Example #1
0
		void clear_ensemble_group()
		{
			if (ensemble_group)
			{
				Cmiss_field *field = ensemble_group->getField();
				Cmiss_field_destroy(&field);
				ensemble_group = NULL;
			}
		}
Example #2
0
StrainMeasures::~StrainMeasures() {

	for (unsigned int i = 0; i < num_elements; i++) {
		Cmiss_element_destroy(&(elements[i]));
	}
	Cmiss_field_module_destroy(&field_module);
	Cmiss_field_cache_destroy(&fieldCache);
	Cmiss_field_destroy(&coordianteField);
	Cmiss_context_destroy(&context_);
}
Example #3
0
ShortAxisFitting::~ShortAxisFitting() {
	for (int i = 0; i < NUMBER_OF_NODES; i++)
	{
		Cmiss_node_destroy(&cmiss_nodes[i]);
	}
	Cmiss_field_cache_destroy(&cache);
	Cmiss_field_destroy(&coordinates_rc_);
	Cmiss_field_module_destroy(&field_module_);
	Cmiss_context_destroy(&context_);
	delete[] initialSegmentLengths;
	for (int i = 0; i < 24; i++)
	{
		delete[] segmentNodes[i];
	}
	delete[] segmentNodes;
}
Example #4
0
	~Cmiss_ensemble_index()
	{
		delete[] indexing;
		Cmiss_field_destroy(&indexee);
	}
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 */
Example #6
0
void StrainMeasures::embedStrainOnElements(std::string fieldname, std::vector<std::string>& strain) {

	const unsigned int num_strains = numberOfModelFrames_;
	double times[1024];
	for (unsigned int j = 0; j < num_strains; j++) {
		times[j] = static_cast<double>(j) / (num_strains - 1.0);
	}
	Cmiss_time_sequence_id time_sequence = Cmiss_field_module_get_matching_time_sequence(field_module, num_strains, times);

	Cmiss_field_module_begin_change(field_module);

	//Create Node template
	Cmiss_nodeset_id nodeset = Cmiss_field_module_find_nodeset_by_name(field_module, "cmiss_nodes");
	Cmiss_node_template_id nodeTemplate = Cmiss_nodeset_create_node_template(nodeset);
	//Create the field
	Cmiss_field_id strainField = Cmiss_field_module_create_field(field_module, fieldname.c_str(), "finite number_of_components 1 component_names value");
	if (!strainField) {
		std::cout << "Unable to create field " << fieldname << std::endl;
		return;
	}

	Cmiss_node_template_define_field(nodeTemplate, strainField);
	Cmiss_node_template_define_time_sequence(nodeTemplate, strainField, time_sequence);

	//Create Element template
	Cmiss_mesh_id mesh = Cmiss_field_module_find_mesh_by_dimension(field_module, 3);
	Cmiss_element_template_id element_template = Cmiss_mesh_create_element_template(mesh);
	Cmiss_element_template_set_shape_type(element_template, CMISS_ELEMENT_SHAPE_CUBE);
	Cmiss_element_template_set_number_of_nodes(element_template, 1);
	Cmiss_element_basis_id constant_basis = Cmiss_field_module_create_element_basis(field_module, 3, CMISS_BASIS_FUNCTION_CONSTANT);
	const int local_node_index = 1;
	Cmiss_element_template_define_field_simple_nodal(element_template, strainField, -1, constant_basis, 1, &local_node_index);
	Cmiss_element_basis_destroy(&constant_basis);

	//Map strains to elements

	std::map<int, int> elemStrainMap; //Cmiss element no is mapped to strain array number
	//APLAX
	elemStrainMap[3] = elemStrainMap[10] = 1; //Array id base 0
	elemStrainMap[15] = elemStrainMap[22] = 18; //Average of strain ids 2 and 8
	elemStrainMap[27] = elemStrainMap[34] = 12;
	elemStrainMap[39] = elemStrainMap[46] = 17;
	elemStrainMap[40] = elemStrainMap[45] = 17;
	elemStrainMap[28] = elemStrainMap[33] = 10;
	elemStrainMap[16] = elemStrainMap[21] = 19; //Average of strain ids 11 and 5
	elemStrainMap[4] = elemStrainMap[9] = 4;

