Public Member Functions

NrrdData Class Reference

Class wrapping teem nrrd for loading nrrd files. More...

#include <NrrdData.h>

Inheritance diagram for NrrdData:
ISignalData ISignalData

List of all members.

Public Member Functions

 NrrdData (double sigma_signal, double sigma_mask)
 ~NrrdData ()
virtual void Interp3Signal (const vec_t &pos, std::vector< double > &signal) const
virtual double Interp3ScalarMask (const vec_t &pos) const
virtual void GetSeeds (const std::vector< int > &labels, std::vector< vec_t > &seeds) const
 Get the seed points from the nrrd file.
virtual const std::vector
< vec_t > & 
gradients () const
virtual const std::vector
< double > & 
GetBValues () const
virtual int GetSignalDimension () const
virtual bool LoadData (const std::string &data_file, const std::string &seed_file, const std::string &mask_file, const bool normalizedDWIData, const bool outputNormalizedDWIData)
 Load all Data.
virtual bool LoadSignal (const std::string &data_file, const bool normalizedDWIData)
virtual vec_t dim () const

Detailed Description

Class wrapping teem nrrd for loading nrrd files.


Constructor & Destructor Documentation

NrrdData::NrrdData ( double  sigma_signal,
double  sigma_mask 
)

Constructor

NrrdData::~NrrdData (  ) 

Destructor


Member Function Documentation

virtual vec_t NrrdData::dim (  )  const [inline, virtual]

Returns the dimensions of the signal in each directions as a vector

Implements ISignalData.

virtual const std::vector<double>& NrrdData::GetBValues (  )  const [inline, virtual]

returns the vector of b-values of the diffusion image
Note: Except for cases recorded with multiple b-values it contains identical values

Implements ISignalData.

void NrrdData::GetSeeds ( const std::vector< int > &  labels,
std::vector< vec_t > &  seeds 
) const [virtual]

Get the seed points from the nrrd file.

Takes care of different seed data types by type casting

Parameters:
[in] labels a vector of labels that define the seed region
[out] seeds a vector containing the positions in ijk-space of the seeds

Implements ISignalData.

virtual int NrrdData::GetSignalDimension (  )  const [inline, virtual]

returns the dimension of the signal
Note: The actual signal vector will be twice this size

Implements ISignalData.

virtual const std::vector<vec_t>& NrrdData::gradients (  )  const [inline, virtual]

returns the gradients of the diffusion image

Implements ISignalData.

double NrrdData::Interp3ScalarMask ( const vec_t pos  )  const [virtual]

Interpolates the brain mask at a certain position

Implements ISignalData.

void NrrdData::Interp3Signal ( const vec_t pos,
std::vector< double > &  signal 
) const [virtual]

Interpolates the DWI signal at a certain position

Implements ISignalData.

bool NrrdData::LoadData ( const std::string &  data_file,
const std::string &  seed_file,
const std::string &  mask_file,
const bool  normalizedDWIData,
const bool  outputNormalizedDWIData 
) [virtual]

Load all Data.

Parameters:
[in] data_file The path of the diffusion image
[in] seed_file The path of the seeds, a binary label map containing the starting points
[in] mask_file The path of the non-optional brain mask
[in] normalizedDWIData If set to 'true', the data will not be normalized
[in] outputNormalizedDWIData If set to 'true' the result of the normalization will be saved

Loads all the data necessary to perform tractography

Implements ISignalData.

bool NrrdData::LoadSignal ( const std::string &  data_file,
const bool  normalizedDWIData 
) [virtual]

Load the signal, called by LoadData

Todo:
Should be a private function of this class, and not implementing ISignalData

Implements ISignalData.


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