loadNrrdStructure.m File Reference

Functions
function otherwise it will not work makes Assumes but needs to be compiled manually on your machine	cd ('../../../../Slicer3-lib/teem/src/matlab')
	elseif (foundKeyword('DWMRI_GRADIENT_', cs))[iGNr
	elseif (foundKeyword('DWMRI_B-VALUE', cs)) headerInfo.bvalue
	elseif (foundKeyword('MODALITY', cs)) headerInfo.modality
	elseif (foundKeyword('MEASUREMENT FRAME:', cs)) iMF
	elseif (foundKeyword('SPACE ORIGIN:', cs)) iSO
	elseif (foundKeyword('SPACE UNITS:', cs)) headerInfo.spaceunits
	elseif (foundKeyword('CENTERINGS:', cs)) headerInfo.centerings
	elseif (foundKeyword('KINDS:', cs)) headerInfo.kinds
	elseif (foundKeyword('THICKNESSES:', cs)) sThicknesses
	elseif (foundKeyword('SIZES:', cs)) iSizes
end	elseif (foundKeyword('SPACE DIRECTIONS:', cs))%iSD
	elseif (foundKeyword('SPACE:', cs)) headerInfo.space
	elseif (foundKeyword('DIMENSION:', cs)) headerInfo.dimension
	elseif (foundKeyword('DATA FILE:', cs))%headerInfo.datafile
	elseif (foundKeyword('ENCODING:', cs)) headerInfo.encoding
	elseif (foundKeyword('ENDIAN:', cs)) headerInfo.endian
	elseif (foundKeyword('TYPE:', cs)) headerInfo.type
if(csTmp(1)~='#'&~strcmp(cs(1:4),'NRRD')) fprintf('Warning end end end	fclose (fidr)
else	fprintf ('Warning:File is not RAS, make sure subsequent matlab processing is consistent!\n')
headerInfo	gradients (iGNr+1,:)
return end	if (strcmp(csU(1:lenKeyword), keyWordU)) fk
	if (len< lenKeyword) fk=0 = iSD
else	if (~iLastWasDelimiter) indxList
	if (numDelimiters >=1) sl
	if (isempty(assgnLoc)) dwiGradient = []
only implemented for RAS	if (iLocation >0) iIsRas
	if (foundKeyword( 'CONTENT:', cs)) headerInfo.content
	iMF (3) iMF(6) iMF(9)]
	iMF (2) iMF(5) iMF(8)
	iSD (3) iSD(6) iSD(9)]
	iSD (2) iSD(5) iSD(8)
	while (iEnd >1 &strList(iEnd)==delim) iEnd
	while (iStart< len &strList(iStart)==delim) iStart
	while (~feof(fidr)) cs
Variables
TODO	__pad0__
find where the assignment is	assgnLoc = strfind( st, ':=' )
headerInfo	centerings = [{'?^} {'cell'} {'cell'} {'cell'}]
else let s see if we are dealing with a comment	csTmp = removeExcessDelimiters( cs, ' ' )
	csU = upper( cs )
headerInfo	data = '?^
	delimiterIndices = strfind(strList,' ')
headerInfo	dimension = '?^
in case of a tensor volume there are	dimensions
	dwiGradient = extractGradient( cs(length('DWMRI_GRADIENT_')+1:end ) )
headerInfo	encoding = '?^
headerInfo	endian = '?^
	fidr = fileparts( nhdrFileName ) fopen( nhdrFileName, 'r' )
return function	fk
return	function [iGNr, dwiGradient]
default	header
function	headerInfo
end	iEnd = len
for	iI
end	iLastWasDelimiter = 0
	iLocation = strfind( csU(length('SPACE:')+1:end ), 'RIGHT-ANTERIOR-SUPERIOR')
end	indxList = []
return function	iNrs
	iSD = extractNumbersWithout( space_dir_tmp, {'(',')',','} )
	iStart = 1
	iThicknesses = []
	keyWordU = upper( keyWord )
tensor has to have headerInfo	kinds
end return function	kvs
	len = length( strList )
	lenKeyword = length( keyWord )
	lenThicknesses = length( sThicknesses )
decided that the none is not needed in	matlab
headerInfo	measurementframe = [NaN NaN NaN
NaN NaN	NaN
function otherwise it will not work makes Assumes	nrrdStructure
	numDelimiters = length(delimiterIndices)
these fields are	optional
if(fidr==-1) fprintf('ABORT	return
headerInfo	sizes = '?^
end return function	sl
headerInfo	space = '?^
in case of a tensor volume there are but only of them are in space	space_dir_tmp = strrep( cs(length('SPACE DIRECTIONS:')+1:end), 'none', 'NaN' )
headerInfo scalar data is expected to have values headerInfo	spacedirections = [NaN NaN NaN
headerInfo	spaceorigin = [NaN NaN NaN]
headerInfo	thicknesses = iThicknesses
headerInfo	type = '?^

