Segmentation Class Reference

#include <segmentation.h>

Public Types
typedef Segmentation	Self
typedef std::shared_ptr< Self >	Pointer

Public Member Functions
	Segmentation ()
	~Segmentation ()
void	clear ()
void	load (const char *ss_img, const char *ss_list)
void	load_cxt (const std::string &input_fn, Rt_study_metadata *rsm)
void	load_prefix (const char *prefix_dir)
void	load_prefix (const std::string &prefix_dir)
void	load_xio (const Xio_studyset &xio_studyset)
size_t	get_num_structures ()
std::string	get_structure_name (size_t index)
void	set_structure_name (size_t index, const std::string &name)
UCharImageType::Pointer	get_structure_image (int index)
void	save_colormap (const std::string &colormap_fn)
void	save_cxt (const Rt_study_metadata::Pointer &rsm, const std::string &cxt_fn, bool prune_empty)
void	save_fcsv (const Rtss_roi *curr_structure, const std::string &fn)
void	save_prefix_fcsv (const std::string &output_prefix)
void	save_ss_image (const std::string &ss_img_fn)
void	save_labelmap (const std::string &labelmap_fn)
void	save_opt4d (const std::string &output_prefix)
void	save_prefix (const std::string &output_prefix, const std::string &extension="mha")
void	save_prefix (const char *output_prefix)
void	save_ss_list (const std::string &ss_list_fn)
void	save_xio (const Rt_study_metadata::Pointer &rsm, Xio_ct_transform *xio_transform, Xio_version xio_version, const std::string &output_dir)
UInt32ImageType::Pointer	get_ss_img_uint32 (void)
UCharVecImageType::Pointer	get_ss_img_uchar_vec (void)
void	apply_dicom_dir (const Rt_study_metadata::Pointer &rsm)
void	convert_ss_img_to_cxt (void)
void	convert_to_uchar_vec (void)
void	cxt_extract (void)
void	cxt_re_extract (void)
void	prune_empty (void)
void	keyholize ()
void	rasterize (Plm_image_header *pih, bool want_labelmap, bool xor_overlapping)
void	set_geometry (const Plm_image_header *pih)
void	find_rasterization_geometry (Plm_image_header *pih)
Segmentation::Pointer	warp_nondestructive (const Xform::Pointer &xf, Plm_image_header *pih, bool use_itk=false) const
void	warp (const Xform::Pointer &xf, Plm_image_header *pih, bool use_itk=false)
void	warp (const Xform::Pointer &xf, Plm_image_header *pih, Warp_parms *parms)
void	add_structure (UCharImageType::Pointer itk_image, const char *structure_name=0, const char *structure_color=0)
Rtss_roi *	add_rtss_roi (const char *structure_name=0, const char *structure_color=0)
bool	have_ss_img ()
void	set_ss_img (UCharImageType::Pointer ss_img)
Plm_image::Pointer	get_ss_img ()
bool	have_structure_set ()
Rtss::Pointer &	get_structure_set ()
Rtss *	get_structure_set_raw ()
void	set_structure_set (Rtss::Pointer &rtss_ss)
void	set_structure_set (Rtss *rtss_ss)
void	set_structure_image (UCharImageType::Pointer uchar_img, unsigned int bit)
void	resample (float spacing[3])

Static Public Member Functions
static Segmentation::Pointer	New ()
static Segmentation::Pointer	New (Segmentation *t)
template<class U1>
static Segmentation::Pointer	New (const U1 &u1)
template<class U1, class U2>
static Segmentation::Pointer	New (const U1 &u1, const U2 &u2)
template<class U1, class U2, class U3>
static Segmentation::Pointer	New (const U1 &u1, const U2 &u2, const U3 &u3)
template<class U1, class U2, class U3, class U4, class U5, class U6>
static Segmentation::Pointer	New (const U1 &u1, const U2 &u2, const U3 &u3, const U4 &u4, const U5 &u5, const U6 &u6)
static bool	valid_extension (const char *filename)

Public Attributes
Segmentation_private *	d_ptr

Protected Member Functions
void	initialize_ss_image (const Plm_image_header &pih, int vector_length)
void	broaden_ss_image (int new_vector_length)

Member Typedef Documentation

Pointer

typedef std::shared_ptr<Self> Segmentation::Pointer

Self

typedef Segmentation Segmentation::Self

Constructor & Destructor Documentation

Segmentation()

Segmentation::Segmentation

(

)

~Segmentation()

Segmentation::~Segmentation

(

)

Member Function Documentation

add_rtss_roi()

Rtss_roi * Segmentation::add_rtss_roi	(	const char *	structure_name = 0,
		const char *	structure_color = 0 )

add_structure()

void Segmentation::add_structure	(	UCharImageType::Pointer	itk_image,
		const char *	structure_name = 0,
		const char *	structure_color = 0 )

apply_dicom_dir()

void Segmentation::apply_dicom_dir

(

const Rt_study_metadata::Pointer &

rsm

)

broaden_ss_image()

void Segmentation::broaden_ss_image ( int new_vector_length )

protected

clear()

void Segmentation::clear

(

)

convert_ss_img_to_cxt()

void Segmentation::convert_ss_img_to_cxt

(

void

)

convert_to_uchar_vec()

void Segmentation::convert_to_uchar_vec

(

void

)

cxt_extract()

void Segmentation::cxt_extract

(

void

)

cxt_re_extract()

void Segmentation::cxt_re_extract

(

void

)

find_rasterization_geometry()

void Segmentation::find_rasterization_geometry

(

Plm_image_header *

pih

)

get_num_structures()

size_t Segmentation::get_num_structures

(

)

get_ss_img()

Plm_image::Pointer Segmentation::get_ss_img

(

)

get_ss_img_uchar_vec()

UCharVecImageType::Pointer Segmentation::get_ss_img_uchar_vec

(

void

)

get_ss_img_uint32()

UInt32ImageType::Pointer Segmentation::get_ss_img_uint32

(

void

)

get_structure_image()

UCharImageType::Pointer Segmentation::get_structure_image

(

int

index

)

get_structure_name()

std::string Segmentation::get_structure_name

(

size_t

index

)

get_structure_set()

Rtss::Pointer & Segmentation::get_structure_set

(

)

get_structure_set_raw()

Rtss * Segmentation::get_structure_set_raw

(

)

have_ss_img()

bool Segmentation::have_ss_img

(

)

have_structure_set()

bool Segmentation::have_structure_set

(

)

initialize_ss_image()

void Segmentation::initialize_ss_image ( const Plm_image_header & pih, int vector_length )

protected

keyholize()

void Segmentation::keyholize

(

)

load()

void Segmentation::load	(	const char *	ss_img,
		const char *	ss_list )

load_cxt()

void Segmentation::load_cxt	(	const std::string &	input_fn,
		Rt_study_metadata *	rsm )

load_prefix() [1/2]

void Segmentation::load_prefix

(

const char *

prefix_dir

)

load_prefix() [2/2]

void Segmentation::load_prefix

(

const std::string &

prefix_dir

)

load_xio()

void Segmentation::load_xio

(

const Xio_studyset &

xio_studyset

)

New() [1/6]

static Segmentation::Pointer Segmentation::New ( )

inlinestatic

New() [2/6]

template<class U1>

static Segmentation::Pointer Segmentation::New ( const U1 & u1 )

inlinestatic

New() [3/6]

template<class U1, class U2>

static Segmentation::Pointer Segmentation::New ( const U1 & u1, const U2 & u2 )

inlinestatic

New() [4/6]

template<class U1, class U2, class U3>

static Segmentation::Pointer Segmentation::New ( const U1 & u1, const U2 & u2, const U3 & u3 )

inlinestatic

New() [5/6]

template<class U1, class U2, class U3, class U4, class U5, class U6>

static Segmentation::Pointer Segmentation::New ( const U1 & u1, const U2 & u2, const U3 & u3, const U4 & u4, const U5 & u5, const U6 & u6 )

inlinestatic

New() [6/6]

static Segmentation::Pointer Segmentation::New ( Segmentation * t )

inlinestatic

prune_empty()

void Segmentation::prune_empty

(

void

)

rasterize()

void Segmentation::rasterize	(	Plm_image_header *	pih,
		bool	want_labelmap,
		bool	xor_overlapping )

resample()

void Segmentation::resample

(

float

spacing[3]

)

save_colormap()

void Segmentation::save_colormap

(

const std::string &

colormap_fn

)

save_cxt()

void Segmentation::save_cxt	(	const Rt_study_metadata::Pointer &	rsm,
		const std::string &	cxt_fn,
		bool	prune_empty )

save_fcsv()

void Segmentation::save_fcsv	(	const Rtss_roi *	curr_structure,
		const std::string &	fn )

save_labelmap()

void Segmentation::save_labelmap

(

const std::string &

labelmap_fn

)

save_opt4d()

void Segmentation::save_opt4d

(

const std::string &

output_prefix

)

save_prefix() [1/2]

void Segmentation::save_prefix

(

const char *

output_prefix

)

save_prefix() [2/2]

void Segmentation::save_prefix	(	const std::string &	output_prefix,
		const std::string &	extension = "mha" )

save_prefix_fcsv()

void Segmentation::save_prefix_fcsv

(

const std::string &

output_prefix

)

save_ss_image()

void Segmentation::save_ss_image

(

const std::string &

ss_img_fn

)

save_ss_list()

void Segmentation::save_ss_list

(

const std::string &

ss_list_fn

)

save_xio()

void Segmentation::save_xio	(	const Rt_study_metadata::Pointer &	rsm,
		Xio_ct_transform *	xio_transform,
		Xio_version	xio_version,
		const std::string &	output_dir )

set_geometry()

void Segmentation::set_geometry

(

const Plm_image_header *

pih

)

set_ss_img()

void Segmentation::set_ss_img

(

UCharImageType::Pointer

ss_img

)

set_structure_image()

void Segmentation::set_structure_image	(	UCharImageType::Pointer	uchar_img,
		unsigned int	bit )

set_structure_name()

void Segmentation::set_structure_name	(	size_t	index,
		const std::string &	name )

set_structure_set() [1/2]

void Segmentation::set_structure_set

(

Rtss *

rtss_ss

)

set_structure_set() [2/2]

void Segmentation::set_structure_set

(

Rtss::Pointer &

rtss_ss

)

valid_extension()

bool Segmentation::valid_extension ( const char * filename )

static

warp() [1/2]

void Segmentation::warp	(	const Xform::Pointer &	xf,
		Plm_image_header *	pih,
		bool	use_itk = false )

warp() [2/2]

void Segmentation::warp	(	const Xform::Pointer &	xf,
		Plm_image_header *	pih,
		Warp_parms *	parms )

warp_nondestructive()

Segmentation::Pointer Segmentation::warp_nondestructive	(	const Xform::Pointer &	xf,
		Plm_image_header *	pih,
		bool	use_itk = false ) const

Member Data Documentation

d_ptr

Segmentation_private* Segmentation::d_ptr

---

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

• src/base/segmentation.h
• src/base/segmentation.cxx