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Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | List of all members
Segmentation Class Reference

#include <segmentation.h>

Public Member Functions

 SMART_POINTER_SUPPORT (Segmentation)
 
 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_roiadd_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 ()
 
Rtssget_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 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)
 

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)

◆ 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)

◆ SMART_POINTER_SUPPORT()

Segmentation::SMART_POINTER_SUPPORT ( Segmentation  )

◆ 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: