feat (WIP): base VTK visualisation of Eulerian flow fields
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.DS_Store
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src/.DS_Store
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src/.cache
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src/build
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.idea
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src/cmake-build-debug
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## Location of data
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The data path is hardcoded such that the following tree structure is assumed:
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```
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data/
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grid.h5
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hydrodynamic_U.h5
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hydrodynamic_V.h5
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interactive-track-and-trace/
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opening-hdf5/
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...
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```
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## Compiling
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Let the current directory be the `src` directory. Run:
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```shell
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mkdir build
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cd build
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cmake ..
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make
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```
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### Building with Linux
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Makes use of `mdspan` which is not supported by glibc++ at time of writing. See [compiler support](https://en.cppreference.com/w/cpp/compiler_support/23) for `mdspan`. The solution to this is to use Clang and libc++; this is configured in our CMake setup, however the default installation of the `netcdf-cxx` package on at least Arch linux (and suspectedly Debian derivatives as well) specifically builds for the glibc implementation. To get the netcdf C++ bindings functional with the libc++ implementation, one needs to build from source. On Linux, this requires a few changes to the CMake file included with the netcdf-cxx source code, which are detailed below.
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Step-by-step to build the program using clang++ and libc++ on linux:
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1. Download the source code of netcdf-cxx, found at 'https://github.com/Unidata/netcdf-cxx4/releases/tag/v4.3.1' (make sure to download the release source code, as the master branch contains non-compilable code).
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2. Edit the CMakeLists.txt file, by appending '-stdlib=libc++' to the `CMAKE_CXX_FLAGS` variable in line 430. This means line 430 should read:
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```cmake
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SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -Wall -Wno-unused-variable -Wno-unused-parameter -stdlib=libc++")
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```
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2. Build the source code with the following:
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```sh
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mkdir build && cd build
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cmake .. -DCMAKE_CXX_COMPILER=/usr/bin/clang++
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make
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ctest
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sudo make install
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```
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3. Now the code should compile through the standard steps described in the Compiling section.
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cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
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project(VtkBase)
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set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
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find_package(VTK COMPONENTS
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CommonColor
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CommonCore
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CommonDataModel
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FiltersGeneral
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InteractionStyle
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RenderingContextOpenGL2
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RenderingCore
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RenderingFreeType
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RenderingGL2PSOpenGL2
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RenderingOpenGL2
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CommonColor
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FiltersGeometry
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RenderingCore)
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if (NOT VTK_FOUND)
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message(FATAL_ERROR "VtkBase: Unable to find the VTK build folder.")
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endif()
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# netcdf setup
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find_package(netCDF REQUIRED)
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add_executable(VtkBase MACOSX_BUNDLE main.cpp )
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execute_process(
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COMMAND nc-config --includedir
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OUTPUT_VARIABLE NETCDF_INCLUDE_DIR
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OUTPUT_STRIP_TRAILING_WHITESPACE
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)
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execute_process(
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COMMAND ncxx4-config --libdir
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OUTPUT_VARIABLE NETCDFCXX_LIB_DIR
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OUTPUT_STRIP_TRAILING_WHITESPACE
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)
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target_include_directories(VtkBase PUBLIC ${netCDF_INCLUDE_DIR})
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find_library(NETCDF_LIB NAMES netcdf-cxx4 netcdf_c++4 PATHS ${NETCDFCXX_LIB_DIR} NO_DEFAULT_PATH)
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# Prevent a "command line is too long" failure in Windows.
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set(CMAKE_NINJA_FORCE_RESPONSE_FILE "ON" CACHE BOOL "Force Ninja to use response files.")
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target_link_libraries(VtkBase ${NETCDF_LIB} ${VTK_LIBRARIES})
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# vtk_module_autoinit is needed
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vtk_module_autoinit(
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TARGETS VtkBase
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MODULES ${VTK_LIBRARIES}
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)
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#include <vtkActor.h>
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#include <vtkActor2D.h>
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#include <vtkCamera.h>
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#include <vtkDoubleArray.h>
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#include <vtkMapper2D.h>
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#include <vtkNamedColors.h>
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#include <vtkNew.h>
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#include <vtkPolyDataMapper.h>
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#include <vtkPolyDataMapper2D.h>
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#include <vtkProperty.h>
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#include <vtkRectilinearGrid.h>
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#include <vtkRectilinearGridGeometryFilter.h>
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#include <vtkRenderWindow.h>
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#include <vtkRenderWindowInteractor.h>
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#include <vtkRenderer.h>
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#include <netcdf>
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#define NLATS 67
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#define NLONS 116
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using namespace std;
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using namespace netCDF;
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template <typename T>
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vector<T> getVarVector(const NcVar &var) {
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int length = 1;
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for (NcDim dim : var.getDims()) {
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length *= dim.getSize();
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}
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vector<T> vec(length);
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var.getVar(vec.data());
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return vec;
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}
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tuple<vector<int>, vector<double>, vector<double>> readGrid() {
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netCDF::NcFile data("../../../../data/grid.h5", netCDF::NcFile::read);
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multimap< string, NcVar > vars = data.getVars();
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vector<int> time = getVarVector<int>(vars.find("times")->second);
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vector<double> longitude = getVarVector<double>(vars.find("longitude")->second);
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vector<double> latitude = getVarVector<double>(vars.find("latitude")->second);
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return {time, latitude, longitude};
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}
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int main() {
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vtkNew<vtkNamedColors> colors;
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vtkNew<vtkDoubleArray> pCoords;
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pCoords->SetNumberOfComponents(3);
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pCoords->SetNumberOfTuples(NLATS*NLONS);
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auto [times, lats, lons] = readGrid();
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double i = 0;
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for (double lat : lats) {
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for (double lon : lons) {
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pCoords->InsertTuple3(i++, 0, lat, lon);
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}
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}
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vtkNew<vtkPoints> points;
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points->SetData(pCoords);
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vtkNew<vtkPolyData> polydata;
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polydata->SetPoints(points);
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vtkNew<vtkPolyDataMapper2D> mapper;
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mapper->SetInputData(polydata);
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mapper->SetScalarRange(0, 40);
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vtkNew<vtkActor2D> actor;
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actor->SetMapper(mapper);
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vtkNew<vtkRenderer> ren;
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ren->AddActor(actor);
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ren->SetBackground(colors->GetColor3d("DarkSlateGray").GetData());
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vtkNew<vtkRenderWindow> renWin;
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renWin->AddRenderer(ren);
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renWin->SetSize(900, 600);
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vtkNew<vtkRenderWindowInteractor> iren;
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iren->SetRenderWindow(renWin);
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iren->Start();
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return EXIT_SUCCESS;
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}
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