Generic Variable-Typed Data Array. More...

#include <cmtkTypedArray.h>

Inheritance diagram for cmtk::TypedArray:

Public Types
typedef TypedArray	Self
	This class.
typedef SmartPointer< Self >	SmartPtr
	Smart pointer.
typedef SmartConstPointer< Self >	SmartConstPtr
	Smart pointer to const.
typedef double(*	FunctionTypeDouble )(const double)
	Function pointer type: double to double.
typedef float(*	FunctionTypeFloat )(const float)
	Function pointer type: float to float.
Public Member Functions
virtual bool	Get (Types::DataItem &, const size_t) const =0
	Get an item from the specified index in the data array.
virtual void	GetSequence (Types::DataItem *const values, const size_t index, const size_t length) const =0
	Get a sequence of items from the array.
virtual void	Set (const Types::DataItem, const size_t)=0
	Sets the specified array element.
virtual ScalarDataType	GetType () const =0
	Return type of stored data.
virtual size_t	GetItemSize () const =0
	Return the number of bytes per stored item.
virtual void *	GetPaddingPtr () const =0
	Get the adress of the real value used for no data present.
virtual Types::DataItem	GetPaddingValue () const =0
	Get the transfer representation of the value used for no data present.
virtual bool	PaddingDataAt (const size_t index) const =0
	Test if there is NULL data at a particular location.
virtual Types::DataItem *	GetData () const =0
	Get complete aray of data values.
virtual void	SetData (Types::DataItem *const data)=0
	Set all data from an Types::DataItem array.
virtual Self::SmartPtr	Convert (const ScalarDataType dtype) const =0
	Convert to typed array of any given template type.
virtual void *	ConvertSubArray (const ScalarDataType dtype, const size_t fromIdx, const size_t len) const =0
	Convert a sub-array to any given primitive data type.
virtual void	ConvertSubArray (void *const destination, const ScalarDataType dtype, const size_t fromIdx, const size_t len) const =0
	Convert a sub-array to given primitive data type into existing array.
virtual void *	ConvertArray (const ScalarDataType dtype) const
	Convert the array to any given data type.
virtual void	ClearArray (const bool usePaddingData=false)=0
	Clear entire array.
virtual void	ChangeEndianness ()=0
	Change endianness of data.
virtual void	Rescale (const Types::DataItem scale=1, const Types::DataItem offset=0)=0
	Scale values in the array.
virtual void	RescaleAndShift (const Types::DataItem scale=1, const Types::DataItem offset=0, const size_t shiftBits=0)=0
	Scale and shift values in the array.
virtual void	RescaleToRange (const Types::DataItemRange &toRange)
	Scale values in the array to a given target range.
virtual void	GammaCorrection (const Types::DataItem gamma)=0
	Apply gamma correction.
virtual void	ApplyFunction (Self::FunctionTypeFloat f)
	Apply real function to data.
virtual void	ApplyFunction (Self::FunctionTypeDouble f)
	Apply real function to data.
virtual void	ApplyFunctionFloat (Self::FunctionTypeFloat f)=0
	Apply real function to data.
virtual void	ApplyFunctionDouble (Self::FunctionTypeDouble f)=0
	Apply real function to data.
virtual void	MakeAbsolute ()=0
	Convert all values to absolute values.
virtual void	Rescale (const Types::DataItem scale, const Types::DataItem offset, const Types::DataItem truncLo, const Types::DataItem truncHi=CMTK_ITEM_MAX)=0
	Scale values in the array with truncation boundaries.
virtual void	Threshold (const Types::DataItemRange &range)=0
	Threshold data.
virtual void	ThresholdToPadding (const Types::DataItemRange &range)=0
	Threshold data.
virtual void	PruneHistogram (const bool pruneHi, const bool pruneLo, const size_t numberOfBinsTarget, const size_t numberOfBinsInternal=1024)
	Prune histogram to trim noise.
virtual void	Binarize (const Types::DataItem threshold=0)=0
	Binarize array values with given threshold.
Self::SmartPtr	Clone () const
	Clone an existing TypedArray.
	TypedArray ()
	Default constructor.
virtual	~TypedArray ()
	Destructor.
virtual void	FreeData ()=0
	Free data pointer.
void	ReleaseDataPointer ()
	Release pointer to data array.
size_t	GetDataSize () const
	Return the number of array elements.
size_t	GetDataSizeBytes () const
	Return the array size in bytes.
virtual void *	GetDataPtr (const size_t offset=0)=0
	Return address of the data array.
virtual const void *	GetDataPtr (const size_t offset=0) const =0
	Return address of the data array.