	//TCH
	elemStrainMap[11] = elemStrainMap[12] = 2; //Array id base 0
	elemStrainMap[23] = elemStrainMap[24] = 20; //Average of strain ids 3 and 9
	elemStrainMap[35] = elemStrainMap[36] = 8;
	elemStrainMap[47] = elemStrainMap[48] = 16;
	elemStrainMap[41] = elemStrainMap[42] = 16;
	elemStrainMap[17] = elemStrainMap[18] = 11;
	elemStrainMap[29] = elemStrainMap[30] = 21; //Average of strain ids 12 and 6
	elemStrainMap[5] = elemStrainMap[6] = 5;

	//FCH
	elemStrainMap[1] = elemStrainMap[2] = 3; //Array id base 0
	elemStrainMap[13] = elemStrainMap[14] = 22; //Average of 10 and 4
	elemStrainMap[25] = elemStrainMap[26] = 4;
	elemStrainMap[37] = elemStrainMap[38] = 23; //Average of strains 14 and 15
	elemStrainMap[43] = elemStrainMap[44] = 24; //Average of strains 16 and 13
	elemStrainMap[31] = elemStrainMap[32] = 6;
	elemStrainMap[19] = elemStrainMap[20] = 25; //Average of strains 7 and 1
	elemStrainMap[7] = elemStrainMap[8] = 0;

	std::vector<std::string> allStrain = strain;

	//Add the additional strains 18 - 23
	std::string s2 = strain[1];
	std::string s8 = strain[7];

	std::string s11 = strain[10];
	std::string s5 = strain[5];

	std::string s9 = strain[8];
	std::string s3 = strain[2];

	std::string s12 = strain[11];
	std::string s6 = strain[6];

	std::string s10 = strain[9];
	std::string s4 = strain[3];

	std::string s14 = strain[13];
	std::string s15 = strain[14];

	std::string s16 = strain[15];
	std::string s13 = strain[12];

	std::string s1 = strain[0];
	std::string s7 = strain[6];

	std::vector<std::string> compute;
	compute.push_back(s2);
	compute.push_back(s8);

	compute.push_back(s11);
	compute.push_back(s5);

	compute.push_back(s9);
	compute.push_back(s3);

	compute.push_back(s12);
	compute.push_back(s6);

	compute.push_back(s10);
	compute.push_back(s4);

	compute.push_back(s14);
	compute.push_back(s15);

	compute.push_back(s16);
	compute.push_back(s13);

	compute.push_back(s7);
	compute.push_back(s1);

	for (int cptc = 0; cptc < 16; cptc += 2) {
		std::vector<std::string> strain1;
		std::vector<std::string> strain2;
		std::ostringstream ss;
		boost::split(strain1, compute[cptc], boost::is_any_of(","));
		boost::split(strain2, compute[cptc + 1], boost::is_any_of(","));
		for (unsigned int j = 0; j < num_strains - 1; j++) {
			double value1 = atof(strain1[j].c_str());
			double value2 = atof(strain2[j].c_str());
			ss << (value1 + value2) * 0.5 << ",";
		}
		ss << "0.0";
		allStrain.push_back(ss.str());
	}

	for (unsigned int i = 0; i < num_elements; i++) {
		Cmiss_node_id temporaryNode = Cmiss_nodeset_create_node(nodeset, extraNodeStartID++, nodeTemplate);
		Cmiss_element_template_set_node(element_template, 1, temporaryNode); //Link node with the element
		Cmiss_element_merge(elements[i], element_template);
		Cmiss_field_cache_set_node(fieldCache, temporaryNode);
		std::vector<std::string> strains;
		boost::split(strains, allStrain[elemStrainMap[i + 1]], boost::is_any_of(","));
		for (unsigned int j = 0; j < num_strains; j++) {
			double value = atof(strains[j].c_str());
			double time = times[j];
			Cmiss_field_cache_set_time(fieldCache, time);
			Cmiss_field_assign_real(strainField,fieldCache,1,&value);
		}
		Cmiss_node_destroy(&temporaryNode);
	}

