Some basic utility functions. More...

#include <algorithm>
#include <functional>
#include <cmath>
#include "itkImage.h"
#include "itkImageRegionConstIterator.h"
#include "itkImageRegionConstIteratorWithIndex.h"
#include "itkImageRegionIterator.h"
#include "itkHistogramMatchingImageFilter.h"
#include "itkAdaptiveHistogramEqualizationImageFilter.h"
#include "itkConnectedThresholdImageFilter.h"
#include "itkOrientImageFilter.h"
#include "itkResampleImageFilter.h"
#include "itkIdentityTransform.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkBSplineInterpolateImageFunction.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
#include "itkTestingComparisonImageFilter.h"
#include "itkStripTsImageFilter.h"
#include "itkMaskImageFilter.h"
#include "cbicaUtilities.h"
#include "cbicaITKImageInfo.h"
#include "gdcmMD5.h"
#include "gdcmReader.h"
#include "DicomIOManager.h"

Include dependency graph for cbicaITKUtilities.h:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Typedefs
using	ImageTypeFloat3D = itk::Image< float, 3 >

Enumerations
enum	DeformRegType { Demons, DiffeomorphicDemons, SymmetricForcesDemons, FastSymmetricForcesDemons }

enum	InterpolatorType { Linear, NearestNeighbor, BSpline }

Functions
template<class TImageType = ImageTypeFloat3D>
TImageType::Pointer	ChangeImageValues (const typename TImageType::Pointer inputImage, const std::string &oldValues, const std::string &newValues)
	Create an empty (optionally pass a value) ITK image based on an input image with same properties. More...

template<class TImageType = ImageTypeFloat3D>
TImageType::Pointer	CreateImage (const typename TImageType::Pointer inputImage, const typename TImageType::PixelType value=0)
	Create an empty (optionally pass a value) ITK image based on an input image with same properties. More...

template<class TImageType = ImageTypeFloat3D>
std::vector< std::vector< typename TImageType::IndexType > >	CreateMaskIndeces (const std::vector< std::vector< typename TImageType::Pointer > > &inputModalitiesAndImages)
	Calculate and preserve the mask indeces. More...

template<typename TImageType = ImageTypeFloat3D>
std::vector< typename TImageType::PixelType >	ExtractPixelValuesFromIndeces (const typename TImageType::Pointer inputImage, const std::vector< typename TImageType::IndexType > &indeces)
	Wrap of GetPixelValues.

template<typename TImageType = ImageTypeFloat3D>
TImageType::Pointer	GetAdaptiveHistogramEqualizedImage (const typename TImageType::Pointer inputImage, const typename TImageType::Pointer referenceImage, const float alpha=0.3, const float beta=0.3, const float radius=1, const int numberOfHistogramLevels=100)
	Get the indeces of the image which are not zero. More...

template<class TImageType = ImageTypeFloat3D>
float	GetDistanceBetweenIndeces (const typename TImageType::IndexType point1, const typename TImageType::IndexType point2)
	Get the distance between 2 indeces of an itk::Image.

float	GetDistanceBetweenIndeces (const float point1, const float point2)
	Get the distance between 2 itk::P of an itk::Image.

template<typename TImageType = ImageTypeFloat3D>
itk::Vector< float, TImageType::ImageDimension >	GetDistances (const typename TImageType::Pointer inputImage)
	Get distances in world coordinates across axes for an image. More...

template<typename TImageType = ImageTypeFloat3D>
TImageType::Pointer	GetHistogramMatchedImage (const typename TImageType::Pointer inputImage, const typename TImageType::Pointer referenceImage, const int numberOfMatchPoints=40, const int numberOfHistogramLevels=100)
	Get the indeces of the image which are not zero. More...

template<class TImageType = ImageTypeFloat3D>
std::pair< std::string, typename TImageType::Pointer >	GetImageOrientation (const typename TImageType::Pointer inputImage)
	Perform the deformable registration. More...

template<typename TImageType = ImageTypeFloat3D>
std::vector< typename TImageType::IndexType >	GetIndexFromNonZeroPixels (const typename TImageType::Pointer inputImage, const std::string valuesToExclude="0")
	Get MD5 sum of a supplied file. More...