virtual Types::DataItem *	GetSubArray (Types::DataItem *const, const size_t, const size_t, const Types::DataItem=0) const =0
	Get part of the stored array.
virtual Types::DataItem *	GetSubArray (const size_t, const size_t, const Types::DataItem=0) const =0
	Allocate memory and get part of the stored array.
bool	GetPaddingFlag () const
	Return the flag for padding data.
void	ClearPaddingFlag ()
	Clear padding flag. This effectively turns padded pixels into actual data.
virtual void	SetPaddingAt (const size_t)=0
	Set the specified array element to no data present.
virtual void	SetPaddingValue (const Types::DataItem paddingData)=0
	Select the value to mark non-existent data.
virtual void	SetPaddingPtr (const void *paddingData)=0
	Select the value to mark non-existent data.
virtual void	ReplacePaddingData (const Types::DataItem value=0)=0
	Replace Padding data (padding) with given value.
virtual bool	IsPaddingAt (const size_t index) const =0
	Check for padding data at given location.
virtual bool	IsPaddingOrZeroAt (const size_t index) const =0
	Check for padding data or zero at given location.
virtual const Types::DataItemRange	GetRange () const =0
	Calculate and return minimum and maximum data value.
virtual double	GetEntropy (const bool fractional=CMTK_HISTOGRAM_DISCRETE, const int numberOfBins=128) const =0
	Calculate entropy of distribution of values in this array.
virtual double	GetEntropy (Histogram< unsigned int > &histogram) const =0
	Calculate entropy of values in this array using existing histogram.
virtual double	GetEntropy (Histogram< double > &histogram, const bool fractional=CMTK_HISTOGRAM_DISCRETE) const =0
	Calculate entropy of values in this array using existing histogram.
virtual double	GetEntropy (Histogram< double > &histogram, const double *kernel, const size_t kernelRadius) const =0
	Calculate entropy of values in this array using existing histogram and kernel for Parzen windowing.
virtual size_t	GetStatistics (Types::DataItem &mean, Types::DataItem &variance) const =0
	Calculate statistics.
virtual Types::DataItem	GetPercentile (const Types::DataItem percentile, const size_t nBins=256) const
	Compute approximate percentile value from histogram.
virtual std::vector < Types::DataItem >	GetPercentileList (const std::vector< Types::DataItem > &percentileList, const size_t nBins=256) const
	Compute list of approximate percentile values from histogram.
virtual Histogram< unsigned int >::SmartPtr	GetHistogram (const unsigned int numberOfBins, const bool centeredBins=false) const =0
	Get data histogram.
virtual void	BlockSet (const Types::DataItem value, const size_t fromOffset, const size_t toOffset)=0
	Set data block to constant value.
virtual void	Fill (const Types::DataItem value)
	Fill entire array with one value.
virtual void	BlockCopy (Self &target, const size_t toOffset, const size_t fromOffset, const size_t blockLength) const
	Copy data block to other array.
virtual void	BlockSwap (const size_t fromOffset, const size_t toOffset, const size_t blockLength)
	Exchange two data blocks.
virtual void	BlockReverse (const size_t fromOffset, const size_t blockLength)
	Revert order of items in a given range.
virtual void	ApplyFunctionObject (const TypedArrayFunction &f)=0
	Apply function class to the values of this array.
Static Public Member Functions
static Self::SmartPtr	Create (const ScalarDataType dtype, void const data, const size_t size, const bool freeArray=true, const bool paddingFlag=false, const void paddingData=NULL)
	Create typed data array from existing array of values.
static Self::SmartPtr	Create (const ScalarDataType dtype, const size_t size)
	Create typed data array, allocating new memory for the items array.
static void	Free (void *const data)
	Free data allocated by this object.
Protected Member Functions
virtual void	Alloc (const size_t datasize)=0
	Allocate array for the given number of elements.
virtual Self *	CloneVirtual () const =0
	Virtual clone function: only to be calle by Clone().
Protected Attributes
ScalarDataType	m_DataType
	Scalar data type ID.
bool	FreeArray
	If not zero, the object should free the allocated array.
size_t	DataSize
	The size of the data array, i.e. the number of items allocated.
bool	PaddingFlag
	If true, PaddingFlag indicates there are items with no data present.
Private Member Functions
	cmtkGetSetMacro (DataClass, DataClass)
	Parameter defining the primitive data class.

