From bdc9581eab93a8ffa31b0c7f78d5e77fe0eab367 Mon Sep 17 00:00:00 2001 From: Martin Pfaller Date: Tue, 5 May 2026 15:58:49 -0400 Subject: [PATCH 01/12] Allow holding parameters constant in calibrator Add an optional `calibrate` field to `calibration_parameters` that lists the parameter names to calibrate (e.g., `["R_poiseuille"]`). Parameters not listed are held constant at their input-file values; the LM optimizer now takes an active-parameter index list and runs the normal equations on the reduced sub-Jacobian, leaving inactive entries of alpha untouched. When the field is absent, all parameters are calibrated, preserving legacy behavior. Adds a regression test (`test_steady_flow_calibration_R_only`) that recovers R=100 from a non-ground-truth initial guess while keeping C, L, and stenosis_coefficient pinned to their ground-truth values. Co-Authored-By: Claude Opus 4.7 (1M context) --- src/optimize/LevenbergMarquardtOptimizer.cpp | 33 ++- src/optimize/LevenbergMarquardtOptimizer.h | 7 +- src/optimize/calibrate.cpp | 61 +++++- .../cases/steadyFlow_calibration_R_only.json | 205 ++++++++++++++++++ tests/test_calibrator.py | 24 ++ 5 files changed, 319 insertions(+), 11 deletions(-) create mode 100644 tests/cases/steadyFlow_calibration_R_only.json diff --git a/src/optimize/LevenbergMarquardtOptimizer.cpp b/src/optimize/LevenbergMarquardtOptimizer.cpp index 40d5fbcef..a91e584db 100644 --- a/src/optimize/LevenbergMarquardtOptimizer.cpp +++ b/src/optimize/LevenbergMarquardtOptimizer.cpp @@ -5,11 +5,14 @@ #include LevenbergMarquardtOptimizer::LevenbergMarquardtOptimizer( - Model* model, int num_obs, int num_params, double lambda0, double tol_grad, + Model* model, int num_obs, int num_params, + const std::vector& active_param_ids, double lambda0, double tol_grad, double tol_inc, int max_iter) { this->model = model; this->num_obs = num_obs; this->num_params = num_params; + this->active_param_ids = active_param_ids; + this->num_active = static_cast(active_param_ids.size()); this->num_eqns = model->dofhandler.get_num_equations(); this->num_vars = model->dofhandler.get_num_variables(); this->num_dpoints = this->num_obs * this->num_eqns; @@ -20,9 +23,9 @@ LevenbergMarquardtOptimizer::LevenbergMarquardtOptimizer( jacobian = Eigen::SparseMatrix(num_dpoints, num_params); residual = Eigen::Matrix::Zero(num_dpoints); - mat = Eigen::Matrix(num_params, - num_params); - vec = Eigen::Matrix::Zero(num_params); + mat = Eigen::Matrix(num_active, + num_active); + vec = Eigen::Matrix::Zero(num_active); } Eigen::Matrix LevenbergMarquardtOptimizer::run( @@ -38,7 +41,9 @@ Eigen::Matrix LevenbergMarquardtOptimizer::run( update_delta(false); } - alpha -= delta; + for (int k = 0; k < num_active; k++) { + alpha[active_param_ids[k]] -= delta[k]; + } double norm_grad = vec.norm(); double norm_inc = delta.norm(); std::cout << std::setprecision(1) << std::scientific << "Iteration " @@ -79,9 +84,23 @@ void LevenbergMarquardtOptimizer::update_gradient( } void LevenbergMarquardtOptimizer::update_delta(bool first_step) { + // Build a reduced Jacobian containing only columns of active parameters. + // Inactive parameters are held constant, so they do not appear in the + // reduced normal equations. + Eigen::SparseMatrix jac_active(num_dpoints, num_active); + std::vector> triplets; + for (int k = 0; k < num_active; k++) { + int col = active_param_ids[k]; + for (Eigen::SparseMatrix::InnerIterator it(jacobian, col); it; + ++it) { + triplets.emplace_back(it.row(), k, it.value()); + } + } + jac_active.setFromTriplets(triplets.begin(), triplets.end()); + // Cache old gradient vector and calulcate new one Eigen::Matrix vec_old = vec; - vec = jacobian.transpose() * residual; + vec = jac_active.transpose() * residual; // Determine new lambda parameter from new and old gradient vector if (!first_step) { @@ -90,7 +109,7 @@ void LevenbergMarquardtOptimizer::update_delta(bool first_step) { // Determine gradient matrix Eigen::Matrix jacobian_sq = - jacobian.transpose() * jacobian; + jac_active.transpose() * jac_active; Eigen::Matrix jacobian_sq_diag = jacobian_sq.diagonal().asDiagonal(); mat = jacobian_sq + lambda * jacobian_sq_diag; diff --git a/src/optimize/LevenbergMarquardtOptimizer.h b/src/optimize/LevenbergMarquardtOptimizer.h index 9578c5090..7d5a93d86 100644 --- a/src/optimize/LevenbergMarquardtOptimizer.h +++ b/src/optimize/LevenbergMarquardtOptimizer.h @@ -80,13 +80,16 @@ class LevenbergMarquardtOptimizer { * * @param model The 0D model * @param num_obs Number of observations in optimization - * @param num_params Number of parameters in optimization + * @param num_params Total number of parameters in alpha + * @param active_param_ids Indices into alpha of parameters that should be + * optimized. Parameters not listed are held constant at their initial value. * @param lambda0 Initial damping factor * @param tol_grad Gradient tolerance * @param tol_inc Parameter increment tolerance * @param max_iter Maximum iterations */ LevenbergMarquardtOptimizer(Model* model, int num_obs, int num_params, + const std::vector& active_param_ids, double lambda0, double tol_grad, double tol_inc, int max_iter); @@ -110,11 +113,13 @@ class LevenbergMarquardtOptimizer { Eigen::Matrix delta; Eigen::Matrix mat; Eigen::Matrix vec; + std::vector active_param_ids; Model* model; double lambda; int num_obs; int num_params; + int num_active; int num_eqns; int num_vars; int num_dpoints; diff --git a/src/optimize/calibrate.cpp b/src/optimize/calibrate.cpp index 28904a312..078d900ae 100644 --- a/src/optimize/calibrate.cpp +++ b/src/optimize/calibrate.cpp @@ -2,6 +2,8 @@ // University of California, and others. SPDX-License-Identifier: BSD-3-Clause #include "calibrate.h" +#include + #include "LevenbergMarquardtOptimizer.h" #include "SimulationParameters.h" @@ -22,10 +24,32 @@ nlohmann::json calibrate(const nlohmann::json& config) { calibration_parameters.value("set_capacitance_to_zero", false); double lambda0 = calibration_parameters.value("initial_damping_factor", 1.0); + // Optional list of parameter names to calibrate. Any parameter not listed is + // held constant at its initial value from the input file. If the field is + // absent or empty, all parameters are calibrated (legacy behavior). + std::set calibrate_names; + bool calibrate_all = true; + if (calibration_parameters.contains("calibrate")) { + auto names = + calibration_parameters["calibrate"].get>(); + if (!names.empty()) { + calibrate_names.insert(names.begin(), names.end()); + calibrate_all = false; + } + } + auto is_active = [&](const std::string& name) { + return calibrate_all || calibrate_names.count(name) > 0; + }; + int num_params = 3; if (calibrate_stenosis) { num_params = 4; } + // Parameter names ordered to match BloodVessel::ParamId. + const std::vector bv_param_names = { + "R_poiseuille", "C", "L", "stenosis_coefficient"}; + // Active parameter ids in alpha (ids of params actually optimized). + std::vector active_param_ids; // Setup model auto model = Model(); @@ -50,6 +74,13 @@ nlohmann::json calibrate(const nlohmann::json& config) { vessel_id_map.insert({vessel_config["vessel_id"], vessel_name}); DEBUG_MSG("Created vessel " << vessel_name); + // Mark which of this block's parameters are active. + for (size_t k = 0; k < num_params; k++) { + if (is_active(bv_param_names[k])) { + active_param_ids.push_back(param_ids[k]); + } + } + // Read connected boundary conditions if (vessel_config.contains("boundary_conditions")) { auto const& vessel_bc_config = vessel_config["boundary_conditions"]; @@ -76,6 +107,23 @@ nlohmann::json calibrate(const nlohmann::json& config) { for (size_t i = 0; i < (num_outlets * (num_params - 1)); i++) param_ids.push_back(param_counter++); model.add_block("BloodVesselJunction", param_ids, junction_name); + + // Mark which of this junction's per-outlet parameters are active. + // Layout: [R0..Rn-1, L0..Ln-1, (S0..Sn-1)?] + for (size_t i = 0; i < num_outlets; i++) { + if (is_active("R_poiseuille")) + active_param_ids.push_back(param_ids[i]); + } + for (size_t i = 0; i < num_outlets; i++) { + if (is_active("L")) + active_param_ids.push_back(param_ids[num_outlets + i]); + } + if (num_params > 3) { + for (size_t i = 0; i < num_outlets; i++) { + if (is_active("stenosis_coefficient")) + active_param_ids.push_back(param_ids[2 * num_outlets + i]); + } + } } // Check for connections to inlet and outlet vessels and append to @@ -203,9 +251,16 @@ nlohmann::json calibrate(const nlohmann::json& config) { // Run optimization DEBUG_MSG("Start optimization"); - auto lm_alg = - LevenbergMarquardtOptimizer(&model, num_obs, param_counter, lambda0, - gradient_tol, increment_tol, max_iter); + DEBUG_MSG("Number of active parameters " << active_param_ids.size()); + if (active_param_ids.empty()) { + throw std::runtime_error( + "[svzerodcalibrator] No parameters selected for calibration. Either " + "omit 'calibrate' from calibration_parameters or list at least one " + "parameter name."); + } + auto lm_alg = LevenbergMarquardtOptimizer( + &model, num_obs, param_counter, active_param_ids, lambda0, gradient_tol, + increment_tol, max_iter); alpha = lm_alg.run(alpha, y_all, dy_all); diff --git a/tests/cases/steadyFlow_calibration_R_only.json b/tests/cases/steadyFlow_calibration_R_only.json new file mode 100644 index 000000000..e91161641 --- /dev/null +++ b/tests/cases/steadyFlow_calibration_R_only.json @@ -0,0 +1,205 @@ +{ + "boundary_conditions": [ + { + "bc_name": "INFLOW", + "bc_type": "FLOW", + "bc_values": { + "Q": [5.0, 5.0], + "t": [0.0, 1.0] + } + }, + { + "bc_name": "OUT", + "bc_type": "RESISTANCE", + "bc_values": { + "Pd": 100.0, + "R": 100.0 + } + } + ], + "junctions": [], + "vessels": [ + { + "boundary_conditions": { + "inlet": "INFLOW", + "outlet": "OUT" + }, + "vessel_id": 0, + "vessel_length": 10.0, + "vessel_name": "branch0_seg0", + "zero_d_element_type": 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The observations were generated by a + ground-truth forward simulation with R=100, C=1e-4, L=1.0, S=0; the input + file starts R at 50 and the other parameters at the ground truth, so the + calibrator should recover R=100 and leave the others untouched.""" + testfile = os.path.join( + this_file_dir, "cases", "steadyFlow_calibration_R_only.json" + ) + + result, _ = execute_pysvzerod(testfile, "calibrator") + + calibrated_parameters = result["vessels"][0]["zero_d_element_values"] + + assert np.isclose( + np.mean(calibrated_parameters["R_poiseuille"]), 100, rtol=RTOL_PRES + ) + assert np.isclose(np.mean(calibrated_parameters["C"]), 0.0001, rtol=RTOL_PRES) + assert np.isclose(np.mean(calibrated_parameters["L"]), 1.0, rtol=RTOL_PRES) + assert np.isclose( + np.mean(calibrated_parameters["stenosis_coefficient"]), 0.0, rtol=RTOL_PRES + ) + + @pytest.mark.parametrize("model_id", ["0080_0001", "0104_0001", "0140_2001"]) def test_calibration_vmr(model_id): """Test actual models from the vascular model repository.""" From aa66adab668a6f0ef751029a14227a98f1247aad Mon Sep 17 00:00:00 2001 From: Martin Pfaller Date: Tue, 5 May 2026 16:14:46 -0400 Subject: [PATCH 02/12] Switch R-only calibration test to a VMR case Replaces the synthetic steady-flow R-only test with one based on the existing VMR calibration fixtures (0104_0001). The test starts from the calibrated reference (so C, L and stenosis_coefficient are at the ground truth), zeros every R_poiseuille in vessels and junctions, and asks the calibrator to recover R only. The reference values are recovered to machine precision and the held-constant parameters are unchanged. Also fixes the clang-format violations CI flagged on the previous commit and removes the steady-flow JSON case (the dirgraph test auto-discovers JSONs in tests/cases/ and would have required a generated reference dot file). Co-Authored-By: Claude Opus 4.7 (1M context) --- src/optimize/calibrate.cpp | 7 +- .../cases/steadyFlow_calibration_R_only.json | 205 ------------------ tests/test_calibrator.py | 86 ++++++-- 3 files changed, 70 insertions(+), 228 deletions(-) delete mode 100644 tests/cases/steadyFlow_calibration_R_only.json diff --git a/src/optimize/calibrate.cpp b/src/optimize/calibrate.cpp index 078d900ae..2fdffed87 100644 --- a/src/optimize/calibrate.cpp +++ b/src/optimize/calibrate.cpp @@ -46,8 +46,8 @@ nlohmann::json calibrate(const nlohmann::json& config) { num_params = 4; } // Parameter names ordered to match BloodVessel::ParamId. - const std::vector bv_param_names = { - "R_poiseuille", "C", "L", "stenosis_coefficient"}; + const std::vector bv_param_names = {"R_poiseuille", "C", "L", + "stenosis_coefficient"}; // Active parameter ids in alpha (ids of params actually optimized). std::vector active_param_ids; @@ -111,8 +111,7 @@ nlohmann::json calibrate(const nlohmann::json& config) { // Mark which of this junction's per-outlet parameters are active. // Layout: [R0..Rn-1, L0..Ln-1, (S0..Sn-1)?] for (size_t i = 0; i < num_outlets; i++) { - if (is_active("R_poiseuille")) - active_param_ids.push_back(param_ids[i]); + if (is_active("R_poiseuille")) active_param_ids.push_back(param_ids[i]); } for (size_t i = 0; i < num_outlets; i++) { if (is_active("L")) diff --git a/tests/cases/steadyFlow_calibration_R_only.json b/tests/cases/steadyFlow_calibration_R_only.json deleted file mode 100644 index e91161641..000000000 --- a/tests/cases/steadyFlow_calibration_R_only.json +++ /dev/null @@ -1,205 +0,0 @@ -{ - "boundary_conditions": [ - { - "bc_name": "INFLOW", - "bc_type": "FLOW", - "bc_values": { - "Q": [5.0, 5.0], - "t": [0.0, 1.0] - } - }, - { - "bc_name": "OUT", - "bc_type": "RESISTANCE", - "bc_values": { - "Pd": 100.0, - "R": 100.0 - } - } - ], - "junctions": [], - "vessels": [ - { - "boundary_conditions": { - "inlet": "INFLOW", - "outlet": "OUT" - }, - "vessel_id": 0, - "vessel_length": 10.0, - "vessel_name": "branch0_seg0", - "zero_d_element_type": "BloodVessel", - "zero_d_element_values": { - "C": 0.0001, - "L": 1.0, - "R_poiseuille": 50.0, - 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"calibrate": ["R_poiseuille"] - } -} diff --git a/tests/test_calibrator.py b/tests/test_calibrator.py index fd1bbe25f..6b94dbd60 100644 --- a/tests/test_calibrator.py +++ b/tests/test_calibrator.py @@ -1,3 +1,4 @@ +import copy import json import os import pytest @@ -26,28 +27,75 @@ def test_steady_flow_calibration(): ) -def test_steady_flow_calibration_R_only(): - """Calibrate only R_poiseuille while holding C, L and stenosis_coefficient - constant at their input-file values. The observations were generated by a - ground-truth forward simulation with R=100, C=1e-4, L=1.0, S=0; the input - file starts R at 50 and the other parameters at the ground truth, so the - calibrator should recover R=100 and leave the others untouched.""" - testfile = os.path.join( - this_file_dir, "cases", "steadyFlow_calibration_R_only.json" - ) +def test_calibration_vmr_R_only(tmp_path): + """Calibrate only R_poiseuille on a VMR model while holding C, L and + stenosis_coefficient constant at their ground-truth values. - result, _ = execute_pysvzerod(testfile, "calibrator") + Starts from the calibrated reference (so C, L, stenosis_coefficient are at + the ground truth), zeros out every R_poiseuille in vessels and junctions, + and runs the calibrator with ``calibrate=["R_poiseuille"]``. The y/dy + observations come from the corresponding input file. The calibrator should + recover the reference R_poiseuille values and leave every other parameter + untouched. + """ + model_id = "0104_0001" - calibrated_parameters = result["vessels"][0]["zero_d_element_values"] + with open( + os.path.join( + this_file_dir, "cases", "vmr", "input", f"{model_id}_calibrate_from_0d.json" + ) + ) as ff: + input_cfg = json.load(ff) + with open( + os.path.join( + this_file_dir, + "cases", + "vmr", + "reference", + f"{model_id}_optimal_from_0d.json", + ) + ) as ff: + reference = json.load(ff) - assert np.isclose( - np.mean(calibrated_parameters["R_poiseuille"]), 100, rtol=RTOL_PRES - ) - assert np.isclose(np.mean(calibrated_parameters["C"]), 0.0001, rtol=RTOL_PRES) - assert np.isclose(np.mean(calibrated_parameters["L"]), 1.0, rtol=RTOL_PRES) - assert np.isclose( - np.mean(calibrated_parameters["stenosis_coefficient"]), 0.0, rtol=RTOL_PRES - ) + cfg = copy.deepcopy(reference) + cfg["y"] = input_cfg["y"] + cfg["dy"] = input_cfg["dy"] + cfg["calibration_parameters"] = copy.deepcopy(input_cfg["calibration_parameters"]) + cfg["calibration_parameters"]["calibrate"] = ["R_poiseuille"] + + # Zero every R_poiseuille; leave C, L, stenosis_coefficient at ground truth + for vessel in cfg["vessels"]: + vessel["zero_d_element_values"]["R_poiseuille"] = 0.0 + for junction in cfg["junctions"]: + if "junction_values" in junction and "R_poiseuille" in junction["junction_values"]: + junction["junction_values"]["R_poiseuille"] = [ + 0.0 for _ in junction["junction_values"]["R_poiseuille"] + ] + + testfile = tmp_path / f"{model_id}_calibrate_R_only.json" + with open(testfile, "w") as ff: + json.dump(cfg, ff) + + result, _ = execute_pysvzerod(str(testfile), "calibrator") + + # R_poiseuille is recovered; other parameters are unchanged + for ref_vessel, res_vessel in zip(reference["vessels"], result["vessels"]): + for key, ref_value in ref_vessel["zero_d_element_values"].items(): + res_value = res_vessel["zero_d_element_values"][key] + assert np.isclose(res_value, ref_value, atol=1e-9, rtol=RTOL_PRES), ( + f"Vessel {ref_vessel['vessel_name']} parameter {key}: " + f"expected {ref_value}, got {res_value}" + ) + + for ref_junction, res_junction in zip(reference["junctions"], result["junctions"]): + if "junction_values" not in ref_junction: + continue + for key, ref_values in ref_junction["junction_values"].items(): + res_values = res_junction["junction_values"][key] + assert np.allclose(res_values, ref_values, atol=1e-9, rtol=RTOL_PRES), ( + f"Junction {ref_junction['junction_name']} parameter {key}: " + f"expected {ref_values}, got {res_values}" + ) @pytest.mark.parametrize("model_id", ["0080_0001", "0104_0001", "0140_2001"]) From 3845bcf732f63b7c5ab32b6138ddb362194d8ae0 Mon Sep 17 00:00:00 2001 From: Martin Pfaller Date: Tue, 5 May 2026 16:23:48 -0400 Subject: [PATCH 03/12] Allow per-block calibrate field to override global default MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Each vessel and BloodVesselJunction can now carry its own optional ``calibrate`` list naming the parameters to optimize. Resolution order for each block: block-level ``calibrate`` > ``calibration_parameters.calibrate`` > calibrate everything (legacy). An explicit empty list at any level means "calibrate nothing for that scope". The active-parameter id list passed to LM is built per block from the resolved set, so the optimizer still operates on a global reduced subspace. Adds two regression tests on the smallest VMR case: - ``test_calibration_vmr_R_only_per_block`` — sets the new field on every vessel and junction with no global default. - ``test_calibration_vmr_block_overrides_global`` — sets a wrong global default (``["C"]``) and overrides each block to recover R; verifies the override actually wins. The previous global-only test is renamed to ``test_calibration_vmr_R_only_global``. Co-Authored-By: Claude Opus 4.7 (1M context) --- src/optimize/calibrate.cpp | 47 +++++++++++------- tests/test_calibrator.py | 97 +++++++++++++++++++++++++++++--------- 2 files changed, 106 insertions(+), 38 deletions(-) diff --git a/src/optimize/calibrate.cpp b/src/optimize/calibrate.cpp index 2fdffed87..e3836e27b 100644 --- a/src/optimize/calibrate.cpp +++ b/src/optimize/calibrate.cpp @@ -2,6 +2,7 @@ // University of California, and others. SPDX-License-Identifier: BSD-3-Clause #include "calibrate.h" +#include #include #include "LevenbergMarquardtOptimizer.h" @@ -24,21 +25,30 @@ nlohmann::json calibrate(const nlohmann::json& config) { calibration_parameters.value("set_capacitance_to_zero", false); double lambda0 = calibration_parameters.value("initial_damping_factor", 1.0); - // Optional list of parameter names to calibrate. Any parameter not listed is - // held constant at its initial value from the input file. If the field is - // absent or empty, all parameters are calibrated (legacy behavior). - std::set calibrate_names; - bool calibrate_all = true; + // Resolve the set of parameter names to calibrate for a given block. The + // block's own ``calibrate`` field takes precedence, followed by the global + // ``calibration_parameters.calibrate`` default. If neither is present, + // returns ``std::nullopt`` meaning "calibrate every parameter of this + // block" (legacy behavior). An explicit empty list means "calibrate + // nothing for this block". + auto parse_set = [](const nlohmann::json& list) { + auto names = list.get>(); + return std::set(names.begin(), names.end()); + }; + std::optional> global_calibrate_set; if (calibration_parameters.contains("calibrate")) { - auto names = - calibration_parameters["calibrate"].get>(); - if (!names.empty()) { - calibrate_names.insert(names.begin(), names.end()); - calibrate_all = false; - } + global_calibrate_set = parse_set(calibration_parameters["calibrate"]); } - auto is_active = [&](const std::string& name) { - return calibrate_all || calibrate_names.count(name) > 0; + auto resolve_calibrate_set = [&](const nlohmann::json& block_config) + -> std::optional> { + if (block_config.contains("calibrate")) { + return parse_set(block_config["calibrate"]); + } + return global_calibrate_set; + }; + auto is_active = [](const std::optional>& set, + const std::string& name) { + return !set.has_value() || set->count(name) > 0; }; int num_params = 3; @@ -75,8 +85,9 @@ nlohmann::json calibrate(const nlohmann::json& config) { DEBUG_MSG("Created vessel " << vessel_name); // Mark which of this block's parameters are active. + auto vessel_calibrate_set = resolve_calibrate_set(vessel_config); for (size_t k = 0; k < num_params; k++) { - if (is_active(bv_param_names[k])) { + if (is_active(vessel_calibrate_set, bv_param_names[k])) { active_param_ids.push_back(param_ids[k]); } } @@ -110,16 +121,18 @@ nlohmann::json calibrate(const nlohmann::json& config) { // Mark which of this junction's per-outlet parameters are active. // Layout: [R0..Rn-1, L0..Ln-1, (S0..Sn-1)?] + auto junction_calibrate_set = resolve_calibrate_set(junction_config); for (size_t i = 0; i < num_outlets; i++) { - if (is_active("R_poiseuille")) active_param_ids.push_back(param_ids[i]); + if (is_active(junction_calibrate_set, "R_poiseuille")) + active_param_ids.push_back(param_ids[i]); } for (size_t i = 0; i < num_outlets; i++) { - if (is_active("L")) + if (is_active(junction_calibrate_set, "L")) active_param_ids.push_back(param_ids[num_outlets + i]); } if (num_params > 3) { for (size_t i = 0; i < num_outlets; i++) { - if (is_active("stenosis_coefficient")) + if (is_active(junction_calibrate_set, "stenosis_coefficient")) active_param_ids.push_back(param_ids[2 * num_outlets + i]); } } diff --git a/tests/test_calibrator.py b/tests/test_calibrator.py index 6b94dbd60..c73b57da3 100644 --- a/tests/test_calibrator.py +++ b/tests/test_calibrator.py @@ -27,19 +27,8 @@ def test_steady_flow_calibration(): ) -def test_calibration_vmr_R_only(tmp_path): - """Calibrate only R_poiseuille on a VMR model while holding C, L and - stenosis_coefficient constant at their ground-truth values. - - Starts from the calibrated reference (so C, L, stenosis_coefficient are at - the ground truth), zeros out every R_poiseuille in vessels and junctions, - and runs the calibrator with ``calibrate=["R_poiseuille"]``. The y/dy - observations come from the corresponding input file. The calibrator should - recover the reference R_poiseuille values and leave every other parameter - untouched. - """ - model_id = "0104_0001" - +def _load_vmr_case(model_id): + """Load the VMR input (with y/dy) and reference (with optimal params).""" with open( os.path.join( this_file_dir, "cases", "vmr", "input", f"{model_id}_calibrate_from_0d.json" @@ -56,14 +45,18 @@ def test_calibration_vmr_R_only(tmp_path): ) ) as ff: reference = json.load(ff) + return input_cfg, reference + +def _build_R_only_config(input_cfg, reference): + """Compose a calibrator config that starts from the reference values, with + every R_poiseuille zeroed; the y/dy/calibration_parameters come from the + forward-simulation input file.""" cfg = copy.deepcopy(reference) cfg["y"] = input_cfg["y"] cfg["dy"] = input_cfg["dy"] cfg["calibration_parameters"] = copy.deepcopy(input_cfg["calibration_parameters"]) - cfg["calibration_parameters"]["calibrate"] = ["R_poiseuille"] - # Zero every R_poiseuille; leave C, L, stenosis_coefficient at ground truth for vessel in cfg["vessels"]: vessel["zero_d_element_values"]["R_poiseuille"] = 0.0 for junction in cfg["junctions"]: @@ -71,14 +64,10 @@ def test_calibration_vmr_R_only(tmp_path): junction["junction_values"]["R_poiseuille"] = [ 0.0 for _ in junction["junction_values"]["R_poiseuille"] ] + return cfg - testfile = tmp_path / f"{model_id}_calibrate_R_only.json" - with open(testfile, "w") as ff: - json.dump(cfg, ff) - - result, _ = execute_pysvzerod(str(testfile), "calibrator") - # R_poiseuille is recovered; other parameters are unchanged +def _assert_recovers_reference(result, reference): for ref_vessel, res_vessel in zip(reference["vessels"], result["vessels"]): for key, ref_value in ref_vessel["zero_d_element_values"].items(): res_value = res_vessel["zero_d_element_values"][key] @@ -98,6 +87,72 @@ def test_calibration_vmr_R_only(tmp_path): ) +def test_calibration_vmr_R_only_global(tmp_path): + """Calibrate only R_poiseuille via the global ``calibrate`` field. + + Starts from the calibrated reference (so C, L, stenosis_coefficient are at + the ground truth), zeros every R_poiseuille and asks the calibrator to + recover R only via ``calibration_parameters.calibrate=["R_poiseuille"]``. + """ + model_id = "0104_0001" + input_cfg, reference = _load_vmr_case(model_id) + cfg = _build_R_only_config(input_cfg, reference) + cfg["calibration_parameters"]["calibrate"] = ["R_poiseuille"] + + testfile = tmp_path / f"{model_id}_calibrate_R_only_global.json" + with open(testfile, "w") as ff: + json.dump(cfg, ff) + + result, _ = execute_pysvzerod(str(testfile), "calibrator") + _assert_recovers_reference(result, reference) + + +def test_calibration_vmr_R_only_per_block(tmp_path): + """Calibrate only R_poiseuille via per-block ``calibrate`` fields, with no + global default. Every vessel and junction independently lists the + parameters it wants calibrated.""" + model_id = "0104_0001" + input_cfg, reference = _load_vmr_case(model_id) + cfg = _build_R_only_config(input_cfg, reference) + + for vessel in cfg["vessels"]: + vessel["calibrate"] = ["R_poiseuille"] + for junction in cfg["junctions"]: + if "junction_values" in junction: + junction["calibrate"] = ["R_poiseuille"] + + testfile = tmp_path / f"{model_id}_calibrate_R_only_per_block.json" + with open(testfile, "w") as ff: + json.dump(cfg, ff) + + result, _ = execute_pysvzerod(str(testfile), "calibrator") + _assert_recovers_reference(result, reference) + + +def test_calibration_vmr_block_overrides_global(tmp_path): + """Per-block ``calibrate`` must override the global default. Sets a + nonsense global default of ``["C"]`` (which would calibrate the wrong + parameter and fail the recovery test) and overrides every block to + ``["R_poiseuille"]``. The global must be ignored where overridden.""" + model_id = "0104_0001" + input_cfg, reference = _load_vmr_case(model_id) + cfg = _build_R_only_config(input_cfg, reference) + cfg["calibration_parameters"]["calibrate"] = ["C"] + + for vessel in cfg["vessels"]: + vessel["calibrate"] = ["R_poiseuille"] + for junction in cfg["junctions"]: + if "junction_values" in junction: + junction["calibrate"] = ["R_poiseuille"] + + testfile = tmp_path / f"{model_id}_calibrate_block_overrides.json" + with open(testfile, "w") as ff: + json.dump(cfg, ff) + + result, _ = execute_pysvzerod(str(testfile), "calibrator") + _assert_recovers_reference(result, reference) + + @pytest.mark.parametrize("model_id", ["0080_0001", "0104_0001", "0140_2001"]) def test_calibration_vmr(model_id): """Test actual models from the vascular model repository.""" From b8897f75eaf74b5b10acaba0d749961b271199d9 Mon Sep 17 00:00:00 2001 From: Martin Pfaller Date: Tue, 5 May 2026 16:34:47 -0400 Subject: [PATCH 04/12] Make calibrator block-agnostic via Block::input_params Removes hardcoded knowledge of BloodVessel/BloodVesselJunction parameter names ("R_poiseuille", "C", "L", "stenosis_coefficient") from calibrate.cpp. Each block now exposes its parameter names via the existing ``Block::input_params`` field, and ``Block::input_params_list`` distinguishes scalar layout (one slot per name) from list layout (``input_params.size() * stride`` slots, name-major). Three small helpers (``num_param_slots``, ``register_active``, ``init_alpha_for_block``, ``write_alpha_for_block``) walk the parameters generically; alpha init, active-id selection, and JSON output writing all use the block's own metadata. New blocks that implement ``update_gradient`` and populate ``input_params`` will be calibrated without further changes to calibrate.cpp. The legacy ``calibrate_stenosis_coefficient: false`` flag is preserved as an additional filter that excludes ``stenosis_coefficient`` from the active set; behavior is observably identical (the slot is always allocated but not optimized). All seven calibrator tests pass; the existing forward-solver tests are unchanged. Co-Authored-By: Claude Opus 4.7 (1M context) --- src/optimize/calibrate.cpp | 249 ++++++++++++++++++------------------- 1 file changed, 120 insertions(+), 129 deletions(-) diff --git a/src/optimize/calibrate.cpp b/src/optimize/calibrate.cpp index e3836e27b..5035d328e 100644 --- a/src/optimize/calibrate.cpp +++ b/src/optimize/calibrate.cpp @@ -8,6 +8,27 @@ #include "LevenbergMarquardtOptimizer.h" #include "SimulationParameters.h" +namespace { + +// Number of alpha slots a block exposes to the calibrator. Scalar blocks +// (``input_params_list == false``) contribute one slot per named input +// parameter. List blocks contribute ``input_params.size() * stride`` slots, +// where ``stride`` is determined by the block's connectivity (e.g. number of +// outlets for BloodVesselJunction). +int num_param_slots(const Block& block, int stride) { + int n = static_cast(block.input_params.size()); + return block.input_params_list ? n * stride : n; +} + +// Stride for a list-style block. The only list block currently in the model +// (``BloodVesselJunction``) groups its parameters per outlet, so the stride +// equals the number of outlets. For scalar blocks the stride is 1. +int param_stride(const Block& block, int num_outlets) { + return block.input_params_list ? num_outlets : 1; +} + +} // namespace + nlohmann::json calibrate(const nlohmann::json& config) { auto output_config = nlohmann::json(config); @@ -46,20 +67,35 @@ nlohmann::json calibrate(const nlohmann::json& config) { } return global_calibrate_set; }; - auto is_active = [](const std::optional>& set, - const std::string& name) { + // Whether ``name`` should be calibrated for this block. The ``set`` argument + // is the resolved per-block calibrate filter (nullopt = calibrate all). The + // legacy ``calibrate_stenosis_coefficient`` flag layers on top: if disabled, + // ``stenosis_coefficient`` is held constant regardless. + auto is_active = [&](const std::optional>& set, + const std::string& name) { + if (!calibrate_stenosis && name == "stenosis_coefficient") return false; return !set.has_value() || set->count(name) > 0; }; - int num_params = 3; - if (calibrate_stenosis) { - num_params = 4; - } - // Parameter names ordered to match BloodVessel::ParamId. - const std::vector bv_param_names = {"R_poiseuille", "C", "L", - "stenosis_coefficient"}; - // Active parameter ids in alpha (ids of params actually optimized). + // Append the active alpha indices contributed by a single block to + // ``active_param_ids``. Walks the block's ``input_params`` and consults the + // resolved calibrate filter to decide whether each parameter (or each + // per-outlet copy of it, for list blocks) is optimized. std::vector active_param_ids; + auto register_active = [&](const Block& block, + const std::vector& param_ids, + const std::optional>& set) { + int stride = static_cast(param_ids.size()) / + static_cast(block.input_params.size()); + if (!block.input_params_list) stride = 1; + for (size_t i = 0; i < block.input_params.size(); i++) { + const std::string& name = block.input_params[i].first; + if (!is_active(set, name)) continue; + for (int s = 0; s < stride; s++) { + active_param_ids.push_back(param_ids[i * stride + s]); + } + } + }; // Setup model auto model = Model(); @@ -73,24 +109,19 @@ nlohmann::json calibrate(const nlohmann::json& config) { int param_counter = 0; for (auto const& vessel_config : config["vessels"]) { std::string vessel_name = vessel_config["vessel_name"]; - - // Create parameter IDs - std::vector param_ids; - for (size_t k = 0; k < num_params; k++) - param_ids.push_back(param_counter++); std::string block_type = vessel_config["zero_d_element_type"].get(); - model.add_block(block_type, param_ids, vessel_name); + + // Instantiate the block so we can introspect its parameter names. + auto* block = model.create_block(block_type); + int num_slots = num_param_slots(*block, /*stride=*/1); + std::vector param_ids; + for (int k = 0; k < num_slots; k++) param_ids.push_back(param_counter++); + model.add_block(block, vessel_name, param_ids); vessel_id_map.insert({vessel_config["vessel_id"], vessel_name}); DEBUG_MSG("Created vessel " << vessel_name); - // Mark which of this block's parameters are active. - auto vessel_calibrate_set = resolve_calibrate_set(vessel_config); - for (size_t k = 0; k < num_params; k++) { - if (is_active(vessel_calibrate_set, bv_param_names[k])) { - active_param_ids.push_back(param_ids[k]); - } - } + register_active(*block, param_ids, resolve_calibrate_set(vessel_config)); // Read connected boundary conditions if (vessel_config.contains("boundary_conditions")) { @@ -112,30 +143,15 @@ nlohmann::json calibrate(const nlohmann::json& config) { if (num_outlets == 1) { model.add_block("NORMAL_JUNCTION", {}, junction_name); - } else { + auto* block = model.create_block("BloodVesselJunction"); + int num_slots = num_param_slots(*block, num_outlets); std::vector param_ids; - for (size_t i = 0; i < (num_outlets * (num_params - 1)); i++) - param_ids.push_back(param_counter++); - model.add_block("BloodVesselJunction", param_ids, junction_name); - - // Mark which of this junction's per-outlet parameters are active. - // Layout: [R0..Rn-1, L0..Ln-1, (S0..Sn-1)?] - auto junction_calibrate_set = resolve_calibrate_set(junction_config); - for (size_t i = 0; i < num_outlets; i++) { - if (is_active(junction_calibrate_set, "R_poiseuille")) - active_param_ids.push_back(param_ids[i]); - } - for (size_t i = 0; i < num_outlets; i++) { - if (is_active(junction_calibrate_set, "L")) - active_param_ids.push_back(param_ids[num_outlets + i]); - } - if (num_params > 3) { - for (size_t i = 0; i < num_outlets; i++) { - if (is_active(junction_calibrate_set, "stenosis_coefficient")) - active_param_ids.push_back(param_ids[2 * num_outlets + i]); - } - } + for (int k = 0; k < num_slots; k++) param_ids.push_back(param_counter++); + model.add_block(block, junction_name, param_ids); + + register_active(*block, param_ids, + resolve_calibrate_set(junction_config)); } // Check for connections to inlet and outlet vessels and append to @@ -208,56 +224,45 @@ nlohmann::json calibrate(const nlohmann::json& config) { // Setup start parameter vector Eigen::Matrix alpha = Eigen::Matrix::Zero(param_counter); + + // Initialize alpha from a JSON values object using the block's own + // ``input_params`` to map names to slot indices. Missing names default to + // 0 (already set by the zero-init above). + auto init_alpha_for_block = [&](const Block& block, + const nlohmann::json& values) { + int total = static_cast(block.global_param_ids.size()); + int stride = param_stride( + block, total / static_cast(block.input_params.size())); + for (size_t i = 0; i < block.input_params.size(); i++) { + const std::string& name = block.input_params[i].first; + if (!values.contains(name)) continue; + if (block.input_params_list) { + auto arr = values[name].get>(); + for (int s = 0; s < stride && s < static_cast(arr.size()); s++) { + alpha[block.global_param_ids[i * stride + s]] = arr[s]; + } + } else { + alpha[block.global_param_ids[i]] = values[name].get(); + } + } + }; + DEBUG_MSG("Reading initial alpha"); for (auto& vessel_config : output_config["vessels"]) { std::string vessel_name = vessel_config["vessel_name"]; DEBUG_MSG("Reading initial alpha for " << vessel_name); auto block = model.get_block(vessel_name); - alpha[block->global_param_ids[0]] = - vessel_config["zero_d_element_values"].value("R_poiseuille", 0.0); - alpha[block->global_param_ids[1]] = - vessel_config["zero_d_element_values"].value("C", 0.0); - alpha[block->global_param_ids[2]] = - vessel_config["zero_d_element_values"].value("L", 0.0); - if (num_params > 3) { - alpha[block->global_param_ids[3]] = - vessel_config["zero_d_element_values"].value("stenosis_coefficient", - 0.0); + if (vessel_config.contains("zero_d_element_values")) { + init_alpha_for_block(*block, vessel_config["zero_d_element_values"]); } } for (auto& junction_config : output_config["junctions"]) { std::string junction_name = junction_config["junction_name"]; DEBUG_MSG("Reading initial alpha for " << junction_name); auto block = model.get_block(junction_name); - int num_outlets = block->outlet_nodes.size(); - - if (num_outlets < 2) { - continue; - } - - for (size_t i = 0; i < num_outlets; i++) { - alpha[block->global_param_ids[i]] = 0.0; - alpha[block->global_param_ids[i + num_outlets]] = 0.0; - if (num_params > 3) { - alpha[block->global_param_ids[i + 2 * num_outlets]] = 0.0; - } - } - if (junction_config["junction_type"] == "BloodVesselJunction") { - auto resistance = junction_config["junction_values"]["R_poiseuille"] - .get>(); - auto inductance = - junction_config["junction_values"]["L"].get>(); - auto stenosis_coeff = - junction_config["junction_values"]["stenosis_coefficient"] - .get>(); - for (size_t i = 0; i < num_outlets; i++) { - alpha[block->global_param_ids[i]] = resistance[i]; - alpha[block->global_param_ids[i + num_outlets]] = inductance[i]; - if (num_params > 3) { - alpha[block->global_param_ids[i + 2 * num_outlets]] = - stenosis_coeff[i]; - } - } + if (block->global_param_ids.empty()) continue; + if (junction_config.contains("junction_values")) { + init_alpha_for_block(*block, junction_config["junction_values"]); } } @@ -276,60 +281,46 @@ nlohmann::json calibrate(const nlohmann::json& config) { alpha = lm_alg.run(alpha, y_all, dy_all); + // Build a JSON values object for a block by reading optimized alpha values + // out using the block's own ``input_params``. + auto post_process = [&](const std::string& name, double v) { + if (name == "C" && zero_capacitance) v = 0.0; + if (name == "C" || name == "L") v = std::max(v, 0.0); + return v; + }; + auto write_alpha_for_block = [&](const Block& block) -> nlohmann::json { + nlohmann::json values = nlohmann::json::object(); + int total = static_cast(block.global_param_ids.size()); + int stride = param_stride( + block, total / static_cast(block.input_params.size())); + for (size_t i = 0; i < block.input_params.size(); i++) { + const std::string& name = block.input_params[i].first; + if (block.input_params_list) { + std::vector arr; + for (int s = 0; s < stride; s++) { + arr.push_back(post_process( + name, alpha[block.global_param_ids[i * stride + s]])); + } + values[name] = arr; + } else { + values[name] = post_process(name, alpha[block.global_param_ids[i]]); + } + } + return values; + }; + // Write optimized simulation config file for (auto& vessel_config : output_config["vessels"]) { std::string vessel_name = vessel_config["vessel_name"]; auto block = model.get_block(vessel_name); - double stenosis_coeff = 0.0; - if (num_params > 3) { - stenosis_coeff = alpha[block->global_param_ids[3]]; - } - double c_value = 0.0; - if (!zero_capacitance) { - c_value = alpha[block->global_param_ids[1]]; - } - vessel_config["zero_d_element_values"] = { - {"R_poiseuille", alpha[block->global_param_ids[0]]}, - {"C", std::max(c_value, 0.0)}, - {"L", std::max(alpha[block->global_param_ids[2]], 0.0)}, - {"stenosis_coefficient", stenosis_coeff}}; + vessel_config["zero_d_element_values"] = write_alpha_for_block(*block); } for (auto& junction_config : output_config["junctions"]) { std::string junction_name = junction_config["junction_name"]; auto block = model.get_block(junction_name); - int num_outlets = block->outlet_nodes.size(); - - if (num_outlets < 2) { - continue; - } - - std::vector r_values; - for (size_t i = 0; i < num_outlets; i++) { - r_values.push_back(alpha[block->global_param_ids[i]]); - } - std::vector l_values; - for (size_t i = 0; i < num_outlets; i++) { - l_values.push_back( - std::max(alpha[block->global_param_ids[i + num_outlets]], 0.0)); - } - - std::vector ste_values; - - if (num_params > 3) { - for (size_t i = 0; i < num_outlets; i++) { - ste_values.push_back( - alpha[block->global_param_ids[i + 2 * num_outlets]]); - } - } else { - for (size_t i = 0; i < num_outlets; i++) { - ste_values.push_back(0.0); - } - } - + if (block->global_param_ids.empty()) continue; junction_config["junction_type"] = "BloodVesselJunction"; - junction_config["junction_values"] = {{"R_poiseuille", r_values}, - {"L", l_values}, - {"stenosis_coefficient", ste_values}}; + junction_config["junction_values"] = write_alpha_for_block(*block); } output_config.erase("y"); From 31c1439619f0266c441862e249252808418d2e67 Mon Sep 17 00:00:00 2001 From: Martin Pfaller Date: Tue, 5 May 2026 16:50:38 -0400 Subject: [PATCH 05/12] Check in R-only calibrator fixtures and document calibrate field Replaces the in-test config builders in tests/test_calibrator.py with three checked-in fixtures derived from the existing 0104_0001 VMR data: tests/cases/vmr/input/0104_0001_calibrate_R_only_global.json tests/cases/vmr/input/0104_0001_calibrate_R_only_per_block.json tests/cases/vmr/input/0104_0001_calibrate_R_only_block_overrides.json Each starts from the calibrated reference (so C, L and stenosis_coefficient are at the ground truth) with every R_poiseuille zeroed; the test parametrizes the same recovery assertion across all three. The Python helpers that built these configs at runtime are gone. Adds docs/pages/calibrator.md describing the new ``calibrate`` field, its global vs per-block resolution order, and pointing readers at the new fixtures as worked examples. Linked from docs/pages/main.md. Co-Authored-By: Claude Opus 4.7 (1M context) --- docs/pages/calibrator.md | 149 + docs/pages/main.md | 1 + ...0001_calibrate_R_only_block_overrides.json | 5569 +++++++++++++++++ .../0104_0001_calibrate_R_only_global.json | 5548 ++++++++++++++++ .../0104_0001_calibrate_R_only_per_block.json | 5568 ++++++++++++++++ tests/test_calibrator.py | 178 +- 6 files changed, 16885 insertions(+), 128 deletions(-) create mode 100644 docs/pages/calibrator.md create mode 100644 tests/cases/vmr/input/0104_0001_calibrate_R_only_block_overrides.json create mode 100644 tests/cases/vmr/input/0104_0001_calibrate_R_only_global.json create mode 100644 tests/cases/vmr/input/0104_0001_calibrate_R_only_per_block.json diff --git a/docs/pages/calibrator.md b/docs/pages/calibrator.md new file mode 100644 index 000000000..8004423e4 --- /dev/null +++ b/docs/pages/calibrator.md @@ -0,0 +1,149 @@ +@page calibrator svZeroDCalibrator + +[TOC] + +svZeroDCalibrator solves the inverse problem: given observations of pressure +and flow, it tunes the parameters of an existing 0D model so that the +solver-predicted state matches the observations. The optimizer is a +Levenberg-Marquardt loop running over the alpha vector of all calibratable +parameters in the model. See `src/optimize/calibrate.cpp` and +`src/optimize/LevenbergMarquardtOptimizer.h` for the implementation. + +## Input file + +The input file is a normal solver configuration extended with three extra +blocks: + +```json +{ + "boundary_conditions": [...], + "junctions": [...], + "vessels": [...], + "calibration_parameters": { ... }, + "y": { ... }, + "dy": { ... } +} +``` + +* `y` and `dy` are dictionaries keyed by the variable names that the model + exposes after assembly (e.g. `pressure:INFLOW:branch0_seg0`, + `flow:branch0_seg0:OUT`). Each value is a list of observed samples; the + number of samples is the same for every variable. `dy` holds the matching + time derivatives. +* `calibration_parameters` collects