template<class TImageType = ImageTypeFloat3D>
std::pair< float, typename TImageType::IndexType >	GetMaxDistanceInLabelMap (const typename TImageType::Pointer inputLabelMap, const typename TImageType::IndexType indexForComputation, bool realCoordinateInput=false, bool realCoordinateOutput=false)
	Get the maximum distance and corresponding coordinate from a seed point in a label map. More...

template<class TImageType = ImageTypeFloat3D>
std::vector< typename TImageType::IndexType >	GetNonZeroIndeces (typename TImageType::Pointer inputImage)
	Get Non-zero indeces of image.

template<typename TImageType = ImageTypeFloat3D>
std::vector< typename TImageType::PixelType >	GetPixelValuesFromIndeces (const typename TImageType::Pointer inputImage, const std::vector< typename TImageType::IndexType > &indeces)
	Get Pixel Values of specified indeces of input Image. More...

template<class TImageType = ImageTypeFloat3D>
bool	GetResultOfImageComparasion (const typename TImageType::Pointer referenceImage, const typename TImageType::Pointer checkImage, const typename TImageType::PixelType differenceThreshold=0, const unsigned int toleranceRadius=0, const unsigned long long numberOfPixelsTolerance=10, const typename TImageType::PixelType averageIntensityDifference=0)
	Get result of Image comparison between 2 images. More...

template<class TImageType = ImageTypeFloat3D, class TAtlasImageType = TImageType, class TAtlasLabelType = TImageType>
TImageType::Pointer	GetSkullStrippedImage (const typename TImageType::Pointer inputImage, const typename TAtlasImageType::Pointer atlasImage, const typename TAtlasLabelType::Pointer atlasLabelImage)
	Get skull stripped image. More...

template<class TImageType = ImageTypeFloat3D>
std::vector< typename TImageType::PixelType >	GetUniqueValuesInImage (typename TImageType::Pointer inputImage, bool sortResult=true)
	Get the unique values in an image. More...

template<typename TImageType >
bool	ImageSanityCheck (const typename TImageType::Pointer image1, const typename TImageType::Pointer image2)
	Check properties of 2 images to see if they are defined in the same space.

bool	ImageSanityCheck (const std::string &image1, const std::string &image2)
	Check properties of 2 images to see if they are defined in the same space. More...

template<class TImageType = ImageTypeFloat3D>
TImageType::Pointer	ResampleImage (const typename TImageType::Pointer inputImage, const itk::Vector< double, TImageType::ImageDimension > &outputSpacing, const std::string interpolator="Linear")
	Resample an image to an isotropic resolution using the specified output spacing vector. More...

template<class TImageType = ImageTypeFloat3D>
TImageType::Pointer	ResampleImage (const typename TImageType::Pointer inputImage, const typename TImageType::SpacingType outputSpacing, typename TImageType::SizeType outputSize, const std::string interpolator="Linear")
	Resample an image to an isotropic resolution using the specified output spacing vector. More...

template<class TImageType = ImageTypeFloat3D>
TImageType::Pointer	ResampleImage (const typename TImageType::Pointer inputImage, const float outputSpacing=1.0, const std::string interpolator="Linear")
	Resample an image to an isotropic resolution using the specified output spacing. More...

template<class TImageType = ImageTypeFloat3D>
TImageType::Pointer	ResizeImage (const typename TImageType::Pointer inputImage, const size_t resizeFactor, const std::string &interpolator="Linear")
	Resize an input image by a factor (expressed as a percentage) More...

Detailed Description

Some basic utility functions.

Dependecies: ITK (module_review, module_skullstrip enabled), OpenMP

https://www.cbica.upenn.edu/sbia/software/
softw.nosp@m.are@.nosp@m.cbica.nosp@m..upe.nosp@m.nn.ed.nosp@m.u

Copyright (c) 2015 University of Pennsylvania. All rights reserved.
See COPYING file or https://www.cbica.upenn.edu/sbia/software/license.html

Function Documentation

◆ ChangeImageValues()

TImageType::Pointer cbica::ChangeImageValues	(	const typename TImageType::Pointer	inputImage,
		const std::string &	oldValues,
		const std::string &	newValues
	)

Create an empty (optionally pass a value) ITK image based on an input image with same properties.

Parameters

inputImage	The image to base the output on
oldValues	Values separated by 'x'
newValues	Values separated by 'x'

References cbica::ChangeImageValues(), and cbica::stringSplit().

Referenced by cbica::ChangeImageValues().

◆ CreateImage()

TImageType::Pointer cbica::CreateImage	(	const typename TImageType::Pointer	inputImage,
		const typename TImageType::PixelType	value = `0`
	)

Create an empty (optionally pass a value) ITK image based on an input image with same properties.

Parameters

inputImage	The image to base the output on
value	The value to populate the new image with; defaults to '0'

References cbica::CreateImage().

Referenced by cbica::CreateImage().

◆ CreateMaskIndeces()

std::vector< std::vector< typename TImageType::IndexType > > cbica::CreateMaskIndeces ( const std::vector< std::vector< typename TImageType::Pointer > > & inputModalitiesAndImages )

Calculate and preserve the mask indeces.

Parameters

inputModalitiesAndImages A collection of images which are stored in a per-modality basis (each entry corresponds to a subject, whose entries contain different modalities)

Returns: A collection of indeces which constitute the non-zero locations per modality (each entry corresponds to a subject, which contains the locations of non-zero pixel values for all modalities)

References cbica::CreateMaskIndeces().

Referenced by cbica::CreateMaskIndeces().

◆ GetAdaptiveHistogramEqualizedImage()

TImageType::Pointer cbica::GetAdaptiveHistogramEqualizedImage	(	const typename TImageType::Pointer	inputImage,
		const typename TImageType::Pointer	referenceImage,
		const float	alpha = `0.3`,
		const float	beta = `0.3`,
		const float	radius = `1`,
		const int	numberOfHistogramLevels = `100`
	)

Get the indeces of the image which are not zero.

Parameters

inputImage	The input image on which the matching needs to be done
referenceImage	The reference image based on which the
alpha	Ranges between 0-1; with 1 giving result same as input image and lower values behaving as unsharp filters; default = 0.3
beta	Ranges between 0-1; with 1 giving result same as input image and lower values behaving as unsharp filters; default = 0.3
radius	Ranges between 1-10 with default = 1

References cbica::GetAdaptiveHistogramEqualizedImage().

Referenced by cbica::GetAdaptiveHistogramEqualizedImage().

◆ GetDistances()

itk::Vector< float, TImageType::ImageDimension > cbica::GetDistances ( const typename TImageType::Pointer inputImage )

Get distances in world coordinates across axes for an image.

Parameters

inputImage

References cbica::GetDistances().

Referenced by cbica::GetDistances().

◆ GetHistogramMatchedImage()

TImageType::Pointer cbica::GetHistogramMatchedImage	(	const typename TImageType::Pointer	inputImage,
		const typename TImageType::Pointer	referenceImage,
		const int	numberOfMatchPoints = `40`,
		const int	numberOfHistogramLevels = `100`
	)

Get the indeces of the image which are not zero.

Parameters

inputImage	The input image on which the matching needs to be done
referenceImage	The reference image based on which the
numberOfMatchPoints	Governs the number of quantile values to be matched
numberOfHistogramLevels	Sets the number of bins used when creating histograms of the source and reference images

References cbica::GetHistogramMatchedImage().

Referenced by cbica::GetHistogramMatchedImage().

◆ GetImageOrientation()

std::pair< std::string, typename TImageType::Pointer > cbica::GetImageOrientation ( const typename TImageType::Pointer inputImage )

Perform the deformable registration.

Parameters

movingImage	The moving image for registration
referenceImage	The reference image for registration
multiResLevels	Number of multi-resolution levels for registration, defaults to 5
iterationStart	Start size of iteration for first multiResLevel, defaults to 10
iterationStep	Step size of the iterations increasing over each MultiResLevel, defaults to 10
iterationEnd	End size of iteration for first multiResLevel, defaults to 50
regType	The type of registration to perform, defaults to 'Demons'
interpolatorType	The type of interpolator to use, defaults to 'Linear'Get the image orientation
inputImage	The input image

Returns: A pair of string (which represents the orientation) and an itk::Image which represents the inputImage in RAI form

References cbica::GetImageOrientation().

Referenced by cbica::GetImageOrientation().

◆ GetIndexFromNonZeroPixels()

std::vector< typename TImageType::IndexType > cbica::GetIndexFromNonZeroPixels	(	const typename TImageType::Pointer	inputImage,
		const std::string	valuesToExclude = `"0"`
	)

Get MD5 sum of a supplied file.

Parameters

fileName The input file

Returns: The MD5 checksumWrap of GetMD5Sum()Get the indeces of the image which are not zero

References cbica::GetIndexFromNonZeroPixels().

Referenced by cbica::GetIndexFromNonZeroPixels().

◆ GetMaxDistanceInLabelMap()

std::pair< float, typename TImageType::IndexType > cbica::GetMaxDistanceInLabelMap	(	const typename TImageType::Pointer	inputLabelMap,
		const typename TImageType::IndexType	indexForComputation,
		bool	realCoordinateInput = `false`,
		bool	realCoordinateOutput = `false`
	)

Get the maximum distance and corresponding coordinate from a seed point in a label map.

Parameters

inputLabelMap	The label map on which to do the calculation
indexForComputation	The index of the seed point from where to do the distance measurements
realCoordinatesPassed	Bool which denotes if indexForComputation is real (e.g. the tumorPoints used by GLISTR) or an image index

Returns: The maximum distance and the corrensponding index

References cbica::GetMaxDistanceInLabelMap().

Referenced by cbica::GetMaxDistanceInLabelMap().

◆ GetPixelValuesFromIndeces()

std::vector< typename TImageType::PixelType > cbica::GetPixelValuesFromIndeces	(	const typename TImageType::Pointer	inputImage,
		const std::vector< typename TImageType::IndexType > &	indeces
	)

Get Pixel Values of specified indeces of input Image.

Parameters

inputImage	The input image in itk::Image format
indeced	The indeces from which pixel values need to be extracted

Returns: Vector of values whose data type is the same as image type

References cbica::GetPixelValuesFromIndeces().

Referenced by cbica::GetPixelValuesFromIndeces().

◆ GetResultOfImageComparasion()

bool cbica::GetResultOfImageComparasion	(	const typename TImageType::Pointer	referenceImage,
		const typename TImageType::Pointer	checkImage,
		const typename TImageType::PixelType	differenceThreshold = `0`,
		const unsigned int	toleranceRadius = `0`,
		const unsigned long long	numberOfPixelsTolerance = `10`,
		const typename TImageType::PixelType	averageIntensityDifference = `0`
	)

Get result of Image comparison between 2 images.

This runs itk::Testing::ComparisonImageFilter inside so the inputs are identical. Always updates the largest possible region.

Parameters

referenceImage	The reference image for comparison
checkImage	The image to check
differenceThreshold	The minimum number of different pixels among both images; default is 0
toleranceRadius	The maximum distance to look for a matching pixel; default is 0
numberOfPixelsTolerance	The maximum maximum number of pixels that can be different; default is 10
averageIntensityDifference	The maximum allowed average intensity difference between both images; default is 0

Returns: True if images are similar in accordance with passed parameters

References cbica::GetResultOfImageComparasion().

Referenced by cbica::GetResultOfImageComparasion().

◆ GetSkullStrippedImage()

TImageType::Pointer cbica::GetSkullStrippedImage	(	const typename TImageType::Pointer	inputImage,
		const typename TAtlasImageType::Pointer	atlasImage,
		const typename TAtlasLabelType::Pointer	atlasLabelImage
	)

Get skull stripped image.

Templated over InputImageType, AtlasImageType and AtlasLabelType

Parameters

inputImage	The input image on which to run the skull stripping
atlasImage	The atlas image
atlasLabelImage	The atlas label

References cbica::GetSkullStrippedImage().

Referenced by cbica::GetSkullStrippedImage().

◆ GetUniqueValuesInImage()

std::vector< typename TImageType::PixelType > cbica::GetUniqueValuesInImage	(	typename TImageType::Pointer	inputImage,
		bool	sortResult = `true`
	)

Get the unique values in an image.

Parameters

inputImage	The input image
sortResult	Whether the output should be sorted in ascending order or not, defaults to true

References cbica::GetUniqueValuesInImage().

Referenced by cbica::GetUniqueValuesInImage().

◆ ImageSanityCheck()

bool cbica::ImageSanityCheck	(	const std::string &	image1,
		const std::string &	image2
	)

inline

Check properties of 2 images to see if they are defined in the same space.

Checks are done based on cbica::ImageInfo class

References cbica::ImageSanityCheck().

◆ ResampleImage() [1/3]

TImageType::Pointer cbica::ResampleImage	(	const typename TImageType::Pointer	inputImage,
		const itk::Vector< double, TImageType::ImageDimension > &	outputSpacing,
		const std::string	interpolator = `"Linear"`
	)

Resample an image to an isotropic resolution using the specified output spacing vector.

This filter uses the example https://itk.org/Wiki/ITK/Examples/ImageProcessing/ResampleImageFilter as a base while processing time-stamped images as well

Parameters

inputImage	The input image to process
outputSpacing	The output spacing, always isotropic
interpolator	The type of interpolator to use; can be Linear, BSpline or NearestNeighbor

Returns: The resized image

References cbica::ResampleImage().

Referenced by cbica::ResampleImage().

◆ ResampleImage() [2/3]

TImageType::Pointer cbica::ResampleImage	(	const typename TImageType::Pointer	inputImage,
		const typename TImageType::SpacingType	outputSpacing,
		typename TImageType::SizeType	outputSize,
		const std::string	interpolator = `"Linear"`
	)

Resample an image to an isotropic resolution using the specified output spacing vector.

This filter uses the example https://itk.org/Wiki/ITK/Examples/ImageProcessing/ResampleImageFilter as a base while processing time-stamped images as well

Parameters

inputImage	The input image to process
outputSpacing	The output spacing, always isotropic
interpolator	The type of interpolator to use; can be Linear, BSpline or NearestNeighbor

Returns: The resized image

References cbica::ResampleImage().

◆ ResampleImage() [3/3]

TImageType::Pointer cbica::ResampleImage	(	const typename TImageType::Pointer	inputImage,
		const float	outputSpacing = `1.0`,
		const std::string	interpolator = `"Linear"`
	)

Resample an image to an isotropic resolution using the specified output spacing.

This filter uses the example https://itk.org/Wiki/ITK/Examples/ImageProcessing/ResampleImageFilter as a base while processing time-stamped images as well

Parameters

inputImage	The input image to process
outputSpacing	The output spacing, always isotropic
interpolator	The type of interpolator to use; can be Linear, BSpline or NearestNeighbor

Returns: The resized image

References cbica::ResampleImage().

◆ ResizeImage()

TImageType::Pointer cbica::ResizeImage	(	const typename TImageType::Pointer	inputImage,
		const size_t	resizeFactor,
		const std::string &	interpolator = `"Linear"`
	)

Resize an input image by a factor (expressed as a percentage)

This filter uses the example https://itk.org/Wiki/ITK/Examples/ImageProcessing/ResampleImageFilter as a base while processing time-stamped images as well

Parameters

inputImage	The input image to process
resizeFactor	The resize factor; can be greater than 100 (which causes an expanded image to be written) but can never be less than zero
interpolator	The type of interpolator to use; can be Linear, BSpline, BiCubic or NearestNeighbor

Returns: The resized image

References cbica::ResizeImage().

Referenced by cbica::ResizeImage().

Typedefs

Enumerations

Functions

Detailed Description

Function Documentation

◆ ChangeImageValues()

◆ CreateImage()

◆ CreateMaskIndeces()

◆ GetAdaptiveHistogramEqualizedImage()

◆ GetDistances()

◆ GetHistogramMatchedImage()

◆ GetImageOrientation()

◆ GetIndexFromNonZeroPixels()

◆ GetMaxDistanceInLabelMap()

◆ GetPixelValuesFromIndeces()

◆ GetResultOfImageComparasion()

◆ GetSkullStrippedImage()

◆ GetUniqueValuesInImage()

◆ ImageSanityCheck()

◆ ResampleImage() [1/3]

◆ ResampleImage() [2/3]

◆ ResampleImage() [3/3]

◆ ResizeImage()