tests actually run now, but take 5 min

Author: mrp089

src/model/Block.cpp

@@ -9,6 +9,8 @@ std::string Block::get_name() { return this->model->get_block_name(this->id); }
 
 void Block::update_vessel_type(VesselType type) { vessel_type = type; }
 
+VesselType Block::get_vessel_type() { return vessel_type; }
+
 Block::~Block() {}
 
 void Block::setup_params_(const std::vector<int>& param_ids) {

src/model/Block.h

@@ -162,6 +162,13 @@ class Block {
    */
   void update_vessel_type(VesselType type);
 
+  /**
+   * @brief Get vessel type of the block
+   *
+   * @return VesselType Type of vessel
+   */
+  VesselType get_vessel_type();
+
   /**
    * @brief Setup parameter IDs for the block
    * @param param_ids Global IDs of the block parameters

src/optimize/calibrate.cpp

@@ -13,7 +13,7 @@ nlohmann::json calibrate(const nlohmann::json& config) {
 
   // Setup model
   auto model = Model();
-  load_calibration_model(config, model);
+  load_calibration_model_legacy(config, model);
 
   // Build mapping between optimization parameters and model parameters
   // todo: have a list of optimization parameters for every block (default

src/solve/Parameters.cpp

@@ -282,15 +282,105 @@ void load_calibration_model(const nlohmann::json& config, Model& model) {
   if (config.contains(component)) {
     create_vessels(model, connections, config, component, vessel_id_map);
   }
-  
+
   // Create junctions
   component = "junctions";
   if (config.contains(component)) {
     create_junctions(model, connections, config, component, vessel_id_map);
   }
 
   // Create Connections
-  create_connections(model, connections);
+  DEBUG_MSG("Create connections");
+  for (auto& cn : connections) {
+    auto ele1 = model.get_block(std::get<0>(cn));
+    auto ele2 = model.get_block(std::get<1>(cn));
+    if (ele1->get_vessel_type() == VesselType::inlet) {
+      model.add_node({}, {ele1}, std::get<0>(cn) + ":" + ele1->get_name());
+    } else if (ele2->get_vessel_type() == VesselType::outlet) {
+      model.add_node({ele2}, {}, ele2->get_name() + ":" + std::get<1>(cn));
+    } else {
+      model.add_node({ele1}, {ele2}, ele1->get_name() + ":" + ele2->get_name());
+    }
+  }
+
+  // Finalize model
+  model.finalize();
+}
+
+void load_calibration_model_legacy(const nlohmann::json& config, Model& model) {
+  std::vector<std::tuple<std::string, std::string>> connections;
+  std::vector<std::tuple<std::string, std::string>> inlet_connections;
+  std::vector<std::tuple<std::string, std::string>> outlet_connections;
+
+  // Create vessels
+  DEBUG_MSG("Load vessels");
+  std::map<std::int64_t, std::string> vessel_id_map;
+  int param_counter = 0;
+  for (auto const& vessel_config : config["vessels"]) {
+    std::string vessel_name = vessel_config["vessel_name"];
+
+    // Create parameter IDs
+    std::vector<int> param_ids;
+    for (size_t k = 0; k < 4; k++) param_ids.push_back(param_counter++);
+    model.add_block("BloodVessel", param_ids, vessel_name);
+    vessel_id_map.insert({vessel_config["vessel_id"], vessel_name});
+    DEBUG_MSG("Created vessel " << vessel_name);
+
+    // Read connected boundary conditions
+    if (vessel_config.contains("boundary_conditions")) {
+      auto const& vessel_bc_config = vessel_config["boundary_conditions"];
+      if (vessel_bc_config.contains("inlet")) {
+        inlet_connections.push_back({vessel_bc_config["inlet"], vessel_name});
+      }
+      if (vessel_bc_config.contains("outlet")) {
+        outlet_connections.push_back({vessel_name, vessel_bc_config["outlet"]});
+      }
+    }
+  }
+
+  // Create junctions
+  for (auto const& junction_config : config["junctions"]) {
+    std::string junction_name = junction_config["junction_name"];
+    auto const& outlet_vessels = junction_config["outlet_vessels"];
+    int num_outlets = outlet_vessels.size();
+
+    if (num_outlets == 1) {
+      model.add_block("NORMAL_JUNCTION", {}, junction_name);
+
+    } else {
+      std::vector<int> param_ids;
+      for (size_t i = 0; i < (num_outlets * 3); i++)
+        param_ids.push_back(param_counter++);
+      model.add_block("BloodVesselJunction", param_ids, junction_name);
+    }
+
+    // Check for connections to inlet and outlet vessels and append to
+    // connections list
+    for (auto vessel_id : junction_config["inlet_vessels"]) {
+      connections.push_back({vessel_id_map[vessel_id], junction_name});
+    }
+
+    for (auto vessel_id : outlet_vessels) {
+      connections.push_back({junction_name, vessel_id_map[vessel_id]});
+    }
+    DEBUG_MSG("Created junction " << junction_name);
+  }
+
+  // Create Connections
+  DEBUG_MSG("Created connection");
+  for (auto& connection : connections) {
+    auto ele1 = model.get_block(std::get<0>(connection));
+    auto ele2 = model.get_block(std::get<1>(connection));
+    model.add_node({ele1}, {ele2}, ele1->get_name() + ":" + ele2->get_name());
+  }
+  for (auto& connection : inlet_connections) {
+    auto ele = model.get_block(std::get<1>(connection));
+    model.add_node({}, {ele}, std::get<0>(connection) + ":" + ele->get_name());
+  }
+  for (auto& connection : outlet_connections) {
+    auto ele = model.get_block(std::get<0>(connection));
+    model.add_node({ele}, {}, ele->get_name() + ":" + std::get<1>(connection));
+  }
 
   // Finalize model
   model.finalize();
@@ -494,9 +584,9 @@ void create_junctions(
   }
 }
 
-void create_connections(Model& model,
-                        std::vector<std::tuple<std::string, std::string>>&
-                            connections) {
+void create_connections(
+    Model& model,
+    std::vector<std::tuple<std::string, std::string>>& connections) {
   DEBUG_MSG("Creating connections");
   for (auto& connection : connections) {
     auto ele1 = model.get_block(std::get<0>(connection));

src/solve/Parameters.h

@@ -176,6 +176,7 @@ CalibrationParameters load_calibration_params(const nlohmann::json& config);
  * @
  */
 void load_calibration_model(const nlohmann::json& config, Model& model);
+void load_calibration_model_legacy(const nlohmann::json& config, Model& model);
 
 /**
  * @brief Check that the JSON configuration has the required inputs

tests/cases/steadyFlow_calibration.json

@@ -38,7 +38,8 @@
                 "C": 0.0001,
                 "L": 1.0,
                 "R_poiseuille": 100.0
-            }
+            },
+            "calibrate_elements": ["R_poiseuille", "C", "L", "stenosis_coefficient"]
         }
     ],
     "y": {