~ElementIterator()
{
if (0 != id)
{
Cmiss_element_iterator_destroy(&id);
}
}
ElementIterator& operator=(const ElementIterator& elementIterator)
{
Cmiss_element_iterator_id temp_id = Cmiss_element_iterator_access(elementIterator.id);
if (0 != id)
{
Cmiss_element_iterator_destroy(&id);
}
id = temp_id;
return *this;
}
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);
}
