ImageD  v2_7_5 (24.06.22)
ImageD is an image processing software designed for rapid prototyping and implementing algorithms and solutions for science, research and teaching.
Public Member Functions | List of all members
D_Bio_NucleusImage Class Reference

#include <d_bio_nucleusimage.h>

Public Member Functions

 D_Bio_NucleusImage ()
 
 D_Bio_NucleusImage (vector< D_Bio_NucleusImage > vNucImgs2Merge, Point P_Offset_coordinates, Point P_Offset_mosaicgrid, size_t time)
 
 D_Bio_NucleusImage (Point P_Offset_coordinates, Point P_Offset_mosaicgrid, size_t time)
 
 D_Bio_NucleusImage (Mat *pMA_NucleiBinary, vector< Mat > *pvMA_FociBinary, vector< Mat > *pvMA_Values, Point P_Offset_coordinates=Point(0, 0), Point P_Offset_mosaicgrid=Point(0, 0), size_t time=0, int neighborhood=4, bool blockSave_StichBorder_BottomRight=false, size_t block_x_right=INFINITY, size_t block_y_bottom=INFINITY)
 
 D_Bio_NucleusImage (D_VisDat_Obj *pVD_NucleiBinary, vector< D_VisDat_Obj > *pvVD_FociBinary, vector< D_VisDat_Obj > *pvVD_Values, Point P_Offset_coordinates=Point(0, 0), Point P_Offset_mosaicgrid=Point(0, 0), size_t time=0, int neighborhood=4, bool blockSave_StichBorder_BottomRight=false, size_t block_x_right=INFINITY, size_t block_y_bottom=INFINITY)
 
 D_Bio_NucleusImage (vector< D_VisDat_Obj > *pvVD_Images, size_t index_NucleiBinary, vector< size_t > vIndices_FociBinary, vector< size_t > vIndices_Values, Point P_Offset_coordinates=Point(0, 0), Point P_Offset_mosaicgrid=Point(0, 0), size_t time=0, int neighborhood=4, bool blockSave_StichBorder_BottomRight=false, size_t block_x_right=INFINITY, size_t block_y_bottom=INFINITY)
 
int calc_NucleiDecomposition (D_VisDat_Obj *pVD_NucleiBinary, vector< D_VisDat_Obj > *pvVD_FociBinary, vector< D_VisDat_Obj > *pvVD_Values, Point P_Offset_coordinates=Point(0, 0), Point P_Offset_mosaicgrid=Point(0, 0), size_t time=0, int neighborhood=4, bool blockSave_StichBorder_BottomRight=false, size_t block_x_right=INFINITY, size_t block_y_bottom=INFINITY)
 
int calc_NucleiDecomposition (vector< D_VisDat_Obj > *pvVD_Images, size_t index_NucleiBinary, vector< size_t > vIndices_FociBinary, vector< size_t > vIndices_Values, Point P_Offset_coordinates=Point(0, 0), Point P_Offset_mosaicgrid=Point(0, 0), size_t time=0, int neighborhood=4, bool blockSave_StichBorder_BottomRight=false, size_t block_x_right=INFINITY, size_t block_y_bottom=INFINITY)
 
int calc_NucleiDecomposition (Mat *pMA_NucleiBinary, vector< Mat > *pvMA_FociBinary, vector< Mat > *pvMA_Values, Point P_Offset_coordinates=Point(0, 0), Point P_Offset_mosaicgrid=Point(0, 0), size_t time=0, int neighborhood=4, bool blockSave_StichBorder_BottomRight=false, size_t block_x_right=INFINITY, size_t block_y_bottom=INFINITY)
 
int load (QString path, bool foci_are_part_of_nuc_files)
 
int load_foci (QFileInfoList FIL_foci)
 
int save (QString path, bool save_foci_in_nuclei, bool save_foci_separate, bool save_name_mosaic_not_coordiante)
 
int save_PathExactDir (QString path, bool save_foci_in_nuclei, bool save_foci_separate, size_t x, size_t y, size_t t)
 
void set_OffsetMosaicGrid (Point OffsetMosaicGrid)
 
void set_OffsetPixels (Point OffsetPixels)
 
int get_Contours_append (vector< vector< Point >> *pvScaledContours, double scale)
 
vector< Point2f > get_Centroids (double scale, Point2f scaled_offset)
 
int get_Centroids_append (vector< Point2f > *pvScaledCentroids, double scale)
 