Detailed Description

Generic Variable-Typed Data Array.

This class delivers the common interface of all variable-typed data arrays.

Author:: Torsten Rohlfing

Definition at line 76 of file cmtkTypedArray.h.

Member Typedef Documentation

typedef double(* cmtk::TypedArray::FunctionTypeDouble)(const double)

Function pointer type: double to double.

Definition at line 232 of file cmtkTypedArray.h.

typedef float(* cmtk::TypedArray::FunctionTypeFloat)(const float)

Function pointer type: float to float.

Definition at line 235 of file cmtkTypedArray.h.

typedef TypedArray cmtk::TypedArray::Self

This class.

Reimplemented in cmtk::TemplateArray< T >.

Definition at line 83 of file cmtkTypedArray.h.

typedef SmartConstPointer<Self> cmtk::TypedArray::SmartConstPtr

Smart pointer to const.

Definition at line 89 of file cmtkTypedArray.h.

typedef SmartPointer<Self> cmtk::TypedArray::SmartPtr

Smart pointer.

Reimplemented in cmtk::TemplateArray< T >.

Definition at line 86 of file cmtkTypedArray.h.

Constructor & Destructor Documentation

cmtk::TypedArray::TypedArray ( ) [inline]

Default constructor.

Definition at line 312 of file cmtkTypedArray.h.

References cmtk::DATACLASS_GREY.

virtual cmtk::TypedArray::~TypedArray ( ) [inline, virtual]

Destructor.

Just has to be declared virtual.

Definition at line 323 of file cmtkTypedArray.h.

Member Function Documentation

virtual void cmtk::TypedArray::Alloc ( const size_t datasize ) [protected, pure virtual]

Allocate array for the given number of elements.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::ApplyFunction ( Self::FunctionTypeFloat f ) [inline, virtual]

Apply real function to data.

Definition at line 238 of file cmtkTypedArray.h.

virtual void cmtk::TypedArray::ApplyFunction ( Self::FunctionTypeDouble f ) [inline, virtual]

Apply real function to data.

Definition at line 244 of file cmtkTypedArray.h.

virtual void cmtk::TypedArray::ApplyFunctionDouble ( Self::FunctionTypeDouble f ) [pure virtual]

Apply real function to data.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::ApplyFunctionFloat ( Self::FunctionTypeFloat f ) [pure virtual]

Apply real function to data.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::ApplyFunctionObject ( const TypedArrayFunction & f ) [pure virtual]

Apply function class to the values of this array.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::Binarize ( const Types::DataItem threshold = 0 ) [pure virtual]

Binarize array values with given threshold.

All values greater than threshold (default: zero) are set to one, all values smaller or equal are set to zero.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::BlockCopy	(	Self &	target,
		const size_t	toOffset,
		const size_t	fromOffset,
		const size_t	blockLength
	)		const `[inline, virtual]`

Copy data block to other array.

This is really just a convenience wrapper for ConvertSubArray().

Definition at line 476 of file cmtkTypedArray.h.

References GetDataPtr(), and GetType().

Referenced by cmtk::DataGrid::GetCroppedData(), cmtk::DataGrid::GetDataMirrored(), and cmtk::DataGrid::SetOrthoSlice().

virtual void cmtk::TypedArray::BlockSet	(	const Types::DataItem	value,
		const size_t	fromOffset,
		const size_t	toOffset
	)		`[pure virtual]`

Set data block to constant value.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::ChangeEndianness ( ) [pure virtual]

Change endianness of data.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::ClearArray ( const bool usePaddingData = false ) [pure virtual]

Clear entire array.

This method is implemented by derived template classes for better efficiency.

Parameters:

usePaddingData If this flag is set, then the array will be filled with the PaddingData value, if one exists. Otherwise, the array will be filled with the respective data type's zero value.

Implemented in cmtk::TemplateArray< T >.

void cmtk::TypedArray::ClearPaddingFlag ( ) [inline]

Clear padding flag. This effectively turns padded pixels into actual data.

Definition at line 378 of file cmtkTypedArray.h.

Self::SmartPtr cmtk::TypedArray::Clone ( ) const [inline]

Clone an existing TypedArray.

Memory is allocated and the source array copied item by item. Data is read by the source object's Get method and stored by the destination object's Set method.

Definition at line 306 of file cmtkTypedArray.h.

Referenced by cmtk::DataGridMorphologicalOperators::EliminatePaddingVoting().

virtual Self* cmtk::TypedArray::CloneVirtual ( ) const [protected, pure virtual]

Virtual clone function: only to be calle by Clone().

Implemented in cmtk::TemplateArray< T >.

cmtk::TypedArray::cmtkGetSetMacro	(	DataClass	,
		DataClass
	)		`[private]`

Parameter defining the primitive data class.

virtual Self::SmartPtr cmtk::TypedArray::Convert ( const ScalarDataType dtype ) const [pure virtual]

Convert to typed array of any given template type.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::VoxelMatchingMetric_Type< T, DT >::ImageData::Init().

virtual void* cmtk::TypedArray::ConvertArray ( const ScalarDataType dtype ) const [inline, virtual]

Convert the array to any given data type.

This function uses ConvertSubArray to convert the complete array.

Returns:: Newly allocated memory of given type. Caller is responsible for freeing this memory with a call to Memory::DeleteArray().

See also:: ConvertSubArray

Definition at line 191 of file cmtkTypedArray.h.

virtual void* cmtk::TypedArray::ConvertSubArray	(	const ScalarDataType	dtype,
		const size_t	fromIdx,
		const size_t	len
	)		const `[pure virtual]`

Convert a sub-array to any given primitive data type.

Returns:: Newly allocated memory of given type. Caller is responsible for freeing this memory with a call to Memory::DeleteArray().

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::ScalarImage::ScalarImage().

virtual void cmtk::TypedArray::ConvertSubArray	(	void *const	destination,
		const ScalarDataType	dtype,
		const size_t	fromIdx,
		const size_t	len
	)		const `[pure virtual]`

Convert a sub-array to given primitive data type into existing array.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::Fill ( const Types::DataItem value ) [inline, virtual]

Fill entire array with one value.

Definition at line 468 of file cmtkTypedArray.h.

static void cmtk::TypedArray::Free ( void *const data ) [inline, static]

Free data allocated by this object.

Definition at line 116 of file cmtkTypedArray.h.

virtual void cmtk::TypedArray::FreeData ( ) [pure virtual]

Free data pointer.

Derived classes may have to overload this method to take care of other memory management libraries.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::GammaCorrection ( const Types::DataItem gamma ) [pure virtual]

Apply gamma correction.

Parameters:

gamma The gamma correction coefficient.

Implemented in cmtk::TemplateArray< T >.

virtual bool cmtk::TypedArray::Get	(	Types::DataItem &	,
		const	size_t
	)		const `[pure virtual]`

Get an item from the specified index in the data array.

If there is no valid data present at the given index, zero is returned and the resulting item is zero, too. This can only happen if PaddingFlag is not zero.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::ImageOperationReplace::Apply(), cmtk::ScalarImage::ApplyBinaryMask(), cmtk::DataGrid::AutoCrop(), cmtk::UniformDistanceMap< TDistanceDataType >::BuildDistanceMap(), cmtk::FilterVolume::ComputeNLWithinWindow(), cmtk::DataGrid::ComputeProjection(), cmtk::GroupwiseRegistrationFunctionalBase::CopyTemplateData(), cmtk::FilterVolume::CoupeFilter(), cmtk::FilterVolume::GaussianFilter(), cmtk::TypedArraySimilarity::GetCorrelationRatio(), cmtk::FilterVolume::GetCoupeBlock(), cmtk::TypedArraySimilarity::GetCrossCorrelation(), cmtk::Image::GetDataAt(), cmtk::DataGridFilter::GetDataMedianFiltered(), cmtk::DataGridFilter::GetDataSobelFiltered(), cmtk::TypedArraySimilarity::GetDifferenceArray(), cmtk::DataGrid::GetDownsampledAndAveraged(), cmtk::HypothesisTests::GetGeneticCovariance(), cmtk::HypothesisTests::GetHeritability(), cmtk::TypedArraySimilarity::GetMinusMeanSquaredDifference(), cmtk::TypedArraySimilarity::GetMutualInformation(), cmtk::TypedArraySimilarity::GetNormalizedMutualInformation(), cmtk::HypothesisTests::GetOneSampleTTest(), cmtk::TypedArraySimilarity::GetOptimalScale(), cmtk::HypothesisTests::GetPairedCorrelation(), cmtk::HypothesisTests::GetPairedTwoTailedTTest(), cmtk::ScalarImage::GetPixelAtCubic(), cmtk::ScalarImageSimilarity::GetRegionalMutualInformation(), cmtk::Volume::GetTrilinear(), cmtk::HypothesisTests::GetUnpairedTwoTailedTTest(), cmtk::HypothesisTests::GetZScores(), cmtk::VoxelMatchingMetric_Type< T, DT >::ImageData::Init(), cmtk::operator-(), cmtk::ScalarImage::operator-=(), cmtk::ReformatVolume::ReformatMasked(), cmtk::FilterVolume::RohlfingFilter(), cmtk::UniformVolumeInterpolatorBase::SetVolume(), cmtk::FilterVolume::StudholmeFilter(), cmtk::DataGrid::TrilinearInterpolation(), cmtk::TypedArrayNoiseEstimatorNaiveGaussian::TypedArrayNoiseEstimatorNaiveGaussian(), cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::UpdateTransformationFixedControlPoints(), cmtk::PGM::Write16bit(), and cmtk::GroupwiseRegistrationOutput::WriteAverageImage().

virtual Types::DataItem* cmtk::TypedArray::GetData ( ) const [pure virtual]

Get complete aray of data values.

The calling routine is responsible for de-allocating the returned array by calling 'free' after use.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::ImageOperationApplyMask::Apply(), cmtk::GroupwiseRegistrationFunctionalBase::CopyTemplateData(), cmtk::DataGridMorphologicalOperators::EliminatePaddingVoting(), cmtk::DataGridFilter::GetDataMedianFiltered(), cmtk::DataGridFilter::GetDataSobelFiltered(), cmtk::Study::ReadVolume(), cmtk::Study::UpdateFromVolume(), cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::UpdateTransformationFixedControlPoints(), cmtk::VolumeInjectionReconstruction::VolumeInjectionReconstruction(), cmtk::VolumeFromFile::WriteAnalyzeHdr(), cmtk::GroupwiseRegistrationOutput::WriteAverageImage(), and cmtk::VolumeFromFile::WriteNifti().

virtual void* cmtk::TypedArray::GetDataPtr ( const size_t offset = 0 ) [pure virtual]

Return address of the data array.

Returns:: A pointer to the real data array.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::Colormap::Apply(), BlockCopy(), cmtk::DataGrid::ExtractSliceVirtual(), cmtk::DataGrid::GetOrthoSlice(), cmtk::DataGrid::GetReoriented(), cmtk::ScalarImageIO::WriteAnalyze(), cmtk::VolumeFromFile::WriteAnalyzeHdr(), cmtk::VolumeFromFile::WriteMetaImage(), and cmtk::VolumeFromFile::WriteNifti().

virtual const void* cmtk::TypedArray::GetDataPtr ( const size_t offset = 0 ) const [pure virtual]

Return address of the data array.

Returns:: A pointer to the real data array.

Implemented in cmtk::TemplateArray< T >.

size_t cmtk::TypedArray::GetDataSize ( ) const [inline]

Return the number of array elements.

Returns:: The number of array elements

Definition at line 342 of file cmtkTypedArray.h.

size_t cmtk::TypedArray::GetDataSizeBytes ( ) const [inline]

Return the array size in bytes.

Definition at line 346 of file cmtkTypedArray.h.

virtual double cmtk::TypedArray::GetEntropy	(	Histogram< double > &	histogram,
		const bool	fractional = `CMTK_HISTOGRAM_DISCRETE`
	)		const `[pure virtual]`

Calculate entropy of values in this array using existing histogram.

