mitk::AutoCropImageFilter Class Reference

Shrink the image borders to a minimum considering a background color. More...

#include <mitkAutoCropImageFilter.h>

Inheritance diagram for mitk::AutoCropImageFilter:

Collaboration diagram for mitk::AutoCropImageFilter:

Public Types
typedef itk::ImageRegion< 3 >	RegionType
Public Types inherited from mitk::SubImageSelector
typedef SubImageSelector	Self
typedef ImageToImageFilter	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer< const Self >	ConstPointer
Public Types inherited from mitk::ImageToImageFilter
typedef ImageToImageFilter	Self
typedef ImageSource	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer< const Self >	ConstPointer
typedef Superclass::OutputImageRegionType	OutputImageRegionType
typedef mitk::Image	InputImageType
typedef InputImageType::Pointer	InputImagePointer
typedef InputImageType::ConstPointer	InputImageConstPointer
typedef SlicedData::RegionType	InputImageRegionType
Public Types inherited from mitk::ImageSource
typedef ImageSource	Self
typedef BaseDataSource	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer< const Self >	ConstPointer
typedef mitk::Image	OutputImageType
	Some convenient typedefs. More...
typedef OutputImageType	OutputType
typedef OutputImageType::Pointer	OutputImagePointer
typedef SlicedData::RegionType	OutputImageRegionType
Public Types inherited from mitk::BaseDataSource
typedef BaseDataSource	Self
typedef itk::ProcessObject	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer< const Self >	ConstPointer
typedef BaseData	OutputType
typedef itk::DataObject::DataObjectIdentifierType	DataObjectIdentifierType

Public Member Functions
	mitkClassMacro (AutoCropImageFilter, SubImageSelector)
Pointer	Clone () const
virtual float	GetBackgroundValue () const
virtual void	SetBackgroundValue (float _arg)
virtual float	GetMarginFactor () const
virtual void	SetMarginFactor (float _arg)
virtual RegionType	GetCroppingRegion ()
void	SetCroppingRegion (RegionType overrideRegion)
virtual const PixelType	GetOutputPixelType ()
Public Member Functions inherited from mitk::SubImageSelector
virtual std::vector< std::string >	GetClassHierarchy () const override
virtual const char *	GetClassName () const
Pointer	Clone () const
virtual void	SetPosNr (int p)
	SubImageSelector ()
virtual	~SubImageSelector ()
Public Member Functions inherited from mitk::ImageToImageFilter
Pointer	Clone () const
virtual void	SetInput (const InputImageType *image)
virtual void	SetInput (unsigned int, const InputImageType *image)
InputImageType *	GetInput (void)
InputImageType *	GetInput (unsigned int idx)
const InputImageType *	GetInput (void) const
const InputImageType *	GetInput (unsigned int idx) const
Public Member Functions inherited from mitk::ImageSource
Pointer	Clone () const
OutputType *	GetOutput ()
	Get the output data of this image source object. More...
const OutputType *	GetOutput () const
OutputType *	GetOutput (DataObjectPointerArraySizeType idx)
const OutputType *	GetOutput (DataObjectPointerArraySizeType idx) const
virtual itk::DataObject::Pointer	MakeOutput (DataObjectPointerArraySizeType idx) override
	Make a DataObject of the correct type to used as the specified output. More...
virtual itk::DataObject::Pointer	MakeOutput (const DataObjectIdentifierType &name) override
virtual vtkImageData *	GetVtkImageData ()
virtual const vtkImageData *	GetVtkImageData () const
Public Member Functions inherited from mitk::BaseDataSource
OutputType *	GetOutput ()
const OutputType *	GetOutput () const
OutputType *	GetOutput (DataObjectPointerArraySizeType idx)
const OutputType *	GetOutput (DataObjectPointerArraySizeType idx) const
virtual void	GraftOutput (OutputType *output)
	Graft the specified BaseData onto this BaseDataSource's output. More...
virtual void	GraftOutput (const DataObjectIdentifierType &key, OutputType *output)
virtual void	GraftNthOutput (unsigned int idx, OutputType *output)
	Graft the specified base data object onto this BaseDataSource's idx'th output. More...
bool	Updating () const
	Access itk::ProcessObject::m_Updating. More...

