~Mesh() { if (0 != id) { Cmiss_mesh_destroy(&id); } }
static int Cmiss_field_group_destroy_all_elements(Cmiss_field_group_id group, void *dummy_void) { USE_PARAMETER(dummy_void); int return_code = 0; if (group) { Cmiss_field_module_id field_module = Cmiss_field_get_field_module(Cmiss_field_group_base_cast(group)); for (int i = 1; i <= 3; i++) { Cmiss_mesh_id master_mesh = Cmiss_field_module_find_mesh_by_dimension(field_module, /*dimension*/i); Cmiss_field_element_group_id element_group = Cmiss_field_group_get_element_group(group, master_mesh); Cmiss_mesh_destroy(&master_mesh); if (element_group) { Cmiss_mesh_group_id mesh_group = Cmiss_field_element_group_get_mesh(element_group); Cmiss_mesh_destroy_all_elements(Cmiss_mesh_group_base_cast(mesh_group)); Cmiss_mesh_group_destroy(&mesh_group); Cmiss_field_element_group_destroy(&element_group); } } Cmiss_field_module_destroy(&field_module); return_code = 1; } return return_code; }
Mesh& operator=(const Mesh& mesh) { Cmiss_mesh_id temp_id = Cmiss_mesh_access(mesh.id); if (0 != id) { Cmiss_mesh_destroy(&id); } id = temp_id; return *this; }
static int set_Cmiss_mesh(struct Parse_state *state, void *region_void, void *mesh_address_void) { Cmiss_region_id region = reinterpret_cast<Cmiss_region_id>(region_void); Cmiss_mesh_id *mesh_address = reinterpret_cast<Cmiss_mesh_id*>(mesh_address_void); if (!(state && region && mesh_address)) return 0; const char *current_token = state->current_token; int return_code = 1; if (!current_token) { display_message(WARNING_MESSAGE, "Missing mesh name"); display_parse_state_location(state); return_code = 0; } else if ((0 == strcmp(PARSER_HELP_STRING, current_token)) || (0 == strcmp(PARSER_RECURSIVE_HELP_STRING, current_token))) { display_message(INFORMATION_MESSAGE, " ELEMENT_GROUP_FIELD_NAME|[GROUP_NAME.]cmiss_mesh_1d|cmiss_mesh_2d|cmiss_mesh_3d["); if (*mesh_address) { char *mesh_name = Cmiss_mesh_get_name(*mesh_address); make_valid_token(&mesh_name); display_message(INFORMATION_MESSAGE, "%s]", mesh_name); DEALLOCATE(mesh_name); } else { display_message(INFORMATION_MESSAGE, "none]"); } } else { Cmiss_field_module_id field_module = Cmiss_region_get_field_module(region); Cmiss_mesh_id new_mesh = Cmiss_field_module_find_mesh_by_name(field_module, current_token); if (new_mesh) { if (*mesh_address) Cmiss_mesh_destroy(mesh_address); *mesh_address = new_mesh; shift_Parse_state(state, 1); } else { display_message(ERROR_MESSAGE, "Invalid mesh: %s", current_token); display_parse_state_location(state); return_code = 0; } Cmiss_field_module_destroy(&field_module); } return return_code; }
static void Element_tool_interactive_event_handler(void *device_id, struct Interactive_event *event,void *element_tool_void, struct Graphics_buffer *graphics_buffer) /******************************************************************************* LAST MODIFIED 18 November 2005 DESCRIPTION : Input handler for input from devices. <device_id> is a unique address enabling the editor to handle input from more than one device at a time. The <event> describes the type of event, button numbers and key modifiers, and the volume of space affected by the interaction. Main events are button press, movement and release. ==============================================================================*/ { enum Interactive_event_type event_type; FE_value time, xi[MAXIMUM_ELEMENT_XI_DIMENSIONS]; int clear_selection, element_dimension, i, input_modifier, number_of_xi_points, shift_pressed; int number_in_xi[MAXIMUM_ELEMENT_XI_DIMENSIONS]; struct FE_element *picked_element; struct FE_element_shape *element_shape; struct Element_tool *element_tool; struct Interaction_volume *interaction_volume,*temp_interaction_volume; struct LIST(Scene_picked_object) *scene_picked_object_list; struct Scene *scene; struct Cmiss_rendition *rendition = NULL; FE_value_triple *xi_points; ENTER(Element_tool_interactive_event_handler); if (device_id&&event&&(element_tool= (struct Element_tool *)element_tool_void)) { Cmiss_region_begin_hierarchical_change(element_tool->region); interaction_volume=Interactive_event_get_interaction_volume(event); scene=Interactive_event_get_scene(event); if (scene != 0) { event_type=Interactive_event_get_type(event); input_modifier=Interactive_event_get_input_modifier(event); shift_pressed=(INTERACTIVE_EVENT_MODIFIER_SHIFT & input_modifier); switch (event_type) { case INTERACTIVE_EVENT_BUTTON_PRESS: { /* interaction only works with first mouse button */ if (1==Interactive_event_get_button_number(event)) { scene_picked_object_list= Scene_pick_objects(scene,interaction_volume,graphics_buffer); if (scene_picked_object_list != 0) { element_tool->picked_element_was_unselected=1; if (0 != (picked_element=Scene_picked_object_list_get_nearest_element( scene_picked_object_list,(struct Cmiss_region *)NULL, element_tool->select_elements_enabled, element_tool->select_faces_enabled, element_tool->select_lines_enabled, (struct Scene_picked_object **)NULL, &rendition, (struct Cmiss_graphic **)NULL))) { /* Open command_field of picked_element in browser */ if (element_tool->command_field) { if (element_tool->time_keeper) { time = Time_keeper_get_time(element_tool->time_keeper); } else { time = 0; } /* since we don't really have fields constant over an element, evaluate at its centre */ element_dimension = get_FE_element_dimension(picked_element); for (i = 0; i < element_dimension; i++) { number_in_xi[i] = 1; } get_FE_element_shape(picked_element, &element_shape); if (FE_element_shape_get_xi_points_cell_centres( element_shape, number_in_xi, &number_of_xi_points, &xi_points)) { /*???debug*/printf("element_tool: xi ="); for (i = 0; i < element_dimension; i++) { xi[i] = xi_points[0][i]; /*???debug*/printf(" %g",xi[i]); } /*???debug*/printf("\n"); Cmiss_field_module_id field_module = Cmiss_field_get_field_module(element_tool->command_field); Cmiss_field_cache_id field_cache = Cmiss_field_module_create_cache(field_module); Cmiss_field_cache_set_time(field_cache, time); Cmiss_field_cache_set_mesh_location(field_cache, picked_element, element_dimension, xi); char *command_string = Cmiss_field_evaluate_string(element_tool->command_field, field_cache); if (command_string) { Execute_command_execute_string(element_tool->execute_command, command_string); DEALLOCATE(command_string); } Cmiss_field_cache_destroy(&field_cache); Cmiss_field_module_destroy(&field_module); DEALLOCATE(xi_points); } } Cmiss_field_group_id group = Cmiss_rendition_get_selection_group(rendition); if (group) { Cmiss_region_id temp_region = Cmiss_rendition_get_region(rendition); Cmiss_field_module_id field_module = Cmiss_region_get_field_module(temp_region); int dimension = Cmiss_element_get_dimension(picked_element); Cmiss_mesh_id master_mesh = Cmiss_field_module_find_mesh_by_dimension(field_module, dimension); Cmiss_field_element_group_id element_group = Cmiss_field_group_get_element_group(group, master_mesh); Cmiss_mesh_destroy(&master_mesh); if (element_group) { Cmiss_mesh_group_id mesh_group = Cmiss_field_element_group_get_mesh(element_group); element_tool->picked_element_was_unselected = !Cmiss_mesh_contains_element(Cmiss_mesh_group_base_cast(mesh_group), picked_element); Cmiss_mesh_group_destroy(&mesh_group); Cmiss_field_element_group_destroy(&element_group); } Cmiss_field_group_destroy(&group); Cmiss_field_module_destroy(&field_module); } } REACCESS(FE_element)(&(element_tool->last_picked_element), picked_element); /*(if ((clear_selection = !shift_pressed) &&((!picked_element)|| (element_tool->picked_element_was_unselected)))*/ clear_selection = !shift_pressed; if (clear_selection) { if (element_tool->region) { Cmiss_rendition *root_rendition = Cmiss_region_get_rendition_internal(element_tool->region); Cmiss_field_group_id root_group = Cmiss_rendition_get_selection_group(root_rendition); if (root_group) { Cmiss_field_group_clear_region_tree_element(root_group); Cmiss_field_group_destroy(&root_group); } Cmiss_rendition_destroy(&root_rendition); } } if (picked_element) { REACCESS(Cmiss_rendition)(&(element_tool->rendition), rendition); Cmiss_region *sub_region = NULL; Cmiss_field_group_id sub_group = NULL; Cmiss_mesh_group_id mesh_group = 0; if (element_tool->rendition) { sub_region = Cmiss_rendition_get_region(element_tool->rendition); sub_group = Cmiss_rendition_get_or_create_selection_group(element_tool->rendition); if (sub_group) { int dimension = Cmiss_element_get_dimension(picked_element); Cmiss_field_module_id field_module = Cmiss_region_get_field_module(sub_region); Cmiss_mesh_id temp_mesh = Cmiss_field_module_find_mesh_by_dimension(field_module, dimension); Cmiss_field_element_group_id element_group = Cmiss_field_group_get_element_group(sub_group, temp_mesh); if (!element_group) element_group = Cmiss_field_group_create_element_group(sub_group, temp_mesh); mesh_group = Cmiss_field_element_group_get_mesh(element_group); Cmiss_field_element_group_destroy(&element_group); Cmiss_mesh_destroy(&temp_mesh); Cmiss_field_module_destroy(&field_module); } } if (mesh_group) { Cmiss_mesh_group_add_element(mesh_group, picked_element); Cmiss_mesh_group_destroy(&mesh_group); } if (sub_group) { Cmiss_field_group_destroy(&sub_group); } } DESTROY(LIST(Scene_picked_object))(&(scene_picked_object_list)); } element_tool->motion_detected=0; REACCESS(Interaction_volume)( &(element_tool->last_interaction_volume),interaction_volume); } } break; case INTERACTIVE_EVENT_MOTION_NOTIFY: case INTERACTIVE_EVENT_BUTTON_RELEASE: { if (element_tool->last_interaction_volume&& ((INTERACTIVE_EVENT_MOTION_NOTIFY==event_type) || (1==Interactive_event_get_button_number(event)))) { if (INTERACTIVE_EVENT_MOTION_NOTIFY==event_type) { element_tool->motion_detected=1; } if (element_tool->last_picked_element) { /* unselect last_picked_element if not just added */ if ((INTERACTIVE_EVENT_BUTTON_RELEASE==event_type)&& shift_pressed&&(!(element_tool->picked_element_was_unselected))) { struct LIST(FE_element) *temp_element_list = CREATE(LIST(FE_element))(); ADD_OBJECT_TO_LIST(FE_element)(element_tool->last_picked_element, temp_element_list); Cmiss_rendition_remove_selection_from_element_list_of_dimension(element_tool->rendition, temp_element_list, Cmiss_element_get_dimension(element_tool->last_picked_element)); DESTROY(LIST(FE_element))(&temp_element_list); } } else if (element_tool->motion_detected) { /* rubber band select */ temp_interaction_volume= create_Interaction_volume_bounding_box( element_tool->last_interaction_volume,interaction_volume); if (temp_interaction_volume != 0) { if (INTERACTIVE_EVENT_MOTION_NOTIFY==event_type) { if (!element_tool->rubber_band) { /* create rubber_band object and put in scene */ element_tool->rubber_band=CREATE(GT_object)( "element_tool_rubber_band",g_POLYLINE, element_tool->rubber_band_material); ACCESS(GT_object)(element_tool->rubber_band); } Interaction_volume_make_polyline_extents( temp_interaction_volume,element_tool->rubber_band); } else { #if defined (USE_SCENE_OBJECT) Scene_remove_graphics_object(scene,element_tool->rubber_band); #endif DEACCESS(GT_object)(&(element_tool->rubber_band)); } if (INTERACTIVE_EVENT_BUTTON_RELEASE==event_type) { scene_picked_object_list= Scene_pick_objects(scene,temp_interaction_volume, graphics_buffer); if (scene_picked_object_list != 0) { Region_element_map *element_map = (Region_element_map *)Scene_picked_object_list_get_picked_region_sorted_elements( scene_picked_object_list, element_tool->select_elements_enabled, element_tool->select_faces_enabled, element_tool->select_lines_enabled); if (element_map) { Cmiss_region *sub_region = NULL; Cmiss_field_group_id sub_group = NULL; Cmiss_rendition *region_rendition = NULL; Cmiss_mesh_group_id mesh_group[MAXIMUM_ELEMENT_XI_DIMENSIONS]; int iter = 0; for (iter = 0; iter < MAXIMUM_ELEMENT_XI_DIMENSIONS; iter++) { mesh_group[iter] = 0; } Region_element_map::iterator pos; for (pos = element_map->begin(); pos != element_map->end(); ++pos) { if (pos->first != sub_region) { if (sub_group) { Cmiss_field_group_destroy(&sub_group); } for (iter = 0; iter < MAXIMUM_ELEMENT_XI_DIMENSIONS; iter++) { if (mesh_group[iter]) { Cmiss_mesh_group_destroy(&(mesh_group[iter])); } } if (region_rendition) { Cmiss_rendition_destroy(®ion_rendition); } sub_region = pos->first; if (sub_region) { region_rendition= Cmiss_region_get_rendition_internal(sub_region); sub_group = Cmiss_rendition_get_or_create_selection_group(region_rendition); } } if (sub_region && sub_group) { Cmiss_field_module_id field_module = Cmiss_region_get_field_module(sub_region); int dimension = Cmiss_element_get_dimension(pos->second); if (dimension <= MAXIMUM_ELEMENT_XI_DIMENSIONS) { if (!mesh_group[dimension - 1]) { Cmiss_mesh_id temp_mesh = Cmiss_field_module_find_mesh_by_dimension(field_module, dimension); Cmiss_field_element_group_id element_group = Cmiss_field_group_get_element_group(sub_group, temp_mesh); if (!element_group) { element_group = Cmiss_field_group_create_element_group(sub_group, temp_mesh); } mesh_group[dimension - 1] = Cmiss_field_element_group_get_mesh(element_group); Cmiss_field_element_group_destroy(&element_group); Cmiss_mesh_destroy(&temp_mesh); } Cmiss_mesh_group_add_element(mesh_group[dimension - 1], pos->second); } Cmiss_field_module_destroy(&field_module); } } if (sub_group) { Cmiss_field_group_destroy(&sub_group); } for (iter = 0; iter < MAXIMUM_ELEMENT_XI_DIMENSIONS; iter++) { if (mesh_group[iter]) { Cmiss_mesh_group_destroy(&(mesh_group[iter])); } } if (region_rendition) { Cmiss_rendition_destroy(®ion_rendition); } delete element_map; } DESTROY(LIST(Scene_picked_object))( &(scene_picked_object_list)); } } DESTROY(Interaction_volume)(&temp_interaction_volume); } } if (INTERACTIVE_EVENT_BUTTON_RELEASE==event_type) { Element_tool_reset((void *)element_tool); } } } break; default: { display_message(ERROR_MESSAGE, "Element_tool_interactive_event_handler. Unknown event type"); } break; }
int define_Computed_field_type_compose(struct Parse_state *state, void *field_modify_void, void *computed_field_compose_package_void) /******************************************************************************* LAST MODIFIED : 24 August 2006 DESCRIPTION : Converts <field> into type COMPUTED_FIELD_COMPOSE (if it is not already) and allows its contents to be modified. ==============================================================================*/ { int return_code; Computed_field_compose_package *computed_field_compose_package; Computed_field_modify_data *field_modify; struct Option_table *find_option_table, *option_table, *out_of_bounds_option_table; struct Set_Computed_field_conditional_data set_calculate_values_field_data, set_find_element_xi_field_data, set_texture_coordinates_field_data; ENTER(define_Computed_field_type_compose); if (state && (field_modify=(Computed_field_modify_data *)field_modify_void) && (computed_field_compose_package = (Computed_field_compose_package *) computed_field_compose_package_void)) { return_code = 1; Cmiss_mesh_id mesh = 0; char *search_group_name = 0; Cmiss_field_id calculate_values_field = 0; Cmiss_field_id find_element_xi_field = 0; Cmiss_field_id texture_coordinates_field = 0; char find_nearest_flag = 0; char find_exact_flag = 0; char use_point_five_when_out_of_bounds_flag = 0; char fail_when_out_of_bounds_flag = 0; int use_point_five_when_out_of_bounds = 0; int element_dimension = 0; /* Maintain the existing behaviour as the default */ int find_nearest = 0; /* get valid parameters for composite field */ if (field_modify->get_field()) { Computed_field_compose* compose_core = dynamic_cast<Computed_field_compose*>(field_modify->get_field()->core); if (compose_core) { return_code = compose_core->get_type( &calculate_values_field, &find_element_xi_field, &texture_coordinates_field, &mesh, &find_nearest, &use_point_five_when_out_of_bounds); if (mesh) { Cmiss_mesh_access(mesh); element_dimension = Cmiss_mesh_get_dimension(mesh); } } } if (return_code) { /* must access objects for set functions */ if (calculate_values_field) { ACCESS(Computed_field)(calculate_values_field); } if (find_element_xi_field) { ACCESS(Computed_field)(find_element_xi_field); } if (texture_coordinates_field) { ACCESS(Computed_field)(texture_coordinates_field); } option_table = CREATE(Option_table)(); Option_table_add_help(option_table, "The value of a compose field is found by evaluating the <texture_coordinates_field>, " "then searching for matching values of the <find_element_xi_field> in the elements of " "the <mesh> (alternatively specified by <group> and <element_dimension>) and then " "finally evaluating the <calculate_values_field> at this found location. You can " "specify the outcome if the matching values cannot be found in the mesh with " "<use_point_five_when_out_of_bounds> or <fail_when_out_of_bounds>. See examples " "a/resample_texture or a/create_slices where the compose field is used to find the " "equivalent coordinate in another element to evaluate a texture."); /* calculate_values_field */ set_calculate_values_field_data.computed_field_manager = field_modify->get_field_manager(); set_calculate_values_field_data.conditional_function = Computed_field_has_numerical_components; set_calculate_values_field_data.conditional_function_user_data = (void *)NULL; Option_table_add_entry(option_table, "calculate_values_field", &calculate_values_field, &set_calculate_values_field_data, set_Computed_field_conditional); Option_table_add_int_positive_entry(option_table,"element_dimension", &element_dimension); /* find_element_xi_field */ set_find_element_xi_field_data.computed_field_manager = field_modify->get_field_manager(); set_find_element_xi_field_data.conditional_function = Computed_field_has_numerical_components; set_find_element_xi_field_data.conditional_function_user_data = (void *)NULL; Option_table_add_entry(option_table, "find_element_xi_field", &find_element_xi_field, &set_find_element_xi_field_data, set_Computed_field_conditional); find_option_table=CREATE(Option_table)(); Option_table_add_char_flag_entry(find_option_table,"find_nearest", &find_nearest_flag); Option_table_add_char_flag_entry(find_option_table,"find_exact", &find_exact_flag); Option_table_add_suboption_table(option_table, find_option_table); /* group */ Option_table_add_string_entry(option_table, "group", &search_group_name, " GROUP_NAME"); // mesh Option_table_add_mesh_entry(option_table, "mesh", field_modify->get_region(), &mesh); /* texture_coordinates_field */ set_texture_coordinates_field_data.computed_field_manager = field_modify->get_field_manager(); set_texture_coordinates_field_data.conditional_function = Computed_field_has_numerical_components; set_texture_coordinates_field_data.conditional_function_user_data = (void *)NULL; Option_table_add_entry(option_table, "texture_coordinates_field", &texture_coordinates_field, &set_texture_coordinates_field_data, set_Computed_field_conditional); out_of_bounds_option_table=CREATE(Option_table)(); /* use_point_five_when_out_of_bounds */ Option_table_add_char_flag_entry(out_of_bounds_option_table, "use_point_five_when_out_of_bounds", &use_point_five_when_out_of_bounds_flag); Option_table_add_char_flag_entry(out_of_bounds_option_table, "fail_when_out_of_bounds", &fail_when_out_of_bounds_flag); Option_table_add_suboption_table(option_table, out_of_bounds_option_table); return_code = Option_table_multi_parse(option_table, state); if (return_code && !mesh) { mesh = Cmiss_field_module_find_mesh_by_dimension( field_modify->get_field_module(), element_dimension); if (search_group_name) { Cmiss_field_id group_field = Cmiss_field_module_find_field_by_name(field_modify->get_field_module(), search_group_name); Cmiss_field_group_id group = Cmiss_field_cast_group(group_field); Cmiss_field_element_group_id element_group = Cmiss_field_group_get_element_group(group, mesh); Cmiss_mesh_destroy(&mesh); mesh = Cmiss_mesh_group_base_cast(Cmiss_field_element_group_get_mesh(element_group)); Cmiss_field_element_group_destroy(&element_group); Cmiss_field_group_destroy(&group); Cmiss_field_destroy(&group_field); } } if (return_code && !mesh) { display_message(ERROR_MESSAGE, "You must specify a mesh (or element_dimension and optional group)."); return_code = 0; } if (return_code) { if (find_nearest_flag && find_exact_flag) { display_message(ERROR_MESSAGE, "Specify only one of find_nearest and find_exact"); return_code = 0; } if (find_nearest_flag) { find_nearest = 1; } else if (find_exact_flag) { find_nearest = 0; } if (use_point_five_when_out_of_bounds_flag && fail_when_out_of_bounds_flag) { display_message(ERROR_MESSAGE, "Specify only one of use_point_five_when_out_of_bounds " "and fail_when_out_of_bounds"); return_code = 0; } if (use_point_five_when_out_of_bounds_flag) { use_point_five_when_out_of_bounds = 1; } else if (fail_when_out_of_bounds_flag) { use_point_five_when_out_of_bounds = 0; } } if (return_code) { return_code = field_modify->update_field_and_deaccess( Computed_field_create_compose(field_modify->get_field_module(), texture_coordinates_field, find_element_xi_field, calculate_values_field, mesh, find_nearest, use_point_five_when_out_of_bounds)); } if (!return_code) { if ((!state->current_token) || (strcmp(PARSER_HELP_STRING, state->current_token)&& strcmp(PARSER_RECURSIVE_HELP_STRING, state->current_token))) { /* error */ display_message(ERROR_MESSAGE, "define_Computed_field_type_compose. Failed"); } } Cmiss_mesh_destroy(&mesh); if (calculate_values_field) { DEACCESS(Computed_field)(&calculate_values_field); } if (find_element_xi_field) { DEACCESS(Computed_field)(&find_element_xi_field); } if (search_group_name) { DEALLOCATE(search_group_name); } if (texture_coordinates_field) { DEACCESS(Computed_field)(&texture_coordinates_field); } DESTROY(Option_table)(&option_table); } } else { display_message(ERROR_MESSAGE, "define_Computed_field_type_compose. Invalid argument(s)"); return_code = 0; } LEAVE; return (return_code); } /* define_Computed_field_type_compose */
StrainMeasures::StrainMeasures(std::vector<std::string> mesh) : mySegments(NULL) { num_level_sets = 10; num_elements = 48; num_nodes = 98; elements.resize(num_elements); x_discret = 25; y_discret = 25; lagrangian = true; modelPGS = 0.0; computeModelPGS = false; ejectionFraction = 0.0; extraNodeStartID = 100000; LVMyocardialVolume* lvm = new LVMyocardialVolume(mesh); volumes = lvm->getMyocardialVolumes(); delete lvm; //Read the mesh context_ = Cmiss_context_create("strainmeasure"); /**< Handle to the context */ Cmiss_region_id root_region = Cmiss_context_get_default_region(context_); //This required for using the cmiss_context_execute_command Cmiss_context_enable_user_interface(context_, NULL); //Load the finite element mesh of the heart std::string region_name = "heart"; Cmiss_region_id heart_region = Cmiss_region_create_child(root_region, region_name.c_str()); //Get the field module of the heart region field_module = Cmiss_region_get_field_module(heart_region); fieldCache = Cmiss_field_module_create_cache(field_module); numberOfModelFrames_ = mesh.size(); double denom = numberOfModelFrames_ - 1; for (unsigned int i = 0; i < numberOfModelFrames_; i++) { double time = static_cast<double>(i) / denom; Cmiss_stream_information_id stream_information = Cmiss_region_create_stream_information(root_region); Cmiss_stream_information_region_id stream_information_region = Cmiss_stream_information_cast_region(stream_information); Cmiss_stream_resource_id stream_resource = Cmiss_stream_information_create_resource_memory_buffer(stream_information, mesh[i].c_str(), mesh[i].length()); Cmiss_stream_information_region_set_resource_attribute_real(stream_information_region, stream_resource, CMISS_STREAM_INFORMATION_REGION_ATTRIBUTE_TIME, time); Cmiss_region_read(root_region, stream_information); Cmiss_stream_resource_destroy(&stream_resource); Cmiss_stream_information_destroy(&stream_information); Cmiss_stream_information_region_destroy(&stream_information_region); } { //Define