See also:: TypedArray::GetEntropy

Implemented in cmtk::TemplateArray< T >.

virtual double cmtk::TypedArray::GetEntropy	(	const bool	fractional = `CMTK_HISTOGRAM_DISCRETE`,
		const int	numberOfBins = `128`
	)		const `[pure virtual]`

Calculate entropy of distribution of values in this array.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::VolumeInjectionReconstruction::SetupHistogramKernels().

virtual double cmtk::TypedArray::GetEntropy ( Histogram< unsigned int > & histogram ) const [pure virtual]

Calculate entropy of values in this array using existing histogram.

By using an already existing histogram, this function ensures that the same numbers and sizes of bins are used for repeated calls of this function, even when the actual data in this array has changed. On the other hand, there is of course a risk that the data may have changed in such a way that the old histogram arrangement does not fit it anymore.

In the process of entropy computation, the histogram is also filled with the data from this array. It is therefore available for subsequent operations after returning from this function.

Implemented in cmtk::TemplateArray< T >.

virtual double cmtk::TypedArray::GetEntropy	(	Histogram< double > &	histogram,
		const double *	kernel,
		const size_t	kernelRadius
	)		const `[pure virtual]`

Calculate entropy of values in this array using existing histogram and kernel for Parzen windowing.

See also:: TypedArray::GetEntropy

Implemented in cmtk::TemplateArray< T >.

virtual Histogram<unsigned int>::SmartPtr cmtk::TypedArray::GetHistogram	(	const unsigned int	numberOfBins,
		const bool	centeredBins = `false`
	)		const `[pure virtual]`

Get data histogram.

Returns:: A histogram object filled with the relative frequencies of values in this array.

Parameters:

numberOfBins	Number of histogram bins
centeredBins	Flag for bins centered around the samples

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::TypedArrayFunctionHistogramEqualization::TypedArrayFunctionHistogramEqualization(), cmtk::TypedArrayFunctionHistogramMatching::TypedArrayFunctionHistogramMatching(), cmtk::TypedArrayNoiseEstimatorBrummer::TypedArrayNoiseEstimatorBrummer(), cmtk::TypedArrayNoiseEstimatorMaximumLikelihood::TypedArrayNoiseEstimatorMaximumLikelihood(), and cmtk::TypedArrayNoiseEstimatorNaiveGaussian::TypedArrayNoiseEstimatorNaiveGaussian().

virtual size_t cmtk::TypedArray::GetItemSize ( ) const [pure virtual]

Return the number of bytes per stored item.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::DataGrid::ExtractSliceVirtual(), cmtk::DataGrid::GetOrthoSlice(), cmtk::DataGrid::GetReoriented(), cmtk::ScalarImageIO::WriteAnalyze(), cmtk::VolumeFromFile::WriteAnalyzeHdr(), cmtk::VolumeFromFile::WriteMetaImage(), and cmtk::VolumeFromFile::WriteNifti().

bool cmtk::TypedArray::GetPaddingFlag ( ) const [inline]

Return the flag for padding data.

Returns:: If return value is zero, all data stored in the array is valid. A non-zero value indicates, that there are locations with no data present.

Definition at line 375 of file cmtkTypedArray.h.

Referenced by cmtk::Colormap::Apply(), cmtk::DataGridMorphologicalOperators::EliminatePaddingVoting(), cmtk::ImageToImageRGB::Execute(), cmtk::DataGrid::ExtractSliceVirtual(), cmtk::DataGrid::GetOrthoSlice(), cmtk::DataGrid::GetReoriented(), cmtk::VoxelMatchingMetric_Type< T, DT >::ImageData::Init(), cmtk::UniformVolume::Resample(), and cmtk::ScalarImage::ScalarImage().

virtual void* cmtk::TypedArray::GetPaddingPtr ( ) const [pure virtual]

Get the adress of the real value used for no data present.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::Colormap::Apply(), and cmtk::ScalarImage::ScalarImage().

virtual Types::DataItem cmtk::TypedArray::GetPaddingValue ( ) const [pure virtual]

Get the transfer representation of the value used for no data present.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::DataGridMorphologicalOperators::EliminatePaddingVoting(), cmtk::DataGrid::ExtractSliceVirtual(), cmtk::DataGrid::GetOrthoSlice(), cmtk::DataGrid::GetReoriented(), cmtk::VoxelMatchingMetric_Type< T, DT >::ImageData::Init(), and cmtk::UniformVolume::Resample().

