Index

A

abort_info_boost (C++ member) abort_info_petsc (C++ member)

abort_with_unhandled_error (C++ function), [1] all_true (C++ function) all_true_varlen (C++ function)

B

BadConfigurationError (C++ class) BadConfigurationError::BadConfigurationError (C++ function) BaseLoader (C++ class) BaseLoader::_comm (C++ member) BaseLoader::_loaders (C++ member) BaseLoader::_path (C++ member) BaseLoader::_shape (C++ member) BaseLoader::BaseLoader (C++ function) BaseLoader::copy_scaled_chunk (C++ function) BaseLoader::find_loader (C++ function) BaseLoader::loader_creator (C++ type) BaseLoader::loader_map (C++ type) BaseLoader::loaders (C++ function) BaseLoader::register_loader (C++ function) BaseLoader::shape (C++ function) BaseLoader::~BaseLoader (C++ function) BaseLoader_unique (C++ type) BaseWriter (C++ class) BaseWriter::_comm (C++ member) BaseWriter::_components (C++ member) BaseWriter::_creators (C++ member) BaseWriter::_extension_handlers (C++ member) BaseWriter::_truncated_files (C++ member) BaseWriter::BaseWriter (C++ function) BaseWriter::check_truncated (C++ function)

BaseWriter::create_writer (C++ function) BaseWriter::creator_map (C++ type) BaseWriter::extension_map (C++ type) BaseWriter::extensions (C++ member) BaseWriter::extra_path (C++ member) BaseWriter::filename (C++ member) BaseWriter::find_writer_for_filename (C++ function) BaseWriter::get_writer_by_name (C++ function) BaseWriter::get_writer_for_filename (C++ function) BaseWriter::mark_truncated (C++ function) BaseWriter::register_writer (C++ function) BaseWriter::split_filespec (C++ function) BaseWriter::string_pair (C++ type) BaseWriter::write_image (C++ function) BaseWriter::write_map (C++ function) BaseWriter::writer_creator (C++ type) BaseWriter::writer_name (C++ member) BaseWriter::~BaseWriter (C++ function) BaseWriter_unique (C++ type) binarize_vector (C++ function), [1] block_precondition (C++ function), [1] build_basis_matrix (C++ function), [1] build_laplacian_autostride (C++ function), [1] build_laplacian_matrix (C++ function), [1] build_warp_matrix (C++ function), [1]

C

calculate_basis_coefficient (C++ function) check_comm_size_and_warn_odd (C++ function), [1] clamp_to_edge (C++ function) command line option debug_frames fixed lambda map max_iterations moved nodespacing registered verbose config_map (C++ type) ConfigurationBase (C++ class) ConfigurationBase::arguments (C++ member) ConfigurationBase::config (C++ member) ConfigurationBase::ConfigurationBase (C++ function) ConfigurationBase::get_invocation_name (C++ function) ConfigurationBase::grab (C++ function), [1], [2], [3]

ConfigurationBase::invocation_name (C++ member) ConfigurationBase::k_extension_token (C++ member) ConfigurationBase::k_inner_token (C++ member) ConfigurationBase::k_outer_token (C++ member) ConfigurationBase::k_stem_token (C++ member) ConfigurationBase::required_options (C++ member) ConfigurationBase::validate_config (C++ function) copy_nth_from_stack_nat_to_petsc (C++ function), [1] create_shared_dm (C++ function) create_shared_is (C++ function) create_shared_ksp (C++ function) create_shared_mat (C++ function) create_shared_vec (C++ function) create_shared_vecscatter (C++ function) create_unique_dm (C++ function) create_unique_imagecache (C++ function) create_unique_is (C++ function) create_unique_ksp (C++ function) create_unique_mat (C++ function) create_unique_vec (C++ function) create_unique_vecscatter (C++ function)

D

DCMLoader (C++ class) DCMLoader::_datafile (C++ member) DCMLoader::copy_scaled_chunk (C++ function) DCMLoader::Create_Loader (C++ function) DCMLoader::DCMLoader (C++ function) DCMLoader::loader_name (C++ member) DCMLoader::~DCMLoader (C++ function) debug_creation (C macro) debug_deletion (C macro)

debug_frames command line option diagonal_sum (C++ function), [1] dilate_dmda (C++ function), [1] DM_shared (C++ type) DM_unique (C++ type) DMDeleter (C++ class) DMDeleter::operator() (C++ function) do_debug_creation (C++ function) do_debug_deletion (C++ function)

E

Elastic (C++ class) Elastic::approximate_optimum_lambda (C++ function) Elastic::autoregister (C++ function) Elastic::calculate_node_spacings (C++ function) Elastic::calculate_tmat (C++ function) Elastic::configuration (C++ member) Elastic::Elastic (C++ function) Elastic::innerloop (C++ function) Elastic::innerstep (C++ function) Elastic::k_lambda_default (C++ member) Elastic::k_lambda_min (C++ member) Elastic::m_comm (C++ member) Elastic::m_convergence_thres (C++ member) Elastic::m_fixed (C++ member) Elastic::m_imgdims (C++ member) Elastic::m_iternum (C++ member)

Elastic::m_lambda (C++ member) Elastic::m_mapdims (C++ member) Elastic::m_mask (C++ member) Elastic::m_max_iter (C++ member) Elastic::m_moved (C++ member) Elastic::m_p_map (C++ member) Elastic::m_p_registered (C++ member) Elastic::m_size (C++ member) Elastic::m_v_final_nodespacing (C++ member) Elastic::m_v_nodespacings (C++ member) Elastic::m_workspace (C++ member) Elastic::normmat (C++ member) Elastic::registered (C++ function) Elastic::save_debug_frame (C++ function) Elastic::save_debug_map (C++ function) ensure_directories_exist (C++ function), [1] explain_memory (C++ function)

F

fd (C++ type) fd::gradient_existing (C++ function) fd::gradient_to_global_unique (C++ function) FileNotFoundError (C++ class) FileNotFoundError::build_errstring (C++ function)

FileNotFoundError::FileNotFoundError (C++ function) fixed command line option floating (C++ type) floatvector (C++ type) floatvector2d (C++ type)

G

get_condnum_by_poweriter (C++ function), [1] get_eigenvalue_by_poweriter (C++ function), [1] get_invocation_name (C++ function)

get_version_string_boost (C++ function), [1] get_version_string_petsc (C++ function), [1] git_commit_string (C++ function) git_version_string (C++ function)

H

HDFWriter (C++ class) HDFWriter::_file_h (C++ member) HDFWriter::extensions (C++ member) HDFWriter::h5_filename (C++ member) HDFWriter::h5_groupname (C++ member) HDFWriter::HDFWriter (C++ function)

HDFWriter::open_or_create_h5 (C++ function) HDFWriter::write_1d_dataset_rank0 (C++ function) HDFWriter::write_3d_dataset_parallel (C++ function) HDFWriter::write_image (C++ function) HDFWriter::write_map (C++ function) HDFWriter::writer_name (C++ member) HDFWriter::~HDFWriter (C++ function)

I

idx_cmaj_to_rmaj (C++ function) Image (C++ class) Image::copy (C++ function) Image::duplicate (C++ function) Image::Image (C++ function), [1] Image::load_file (C++ function) Image::operator= (C++ function) ImageBase (C++ class) ImageBase::binarize (C++ function) ImageBase::comm (C++ function) ImageBase::copy (C++ function) ImageBase::copy_data (C++ function) ImageBase::dmda (C++ function) ImageBase::duplicate (C++ function) ImageBase::get_raw_data_natural (C++ function) ImageBase::get_raw_data_ro (C++ function) ImageBase::get_raw_data_row_major (C++ function) ImageBase::global_vec (C++ function) ImageBase::gradient (C++ function) ImageBase::ImageBase (C++ function), [1] ImageBase::initialize_dmda (C++ function) ImageBase::initialize_vectors (C++ function) ImageBase::instance_id (C++ member) ImageBase::instance_id_counter (C++ member) ImageBase::local_vec (C++ function) ImageBase::m_comm (C++ member) ImageBase::m_dmda (C++ member) ImageBase::m_globalvec (C++ member) ImageBase::m_localvec (C++ member) ImageBase::m_ndim (C++ member) ImageBase::m_shape (C++ member) ImageBase::masked_normalize (C++ function) ImageBase::mi_resolution (C++ member) ImageBase::mpi_get_chunksize (C++ function) ImageBase::mpi_get_offset (C++ function) ImageBase::mutual_information (C++ function) ImageBase::ndim (C++ function) ImageBase::normalize (C++ function) ImageBase::operator= (C++ function)

ImageBase::release_raw_data_ro (C++ function) ImageBase::scatter_to_zero (C++ function) ImageBase::shape (C++ function) ImageBase::size (C++ function) ImageBase::update_local_from_global (C++ function) ImageCache_unique (C++ type) ImageCacheDeleter (C++ class) ImageCacheDeleter::operator() (C++ function) infix_ostream_iterator (C++ class) infix_ostream_iterator::char_type (C++ type) infix_ostream_iterator::delimiter (C++ member) infix_ostream_iterator::infix_ostream_iterator (C++ function), [1] infix_ostream_iterator::operator* (C++ function) infix_ostream_iterator::operator++ (C++ function), [1] infix_ostream_iterator::operator= (C++ function) infix_ostream_iterator::os (C++ member) infix_ostream_iterator::ostream_type (C++ type) infix_ostream_iterator::real_delim (C++ member) infix_ostream_iterator::traits_type (C++ type) IniConfig (C++ class) IniConfig::IniConfig (C++ function) IniConfig::parse_arguments (C++ function) IniConfig::read_config_file (C++ function) IniConfig::usage (C++ function) IniConfig::valid_invocation (C++ function) integer (C++ type) InternalError (C++ class) InternalError::build_errstring (C++ function) InternalError::InternalError (C++ function) intvector (C++ type) intvector2d (C++ type) InvalidLoaderError (C++ class) InvalidLoaderError::build_errstring (C++ function) InvalidLoaderError::InvalidLoaderError (C++ function) InvalidWriterError (C++ class) InvalidWriterError::InvalidWriterError (C++ function) IS_shared (C++ type) IS_unique (C++ type) ISDeleter (C++ class) ISDeleter::operator() (C++ function)

K

kbanner_text_lower (C++ member) kbanner_text_upper (C++ member) kGitDirty (C++ member), [1] kGitSHA (C++ member), [1]

kGitTag (C++ member), [1] KSP_shared (C++ type) KSP_unique (C++ type) KSPDeleter (C++ class) KSPDeleter::operator() (C++ function)

L

lambda command line option

M

main (C++ function) mainflow (C++ function) map command line option Map (C++ class) Map::alloc_displacements (C++ function) Map::apply_mask_to_basis (C++ function) Map::basis (C++ function) Map::calculate_basis (C++ function) Map::calculate_laplacian (C++ function) Map::calculate_map_mask (C++ function) Map::calculate_map_shape (C++ function) Map::calculate_node_info (C++ function) Map::calculate_warp_matrix (C++ function) Map::comm (C++ function) Map::displacements (C++ function) Map::get_displacement_ownershiprange (C++ function) Map::get_dmda_local_extents (C++ function) Map::get_raw_data_ro (C++ function) Map::get_raw_data_row_major (C++ function) Map::get_single_dim_natural (C++ function) Map::get_single_dim_petsc (C++ function) Map::image_shape (C++ function) Map::initialize_dmda (C++ function) Map::interpolate (C++ function) Map::laplacian (C++ function) Map::low_corner (C++ function) Map::m_basis (C++ member) Map::m_comm (C++ member) Map::m_displacements (C++ member) Map::m_lapl (C++ member) Map::m_mask (C++ member) Map::m_ndim (C++ member)

Map::m_v_image_shape (C++ member) Map::m_v_node_spacing (C++ member) Map::m_v_offsets (C++ member) Map::m_vv_node_locs (C++ member) Map::Map (C++ function) Map::map_dmda (C++ member) Map::map_shape (C++ member) Map::ndim (C++ function) Map::node_locs (C++ function) Map::print_dm_info (C++ function) Map::release_raw_data_ro (C++ function) Map::shape (C++ function) Map::size (C++ function) Map::spacing (C++ function) Map::update (C++ function) Map::warp (C++ function) Mask (C++ class) Mask::copy (C++ function) Mask::duplicate (C++ function) Mask::full_image (C++ function) Mask::load_file (C++ function) Mask::Mask (C++ function), [1] Mask::npoints (C++ function) Mat_shared (C++ type) mat_size (C++ function) Mat_unique (C++ type) MatDeleter (C++ class) MatDeleter::operator() (C++ function) matrix_dbg_print (C++ function), [1] max_iterations command line option METADATA_MAX_BYTES (C++ member) moved command line option

N

n_ary_for_each (C++ function) n_ary_transform (C++ function)

nodespacing command line option norm_convert (C++ function)

O

OIIOLoader (C++ class) OIIOLoader::cache (C++ member) OIIOLoader::copy_scaled_chunk (C++ function) OIIOLoader::Create_Loader (C++ function) OIIOLoader::loader_name (C++ member) OIIOLoader::OIIOLoader (C++ function) OIIOLoader::~OIIOLoader (C++ function)

OIIOWriter (C++ class) OIIOWriter::extensions (C++ member) OIIOWriter::OIIOWriter (C++ function) OIIOWriter::write_image (C++ function) OIIOWriter::write_map (C++ function) OIIOWriter::writer_name (C++ member) OIIOWriter::~OIIOWriter (C++ function)

P

pfire_setup (C++ function), [1] pfire_teardown (C++ function), [1] pFIREBaseError (C++ class) pFIREBaseError::_where (C++ member) pFIREBaseError::build_errstring (C++ function) pFIREBaseError::build_wherestring (C++ function)

pFIREBaseError::pFIREBaseError (C++ function) pFIREBaseError::where (C++ function) pFIREExpectedError (C++ class) pFIREExpectedError::pFIREExpectedError (C++ function) print_abort_message (C++ function), [1] print_welcome_message (C++ function), [1]

Q

quadratic_from_points (C++ function), [1]

quadratic_vertex (C++ function), [1]

R

ravel (C++ function) register_plugins (C++ function) registered command line option

repeat_stack (C++ function), [1] repeat_stack_petsc_to_nat (C++ function), [1] replace_token (C++ function), [1]

S

ShirtConfig (C++ class) ShirtConfig::parse_arguments (C++ function) ShirtConfig::shirt_synonyms (C++ member) ShirtConfig::ShirtConfig (C++ function) ShirtConfig::usage (C++ function) ShirtConfig::valid_invocation (C++ function) ShIRTLoader (C++ class) ShIRTLoader::_file_type (C++ member) ShIRTLoader::copy_chunk_image (C++ function) ShIRTLoader::copy_chunk_mask (C++ function) ShIRTLoader::copy_scaled_chunk (C++ function) ShIRTLoader::Create_Loader (C++ function) ShIRTLoader::image (C++ enumerator) ShIRTLoader::image_data_dtype (C++ type) ShIRTLoader::image_data_mpi_type (C++ member) ShIRTLoader::image_header_bytes (C++ member)

ShIRTLoader::image_header_length (C++ member) ShIRTLoader::loader_name (C++ member) ShIRTLoader::mask (C++ enumerator) ShIRTLoader::mask_data_dtype (C++ type) ShIRTLoader::mask_data_mpi_type (C++ member) ShIRTLoader::mask_header_bytes (C++ member) ShIRTLoader::mask_header_length (C++ member) ShIRTLoader::read_and_validate_image_header (C++ function) ShIRTLoader::read_and_validate_mask_header (C++ function) ShIRTLoader::shirt_file_type (C++ enum) ShIRTLoader::shirt_header_dtype (C++ type) ShIRTLoader::ShIRTLoader (C++ function) ShIRTLoader::undef (C++ enumerator) ShIRTLoader::~ShIRTLoader (C++ function) sigterm_handler (C++ function), [1] std (C++ type) stringset (C++ type)

T

throw_if_nonexistent (C++ function), [1]

U

uintvector (C++ type)

unravel (C++ function) usage (C++ function)

V

Vec_shared (C++ type) Vec_unique (C++ type) VecDeleter (C++ class) VecDeleter::operator() (C++ function) vecs_equivalent (C++ function), [1]

VecScatter_shared (C++ type) VecScatter_unique (C++ type) VecScatterDeleter (C++ class) VecScatterDeleter::operator() (C++ function) verbose command line option

W

WorkSpace (C++ class) WorkSpace::allocate_persistent_workspace (C++ function) WorkSpace::create_nonreordering_scatterers (C++ function) WorkSpace::create_reordering_scatterers (C++ function) WorkSpace::duplicate_single_grad_to_stacked (C++ function) WorkSpace::ephemeral_count (C++ member) WorkSpace::m_comm (C++ member) WorkSpace::m_delta (C++ member) WorkSpace::m_dmda (C++ member) WorkSpace::m_globaltmps (C++ member) WorkSpace::m_iss (C++ member) WorkSpace::m_localtmp (C++ member)

WorkSpace::m_nr_scatterers (C++ member) WorkSpace::m_r_scatterers (C++ member) WorkSpace::m_rhs (C++ member) WorkSpace::m_size (C++ member) WorkSpace::m_stacktmp (C++ member) WorkSpace::m_tmat (C++ member) WorkSpace::reallocate_ephemeral_workspace (C++ function) WorkSpace::scatter_grads_to_stacked (C++ function) WorkSpace::scatter_stacked_to_grads (C++ function) WorkSpace::scatter_stacked_to_grads_noreorder (C++ function) WorkSpace::WorkSpace (C++ function) WriterError (C++ class) WriterError::WriterError (C++ function)

X

XDMFWriter (C++ class) XDMFWriter::extensions (C++ member) XDMFWriter::h5name_from_xdmfname (C++ function) XDMFWriter::prepopulate_xdmf_ptree (C++ function) XDMFWriter::rank (C++ member) XDMFWriter::write_image (C++ function)

XDMFWriter::write_map (C++ function) XDMFWriter::writer_name (C++ member) XDMFWriter::xdmf_filename (C++ member) XDMFWriter::xdmf_groupname (C++ member) XDMFWriter::xdmf_tree (C++ member) XDMFWriter::XDMFWriter (C++ function) XDMFWriter::~XDMFWriter (C++ function)