	Cmiss_field_module_end_change(field_module);
	Cmiss_field_destroy(&strainField);
	Cmiss_element_template_destroy(&element_template);
	Cmiss_node_template_destroy(&nodeTemplate);
	Cmiss_nodeset_destroy(&nodeset);
	//Calling the following leads to the error ERROR: DESTROY(FE_time_sequence).  Positive access_count
	//Cmiss_time_sequence_destroy(&time_sequence);

}
Example #7
0
std::vector<std::string> StrainMeasures::getLinearDistortion(double* wall_xi, unsigned int cnt, double power) {
	unsigned int xdiscret = 25;
	unsigned int ydiscret = 25;
	//Create points of interest array
	double **pointsOfInterest_x = new double*[xdiscret + 1];
	double **pointsOfInterest_y = new double*[xdiscret + 1];
	for (unsigned int i = 0; i <= xdiscret; i++) {
		pointsOfInterest_x[i] = new double[ydiscret + 1];
		pointsOfInterest_y[i] = new double[ydiscret + 1];
	}
	double delx = 1.0 / xdiscret;
	double dely = 1.0 / ydiscret;

	for (unsigned int xd = 0; xd <= xdiscret; xd++) {
		double xinc = xd * delx;
		if (xinc == 0.0)
			xinc = 0.001;
		if (xinc == 1.0)
			xinc = 0.99;
		for (unsigned int yd = 0; yd <= ydiscret; yd++) {
			double yinc = yd * dely;
			if (yinc == 0.0)
				yinc = 0.001;
			if (yinc == 1.0)
				yinc = 0.99;
			pointsOfInterest_x[xd][yd] = xinc;
			pointsOfInterest_y[xd][yd] = yinc;
		}
	}

	Cmiss_field_id principleStarinsField = Cmiss_field_module_find_field_by_name(field_module, "principal_strains");
	double temp_array[3];
	double coordinates[3];
	long nan_count = 0;

	std::vector<std::string> results;

	std::vector<LevelSet*>* coordSets = new std::vector<LevelSet*>();
	std::vector<LevelSet*>* deformSets = new std::vector<LevelSet*>();
	for (unsigned int ls = 0; ls < cnt; ls++) {
		coordSets->clear();
		deformSets->clear();
		for (unsigned int mt = 0; mt < numberOfModelFrames_; mt++) {
			double time = ((double) mt) / (numberOfModelFrames_ - 1.0);
			LevelSet* myCoordLevelSet = new LevelSet(num_elements, xdiscret + 1, ydiscret + 1);
			LevelSet* myDeformLevelSet = new LevelSet(num_elements, xdiscret + 1, ydiscret + 1, 1);

			Cmiss_field_cache_set_time(fieldCache, time);
			nan_count = 0;
			for (unsigned int xd = 0; xd <= xdiscret; xd++) {
				for (unsigned int yd = 0; yd <= ydiscret; yd++) {
					for (unsigned int elementId = 0; elementId < num_elements; elementId++) {
						coordinates[0] = pointsOfInterest_x[xd][yd];
						coordinates[1] = pointsOfInterest_y[xd][yd];
						coordinates[2] = wall_xi[ls];
						//std::cout<<coordinates[0]<<" "<<coordinates[1]<<" "<<coordinates[2]<<std::endl;
						temp_array[0] = temp_array[1] = temp_array[2] = 0.0;

						Cmiss_field_cache_set_mesh_location(fieldCache, elements[elementId], 3, coordinates);
						Cmiss_field_evaluate_real(principleStarinsField, fieldCache, 3, temp_array);
						double result = getLocalDeformation(temp_array, &nan_count);
						myDeformLevelSet->setData(elementId, xd, yd, &result, 1);