Static Public Member Functions
static Pointer	New ()
Static Public Member Functions inherited from mitk::SubImageSelector
static const char *	GetStaticNameOfClass ()
static Pointer	New ()
Static Public Member Functions inherited from mitk::ImageToImageFilter
static const char *	GetStaticNameOfClass ()
static Pointer	New ()
Static Public Member Functions inherited from mitk::ImageSource
static const char *	GetStaticNameOfClass ()
static Pointer	New ()
	Method for creation through the object factory. More...
Static Public Member Functions inherited from mitk::BaseDataSource
static const char *	GetStaticNameOfClass ()

Protected Types
typedef itk::Image< float, 3 >	ImageType
typedef ImageType::Pointer	ImagePointer

Protected Member Functions
	AutoCropImageFilter ()
virtual	~AutoCropImageFilter ()
void	ComputeNewImageBounds ()
template<typename TPixel , unsigned int VImageDimension>
void	ITKCrop3DImage (itk::Image< TPixel, VImageDimension > *inputItkImage, unsigned int timestep)
virtual void	GenerateOutputInformation () override
virtual void	GenerateInputRequestedRegion () override
virtual void	GenerateData () override
	A version of GenerateData() specific for image processing filters. More...
Protected Member Functions inherited from mitk::SubImageSelector
mitk::Image::ImageDataItemPointer	GetSliceData (int s=0, int t=0, int n=0)
mitk::Image::ImageDataItemPointer	GetVolumeData (int t=0, int n=0)
mitk::Image::ImageDataItemPointer	GetChannelData (int n=0)
void	SetSliceItem (mitk::Image::ImageDataItemPointer dataItem, int s=0, int t=0, int n=0)
void	SetVolumeItem (mitk::Image::ImageDataItemPointer dataItem, int t=0, int n=0)
void	SetChannelItem (mitk::Image::ImageDataItemPointer dataItem, int n=0)
Protected Member Functions inherited from mitk::ImageToImageFilter
	ImageToImageFilter ()
virtual	~ImageToImageFilter ()
virtual void	PrintSelf (std::ostream &os, itk::Indent indent) const override
Protected Member Functions inherited from mitk::ImageSource
	ImageSource ()
virtual	~ImageSource ()
virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, itk::ThreadIdType threadId)
	If an imaging filter can be implemented as a multithreaded algorithm, the filter will provide an implementation of ThreadedGenerateData(). More...
virtual void	PrepareOutputs () override
	This method is intentionally left blank. More...
virtual void	AllocateOutputs ()
	The GenerateData method normally allocates the buffers for all of the outputs of a filter. More...
virtual void	BeforeThreadedGenerateData ()
	If an imaging filter needs to perform processing after the buffer has been allocated but before threads are spawned, the filter can can provide an implementation for BeforeThreadedGenerateData(). More...
virtual void	AfterThreadedGenerateData ()
	If an imaging filter needs to perform processing after all processing threads have completed, the filter can can provide an implementation for AfterThreadedGenerateData(). More...
virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int num, OutputImageRegionType &splitRegion)
	Split the output's RequestedRegion into "num" pieces, returning region "i" as "splitRegion". More...
Protected Member Functions inherited from mitk::BaseDataSource
	BaseDataSource ()
virtual	~BaseDataSource ()

Protected Attributes
float	m_BackgroundValue
RegionType	m_CroppingRegion
float	m_MarginFactor
RegionType::SizeType	m_RegionSize
RegionType::IndexType	m_RegionIndex
mitk::ImageTimeSelector::Pointer	m_TimeSelector
mitk::SlicedData::RegionType	m_InputRequestedRegion
itk::TimeStamp	m_TimeOfHeaderInitialization
bool	m_OverrideCroppingRegion

Additional Inherited Members
Static Protected Member Functions inherited from mitk::ImageSource
static ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)
	Static function used as a "callback" by the MultiThreader. More...
Static Protected Member Functions inherited from mitk::BaseDataSource
static Pointer	New ()

Detailed Description

Shrink the image borders to a minimum considering a background color.

