Add Levenberg-Marquardt model calibration (SimVascular#31)

* Split json handling from config reader
Fix Debug build
Set debug messages  to be printed in debug build
Fix deprecation warnings

* Add documentation

* Try to fix ubuntu build problems by fixing simdjson version

* try with CMAKE_POSITION_INDEPENDENT_CODE again

* Adress reviewers comments

* Move block count increment out of loop

* Rename time dependent parameter

* Add block method for model class

* Revise parameter class

* Make elements use parameter IDs

* Fix bug and support more elements

* Support blood vessel junction

* Fix gradient of blood vessel and add calibrator

* Add gradient update to blood vessel junction

* Support normal BC names

* Write calibrated parameter values back into config

* Add support for open loop coronary back

* Add support for resistive junction back

* Clean up

* Fix bugs in calibrator and adapt after cleanup

* Reduce blood vessel system size

* Update bloodvessel junction to new blood vessel system

* Some fixes

* Fix bugs

* Fix stenosis coeff gradient

* Add support for remaining blocks back

* Move determination of cardiac cycle period to model

* Clean up reader

* Use nlohmann json

* Add gradient info to documentation

* Fix calibrator

* Improve python binding

* Adapt solver interface

* Add Levenberg Marquardt optimizer

* Full LM algorithm and fixes for capacitance

* Fix bug with calibrating stenosis coefficient

* Fix bug with capacitance in steady model

* Add termination criteria

* Fix pytest

* Move solver to own class

* New python binding with thread safety

* Dockerfile

* Fix profiling

* Allow installation via pip

* Add reading derivative of initial condition

* Get rid of Jsonhandler

* Dockerize profiling

* Adapt svzerodcalibrator

* Use output last cycle only as default

* Clean up

* Fix interface

* Fix tests

* Setup for new documentation

* update main page

* Add svzerodsolver Guide

* Finalize

* Fix clang-format

* Fix bug

* Try to fix documentation

* Another try

* New try

* fix typo

* fix bug using calibration_parameters

* clang format

* add script to generate calibration problems from test cases

* add VMR model 0075_1001

* Blood vessel junction without internal variables

* exit normally if LM doesn't converge and use sci notation

* add vmr 0d models. tried calibration from 3d, doesn't work. giving up

* Fix bug

* clang format

* Address reviewer's comments

* Typo in error msg

* Make specifying the output file optional

* default cardiac cycle period

* Fix bug

* make cmake compile interface by default

* make specifying output file optional

* added get_block_type

* bug fix: update_parameter_value

* update initial condition reading and other debugging

* interface working again

* clang format

* updated parameter descriptions for heart model

* Add calibration tests using vmr geometries

* remove python script for plotting calibration

---------

Co-authored-by: Jakob Richter <[email protected]>
Co-authored-by: Martin R. Pfaller <[email protected]>
Co-authored-by: Karthik Menon <[email protected]>

.github/workflows/documentation.yml

@@ -12,7 +12,7 @@ jobs:
  run: mkdir docs/html
  - name: Build doxygen documentation
  continue-on-error: true
- uses: mattnotmitt/[email protected].4
+ uses: mattnotmitt/[email protected].5
  with:
  working-directory: '.'
  doxyfile-path: 'docs/cpp/Doxyfile'

.github/workflows/test.yml

@@ -8,20 +8,14 @@ jobs:
  runs-on: ${{ matrix.os }}
  strategy:
  matrix:
- os: [ubuntu-18.04, ubuntu-20.04, ubuntu-22.04, macos-11, macos-12]
+ os: [ubuntu-20.04, ubuntu-22.04, macos-11, macos-12]
  fail-fast: false
  steps:
  - uses: actions/checkout@v2
  - name: Install ubuntu dependencies
  if: ${{ matrix.os == 'ubuntu-*' }}
  run: sudo apt update && sudo apt install build-essential cmake
- - name: Build svZeroDSolver
- run: |
- mkdir Release
- cd Release
- cmake -DCMAKE_BUILD_TYPE=Release ..
- cmake --build .
- - name: Install test dependencies
+ - name: Install svZeroDPlus
  run: |
  conda create -n zerod python=3.9
  conda run -n zerod pip install pytest pytest-cov pytest-mock

.gitignore

@@ -28,3 +28,5 @@ docs/python/build
 Release*/
 Debug*/
 externals/
+*.so
+build

CMakeLists.txt

@@ -4,17 +4,6 @@ set(CMAKE_CXX_STANDARD_REQUIRED True)
 project(svZeroDSolver)
 include(FetchContent)
 
-# -----------------------------------------------------------------------------
-# Fetch simdjson
-# -----------------------------------------------------------------------------
-set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-FetchContent_Declare(
- simdjson
- GIT_REPOSITORY https://github.com/simdjson/simdjson.git
- GIT_TAG master
- GIT_SHALLOW TRUE)
-FetchContent_MakeAvailable(simdjson)
-
 # -----------------------------------------------------------------------------
 # Fetch Eigen
 # -----------------------------------------------------------------------------
@@ -44,17 +33,41 @@ if(NOT pybind11_POPULATED)
  add_subdirectory(${pybind11_SOURCE_DIR} ${pybind11_BINARY_DIR})
 endif()
 
+# -----------------------------------------------------------------------------
+# Fetch nlohmann/json
+# -----------------------------------------------------------------------------
+FetchContent_Declare(
+ json
+ URL https://github.com/nlohmann/json/releases/download/v3.11.2/json.tar.xz
+)
+FetchContent_MakeAvailable(json)
+
+# -----------------------------------------------------------------------------
+# Fetch pybind11_json
+# -----------------------------------------------------------------------------
+FetchContent_Declare(
+ pybind11_json
+ GIT_REPOSITORY https://github.com/pybind/pybind11_json.git
+ GIT_TAG master
+)
+FetchContent_MakeAvailable(pybind11_json)
+
 # -----------------------------------------------------------------------------
 # Set executable and python library
 # -----------------------------------------------------------------------------
-add_executable(svzerodsolver src/main.cpp)
-pybind11_add_module(libsvzerodsolver src/python.cpp)
+include_directories(src)
+add_executable(svzerodsolver applications/svzerodsolver.cpp)
+add_executable(svzerodcalibrator applications/svzerodcalibrator.cpp)
+pybind11_add_module(svzerodplus EXCLUDE_FROM_ALL applications/svzerodplus.cpp)
 add_subdirectory("src/interface")
 
 # -----------------------------------------------------------------------------
 # Link libraries
 # -----------------------------------------------------------------------------
 target_link_libraries(svzerodsolver PRIVATE Eigen3::Eigen)
-target_link_libraries(svzerodsolver PRIVATE simdjson)
-target_link_libraries(libsvzerodsolver PRIVATE Eigen3::Eigen)
-target_link_libraries(libsvzerodsolver PRIVATE simdjson)
+target_link_libraries(svzerodsolver PRIVATE nlohmann_json::nlohmann_json)
+target_link_libraries(svzerodcalibrator PRIVATE Eigen3::Eigen)
+target_link_libraries(svzerodcalibrator PRIVATE nlohmann_json::nlohmann_json)
+target_link_libraries(svzerodplus PRIVATE Eigen3::Eigen)
+target_link_libraries(svzerodplus PRIVATE nlohmann_json::nlohmann_json)
+target_link_libraries(svzerodplus PRIVATE pybind11_json)

applications/svzerodcalibrator.cpp

@@ -0,0 +1,64 @@
+// Copyright (c) Stanford University, The Regents of the University of
+// California, and others.
+//
+// All Rights Reserved.
+//
+// See Copyright-SimVascular.txt for additional details.
+//
+// Permission is hereby granted, free of charge, to any person obtaining
+// a copy of this software and associated documentation files (the
+// "Software"), to deal in the Software without restriction, including
+// without limitation the rights to use, copy, modify, merge, publish,
+// distribute, sublicense, and/or sell copies of the Software, and to
+// permit persons to whom the Software is furnished to do so, subject
+// to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included
+// in all copies or substantial portions of the Software.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+// IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+// TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+// PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+// OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+/**
+ * @file svzerodcalibrator.cpp
+ * @brief Main routine for svZeroDCalibrator
+ */
+#include "optimize/calibrate.hpp"
+
+// Setting scalar type to double
+typedef double T;
+
+int main(int argc, char* argv[]) {
+ DEBUG_MSG("Starting svZeroDCalibrator");
+
+ // Get input and output file name
+ if (argc != 3) {
+ std::cout
+ << "Usage: svzerodcalibrator path/to/config.json path/to/output.json"
+ << std::endl;
+ exit(1);
+ }
+
+ // Get input and output file names
+ std::string input_file = argv[1];
+ std::string output_file = argv[2];
+
+ // Parse the configuration
+ DEBUG_MSG("Parse configuration");
+ std::ifstream ifs(input_file);
+ const auto& config = nlohmann::json::parse(ifs);
+
+ auto output_config = OPT::calibrate<T>(config);
+
+ // Write optimized simulation config
+ std::ofstream o(output_file);
+ o << std::setw(4) << output_config << std::endl;
+}

applications/svzerodplus.cpp

@@ -0,0 +1,104 @@
+// Copyright (c) Stanford University, The Regents of the University of
+// California, and others.
+//
+// All Rights Reserved.
+//
+// See Copyright-SimVascular.txt for additional details.
+//
+// Permission is hereby granted, free of charge, to any person obtaining
+// a copy of this software and associated documentation files (the
+// "Software"), to deal in the Software without restriction, including
+// without limitation the rights to use, copy, modify, merge, publish,
+// distribute, sublicense, and/or sell copies of the Software, and to
+// permit persons to whom the Software is furnished to do so, subject
+// to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included
+// in all copies or substantial portions of the Software.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+// IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+// TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+// PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+// OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+/**
+ * @file svzerodplus.cpp
+ * @brief Python interface for svZeroDSolver
+ */
+#include <pybind11/eigen.h>
+#include <pybind11/operators.h>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+#include "optimize/calibrate.hpp"
+#include "pybind11_json/pybind11_json.hpp"
+#include "solve/solver.hpp"
+
+namespace py = pybind11;
+
+PYBIND11_MODULE(svzerodplus, m) {
+ using Solver = SOLVE::Solver<double>;
+ m.doc() = "svZeroDSolver";
+ py::class_<Solver>(m, "Solver")
+ .def(py::init([](py::dict& config) {
+ const nlohmann::json& config_json = config;
+ return Solver(config_json);
+ }))
+ .def(py::init([](std::string config_file) {
+ std::ifstream ifs(config_file);
+ const auto& config_json = nlohmann::json::parse(ifs);
+ return Solver(config_json);
+ }))
+ .def("copy", [](Solver& solver) { return Solver(solver); })
+ .def("run", &Solver::run)
+ .def("get_single_result", &Solver::get_single_result)
+ .def("get_single_result_avg", &Solver::get_single_result_avg)
+ .def("update_block_params", &Solver::update_block_params);
+
+ m.def("simulate", [](py::dict& config) {
+ const nlohmann::json& config_json = config;
+ auto solver = Solver(config_json);
+ solver.run();
+ return solver.get_full_result();
+ });
+ m.def("calibrate", [](py::dict& config) {
+ const nlohmann::json& config_json = config;
+ return OPT::calibrate<double>(config);
+ });
+ m.def("run_simulation_cli", []() {
+ py::module_ sys = py::module_::import("sys");
+ auto argv = sys.attr("argv").cast<std::vector<std::string>>();
+ if (argv.size() != 3) {
+ std::cout
+ << "Usage: svzerodsolver path/to/config.json path/to/output.json"
+ << std::endl;
+ exit(1);
+ }
+ std::ifstream ifs(argv[1]);
+ const auto& config = nlohmann::json::parse(ifs);
+ auto solver = SOLVE::Solver<double>(config);
+ solver.run();
+ solver.write_result_to_csv(argv[2]);
+ });
+ m.def("run_calibration_cli", []() {
+ py::module_ sys = py::module_::import("sys");
+ auto argv = sys.attr("argv").cast<std::vector<std::string>>();
+ if (argv.size() != 3) {
+ std::cout
+ << "Usage: svzerodcalibrator path/to/config.json path/to/output.json"
+ << std::endl;
+ exit(1);
+ }
+ std::ifstream ifs(argv[1]);
+ const auto& config = nlohmann::json::parse(ifs);
+ auto output_config = OPT::calibrate<double>(config);
+ std::ofstream o(argv[2]);
+ o << std::setw(4) << output_config << std::endl;
+ });
+}

src/main.cpp → applications/svzerodsolver.cpp

@@ -28,10 +28,10 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file main.cpp
+ * @file svzerodsolver.cpp
  * @brief Main routine of svZeroDSolver
  */
-#include "main.hpp"
+#include "solve/solver.hpp"
 
 /**
  *
@@ -50,28 +50,37 @@
  * @param argv Command line arguments
  * @return Return code
  */
-int main(int argc, char *argv[]) {
+int main(int argc, char* argv[]) {
  DEBUG_MSG("Starting svZeroDSolver");
 
  // Get input and output file name
- if (argc != 3) {
- std::cout << "Usage: svzerodsolver path/to/config.json path/to/output.csv"
-  << std::endl;
- exit(1);
+ if (argc < 2 && argc > 3) {
+ std::runtime_error(
+ "Usage: svzerodsolver path/to/config.json "
+  "(optional:path/to/output.csv)");
  }
  std::string input_file = argv[1];
- std::string output_file = argv[2];
-
- std::ifstream input_file_stream(input_file);
- std::stringstream buffer;
- buffer << input_file_stream.rdbuf();
- std::string config = buffer.str();
+ std::string output_file;
+ if (argc == 3) {
+ output_file = argv[2];
+ } else {
+ // If output file is not provided, default is <path to .json>+"output.csv"
+ std::size_t end_of_path = input_file.rfind("/");
+ if (end_of_path == std::string::npos) {
+ end_of_path = input_file.rfind("\\"); // For Windows paths (?)
+ if (end_of_path == std::string::npos) {
+ std::runtime_error("Could not find path to .json file.");
+ }
+ }
+ output_file = input_file.substr(0, end_of_path) + "output.csv";
+ }
 
- auto output = run(config);
+ std::ifstream ifs(input_file);
+ const auto& config = nlohmann::json::parse(ifs);
 
- std::ofstream ofs(output_file);
- ofs << output;
- ofs.close();
+ auto solver = SOLVE::Solver<double>(config);
+ solver.run();
+ solver.write_result_to_csv(output_file);
 
  return 0;
 }

container/profiling/Dockerfile

@@ -0,0 +1,32 @@
+FROM ubuntu:22.04
+
+# Install dependencies
+RUN apt-get -q update && \
+ DEBIAN_FRONTEND=noninteractive \
+ TZ=Europe/Berlin \
+ apt-get -q -y --no-install-recommends install \
+ git \
+ gcc \
+ g++ \
+ make \
+ cmake \
+ python3 \
+ python3-dev \
+ ca-certificates \
+ google-perftools \
+ libgoogle-perftools-dev \
+ graphviz \
+ ghostscript \
+ && apt-get clean \
+ && rm -rf /var/lib/apt/lists/*
+
+COPY . /opt/svzerodplus
+
+RUN mkdir -p /opt/svzerodplus-build/relwithdebinfo && \
+ cd /opt/svzerodplus-build/relwithdebinfo && \
+ cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo /opt/svzerodplus && \
+ cmake --build . --target svzerodsolver
+
+WORKDIR /opt/data
+RUN chmod +x /opt/svzerodplus/container/profiling/entrypoint.sh
+ENTRYPOINT ["/opt/svzerodplus/container/profiling/entrypoint.sh"]

container/profiling/entrypoint.sh

@@ -0,0 +1,5 @@
+#! /bin/bash
+
+export LIBPROFILER=$(find /usr/lib -name "libprofiler.so")
+LD_PRELOAD=$LIBPROFILER CPUPROFILE=/opt/main.prof CPUPROFILE_FREQUENCY=100000 /opt/svzerodplus-build/relwithdebinfo/svzerodsolver $@ /opt/output.csv
+google-pprof --pdf /opt/svzerodplus-build/relwithdebinfo/svzerodsolver /opt/main.prof > profiling_report.pdf