QStringList get_FociCounts ()
 
int get_FociCount_append (QStringList *pQSL_FociCounts)
 
int get_ShapeInfo_append (QStringList *pQSL_ShapeInfo)
 
int get_ChannelStat_append (QStringList *pQSL_Stat, size_t stat_index_bio_enum)
 
vector< D_Contour > get_nuclei_contour_objects ()
 
void get_nuclei_contour_objects_append (vector< D_Contour > *pvContours)
 
size_t get_nuclei_count ()
 
size_t get_foci_channel_count ()
 
size_t get_foci_count (size_t foci_channel)
 
vector< vector< Point > > get_nuclei_contours (double scale=1, Point scaled_offset=Point(0, 0))
 
vector< Point2f > get_nuclei_centers (double scale=1, Point scaled_offset=Point(0, 0))
 
vector< Point2f > get_foci_centers (size_t channel, double scale=1, Point scaled_offset=Point(0, 0))
 
vector< double > get_foci_radii (size_t channel, double scale=1)
 
vector< double > get_foci_diameters (size_t channel, double scale=1)
 
vector< D_Bio_NucleusBlob > get_nuclei ()
 
D_Bio_NucleusBlob get_nucleus (size_t nuc)
 
D_Bio_Focus get_focus (size_t ch, size_t foc)
 
QString info ()
 
void add_focus (size_t channel, D_Bio_Focus Foc)
 
void add_foci (size_t channel, vector< D_Bio_Focus > vFoc)
 
void add_nucleus (D_Bio_NucleusBlob Nuc)
 
void add_nuclei (vector< D_Bio_NucleusBlob > vNuc)
 
bool remove_focus (Point P, size_t channel, double margin=0)
 
void remove_foci (vector< Point > vP, size_t channel, double margin=0)
 
bool remove_nucleus (Point P, double margin=0)
 
void remove_nuclei (vector< Point > vP, double margin=0)
 
void remove_nuclei_foci_all ()
 
void remove_foci_all ()
 
void remove_nuclei_all ()
 
void remove_nuclei_dulicates (vector< D_Bio_NucleusImage > vNucImgOther, double min_rel_intersection_for_remove=0.5)
 

Constructor & Destructor Documentation

◆ D_Bio_NucleusImage() [1/6]

D_Bio_NucleusImage::D_Bio_NucleusImage ( )

◆ D_Bio_NucleusImage() [2/6]

D_Bio_NucleusImage::D_Bio_NucleusImage ( vector< D_Bio_NucleusImage >  vNucImgs2Merge,
Point  P_Offset_coordinates,
Point  P_Offset_mosaicgrid,
size_t  time 
)

◆ D_Bio_NucleusImage() [3/6]

D_Bio_NucleusImage::D_Bio_NucleusImage ( Point  P_Offset_coordinates,
Point  P_Offset_mosaicgrid,
size_t  time 
)

◆ D_Bio_NucleusImage() [4/6]

D_Bio_NucleusImage::D_Bio_NucleusImage ( Mat *  pMA_NucleiBinary,
vector< Mat > *  pvMA_FociBinary,
vector< Mat > *  pvMA_Values,
Point  P_Offset_coordinates = Point(0, 0),
Point  P_Offset_mosaicgrid = Point(0, 0),
size_t  time = 0,
int  neighborhood = 4,
bool  blockSave_StichBorder_BottomRight = false,
size_t  block_x_right = INFINITY,
size_t  block_y_bottom = INFINITY 
)

◆ D_Bio_NucleusImage() [5/6]

D_Bio_NucleusImage::D_Bio_NucleusImage ( D_VisDat_Obj *  pVD_NucleiBinary,
vector< D_VisDat_Obj > *  pvVD_FociBinary,
vector< D_VisDat_Obj > *  pvVD_Values,
Point  P_Offset_coordinates = Point(0, 0),
Point  P_Offset_mosaicgrid = Point(0, 0),
size_t  time = 0,
int  neighborhood = 4,
bool  blockSave_StichBorder_BottomRight = false,
size_t  block_x_right = INFINITY,
size_t  block_y_bottom = INFINITY 
)

◆ D_Bio_NucleusImage() [6/6]

D_Bio_NucleusImage::D_Bio_NucleusImage ( vector< D_VisDat_Obj > *  pvVD_Images,
size_t  index_NucleiBinary,
vector< size_t >  vIndices_FociBinary,
vector< size_t >  vIndices_Values,
Point  P_Offset_coordinates = Point(0, 0),
Point  P_Offset_mosaicgrid = Point(0, 0),
size_t  time = 0,
int  neighborhood = 4,
bool  blockSave_StichBorder_BottomRight = false,
size_t  block_x_right = INFINITY,
size_t  block_y_bottom = INFINITY 
)

Member Function Documentation

◆ add_foci()

void D_Bio_NucleusImage::add_foci ( size_t  channel,
vector< D_Bio_Focus >  vFoc 
)

◆ add_focus()

void D_Bio_NucleusImage::add_focus ( size_t  channel,
D_Bio_Focus  Foc 
)

◆ add_nuclei()

void D_Bio_NucleusImage::add_nuclei ( vector< D_Bio_NucleusBlob >  vNuc)

◆ add_nucleus()

void D_Bio_NucleusImage::add_nucleus ( D_Bio_NucleusBlob  Nuc)

◆ calc_NucleiDecomposition() [1/3]

int D_Bio_NucleusImage::calc_NucleiDecomposition ( D_VisDat_Obj *  pVD_NucleiBinary,
vector< D_VisDat_Obj > *  pvVD_FociBinary,
vector< D_VisDat_Obj > *  pvVD_Values,
Point  P_Offset_coordinates = Point(0, 0),
Point  P_Offset_mosaicgrid = Point(0, 0),
size_t  time = 0,
int  neighborhood = 4,
bool  blockSave_StichBorder_BottomRight = false,
size_t  block_x_right = INFINITY,
size_t  block_y_bottom = INFINITY 
)

◆ calc_NucleiDecomposition() [2/3]

int D_Bio_NucleusImage::calc_NucleiDecomposition ( Mat *  pMA_NucleiBinary,
vector< Mat > *  pvMA_FociBinary,
vector< Mat > *  pvMA_Values,
Point  P_Offset_coordinates = Point(0, 0),
Point  P_Offset_mosaicgrid = Point(0, 0),
size_t  time = 0,
int  neighborhood = 4,
bool  blockSave_StichBorder_BottomRight = false,
size_t  block_x_right = INFINITY,
size_t  block_y_bottom = INFINITY 
)

◆ calc_NucleiDecomposition() [3/3]

int D_Bio_NucleusImage::calc_NucleiDecomposition ( vector< D_VisDat_Obj > *  pvVD_Images,
size_t  index_NucleiBinary,
vector< size_t >  vIndices_FociBinary,
vector< size_t >  vIndices_Values,
Point  P_Offset_coordinates = Point(0, 0),
Point  P_Offset_mosaicgrid = Point(0, 0),
size_t  time = 0,
int  neighborhood = 4,
bool  blockSave_StichBorder_BottomRight = false,
size_t  block_x_right = INFINITY,
size_t  block_y_bottom = INFINITY 
)

◆ get_Centroids()

vector< Point2f > D_Bio_NucleusImage::get_Centroids ( double  scale,
Point2f  scaled_offset 
)

◆ get_Centroids_append()

int D_Bio_NucleusImage::get_Centroids_append ( vector< Point2f > *  pvScaledCentroids,
double  scale 
)

◆ get_ChannelStat_append()

int D_Bio_NucleusImage::get_ChannelStat_append ( QStringList *  pQSL_Stat,
size_t  stat_index_bio_enum 
)

◆ get_Contours_append()

int D_Bio_NucleusImage::get_Contours_append ( vector< vector< Point >> *  pvScaledContours,
double  scale 
)

◆ get_foci_centers()

vector< Point2f > D_Bio_NucleusImage::get_foci_centers ( size_t  channel,
double  scale = 1,
Point  scaled_offset = Point(0, 0) 
)

