SIVIC API  0.9.26
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svkPhilipsSMapper Class Reference

#include <svkPhilipsSMapper.h>

Inheritance diagram for svkPhilipsSMapper:

Public Member Functions

 vtkTypeMacro (svkPhilipsSMapper, vtkObject)
 
virtual void InitializeDcmHeader (map< string, string > sparMap, svkDcmHeader *header, svkMRSIOD *iod, int swapBytes)
 
virtual void ReadSDATFile (string sdatFileName, svkImageData *data)
 

Static Public Member Functions

static svkPhilipsSMapper * New ()
 

Protected Member Functions

 svkPhilipsSMapper ()
 
 ~svkPhilipsSMapper ()
 
void InitPatientModule ()
 
void InitGeneralStudyModule ()
 
void InitGeneralSeriesModule ()
 
void InitGeneralEquipmentModule ()
 
virtual void InitMultiFrameFunctionalGroupsModule ()
 
virtual void InitMultiFrameDimensionModule ()
 
virtual void InitAcquisitionContextModule ()
 
virtual void InitSharedFunctionalGroupMacros ()
 
virtual void InitPerFrameFunctionalGroupMacros ()
 
virtual void InitMRModifierMacro ()
 
virtual void InitMRTransmitCoilMacro ()
 
virtual void InitMRAveragesMacro ()
 
virtual void InitPixelMeasuresMacro ()
 
virtual void InitPlaneOrientationMacro ()
 
virtual void InitMREchoMacro ()
 
virtual void InitMRTimingAndRelatedParametersMacro ()
 
virtual void InitMRReceiveCoilMacro ()
 
virtual void InitMRSpectroscopyPulseSequenceModule ()
 
virtual void InitMRSpectroscopyModule ()
 
virtual void InitMRSpectroscopyFOVGeometryMacro ()
 
virtual void InitMRSpectroscopyDataModule ()
 
string GetDcmPatientPositionString ()
 
int GetHeaderValueAsInt (string keyString)
 
float GetHeaderValueAsFloat (string keyString)
 
virtual void SetCellSpectrum (vtkImageData *data, int x, int y, int z, int timePt, int coilNum)
 
string GetDcmDate ()
 
void VaxToFloat (const void *inbuf, void *outbuf, const int *count)
 
void GetFOV (float *fov)
 
void GetDimPnts (int *numPixels)
 

Protected Attributes

map< string, string > sparMap
 
svkDcmHeader * dcmHeader
 
float * specData
 
svkDcmHeader::DcmDataOrderingDirection dataSliceOrder
 
int numSlices
 
int numFrames
 
svkMRSIOD * iod
 
int swapBytes
 

Detailed Description

Mapper base class for converting from Philips SPAR header format to DICOM MR Spectrosocpy IOD/SOP Class instance. The mapper receives the SPAR fields from the svkPhilipsSReader. The spar fields are in the form of a map of of key value pairs (sparMap). Map values are key value pairs and can be accessed by key string name and value index (GetHeaderValueAsType methods).

Concrete mappers need to be implemented to map sequence specific content from Varian acquisitions to DICOM MR Spectroscopy. It is the svkPhilipsSReader's responsibility to select the appropriate svkPhilipsSMapper instance for any give data set.

Constructor & Destructor Documentation

svkPhilipsSMapper ( )
protected

References svkPhilipsSMapper::numFrames, and svkPhilipsSMapper::specData.

~svkPhilipsSMapper ( )
protected

References svkPhilipsSMapper::specData.

Member Function Documentation

string GetDcmDate ( )
protected

References svkImageReader2::RemoveDelimFromDate(), and svkPhilipsSMapper::sparMap.

Referenced by svkPhilipsSMapper::InitGeneralStudyModule(), and svkPhilipsSMapper::InitMultiFrameFunctionalGroupsModule().

string GetDcmPatientPositionString ( )
protected

Use the Procpar patient position string to set the DCM_PatientPosition data element.

References svkPhilipsSMapper::sparMap.

Referenced by svkPhilipsSMapper::InitGeneralSeriesModule().

void GetDimPnts ( int *  numPixels)
protected

References svkPhilipsSMapper::GetHeaderValueAsInt().