Function Documentation

function otherwise it will not work makes Assumes but needs to be compiled manually on your machine cd ( '../../../../Slicer3-lib/teem/src/matlab' )

Type Constraints

elseif ( foundKeyword('DWMRI_GRADIENT_', cs) )

elseif ( foundKeyword('DWMRI_B-VALUE', cs) )

elseif ( foundKeyword('MODALITY', cs) )

elseif ( foundKeyword('MEASUREMENT FRAME:', cs) )

elseif ( foundKeyword('SPACE ORIGIN:', cs) )

elseif ( foundKeyword('SPACE UNITS:', cs) )

elseif ( foundKeyword('CENTERINGS:', cs) )

elseif ( foundKeyword('KINDS:', cs) )

elseif ( foundKeyword('THICKNESSES:', cs) )

elseif ( foundKeyword('SIZES:', cs) )

end elseif ( foundKeyword('SPACE DIRECTIONS:', cs) )

elseif ( foundKeyword('SPACE:', cs) )

elseif ( foundKeyword('DIMENSION:', cs) )

elseif ( foundKeyword('DATA FILE:', cs) )

elseif ( foundKeyword('ENCODING:', cs) )

elseif ( foundKeyword('ENDIAN:', cs) )

elseif ( foundKeyword('TYPE:', cs) )

if ( csTmp(1)~='#' & ~strcmp(cs(1:4),'NRRD') ) fprintf('Warning end end end fclose ( fidr )

else fprintf	(	'Warning:File is not	RAS,
		make sure subsequent matlab processing is consistent!\n'
	)

headerInfo gradients	(	iGNr+	1,
		:
	)

Referenced by itk::MRMLIDImageIO::SetDWNodeValues().

return end if ( strcmp(csU(1:lenKeyword), keyWordU) )

if ( ) = iSD [pure virtual]

else if ( ~ iLastWasDelimiter )

end if ( numDelimiters >= 1 )

References numDelimiters.

if ( isempty(assgnLoc) ) = []

only implemented for RAS if	(	iLocation	,
		0
	)

if ( foundKeyword( 'CONTENT:', cs) )

Referenced by EMLocalRegistrationCostFunction::CostFunction_Sum_WeightxProbability(), vtkTextureText::getLineLength(), vtkTextureText::getLineWordCount(), MatrixRowCol::KP(), vtkTextureText::Modified(), and vtkCudaVolumeInformationHandler::UpdateGradient().

iMF ( 3 )

iMF ( 2 )

iSD ( 3 )

iSD ( 2 )

while	(	iEnd	,
		1 &	strListiEnd = `=delim`
	)

while ( )

while ( ~ feoffidr )

Variable Documentation

TODO __pad0__

find where the assignment is assgnLoc = strfind( st, ':=' )

headerInfo centerings = [{'?^} {'cell'} {'cell'} {'cell'}]

else let s see if we are dealing with a comment csTmp = removeExcessDelimiters( cs, ' ' )

csU = upper( cs )

