PixelDumpMiniApp.cpp File Reference

#include <string>
#include "itksys/SystemTools.hxx"
#include "itkImageRegionConstIteratorWithIndex.h"
#include "itkCastImageFilter.h"
#include "itkExtractImageFilter.h"
#include "mitkCommandLineParser.h"
#include <mitkIOUtil.h>
#include <mitkPreferenceListReaderOptionsFunctor.h>
#include <mitkImageTimeSelector.h>
#include "mitkImageAccessByItk.h"
#include "mitkImageCast.h"

Go to the source code of this file.

Typedefs
using	ImageVectorType = std::vector< mitk::Image::Pointer >
typedef itk::Image< mitk::ScalarType, 3 >	InternalImageType
typedef std::map< std::string, InternalImageType::Pointer >	InternalImageMapType
typedef itk::Index< 3 >	DumpIndexType
typedef std::vector< mitk::ScalarType >	DumpedValuesType
typedef std::map< DumpIndexType, DumpedValuesType, DumpIndexCompare >	DumpPixelMapType

Functions
bool	verbose (false)
void	setupParser (mitkCommandLineParser &parser)
bool	configureApplicationSettings (std::map< std::string, us::Any > parsedArgs)
template<typename TPixel , unsigned int VImageDimension>
void	ExtractRelevantInformation (const itk::Image< TPixel, VImageDimension > *image)
template<typename TPixel , unsigned int VImageDimension>
void	DoInternalImageConversion (const itk::Image< TPixel, VImageDimension > *image, InternalImageType::Pointer &internalImage)
template<typename TPixel , unsigned int VImageDimension>
void	DoMaskedCollecting (const itk::Image< TPixel, VImageDimension > *image)
InternalImageMapType	ConvertImageTimeSteps (mitk::Image *image)
void	doDumping ()
void	storeCSV ()
int	main (int argc, char *argv[])

Variables
mitkCommandLineParser::StringContainerType	inFilenames
std::string	outFileName
std::string	maskFileName
mitkCommandLineParser::StringContainerType	captions
ImageVectorType	images
mitk::Image::Pointer	mask
InternalImageMapType	internalImages
itk::ImageRegion< 3 >	relevantRegion
InternalImageType::PointType	relevantOrigin
InternalImageType::SpacingType	relevantSpacing
InternalImageType::DirectionType	relevantDirection
DumpPixelMapType	dumpedPixels

Typedef Documentation

DumpedValuesType

typedef std::vector<mitk::ScalarType> DumpedValuesType

Definition at line 55 of file PixelDumpMiniApp.cpp.

DumpIndexType

typedef itk::Index<3> DumpIndexType

Definition at line 54 of file PixelDumpMiniApp.cpp.

DumpPixelMapType

typedef std::map<DumpIndexType, DumpedValuesType, DumpIndexCompare> DumpPixelMapType

Definition at line 83 of file PixelDumpMiniApp.cpp.

ImageVectorType

using ImageVectorType = std::vector<mitk::Image::Pointer>

Definition at line 38 of file PixelDumpMiniApp.cpp.

InternalImageMapType

typedef std::map<std::string, InternalImageType::Pointer> InternalImageMapType

Definition at line 46 of file PixelDumpMiniApp.cpp.

InternalImageType

typedef itk::Image<mitk::ScalarType, 3> InternalImageType

Definition at line 45 of file PixelDumpMiniApp.cpp.

Function Documentation

configureApplicationSettings()

bool configureApplicationSettings

(

std::map< std::string, us::Any >

parsedArgs

)

Definition at line 122 of file PixelDumpMiniApp.cpp.

References us::any_cast(), captions, inFilenames, maskFileName, and outFileName.

Referenced by main().

ConvertImageTimeSteps()

InternalImageMapType ConvertImageTimeSteps

(

mitk::Image *

image

)

Definition at line 252 of file PixelDumpMiniApp.cpp.

References AccessFixedDimensionByItk_1, DoInternalImageConversion(), mitk::BaseData::GetTimeSteps(), mitk::ImageMappingHelper::map(), and mitk::ImageTimeSelector::New().

Referenced by doDumping().

doDumping()

void doDumping

(

)

Definition at line 280 of file PixelDumpMiniApp.cpp.

References AccessFixedDimensionByItk, captions, ConvertImageTimeSteps(), DoMaskedCollecting(), ExtractRelevantInformation(), images, internalImages, and mitk::ImageTimeSelector::New().

Referenced by main().

DoInternalImageConversion()

template<typename TPixel , unsigned int VImageDimension>

void DoInternalImageConversion	(	const itk::Image< TPixel, VImageDimension > *	image,
		InternalImageType::Pointer &	internalImage
	)

Definition at line 158 of file PixelDumpMiniApp.cpp.

References mitkThrow, relevantDirection, relevantOrigin, relevantRegion, and relevantSpacing.

Referenced by ConvertImageTimeSteps().

DoMaskedCollecting()

template<typename TPixel , unsigned int VImageDimension>

void DoMaskedCollecting

(

const itk::Image< TPixel, VImageDimension > *

image

)

Definition at line 223 of file PixelDumpMiniApp.cpp.

References dumpedPixels, internalImages, and relevantRegion.

Referenced by doDumping().

ExtractRelevantInformation()

template<typename TPixel , unsigned int VImageDimension>

void ExtractRelevantInformation

(

const itk::Image< TPixel, VImageDimension > *

image

)

Definition at line 148 of file PixelDumpMiniApp.cpp.

References relevantDirection, relevantOrigin, relevantRegion, and relevantSpacing.

Referenced by doDumping().

main()

int main	(	int	argc,
		char *	argv[]
	)

[do processing]

Definition at line 377 of file PixelDumpMiniApp.cpp.

References captions, configureApplicationSettings(), doDumping(), mitkCommandLineParser::helpText(), image, images, inFilenames, maskFileName, MITK_ERROR, mitkCommandLineParser::parseArguments(), setupParser(), and storeCSV().

setupParser()

void setupParser

(

mitkCommandLineParser &

parser

)

[create parser]

[add arguments]

[add arguments]

Definition at line 86 of file PixelDumpMiniApp.cpp.

References mitkCommandLineParser::addArgument(), mitkCommandLineParser::beginGroup(), mitkCommandLineParser::Bool, mitkCommandLineParser::endGroup(), mitkCommandLineParser::File, mitkCommandLineParser::Input, mitkCommandLineParser::Output, mitkCommandLineParser::setArgumentPrefix(), mitkCommandLineParser::setCategory(), mitkCommandLineParser::setContributor(), mitkCommandLineParser::setDescription(), mitkCommandLineParser::setTitle(), and mitkCommandLineParser::StringList.

Referenced by main().

storeCSV()

void storeCSV

(

)

Definition at line 352 of file PixelDumpMiniApp.cpp.

References dumpedPixels, internalImages, and outFileName.

Referenced by main().

verbose()

bool verbose

(

false

)

Variable Documentation

captions

mitkCommandLineParser::StringContainerType captions

Definition at line 36 of file PixelDumpMiniApp.cpp.

Referenced by configureApplicationSettings(), doDumping(), and main().

dumpedPixels

DumpPixelMapType dumpedPixels

Definition at line 84 of file PixelDumpMiniApp.cpp.

Referenced by DoMaskedCollecting(), and storeCSV().

images

ImageVectorType images

Definition at line 39 of file PixelDumpMiniApp.cpp.

Referenced by doDumping(), main(), mitkDICOMLocaleTestWithReferenceImage(), mitkDICOMPreloadedVolumeTest(), mitkDICOMTestingSanityTest(), mitkViewportRenderingTest(), and berry::Window::SetDefaultImages().

inFilenames

mitkCommandLineParser::StringContainerType inFilenames

Definition at line 33 of file PixelDumpMiniApp.cpp.

Referenced by configureApplicationSettings(), and main().

internalImages

InternalImageMapType internalImages

Definition at line 47 of file PixelDumpMiniApp.cpp.

Referenced by doDumping(), DoMaskedCollecting(), and storeCSV().

mask

mitk::Image::Pointer mask

Definition at line 41 of file PixelDumpMiniApp.cpp.

maskFileName

std::string maskFileName

Definition at line 35 of file PixelDumpMiniApp.cpp.

Referenced by configureApplicationSettings(), and main().

outFileName

std::string outFileName

Definition at line 34 of file PixelDumpMiniApp.cpp.

Referenced by configureApplicationSettings(), and storeCSV().

relevantDirection

InternalImageType::DirectionType relevantDirection

Definition at line 52 of file PixelDumpMiniApp.cpp.

Referenced by DoInternalImageConversion(), and ExtractRelevantInformation().

relevantOrigin

InternalImageType::PointType relevantOrigin

Definition at line 50 of file PixelDumpMiniApp.cpp.

Referenced by DoInternalImageConversion(), and ExtractRelevantInformation().

relevantRegion

itk::ImageRegion<3> relevantRegion

Definition at line 49 of file PixelDumpMiniApp.cpp.

Referenced by DoInternalImageConversion(), DoMaskedCollecting(), and ExtractRelevantInformation().

relevantSpacing

InternalImageType::SpacingType relevantSpacing

Definition at line 51 of file PixelDumpMiniApp.cpp.

Referenced by DoInternalImageConversion(), and ExtractRelevantInformation().