Referenced by svkPhilipsSMapper::InitMRSpectroscopyDataModule(), svkPhilipsSMapper::InitMRSpectroscopyFOVGeometryMacro(), svkPhilipsSMapper::InitPerFrameFunctionalGroupMacros(), and svkPhilipsSMapper::InitPixelMeasuresMacro().

void GetFOV ( float *  fov)
protected

References svkPhilipsSMapper::GetHeaderValueAsFloat().

Referenced by svkPhilipsSMapper::InitMRSpectroscopyFOVGeometryMacro(), svkPhilipsSMapper::InitPerFrameFunctionalGroupMacros(), and svkPhilipsSMapper::InitPixelMeasuresMacro().

float GetHeaderValueAsFloat ( string  keyString)
protected

References svkPhilipsSMapper::sparMap.

Referenced by svkPhilipsSMapper::GetFOV(), svkPhilipsSMapper::InitMREchoMacro(), svkPhilipsSMapper::InitMRModifierMacro(), svkPhilipsSMapper::InitMRSpectroscopyModule(), svkPhilipsSMapper::InitMRTimingAndRelatedParametersMacro(), svkPhilipsSMapper::InitPerFrameFunctionalGroupMacros(), and svkPhilipsSMapper::InitPlaneOrientationMacro().

int GetHeaderValueAsInt ( string  keyString)
protected
Parameters
keystring
Returns
value if key is found, or INT_MIN otherwise

References svkPhilipsSMapper::sparMap.

Referenced by svkPhilipsSMapper::GetDimPnts(), svkPhilipsSMapper::InitMRSpectroscopyDataModule(), svkPhilipsSMapper::InitMRSpectroscopyFOVGeometryMacro(), and svkPhilipsSMapper::InitMultiFrameFunctionalGroupsModule().

void InitAcquisitionContextModule ( )
protectedvirtual
void InitGeneralEquipmentModule ( )
protected

DDF is historically the UCSF representation of a GE raw file so initialize to svkPhilipsSMapper::MFG_STRING.

References svkPhilipsSMapper::dcmHeader, and svkDcmHeader::SetValue().

Referenced by svkPhilipsSMapper::InitializeDcmHeader().

void InitGeneralSeriesModule ( )
protected

References svkPhilipsSMapper::dcmHeader, svkPhilipsSMapper::GetDcmPatientPositionString(), and svkDcmHeader::InitGeneralSeriesModule().

Referenced by svkPhilipsSMapper::InitializeDcmHeader().

void InitGeneralStudyModule ( )
protected

References svkPhilipsSMapper::dcmHeader, svkPhilipsSMapper::GetDcmDate(), and svkDcmHeader::InitGeneralStudyModule().

Referenced by svkPhilipsSMapper::InitializeDcmHeader().

void InitializeDcmHeader ( map< string, string >  sparMap,
svkDcmHeader *  header,
svkMRSIOD *  iod,
int  swapBytes 
)
virtual

Initializes the svkDcmHeader adapter to a specific IOD type and initizlizes the svkDcmHeader member of the svkImageData object.

References svkPhilipsSMapper::dcmHeader, svkPhilipsSMapper::InitGeneralEquipmentModule(), svkPhilipsSMapper::InitGeneralSeriesModule(), svkPhilipsSMapper::InitGeneralStudyModule(), svkPhilipsSMapper::InitMRSpectroscopyDataModule(), svkPhilipsSMapper::InitMRSpectroscopyModule(), svkPhilipsSMapper::InitMRSpectroscopyPulseSequenceModule(), svkPhilipsSMapper::InitMultiFrameFunctionalGroupsModule(), svkPhilipsSMapper::InitPatientModule(), svkPhilipsSMapper::iod, svkDcmHeader::SetValue(), svkPhilipsSMapper::sparMap, and svkPhilipsSMapper::swapBytes.

void InitMRAveragesMacro ( )
protectedvirtual

References svkPhilipsSMapper::dcmHeader, and svkDcmHeader::InitMRAveragesMacro().

