~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);
}