This filter determines the smallest bounding box of all pixels different from the background, and returns an output image which has been cropped to this size. The box calculated this way is not the smallest possible box, but the box with the smallest sides perpendicular to the world coordinate system.

The filter works on 3D and 4D image data. For the 4D case, the smallest box is calculated with side lengths as the maximum of single side lengths from all time steps.

2D images are not supported, and will never be.

It is also possible to set the region to be cropped manually using the SetCroppingRegion() method.

A margin can be set to enlarge the cropped region with a constant factor in all directions around the smallest possible.

Author

Thomas Boettger; revised by Tobias Schwarz and Daniel Stein; Division of Medical and Biological Informatics

Definition at line 58 of file mitkAutoCropImageFilter.h.

Member Typedef Documentation

typedef ImageType::Pointer mitk::AutoCropImageFilter::ImagePointer

protected

Definition at line 110 of file mitkAutoCropImageFilter.h.

typedef itk::Image<float, 3> mitk::AutoCropImageFilter::ImageType

protected

Definition at line 109 of file mitkAutoCropImageFilter.h.

typedef itk::ImageRegion<3> mitk::AutoCropImageFilter::RegionType

Definition at line 61 of file mitkAutoCropImageFilter.h.

Constructor & Destructor Documentation

mitk::AutoCropImageFilter::AutoCropImageFilter ( )

protected

Definition at line 30 of file mitkAutoCropImageFilter.cpp.

mitk::AutoCropImageFilter::~AutoCropImageFilter ( )

protectedvirtual

Definition at line 35 of file mitkAutoCropImageFilter.cpp.

Member Function Documentation

Pointer mitk::AutoCropImageFilter::Clone

(

)

const

void mitk::AutoCropImageFilter::ComputeNewImageBounds ( )

protected

Definition at line 232 of file mitkAutoCropImageFilter.cpp.

References mitk::CastToItkImage(), mitk::eps, mitk::ImageTimeSelector::New(), and mitk::New().

void mitk::AutoCropImageFilter::GenerateData ( )

overrideprotectedvirtual

A version of GenerateData() specific for image processing filters.

This implementation will split the processing across multiple threads. The buffer is allocated by this method. Then the BeforeThreadedGenerateData() method is called (if provided). Then, a series of threads are spawned each calling ThreadedGenerateData(). After all the threads have completed processing, the AfterThreadedGenerateData() method is called (if provided). If an image processing filter cannot be threaded, the filter should provide an implementation of GenerateData(). That implementation is responsible for allocating the output buffer. If a filter an be threaded, it should NOT provide a GenerateData() method but should provide a ThreadedGenerateData() instead.

See also

ThreadedGenerateData()

Reimplemented from mitk::ImageSource.

Definition at line 192 of file mitkAutoCropImageFilter.cpp.

References AccessFixedDimensionByItk_1, MITK_ERROR, and mitk::ImageTimeSelector::New().

void mitk::AutoCropImageFilter::GenerateInputRequestedRegion ( )

overrideprotectedvirtual

What is the input requested region that is required to produce the output requested region? The base assumption for image processing filters is that the input requested region can be set to match the output requested region. If a filter requires more input (for instance a filter that uses neighborhoods needs more input than output to avoid introducing artificial boundary conditions) or less input (for instance a magnify filter) will have to override this method. In doing so, it should call its superclass' implementation as its first step. Note that this imaging filters operate differently than the classes to this point in the class hierachy. Up till now, the base assumption has been that the largest possible region will be requested of the input.

See also

ProcessObject::GenerateInputRequestedRegion(), ImageSource::GenerateInputRequestedRegion()

Reimplemented from mitk::ImageToImageFilter.

Definition at line 353 of file mitkAutoCropImageFilter.cpp.

void mitk::AutoCropImageFilter::GenerateOutputInformation ( )

overrideprotectedvirtual

Definition at line 75 of file mitkAutoCropImageFilter.cpp.

References mitk::ProportionalTimeGeometry::Initialize(), mitk::SlicedGeometry3D::InitializeEvenlySpaced(), mitk::itk2vtk(), MITK_ERROR, mitk::New(), mitk::BaseGeometry::SetOrigin(), and mitk::vtk2itk().

virtual float mitk::AutoCropImageFilter::GetBackgroundValue ( ) const

virtual

virtual RegionType mitk::AutoCropImageFilter::GetCroppingRegion ( )

virtual

virtual float mitk::AutoCropImageFilter::GetMarginFactor ( ) const

virtual

const mitk::PixelType mitk::AutoCropImageFilter::GetOutputPixelType ( )

virtual

Definition at line 357 of file mitkAutoCropImageFilter.cpp.

References mitk::PixelType::GetPixelType().

template<typename TPixel , unsigned int VImageDimension>

void mitk::AutoCropImageFilter::ITKCrop3DImage ( itk::Image< TPixel, VImageDimension > *  inputItkImage, unsigned int  timestep  )

protected

Definition at line 40 of file mitkAutoCropImageFilter.cpp.

References mitk::CastToMitkImage(), mitk::StatusBar::DisplayErrorText(), mitk::ImageAccessorBase::GetData(), mitk::StatusBar::GetInstance(), MITK_ERROR, MITK_INFO, mitk::New(), and mitk::Image::New().

mitk::AutoCropImageFilter::mitkClassMacro	(	AutoCropImageFilter	,
		SubImageSelector
	)

static Pointer mitk::AutoCropImageFilter::New ( )

static

Referenced by mitk::MaskAndCutRoiImageFilter::MaskAndCutRoiImageFilter(), mitkAutoCropImageFilterTest(), and mitk::AutoCropTool::ProcessOneWorkingData().

virtual void mitk::AutoCropImageFilter::SetBackgroundValue ( float  _arg )

virtual

void mitk::AutoCropImageFilter::SetCroppingRegion

(

RegionType

overrideRegion

)

Definition at line 362 of file mitkAutoCropImageFilter.cpp.

virtual void mitk::AutoCropImageFilter::SetMarginFactor ( float  _arg )

virtual

Member Data Documentation

float mitk::AutoCropImageFilter::m_BackgroundValue

protected

Definition at line 103 of file mitkAutoCropImageFilter.h.

RegionType mitk::AutoCropImageFilter::m_CroppingRegion

protected

Definition at line 105 of file mitkAutoCropImageFilter.h.

mitk::SlicedData::RegionType mitk::AutoCropImageFilter::m_InputRequestedRegion

protected

Definition at line 117 of file mitkAutoCropImageFilter.h.

float mitk::AutoCropImageFilter::m_MarginFactor

protected

Definition at line 107 of file mitkAutoCropImageFilter.h.

bool mitk::AutoCropImageFilter::m_OverrideCroppingRegion

protected

Definition at line 120 of file mitkAutoCropImageFilter.h.

RegionType::IndexType mitk::AutoCropImageFilter::m_RegionIndex

protected

Definition at line 113 of file mitkAutoCropImageFilter.h.

RegionType::SizeType mitk::AutoCropImageFilter::m_RegionSize

protected

Definition at line 112 of file mitkAutoCropImageFilter.h.

itk::TimeStamp mitk::AutoCropImageFilter::m_TimeOfHeaderInitialization

protected

Definition at line 118 of file mitkAutoCropImageFilter.h.

mitk::ImageTimeSelector::Pointer mitk::AutoCropImageFilter::m_TimeSelector

protected

Definition at line 115 of file mitkAutoCropImageFilter.h.

---

The documentation for this class was generated from the following files:

• mitkAutoCropImageFilter.h
• mitkAutoCropImageFilter.cpp