the calibrator-specific options described + below. + +The output file has the same shape as a solver input but with calibrated +values written into `zero_d_element_values` (vessels) and `junction_values` +(multi-outlet junctions). The `y`, `dy` and `calibration_parameters` keys are +removed from the output. + +## Selecting which parameters to calibrate + +By default every parameter exposed by every supported block is calibrated. +Two optional fields restrict the set of parameters that are optimized; any +parameter that is not selected is held constant at the value found in the +input file. + +### Global default: `calibration_parameters.calibrate` + +The list of parameter names under `calibration_parameters.calibrate` applies +to every block that does not override it. The names must match the parameter +names a block exposes through its `input_params` list (e.g. `R_poiseuille`, +`C`, `L`, `stenosis_coefficient` for `BloodVessel`). + +```json +"calibration_parameters": { + "tolerance_gradient": 1e-5, + "tolerance_increment": 1e-10, + "maximum_iterations": 100, + "initial_damping_factor": 1.0, + "calibrate": ["R_poiseuille"] +} +``` + +In the example above only the Poiseuille resistance is calibrated for every +block; capacitance, inductance, and stenosis coefficient stay at the values +provided by the input file. + +### Per-block override: `calibrate` field on a vessel or junction + +A vessel or junction can carry its own `calibrate` field at the top level of +its block entry. When present, this list takes precedence over the global +default for that one block: + +```json +{ + "vessel_id": 0, + "vessel_name": "branch0_seg0", + "zero_d_element_type": "BloodVessel", + "zero_d_element_values": { + "R_poiseuille": 0.0, + "C": 1.2e-6, + "L": 0.25, + "stenosis_coefficient": 1.06e-5 + }, + "calibrate": ["R_poiseuille"] +} +``` + +```json +{ + "junction_name": "J0", + "junction_type": "BloodVesselJunction", + "junction_values": { + "R_poiseuille": [0.0, 0.0], + "L": [0.0, 0.0], + "stenosis_coefficient": [0.0, 0.0] + }, + "inlet_vessels": [0], + "outlet_vessels": [1, 2], + "calibrate": ["R_poiseuille"] +} +``` + +### Resolution order + +For each block, the calibrator picks the active set of parameter names with +the following precedence: + +1. The block's own `calibrate` field, if present. +2. Otherwise, `calibration_parameters.calibrate`. +3. Otherwise, every parameter the block exposes (legacy behavior). + +An explicit empty list (`"calibrate": []`) at any level means "calibrate +nothing for that scope". The calibrator errors out if no parameter is +selected in any block. + +### Worked examples + +The repository ships three small fixtures derived from the +`0104_0001` Vascular Model Repository case that exercise each path: + +* `tests/cases/vmr/input/0104_0001_calibrate_R_only_global.json` - + uses `calibration_parameters.calibrate`. +* `tests/cases/vmr/input/0104_0001_calibrate_R_only_per_block.json` - + uses per-block `calibrate` fields with no global default. +* `tests/cases/vmr/input/0104_0001_calibrate_R_only_block_overrides.json` - + sets a misleading global default and overrides every block; the override + must win. + +In each case every `R_poiseuille` value is zeroed in the input file while +`C`, `L`, and `stenosis_coefficient` are kept at their ground-truth values. +The calibrator recovers the reference R values to machine precision and +leaves the other parameters untouched. The matching test is +`tests/test_calibrator.py::test_calibration_R_only`. + +## Block requirements + +A block is calibratable as long as it implements `update_gradient` and +exposes its parameter names through the standard `Block::input_params` +field. The calibrator reads this metadata at runtime via +`Block::input_params` and `Block::input_params_list`, so adding a new +calibratable block does not require any changes to `calibrate.cpp`. + +The legacy flag `calibration_parameters.calibrate_stenosis_coefficient` +(default `true`) layers on top of the selection logic: when set to `false`, +`stenosis_coefficient` is held constant regardless of any `calibrate` field. +The flag predates the `calibrate` field and is preserved for backward +compatibility; new input files should prefer `calibrate`. diff --git a/docs/pages/main.md b/docs/pages/main.md index e001e6d0b..baeaab9e9 100644 --- a/docs/pages/main.md +++ b/docs/pages/main.md @@ -9,6 +9,7 @@ Below are links to important sections of the documentation: * [Installing svZeroDSolver](https://simvascular.github.io/documentation/rom_simulation.html#0d-solver-install) * [User guide for svZeroDSolver](https://simvascular.github.io/documentation/rom_simulation.html#0d-solver-user-guide) * [User guide for svZeroDCalibrator](https://simvascular.github.io/documentation/rom_simulation.html#0d-solver-calibrator) +* [Selecting parameters to calibrate](@ref calibrator) * [User guide for svZeroDVisualization](https://simvascular.github.io/documentation/rom_simulation.html#0d-solver-visualization) * [User guide for svZeroDGUI](https://simvascular.github.io/documentation/rom_simulation.html#0d-solver-gui) diff --git a/tests/cases/vmr/input/0104_0001_calibrate_R_only_block_overrides.json b/tests/cases/vmr/input/0104_0001_calibrate_R_only_block_overrides.json new file mode 100644 index 000000000..3c089ac8c --- /dev/null +++ b/tests/cases/vmr/input/0104_0001_calibrate_R_only_block_overrides.json @@ -0,0 +1,5569 @@ +{ + "boundary_conditions": [ + { + "bc_name": "INFLOW", + "bc_type": "FLOW", + "bc_values": { + "Q": [ + 19.581907481595668, 29.24682998044782, 42.0511165296033, + 58.583913202644474, 78.95362616027712, 103.27506735565193, + 130.16534882450802, 158.11460426170575, 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{ + "bc_name": "RCR_0", + "bc_type": "RCR", + "bc_values": { + "C": 0.00012993, + "Pd": 0.0, + "Rd": 14964.0, + "Rp": 888.0 + } + }, + { + "bc_name": "RCR_1", + "bc_type": "RCR", + "bc_values": { + "C": 0.00060244, + "Pd": 0.0, + "Rd": 3163.0000000000005, + "Rp": 256.0 + } + }, + { + "bc_name": "RCR_2", + "bc_type": "RCR", + "bc_values": { + "C": 0.00011318999999999999, + "Pd": 0.0, + "Rd": 17177.0, + "Rp": 1019.0 + } + }, + { + "bc_name": "RCR_3", + "bc_type": "RCR", + "bc_values": { + "C": 4.123e-5, + "Pd": 0.0, + "Rd": 44958.0, + "Rp": 4995.0 + } + }, + { + "bc_name": "RCR_4", + "bc_type": "RCR", + "bc_values": { + "C": 0.00011318999999999999, + "Pd": 0.0, + "Rd": 17177.0, + "Rp": 1019.0 + } + } + ], + "junctions": [ + { + "inlet_vessels": [0], + "junction_name": "J0", + "junction_type": "BloodVesselJunction", + "junction_values": { + "L": [0.0, 0.0, 0.0], + "R_poiseuille": [0.0, 0.0, 0.0], + "stenosis_coefficient": [0.0, 0.0, 0.0] + }, + "outlet_vessels": [1, 5, 9], + "calibrate": ["R_poiseuille"] + }, + { + "inlet_vessels": [1], + "junction_name": "J1", + "junction_type": "BloodVesselJunction", + "junction_values": { + "L": [0.0, 0.0], + "R_poiseuille": [0.0, 0.0], + "stenosis_coefficient": [0.0, 0.0] + }, + "outlet_vessels": [2, 15], + "calibrate": ["R_poiseuille"] + }, + { + "inlet_vessels": [5], + "junction_name": "J2", + "junction_type": "BloodVesselJunction", + "junction_values": { + "L": [0.0, 0.0], + "R_poiseuille": [0.0, 0.0], + "stenosis_coefficient": [0.0, 0.0] + }, + "outlet_vessels": [6, 12], + "calibrate": ["R_poiseuille"] + }, + { + "inlet_vessels": [2], + "junction_name": "J3", + "junction_type": "NORMAL_JUNCTION", + "outlet_vessels": [3] + }, + { + "inlet_vessels": [3], + "junction_name": "J4", + "junction_type": "NORMAL_JUNCTION", + "outlet_vessels": [4] + }, + { + "inlet_vessels": [6], + "junction_name": "J5", + "junction_type": "NORMAL_JUNCTION", + "outlet_vessels": [7] + }, + { + "inlet_vessels": [7], + "junction_name": "J6", + 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"tolerance_increment": 1e-9, + "maximum_iterations": 20, + "calibrate_stenosis_coefficient": true, + "set_capacitance_to_zero": false + } +} diff --git a/tests/test_calibrator.py b/tests/test_calibrator.py index c73b57da3..e8d857fc6 100644 --- a/tests/test_calibrator.py +++ b/tests/test_calibrator.py @@ -1,9 +1,8 @@ -import copy import json import os -import pytest import numpy as np +import pytest from .utils import execute_pysvzerod, RTOL_PRES @@ -27,132 +26,6 @@ def test_steady_flow_calibration(): ) -def _load_vmr_case(model_id): - """Load the VMR input (with y/dy) and reference (with optimal params).""" - with open( - os.path.join( - this_file_dir, "cases", "vmr", "input", f"{model_id}_calibrate_from_0d.json" - ) - ) as ff: - input_cfg = json.load(ff) - with open( - os.path.join( - this_file_dir, - "cases", - "vmr", - "reference", - f"{model_id}_optimal_from_0d.json", - ) - ) as ff: - reference = json.load(ff) - return input_cfg, reference - - -def _build_R_only_config(input_cfg, reference): - """Compose a calibrator config that starts from the reference values, with - every R_poiseuille zeroed; the y/dy/calibration_parameters come from the - forward-simulation input file.""" - cfg = copy.deepcopy(reference) - cfg["y"] = input_cfg["y"] - cfg["dy"] = input_cfg["dy"] - cfg["calibration_parameters"] = copy.deepcopy(input_cfg["calibration_parameters"]) - - for vessel in cfg["vessels"]: - vessel["zero_d_element_values"]["R_poiseuille"] = 0.0 - for junction in cfg["junctions"]: - if "junction_values" in junction and "R_poiseuille" in junction["junction_values"]: - junction["junction_values"]["R_poiseuille"] = [ - 0.0 for _ in junction["junction_values"]["R_poiseuille"] - ] - return cfg - - -def _assert_recovers_reference(result, reference): - for ref_vessel, res_vessel in zip(reference["vessels"], result["vessels"]): - for key, ref_value in ref_vessel["zero_d_element_values"].items(): - res_value = res_vessel["zero_d_element_values"][key] - assert np.isclose(res_value, ref_value, atol=1e-9, rtol=RTOL_PRES), ( - f"Vessel {ref_vessel['vessel_name']} parameter {key}: " - f"expected {ref_value}, got {res_value}" - ) - - for ref_junction, res_junction in zip(reference["junctions"], result["junctions"]): - if "junction_values" not in ref_junction: - continue - for key, ref_values in ref_junction["junction_values"].items(): - res_values = res_junction["junction_values"][key] - assert np.allclose(res_values, ref_values, atol=1e-9, rtol=RTOL_PRES), ( - f"Junction {ref_junction['junction_name']} parameter {key}: " - f"expected {ref_values}, got {res_values}" - ) - - -def test_calibration_vmr_R_only_global(tmp_path): - """Calibrate only R_poiseuille via the global ``calibrate`` field. - - Starts from the calibrated reference (so C, L, stenosis_coefficient are at - the ground truth), zeros every R_poiseuille and asks the calibrator to - recover R only via ``calibration_parameters.calibrate=["R_poiseuille"]``. - """ - model_id = "0104_0001" - input_cfg, reference = _load_vmr_case(model_id) - cfg = _build_R_only_config(input_cfg, reference) - cfg["calibration_parameters"]["calibrate"] = ["R_poiseuille"] - - testfile = tmp_path / f"{model_id}_calibrate_R_only_global.json" - with open(testfile, "w") as ff: - json.dump(cfg, ff) - - result, _ = execute_pysvzerod(str(testfile), "calibrator") - _assert_recovers_reference(result, reference) - - -def test_calibration_vmr_R_only_per_block(tmp_path): - """Calibrate only R_poiseuille via per-block ``calibrate`` fields, with no - global default. Every vessel and junction independently lists the - parameters it wants calibrated.""" - model_id = "0104_0001" - input_cfg, reference = _load_vmr_case(model_id) - cfg = _build_R_only_config(input_cfg, reference) - - for vessel in cfg["vessels"]: - vessel["calibrate"] = ["R_poiseuille"] - for junction in cfg["junctions"]: - if "junction_values" in junction: - junction["calibrate"] = ["R_poiseuille"] - - testfile = tmp_path / f"{model_id}_calibrate_R_only_per_block.json" - with open(testfile, "w") as ff: - json.dump(cfg, ff) - - result, _ = execute_pysvzerod(str(testfile), "calibrator") - _assert_recovers_reference(result, reference) - - -def test_calibration_vmr_block_overrides_global(tmp_path): - """Per-block ``calibrate`` must override the global default. Sets a - nonsense global default of ``["C"]`` (which would calibrate the wrong - parameter and fail the recovery test) and overrides every block to - ``["R_poiseuille"]``. The global must be ignored where overridden.""" - model_id = "0104_0001" - input_cfg, reference = _load_vmr_case(model_id) - cfg = _build_R_only_config(input_cfg, reference) - cfg["calibration_parameters"]["calibrate"] = ["C"] - - for vessel in cfg["vessels"]: - vessel["calibrate"] = ["R_poiseuille"] - for junction in cfg["junctions"]: - if "junction_values" in junction: - junction["calibrate"] = ["R_poiseuille"] - - testfile = tmp_path / f"{model_id}_calibrate_block_overrides.json" - with open(testfile, "w") as ff: - json.dump(cfg, ff) - - result, _ = execute_pysvzerod(str(testfile), "calibrator") - _assert_recovers_reference(result, reference) - - @pytest.mark.parametrize("model_id", ["0080_0001", "0104_0001", "0140_2001"]) def test_calibration_vmr(model_id): """Test actual models from the vascular model repository.""" @@ -185,3 +58,52 @@ def test_calibration_vmr(model_id): value, rtol=RTOL_PRES, ) + + +@pytest.mark.parametrize( + "case", + [ + # Selects parameters via the global ``calibration_parameters.calibrate``. + "0104_0001_calibrate_R_only_global", + # Selects parameters via per-block ``calibrate`` fields, no global default. + "0104_0001_calibrate_R_only_per_block", + # Per-block ``calibrate`` overrides a misleading global default. + "0104_0001_calibrate_R_only_block_overrides", + ], +) +def test_calibration_R_only(case): + """Calibrate only ``R_poiseuille`` on a VMR model while holding C, L and + stenosis_coefficient at their ground-truth values. The test fixtures start + from the calibrated reference (so non-R parameters are at the optimum) with + every R_poiseuille zeroed; the calibrator should recover R_poiseuille and + leave the rest untouched. The reference values to compare against live in + ``tests/cases/vmr/reference/0104_0001_optimal_from_0d.json``. + """ + testfile = os.path.join(this_file_dir, "cases", "vmr", "input", f"{case}.json") + reference_file = os.path.join( + this_file_dir, "cases", "vmr", "reference", "0104_0001_optimal_from_0d.json" + ) + with open(reference_file) as ff: + reference = json.load(ff) + + result, _ = execute_pysvzerod(testfile, "calibrator") + + for ref_vessel, res_vessel in zip(reference["vessels"], result["vessels"]): + for key, ref_value in ref_vessel["zero_d_element_values"].items(): + res_value = res_vessel["zero_d_element_values"][key] + assert np.isclose(res_value, ref_value, atol=1e-9, rtol=RTOL_PRES), ( + f"Vessel {ref_vessel['vessel_name']} parameter {key}: " + f"expected {ref_value}, got {res_value}" + ) + + for ref_junction, res_junction in zip( + reference["junctions"], result["junctions"] + ): + if "junction_values" not in ref_junction: + continue + for key, ref_values in ref_junction["junction_values"].items(): + res_values = res_junction["junction_values"][key] + assert np.allclose(res_values, ref_values, atol=1e-9, rtol=RTOL_PRES), ( + f"Junction {ref_junction['junction_name']} parameter {key}: " + f"expected {ref_values}, got {res_values}" + ) From c13064e2412d88115ef9b6c910c20692acdda3cc Mon Sep 17 00:00:00 2001 From: Martin Pfaller Date: Tue, 5 May 2026 17:08:32 -0400 Subject: [PATCH 06/12] Drop global calibrate field in favor of per-block only Removes the global ``calibration_parameters.calibrate`` option. The ``calibrate`` field is now exclusively a per-block setting on vessels and multi-outlet junctions. If no block sets it, the legacy "calibrate every parameter" behavior still applies. Consolidates the three R-only fixtures into a single ``tests/cases/vmr/input/0104_0001_calibrate_R_only.json`` (the former per-block variant); the global and block-overrides fixtures, which exercised paths that no longer exist, are deleted. The parametrized ``test_calibration_R_only`` collapses to one assertion. Updates ``docs/pages/calibrator.md`` to document only the per-block form, drops the resolution-precedence section, and points readers at the single new fixture as a worked example. Co-Authored-By: Claude Opus 4.7 (1M context) --- docs/pages/calibrator.md | 92 +- src/optimize/calibrate.cpp | 32 +- ...k.json => 0104_0001_calibrate_R_only.json} | 0 ...0001_calibrate_R_only_block_overrides.json | 5569 ----------------- .../0104_0001_calibrate_R_only_global.json | 5548 ---------------- tests/test_calibrator.py | 36 +- 6 files changed, 59 insertions(+), 11218 deletions(-) rename tests/cases/vmr/input/{0104_0001_calibrate_R_only_per_block.json => 0104_0001_calibrate_R_only.json} (100%) delete mode 100644 tests/cases/vmr/input/0104_0001_calibrate_R_only_block_overrides.json delete mode 100644 tests/cases/vmr/input/0104_0001_calibrate_R_only_global.json diff --git a/docs/pages/calibrator.md b/docs/pages/calibrator.md index 8004423e4..7050bcb8e 100644 --- a/docs/pages/calibrator.md +++ b/docs/pages/calibrator.md @@ -30,8 +30,9 @@ blocks: `flow:branch0_seg0:OUT`). Each value is a list of observed samples; the number of samples is the same for every variable. `dy` holds the matching time derivatives. -* `calibration_parameters` collects the calibrator-specific options described - below. +* `calibration_parameters` collects the calibrator-specific options + (tolerances, iteration cap, damping factor, legacy + `calibrate_stenosis_coefficient` switch). The output file has the same shape as a solver input but with calibrated values written into `zero_d_element_values` (vessels) and `junction_values` @@ -41,36 +42,14 @@ removed from the output. ## Selecting which parameters to calibrate By default every parameter exposed by every supported block is calibrated. -Two optional fields restrict the set of parameters that are optimized; any -parameter that is not selected is held constant at the value found in the -input file. +To restrict the optimization, add an optional `calibrate` field to a vessel +or junction listing the parameter names that should be optimized for that +block. Any parameter not in the list is held constant at the value found in +the input file. -### Global default: `calibration_parameters.calibrate` - -The list of parameter names under `calibration_parameters.calibrate` applies -to every block that does not override it. The names must match the parameter -names a block exposes through its `input_params` list (e.g. `R_poiseuille`, -`C`, `L`, `stenosis_coefficient` for `BloodVessel`). - -```json -"calibration_parameters": { - "tolerance_gradient": 1e-5, - "tolerance_increment": 1e-10, - "maximum_iterations": 100, - "initial_damping_factor": 1.0, - "calibrate": ["R_poiseuille"] -} -``` - -In the example above only the Poiseuille resistance is calibrated for every -block; capacitance, inductance, and stenosis coefficient stay at the values -provided by the input file. - -### Per-block override: `calibrate` field on a vessel or junction - -A vessel or junction can carry its own `calibrate` field at the top level of -its block entry. When present, this list takes precedence over the global -default for that one block: +The names must match the parameter names a block exposes through its +`input_params` list (e.g. `R_poiseuille`, `C`, `L`, `stenosis_coefficient` +for `BloodVessel`). ```json { @@ -102,36 +81,25 @@ default for that one block: } ``` -### Resolution order - -For each block, the calibrator picks the active set of parameter names with -the following precedence: - -1. The block's own `calibrate` field, if present. -2. Otherwise, `calibration_parameters.calibrate`. -3. Otherwise, every parameter the block exposes (legacy behavior). - -An explicit empty list (`"calibrate": []`) at any level means "calibrate -nothing for that scope". The calibrator errors out if no parameter is -selected in any block. - -### Worked examples - -The repository ships three small fixtures derived from the -`0104_0001` Vascular Model Repository case that exercise each path: - -* `tests/cases/vmr/input/0104_0001_calibrate_R_only_global.json` - - uses `calibration_parameters.calibrate`. -* `tests/cases/vmr/input/0104_0001_calibrate_R_only_per_block.json` - - uses per-block `calibrate` fields with no global default. -* `tests/cases/vmr/input/0104_0001_calibrate_R_only_block_overrides.json` - - sets a misleading global default and overrides every block; the override - must win. - -In each case every `R_poiseuille` value is zeroed in the input file while -`C`, `L`, and `stenosis_coefficient` are kept at their ground-truth values. -The calibrator recovers the reference R values to machine precision and -leaves the other parameters untouched. The matching test is +### Resolution rules + +* If a block has a `calibrate` field, only the listed parameters are + optimized for that block. +* If a block has no `calibrate` field, every parameter the block exposes is + optimized (legacy behavior). +* An explicit empty list (`"calibrate": []`) means "calibrate nothing for + this block". The calibrator errors out if no parameter ends up selected + in any block. + +### Worked example + +The repository ships a small fixture derived from the `0104_0001` Vascular +Model Repository case at +`tests/cases/vmr/input/0104_0001_calibrate_R_only.json`. Every vessel and +multi-outlet junction in that file carries `"calibrate": ["R_poiseuille"]`, +the non-R parameters are fixed at the calibrated reference, and every R +value is zeroed. The calibrator recovers the reference R values to machine +precision and leaves the other parameters untouched. The matching test is `tests/test_calibrator.py::test_calibration_R_only`. ## Block requirements @@ -146,4 +114,4 @@ The legacy flag `calibration_parameters.calibrate_stenosis_coefficient` (default `true`) layers on top of the selection logic: when set to `false`, `stenosis_coefficient` is held constant regardless of any `calibrate` field. The flag predates the `calibrate` field and is preserved for backward -compatibility; new input files should prefer `calibrate`. +compatibility; new input files should prefer per-block `calibrate`. diff --git a/src/optimize/calibrate.cpp b/src/optimize/calibrate.cpp index 5035d328e..92dcfac7c 100644 --- a/src/optimize/calibrate.cpp +++ b/src/optimize/calibrate.cpp @@ -46,26 +46,16 @@ nlohmann::json calibrate(const