◆ get_foci_channel_count()

size_t D_Bio_NucleusImage::get_foci_channel_count ( )
inline

◆ get_foci_count()

size_t D_Bio_NucleusImage::get_foci_count ( size_t  foci_channel)
inline

◆ get_foci_diameters()

vector< double > D_Bio_NucleusImage::get_foci_diameters ( size_t  channel,
double  scale = 1 
)

◆ get_foci_radii()

vector< double > D_Bio_NucleusImage::get_foci_radii ( size_t  channel,
double  scale = 1 
)

◆ get_FociCount_append()

int D_Bio_NucleusImage::get_FociCount_append ( QStringList *  pQSL_FociCounts)

◆ get_FociCounts()

QStringList D_Bio_NucleusImage::get_FociCounts ( )

◆ get_focus()

D_Bio_Focus D_Bio_NucleusImage::get_focus ( size_t  ch,
size_t  foc 
)
inline

◆ get_nuclei()

vector<D_Bio_NucleusBlob> D_Bio_NucleusImage::get_nuclei ( )
inline

◆ get_nuclei_centers()

vector< Point2f > D_Bio_NucleusImage::get_nuclei_centers ( double  scale = 1,
Point  scaled_offset = Point(0, 0) 
)

◆ get_nuclei_contour_objects()

vector< D_Contour > D_Bio_NucleusImage::get_nuclei_contour_objects ( )

◆ get_nuclei_contour_objects_append()

void D_Bio_NucleusImage::get_nuclei_contour_objects_append ( vector< D_Contour > *  pvContours)

◆ get_nuclei_contours()

vector< vector< Point > > D_Bio_NucleusImage::get_nuclei_contours ( double  scale = 1,
Point  scaled_offset = Point(0, 0) 
)

◆ get_nuclei_count()

size_t D_Bio_NucleusImage::get_nuclei_count ( )
inline

◆ get_nucleus()

D_Bio_NucleusBlob D_Bio_NucleusImage::get_nucleus ( size_t  nuc)
inline

◆ get_ShapeInfo_append()

int D_Bio_NucleusImage::get_ShapeInfo_append ( QStringList *  pQSL_ShapeInfo)

◆ info()

QString D_Bio_NucleusImage::info ( )

◆ load()

int D_Bio_NucleusImage::load ( QString  path,
bool  foci_are_part_of_nuc_files 
)

◆ load_foci()

int D_Bio_NucleusImage::load_foci ( QFileInfoList  FIL_foci)

◆ remove_foci()

void D_Bio_NucleusImage::remove_foci ( vector< Point >  vP,
size_t  channel,
double  margin = 0 
)

◆ remove_foci_all()

void D_Bio_NucleusImage::remove_foci_all ( )

◆ remove_focus()

bool D_Bio_NucleusImage::remove_focus ( Point  P,
size_t  channel,
double  margin = 0 
)

◆ remove_nuclei()

void D_Bio_NucleusImage::remove_nuclei ( vector< Point >  vP,
double  margin = 0 
)

◆ remove_nuclei_all()

void D_Bio_NucleusImage::remove_nuclei_all ( )

◆ remove_nuclei_dulicates()

void D_Bio_NucleusImage::remove_nuclei_dulicates ( vector< D_Bio_NucleusImage >  vNucImgOther,
double  min_rel_intersection_for_remove = 0.5 
)

◆ remove_nuclei_foci_all()

void D_Bio_NucleusImage::remove_nuclei_foci_all ( )

◆ remove_nucleus()

bool D_Bio_NucleusImage::remove_nucleus ( Point  P,
double  margin = 0 
)

◆ save()

int D_Bio_NucleusImage::save ( QString  path,
bool  save_foci_in_nuclei,
bool  save_foci_separate,
bool  save_name_mosaic_not_coordiante 
)

◆ save_PathExactDir()

int D_Bio_NucleusImage::save_PathExactDir ( QString  path,
bool  save_foci_in_nuclei,
bool  save_foci_separate,
size_t  x,
size_t  y,
size_t  t 
)

◆ set_OffsetMosaicGrid()

void D_Bio_NucleusImage::set_OffsetMosaicGrid ( Point  OffsetMosaicGrid)
inline

◆ set_OffsetPixels()

void D_Bio_NucleusImage::set_OffsetPixels ( Point  OffsetPixels)
inline
The documentation for this class was generated from the following files: