Seg3D
2.4
Seg3D is a free volume segmentation and processing tool developed by the NIH Center for Integrative Biomedical Computing at the University of Utah Scientific Computing and Imaging (SCI) Institute.
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Public Member Functions | |
DataLayer (const std::string &name, const Core::DataVolumeHandle &volume) | |
DataLayer (const std::string &state_id) | |
virtual Core::VolumeType | get_type () const |
virtual size_t | get_byte_size () const |
virtual Core::GridTransform | get_grid_transform () const |
virtual void | set_grid_transform (const Core::GridTransform &grid_transform, bool preserve_centering) |
virtual bool | has_valid_data () const |
virtual Core::DataType | get_data_type () const |
virtual Core::VolumeHandle | get_volume () const |
virtual LayerHandle | duplicate () const |
Core::DataVolumeHandle | get_data_volume () const |
bool | set_data_volume (Core::DataVolumeHandle data_volume) |
Public Member Functions inherited from Seg3D::Layer | |
void | update_progress (double amount, double progress_start=0.0f, double progress_amount=1.0f) |
bool | is_visible (size_t viewer_id) const |
LayerGroupHandle | get_layer_group () |
void | set_layer_group (LayerGroupWeakHandle layer_group) |
std::string | get_layer_id () const |
std::string | get_layer_name () const |
Core::DataBlock::generation_type | get_generation () const |
LayerMetaData | get_meta_data () const |
void | set_meta_data (const LayerMetaData &meta_data) |
bool | check_abort () |
void | reset_abort () |
bool | check_stop () |
void | reset_stop () |
bool | check_filter_key (filter_key_type key) const |
void | add_filter_key (filter_key_type key) |
void | remove_filter_key (filter_key_type key) |
void | clear_filter_keys () |
size_t | num_filter_keys () const |
void | set_filter_handle (LayerAbstractFilterHandle layer) |
void | reset_filter_handle () |
LayerAbstractFilterHandle | get_filter_handle () |
void | set_allow_stop () |
void | reset_allow_stop () |
Public Member Functions inherited from Core::StateHandler | |
StateHandler (const std::string &type_str, bool auto_id) | |
template<class HANDLE , class T > | |
bool | add_state (const std::string &key, HANDLE &state, const T &default_value) |
Add a local state variable with default value. | |
template<class HANDLE , class T > | |
bool | add_state (const std::string &key, HANDLE &state, const T &default_value, const T &min_value, const T &max_value, const T &step) |
Add a local state variable with default value and min and max. | |
template<class HANDLE > | |
bool | add_state (const std::string &key, HANDLE &state) |
Add a local state variable without default value. | |
template<class HANDLE > | |
bool | add_state (const std::string &key, HANDLE &state, const std::string &default_option, const std::string &option_list) |
Add a local state variable with option list. | |
template<class HANDLE > | |
bool | add_state (const std::string &key, HANDLE &state, const std::string &default_option, const std::vector< std::string > option_list) |
Add a local state variable with option list. | |
template<class HANDLE > | |
bool | add_state (const std::string &key, HANDLE &state, const std::string &default_option, const std::vector< OptionLabelPair > option_list) |
Add a local state variable with option list. | |
template<class HANDLE > | |
bool | add_state (const std::string &key, HANDLE &state, const std::vector< std::string > &default_options, const std::vector< OptionLabelPair > option_list) |
Add a local state variable with option list. | |
template<class HANDLE > | |
bool | add_state (const std::string &key, HANDLE &state, const std::vector< std::string > &default_options, const std::string &option_list) |
Add a local state variable with option list. | |
template<class HANDLE , class T > | |
bool | add_state (const std::string &key, HANDLE &state, const std::vector< T > &default_value) |
Add a local state variable without default value. | |
void | invalidate () |
this function is called when you need to delete something from the state engine, but may have More... | |
bool | is_valid () |
returns true if the function hasn't been invalidated | |
void | mark_as_project_data () |
Mask the states that are added to this state handler as project data. | |
void | do_not_save_id_number () |
The id number of the statehandler will not be saved. | |
void | set_initializing (bool initializing) |
bool | load_states (const StateIO &state_io) |
Load the states into the StateIO variable. | |
bool | save_states (StateIO &state_io) |
Save the states into the StateIO variable. | |
const std::string & | get_statehandler_id () const |
The id of the handler that will be the prefix of the state variables. | |
const std::string & | get_statehandler_id_base () const |
The id of the handler that will be the prefix of the state variables. | |
size_t | get_statehandler_id_number () const |
The id number of the handler that will be at the end of the prefix. | |
Public Attributes | |
Core::StateRangedDoubleHandle | contrast_state_ |
State describing contrast. | |
Core::StateRangedDoubleHandle | brightness_state_ |
State describing brightness. | |
Core::StateRangedDoubleHandle | display_min_value_state_ |
Core::StateRangedDoubleHandle | display_max_value_state_ |
Core::StateBoolHandle | adjust_display_min_max_state_ |
Core::StateBoolHandle | volume_rendered_state_ |
State describing whether volume is volume rendered. | |
Core::StateStringHandle | data_type_state_ |
Core::StateDoubleHandle | min_value_state_ |
Core::StateDoubleHandle | max_value_state_ |
Public Attributes inherited from Seg3D::Layer | |
update_progress_signal_type | update_progress_signal_ |
layer_updated_signal_type | layer_updated_signal_ |
abort_signal_type | abort_signal_ |
stop_signal_type | stop_signal_ |
Core::StateNameHandle | name_state_ |
The name of the layer. | |
std::vector< Core::StateBoolHandle > | visible_state_ |
Per viewer state of whether this layer is visible. | |
Core::StateBoolHandle | master_visible_state_ |
Master state of the layer visibility. | |
Core::StateBoolHandle | locked_state_ |
State indicating whether the layer is locked. | |
Core::StateRangedDoubleHandle | opacity_state_ |
State that describes the opacity with which the layer is displayed. | |
Core::StateOptionHandle | data_state_ |
State that stores the current layer state. | |
Core::StateBoolHandle | show_information_state_ |
Whether to show the layer information. | |
Core::StateBoolHandle | show_appearance_state_ |
Whether to show the layer information. | |
Core::StateBoolHandle | show_advanced_visibility_state_ |
Whether to show the layer information. | |
Core::StateBoolHandle | show_opacity_state_ |
Whether to show the opacity control. | |
Core::StateBoolHandle | show_progress_bar_state_ |
Whether to show the progress bar. | |
Core::StateBoolHandle | show_abort_message_state_ |
Whether to show the abort message. | |
Core::StateBoolHandle | show_stop_button_state_ |
Whether to show the stop button. | |
Core::BooleanStateGroupHandle | gui_state_group_ |
An exclusive group of boolean states that control the visibility of different parts. | |
Core::StateLongLongHandle | provenance_id_state_ |
State that keeps track of the provenance number. More... | |
Core::StateStringHandle | meta_data_state_ |
State of the MetaData associated with this layer. | |
Core::StateStringHandle | meta_data_info_state_ |
State variable that keeps track of what type of meta data was provided by the importer. | |
Core::StateStringHandle | centering_state_ |
Centering (node vs. cell) is stored per layer for all layers (mask and data) | |
Protected Member Functions | |
virtual bool | pre_save_states (Core::StateIO &state_io) |
virtual bool | post_load_states (const Core::StateIO &state_io) |
virtual void | clean_up () |
Protected Member Functions inherited from Seg3D::Layer | |
Layer (const std::string &name, bool creating=false) | |
Layer (const std::string &name, const std::string &state_id, bool creating=false) | |
virtual bool | post_save_states (Core::StateIO &state_io) |
virtual int | get_version () |
Protected Member Functions inherited from Core::StateHandler | |
void | enable_signals (bool enabled) |
This function enables/disables signals in the state variables. | |
virtual bool | pre_load_states (const StateIO &state_io) |
virtual void | state_changed () |
virtual int | get_session_priority () |
int | get_loaded_version () |
Get the version number of the data that was loaded. | |
void | set_loaded_version (int loaded_version) |
Set the version number of the data that was loaded. | |
Protected Member Functions inherited from Core::ConnectionHandler | |
void | add_connection (const boost::signals2::connection &connection) |
void | add_connection (const ConnectionHandlerConnectionHandle &connection) |
void | disconnect_all () |
Friends | |
class | DataLayerPrivate |
Additional Inherited Members | |
Public Types inherited from Seg3D::Layer | |
typedef boost::signals2::signal< void(double) > | update_progress_signal_type |
typedef boost::signals2::signal< void() > | layer_updated_signal_type |
typedef boost::signals2::signal< void() > | abort_signal_type |
typedef boost::signals2::signal< void() > | stop_signal_type |
typedef long long | filter_key_type |
typedef Core::StateEngine::mutex_type | mutex_type |
This code just aligns the layer locking with the StateEngine locking. | |
typedef Core::StateEngine::lock_type | lock_type |
Static Public Member Functions inherited from Seg3D::Layer | |
static mutex_type & | GetMutex () |
static filter_key_type | GenerateFilterKey () |
Static Public Attributes inherited from Seg3D::Layer | |
static const std::string | CREATING_C |
static const std::string | PROCESSING_C |
static const std::string | AVAILABLE_C |
static const std::string | IN_USE_C |
Protected Attributes inherited from Seg3D::Layer | |
Core::StateLongLongHandle | generation_state_ |
State that stores the generation of its datablock. | |
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protectedvirtual |
CLEAN_UP: this function cleans up the data volume for when you are deleting the data layer and reloading
Reimplemented from Core::StateHandler.
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virtual |
DUPLICATE_LAYER: Duplicate layer
Implements Seg3D::Layer.
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virtual |
GET_BYTE_SIZE: Get the size of the data contained in the layer in bytes
Implements Seg3D::Layer.
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virtual |
GET_DATA_TYPE: Get the data type of the data volume
Implements Seg3D::Layer.
Core::DataVolumeHandle Seg3D::DataLayer::get_data_volume | ( | ) | const |
GET_DATA_VOLUME: this function returns the data volume
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virtual |
GET_GRID_TRANSFORM: this function returns the grid transform of the data volume Locks: StateEngine
Implements Seg3D::Layer.
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inlinevirtual |
GET_TYPE: this function returns the a Core::VolumeType indicating that this is a DataLayer
Implements Seg3D::Layer.
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virtual |
GET_VOLUME: Get the underlying volume.
Implements Seg3D::Layer.
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virtual |
HAS_VALID_DATA: Check whether the layer has valid data.
Implements Seg3D::Layer.
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protectedvirtual |
POST_LOAD_STATES: this function takes care of connecting the DataVolume to the data layer after it's settings
Reimplemented from Core::StateHandler.
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protectedvirtual |
PRE_SAVE_STATES: this function synchronize the generation number for the session saving
Reimplemented from Core::StateHandler.
bool Seg3D::DataLayer::set_data_volume | ( | Core::DataVolumeHandle | data_volume | ) |
SET_DATA_VOLUME: this function sets the data_volume
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virtual |
SET_GRID_TRANSFORM: Set the grid transform of the data volume
Implements Seg3D::Layer.