nlohmann::json& config) { calibration_parameters.value("set_capacitance_to_zero", false); double lambda0 = calibration_parameters.value("initial_damping_factor", 1.0); - // Resolve the set of parameter names to calibrate for a given block. The - // block's own ``calibrate`` field takes precedence, followed by the global - // ``calibration_parameters.calibrate`` default. If neither is present, - // returns ``std::nullopt`` meaning "calibrate every parameter of this - // block" (legacy behavior). An explicit empty list means "calibrate - // nothing for this block". - auto parse_set = [](const nlohmann::json& list) { - auto names = list.get>(); - return std::set(names.begin(), names.end()); - }; - std::optional> global_calibrate_set; - if (calibration_parameters.contains("calibrate")) { - global_calibrate_set = parse_set(calibration_parameters["calibrate"]); - } - auto resolve_calibrate_set = [&](const nlohmann::json& block_config) + // Resolve the set of parameter names to calibrate for a given block from + // its own ``calibrate`` field. If the field is absent the block falls back + // to ``std::nullopt`` meaning "calibrate every parameter of this block" + // (legacy behavior); an explicit empty list means "calibrate nothing for + // this block". + auto resolve_calibrate_set = [](const nlohmann::json& block_config) -> std::optional> { - if (block_config.contains("calibrate")) { - return parse_set(block_config["calibrate"]); - } - return global_calibrate_set; + if (!block_config.contains("calibrate")) return std::nullopt; + auto names = block_config["calibrate"].get>(); + return std::set(names.begin(), names.end()); }; // Whether ``name`` should be calibrated for this block. The ``set`` argument // is the resolved per-block calibrate filter (nullopt = calibrate all). The @@ -272,8 +262,8 @@ nlohmann::json calibrate(const nlohmann::json& config) { if (active_param_ids.empty()) { throw std::runtime_error( "[svzerodcalibrator] No parameters selected for calibration. Either " - "omit 'calibrate' from calibration_parameters or list at least one " - "parameter name."); + "omit the 'calibrate' field from every block, or list at least one " + "parameter name in some block."); } auto lm_alg = LevenbergMarquardtOptimizer( &model, num_obs, param_counter, active_param_ids, lambda0, gradient_tol, diff --git a/tests/cases/vmr/input/0104_0001_calibrate_R_only_per_block.json b/tests/cases/vmr/input/0104_0001_calibrate_R_only.json similarity index 100% rename from tests/cases/vmr/input/0104_0001_calibrate_R_only_per_block.json rename to tests/cases/vmr/input/0104_0001_calibrate_R_only.json diff --git a/tests/cases/vmr/input/0104_0001_calibrate_R_only_block_overrides.json b/tests/cases/vmr/input/0104_0001_calibrate_R_only_block_overrides.json deleted file mode 100644 index 3c089ac8c..000000000 --- a/tests/cases/vmr/input/0104_0001_calibrate_R_only_block_overrides.json +++ /dev/null @@ -1,5569 +0,0 @@ -{ - "boundary_conditions": [ - { - "bc_name": "INFLOW", - "bc_type": "FLOW", - 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40068.06819664574, 66870.74993784717, 181485.5111444608 - ] - }, - "calibration_parameters": { - "tolerance_gradient": 1e-5, - "tolerance_increment": 1e-9, - "maximum_iterations": 20, - "calibrate_stenosis_coefficient": true, - "set_capacitance_to_zero": false, - "calibrate": ["R_poiseuille"] - } -} diff --git a/tests/test_calibrator.py b/tests/test_calibrator.py index e8d857fc6..f38113c99 100644 --- a/tests/test_calibrator.py +++ b/tests/test_calibrator.py @@ -60,28 +60,28 @@ def test_calibration_vmr(model_id): ) -@pytest.mark.parametrize( - "case", - [ - # Selects parameters via the global ``calibration_parameters.calibrate``. - "0104_0001_calibrate_R_only_global", - # Selects parameters via per-block ``calibrate`` fields, no global default. - "0104_0001_calibrate_R_only_per_block", - # Per-block ``calibrate`` overrides a misleading global default. - "0104_0001_calibrate_R_only_block_overrides", - ], -) -def test_calibration_R_only(case): +def test_calibration_R_only(): """Calibrate only ``R_poiseuille`` on a VMR model while holding C, L and - stenosis_coefficient at their ground-truth values. The test fixtures start - from the calibrated reference (so non-R parameters are at the optimum) with - every R_poiseuille zeroed; the calibrator should recover R_poiseuille and - leave the rest untouched. The reference values to compare against live in + stenosis_coefficient at their ground-truth values via per-block + ``calibrate`` fields. The fixture starts from the calibrated reference (so + non-R parameters are at the optimum) with every R_poiseuille zeroed; the + calibrator should recover R_poiseuille and leave the rest untouched. The + reference values to compare against live in ``tests/cases/vmr/reference/0104_0001_optimal_from_0d.json``. """ - testfile = os.path.join(this_file_dir, "cases", "vmr", "input", f"{case}.json") + testfile = os.path.join( + this_file_dir, + "cases", + "vmr", + "input", + "0104_0001_calibrate_R_only.json", + ) reference_file = os.path.join( - this_file_dir, "cases", "vmr", "reference", "0104_0001_optimal_from_0d.json" + this_file_dir, + "cases", + "vmr", + "reference", + "0104_0001_optimal_from_0d.json", ) with open(reference_file) as ff: reference = json.load(ff) From d5d56864565b281fc2f50e9bcacc168c6571c74a Mon Sep 17 00:00:00 2001 From: Martin Pfaller Date: Tue, 5 May 2026 17:16:31 -0400 Subject: [PATCH 07/12] Make calibrate field mandatory per block Removes the legacy "no calibrate field => calibrate everything" fallback. Each block must now declare a ``calibrate`` list naming the parameters to optimize; a missing or empty list means every parameter of that block is held at its input value. Drops the ``calibrate_stenosis_coefficient`` flag from ``calibration_parameters``: with explicit per-block selection it is redundant. Removed from the reader in calibrate.cpp and from the fixtures that still carried it. Updates every checked-in calibrator fixture to the new schema: * ``tests/cases/steadyFlow_calibration.json`` * ``tests/cases/vmr/input/0080_0001_calibrate_from_0d.json`` * ``tests/cases/vmr/input/0104_0001_calibrate_from_0d.json`` * ``tests/cases/vmr/input/0140_2001_calibrate_from_0d.json`` Each gets ``calibrate: ["R_poiseuille", "C", "L", "stenosis_coefficient"]`` on every vessel and ``calibrate: ["R_poiseuille", "L", "stenosis_coefficient"]`` on every multi-outlet junction so the existing test expectations (``test_steady_flow_calibration``, ``test_calibration_vmr``) still hold. Updates ``docs/pages/calibrator.md`` to document the mandatory form and shows the explicit lists needed to opt every parameter into calibration. Co-Authored-By: Claude Opus 4.7 (1M context) --- docs/pages/calibrator.md | 32 +- src/optimize/calibrate.cpp | 47 +- tests/cases/steadyFlow_calibration.json | 4 +- .../input/0080_0001_calibrate_from_0d.json | 807 ++++++++++++------ .../vmr/input/0104_0001_calibrate_R_only.json | 1 - .../input/0104_0001_calibrate_from_0d.json | 64 +- .../input/0140_2001_calibrate_from_0d.json | 139 ++- 7 files changed, 704 insertions(+), 390 deletions(-) diff --git a/docs/pages/calibrator.md b/docs/pages/calibrator.md index 7050bcb8e..82e3b9449 100644 --- a/docs/pages/calibrator.md +++ b/docs/pages/calibrator.md @@ -31,8 +31,7 @@ blocks: number of samples is the same for every variable. `dy` holds the matching time derivatives. * `calibration_parameters` collects the calibrator-specific options - (tolerances, iteration cap, damping factor, legacy - `calibrate_stenosis_coefficient` switch). + (tolerances, iteration cap, damping factor, capacitance clamp). The output file has the same shape as a solver input but with calibrated values written into `zero_d_element_values` (vessels) and `junction_values` @@ -41,11 +40,10 @@ removed from the output. ## Selecting which parameters to calibrate -By default every parameter exposed by every supported block is calibrated. -To restrict the optimization, add an optional `calibrate` field to a vessel -or junction listing the parameter names that should be optimized for that -block. Any parameter not in the list is held constant at the value found in -the input file. +Every vessel and multi-outlet junction must declare which of its parameters +should be calibrated through a `calibrate` field listing the parameter names. +Parameters that are not listed are held constant at the value found in the +input file. The names must match the parameter names a block exposes through its `input_params` list (e.g. `R_poiseuille`, `C`, `L`, `stenosis_coefficient` @@ -85,11 +83,15 @@ for `BloodVessel`). * If a block has a `calibrate` field, only the listed parameters are optimized for that block. -* If a block has no `calibrate` field, every parameter the block exposes is - optimized (legacy behavior). -* An explicit empty list (`"calibrate": []`) means "calibrate nothing for - this block". The calibrator errors out if no parameter ends up selected - in any block. +* If a block has no `calibrate` field (or an empty list), every parameter of + that block is held at its input value. +* The calibrator errors out if no parameter ends up selected anywhere in the + model. + +To calibrate every parameter of a block (the previous default), list every +name explicitly, e.g. `"calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"]` +for a `BloodVessel` or `"calibrate": ["R_poiseuille", "L", "stenosis_coefficient"]` +for a `BloodVesselJunction`. ### Worked example @@ -109,9 +111,3 @@ exposes its parameter names through the standard `Block::input_params` field. The calibrator reads this metadata at runtime via `Block::input_params` and `Block::input_params_list`, so adding a new calibratable block does not require any changes to `calibrate.cpp`. - -The legacy flag `calibration_parameters.calibrate_stenosis_coefficient` -(default `true`) layers on top of the selection logic: when set to `false`, -`stenosis_coefficient` is held constant regardless of any `calibrate` field. -The flag predates the `calibrate` field and is preserved for backward -compatibility; new input files should prefer per-block `calibrate`. diff --git a/src/optimize/calibrate.cpp b/src/optimize/calibrate.cpp index 92dcfac7c..b25e1bc42 100644 --- a/src/optimize/calibrate.cpp +++ b/src/optimize/calibrate.cpp @@ -2,7 +2,6 @@ // University of California, and others. SPDX-License-Identifier: BSD-3-Clause #include "calibrate.h" -#include #include #include "LevenbergMarquardtOptimizer.h" @@ -40,47 +39,37 @@ nlohmann::json calibrate(const nlohmann::json& config) { double increment_tol = calibration_parameters.value("tolerance_increment", 1e-10); int max_iter = calibration_parameters.value("maximum_iterations", 100); - bool calibrate_stenosis = - calibration_parameters.value("calibrate_stenosis_coefficient", true); bool zero_capacitance = calibration_parameters.value("set_capacitance_to_zero", false); double lambda0 = calibration_parameters.value("initial_damping_factor", 1.0); // Resolve the set of parameter names to calibrate for a given block from - // its own ``calibrate`` field. If the field is absent the block falls back - // to ``std::nullopt`` meaning "calibrate every parameter of this block" - // (legacy behavior); an explicit empty list means "calibrate nothing for - // this block". - auto resolve_calibrate_set = [](const nlohmann::json& block_config) - -> std::optional> { - if (!block_config.contains("calibrate")) return std::nullopt; - auto names = block_config["calibrate"].get>(); - return std::set(names.begin(), names.end()); - }; - // Whether ``name`` should be calibrated for this block. The ``set`` argument - // is the resolved per-block calibrate filter (nullopt = calibrate all). The - // legacy ``calibrate_stenosis_coefficient`` flag layers on top: if disabled, - // ``stenosis_coefficient`` is held constant regardless. - auto is_active = [&](const std::optional>& set, - const std::string& name) { - if (!calibrate_stenosis && name == "stenosis_coefficient") return false; - return !set.has_value() || set->count(name) > 0; + // its own ``calibrate`` field. The field is mandatory: a block without a + // ``calibrate`` field has no parameters optimized (every parameter of that + // block is held at its input value). An explicit empty list is equivalent + // to omitting the field. + auto resolve_calibrate_set = [](const nlohmann::json& block_config) { + std::set names; + if (!block_config.contains("calibrate")) return names; + auto list = block_config["calibrate"].get>(); + names.insert(list.begin(), list.end()); + return names; }; // Append the active alpha indices contributed by a single block to - // ``active_param_ids``. Walks the block's ``input_params`` and consults the - // resolved calibrate filter to decide whether each parameter (or each - // per-outlet copy of it, for list blocks) is optimized. + // ``active_param_ids``. Walks the block's ``input_params`` and includes + // each parameter (or, for list blocks, each per-outlet copy of it) whose + // name appears in the resolved calibrate filter. std::vector active_param_ids; auto register_active = [&](const Block& block, const std::vector& param_ids, - const std::optional>& set) { + const std::set& set) { int stride = static_cast(param_ids.size()) / static_cast(block.input_params.size()); if (!block.input_params_list) stride = 1; for (size_t i = 0; i < block.input_params.size(); i++) { const std::string& name = block.input_params[i].first; - if (!is_active(set, name)) continue; + if (set.count(name) == 0) continue; for (int s = 0; s < stride; s++) { active_param_ids.push_back(param_ids[i * stride + s]); } @@ -261,9 +250,9 @@ nlohmann::json calibrate(const nlohmann::json& config) { DEBUG_MSG("Number of active parameters " << active_param_ids.size()); if (active_param_ids.empty()) { throw std::runtime_error( - "[svzerodcalibrator] No parameters selected for calibration. Either " - "omit the 'calibrate' field from every block, or list at least one " - "parameter name in some block."); + "[svzerodcalibrator] No parameters selected for calibration. Add a " + "'calibrate' field listing parameter names to at least one vessel or " + "junction."); } auto lm_alg = LevenbergMarquardtOptimizer( &model, num_obs, param_counter, active_param_ids, lambda0, gradient_tol, diff --git a/tests/cases/steadyFlow_calibration.json b/tests/cases/steadyFlow_calibration.json index 69122f2c0..eeb7aa7b1 100644 --- a/tests/cases/steadyFlow_calibration.json +++ b/tests/cases/steadyFlow_calibration.json @@ -32,7 +32,8 @@ "C": 0.0001, "L": 1.0, "R_poiseuille": 100.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] } ], "y": { @@ -196,7 +197,6 @@ "tolerance_gradient": 1e-5, "tolerance_increment": 1e-10, "maximum_iterations": 100, - "calibrate_stenosis_coefficient": true, "set_capacitance_to_zero": false, "initial_damping_factor": 1.0 } diff --git a/tests/cases/vmr/input/0080_0001_calibrate_from_0d.json b/tests/cases/vmr/input/0080_0001_calibrate_from_0d.json index 9a3663b53..2458744e6 100644 --- a/tests/cases/vmr/input/0080_0001_calibrate_from_0d.json +++ b/tests/cases/vmr/input/0080_0001_calibrate_from_0d.json @@ -835,321 +835,372 @@ "inlet_vessels": [0], "junction_name": "J0", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [1, 8] + "outlet_vessels": [1, 8], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [3], "junction_name": "J1", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [ - 4, 37, 49, 59, 70, 73, 91, 94, 100, 137, 156, 168, 186, 198 - ] + "outlet_vessels": [4, 37, 49, 59, 70, 73, 91, 94, 100, 137, 156, 168, 186, 198], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [4], "junction_name": "J2", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [5, 48] + "outlet_vessels": [5, 48], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [8], "junction_name": "J3", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [9, 18, 26, 28, 41, 51, 68, 92, 105, 164, 183, 212] + "outlet_vessels": [9, 18, 26, 28, 41, 51, 68, 92, 105, 164, 183, 212], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [9], "junction_name": "J4", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [10, 125, 185] + "outlet_vessels": [10, 125, 185], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [10], "junction_name": "J5", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [11, 16, 69, 83, 87] + "outlet_vessels": [11, 16, 69, 83, 87], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [11], "junction_name": "J6", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [12, 21] + "outlet_vessels": [12, 21], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [12], "junction_name": "J7", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [13, 65] + "outlet_vessels": [13, 65], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [16], "junction_name": "J8", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [17, 184] + "outlet_vessels": [17, 184], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [18], "junction_name": "J9", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [19, 106, 130] + "outlet_vessels": [19, 106, 130], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [19], "junction_name": "J10", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [20, 148] + "outlet_vessels": [20, 148], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [21], "junction_name": "J11", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [22, 30] + "outlet_vessels": [22, 30], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [22], "junction_name": "J12", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [23, 162] + "outlet_vessels": [23, 162], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [23], "junction_name": "J13", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [24, 63] + "outlet_vessels": [24, 63], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [24], "junction_name": "J14", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [25, 29] + "outlet_vessels": [25, 29], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [26], "junction_name": "J15", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [27, 76, 149] + "outlet_vessels": [27, 76, 149], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [30], "junction_name": "J16", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [31, 204] + "outlet_vessels": [31, 204], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [31], "junction_name": "J17", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [32, 58] + "outlet_vessels": [32, 58], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [32], "junction_name": "J18", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [33, 170] + "outlet_vessels": [33, 170], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [33], "junction_name": "J19", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [34, 61] + "outlet_vessels": [34, 61], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [37], "junction_name": "J20", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [38, 43, 56, 62, 90, 113, 145, 171] + "outlet_vessels": [38, 43, 56, 62, 90, 113, 145, 171], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [41], "junction_name": "J21", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [42, 139] + "outlet_vessels": [42, 139], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [43], "junction_name": "J22", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [44, 107, 163] + "outlet_vessels": [44, 107, 163], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [44], "junction_name": "J23", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [45, 143] + "outlet_vessels": [45, 143], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [49], "junction_name": "J24", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [50, 140] + "outlet_vessels": [50, 140], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [51], "junction_name": "J25", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [52, 154] + "outlet_vessels": [52, 154], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [52], "junction_name": "J26", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [53, 136] + "outlet_vessels": [53, 136], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [56], "junction_name": "J27", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [57, 192] + "outlet_vessels": [57, 192], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [59], "junction_name": "J28", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [60, 121] + "outlet_vessels": [60, 121], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [63], "junction_name": "J29", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [64, 120] + "outlet_vessels": [64, 120], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [70], "junction_name": "J30", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [71, 144, 205] + "outlet_vessels": [71, 144, 205], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [71], "junction_name": "J31", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [72, 112] + "outlet_vessels": [72, 112], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [73], "junction_name": "J32", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [74, 79, 197] + "outlet_vessels": [74, 79, 197], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [74], "junction_name": "J33", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [75, 211] + "outlet_vessels": [75, 211], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [81], "junction_name": "J34", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [82, 178] + "outlet_vessels": [82, 178], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [83], "junction_name": "J35", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [84, 109, 135] + "outlet_vessels": [84, 109, 135], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [87], "junction_name": "J36", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [88, 89, 108] + "outlet_vessels": [88, 89, 108], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [92], "junction_name": "J37", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [93, 97] + "outlet_vessels": [93, 97], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [94], "junction_name": "J38", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [95, 104] + "outlet_vessels": [95, 104], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [95], "junction_name": "J39", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [96, 122] + "outlet_vessels": [96, 122], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [100], "junction_name": "J40", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [101, 126] + "outlet_vessels": [101, 126], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [113], "junction_name": "J41", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [114, 151] + "outlet_vessels": [114, 151], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [116], "junction_name": "J42", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [117, 210] + "outlet_vessels": [117, 210], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [126], "junction_name": "J43", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [127, 195, 201] + "outlet_vessels": [127, 195, 201], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [130], "junction_name": "J44", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [131, 159] + "outlet_vessels": [131, 159], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [131], "junction_name": "J45", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [132, 155] + "outlet_vessels": [132, 155], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [137], "junction_name": "J46", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [138, 209] + "outlet_vessels": [138, 209], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [149], "junction_name": "J47", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [150, 206] + "outlet_vessels": [150, 206], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [156], "junction_name": "J48", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [157, 189] + "outlet_vessels": [157, 189], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [157], "junction_name": "J49", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [158, 174] + "outlet_vessels": [158, 174], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [164], "junction_name": "J50", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [165, 179] + "outlet_vessels": [165, 179], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [168], "junction_name": "J51", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [169, 182] + "outlet_vessels": [169, 182], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [176], "junction_name": "J52", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [177, 196] + "outlet_vessels": [177, 196], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [1], @@ -1582,7 +1633,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 1, @@ -1594,7 +1646,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 2, @@ -1606,7 +1659,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 3, @@ -1618,7 +1672,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 4, @@ -1630,7 +1685,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 5, @@ -1642,7 +1698,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 6, @@ -1654,7 +1711,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -1669,7 +1727,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 8, @@ -1681,7 +1740,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 9, @@ -1693,7 +1753,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 10, @@ -1705,7 +1766,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 11, @@ -1717,7 +1779,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 12, @@ -1729,7 +1792,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 13, @@ -1741,7 +1805,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 14, @@ -1753,7 +1818,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -1768,7 +1834,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 16, @@ -1780,7 +1847,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -1795,7 +1863,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 18, @@ -1807,7 +1876,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 19, @@ -1819,7 +1889,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -1834,7 +1905,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 21, @@ -1846,7 +1918,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 22, @@ -1858,7 +1931,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 23, @@ -1870,7 +1944,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 24, @@ -1882,7 +1957,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -1897,7 +1973,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 26, @@ -1909,7 +1986,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -1924,7 +2002,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -1939,7 +2018,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -1954,7 +2034,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 30, @@ -1966,7 +2047,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 31, @@ -1978,7 +2060,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 32, @@ -1990,7 +2073,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 33, @@ -2002,7 +2086,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 34, @@ -2014,7 +2099,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 35, @@ -2026,7 +2112,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2041,7 +2128,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 37, @@ -2053,7 +2141,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 38, @@ -2065,7 +2154,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 39, @@ -2077,7 +2167,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2092,7 +2183,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 41, @@ -2104,7 +2196,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2119,7 +2212,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 43, @@ -2131,7 +2225,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 44, @@ -2143,7 +2238,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 45, @@ -2155,7 +2251,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 46, @@ -2167,7 +2264,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2182,7 +2280,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2197,7 +2296,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 49, @@ -2209,7 +2309,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2224,7 +2325,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 51, @@ -2236,7 +2338,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 52, @@ -2248,7 +2351,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 53, @@ -2260,7 +2364,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 54, @@ -2272,7 +2377,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2287,7 +2393,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 56, @@ -2299,7 +2406,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2314,7 +2422,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2329,7 +2438,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 59, @@ -2341,7 +2451,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2356,7 +2467,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2371,7 +2483,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2386,7 +2499,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 63, @@ -2398,7 +2512,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2413,7 +2528,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 65, @@ -2425,7 +2541,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 66, @@ -2437,7 +2554,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2452,7 +2570,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2467,7 +2586,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2482,7 +2602,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 70, @@ -2494,7 +2615,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 71, @@ -2506,7 +2628,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2521,7 +2644,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 73, @@ -2533,7 +2657,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 74, @@ -2545,7 +2670,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2560,7 +2686,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 76, @@ -2572,7 +2699,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 77, @@ -2584,7 +2712,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2599,7 +2728,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 79, @@ -2611,7 +2741,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 80, @@ -2623,7 +2754,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 81, @@ -2635,7 +2767,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2650,7 +2783,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 83, @@ -2662,7 +2796,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 84, @@ -2674,7 +2809,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 85, @@ -2686,7 +2822,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2701,7 +2838,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 87, @@ -2713,7 +2851,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2728,7 +2867,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2743,7 +2883,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2758,7 +2899,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2773,7 +2915,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 92, @@ -2785,7 +2928,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2800,7 +2944,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 94, @@ -2812,7 +2957,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 95, @@ -2824,7 +2970,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2839,7 +2986,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 97, @@ -2851,7 +2999,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 98, @@ -2863,7 +3012,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2878,7 +3028,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 100, @@ -2890,7 +3041,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 101, @@ -2902,7 +3054,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 102, @@ -2914,7 +3067,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2929,7 +3083,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2944,7 +3099,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2959,7 +3115,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2974,7 +3131,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -2989,7 +3147,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3004,7 +3163,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 109, @@ -3016,7 +3176,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 110, @@ -3028,7 +3189,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3043,7 +3205,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3058,7 +3221,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 113, @@ -3070,7 +3234,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 114, @@ -3082,7 +3247,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 115, @@ -3094,7 +3260,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 116, @@ -3106,7 +3273,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 117, @@ -3118,7 +3286,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 118, @@ -3130,7 +3299,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3145,7 +3315,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3160,7 +3331,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3175,7 +3347,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 122, @@ -3187,7 +3360,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 123, @@ -3199,7 +3373,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3214,7 +3389,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3229,7 +3405,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 126, @@ -3241,7 +3418,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 127, @@ -3253,7 +3431,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 128, @@ -3265,7 +3444,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3280,7 +3460,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 130, @@ -3292,7 +3473,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 131, @@ -3304,7 +3486,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 132, @@ -3316,7 +3499,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 133, @@ -3328,7 +3512,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3343,7 +3528,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3358,7 +3544,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3373,7 +3560,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 137, @@ -3385,7 +3573,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3400,7 +3589,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3415,7 +3605,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 140, @@ -3427,7 +3618,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 141, @@ -3439,7 +3631,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3454,7 +3647,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3469,7 +3663,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3484,7 +3679,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 145, @@ -3496,7 +3692,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 146, @@ -3508,7 +3705,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3523,7 +3721,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3538,7 +3737,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 149, @@ -3550,7 +3750,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3565,7 +3766,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 151, @@ -3577,7 +3779,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 152, @@ -3589,7 +3792,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3604,7 +3808,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3619,7 +3824,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3634,7 +3840,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 156, @@ -3646,7 +3853,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 157, @@ -3658,7 +3866,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3673,7 +3882,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 159, @@ -3685,7 +3895,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 160, @@ -3697,7 +3908,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3712,7 +3924,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3727,7 +3940,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3742,7 +3956,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 164, @@ -3754,7 +3969,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 165, @@ -3766,7 +3982,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 166, @@ -3778,7 +3995,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3793,7 +4011,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 168, @@ -3805,7 +4024,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3820,7 +4040,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3835,7 +4056,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 171, @@ -3847,7 +4069,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 172, @@ -3859,7 +4082,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3874,7 +4098,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 174, @@ -3886,7 +4111,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 175, @@ -3898,7 +4124,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 176, @@ -3910,7 +4137,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3925,7 +4153,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3940,7 +4169,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 179, @@ -3952,7 +4182,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 180, @@ -3964,7 +4195,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3979,7 +4211,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -3994,7 +4227,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4009,7 +4243,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4024,7 +4259,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4039,7 +4275,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 186, @@ -4051,7 +4288,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 187, @@ -4063,7 +4301,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4078,7 +4317,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 189, @@ -4090,7 +4330,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 190, @@ -4102,7 +4343,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4117,7 +4359,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 192, @@ -4129,7 +4372,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 193, @@ -4141,7 +4385,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4156,7 +4401,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4171,7 +4417,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4186,7 +4433,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4201,7 +4449,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 198, @@ -4213,7 +4462,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 199, @@ -4225,7 +4475,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4240,7 +4491,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 201, @@ -4252,7 +4504,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 202, @@ -4264,7 +4517,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4279,7 +4533,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4294,7 +4549,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4309,7 +4565,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 206, @@ -4321,7 +4578,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 207, @@ -4333,7 +4591,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4348,7 +4607,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4363,7 +4623,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4378,7 +4639,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4393,7 +4655,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 212, @@ -4405,7 +4668,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 213, @@ -4417,7 +4681,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -4432,14 +4697,14 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] } ], "calibration_parameters": { "tolerance_gradient": 1e-5, "tolerance_increment": 1e-9, "maximum_iterations": 20, - "calibrate_stenosis_coefficient": true, "set_capacitance_to_zero": false }, "y": { diff --git a/tests/cases/vmr/input/0104_0001_calibrate_R_only.json b/tests/cases/vmr/input/0104_0001_calibrate_R_only.json index 4a7b1c721..517784069 100644 --- a/tests/cases/vmr/input/0104_0001_calibrate_R_only.json +++ b/tests/cases/vmr/input/0104_0001_calibrate_R_only.json @@ -5562,7 +5562,6 @@ "tolerance_gradient": 1e-5, "tolerance_increment": 1e-9, "maximum_iterations": 20, - "calibrate_stenosis_coefficient": true, "set_capacitance_to_zero": false } } diff --git a/tests/cases/vmr/input/0104_0001_calibrate_from_0d.json b/tests/cases/vmr/input/0104_0001_calibrate_from_0d.json index e1badeafe..1224fda40 100644 --- a/tests/cases/vmr/input/0104_0001_calibrate_from_0d.json +++ b/tests/cases/vmr/input/0104_0001_calibrate_from_0d.json @@ -133,19 +133,22 @@ "inlet_vessels": [0], "junction_name": "J0", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [1, 5, 9] + "outlet_vessels": [1, 5, 9], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [1], "junction_name": "J1", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [2, 15] + "outlet_vessels": [2, 15], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [5], "junction_name": "J2", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [6, 12] + "outlet_vessels": [6, 12], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [2], @@ -230,7 +233,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 1, @@ -242,7 +246,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 2, @@ -254,7 +259,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 3, @@ -266,7 +272,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -281,7 +288,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 5, @@ -293,7 +301,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 6, @@ -305,7 +314,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 7, @@ -317,7 +327,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -332,7 +343,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 9, @@ -344,7 +356,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 10, @@ -356,7 +369,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -371,7 +385,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 12, @@ -383,7 +398,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 13, @@ -395,7 +411,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -410,7 +427,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 15, @@ -422,7 +440,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 16, @@ -434,7 +453,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -449,14 +469,14 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] } ], "calibration_parameters": { "tolerance_gradient": 1e-5, "tolerance_increment": 1e-9, "maximum_iterations": 20, - "calibrate_stenosis_coefficient": true, "set_capacitance_to_zero": false }, "y": { diff --git a/tests/cases/vmr/input/0140_2001_calibrate_from_0d.json b/tests/cases/vmr/input/0140_2001_calibrate_from_0d.json index ca7ab3fc6..713a218f7 100644 --- a/tests/cases/vmr/input/0140_2001_calibrate_from_0d.json +++ b/tests/cases/vmr/input/0140_2001_calibrate_from_0d.json @@ -183,37 +183,43 @@ "inlet_vessels": [0], "junction_name": "J0", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [1, 9, 21, 34, 37] + "outlet_vessels": [1, 9, 21, 34, 37], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [1], "junction_name": "J1", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [2, 27] + "outlet_vessels": [2, 27], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [2], "junction_name": "J2", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [3, 15] + "outlet_vessels": [3, 15], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [5], "junction_name": "J3", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [6, 24] + "outlet_vessels": [6, 24], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [11], "junction_name": "J4", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [12, 31] + "outlet_vessels": [12, 31], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [17], "junction_name": "J5", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [18, 28] + "outlet_vessels": [18, 28], + "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { "inlet_vessels": [3], @@ -382,7 +388,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 1, @@ -394,7 +401,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 2, @@ -406,7 +414,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 3, @@ -418,7 +427,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 4, @@ -430,7 +440,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 5, @@ -442,7 +453,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 6, @@ -454,7 +466,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 7, @@ -466,7 +479,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -481,7 +495,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 9, @@ -493,7 +508,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 10, @@ -505,7 +521,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 11, @@ -517,7 +534,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 12, @@ -529,7 +547,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 13, @@ -541,7 +560,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -556,7 +576,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 15, @@ -568,7 +589,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 16, @@ -580,7 +602,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 17, @@ -592,7 +615,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 18, @@ -604,7 +628,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 19, @@ -616,7 +641,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -631,7 +657,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 21, @@ -643,7 +670,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 22, @@ -655,7 +683,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -670,7 +699,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 24, @@ -682,7 +712,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 25, @@ -694,7 +725,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -709,7 +741,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -724,7 +757,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 28, @@ -736,7 +770,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 29, @@ -748,7 +783,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -763,7 +799,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 31, @@ -775,7 +812,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 32, @@ -787,7 +825,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -802,7 +841,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 34, @@ -814,7 +854,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 35, @@ -826,7 +867,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -841,7 +883,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 37, @@ -853,7 +896,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "vessel_id": 38, @@ -865,7 +909,8 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] }, { "boundary_conditions": { @@ -880,14 +925,14 @@ "L": 0.0, "R_poiseuille": 0.0, "stenosis_coefficient": 0.0 - } + }, + "calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"] } ], "calibration_parameters": { "tolerance_gradient": 1e-5, "tolerance_increment": 1e-9, "maximum_iterations": 20, - "calibrate_stenosis_coefficient": true, "set_capacitance_to_zero": false }, "y": { From aad64f7f43d676427a4fb989e220d65ae004a2a5 Mon Sep 17 00:00:00 2001 From: Martin Pfaller Date: Tue, 5 May 2026 17:24:23 -0400 Subject: [PATCH 08/12] Drop set_capacitance_to_zero, consolidate VMR test Removes the BloodVessel-specific ``set_capacitance_to_zero`` switch from ``calibration_parameters`` along with the name-based output post-processing (``std::max(C, 0)``, ``std::max(L, 0)``). With explicit per-block ``calibrate`` selection, these legacy clamps are unnecessary and the calibrator no longer special-cases parameter names by string. Folds the new R-only test case into the existing ``test_calibration_vmr`` parametrize and switches the comparison to the proper ``reference/`` files (which were always intended). Fixes the latent bug where ``np.isclose`` was called without ``assert`` and the comparison referenced ``input/`` instead of ``reference/`` - ``calibrator(input)`` matches every reference to ~1e-13, so the existing three VMR cases now actually verify their output. The R-only case is just one more entry with the same comparison code. Removes the local ``docs/pages/calibrator.md`` and link from ``main.md``: the canonical user guide is in the SimVascular documentation site repo and will be updated there. Drops ``set_capacitance_to_zero`` from every checked-in fixture. Co-Authored-By: Claude Opus 4.7 (1M context) --- docs/pages/calibrator.md | 113 ------------------ docs/pages/main.md | 1 - src/optimize/calibrate.cpp | 12 +- tests/cases/steadyFlow_calibration.json | 1 - .../input/0080_0001_calibrate_from_0d.json | 3 +- .../vmr/input/0104_0001_calibrate_R_only.json | 3 +- .../input/0104_0001_calibrate_from_0d.json | 3 +- .../input/0140_2001_calibrate_from_0d.json | 3 +- tests/test_calibrator.py | 87 ++++---------- 9 files changed, 31 insertions(+), 195 deletions(-) delete mode 100644 docs/pages/calibrator.md diff --git a/docs/pages/calibrator.md b/docs/pages/calibrator.md deleted file mode 100644 index 82e3b9449..000000000 --- a/docs/pages/calibrator.md +++ /dev/null @@ -1,113 +0,0 @@ -@page calibrator svZeroDCalibrator - -[TOC] - -svZeroDCalibrator solves the inverse problem: given observations of pressure -and flow, it tunes the parameters of an existing 0D model so that the -solver-predicted state matches the observations. The optimizer is a -Levenberg-Marquardt loop running over the alpha vector of all calibratable -parameters in the model. See `src/optimize/calibrate.cpp` and -`src/optimize/LevenbergMarquardtOptimizer.h` for the implementation. - -## Input file - -The input file is a normal solver configuration extended with three extra -blocks: - -```json -{ - "boundary_conditions": [...], - "junctions": [...], - "vessels": [...], - "calibration_parameters": { ... }, - "y": { ... }, - "dy": { ... } -} -``` - -* `y` and `dy` are dictionaries keyed by the variable names that the model - exposes after assembly (e.g. `pressure:INFLOW:branch0_seg0`, - `flow:branch0_seg0:OUT`). Each value is a list of observed samples; the - number of samples is the same for every variable. `dy` holds the matching - time derivatives. -* `calibration_parameters` collects the calibrator-specific options - (tolerances, iteration cap, damping factor, capacitance clamp). - -The output file has the same shape as a solver input but with calibrated -values written into `zero_d_element_values` (vessels) and `junction_values` -(multi-outlet junctions). The `y`, `dy` and `calibration_parameters` keys are -removed from the output. - -## Selecting which parameters to calibrate - -Every vessel and multi-outlet junction must declare which of its parameters -should be calibrated through a `calibrate` field listing the parameter names. -Parameters that are not listed are held constant at the value found in the -input file. - -The names must match the parameter names a block exposes through its -`input_params` list (e.g. `R_poiseuille`, `C`, `L`, `stenosis_coefficient` -for `BloodVessel`). - -```json -{ - "vessel_id": 0, - "vessel_name": "branch0_seg0", - "zero_d_element_type": "BloodVessel", - "zero_d_element_values": { - "R_poiseuille": 0.0, - "C": 1.2e-6, - "L": 0.25, - "stenosis_coefficient": 1.06e-5 - }, - "calibrate": ["R_poiseuille"] -} -``` - -```json -{ - "junction_name": "J0", - "junction_type": "BloodVesselJunction", - "junction_values": { - "R_poiseuille": [0.0, 0.0], - "L": [0.0, 0.0], - "stenosis_coefficient": [0.0, 0.0] - }, - "inlet_vessels": [0], - "outlet_vessels": [1, 2], - "calibrate": ["R_poiseuille"] -} -``` - -### Resolution rules - -* If a block has a `calibrate` field, only the listed parameters are - optimized for that block. -* If a block has no `calibrate` field (or an empty list), every parameter of - that block is held at its input value. -* The calibrator errors out if no parameter ends up selected anywhere in the - model. - -To calibrate every parameter of a block (the previous default), list every -name explicitly, e.g. `"calibrate": ["R_poiseuille", "C", "L", "stenosis_coefficient"]` -for a `BloodVessel` or `"calibrate": ["R_poiseuille", "L", "stenosis_coefficient"]` -for a `BloodVesselJunction`. - -### Worked example - -The repository ships a small fixture derived from the `0104_0001` Vascular -Model Repository case at -`tests/cases/vmr/input/0104_0001_calibrate_R_only.json`. Every vessel and -multi-outlet junction in that file carries `"calibrate": ["R_poiseuille"]`, -the non-R parameters are fixed at the calibrated reference, and every R -value is zeroed. The calibrator recovers the reference R values to machine -precision and leaves the other parameters untouched. The matching test is -`tests/test_calibrator.py::test_calibration_R_only`. - -## Block requirements - -A block is calibratable as long as it implements `update_gradient` and -exposes its parameter names through the standard `Block::input_params` -field. The calibrator reads this metadata at runtime via -`Block::input_params` and `Block::input_params_list`, so adding a new -calibratable block does not require any changes to `calibrate.cpp`. diff --git a/docs/pages/main.md b/docs/pages/main.md index baeaab9e9..e001e6d0b 100644 --- a/docs/pages/main.md +++ b/docs/pages/main.md @@ -9,7 +9,6 @@ Below are links to important sections of the documentation: * [Installing svZeroDSolver](https://simvascular.github.io/documentation/rom_simulation.html#0d-solver-install) * [User guide for svZeroDSolver](https://simvascular.github.io/documentation/rom_simulation.html#0d-solver-user-guide) * [User guide for svZeroDCalibrator](https://simvascular.github.io/documentation/rom_simulation.html#0d-solver-calibrator) -* [Selecting parameters to calibrate](@ref calibrator) * [User guide for svZeroDVisualization](https://simvascular.github.io/documentation/rom_simulation.html#0d-solver-visualization) * [User guide for svZeroDGUI](https://simvascular.github.io/documentation/rom_simulation.html#0d-solver-gui) diff --git a/src/optimize/calibrate.cpp b/src/optimize/calibrate.cpp index b25e1bc42..0d880c3e3 100644 --- a/src/optimize/calibrate.cpp +++ b/src/optimize/calibrate.cpp @@ -39,8 +39,6 @@ nlohmann::json calibrate(const nlohmann::json& config) { double increment_tol = calibration_parameters.value("tolerance_increment", 1e-10); int max_iter = calibration_parameters.value("maximum_iterations", 100); - bool zero_capacitance = - calibration_parameters.value("set_capacitance_to_zero", false); double lambda0 = calibration_parameters.value("initial_damping_factor", 1.0); // Resolve the set of parameter names to calibrate for a given block from @@ -262,11 +260,6 @@ nlohmann::json calibrate(const nlohmann::json& config) { // Build a JSON values object for a block by reading optimized alpha values // out using the block's own ``input_params``. - auto post_process = [&](const std::string& name, double v) { - if (name == "C" && zero_capacitance) v = 0.0; - if (name == "C" || name == "L") v = std::max(v, 0.0); - return v; - }; auto write_alpha_for_block = [&](const Block& block) -> nlohmann::json { nlohmann::json values = nlohmann::json::object(); int total = static_cast(block.global_param_ids.size()); @@ -277,12 +270,11 @@ nlohmann::json calibrate(const nlohmann::json& config) { if (block.input_params_list) { std::vector arr; for (int s = 0; s < stride; s++) { - arr.push_back(post_process( - name, alpha[block.global_param_ids[i * stride + s]])); + arr.push_back(alpha[block.global_param_ids[i * stride + s]]); } values[name] = arr; } else { - values[name] = post_process(name, alpha[block.global_param_ids[i]]); + values[name] = alpha[block.global_param_ids[i]]; } } return values; diff --git a/tests/cases/steadyFlow_calibration.json b/tests/cases/steadyFlow_calibration.json index eeb7aa7b1..0d0660708 100644 --- a/tests/cases/steadyFlow_calibration.json +++ b/tests/cases/steadyFlow_calibration.json @@ -197,7 +197,6 @@ "tolerance_gradient": 1e-5, "tolerance_increment": 1e-10, "maximum_iterations": 100, - "set_capacitance_to_zero": false, "initial_damping_factor": 1.0 } } diff --git a/tests/cases/vmr/input/0080_0001_calibrate_from_0d.json b/tests/cases/vmr/input/0080_0001_calibrate_from_0d.json index 2458744e6..76532ef44 100644 --- a/tests/cases/vmr/input/0080_0001_calibrate_from_0d.json +++ b/tests/cases/vmr/input/0080_0001_calibrate_from_0d.json @@ -4704,8 +4704,7 @@ "calibration_parameters": { "tolerance_gradient": 1e-5, "tolerance_increment": 1e-9, - "maximum_iterations": 20, - "set_capacitance_to_zero": false + "maximum_iterations": 20 }, "y": { "flow:branch0_seg0:J0": [ diff --git a/tests/cases/vmr/input/0104_0001_calibrate_R_only.json b/tests/cases/vmr/input/0104_0001_calibrate_R_only.json index 517784069..1020ea8e1 100644 --- a/tests/cases/vmr/input/0104_0001_calibrate_R_only.json +++ b/tests/cases/vmr/input/0104_0001_calibrate_R_only.json @@ -5561,7 +5561,6 @@ "calibration_parameters": { "tolerance_gradient": 1e-5, "tolerance_increment": 1e-9, - "maximum_iterations": 20, - "set_capacitance_to_zero": false + "maximum_iterations": 20 } } diff --git a/tests/cases/vmr/input/0104_0001_calibrate_from_0d.json b/tests/cases/vmr/input/0104_0001_calibrate_from_0d.json index 1224fda40..c12458f5c 100644 --- a/tests/cases/vmr/input/0104_0001_calibrate_from_0d.json +++ b/tests/cases/vmr/input/0104_0001_calibrate_from_0d.json @@ -476,8 +476,7 @@ "calibration_parameters": { "tolerance_gradient": 1e-5, "tolerance_increment": 1e-9, - "maximum_iterations": 20, - "set_capacitance_to_zero": false + "maximum_iterations": 20 }, "y": { "flow:branch0_seg0:J0": [ diff --git a/tests/cases/vmr/input/0140_2001_calibrate_from_0d.json b/tests/cases/vmr/input/0140_2001_calibrate_from_0d.json index 713a218f7..dca31ca4b 100644 --- a/tests/cases/vmr/input/0140_2001_calibrate_from_0d.json +++ b/tests/cases/vmr/input/0140_2001_calibrate_from_0d.json @@ -932,8 +932,7 @@ "calibration_parameters": { "tolerance_gradient": 1e-5, "tolerance_increment": 1e-9, - "maximum_iterations": 20, - "set_capacitance_to_zero": false + "maximum_iterations": 20 }, "y": { "flow:branch0_seg0:J0": [ diff --git a/tests/test_calibrator.py b/tests/test_calibrator.py index f38113c99..6e7dbb5b1 100644 --- a/tests/test_calibrator.py +++ b/tests/test_calibrator.py @@ -26,25 +26,37 @@ def test_steady_flow_calibration(): ) -@pytest.mark.parametrize("model_id", ["0080_0001", "0104_0001", "0140_2001"]) -def test_calibration_vmr(model_id): - """Test actual models from the vascular model repository.""" - with open( - os.path.join( - this_file_dir, "cases", "vmr", "input", f"{model_id}_calibrate_from_0d.json" - ) - ) as ff: - reference = json.load(ff) - +@pytest.mark.parametrize( + "test_case", + [ + "0080_0001_calibrate_from_0d", + "0104_0001_calibrate_from_0d", + "0140_2001_calibrate_from_0d", + # Calibrates only R_poiseuille via per-block ``calibrate`` fields, + # starting from the reference values for C, L and + # stenosis_coefficient and zeroed R_poiseuille. The calibrator should + # recover R_poiseuille while leaving the other parameters untouched. + "0104_0001_calibrate_R_only", + ], +) +def test_calibration_vmr(test_case): + """Calibrate a model from the vascular model repository and check that + every parameter matches the corresponding reference.""" test = os.path.join( - this_file_dir, "cases", "vmr", "input", f"{model_id}_calibrate_from_0d.json" + this_file_dir, "cases", "vmr", "input", f"{test_case}.json" ) + model_id = test_case[:9] + reference_file = os.path.join( + this_file_dir, "cases", "vmr", "reference", f"{model_id}_optimal_from_0d.json" + ) + with open(reference_file) as ff: + reference = json.load(ff) result, _ = execute_pysvzerod(test, "calibrator") for i, vessel in enumerate(reference["vessels"]): for key, value in vessel["zero_d_element_values"].items(): - np.isclose( + assert np.isclose( result["vessels"][i]["zero_d_element_values"][key], value, rtol=RTOL_PRES, @@ -53,57 +65,8 @@ def test_calibration_vmr(model_id): for i, junction in enumerate(reference["junctions"]): if "junction_values" in junction: for key, value in junction["junction_values"].items(): - np.allclose( + assert np.allclose( result["junctions"][i]["junction_values"][key], value, rtol=RTOL_PRES, ) - - -def test_calibration_R_only(): - """Calibrate only ``R_poiseuille`` on a VMR model while holding C, L and - stenosis_coefficient at their ground-truth values via per-block - ``calibrate`` fields. The fixture starts from the calibrated reference (so - non-R parameters are at the optimum) with every R_poiseuille zeroed; the - calibrator should recover R_poiseuille and leave the rest untouched. The - reference values to compare against live in - ``tests/cases/vmr/reference/0104_0001_optimal_from_0d.json``. - """ - testfile = os.path.join( - this_file_dir, - "cases", - "vmr", - "input", - "0104_0001_calibrate_R_only.json", - ) - reference_file = os.path.join( - this_file_dir, - "cases", - "vmr", - "reference", - "0104_0001_optimal_from_0d.json", - ) - with open(reference_file) as ff: - reference = json.load(ff) - - result, _ = execute_pysvzerod(testfile, "calibrator") - - for ref_vessel, res_vessel in zip(reference["vessels"], result["vessels"]): - for key, ref_value in ref_vessel["zero_d_element_values"].items(): - res_value = res_vessel["zero_d_element_values"][key] - assert np.isclose(res_value, ref_value, atol=1e-9, rtol=RTOL_PRES), ( - f"Vessel {ref_vessel['vessel_name']} parameter {key}: " - f"expected {ref_value}, got {res_value}" - ) - - for ref_junction, res_junction in zip( - reference["junctions"], result["junctions"] - ): - if "junction_values" not in ref_junction: - continue - for key, ref_values in ref_junction["junction_values"].items(): - res_values = res_junction["junction_values"][key] - assert np.allclose(res_values, ref_values, atol=1e-9, rtol=RTOL_PRES), ( - f"Junction {ref_junction['junction_name']} parameter {key}: " - f"expected {ref_values}, got {res_values}" - ) From bd855e2785cc16d8d5a71f816a28c863766d0ddd Mon Sep 17 00:00:00 2001 From: Martin Pfaller Date: Tue, 5 May 2026 17:33:39 -0400 Subject: [PATCH 09/12] Fix prettier formatting on long inline arrays in fixtures The Python formatter that re-emitted the calibrator fixtures was ignoring the parent dict key's prefix when deciding whether an array fits inline. That left one over-80 line in ``0080_0001_calibrate_from_0d.json`` (``"outlet_vessels": [4, 37, 49, 59, 70, 73, 91, 94, 100, 137, 156, 168, 186, 198],``, 86 chars) which prettier flagged in CI. Re-emitted all calibrator fixtures with the fixed formatter; round-trip on the master VMR files matches byte-for-byte and no line in any fixture is over 80 chars. Co-Authored-By: Claude Opus 4.7 (1M context) --- tests/cases/vmr/input/0080_0001_calibrate_from_0d.json | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/cases/vmr/input/0080_0001_calibrate_from_0d.json b/tests/cases/vmr/input/0080_0001_calibrate_from_0d.json index 76532ef44..01b22b151 100644 --- a/tests/cases/vmr/input/0080_0001_calibrate_from_0d.json +++ b/tests/cases/vmr/input/0080_0001_calibrate_from_0d.json @@ -842,7 +842,9 @@ "inlet_vessels": [3], "junction_name": "J1", "junction_type": "NORMAL_JUNCTION", - "outlet_vessels": [4, 37, 49, 59, 70, 73, 91, 94, 100, 137, 156, 168, 186, 198], + "outlet_vessels": [ + 4, 37, 49, 59, 70, 73, 91, 94, 100, 137, 156, 168, 186, 198 + ], "calibrate": ["R_poiseuille", "L", "stenosis_coefficient"] }, { From 877dfd766b3b2c1b4fd234af295e0c8a5b2c7eb7 Mon Sep 17 00:00:00 2001 From: Martin Pfaller Date: Tue, 5 May 2026 18:13:01 -0400 Subject: [PATCH 10/12] Reuse the forward-solver assembly for the calibrator residual Until now the per-block ``update_gradient`` re-implemented two things: the parameter Jacobian columns and the residual itself, with the latter duplicating the (E, F, c) algebra that the forward solver already owns. This commit splits the two concerns: * ``Block::update_gradient`` is contracted to populate only the parameter Jacobian columns; the residual argument is removed from the signature and the implementations of BloodVessel, BloodVesselCRL and BloodVesselJunction lose their residual-formula branch. Junction's override (which only wrote the residual and had no parameters) is dropped entirely; the new base-class default is a no-op so blocks without parameters need no override. * The Levenberg-Marquardt optimizer now owns a SparseSystem and, at each iteration, syncs alpha into the model's parameter storage, calls ``Model::update_constant`` once and ``Model::update_solution`` per observation, and reads the residual chunk straight off the assembly (``r_i = c + E*dy + F*y``). This is the same residual the forward solver computes (up to the sign that cancels in the LM normal equations). Two practical wrinkles addressed: * Calibrator models contain no boundary-condition blocks, so ``num_vars > num_eqns``. The system is sized with the larger of the two; matrix-vector products run on padded vectors and the residual segment is sliced to the equation count. * ``calibrate.cpp`` now registers each parameter slot through ``Model::add_parameter`` so ``parameter_values`` is sized for the assembly path. The LM loop syncs alpha through ``Model::update_parameter_value``; ``update_time`` is intentionally skipped because it would overwrite the synced values from the Parameter objects. All seven calibrator tests still pass, every solver/io test still passes, and ``make codeformat`` produces no diff. Co-Authored-By: Claude Opus 4.7 (1M context) --- src/model/Block.cpp | 5 +- src/model/Block.h | 22 ++++---- src/model/BloodVessel.cpp | 15 ------ src/model/BloodVessel.h | 9 ++-- src/model/BloodVesselCRL.cpp | 22 -------- src/model/BloodVesselCRL.h | 9 ++-- src/model/BloodVesselJunction.cpp | 23 +------- src/model/BloodVesselJunction.h | 9 ++-- src/model/Junction.cpp | 11 ---- src/model/Junction.h | 15 ------ src/optimize/LevenbergMarquardtOptimizer.cpp | 56 ++++++++++++++++++-- src/optimize/LevenbergMarquardtOptimizer.h | 3 ++ src/optimize/calibrate.cpp | 14 +++-- 13 files changed, 90 insertions(+), 123 deletions(-) diff --git a/src/model/Block.cpp b/src/model/Block.cpp index 7800fa10d..c33fc2cfb 100644 --- a/src/model/Block.cpp +++ b/src/model/Block.cpp @@ -62,11 +62,10 @@ void Block::update_solution( void Block::post_solve(Eigen::Matrix& y) {} void Block::update_gradient(Eigen::SparseMatrix& jacobian, - Eigen::Matrix& residual, Eigen::Matrix& alpha, std::vector& y, std::vector& dy) { - throw std::runtime_error("Gradient calculation not implemented for block " + - get_name()); + // Default: block has no calibratable parameters, so it contributes no + // columns to the parameter Jacobian. Blocks with parameters override this. } TripletsContributions Block::get_num_triplets() { return num_triplets; } diff --git a/src/model/Block.h b/src/model/Block.h index 849aeb956..1f1017f7b 100644 --- a/src/model/Block.h +++ b/src/model/Block.h @@ -252,20 +252,22 @@ class Block { virtual void post_solve(Eigen::Matrix& y); /** - * @brief Set the gradient of the block contributions with respect to the - * parameters + * @brief Write this block's contributions to the parameter Jacobian + * \f$\partial r / \partial \alpha\f$. + * + * The residual is recomputed at the top level of the calibrator from the + * solver assembly (E, F, c via update_constant / update_time / + * update_solution); each block only needs to populate the columns of the + * sparse Jacobian that correspond to its own parameters. * * @param jacobian Jacobian with respect to the parameters * @param alpha Current parameter vector - * @param residual Residual with respect to the parameters - * @param y Current solution - * @param dy Time-derivative of the current solution + * @param y Observed solution at the current data point + * @param dy Observed time derivative at the current data point */ - virtual void update_gradient( - Eigen::SparseMatrix& jacobian, - Eigen::Matrix& residual, - Eigen::Matrix& alpha, std::vector& y, - std::vector& dy); + virtual void update_gradient(Eigen::SparseMatrix& jacobian, + Eigen::Matrix& alpha, + std::vector& y, std::vector& dy); /** * @brief Number of triplets of element diff --git a/src/model/BloodVessel.cpp b/src/model/BloodVessel.cpp index faa6f25c1..a77209f7f 100644 --- a/src/model/BloodVessel.cpp +++ b/src/model/BloodVessel.cpp @@ -58,23 +58,16 @@ void BloodVessel::update_solution( void BloodVessel::update_gradient( Eigen::SparseMatrix& jacobian, - Eigen::Matrix& residual, Eigen::Matrix& alpha, std::vector& y, std::vector& dy) { - auto y0 = y[global_var_ids[0]]; auto y1 = y[global_var_ids[1]]; - auto y2 = y[global_var_ids[2]]; - auto y3 = y[global_var_ids[3]]; - auto dy0 = dy[global_var_ids[0]]; auto dy1 = dy[global_var_ids[1]]; auto dy3 = dy[global_var_ids[3]]; auto resistance = alpha[global_param_ids[ParamId::RESISTANCE]]; auto capacitance = alpha[global_param_ids[ParamId::CAPACITANCE]]; - auto inductance = alpha[global_param_ids[ParamId::INDUCTANCE]]; double stenosis_coeff = 0.0; - if (global_param_ids.size() > 3) { stenosis_coeff = alpha[global_param_ids[ParamId::STENOSIS_COEFFICIENT]]; } @@ -82,7 +75,6 @@ void BloodVessel::update_gradient( jacobian.coeffRef(global_eqn_ids[0], global_param_ids[0]) = -y1; jacobian.coeffRef(global_eqn_ids[0], global_param_ids[2]) = -dy3; - if (global_param_ids.size() > 3) { jacobian.coeffRef(global_eqn_ids[0], global_param_ids[3]) = -fabs(y1) * y1; } @@ -90,15 +82,8 @@ void BloodVessel::update_gradient( jacobian.coeffRef(global_eqn_ids[1], global_param_ids[0]) = capacitance * dy1; jacobian.coeffRef(global_eqn_ids[1], global_param_ids[1]) = -dy0 + (resistance + 2 * stenosis_resistance) * dy1; - if (global_param_ids.size() > 3) { jacobian.coeffRef(global_eqn_ids[1], global_param_ids[3]) = 2.0 * capacitance * fabs(y1) * dy1; } - - residual(global_eqn_ids[0]) = - y0 - (resistance + stenosis_resistance) * y1 - y2 - inductance * dy3; - residual(global_eqn_ids[1]) = - y1 - y3 - capacitance * dy0 + - capacitance * (resistance + 2.0 * stenosis_resistance) * dy1; } diff --git a/src/model/BloodVessel.h b/src/model/BloodVessel.h index fcf9a398d..5928d8593 100644 --- a/src/model/BloodVessel.h +++ b/src/model/BloodVessel.h @@ -195,17 +195,14 @@ class BloodVessel : public Block { const Eigen::Matrix& dy); /** - * @brief Set the gradient of the block contributions with respect to the - * parameters + * @brief Write this block's columns of the parameter Jacobian. * * @param jacobian Jacobian with respect to the parameters * @param alpha Current parameter vector - * @param residual Residual with respect to the parameters - * @param y Current solution - * @param dy Time-derivative of the current solution + * @param y Observed solution + * @param dy Observed time derivative of the solution */ void update_gradient(Eigen::SparseMatrix& jacobian, - Eigen::Matrix& residual, Eigen::Matrix& alpha, std::vector& y, std::vector& dy); diff --git a/src/model/BloodVesselCRL.cpp b/src/model/BloodVesselCRL.cpp index 5c264ca35..06785cf5d 100644 --- a/src/model/BloodVesselCRL.cpp +++ b/src/model/BloodVesselCRL.cpp @@ -50,38 +50,16 @@ void BloodVesselCRL::update_solution( void BloodVesselCRL::update_gradient( Eigen::SparseMatrix& jacobian, - Eigen::Matrix& residual, Eigen::Matrix& alpha, std::vector& y, std::vector& dy) { - auto y0 = y[global_var_ids[0]]; - auto y1 = y[global_var_ids[1]]; - auto y2 = y[global_var_ids[2]]; auto y3 = y[global_var_ids[3]]; - auto dy0 = dy[global_var_ids[0]]; - auto dy1 = dy[global_var_ids[1]]; auto dy3 = dy[global_var_ids[3]]; - auto resistance = alpha[global_param_ids[ParamId::RESISTANCE]]; - auto capacitance = alpha[global_param_ids[ParamId::CAPACITANCE]]; - auto inductance = alpha[global_param_ids[ParamId::INDUCTANCE]]; - double stenosis_coeff = 0.0; - - if (global_param_ids.size() > 3) { - stenosis_coeff = alpha[global_param_ids[ParamId::STENOSIS_COEFFICIENT]]; - } - auto stenosis_resistance = stenosis_coeff * fabs(y3); - jacobian.coeffRef(global_eqn_ids[0], global_param_ids[0]) = -y3; jacobian.coeffRef(global_eqn_ids[0], global_param_ids[2]) = -dy3; - if (global_param_ids.size() > 3) { jacobian.coeffRef(global_eqn_ids[0], global_param_ids[3]) = -fabs(y3) * y3; } - jacobian.coeffRef(global_eqn_ids[1], global_param_ids[1]) = -dy0; - - residual(global_eqn_ids[0]) = - y0 - (resistance + stenosis_resistance) * y3 - y2 - inductance * dy3; - residual(global_eqn_ids[1]) = y1 - y3 - capacitance * dy0; } diff --git a/src/model/BloodVesselCRL.h b/src/model/BloodVesselCRL.h index ca220fff0..593945e4b 100644 --- a/src/model/BloodVesselCRL.h +++ b/src/model/BloodVesselCRL.h @@ -174,17 +174,14 @@ class BloodVesselCRL : public Block { const Eigen::Matrix& dy); /** - * @brief Set the gradient of the block contributions with respect to the - * parameters + * @brief Write this block's columns of the parameter Jacobian. * * @param jacobian Jacobian with respect to the parameters * @param alpha Current parameter vector - * @param residual Residual with respect to the parameters - * @param y Current solution - * @param dy Time-derivative of the current solution + * @param y Observed solution + * @param dy Observed time derivative of the solution */ void update_gradient(Eigen::SparseMatrix& jacobian, - Eigen::Matrix& residual, Eigen::Matrix& alpha, std::vector& y, std::vector& dy); diff --git a/src/model/BloodVesselJunction.cpp b/src/model/BloodVesselJunction.cpp index 56469e31e..c5cf83d70 100644 --- a/src/model/BloodVesselJunction.cpp +++ b/src/model/BloodVesselJunction.cpp @@ -54,43 +54,22 @@ void BloodVesselJunction::update_solution( void BloodVesselJunction::update_gradient( Eigen::SparseMatrix& jacobian, - Eigen::Matrix& residual, Eigen::Matrix& alpha, std::vector& y, std::vector& dy) { - auto p_in = y[global_var_ids[0]]; - auto q_in = y[global_var_ids[1]]; - - residual(global_eqn_ids[0]) = q_in; for (size_t i = 0; i < num_outlets; i++) { - // Get parameters - auto resistance = alpha[global_param_ids[i]]; - auto inductance = alpha[global_param_ids[num_outlets + i]]; - double stenosis_coeff = 0.0; - if (global_param_ids.size() / num_outlets > 2) { - stenosis_coeff = alpha[global_param_ids[2 * num_outlets + i]]; - } auto q_out = y[global_var_ids[3 + 2 * i]]; - auto p_out = y[global_var_ids[2 + 2 * i]]; auto dq_out = dy[global_var_ids[3 + 2 * i]]; - auto stenosis_resistance = stenosis_coeff * fabs(q_out); // Resistance jacobian.coeffRef(global_eqn_ids[i + 1], global_param_ids[i]) = -q_out; - // Inductance jacobian.coeffRef(global_eqn_ids[i + 1], global_param_ids[num_outlets + i]) = -dq_out; - - // Stenosis Coefficent + // Stenosis coefficient if (global_param_ids.size() / num_outlets > 2) { jacobian.coeffRef(global_eqn_ids[i + 1], global_param_ids[2 * num_outlets + i]) = -fabs(q_out) * q_out; } - - residual(global_eqn_ids[0]) -= q_out; - residual(global_eqn_ids[i + 1]) = - p_in - p_out - (resistance + stenosis_resistance) * q_out - - inductance * dq_out; } } diff --git a/src/model/BloodVesselJunction.h b/src/model/BloodVesselJunction.h index 0e477db0f..d098d0859 100644 --- a/src/model/BloodVesselJunction.h +++ b/src/model/BloodVesselJunction.h @@ -204,17 +204,14 @@ class BloodVesselJunction : public Block { const Eigen::Matrix& dy); /** - * @brief Set the gradient of the block contributions with respect to the - * parameters + * @brief Write this block's columns of the parameter Jacobian. * * @param jacobian Jacobian with respect to the parameters * @param alpha Current parameter vector - * @param residual Residual with respect to the parameters - * @param y Current solution - * @param dy Time-derivative of the current solution + * @param y Observed solution + * @param dy Observed time derivative of the solution */ void update_gradient(Eigen::SparseMatrix& jacobian, - Eigen::Matrix& residual, Eigen::Matrix& alpha, std::vector& y, std::vector& dy); diff --git a/src/model/Junction.cpp b/src/model/Junction.cpp index 4f773df09..64391e39b 100644 --- a/src/model/Junction.cpp +++ b/src/model/Junction.cpp @@ -31,14 +31,3 @@ void Junction::update_constant(SparseSystem& system, global_var_ids[i]) = -1.0; } } - -void Junction::update_gradient( - Eigen::SparseMatrix& jacobian, - Eigen::Matrix& residual, - Eigen::Matrix& alpha, std::vector& y, - std::vector& dy) { - // Pressure conservation - residual(global_eqn_ids[0]) = y[global_var_ids[0]] - y[global_var_ids[2]]; - - residual(global_eqn_ids[1]) = y[global_var_ids[1]] - y[global_var_ids[3]]; -} diff --git a/src/model/Junction.h b/src/model/Junction.h index ea82b4d97..3b5389b7c 100644 --- a/src/model/Junction.h +++ b/src/model/Junction.h @@ -119,21 +119,6 @@ class Junction : public Block { */ void update_constant(SparseSystem& system, std::vector& parameters); - /** - * @brief Set the gradient of the block contributions with respect to the - * parameters - * - * @param jacobian Jacobian with respect to the parameters - * @param alpha Current parameter vector - * @param residual Residual with respect to the parameters - * @param y Current solution - * @param dy Time-derivative of the current solution - */ - void update_gradient(Eigen::SparseMatrix& jacobian, - Eigen::Matrix& residual, - Eigen::Matrix& alpha, - std::vector& y, std::vector& dy); - /** * @brief Number of triplets of element * diff --git a/src/optimize/LevenbergMarquardtOptimizer.cpp b/src/optimize/LevenbergMarquardtOptimizer.cpp index a91e584db..7ab932ae5 100644 --- a/src/optimize/LevenbergMarquardtOptimizer.cpp +++ b/src/optimize/LevenbergMarquardtOptimizer.cpp @@ -7,7 +7,13 @@ LevenbergMarquardtOptimizer::LevenbergMarquardtOptimizer( Model* model, int num_obs, int num_params, const std::vector& active_param_ids, double lambda0, double tol_grad, - double tol_inc, int max_iter) { + double tol_inc, int max_iter) + // Size the assembly system with max(num_eqns, num_vars). The calibrator + // has no boundary-condition blocks so it can have num_vars > num_eqns; + // sizing with the larger ensures coeffRef writes (eqn_id < num_eqns, + // var_id < num_vars) stay in bounds. + : system(std::max(model->dofhandler.get_num_equations(), + model->dofhandler.get_num_variables())) { this->model = model; this->num_obs = num_obs; this->num_params = num_params; @@ -26,6 +32,11 @@ LevenbergMarquardtOptimizer::LevenbergMarquardtOptimizer( mat = Eigen::Matrix(num_active, num_active); vec = Eigen::Matrix::Zero(num_active); + + // Establish the sparsity pattern of E, F, dC/dy, dC/dydot using dummy + // values; subsequent calls to update_constant / update_solution overwrite + // the entries via coeffRef without changing the pattern. + system.reserve(model); } Eigen::Matrix LevenbergMarquardtOptimizer::run( @@ -64,18 +75,55 @@ void LevenbergMarquardtOptimizer::update_gradient( Eigen::Matrix& alpha, std::vector>& y_obs, std::vector>& dy_obs) { - // Set jacobian and residual to zero jacobian.setZero(); residual.setZero(); - // Assemble gradient and residual + // Sync the LM parameter vector into the model's parameter storage so the + // solver assembly (update_constant / update_solution below) sees the same + // values that the per-block Jacobians do. + for (int p = 0; p < num_params; p++) { + model->update_parameter_value(p, alpha[p]); + } + + // E and F are constant in the parameters within one LM iteration; refresh + // them once before walking the observations. ``update_time`` is skipped + // because it would overwrite ``parameter_values`` from the model's + // ``Parameter`` objects, undoing the alpha sync above. + model->update_constant(system); + + // The system is sized to max(num_eqns, num_vars); pad y and dy so that + // matrix-vector products E*dy and F*y are well-formed. + int n = static_cast(system.C.size()); + Eigen::Matrix y = + Eigen::Matrix::Zero(n); + Eigen::Matrix dy = + Eigen::Matrix::Zero(n); for (size_t i = 0; i < num_obs; i++) { + // Copy the observation into Eigen vectors so the forward-solver assembly + // (update_solution) can reuse its existing API. + for (int k = 0; k < num_vars; k++) { + y[k] = y_obs[i][k]; + dy[k] = dy_obs[i][k]; + } + model->update_solution(system, y, dy); + + // r_i = c + E * dy + F * y, identical to the residual the forward solver + // computes (up to a sign that cancels in the LM normal equations). Only + // the first num_eqns rows of the assembly are populated by vessel and + // junction blocks; ignore the trailing padding that exists when the + // calibrator's model has more variables than equations. + Eigen::Matrix r = system.C; + r.noalias() += system.E * dy; + r.noalias() += system.F * y; + residual.segment(i * num_eqns, num_eqns) = r.head(num_eqns); + + // Each block contributes its own columns of the parameter Jacobian. for (size_t j = 0; j < model->get_num_blocks(true); j++) { auto block = model->get_block(j); for (size_t l = 0; l < block->global_eqn_ids.size(); l++) { block->global_eqn_ids[l] += num_eqns * i; } - block->update_gradient(jacobian, residual, alpha, y_obs[i], dy_obs[i]); + block->update_gradient(jacobian, alpha, y_obs[i], dy_obs[i]); for (size_t l = 0; l < block->global_eqn_ids.size(); l++) { block->global_eqn_ids[l] -= num_eqns * i; } diff --git a/src/optimize/LevenbergMarquardtOptimizer.h b/src/optimize/LevenbergMarquardtOptimizer.h index 7d5a93d86..41e23cd22 100644 --- a/src/optimize/LevenbergMarquardtOptimizer.h +++ b/src/optimize/LevenbergMarquardtOptimizer.h @@ -11,6 +11,7 @@ #include #include "Model.h" +#include "SparseSystem.h" /** * @brief Levenberg-Marquardt optimization class @@ -114,6 +115,8 @@ class LevenbergMarquardtOptimizer { Eigen::Matrix mat; Eigen::Matrix vec; std::vector active_param_ids; + SparseSystem system; ///< Forward-solver assembly used to compute the + ///< residual at each observation Model* model; double lambda; diff --git a/src/optimize/calibrate.cpp b/src/optimize/calibrate.cpp index 0d880c3e3..266720012 100644 --- a/src/optimize/calibrate.cpp +++ b/src/optimize/calibrate.cpp @@ -89,11 +89,16 @@ nlohmann::json calibrate(const nlohmann::json& config) { std::string block_type = vessel_config["zero_d_element_type"].get(); - // Instantiate the block so we can introspect its parameter names. + // Instantiate the block so we can introspect its parameter names. Each + // parameter slot is registered with the model so that ``parameter_values`` + // is sized for the assembly path used by the Levenberg-Marquardt loop. auto* block = model.create_block(block_type); int num_slots = num_param_slots(*block, /*stride=*/1); std::vector param_ids; - for (int k = 0; k < num_slots; k++) param_ids.push_back(param_counter++); + for (int k = 0; k < num_slots; k++) { + param_ids.push_back(model.add_parameter(0.0)); + param_counter++; + } model.add_block(block, vessel_name, param_ids); vessel_id_map.insert({vessel_config["vessel_id"], vessel_name}); DEBUG_MSG("Created vessel " << vessel_name); @@ -124,7 +129,10 @@ nlohmann::json calibrate(const nlohmann::json& config) { auto* block = model.create_block("BloodVesselJunction"); int num_slots = num_param_slots(*block, num_outlets); std::vector param_ids; - for (int k = 0; k < num_slots; k++) param_ids.push_back(param_counter++); + for (int k = 0; k < num_slots; k++) { + param_ids.push_back(model.add_parameter(0.0)); + param_counter++; + } model.add_block(block, junction_name, param_ids); register_active(*block, param_ids, From 244734f086cf6fcd0e715d0fb98c076884cdad0f Mon Sep 17 00:00:00 2001 From: Martin Pfaller Date: Tue, 5 May 2026 18:34:21 -0400 Subject: [PATCH 11/12] Reject time-dependent blocks; throw on missing parameter Jacobian The calibrator residual is computed at observation samples that carry no time stamp, so any block with non-trivial ``update_time`` cannot be calibrated correctly. ``Block`` gains a virtual ``has_time_dependent_assembly()`` (default false); chambers and the time-dependent boundary conditions override it to return true. ``calibrate.cpp`` walks the model after ``finalize`` and throws before reading observations or constructing the optimizer if any such block is present. Restores ``Block::update_gradient``'s default to throw "not implemented" so a parameterized block that forgets to override is caught instead of silently producing a zero Jacobian column. The Levenberg-Marquardt loop skips blocks with no parameters (``global_param_ids.empty()``) so parameterless blocks like NORMAL_JUNCTION don't trip the throw and don't need their own no-op override. Co-Authored-By: Claude Opus 4.7 (1M context) --- src/model/Block.cpp | 4 ++-- src/model/Block.h | 13 +++++++++++++ src/model/ChamberElastanceInductor.h | 2 ++ src/model/ChamberElastanceInductorExponential.h | 1 + src/model/ChamberSphere.h | 2 ++ src/model/ClosedLoopHeartPulmonary.h | 2 ++ src/model/FlowReferenceBC.h | 2 ++ src/model/LinearElastanceChamber.h | 2 ++ src/model/OpenLoopCoronaryBC.h | 2 ++ src/model/PressureReferenceBC.h | 2 ++ src/model/ResistanceBC.h | 2 ++ src/model/WindkesselBC.h | 2 ++ src/optimize/LevenbergMarquardtOptimizer.cpp | 4 ++++ src/optimize/calibrate.cpp | 15 +++++++++++++++ 14 files changed, 53 insertions(+), 2 deletions(-) diff --git a/src/model/Block.cpp b/src/model/Block.cpp index c33fc2cfb..ac775e50e 100644 --- a/src/model/Block.cpp +++ b/src/model/Block.cpp @@ -64,8 +64,8 @@ void Block::post_solve(Eigen::Matrix& y) {} void Block::update_gradient(Eigen::SparseMatrix& jacobian, Eigen::Matrix& alpha, std::vector& y, std::vector& dy) { - // Default: block has no calibratable parameters, so it contributes no - // columns to the parameter Jacobian. Blocks with parameters override this. + throw std::runtime_error( + "Calibrator parameter Jacobian not implemented for block " + get_name()); } TripletsContributions Block::get_num_triplets() { return num_triplets; } diff --git a/src/model/Block.h b/src/model/Block.h index 1f1017f7b..42defc814 100644 --- a/src/model/Block.h +++ b/src/model/Block.h @@ -230,6 +230,19 @@ class Block { virtual void update_time(SparseSystem& system, std::vector& parameters); + /** + * @brief Whether this block contributes time-dependent terms to the + * assembly. + * + * The calibrator does not support models containing time-dependent blocks + * because the observations passed to it carry no time stamp. Blocks that + * implement non-trivial ``update_time`` logic must override this to return + * true; the calibrator throws on setup if any such block is present. + * + * @return true if ``update_time`` writes time-dependent contributions + */ + virtual bool has_time_dependent_assembly() const { return false; } + /** * @brief Update the solution-dependent contributions of the element in a * sparse system diff --git a/src/model/ChamberElastanceInductor.h b/src/model/ChamberElastanceInductor.h index 0e95b476a..dacbb70fe 100644 --- a/src/model/ChamberElastanceInductor.h +++ b/src/model/ChamberElastanceInductor.h @@ -170,6 +170,8 @@ class ChamberElastanceInductor : public Block { void update_time(SparseSystem& system, std::vector& parameters) override; + bool has_time_dependent_assembly() const override { return true; } + /// @brief Number of triplets of element TripletsContributions num_triplets{6, 2, 0}; diff --git a/src/model/ChamberElastanceInductorExponential.h b/src/model/ChamberElastanceInductorExponential.h index 37492a2a2..6e0338ba4 100644 --- a/src/model/ChamberElastanceInductorExponential.h +++ b/src/model/ChamberElastanceInductorExponential.h @@ -66,6 +66,7 @@ class ChamberElastanceInductorExponential : public ChamberElastanceInductor { }; void update_time(SparseSystem& system, std::vector& parameters); + bool has_time_dependent_assembly() const override { return true; } void update_solution(SparseSystem& system, std::vector& parameters, const Eigen::Matrix& y, const Eigen::Matrix& dy); diff --git a/src/model/ChamberSphere.h b/src/model/ChamberSphere.h index a0c60cc05..06a4d0d51 100644 --- a/src/model/ChamberSphere.h +++ b/src/model/ChamberSphere.h @@ -202,6 +202,8 @@ class ChamberSphere : public Block { */ void update_time(SparseSystem& system, std::vector& parameters); + bool has_time_dependent_assembly() const override { return true; } + /** * @brief Update the solution-dependent contributions of the element in a * sparse system diff --git a/src/model/ClosedLoopHeartPulmonary.h b/src/model/ClosedLoopHeartPulmonary.h index dd9e8841a..489a47bca 100644 --- a/src/model/ClosedLoopHeartPulmonary.h +++ b/src/model/ClosedLoopHeartPulmonary.h @@ -215,6 +215,8 @@ class ClosedLoopHeartPulmonary : public Block { */ void update_time(SparseSystem& system, std::vector& parameters); + bool has_time_dependent_assembly() const override { return true; } + /** * @brief Update the solution-dependent contributions of the element in a * sparse system diff --git a/src/model/FlowReferenceBC.h b/src/model/FlowReferenceBC.h index f626c710e..0a7b9ff27 100644 --- a/src/model/FlowReferenceBC.h +++ b/src/model/FlowReferenceBC.h @@ -116,6 +116,8 @@ class FlowReferenceBC : public Block { */ void