headerInfo data = '?^

Referenced by qMRMLNodeComboBox::activateExtraItem(), CompareTwoVolumes(), vtkSlicerViewControlGUI::ConfigureNavigationWidgetRender(), MatrixRowCol::Data(), MeshContourEvolver::entry_main(), vtkImageGraph::ExecuteData(), vtkTensorMask::ExecuteData(), vtkTeemEstimateDiffusionTensor::ExecuteData(), vtkNRRDReader::ExecuteData(), vtkImageSetTensorComponents::ExecuteData(), vtkITKTimeSeriesDatabase::ExecuteData(), vtkITKArchetypeImageSeriesVectorReaderSeries::ExecuteData(), vtkITKArchetypeImageSeriesVectorReaderFile::ExecuteData(), vtkITKArchetypeImageSeriesScalarReader::ExecuteData(), vtkImageRectangularSource::ExecuteData(), vtkImageCurveRegion::ExecuteDataGauss(), vtkImageCurveRegion::ExecuteDataReadFile(), vtkImageRectangularSource::ExecuteInformation(), qSlicermiAnnotationModuleImageUtil::fromImageData(), vtkSlicerFixedPointVolumeRayCastCompositeShadeHelper::GenerateImage(), vtkSlicerFixedPointVolumeRayCastCompositeGOShadeHelper::GenerateImage(), vtkSlicerFixedPointVolumeRayCastCompositeGOHelper::GenerateImage(), vtkMRMLVolumePropertyNode::GetColorTransferFunctionFromString(), vtkMRMLVolumePropertyNode::GetColorTransferFunctionString(), vtkMRMLArrayPlotNode::GetDrawObject(), vtkMRMLVolumePropertyNode::GetPiecewiseFunctionFromString(), vtkMRMLVolumePropertyNode::GetPiecewiseFunctionString(), MatrixRowCol::IncrDiag(), MatrixRowCol::IncrLT(), MatrixRowCol::IncrMat(), MatrixRowCol::IncrUT(), ipAllocateData(), mexFunction(), qMRMLNodeSelector::node(), vtkPETCTFusionPlots::OutputAllDataInCSV(), vtkPharmacokineticsIntensityCurves::OutputDataInCSV(), vtkPETCTFusionPlots::OutputDataInCSV(), PaddedImageBaseOf< DATA, 3 >::Pad(), SourceAccessorEqualizeBaseOf< DATA, 2, PRECISION, SOURCE >::PrepareForAccessAction(), PrintImage(), vtkUDPServerGUI::ProcessTimerEvents(), vtkFetchMIResourceUploadWidget::ProcessWidgetEvents(), vtkSlicerMRMLSaveDataWidget::ProcessWidgetEvents(), vtkHyperStreamlineTeem::ProduceFiberContext(), qCTKTestApplication::qCTKTestApplication(), vtkTeemEstimateDiffusionTensor::SetGradientsToContext(), SourceAccessorRangeScaleBaseOf< DATA, 2, PRECISION, SOURCE >::SetMinMaxRangeScale(), SourceAccessorRangeScaleBaseOf< DATA, 2, PRECISION, SOURCE >::SetNormalRangeScale(), sort_ascending(), sort_descending(), and itk::EncodedTransformFileReader::Update().

delimiterIndices = strfind(strList,' ')

headerInfo dimension = '?^

Referenced by vtkCTHandBoneClass::largest_component(), and vtkSlicerViewControlGUI::UpdateNavigationWidgetViewActors().

in case of a tensor volume there are dimensions

Referenced by mimxCheckTypeOfFile::Check(), vtkChangeTrackerLogic::CheckROI(), vtkZFrameRobotToImageRegistration::DoRegistration(), vtkSlicerSlicesControlGUI::FitFOVToBackground(), vtkSlicerSliceLogic::GetVolumeRASBox(), main(), vtkEMSegmentRunSegmentationStep::RetrieveInteractorCoordinates(), vtkChangeTrackerROIStep::RetrieveInteractorCoordinates(), vtkEMSegmentRunSegmentationStep::ROICheck(), vtkEMSegmentRunSegmentationStep::ROIMapShow(), vtkChangeTrackerROIStep::ROIMapShow(), vtkPharmacokineticsGUI::SelectActive4DBundle(), vtkEMSegmentRunSegmentationStep::ShowROIGUI(), vtkChangeTrackerROIStep::ShowUserInterface(), vtkSlicerSliceLayerLogic::UpdateTransforms(), and vtkImageSlicePaintPaint().

else dwiGradient = extractGradient( cs(length('DWMRI_GRADIENT_')+1:end ) )

headerInfo encoding = '?^

headerInfo endian = '?^

fidr = fileparts( nhdrFileName ) fopen( nhdrFileName, 'r' )

return else fk

Initial value:

 foundKeyword( keyWord, cs )

csU = upper( cs )

return function[iGNr, dwiGradient]

Initial value:

 extractGradient( st )

% first get the gradient number

iGNr = str2num( st(1:4) )

default header

end clear headerInfo

Initial value:

 loadNrrdStructure( nhdrFileName )

% reads all the header information from a nrrd file
% assumes a nhdr

end iEnd = len

for iI

Initial value:

1:lenThicknesses
      iThicknesses = [iThicknesses, str2num( sThicknesses{iI} ) ]

Referenced by DoIt().

end iLastWasDelimiter = 0

iLocation = strfind( csU(length('SPACE:')+1:end ), 'RIGHT-ANTERIOR-SUPERIOR')

end indxList = []

end iNrs

Initial value:

 extractNumbersWithout( inputString, withoutTokens )

auxStr = inputString

iSD = extractNumbersWithout( space_dir_tmp, {'(',')',','} )

iStart = 1

iThicknesses = []

keyWordU = upper( keyWord )

headerInfo kinds

Initial value:

 [{'3D-masked-symmetric-matrix'} 
% {'space'} {'space'} {'space'}]

else kvs

Initial value:

 extractKeyValueString( st )

assgnLoc = strfind( st, ':=' )

len = length( strList )

Referenced by vtkSlicerApplication::ArrayToString(), ComputeAdjacency(), vtkPETCTFusionLogic::GetParametersFromDICOMHeader(), main(), mexFunction(), vtkFileOps::pathComponent(), vtkSlicerModuleChooseGUI::PopulateModuleSearchMenu(), vtkFSSurfaceAnnotationReader::ReadEmbeddedColorTable(), vtkMRMLViewNode::ReadXMLAttributes(), recursive_copy(), vtkMRMLSliceNode::RotateToVolumePlane(), SkelGraph::Sample_along_axis(), vtkTransRectalFiducialCalibrationAlgo::SegmentCircle(), vtkMRMLVolumeNode::SetIJKToRASMatrix(), vtkCacheManager::SetRemoteCacheDirectory(), Slicer3_main(), TCLAP::StdOutput::spacePrint(), vtkQueryAtlasUseSearchTermWidget::ToggleQuotesOnSelectedSearchTerms(), vtkNeuroNavLogic::UpdateFiducialSeeding(), vtkSlicerModulesStep::UpdateModulesFromRepository(), vtkCommandLineModuleGUI::UpdateMRML(), and vtkImageConnectivityExecute().

lenKeyword = length( keyWord )

lenThicknesses = length( sThicknesses )

decided that the none is not needed in matlab

headerInfo measurementframe = [NaN NaN NaN

NaN NaN NaN

function otherwise it will not work makes Assumes nrrdStructure

Initial value:

 loadNrrdStructure( nhdrFileName )
%
% marc@bwh.harvard.edu
% kquintus@bwh.harvard.edu

% make sure to add path for nrrdLoad in the teem library. 
% comes with Slicer3

numDelimiters = length(delimiterIndices)

Referenced by if().

these fields are optional

const const T2 &t2 return [inline]

