feat (WIP): base VTK visualisation of Eulerian flow fields

vtk/.gitignore

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+.DS_Store
+src/.DS_Store
+src/.cache
+src/build
+.idea
+src/cmake-build-debug

vtk/README.md

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+## Location of data
+The data path is hardcoded such that the following tree structure is assumed:
+```
+data/
+  grid.h5
+  hydrodynamic_U.h5
+  hydrodynamic_V.h5
+interactive-track-and-trace/
+  opening-hdf5/
+     ...
+```
+
+## Compiling
+Let the current directory be the `src` directory. Run:
+```shell
+mkdir build
+cd build
+cmake ..
+make
+```
+
+### Building with Linux
+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.
+
+Step-by-step to build the program using clang++ and libc++ on linux:
+ 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).
+ 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: 
+    ```cmake 
+    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -Wall -Wno-unused-variable -Wno-unused-parameter -stdlib=libc++")
+    ```
+ 2. Build the source code with the following: 
+  ```sh 
+    mkdir build && cd build
+    cmake .. -DCMAKE_CXX_COMPILER=/usr/bin/clang++
+    make
+    ctest
+    sudo make install
+  ```
+ 3. Now the code should compile through the standard steps described in the Compiling section.

vtk/src/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
+
+project(VtkBase)
+
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
+find_package(VTK COMPONENTS 
+  CommonColor
+  CommonCore
+  CommonDataModel
+  FiltersGeneral
+  InteractionStyle
+  RenderingContextOpenGL2
+  RenderingCore
+  RenderingFreeType
+  RenderingGL2PSOpenGL2
+  RenderingOpenGL2
+    CommonColor
+    FiltersGeometry
+    RenderingCore)
+
+if (NOT VTK_FOUND)
+  message(FATAL_ERROR "VtkBase: Unable to find the VTK build folder.")
+endif()
+
+# netcdf setup
+find_package(netCDF REQUIRED)
+
+add_executable(VtkBase MACOSX_BUNDLE main.cpp )
+
+execute_process(
+    COMMAND nc-config --includedir
+    OUTPUT_VARIABLE NETCDF_INCLUDE_DIR
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+execute_process(
+    COMMAND ncxx4-config --libdir
+    OUTPUT_VARIABLE NETCDFCXX_LIB_DIR
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+target_include_directories(VtkBase PUBLIC ${netCDF_INCLUDE_DIR})
+
+find_library(NETCDF_LIB NAMES netcdf-cxx4 netcdf_c++4 PATHS ${NETCDFCXX_LIB_DIR} NO_DEFAULT_PATH)
+
+# Prevent a "command line is too long" failure in Windows.
+set(CMAKE_NINJA_FORCE_RESPONSE_FILE "ON" CACHE BOOL "Force Ninja to use response files.")
+target_link_libraries(VtkBase ${NETCDF_LIB} ${VTK_LIBRARIES})
+
+# vtk_module_autoinit is needed
+vtk_module_autoinit(
+  TARGETS VtkBase
+  MODULES ${VTK_LIBRARIES}
+)

vtk/src/main.cpp

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+#include <vtkActor.h>
+#include <vtkActor2D.h>
+#include <vtkCamera.h>
+#include <vtkDoubleArray.h>
+#include <vtkMapper2D.h>
+#include <vtkNamedColors.h>
+#include <vtkNew.h>
+#include <vtkPolyDataMapper.h>
+#include <vtkPolyDataMapper2D.h>
+#include <vtkProperty.h>
+#include <vtkRectilinearGrid.h>
+#include <vtkRectilinearGridGeometryFilter.h>
+#include <vtkRenderWindow.h>
+#include <vtkRenderWindowInteractor.h>
+#include <vtkRenderer.h>
+
+#include <netcdf>
+
+#define NLATS 67
+#define NLONS 116
+
+using namespace std;
+using namespace netCDF;
+
+template <typename T>
+vector<T> getVarVector(const NcVar &var) {
+    int length = 1;
+    for (NcDim dim : var.getDims()) {
+        length *= dim.getSize();
+    }
+
+    vector<T> vec(length);
+
+    var.getVar(vec.data());
+
+    return vec;
+}
+
+tuple<vector<int>, vector<double>, vector<double>> readGrid() {
+    netCDF::NcFile data("../../../../data/grid.h5", netCDF::NcFile::read);
+    multimap< string, NcVar > vars = data.getVars();
+    vector<int> time = getVarVector<int>(vars.find("times")->second);
+    vector<double> longitude = getVarVector<double>(vars.find("longitude")->second);
+    vector<double> latitude = getVarVector<double>(vars.find("latitude")->second);
+
+    return {time, latitude, longitude};
+}
+
+int main() {
+  vtkNew<vtkNamedColors> colors;
+
+
+  vtkNew<vtkDoubleArray> pCoords;
+  pCoords->SetNumberOfComponents(3);
+  pCoords->SetNumberOfTuples(NLATS*NLONS);
+  auto [times, lats, lons] = readGrid();
+
+  double i = 0;
+  for (double lat : lats) {
+    for (double lon : lons) {
+      pCoords->InsertTuple3(i++, 0, lat, lon);
+    }
+  }
+
+
+  vtkNew<vtkPoints> points;
+  points->SetData(pCoords);
+
+  vtkNew<vtkPolyData> polydata;
+  polydata->SetPoints(points);
+
+
+  vtkNew<vtkPolyDataMapper2D> mapper;
+  mapper->SetInputData(polydata);
+  mapper->SetScalarRange(0, 40);
+
+  vtkNew<vtkActor2D> actor;
+  actor->SetMapper(mapper);
+
+  vtkNew<vtkRenderer> ren;
+  ren->AddActor(actor);
+  ren->SetBackground(colors->GetColor3d("DarkSlateGray").GetData());
+
+  vtkNew<vtkRenderWindow> renWin;
+  renWin->AddRenderer(ren);
+  renWin->SetSize(900, 600);
+
+  vtkNew<vtkRenderWindowInteractor> iren;
+  iren->SetRenderWindow(renWin);
+  iren->Start();
+
+  return EXIT_SUCCESS;
+}
+