virtual const Types::DataItemRange cmtk::TypedArray::GetRange ( ) const [pure virtual]

Calculate and return minimum and maximum data value.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::TypedArraySimilarity::GetCorrelationRatio(), cmtk::TypedArraySimilarity::GetMutualInformation(), cmtk::TypedArraySimilarity::GetNormalizedMutualInformation(), cmtk::TypedArraySimilarity::GetPeakSignalToNoiseRatio(), cmtk::TypedArraySimilarityMemory::GetRangeX(), cmtk::TypedArraySimilarityMemory::GetRangeY(), cmtk::VolumeIO::Read(), cmtk::Study::ReadVolume(), cmtk::FilterVolume::RohlfingFilter(), cmtk::VolumeInjectionReconstruction::SetupHistogramKernels(), cmtk::FilterVolume::StudholmeFilter(), cmtk::TypedArrayFunctionHistogramEqualization::TypedArrayFunctionHistogramEqualization(), cmtk::Study::UpdateFromVolume(), cmtk::ImageSymmetryPlaneCommandLineBase::WriteAligned(), cmtk::ScalarImageIO::WriteAnalyze(), cmtk::VolumeFromFile::WriteAnalyzeHdr(), and cmtk::VolumeFromFile::WriteNifti().

virtual void cmtk::TypedArray::GetSequence	(	Types::DataItem *const	values,
		const size_t	index,
		const size_t	length
	)		const `[pure virtual]`

Get a sequence of items from the array.

Parameters:

values	This must point to an allocated array of at least as many Types::DataItem objects as given in the "length" parameter.
index	The index of the item to retrieve. Valid values are in the range [0..Datasize()-1].
length	Number of consecutive values to get.

Implemented in cmtk::TemplateArray< T >.

virtual size_t cmtk::TypedArray::GetStatistics	(	Types::DataItem &	mean,
		Types::DataItem &	variance
	)		const `[pure virtual]`

Calculate statistics.

Results will be both zero if there is not data in the array.

Returns:: The number of valid (i.e., non-padding) values that constitute the given results.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::TypedArraySimilarity::GetCorrelationRatio(), cmtk::TypedArraySimilarity::GetCrossCorrelation(), and cmtk::QtWindowLevelControls::slotSetStudy().

virtual Types::DataItem* cmtk::TypedArray::GetSubArray	(	Types::DataItem *	const,
		const	size_t,
		const	size_t,
		const Types::DataItem	= `0`
	)		const `[pure virtual]`

Get part of the stored array.

Returns:: A pointer to the buffer given is returned.

Implemented in cmtk::TemplateArray< T >.

virtual Types::DataItem* cmtk::TypedArray::GetSubArray	(	const	size_t,
		const	size_t,
		const Types::DataItem	= `0`
	)		const `[pure virtual]`

Allocate memory and get part of the stored array.

Returns:: A pointer to the newly allocated buffer is returned.

Implemented in cmtk::TemplateArray< T >.

virtual ScalarDataType cmtk::TypedArray::GetType ( ) const [pure virtual]

Return type of stored data.

Implemented in cmtk::TemplateArray< T >.

virtual bool cmtk::TypedArray::IsPaddingAt ( const size_t index ) const [pure virtual]

Check for padding data at given location.

Implemented in cmtk::TemplateArray< T >.

virtual bool cmtk::TypedArray::IsPaddingOrZeroAt ( const size_t index ) const [pure virtual]

Check for padding data or zero at given location.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::ImageOperationApplyMask::Apply().

virtual void cmtk::TypedArray::MakeAbsolute ( ) [pure virtual]

Convert all values to absolute values.

Implemented in cmtk::TemplateArray< T >.

virtual bool cmtk::TypedArray::PaddingDataAt ( const size_t index ) const [pure virtual]

Test if there is NULL data at a particular location.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::DataGridMorphologicalOperators::EliminatePaddingVoting(), and cmtk::ImageToImageRGB::MarkPaddingData().

void cmtk::TypedArray::ReleaseDataPointer ( ) [inline]

Release pointer to data array.

The pointer must remain valid until object is destructed itself.