update_time(SparseSystem& system, std::vector& parameters); + bool has_time_dependent_assembly() const override { return true; } + /** * @brief Number of triplets of element * diff --git a/src/model/LinearElastanceChamber.h b/src/model/LinearElastanceChamber.h index a4c0c8c56..0b9815fa7 100644 --- a/src/model/LinearElastanceChamber.h +++ b/src/model/LinearElastanceChamber.h @@ -171,6 +171,8 @@ class LinearElastanceChamber : public Block { void update_time(SparseSystem& system, std::vector& parameters) override; + bool has_time_dependent_assembly() const override { return true; } + /** * @brief Number of triplets of element * diff --git a/src/model/OpenLoopCoronaryBC.h b/src/model/OpenLoopCoronaryBC.h index 2c0803684..dfb215042 100644 --- a/src/model/OpenLoopCoronaryBC.h +++ b/src/model/OpenLoopCoronaryBC.h @@ -171,6 +171,8 @@ class OpenLoopCoronaryBC : public Block { */ void update_time(SparseSystem& system, std::vector& parameters); + bool has_time_dependent_assembly() const override { return true; } + /** * @brief Number of triplets of element * diff --git a/src/model/PressureReferenceBC.h b/src/model/PressureReferenceBC.h index 7a5bda0e6..fc281d08c 100644 --- a/src/model/PressureReferenceBC.h +++ b/src/model/PressureReferenceBC.h @@ -117,6 +117,8 @@ class PressureReferenceBC : public Block { */ void update_time(SparseSystem& system, std::vector& parameters); + bool has_time_dependent_assembly() const override { return true; } + /** * @brief Number of triplets of element * diff --git a/src/model/ResistanceBC.h b/src/model/ResistanceBC.h index d985816b2..c1221ac44 100644 --- a/src/model/ResistanceBC.h +++ b/src/model/ResistanceBC.h @@ -110,6 +110,8 @@ class ResistanceBC : public Block { */ void update_time(SparseSystem& system, std::vector& parameters); + bool has_time_dependent_assembly() const override { return true; } + /** * @brief Number of triplets of element * diff --git a/src/model/WindkesselBC.h b/src/model/WindkesselBC.h index 3477b00da..41a0169e2 100644 --- a/src/model/WindkesselBC.h +++ b/src/model/WindkesselBC.h @@ -144,6 +144,8 @@ class WindkesselBC : public Block { */ void update_time(SparseSystem& system, std::vector& parameters); + bool has_time_dependent_assembly() const override { return true; } + /** * @brief Number of triplets of element * diff --git a/src/optimize/LevenbergMarquardtOptimizer.cpp b/src/optimize/LevenbergMarquardtOptimizer.cpp index 7ab932ae5..f0fc3b6be 100644 --- a/src/optimize/LevenbergMarquardtOptimizer.cpp +++ b/src/optimize/LevenbergMarquardtOptimizer.cpp @@ -118,8 +118,12 @@ void LevenbergMarquardtOptimizer::update_gradient( residual.segment(i * num_eqns, num_eqns) = r.head(num_eqns); // Each block contributes its own columns of the parameter Jacobian. + // Blocks without parameters (e.g. NORMAL_JUNCTION) are skipped so that + // the base-class default - which throws to flag missing implementations + // - is reached only when a parameterized block forgets to override. for (size_t j = 0; j < model->get_num_blocks(true); j++) { auto block = model->get_block(j); + if (block->global_param_ids.empty()) continue; for (size_t l = 0; l < block->global_eqn_ids.size(); l++) { block->global_eqn_ids[l] += num_eqns * i; } diff --git a/src/optimize/calibrate.cpp b/src/optimize/calibrate.cpp index 266720012..7feb107d1 100644 --- a/src/optimize/calibrate.cpp +++ b/src/optimize/calibrate.cpp @@ -170,6 +170,21 @@ nlohmann::json calibrate(const nlohmann::json& config) { // Finalize model model.finalize(); + // The calibrator computes residuals from per-observation (y, dy) snapshots + // without an associated time stamp, so any block contributing + // time-dependent terms to the assembly cannot be calibrated correctly. + // Reject such models up front, before reading observations or constructing + // the optimizer. + for (int j = 0; j < model.get_num_blocks(true); j++) { + auto* block = model.get_block(j); + if (block->has_time_dependent_assembly()) { + throw std::runtime_error( + "[svzerodcalibrator] Block " + block->get_name() + + " contributes time-dependent terms to the assembly; the calibrator " + "does not support time-dependent blocks."); + } + } + DEBUG_MSG("Number of parameters " << param_counter); // Read observations From f92836e4b00c67e5fadbc55f8951512e2229cec9 Mon Sep 17 00:00:00 2001 From: Martin Pfaller Date: Wed, 6 May 2026 09:19:06 -0400 Subject: [PATCH 12/12] Allow time-dependent calibration via per-observation t array Adds an optional ``t`` array (one entry per observation) that lets the calibrator handle blocks whose assembly varies with time. Behavior changes: * ``calibrate.cpp`` now parses ``t`` from the input alongside ``y`` and ``dy``. ``dy`` becomes optional: when omitted but ``t`` is present, the time derivative is reconstructed internally from ``y`` via the generalized-alpha relation ``dy_{n+1} = (y_{n+1} - y_n)/(gamma*dt) + (1 - 1/gamma)*dy_n``, iterated with periodic seed (``dy_0 := dy_{N-1}``) until ``dy_0`` converges so the first cycle is at periodic steady state. The ``rho_infty`` used for the gen-alpha coefficients is read from ``simulation_parameters`` (default 0.5, matching the solver). The reconstruction is first-order accurate at integer time steps; for exact recovery to machine precision, callers can still pass an explicit ``dy``. * The time-dependent-block check is now gated on whether ``t`` was provided. With ``t`` absent, the calibrator continues to refuse blocks with ``has_time_dependent_assembly() == true``. With ``t`` present, those blocks are allowed and the per-observation assembly loop in the LM optimizer calls ``update_time(system, t_i)``, re-syncs alpha (because ``update_time`` clobbers ``parameter_values`` from the model's ``Parameter`` objects), and calls ``update_constant`` again so the assembly reflects alpha for the current observation. * When ``dy`` and ``t`` are both absent the calibrator throws a clear error rather than silently using stale data. * Errors from missing observations are now ``runtime_error`` instead of ``cout`` + ``exit(1)``, matching the rest of the calibrator. Tests: * ``tests/cases/vmr/input/pulsatileFlow_R_calibrate_R_only.json`` is a new fixture generated by ``pysvzerod.simulate`` of a pulsatile single-vessel model with R=100, C=1e-4, L=1; ``y`` and ``t`` are the solver output, ``dy`` is omitted. * ``test_pulsatile_R_only_recovers_from_y_and_t`` runs the calibrator on the new fixture and checks ``R`` is recovered to ~1% (the reconstruction is first-order at integer steps; the solver writes zero residual at gen-alpha midpoints, so the integer-step residual the calibrator sees has a small bias). * ``test_calibration_rejects_time_dependent_block_without_t`` swaps the steady-flow vessel for a ``ChamberSphere`` and asserts the calibrator refuses with the expected ``time-dependent`` error. Co-Authored-By: Claude Opus 4.7 (1M context) --- src/optimize/LevenbergMarquardtOptimizer.cpp | 45 +++- src/optimize/LevenbergMarquardtOptimizer.h | 5 + src/optimize/calibrate.cpp | 127 +++++++-- .../pulsatileFlow_R_calibrate_R_only.json | 241 ++++++++++++++++++ tests/test_calibrator.py | 37 +++ 5 files changed, 415 insertions(+), 40 deletions(-) create mode 100644 tests/cases/vmr/input/pulsatileFlow_R_calibrate_R_only.json diff --git a/src/optimize/LevenbergMarquardtOptimizer.cpp b/src/optimize/LevenbergMarquardtOptimizer.cpp index f0fc3b6be..e0a895821 100644 --- a/src/optimize/LevenbergMarquardtOptimizer.cpp +++ b/src/optimize/LevenbergMarquardtOptimizer.cpp @@ -6,7 +6,8 @@ LevenbergMarquardtOptimizer::LevenbergMarquardtOptimizer( Model* model, int num_obs, int num_params, - const std::vector& active_param_ids, double lambda0, double tol_grad, + const std::vector& active_param_ids, + const std::vector& time_obs, double lambda0, double tol_grad, double tol_inc, int max_iter) // Size the assembly system with max(num_eqns, num_vars). The calibrator // has no boundary-condition blocks so it can have num_vars > num_eqns; @@ -18,6 +19,7 @@ LevenbergMarquardtOptimizer::LevenbergMarquardtOptimizer( this->num_obs = num_obs; this->num_params = num_params; this->active_param_ids = active_param_ids; + this->time_obs = time_obs; this->num_active = static_cast(active_param_ids.size()); this->num_eqns = model->dofhandler.get_num_equations(); this->num_vars = model->dofhandler.get_num_variables(); @@ -78,19 +80,28 @@ void LevenbergMarquardtOptimizer::update_gradient( jacobian.setZero(); residual.setZero(); - // Sync the LM parameter vector into the model's parameter storage so the - // solver assembly (update_constant / update_solution below) sees the same - // values that the per-block Jacobians do. - for (int p = 0; p < num_params; p++) { - model->update_parameter_value(p, alpha[p]); + // Helper to sync the LM parameter vector into the model's parameter storage + // so the solver assembly (update_constant / update_solution below) sees the + // same values that the per-block Jacobians do. + auto sync_alpha = [&]() { + for (int p = 0; p < num_params; p++) { + model->update_parameter_value(p, alpha[p]); + } + }; + + sync_alpha(); + + // For models without time-dependent blocks, ``E`` and ``F`` are constant + // within one LM iteration; refresh them once before walking the + // observations. When time stamps are provided, ``update_time`` is called + // per observation below, which clobbers parameter_values for time-dependent + // parameters; ``sync_alpha`` + ``update_constant`` are repeated each + // observation in that case. + bool time_dependent = !time_obs.empty(); + if (!time_dependent) { + model->update_constant(system); } - // E and F are constant in the parameters within one LM iteration; refresh - // them once before walking the observations. ``update_time`` is skipped - // because it would overwrite ``parameter_values`` from the model's - // ``Parameter`` objects, undoing the alpha sync above. - model->update_constant(system); - // The system is sized to max(num_eqns, num_vars); pad y and dy so that // matrix-vector products E*dy and F*y are well-formed. int n = static_cast(system.C.size()); @@ -99,6 +110,16 @@ void LevenbergMarquardtOptimizer::update_gradient( Eigen::Matrix dy = Eigen::Matrix::Zero(n); for (size_t i = 0; i < num_obs; i++) { + if (time_dependent) { + // Refresh time-dependent assembly entries and time-dependent + // parameter_values from their Parameter objects, then re-sync alpha so + // the calibratable parameters keep their LM values, and re-run + // update_constant so the assembly reflects alpha for the current + // observation. + model->update_time(system, time_obs[i]); + sync_alpha(); + model->update_constant(system); + } // Copy the observation into Eigen vectors so the forward-solver assembly // (update_solution) can reuse its existing API. for (int k = 0; k < num_vars; k++) { diff --git a/src/optimize/LevenbergMarquardtOptimizer.h b/src/optimize/LevenbergMarquardtOptimizer.h index 41e23cd22..70d356be3 100644 --- a/src/optimize/LevenbergMarquardtOptimizer.h +++ b/src/optimize/LevenbergMarquardtOptimizer.h @@ -84,6 +84,9 @@ class LevenbergMarquardtOptimizer { * @param num_params Total number of parameters in alpha * @param active_param_ids Indices into alpha of parameters that should be * optimized. Parameters not listed are held constant at their initial value. + * @param time_obs Per-observation time stamps. If empty, observations are + * treated as time-independent and the model must not contain any + * time-dependent blocks. * @param lambda0 Initial damping factor * @param tol_grad Gradient tolerance * @param tol_inc Parameter increment tolerance @@ -91,6 +94,7 @@ class LevenbergMarquardtOptimizer { */ LevenbergMarquardtOptimizer(Model* model, int num_obs, int num_params, const std::vector& active_param_ids, + const std::vector& time_obs, double lambda0, double tol_grad, double tol_inc, int max_iter); @@ -115,6 +119,7 @@ class LevenbergMarquardtOptimizer { Eigen::Matrix mat; Eigen::Matrix vec; std::vector active_param_ids; + std::vector time_obs; SparseSystem system; ///< Forward-solver assembly used to compute the ///< residual at each observation Model* model; diff --git a/src/optimize/calibrate.cpp b/src/optimize/calibrate.cpp index 7feb107d1..9dcc1ddf3 100644 --- a/src/optimize/calibrate.cpp +++ b/src/optimize/calibrate.cpp @@ -170,46 +170,117 @@ nlohmann::json calibrate(const nlohmann::json& config) { // Finalize model model.finalize(); - // The calibrator computes residuals from per-observation (y, dy) snapshots - // without an associated time stamp, so any block contributing - // time-dependent terms to the assembly cannot be calibrated correctly. - // Reject such models up front, before reading observations or constructing - // the optimizer. - for (int j = 0; j < model.get_num_blocks(true); j++) { - auto* block = model.get_block(j); - if (block->has_time_dependent_assembly()) { - throw std::runtime_error( - "[svzerodcalibrator] Block " + block->get_name() + - " contributes time-dependent terms to the assembly; the calibrator " - "does not support time-dependent blocks."); - } - } - DEBUG_MSG("Number of parameters " << param_counter); - // Read observations + // Read observations. + // + // ``y`` and ``t`` are required. ``dy`` is optional: when omitted, the time + // derivative is computed internally from ``y`` and ``t`` using the + // generalized-alpha relation that the forward solver uses, so the residual + // the calibrator sees matches the residual the solver would see at the + // same observation. When ``t`` is absent the calibrator runs in legacy + // mode (residual evaluated at t = 0); time-dependent blocks are rejected + // in that case. DEBUG_MSG("Reading observations"); int num_obs = 0; std::vector> y_all; std::vector> dy_all; auto y_values = config["y"]; - auto dy_values = config["dy"]; + bool has_dy = config.contains("dy"); + auto dy_values = has_dy ? config["dy"] : nlohmann::json::object(); + std::vector time_obs; + if (config.contains("t")) { + time_obs = config["t"].get>(); + } + bool has_time = !time_obs.empty(); + + // The calibrator computes residuals from per-observation (y, dy) snapshots. + // Time-dependent blocks need an associated time stamp (``t``) to evaluate + // their assembly correctly; reject such models up front when no ``t`` was + // provided. + if (!has_time) { + for (int j = 0; j < model.get_num_blocks(true); j++) { + auto* block = model.get_block(j); + if (block->has_time_dependent_assembly()) { + throw std::runtime_error( + "[svzerodcalibrator] Block " + block->get_name() + + " contributes time-dependent terms to the assembly; provide a " + "'t' array of observation time stamps to calibrate it."); + } + } + } + + if (!has_dy && !has_time) { + throw std::runtime_error( + "[svzerodcalibrator] Observations need either explicit 'dy' values " + "or a 't' array from which 'dy' can be computed."); + } + + // Generalized-alpha parameters used to derive ``dy`` from ``y`` (so the + // calibrator's residual matches the residual the forward solver would see + // at the same observations). Default rho_infty matches the solver default. + double rho_infty = 0.5; + if (config.contains("simulation_parameters") && + config["simulation_parameters"].contains("rho_infty")) { + rho_infty = config["simulation_parameters"]["rho_infty"].get(); + } + double alpha_m = 0.5 * (3.0 - rho_infty) / (1.0 + rho_infty); + double alpha_f = 1.0 / (1.0 + rho_infty); + double gamma = 0.5 + alpha_m - alpha_f; + for (size_t i = 0; i < model.dofhandler.get_num_variables(); i++) { std::string var_name = model.dofhandler.variables[i]; DEBUG_MSG("Reading observations for variable " << var_name); if (!y_values.contains(var_name)) { - std::cout << "ERROR: Missing y observation for '" << var_name << "'" - << std::endl; - exit(1); - } - if (!dy_values.contains(var_name)) { - std::cout << "ERROR: Missing dy observation for '" << var_name << "'" - << std::endl; - exit(1); + throw std::runtime_error( + "[svzerodcalibrator] Missing y observation for '" + var_name + "'"); } auto y_array = y_values[var_name].get>(); - auto dy_array = dy_values[var_name].get>(); num_obs = y_array.size(); + if (has_time && static_cast(time_obs.size()) != num_obs) { + throw std::runtime_error( + "[svzerodcalibrator] Length of 't' (" + + std::to_string(time_obs.size()) + + ") does not match the number of observations of '" + var_name + + "' (" + std::to_string(num_obs) + ")"); + } + + // Get explicit dy if available; otherwise integrate gen-alpha forward + // from a periodic dy_0. Two passes through the cycle to converge the + // initial value when t spans (approximately) one cardiac cycle. + std::vector dy_array(num_obs, 0.0); + if (has_dy) { + if (!dy_values.contains(var_name)) { + throw std::runtime_error( + "[svzerodcalibrator] Missing dy observation for '" + var_name + + "'"); + } + dy_array = dy_values[var_name].get>(); + } else { + // gen-alpha: dy_{n+1} = (y_{n+1} - y_n) / (gamma * dt) + // + (1 - 1/gamma) * dy_n + // + // Iterate with a periodic seed (dy_0 := dy_{N-1}) until dy_0 converges, + // so the first cycle of the reconstructed derivative matches what the + // forward solver sees at the same grid points after enough cycles to + // reach periodic steady state. + const int max_periodic_iter = 200; + const double periodic_tol = 1e-12; + for (int pass = 0; pass < max_periodic_iter; pass++) { + double dy0_prev = dy_array[0]; + for (int n = 0; n + 1 < num_obs; n++) { + double dt = time_obs[n + 1] - time_obs[n]; + dy_array[n + 1] = (y_array[n + 1] - y_array[n]) / (gamma * dt) + + (1.0 - 1.0 / gamma) * dy_array[n]; + } + dy_array[0] = dy_array[num_obs - 1]; + if (std::abs(dy_array[0] - dy0_prev) < + periodic_tol * (1.0 + std::abs(dy_array[0]))) { + break; + } + } + } + if (i == 0) { y_all.resize(num_obs); dy_all.resize(num_obs); @@ -276,8 +347,8 @@ nlohmann::json calibrate(const nlohmann::json& config) { "junction."); } auto lm_alg = LevenbergMarquardtOptimizer( - &model, num_obs, param_counter, active_param_ids, lambda0, gradient_tol, - increment_tol, max_iter); + &model, num_obs, param_counter, active_param_ids, time_obs, lambda0, + gradient_tol, increment_tol, max_iter); alpha = lm_alg.run(alpha, y_all, dy_all); diff --git a/tests/cases/vmr/input/pulsatileFlow_R_calibrate_R_only.json b/tests/cases/vmr/input/pulsatileFlow_R_calibrate_R_only.json new file mode 100644 index 000000000..29d99d4ea --- /dev/null +++ b/tests/cases/vmr/input/pulsatileFlow_R_calibrate_R_only.json @@ -0,0 +1,241 @@ +{ + "boundary_conditions": [ + { + "bc_name": "INFLOW", + "bc_type": "FLOW", + "bc_values": { + "Q": [ + 5.0, 5.2506664671286085, 5.497379774329709, 5.736249105369356, + 5.96350734820343, 6.175570504584947, 6.3690942118573775, + 6.541026485551578, 6.688655851004031, 6.809654104932039, + 6.902113032590307, 6.964574501457378, 6.996053456856544, + 6.996053456856544, 6.964574501457378, 6.902113032590307, + 6.809654104932039, 6.68865585100403, 6.541026485551578, + 6.3690942118573775, 6.175570504584947, 5.963507348203431, + 5.736249105369357, 5.497379774329709, 5.250666467128609, 5.0, + 4.7493335328713915, 4.50262022567029, 4.263750894630643, + 4.03649265179657, 3.824429495415054, 3.6309057881426225, + 3.458973514448421, 3.3113441489959694, 3.1903458950679604, + 3.0978869674096927, 3.0354254985426223, 3.003946543143457, + 3.003946543143457, 3.0354254985426223, 3.0978869674096927, + 3.190345895067961, 3.311344148995969, 3.458973514448421, + 3.630905788142622, 3.8244294954150533, 4.03649265179657, + 4.263750894630644, 4.502620225670289, 4.749333532871391, + 4.999999999999999 + ], + "t": [ + 0.0, 0.02, 0.04, 0.06, 0.08, 0.1, 0.12, 0.14, 0.16, 0.18, 0.2, 0.22, + 0.24, 0.26, 0.28, 0.3, 0.32, 0.34, 0.36, 0.38, 0.4, 0.42, 0.44, 0.46, + 0.48, 0.5, 0.52, 0.54, 0.56, 0.58, 0.6, 0.62, 0.64, 0.66, 0.68, + 0.7000000000000001, 0.72, 0.74, 0.76, 0.78, 0.8, 0.8200000000000001, + 0.84, 0.86, 0.88, 0.9, 0.92, 0.9400000000000001, 0.96, 0.98, 1.0 + ] + } + }, + { + "bc_name": "OUT", + "bc_type": "RESISTANCE", + "bc_values": { + "Pd": 100.0, + "R": 100.0 + } + } + ], + "junctions": [], + "vessels": [ + { + "boundary_conditions": { + "inlet": "INFLOW", + "outlet": "OUT" + }, + "vessel_id": 0, + "vessel_length": 10.0, + "vessel_name": "branch0_seg0", + "zero_d_element_type": "BloodVessel", + "zero_d_element_values": { + "R_poiseuille": 0.0, + "C": 0.0001, + "L": 1.0, + "stenosis_coefficient": 0.0 + }, + "calibrate": ["R_poiseuille"] + } + ], + "simulation_parameters": { + "number_of_cardiac_cycles": 3, + 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0.9700000000000002, 0.98, 0.9900000000000002, 1.0 + ], + "calibration_parameters": { + "tolerance_gradient": 1e-5, + "tolerance_increment": 1e-10, + "maximum_iterations": 100, + "initial_damping_factor": 1.0 + } +} diff --git a/tests/test_calibrator.py b/tests/test_calibrator.py index 6e7dbb5b1..ee9178d0e 100644 --- a/tests/test_calibrator.py +++ b/tests/test_calibrator.py @@ -26,6 +26,43 @@ def test_steady_flow_calibration(): ) +def test_pulsatile_R_only_recovers_from_y_and_t(): + """Calibrate only ``R_poiseuille`` from a pulsatile forward simulation + using only ``y`` and ``t``; ``dy`` is reconstructed internally from ``y`` + via the generalized-alpha relation. The fixture was produced by + ``pysvzerod.simulate`` with R=100, C=1e-4, L=1; the calibrator should + recover R close to 100 (the reconstruction is first-order accurate so the + error is small but non-zero).""" + testfile = os.path.join( + this_file_dir, + "cases", + "vmr", + "input", + "pulsatileFlow_R_calibrate_R_only.json", + ) + result, _ = execute_pysvzerod(testfile, "calibrator") + R = result["vessels"][0]["zero_d_element_values"]["R_poiseuille"] + assert np.isclose(R, 100.0, rtol=1e-2), f"R = {R}, expected ~100" + + +def test_calibration_rejects_time_dependent_block_without_t(tmp_path): + """The calibrator must refuse a model containing a time-dependent block + when the input lacks an observation time vector ``t``.""" + with open( + os.path.join(this_file_dir, "cases", "steadyFlow_calibration.json") + ) as ff: + cfg = json.load(ff) + cfg["vessels"][0]["zero_d_element_type"] = "ChamberSphere" + cfg["vessels"][0]["calibrate"] = ["W1"] + + testfile = tmp_path / "rejects_time_dependent.json" + with open(testfile, "w") as ff: + json.dump(cfg, ff) + + with pytest.raises(RuntimeError, match="time-dependent"): + execute_pysvzerod(str(testfile), "calibrator") + + @pytest.mark.parametrize( "test_case", [