the necessary fields std::string referenceMesh = mesh[0]; //Change coordinate name to reference_coordinates boost::replace_all(referenceMesh, "1) coordinates", "1) reference_coordinates"); //Load the reference coordinates mesh Cmiss_stream_information_id stream_information = Cmiss_region_create_stream_information(root_region); Cmiss_stream_information_region_id stream_information_region = Cmiss_stream_information_cast_region(stream_information); Cmiss_stream_resource_id stream_resource = Cmiss_stream_information_create_resource_memory_buffer(stream_information, referenceMesh.c_str(), referenceMesh.length()); Cmiss_region_read(root_region, stream_information); Cmiss_stream_resource_destroy(&stream_resource); Cmiss_stream_information_destroy(&stream_information); } coordianteField = Cmiss_field_module_find_field_by_name(field_module, "reference_coordinates"); if (!coordianteField) { std::cout << "reference_coordinates field not found " << std::endl; } Cmiss_region_destroy(&heart_region); //#Calculate the strains Cmiss_field_module_define_field(field_module, "F", "gradient coordinate reference_coordinates field coordinates"); Cmiss_field_module_define_field(field_module, "F_transpose", "transpose source_number_of_rows 3 field F"); Cmiss_field_module_define_field(field_module, "C", "matrix_multiply number_of_rows 3 fields F_transpose F"); Cmiss_field_module_define_field(field_module, "principal_strains", "eigenvalues field C"); Cmiss_field_destroy(&coordianteField); //Assign the coordinates field to the handle for downstream use coordianteField = Cmiss_field_module_find_field_by_name(field_module, "coordinates"); //Define the fibre field { //Load the reference fibre data and reference coordinates { if (Cmiss_field_module_find_field_by_name(field_module, "fibres") == NULL) { Cmiss_stream_information_id stream_information = Cmiss_region_create_stream_information(root_region); Cmiss_stream_information_region_id stream_information_region = Cmiss_stream_information_cast_region(stream_information); //Cmiss_stream_resource_id stream_resource = Cmiss_stream_information_create_resource_memory_buffer(stream_information, reffibre_exregion, reffibre_exregion_len); Cmiss_stream_resource_id stream_resource = Cmiss_stream_information_create_resource_memory_buffer(stream_information, humandtifibre_exregion, humandtifibre_exregion_len); Cmiss_region_read(root_region, stream_information); Cmiss_stream_resource_destroy(&stream_resource); Cmiss_stream_information_destroy(&stream_information); } //Define fibre field //#Calculate the deformed fibre axes Cmiss_field_module_define_field(field_module, "fibre_axes", "fibre_axes coordinate reference_coordinates fibre fibres"); Cmiss_field_module_define_field(field_module, "deformed_fibre_axes", "matrix_multiply number_of_rows 3 fields fibre_axes F_transpose"); Cmiss_field_module_define_field(field_module, "deformed_fibre", "composite deformed_fibre_axes.1 deformed_fibre_axes.2 deformed_fibre_axes.3"); Cmiss_field_module_define_field(field_module, "principal_fibre_strain1", "composite deformed_fibre_axes.1"); } } //Determine the myocardial volume //Get the element and node handles Cmiss_mesh_id cmiss_mesh = Cmiss_field_module_find_mesh_by_name(field_module, "cmiss_mesh_3d"); Cmiss_element_iterator_id elementIterator = Cmiss_mesh_create_element_iterator(cmiss_mesh); Cmiss_element_id element = Cmiss_element_iterator_next(elementIterator); while (element != NULL) { int elementId = Cmiss_element_get_identifier(element) - 1; //Cmiss numbering starts at 1 elements[elementId] = element; element = Cmiss_element_iterator_next(elementIterator); } Cmiss_element_iterator_destroy(&elementIterator); Cmiss_mesh_destroy(&cmiss_mesh); Cmiss_region_destroy(&root_region); }