Developer documentation
Version 3.0.3-105-gd3941f44
MR::DWI::Tractography Namespace Reference

Namespaces

namespace  ACT
 
namespace  Algorithms
 
namespace  Connectome
 
namespace  Editing
 
namespace  GT
 
namespace  Mapping
 
namespace  Resampling
 
namespace  Seeding
 
namespace  SIFT
 
namespace  SIFT2
 
namespace  Tracking
 

Classes

class  DataIndex
 
class  IncludeROIVisitation
 
class  Mask
 
class  Properties
 
class  Reader
 A class to read streamlines data. More...
 
class  ReaderInterface
 
class  ROI
 
class  ROIOrderedSet
 
class  ROISetBase
 
class  ROIUnorderedSet
 
class  ScalarReader
 
class  ScalarWriter
 class to handle writing track scalars to file More...
 
class  Streamline
 
class  TrackScalar
 
class  Writer
 class to handle writing tracks to file, with RAM buffer More...
 
class  WriterInterface
 
class  WriterUnbuffered
 class to handle unbuffered writing of tracks to file More...
 

Functions

void check_timestamps (const Properties &, const Properties &, const std::string &)
 
void check_counts (const Properties &, const Properties &, const std::string &, bool abort_on_fail)
 
void load_rois (Properties &properties)
 
void check_properties_match (const Properties &p_tck, const Properties &p_tsf, const std::string &type, bool abort_on_fail=true)
 convenience function to verify that tck/tsf files match More...
 
template<typename PointType >
PointType::Scalar length (const vector< PointType > &tck)
 

Variables

thread_local Math::RNG rng
 thread-local, but globally accessible RNG to vastly simplify multi-threading More...
 
const App::OptionGroup ROIOption
 
const App::Option TrackWeightsInOption
 
const App::Option TrackWeightsOutOption
 

Function Documentation

◆ check_counts()

void MR::DWI::Tractography::check_counts ( const Properties ,
const Properties ,
const std::string &  ,
bool  abort_on_fail 
)

◆ check_properties_match()

void MR::DWI::Tractography::check_properties_match ( const Properties p_tck,
const Properties p_tsf,
const std::string &  type,
bool  abort_on_fail = true 
)
inline

convenience function to verify that tck/tsf files match

in order to be interpreted correctly, track scalar files must match some corresponding streamline data (.tck) file; this is handled using the timestamp field in the Properties class. Alternatively two .tsf files may be processed, but these must both correspond to the same .tck file (even if that file is not explicitly read).

Furthermore, in some contexts it may be necessary to ensure that two files contain the same number of streamlines (or scalar data corresponding to the same number of streamlines). This check is also provided: if abort_on_fail is true, a mis-match of the 'count' field results in an exception being thrown, otherwise only a warning is issued and processing is free to continue.

The type argument is used to specify the type of files being compared, so that more appropriate information can be shown to the user in the event of a mismatch.

Definition at line 58 of file scalar_file.h.

◆ check_timestamps()

void MR::DWI::Tractography::check_timestamps ( const Properties ,
const Properties ,
const std::string &   
)

◆ length()

template<typename PointType >
PointType::Scalar MR::DWI::Tractography::length ( const vector< PointType > &  tck)

Definition at line 134 of file streamline.h.

◆ load_rois()

void MR::DWI::Tractography::load_rois ( Properties properties)

Variable Documentation

◆ rng

thread_local Math::RNG MR::DWI::Tractography::rng
extern

thread-local, but globally accessible RNG to vastly simplify multi-threading

◆ ROIOption

const App::OptionGroup MR::DWI::Tractography::ROIOption
extern

◆ TrackWeightsInOption

const App::Option MR::DWI::Tractography::TrackWeightsInOption
extern

◆ TrackWeightsOutOption

const App::Option MR::DWI::Tractography::TrackWeightsOutOption
extern