						Cmiss_field_evaluate_real(coordianteField, fieldCache, 3, temp_array);
						myCoordLevelSet->setData(elementId, xd, yd, temp_array, 3);
					}
				}
			}
			coordSets->push_back(myCoordLevelSet);
			deformSets->push_back(myDeformLevelSet);
		}
		std::stringstream ss;
		unsigned int numpoints = coordSets->size();
		for (unsigned int i = 0; i < numpoints; i++) {
			LevelSet* myCoordLevelSet = coordSets->at(i);
			LevelSet* myDeformLevelSet = deformSets->at(i);
			ss << myDeformLevelSet->getLPSum(0, power) / myCoordLevelSet->getArea();
			if (i < (numpoints - 1))
				ss << ",";
			delete myCoordLevelSet;
			delete myDeformLevelSet;
		}
		results.push_back(ss.str());
	}
	//Clean up
	delete deformSets;
	delete coordSets;

	for (unsigned int i = 0; i <= xdiscret; i++) {
		delete[] pointsOfInterest_x[i];
		delete[] pointsOfInterest_y[i];
	}

	delete[] pointsOfInterest_x;
	delete[] pointsOfInterest_y;

	Cmiss_field_destroy(&principleStarinsField);
	return results;
}
Example #8
0
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);
}
Example #9
0
std::vector<std::string> StrainMeasures::getSegmentStrains(std::string fieldName) {
	std::vector<std::string> strains(19);
	Cmiss_field_id field = Cmiss_field_module_find_field_by_name(field_module, fieldName.c_str());

	//Compute strains
	unsigned int numSegments = mySegments->size();
	double temp_array1[3];
	double temp_array2[3];
//#define printcoord
#ifdef printcoord
#include "MeshTopology.h"

	std::vector<Cmiss_node_id> myNodes(100);
	Cmiss_nodeset_id nodeset = Cmiss_field_module_find_nodeset_by_name(field_module, "cmiss_nodes");
	Cmiss_node_iterator_id nodeIterator = Cmiss_nodeset_create_node_iterator(nodeset);
	Cmiss_node_id node = Cmiss_node_iterator_next(nodeIterator);
	if (node != 0) {
		double temp_array[3];

		while (node) {
			int node_id = Cmiss_node_get_identifier(node);
			myNodes[node_id - 1] = node;
			node = Cmiss_node_iterator_next(nodeIterator);
		}
	}
	Cmiss_nodeset_destroy(&nodeset);
	Cmiss_node_iterator_destroy(&nodeIterator);

	std::vector<int> Nodes(27);

	Nodes[8] = aplaxNodes8;
	Nodes[7] = aplaxNodes7;
	Nodes[6] = aplaxNodes6;
	Nodes[5] = aplaxNodes5;
	Nodes[4] = aplaxNodes4;
	Nodes[3] = aplaxNodes3;
	Nodes[2] = aplaxNodes2;
	Nodes[1] = aplaxNodes1;
	Nodes[0] = aplaxNodes0;

	Nodes[9] = tchNodes0;
	Nodes[10] = tchNodes1;
	Nodes[11] = tchNodes2;
	Nodes[12] = tchNodes3;
	Nodes[13] = tchNodes4;
	Nodes[14] = tchNodes5;
	Nodes[15] = tchNodes6;
	Nodes[16] = tchNodes7;
	Nodes[17] = tchNodes8;

	Nodes[18] = fchNodes0;
	Nodes[19] = fchNodes1;
	Nodes[20] = fchNodes2;
	Nodes[21] = fchNodes3;
	Nodes[22] = fchNodes4;
	Nodes[23] = fchNodes5;
	Nodes[24] = fchNodes6;
	Nodes[25] = fchNodes7;
	Nodes[26] = fchNodes8;

#endif
	std::vector<std::vector<double> > aplaxLengths;
	std::vector<std::vector<double> > tchLengths;
	std::vector<std::vector<double> > fchLengths;
	double denomj = (numberOfModelFrames_ - 1.0);
	for (int i = 0; i < numberOfModelFrames_; i++) {
		std::vector<double> cLengths;
		double time = ((double) i) / denomj;
		Cmiss_field_cache_set_time(fieldCache, time);
#ifdef printcoord
		std::cout<<"Frame "<<i<<"\t"<<time<<"\t"<<mySegments->at(0).xia[2]<<std::endl;
#endif
		for (int j = 0; j < numSegments; j++) {
			WallSegment& seg = mySegments->at(j);
			//The the lengths
			temp_array1[0] = temp_array1[1] = temp_array1[2] = 0.0;
			temp_array2[0] = temp_array2[1] = temp_array2[2] = 0.0;
			//Since cmiss id starts at 1 subtract 1 from seg.elemeid?
			//Note that accessing some computed field (those that involve gradients), with multiple versions leads to gradient set to 0 warning
			Cmiss_field_cache_set_mesh_location(fieldCache, elements[seg.elementida - 1], 3, seg.xia);
			Cmiss_field_evaluate_real(field, fieldCache, 3, temp_array1);
			Cmiss_field_cache_set_mesh_location(fieldCache, elements[seg.elementidb - 1], 3, seg.xib);
			Cmiss_field_evaluate_real(field, fieldCache, 3, temp_array2);
			Point3D p1(temp_array1);
			Point3D p2(temp_array2);
			double dist = p1.distance(p2);
#ifdef printcoord
			{
				int nodeCtr = (j / 8) * 9 + j % 8;
				Cmiss_field_cache_set_node(fieldCache, myNodes[Nodes[nodeCtr]]);
				temp_array1[0] = temp_array1[1] = temp_array1[2] = 0.0;
				Cmiss_field_evaluate_real(field, fieldCache, 3, temp_array1);
				Point3D p3(temp_array1);
				Cmiss_field_cache_set_node(fieldCache, myNodes[Nodes[nodeCtr + 1]]);
				temp_array1[0] = temp_array1[1] = temp_array1[2] = 0.0;
				Cmiss_field_evaluate_real(field, fieldCache, 3, temp_array1);
				Point3D p4(temp_array1);
				std::cout << p1 << "\t" << p2 << " = " << dist << "\t:\t Value at " << Nodes[nodeCtr] + 1 << "\t" << p3 << "\t" << p1.distance(p3) << "\t" << Nodes[nodeCtr + 1] + 1
						<< "\t" << p4 << "\t" << p2.distance(p4) << "\t distance \t " << p3.distance(p4) << std::endl;
			}
#endif
			cLengths.push_back(dist);
		}

		for (int segc = 0; segc < numSegments / 8; segc++) {
			int offset = segc * 8;
			std::vector<double> sLengths;

			sLengths.push_back(cLengths[0 + offset] + (1 / 3.0 - 1 / 4.0) * 4 * cLengths[1 + offset]);
			sLengths.push_back((1.0 - (1 / 3.0 - 1 / 4.0)) * 4 * cLengths[1 + offset] + (2 / 3.0 - 1 / 2.0) * 4 * cLengths[2 + offset]);
			sLengths.push_back((1.0 - (2 / 3.0 - 1 / 2.0)) * 4 * cLengths[2 + offset] + cLengths[3 + offset]);
			sLengths.push_back(cLengths[4 + offset] + (1.0 - (2 / 3.0 - 1 / 2.0)) * 4 * cLengths[5 + offset]);
			sLengths.push_back((2 / 3.0 - 1 / 2.0) * 4 * cLengths[5 + offset] + (1.0 - (1 / 3.0 - 1 / 4.0)) * 4 * cLengths[6 + offset]);
			sLengths.push_back((1 / 3.0 - 1 / 4.0) * 4 * cLengths[6 + offset] + cLengths[7 + offset]);