Definition at line 334 of file cmtkTypedArray.h.

virtual void cmtk::TypedArray::ReplacePaddingData ( const Types::DataItem value = 0 ) [pure virtual]

Replace Padding data (padding) with given value.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::ImageOperationReplace::Apply().

virtual void cmtk::TypedArray::Rescale	(	const Types::DataItem	scale,
		const Types::DataItem	offset,
		const Types::DataItem	truncLo,
		const Types::DataItem	truncHi = `CMTK_ITEM_MAX`
	)		`[pure virtual]`

Scale values in the array with truncation boundaries.

A call to this member function will perform an in-place rescaling of the values in the array with value range truncation. Truncation takes place after the scaling itself, i.e., the truncation boundaries refer to the already scaled values.

Parameters:

scale	The original data value is multiplied by the parameter first.
offset	This value is added to the original data value after multiplying it by the scale parameter.
truncLo	Lower truncation boundary. Scaled items below this threshold will be set to equal its value.
truncHi	Upper truncation boundary. Scaled items above this threshold will be set to equal its value.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::Rescale	(	const Types::DataItem	scale = `1`,
		const Types::DataItem	offset = `0`
	)		`[pure virtual]`

Scale values in the array.

A call to this member function will perform an in-place rescaling of the values in the array.

Parameters:

scale	The original data value is multiplied by the parameter first.
offset	This value is added to the original data value after multiplying it by the scale parameter.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::RescaleAndShift	(	const Types::DataItem	scale = `1`,
		const Types::DataItem	offset = `0`,
		const size_t	shiftBits = `0`
	)		`[pure virtual]`

Scale and shift values in the array.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::Set	(	const Types::DataItem	,
		const	size_t
	)		`[pure virtual]`

Sets the specified array element.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::ImageOperationReplace::Apply(), cmtk::ScalarImage::InterpolateFrom(), and cmtk::ScalarImage::operator-=().

virtual void cmtk::TypedArray::SetData ( Types::DataItem *const data ) [pure virtual]

Set all data from an Types::DataItem array.

This function sets all values stored in the present array from a memory region with Types::DataItem values.

Parameters:

data	Pointer to an array of Types::DataItem values. Control over the source array is not taken by this object. If it is on the heap, then the calling routine remains responsible for de-allocating the array afterwards.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::SetPaddingAt ( const size_t ) [pure virtual]

Set the specified array element to no data present.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::ScalarImage::InterpolateFrom(), and cmtk::ScalarImage::operator-=().

virtual void cmtk::TypedArray::SetPaddingPtr ( const void * paddingData ) [pure virtual]

Select the value to mark non-existent data.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::SetPaddingValue ( const Types::DataItem paddingData ) [pure virtual]

Select the value to mark non-existent data.

Implemented in cmtk::TemplateArray< T >.

Referenced by cmtk::DataGrid::GetReoriented().

virtual void cmtk::TypedArray::Threshold ( const Types::DataItemRange & range ) [pure virtual]

Threshold data.

All values above upper threshold are set to upper thrershold. All values below lower threshold are set to lower threshold.

Implemented in cmtk::TemplateArray< T >.

virtual void cmtk::TypedArray::ThresholdToPadding ( const Types::DataItemRange & range ) [pure virtual]

Threshold data.

All values outside the threshold range are set to the Padding (padding) value.

Implemented in cmtk::TemplateArray< T >.

Member Data Documentation

size_t cmtk::TypedArray::DataSize [protected]

The size of the data array, i.e. the number of items allocated.

Definition at line 509 of file cmtkTypedArray.h.

bool cmtk::TypedArray::FreeArray [protected]

If not zero, the object should free the allocated array.

Definition at line 506 of file cmtkTypedArray.h.

ScalarDataType cmtk::TypedArray::m_DataType [protected]

Scalar data type ID.

This field is not yet actually used anywhere. It merely serves a debugging purpose since it allows easy identification of the type of this array from inspecting its data.

Definition at line 503 of file cmtkTypedArray.h.

bool cmtk::TypedArray::PaddingFlag [protected]

If true, PaddingFlag indicates there are items with no data present.

Definition at line 513 of file cmtkTypedArray.h.

Referenced by cmtk::TemplateArray< T >::CloneVirtual().

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