Referenced by svkPhilipsSMapper::InitSharedFunctionalGroupMacros().

void InitMREchoMacro ( )
protectedvirtual

References svkPhilipsSMapper::dcmHeader, svkPhilipsSMapper::GetHeaderValueAsFloat(), and svkDcmHeader::InitMREchoMacro().

Referenced by svkPhilipsSMapper::InitSharedFunctionalGroupMacros().

void InitMRModifierMacro ( )
protectedvirtual

Override in concrete mapper for specific acquisitino

References svkPhilipsSMapper::dcmHeader, svkPhilipsSMapper::GetHeaderValueAsFloat(), and svkDcmHeader::InitMRModifierMacro().

Referenced by svkPhilipsSMapper::InitSharedFunctionalGroupMacros().

void InitMRReceiveCoilMacro ( )
protectedvirtual

Receive Coil:

References svkDcmHeader::AddSequenceItemElement(), and svkPhilipsSMapper::dcmHeader.

Referenced by svkPhilipsSMapper::InitSharedFunctionalGroupMacros().

void InitMRSpectroscopyDataModule ( )
protectedvirtual

References svkPhilipsSMapper::dcmHeader, svkPhilipsSMapper::GetDimPnts(), svkPhilipsSMapper::GetHeaderValueAsInt(), and svkDcmHeader::SetValue().

Referenced by svkPhilipsSMapper::InitializeDcmHeader().

void InitMRSpectroscopyFOVGeometryMacro ( )
protectedvirtual

References svkDcmHeader::AddSequenceItemElement(), svkPhilipsSMapper::dcmHeader, svkPhilipsSMapper::GetDimPnts(), svkPhilipsSMapper::GetFOV(), svkPhilipsSMapper::GetHeaderValueAsInt(), and svkDcmHeader::GetPixelSize().

Referenced by svkPhilipsSMapper::InitSharedFunctionalGroupMacros().

void InitMRSpectroscopyModule ( )
protectedvirtual

References svkPhilipsSMapper::dcmHeader, svkSpecUtils::GetFieldStrength(), svkPhilipsSMapper::GetHeaderValueAsFloat(), svkDcmHeader::SetValue(), and svkPhilipsSMapper::sparMap.

Referenced by svkPhilipsSMapper::InitializeDcmHeader().

void InitMRSpectroscopyPulseSequenceModule ( )
protectedvirtual

Referenced by svkPhilipsSMapper::InitializeDcmHeader().

void InitMRTimingAndRelatedParametersMacro ( )
protectedvirtual

References svkPhilipsSMapper::dcmHeader, svkPhilipsSMapper::GetHeaderValueAsFloat(), and svkDcmHeader::InitMRTimingAndRelatedParametersMacro().

Referenced by svkPhilipsSMapper::InitSharedFunctionalGroupMacros().

void InitMRTransmitCoilMacro ( )
protectedvirtual

References svkPhilipsSMapper::dcmHeader, and svkDcmHeader::InitMRTransmitCoilMacro().

void InitMultiFrameDimensionModule ( )
protectedvirtual

References svkDcmHeader::AddSequenceItemElement(), and svkPhilipsSMapper::dcmHeader.

void InitMultiFrameFunctionalGroupsModule ( )
protectedvirtual

References svkPhilipsSMapper::dcmHeader, svkPhilipsSMapper::GetDcmDate(), svkPhilipsSMapper::GetHeaderValueAsInt(), svkPhilipsSMapper::InitPerFrameFunctionalGroupMacros(), svkPhilipsSMapper::InitSharedFunctionalGroupMacros(), svkPhilipsSMapper::numFrames, svkPhilipsSMapper::numSlices, and svkDcmHeader::SetValue().

Referenced by svkPhilipsSMapper::InitializeDcmHeader().

void InitPatientModule ( )
protected

References svkPhilipsSMapper::dcmHeader, svkDcmHeader::GetDcmPatientName(), svkDcmHeader::InitPatientModule(), and svkPhilipsSMapper::sparMap.

Referenced by svkPhilipsSMapper::InitializeDcmHeader().

void InitPerFrameFunctionalGroupMacros ( )
protectedvirtual

The SPAR toplc is the center of the first voxel. Best guess at field interpretation all dims in mm. Not positive about difference between two sets of fields, e.g. ap_off_center and si_ap_off_center, etc. ap_size : AP FOV lr_size : RL FOV cc_size : SI FOV ap_off_center : AP displacment from center (from origin) lr_off_center : LR displacement from center (from origin) cc_off_center : SI displacment from center (from origin) // these may be euler angles. ap_angulation : angulation of or about AP axis (tilt forward/backwards) lr_angulation : angluation of or aboutLR axis (tilt left right) cc_angulation : angulation of or aboutSI axis( volume_selection_method : 2 si_ap_off_center : 1.225752473 si_lr_off_center : 1.05771184 si_cc_off_center : -2.013401001e-008 si_ap_off_angulation : 0 si_lr_off_angulation : 0 si_cc_off_angulation : 0 phase_encoding_fov : slice_thickness : 10

References svkPhilipsSMapper::dataSliceOrder, svkPhilipsSMapper::dcmHeader, svkDcmHeader::GetDataDcos(), svkDcmHeader::GetDimensionIndexVector(), svkPhilipsSMapper::GetDimPnts(), svkPhilipsSMapper::GetFOV(), svkPhilipsSMapper::GetHeaderValueAsFloat(), svkDcmHeader::GetPixelSize(), svkDcmHeader::InitPerFrameFunctionalGroupSequence(), svkPhilipsSMapper::numFrames, svkDcmHeader::SetDimensionVectorValue(), svkDcmHeader::SetSliceOrder(), and svkDcmHeader::SLICE_INDEX.

Referenced by svkPhilipsSMapper::InitMultiFrameFunctionalGroupsModule().

void InitPixelMeasuresMacro ( )
protectedvirtual

Pixel Spacing:

References svkPhilipsSMapper::dcmHeader, svkPhilipsSMapper::GetDimPnts(), svkPhilipsSMapper::GetFOV(), and svkDcmHeader::InitPixelMeasuresMacro().

Referenced by svkPhilipsSMapper::InitSharedFunctionalGroupMacros().

void InitPlaneOrientationMacro ( )
protectedvirtual

The DICOM PlaneOrientationSequence is set from orientational params defined in the Philips sdat file.

References svkDcmHeader::AddSequenceItemElement(), svkPhilipsSMapper::dataSliceOrder, svkPhilipsSMapper::dcmHeader, svkPhilipsSMapper::GetHeaderValueAsFloat(), svkDcmHeader::GetNormalVector(), svkDcmHeader::INCREMENT_ALONG_NEG_NORMAL, and svkDcmHeader::INCREMENT_ALONG_POS_NORMAL.

Referenced by svkPhilipsSMapper::InitSharedFunctionalGroupMacros().

void InitSharedFunctionalGroupMacros ( )
protectedvirtual

References svkPhilipsSMapper::InitMRAveragesMacro(), svkPhilipsSMapper::InitMREchoMacro(), svkPhilipsSMapper::InitMRModifierMacro(), svkPhilipsSMapper::InitMRReceiveCoilMacro(), svkPhilipsSMapper::InitMRSpectroscopyFOVGeometryMacro(), svkPhilipsSMapper::InitMRTimingAndRelatedParametersMacro(), svkPhilipsSMapper::InitPixelMeasuresMacro(), and svkPhilipsSMapper::InitPlaneOrientationMacro().

Referenced by svkPhilipsSMapper::InitMultiFrameFunctionalGroupsModule().

static svkPhilipsSMapper* New ( )
static
void ReadSDATFile ( string  sdatFileName,
svkImageData *  data 
)
virtual

Reads spec data from sdat file.

References svkPhilipsSMapper::dcmHeader, svkImageReader2::GetFileRoot(), svkDcmHeader::GetIntValue(), svkDcmHeader::GetNumberOfCoils(), svkDcmHeader::GetNumberOfSlices(), svkDcmHeader::GetNumberOfTimePoints(), svkPhilipsSMapper::SetCellSpectrum(), svkPhilipsSMapper::specData, and svkPhilipsSMapper::VaxToFloat().