			if (segc == 0)
				aplaxLengths.push_back(sLengths);
			else if (segc == 1)
				tchLengths.push_back(sLengths);
			else
				fchLengths.push_back(sLengths);
		}
	}
	std::vector<double> avgStrains(numberOfModelFrames_, 0.0);

	for (int segc = 0; segc < numSegments / 8; segc++) {
		std::vector<std::vector<double> > dstrains;
		std::vector<std::vector<double> > distances;
		if (segc == 0)
			distances = aplaxLengths;
		else if (segc == 1)
			distances = tchLengths;
		else if (segc == 2)
			distances = fchLengths;

		std::vector<double>& initStrain = distances[0];
		for (int frame = 1; frame < numberOfModelFrames_; frame++) { //Compute Strains
			std::vector<double>& curStrainLengths = distances[frame];
			std::vector<double> curStrain;
			double c = 0;
			unsigned int ulimit = initStrain.size();
			for (int j = 0; j < ulimit; j++) {
				c = 100.0 * (curStrainLengths[j] - initStrain[j]) / initStrain[j];
				curStrain.push_back(c);
			}
			dstrains.push_back(curStrain);
		}

		std::vector<std::string> strainSeries;

		for (int j = 0; j < initStrain.size(); j++) {
			std::ostringstream ss;
			ss << 0.0; //For init step

			int denom = numberOfModelFrames_ - 1;
			double maxStrain = dstrains[denom - 1][j];
			//Note that frame goes from 1 to heart.numberOfModelFrames_ when computing strain
			//so shift down by 1
			for (int i = 0; i < denom; i++) { //Compute Strains
											  //Drift compensate
				double stc = dstrains[i][j] - (i + 1) * maxStrain / denom;
				ss << "," << stc;
				avgStrains[i] += stc;
			}
			strainSeries.push_back(ss.str());
		}
		if (segc == 0) {
			strains[2 - 1] = strainSeries[5];
			strains[8 - 1] = strainSeries[4];
			strains[17 - 1] = strainSeries[3];
			strains[18 - 1] = strainSeries[2];
			strains[11 - 1] = strainSeries[1];
			strains[5 - 1] = strainSeries[0];
		} else if (segc == 2) {
			strains[3 - 1] = strainSeries[0];
			strains[9 - 1] = strainSeries[1];
			strains[14 - 1] = strainSeries[2];
			strains[16 - 1] = strainSeries[3];
			strains[12 - 1] = strainSeries[4];
			strains[6 - 1] = strainSeries[5];
		} else if (segc == 1) {
			strains[4 - 1] = strainSeries[0];
			strains[10 - 1] = strainSeries[1];
			strains[15 - 1] = strainSeries[2];
			strains[13 - 1] = strainSeries[3];
			strains[7 - 1] = strainSeries[4];
			strains[1 - 1] = strainSeries[5];
		}
	}
#ifdef printcoord
	std::cout << "Linear 3D " << fieldName << std::endl;
	for (int i = 1; i < 100; i++)
		Cmiss_node_destroy(&myNodes[i]);

#endif
	//Add the average strain
	//Num strain segments depends on the number of active segments (6 strain segments per view, which has 8 active segments)
	double denom = (numSegments / 8) * 6;

	std::ostringstream ss;
	ss << 0.0; //For init step
	for (int i = 0; i < numberOfModelFrames_ - 1; i++) { //Compute the Average
		ss << "," << avgStrains[i] / denom;
	}
	strains[18] = ss.str();

	//Check if model PGS should be calculated
	if (computeModelPGS) {
		double max = fabs(avgStrains[0]);
		int idx = 0;
		for (int i = 1; i < numberOfModelFrames_ - 1; i++) {
			if (fabs(avgStrains[i]) > max) {
				max = fabs(avgStrains[i]);
				idx = i;
			}
		}
		modelPGS = avgStrains[idx] / denom;
		computeModelPGS = false; //set it so that it is not computed in subsequent calls
	}

	Cmiss_field_destroy(&field);

	return strains;
}