Referenced by vtkEMSegmentNodeParametersStep::ClassWeightChangedCallback(), vtkKWMimxCreateBBFromRubberBandPickGroup::CreateBBFromRubberBandPickCallback(), vtkKWMimxCreateSurfaceFromContourGroup::CreateSurfaceFromContourTraceContourCallback(), vtkEMSegmentKWDynamicFrame::DefineCheckButton(), vtkEMSegmentKWDynamicFrame::DefineTextEntry(), vtkEMSegmentKWDynamicFrame::DefineTextLabel(), vtkEMSegmentKWDynamicFrame::DefineVolumeMenuButton(), vtkMRMLAnnotationControlPointsNode::DeleteControlPoint(), vtkMRMLAnnotationLinesNode::DeleteLine(), vtkKWMimxEditBBMeshSeedGroup::EditBBMeshSeedPickCellCallback(), vtkKWMimxAssignBoundaryConditionsGroup::ElementSetOutputApplyCallback(), vtkImageEMLocalClass::ExecuteData(), vtkImageEMAtlasClass::ExecuteData(), vtkImageSumOverVoxels::ExecuteData(), vtkMimxCreateElementSetWidgetFEMesh::ExtractElementsBelongingToAFace(), vtkKWMimxCreateBBFromBoundsGroup::ManualBoundCallback(), vtkKWMimxAssignBoundaryConditionsGroup::NodeSetOutputApplyCallback(), vtkMimxPatchSurfaceMesh::PolyDataExecute(), vtkEMSegmentParametersSetStep::SelectedParameterSetChangedCallback(), vtkMimxSelectPointsWidget::SelectPointsOnAFaceFunction(), qSlicerWidget::setMRMLScene(), vtkEMSegmentMRMLManager::SetTargetSelectedVolumeNthID(), vtkEMSegmentMRMLManager::SetTreeNodeDistributionLogCovarianceOffDiagonal(), vtkEMSegmentMRMLManager::SetTreeNodeDistributionLogCovarianceWithCorrection(), vtkKWMimxEditBBMeshSeedGroup::ShowMeshSeedCallback(), vtkSlicermiAnnotationModuleLogic::StartAddingFiducials(), vtkSlicermiAnnotationModuleLogic::StopAddingFiducials(), vtkEMSegmentKWLogic::UpdateIntensityDistributionAuto(), and vtkEMSegmentMRMLManager::UpdateIntensityDistributionFromSample().

parse sizes headerInfo sizes = '?^

Referenced by CountSamplesTest(), DownsampleHeuristicsTest(), qCTKTitleComboBox::paintEvent(), and ScalingHeuristicsTest().

end end sl

Initial value:

 extractStringList( strList )

strList = removeExcessDelimiters( strList, ' ' )

Referenced by vtkQueryAtlasGUI::BuildQueriesGUI().

headerInfo space = '?^

Referenced by main(), vtkMRMLScriptedModuleNode::ReadXMLAttributes(), and itk::CommandIO::Write().

decided that the none is not needed in it s nicer to have a matrix space_dir_tmp = strrep( cs(length('SPACE DIRECTIONS:')+1:end), 'none', 'NaN' )

if (length(iSD)~=9 & length(iSD)~=10) fprintf('Warning end headerInfo spacedirections = [NaN NaN NaN

if (length(iSO)~=3) % fprintf('Warning end headerInfo spaceorigin = [NaN NaN NaN]

end headerInfo thicknesses = iThicknesses

headerInfo type = '?^

Referenced by vtkPETCTFusionGUI::ApplyDefaultCTLUT(), vtkPETCTFusionGUI::ApplyDefaultPETLUT(), vtkMRMLIGTLConnectorNode::Copy(), qSlicerCLIModuleWidgetPrivate::createGeometryTagWidget(), qSlicerCLIModuleWidgetPrivate::createImageTagWidget(), qSlicerCLIModuleWidgetPrivate::createTableTagWidget(), qSlicerCLIModuleWidgetPrivate::createTransformTagWidget(), vtkImageAccumulateDiscrete::ExecuteData(), vtkOpenIGTLinkIFGUI::IOConfigTreeContextMenu(), IsEnumeration(), IsVectorOfVectors(), NeedsQuotes(), NeedsTemp(), nricMatrix::operator<<(), GeneralMatrix::operator<<(), itk::MGHImageIO::ReadVolumeHeader(), vtkMRMLIGTLConnectorNode::ReadXMLAttributes(), vtkMRMLColorTableNode::ReadXMLAttributes(), vtkMRMLColorNode::ReadXMLAttributes(), vtkMRMLColorTableNode::Reset(), vtkTeemEstimateDiffusionTensor::SetGradientsToContext(), vtkKWMimxAssignBoundaryConditionsGroup::ShowBoundaryConditionRepresentation(), sock_initobj(), GeneralMatrix::Type(), vtkPETCTFusionGUI::UpdateColorRadioButtonsFromMRML(), and qSlicerCLIModuleWidgetPrivate::updateMRMLCommandLineModuleNode().

loadNrrdStructure.m File Reference

Functions

Variables

Function Documentation

Variable Documentation