Referenced by svkPhilipsSReader::ExecuteDataWithInformation().

void SetCellSpectrum ( vtkImageData *  data,
int  x,
int  y,
int  z,
int  timePt,
int  coilNum 
)
protectedvirtual

References svkPhilipsSMapper::dcmHeader, svkDcmHeader::GetIntValue(), svkDcmHeader::GetNumberOfSlices(), svkDcmHeader::GetStringValue(), and svkPhilipsSMapper::specData.

Referenced by svkPhilipsSMapper::ReadSDATFile().

void VaxToFloat ( const void *  inbuf,
void *  outbuf,
const int *  count 
)
protected

References EXPONENT_ADJUSTMENT, HIDDEN_BIT, IN_PLACE_EXPONENT_ADJUSTMENT, MANTISSA_MASK, MANTISSA_SIZE, SIGN_BIT, and VAX_F_EXPONENT_MASK.

Referenced by svkPhilipsSMapper::ReadSDATFile().

vtkTypeMacro ( svkPhilipsSMapper  ,
vtkObject   
)

Member Data Documentation

svkDcmHeader::DcmDataOrderingDirection dataSliceOrder
protected

Referenced by svkPhilipsSMapper::InitPerFrameFunctionalGroupMacros(), and svkPhilipsSMapper::InitPlaneOrientationMacro().

svkDcmHeader* dcmHeader
protected

Referenced by svkPhilipsSMapper::InitGeneralEquipmentModule(), svkPhilipsSMapper::InitGeneralSeriesModule(), svkPhilipsSMapper::InitGeneralStudyModule(), svkPhilipsSMapper::InitializeDcmHeader(), svkPhilipsSMapper::InitMRAveragesMacro(), svkPhilipsSMapper::InitMREchoMacro(), svkPhilipsSMapper::InitMRModifierMacro(), svkPhilipsSMapper::InitMRReceiveCoilMacro(), svkPhilipsSMapper::InitMRSpectroscopyDataModule(), svkPhilipsSMapper::InitMRSpectroscopyFOVGeometryMacro(), svkPhilipsSMapper::InitMRSpectroscopyModule(), svkPhilipsSMapper::InitMRTimingAndRelatedParametersMacro(), svkPhilipsSMapper::InitMRTransmitCoilMacro(), svkPhilipsSMapper::InitMultiFrameDimensionModule(), svkPhilipsSMapper::InitMultiFrameFunctionalGroupsModule(), svkPhilipsSMapper::InitPatientModule(), svkPhilipsSMapper::InitPerFrameFunctionalGroupMacros(), svkPhilipsSMapper::InitPixelMeasuresMacro(), svkPhilipsSMapper::InitPlaneOrientationMacro(), svkPhilipsSMapper::ReadSDATFile(), and svkPhilipsSMapper::SetCellSpectrum().

svkMRSIOD* iod
protected

Referenced by svkPhilipsSMapper::InitializeDcmHeader().

int numFrames
protected

Referenced by svkPhilipsSMapper::InitMultiFrameFunctionalGroupsModule(), svkPhilipsSMapper::InitPerFrameFunctionalGroupMacros(), and svkPhilipsSMapper::svkPhilipsSMapper().

int numSlices
protected

Referenced by svkPhilipsSMapper::InitMultiFrameFunctionalGroupsModule().

map<string, string > sparMap
protected

Referenced by svkPhilipsSMapper::GetDcmDate(), svkPhilipsSMapper::GetDcmPatientPositionString(), svkPhilipsSMapper::GetHeaderValueAsFloat(), svkPhilipsSMapper::GetHeaderValueAsInt(), svkPhilipsSMapper::InitializeDcmHeader(), svkPhilipsSMapper::InitMRSpectroscopyModule(), and svkPhilipsSMapper::InitPatientModule().

float* specData
protected

Referenced by svkPhilipsSMapper::ReadSDATFile(), svkPhilipsSMapper::SetCellSpectrum(), svkPhilipsSMapper::svkPhilipsSMapper(), and svkPhilipsSMapper::~svkPhilipsSMapper().

int swapBytes
protected

Referenced by svkPhilipsSMapper::InitializeDcmHeader().

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