

@@ -26,7 +26,7 @@ namespace itk
  * \brief Deformable transform using a BSpline representation
  *
  * This class encapsulates a deformable transform of points from one
- * N-dimensional one space to another N-dimensional space.
+ * N-dimensional space to another N-dimensional space.
  * The deformation field is modelled using B-splines.
  * A deformation is defined on a sparse regular grid of control points
  * \f$ \vec{\lambda}_j \f$ and is varied by defining a deformation

Modules/Core/Transform/include/itkBSplineTransformInitializer.h

@@ -27,6 +27,10 @@ namespace itk
  * \brief BSplineTransformInitializer is a helper class intended to
  * initialize the control point grid such that it has a physically consistent
  * definition.
+ * It sets the transform domain origin, physical dimensions and direction from
+ * information obtained from the image. It also sets the mesh size if asked
+ * to do so by calling SetTransformDomainMeshSize() before calling
+ * InitializeTransform().
  *
  * \author Luis Ibanez
  * \author Nick Tustison

Modules/Filtering/ImageFeature/include/itkBilateralImageFilter.h

@@ -133,6 +133,8 @@ class ITK_EXPORT BilateralImageFilter:
    * RangeSigma is specified in the units of intensity. */
   itkSetMacro(DomainSigma, ArrayType);
   itkGetConstMacro(DomainSigma, const ArrayType);
+  itkSetMacro(DomainMu, double);
+  itkGetConstReferenceMacro(DomainMu, double);
   itkSetMacro(RangeSigma, double);
   itkGetConstMacro(RangeSigma, double);
   itkGetConstMacro(FilterDimensionality, unsigned int);
@@ -175,24 +177,13 @@ class ITK_EXPORT BilateralImageFilter:
 #endif
 
 protected:
-  /** Constructor.  Default value for DomainSigma is 4. Default value
-   * RangeSigma is 50. */
-  BilateralImageFilter()
-  {
-    m_Radius.Fill(1);
-    m_AutomaticKernelSize = true;
-    m_DomainSigma.Fill(4.0);
-    m_RangeSigma = 50.0;
-    m_FilterDimensionality = ImageDimension;
-    m_NumberOfRangeGaussianSamples = 100;
-    m_DynamicRange = 0.0;
-    m_DynamicRangeUsed = 0.0;
-    m_DomainMu = 2.5;  // keep small to keep kernels small
-    m_RangeMu = 4.0;   // can be bigger then DomainMu since we only
-                       // index into a single table
-  }
+  /** Constructor. */
+  BilateralImageFilter();
 
+  /** Destructor. */
   virtual ~BilateralImageFilter() {}
+
+  /** PrintSelf. */
   void PrintSelf(std::ostream & os, Indent indent) const;
 
   /** Do some setup before the ThreadedGenerateData */

Modules/Filtering/ImageFeature/include/itkBilateralImageFilter.hxx

@@ -28,6 +28,23 @@
 
 namespace itk
 {
+template< class TInputImage, class TOutputImage >
+BilateralImageFilter< TInputImage, TOutputImage >
+::BilateralImageFilter()
+{
+  this->m_Radius.Fill(1);
+  this->m_AutomaticKernelSize = true;
+  this->m_DomainSigma.Fill(4.0);
+  this->m_RangeSigma = 50.0;
+  this->m_FilterDimensionality = ImageDimension;
+  this->m_NumberOfRangeGaussianSamples = 100;
+  this->m_DynamicRange = 0.0;
+  this->m_DynamicRangeUsed = 0.0;
+  this->m_DomainMu = 2.5;  // keep small to keep kernels small
+  this->m_RangeMu = 4.0;   // can be bigger then DomainMu since we only
+                           // index into a single table
+}
+
 template< class TInputImage, class TOutputImage >
 void
 BilateralImageFilter< TInputImage, TOutputImage >

Modules/Filtering/ImageFeature/test/itkBilateralImageFilterTest.cxx

@@ -35,6 +35,7 @@ int itkBilateralImageFilterTest(int, char* [] )
         filter = itk::BilateralImageFilter<ImageType,
         ImageType>::New();
       filter->SetDomainSigma(2.0);
+      filter->SetDomainMu(2.5);
       filter->SetRangeSigma(35.0f);
 
       // Run Test

Modules/Filtering/ImageFeature/test/itkBilateralImageFilterTest2.cxx

@@ -49,7 +49,7 @@ int itkBilateralImageFilterTest2(int ac, char* av[] )
   // when the original signal to noise level is 5
   filter->SetDomainSigma( 4.0 );
   filter->SetRangeSigma( 50.0 );
-
+  filter->SetDomainMu(2.5);
 
   // Test itkSetVectorMacro
   double domainSigma[dimension];
@@ -75,6 +75,8 @@ int itkBilateralImageFilterTest2(int ac, char* av[] )
   std::cout << "filter->GetFilterDimensionality(): " << filterDimensionality2 << std::endl;
   unsigned long numberOfRangeGaussianSamples2 = filter->GetNumberOfRangeGaussianSamples();
   std::cout << "filter->GetNumberOfRangeGaussianSamples(): " << numberOfRangeGaussianSamples2 << std::endl;
+  double domainMu = filter->GetDomainMu();
+  std::cout << "filter->GetDomainMu(): " << domainMu << std::endl;
 
   try
     {

Modules/Filtering/ImageFeature/test/itkBilateralImageFilterTest3.cxx

@@ -59,10 +59,13 @@ int itkBilateralImageFilterTest3(int ac, char* av[] )
     // the edges are preserved better.
     filter1->SetDomainSigma( 4.0 );
     filter1->SetRangeSigma( 20.0 );
+    filter1->SetDomainMu( 2.5 );
     filter2->SetDomainSigma( 4.0 );
     filter2->SetRangeSigma( 20.0 );
+    filter2->SetDomainMu( 2.5 );
     filter3->SetDomainSigma( 4.0 );
     filter3->SetRangeSigma( 20.0 );
+    filter3->SetDomainMu( 2.5 );
 
   try
     {

Modules/Filtering/ImageStatistics/include/itkBinaryProjectionImageFilter.h

@@ -27,14 +27,12 @@ namespace itk
  * \brief Binary projection
  *
  * This class was contributed to the Insight Journal by Gaetan Lehmann.
- * the original paper can be found at
+ * The original paper can be found at
  *   http://hdl.handle.net/1926/164
  *
- *
  * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
  *  INRA de Jouy-en-Josas, France.
  *
- *
  * \sa ProjectionImageFilter
  * \sa MedianProjectionImageFilter
  * \sa MeanProjectionImageFilter

Modules/Filtering/ImageStatistics/include/itkMaximumProjectionImageFilter.h

@@ -26,8 +26,8 @@ namespace itk
 /** \class MaximumProjectionImageFilter
  * \brief Maximum projection
  *
- * this class was contributed to the insight journal by Gaetan Lehmann.
- * the original paper can be found at
+ * This class was contributed to the insight journal by Gaetan Lehmann.
+ * The original paper can be found at
  *    http://hdl.handle.net/1926/164
  *
  * \author Gaetan Lehmann. Biologie du Developpement et de la reproduction,

Modules/Filtering/ImageStatistics/include/itkMeanProjectionImageFilter.h

@@ -33,7 +33,6 @@ namespace itk
  * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
  * INRA de Jouy-en-Josas, France.
  *
- *
  * \sa ProjectionImageFilter
  * \sa MedianProjectionImageFilter
  * \sa MinimumProjectionImageFilter

Modules/Filtering/ImageStatistics/include/itkMedianProjectionImageFilter.h

@@ -33,7 +33,6 @@ namespace itk
  * The original paper can be found at
  *      http://hdl.handle.net/1926/164
  *
- *
  * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
  * INRA de Jouy-en-Josas, France.
  *

Modules/Filtering/ImageStatistics/include/itkMinimumProjectionImageFilter.h

@@ -30,7 +30,6 @@ namespace itk
  * The original paper can be found at
  *      http://hdl.handle.net/1926/164
  *
- *
  * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
  * INRA de Jouy-en-Josas, France.
  *