brainrat-private 6.0.4
Public Member Functions | Protected Member Functions | List of all members
HistologyScanSlicesDetector Class Reference

#include <brainrat/data/slices.h>

Public Member Functions

 HistologyScanSlicesDetector (float slice_min_surface=1., float slice_median_variation=1./FRACTION, int32_t histogram_modes=NB_MODES, int32_t histogram_bins=MAX_HISTO, bool check_slices=true)
 
carto::Object boundingBoxes (const carto::VolumeRef< int16_t > &vol, const std::vector< Component > &components)
 
std::vector< Component > analyze (carto::VolumeRef< int16_t > &vol, const int32_t slices_number=6, const int32_t scan_resolution=0, const int32_t threshold_lowerbound=0, const int32_t threshold_upperbound=0)
 

Protected Member Functions

bool detectHistogramModes (const carto::VolumeRef< int32_t > &histogram, const int32_t slices_number, const int32_t slices_min_voxels, const HistoAnalysisFunction analysis_function, int32_t &background, int32_t &slices_mode_lowerbound, int32_t &slices_mode_upperbound)
 
std::vector< Component > detectComponents (carto::VolumeRef< int16_t > &vol, const int32_t slices_number, const int32_t threshold_lowerbound, const int32_t threshold_upperbound)
 
std::vector< Component > checkComponents (carto::VolumeRef< int16_t > &vol, std::vector< Component > &components, const int32_t slices_number)
 
std::vector< Component > processOutlierComponents (std::vector< Component > &components, carto::VolumeRef< int16_t > &vol, const int32_t slices_number)
 
std::vector< Component > openComponent (const std::vector< Component > &components, const int32_t component, carto::VolumeRef< int16_t > &vol)
 
std::vector< Component > separateComponent (const std::vector< Component > &components, const int32_t component, carto::VolumeRef< int16_t > &vol, const Direction dir)
 
void writeTestsWarnings (const Tests &t)
 

Detailed Description

Definition at line 186 of file slices.h.

Constructor & Destructor Documentation

◆ HistologyScanSlicesDetector()

HistologyScanSlicesDetector::HistologyScanSlicesDetector ( float slice_min_surface = 1.,
float slice_median_variation = 1./FRACTION,
int32_t histogram_modes = NB_MODES,
int32_t histogram_bins = MAX_HISTO,
bool check_slices = true )

References FRACTION, MAX_HISTO, and NB_MODES.

Member Function Documentation

◆ analyze()

std::vector< Component > HistologyScanSlicesDetector::analyze ( carto::VolumeRef< int16_t > & vol,
const int32_t slices_number = 6,
const int32_t scan_resolution = 0,
const int32_t threshold_lowerbound = 0,
const int32_t threshold_upperbound = 0 )

Referenced by detectSlices(), and individStackSlices().

◆ boundingBoxes()

carto::Object HistologyScanSlicesDetector::boundingBoxes ( const carto::VolumeRef< int16_t > & vol,
const std::vector< Component > & components )

Referenced by detectSlices().

◆ checkComponents()

std::vector< Component > HistologyScanSlicesDetector::checkComponents ( carto::VolumeRef< int16_t > & vol,
std::vector< Component > & components,
const int32_t slices_number )
protected

◆ detectComponents()

std::vector< Component > HistologyScanSlicesDetector::detectComponents ( carto::VolumeRef< int16_t > & vol,
const int32_t slices_number,
const int32_t threshold_lowerbound,
const int32_t threshold_upperbound )
protected

◆ detectHistogramModes()

bool HistologyScanSlicesDetector::detectHistogramModes ( const carto::VolumeRef< int32_t > & histogram,
const int32_t slices_number,
const int32_t slices_min_voxels,
const HistoAnalysisFunction analysis_function,
int32_t & background,
int32_t & slices_mode_lowerbound,
int32_t & slices_mode_upperbound )
protected

References background().

◆ openComponent()

std::vector< Component > HistologyScanSlicesDetector::openComponent ( const std::vector< Component > & components,
const int32_t component,
carto::VolumeRef< int16_t > & vol )
protected

◆ processOutlierComponents()

std::vector< Component > HistologyScanSlicesDetector::processOutlierComponents ( std::vector< Component > & components,
carto::VolumeRef< int16_t > & vol,
const int32_t slices_number )
protected

◆ separateComponent()

std::vector< Component > HistologyScanSlicesDetector::separateComponent ( const std::vector< Component > & components,
const int32_t component,
carto::VolumeRef< int16_t > & vol,
const Direction dir )
protected

◆ writeTestsWarnings()

void HistologyScanSlicesDetector::writeTestsWarnings ( const Tests & t)
protected
The documentation for this class was generated from the following file: