Merge branch 'djairo-vtk-pause' into djairo-vtk-camera

.gitignore

@@ -1,2 +1,3 @@
 .DS_Store
 .idea
+

advection/.gitignore

@@ -0,0 +1,7 @@
+.DS_Store
+src/.DS_Store
+src/.cache
+src/build
+.idea
+src/cmake-build-debug
+src/cmake-build-release

advection/README.md

@@ -0,0 +1,46 @@
+## What is new?
+There is one new added component: `AdvectionKernel`s which is an "interface" (i.e an abstract class).
+There are two implementations simple Euler integration called `EulerIntegrationKernel` and 
+Runge Kutta integration called `RK4AdvectionKernel`.
+
+Main function gives a good example of how to use the library. Especially the following function which prints the
+position of the particle at every time step.
+```Cpp
+template <typename AdvectionKernelImpl>
+void advectForSomeTime(const UVGrid &uvGrid, const AdvectionKernelImpl &kernel, double latstart, double lonstart) {
+
+    // Require at compile time that kernel derives from the abstract class AdvectionKernel
+    static_assert(std::is_base_of<AdvectionKernel, AdvectionKernelImpl>::value, NotAKernelError);
+
+    double lat1 = latstart, lon1 = lonstart;
+    for(int time = 100; time <= 10000; time += AdvectionKernel::DT) {
+        cout << "lat = " << lat1 << " lon = " << lon1 << endl;
+        auto [templat, templon] = kernel.advect(time, lat1, lon1);
+        lat1 = templat;
+        lon1 = templon;
+    }
+}
+```
+
+
+## Location of data
+The data path is hardcoded such that the following tree structure is assumed:
+The current assumption is that the name of the `u`s and `v`s are flipped since this is the way the data was given to us.
+```
+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
+```

advection/src/AdvectionKernel.h

@@ -0,0 +1,32 @@
+#ifndef ADVECTION_ADVECTIONKERNEL_H
+#define ADVECTION_ADVECTIONKERNEL_H
+
+#include <tuple>
+
+#include "Vel.h"
+
+
+/*
+ * Implement this class for every integration method.
+ */
+class AdvectionKernel {
+public:
+    const static int DT = 60 * 15; // 60 sec/min * 15 mins
+    /**
+     * This function must take a time, latitude and longitude of a particle and must output
+     * a new latitude and longitude after being advected once for AdvectionKernel::DT time as defined above.
+     * @param time Time since the beginning of the data
+     * @param latitude Latitude of particle
+     * @param longitude Longitude of particle
+     * @return A pair of latitude and longitude of particle.
+     */
+    virtual std::pair<double, double> advect(int time, double latitude, double longitude) const = 0;
+
+    // Taken from Parcels https://github.com/OceanParcels/parcels/blob/daa4b062ed8ae0b2be3d87367d6b45599d6f95db/parcels/tools/converters.py#L155
+    const static double metreToDegrees(double metre) {
+        return metre / 1000. / 1.852 / 60.;
+    }
+
+};
+
+#endif //ADVECTION_ADVECTIONKERNEL_H

advection/src/CMakeLists.txt

@@ -0,0 +1,42 @@
+cmake_minimum_required (VERSION 3.28)
+project (Advection)
+
+set(CMAKE_CXX_STANDARD 23)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
+find_package(netCDF REQUIRED)
+
+add_executable(Advection main.cpp
+        readdata.cpp
+        readdata.h
+        interpolate.cpp
+        interpolate.h
+        UVGrid.cpp
+        UVGrid.h
+        Vel.h
+        Vel.cpp
+        AdvectionKernel.h
+        EulerAdvectionKernel.cpp
+        EulerAdvectionKernel.h
+        RK4AdvectionKernel.cpp
+        RK4AdvectionKernel.h
+)
+
+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(Advection PUBLIC ${netCDF_INCLUDE_DIR})
+
+find_library(NETCDF_LIB NAMES netcdf-cxx4 netcdf_c++4 PATHS ${NETCDFCXX_LIB_DIR} NO_DEFAULT_PATH)
+target_link_libraries(Advection ${NETCDF_LIB})

advection/src/EulerAdvectionKernel.cpp

@@ -0,0 +1,13 @@
+
+#include "EulerAdvectionKernel.h"
+#include "interpolate.h"
+
+using namespace std;
+
+EulerAdvectionKernel::EulerAdvectionKernel(std::shared_ptr<UVGrid> grid): grid(grid) { }
+
+std::pair<double, double> EulerAdvectionKernel::advect(int time, double latitude, double longitude) const {
+    auto [u, v] = bilinearinterpolate(*grid, time, latitude, longitude);
+
+    return {latitude+metreToDegrees(v*DT), longitude+metreToDegrees(u*DT)};
+}

advection/src/EulerAdvectionKernel.h

@@ -0,0 +1,25 @@
+#ifndef ADVECTION_EULERADVECTIONKERNEL_H
+#define ADVECTION_EULERADVECTIONKERNEL_H
+
+#include "AdvectionKernel.h"
+#include "UVGrid.h"
+
+/**
+ * Implementation of AdvectionKernel.
+ * The basic equation is:
+ * new_latitude = latitude + v*DT
+ * new_longitude = longitude + u*DT
+ *
+ * Uses bilinear interpolation as implemented in interpolate.h
+ */
+class EulerAdvectionKernel: public AdvectionKernel {
+private:
+    std::shared_ptr<UVGrid> grid;
+public:
+    explicit EulerAdvectionKernel(std::shared_ptr<UVGrid> grid);
+    std::pair<double, double> advect(int time, double latitude, double longitude) const override;
+
+};
+
+
+#endif //ADVECTION_EULERADVECTIONKERNEL_H

advection/src/RK4AdvectionKernel.cpp

@@ -0,0 +1,35 @@
+#include "RK4AdvectionKernel.h"
+#include "interpolate.h"
+
+using namespace std;
+
+RK4AdvectionKernel::RK4AdvectionKernel(std::shared_ptr<UVGrid> grid): grid(grid) { }
+
+std::pair<double, double> RK4AdvectionKernel::advect(int time, double latitude, double longitude) const {
+    auto [u1, v1] = bilinearinterpolate(*grid, time, latitude, longitude);
+//    lon1, lat1 = (particle.lon + u1*.5*particle.dt, particle.lat + v1*.5*particle.dt);
+    double lon1 = longitude + metreToDegrees(u1 * 0.5*DT);
+    double lat1 = latitude + metreToDegrees(v1 * 0.5*DT);
+
+//    (u2, v2) = fieldset.UV[time + .5 * particle.dt, particle.depth, lat1, lon1, particle]
+    auto [u2, v2] = bilinearinterpolate(*grid, time + 0.5 * DT, lat1, lon1);
+
+//    lon2, lat2 = (particle.lon + u2*.5*particle.dt, particle.lat + v2*.5*particle.dt)
+    double lon2 = longitude + metreToDegrees(u2 * 0.5 * DT);
+    double lat2 = latitude + metreToDegrees(v2 * 0.5 * DT);
+
+//    (u3, v3) = fieldset.UV[time + .5 * particle.dt, particle.depth, lat2, lon2, particle]
+    auto [u3, v3] = bilinearinterpolate(*grid, time + 0.5 * DT, lat2, lon2);
+
+//    lon3, lat3 = (particle.lon + u3*particle.dt, particle.lat + v3*particle.dt)
+    double lon3 = longitude + metreToDegrees(u3 * DT);
+    double lat3 = latitude + metreToDegrees(v3 * DT);
+
+//    (u4, v4) = fieldset.UV[time + particle.dt, particle.depth, lat3, lon3, particle]
+    auto [u4, v4] = bilinearinterpolate(*grid, time + DT, lat3, lon3);
+
+    double lonFinal = longitude + metreToDegrees((u1 + 2 * u2 + 2 * u3 + u4) / 6.0 * DT);
+    double latFinal = latitude + metreToDegrees((v1 + 2 * v2 + 2 * v3 + v4) / 6.0 * DT);
+
+    return {latFinal, lonFinal};
+}

advection/src/RK4AdvectionKernel.h

@@ -0,0 +1,22 @@
+#ifndef ADVECTION_RK4ADVECTIONKERNEL_H
+#define ADVECTION_RK4ADVECTIONKERNEL_H
+
+#include "AdvectionKernel.h"
+#include "UVGrid.h"
+
+/**
+ * Implementation of Advection kernel using RK4 integration
+ * See https://en.wikipedia.org/wiki/Runge%E2%80%93Kutta_methods for more details.
+ * Uses bilinear interpolation as implemented in interpolate.h
+ */
+class RK4AdvectionKernel: public AdvectionKernel {
+private:
+    std::shared_ptr<UVGrid> grid;
+public:
+    explicit RK4AdvectionKernel(std::shared_ptr<UVGrid> grid);
+    std::pair<double, double> advect(int time, double latitude, double longitude) const override;
+
+};
+
+
+#endif //ADVECTION_RK4ADVECTIONKERNEL_H

advection/src/UVGrid.cpp

@@ -0,0 +1,66 @@
+#include <ranges>
+
+#include "UVGrid.h"
+#include "readdata.h"
+
+#define sizeError2 "The sizes of the hydrodynamic data files are different"
+#define sizeError "The sizes of the hydrodynamicU or -V files does not correspond with the sizes of the grid file"
+
+using namespace std;
+
+UVGrid::UVGrid() {
+    auto us = readHydrodynamicU();
+    auto vs = readHydrodynamicV();
+    if (us.size() != vs.size()) {
+        throw domain_error(sizeError2);
+    }
+
+    tie(times, lats, lons) = readGrid();
+
+    timeSize = times.size();
+    latSize = lats.size();
+    lonSize = lons.size();
+
+    size_t gridSize = timeSize * latSize * lonSize;
+    if (gridSize != us.size()) {
+        throw domain_error(sizeError);
+    }
+
+    uvData.reserve(gridSize);
+
+    for (auto vel: views::zip(us, vs)) {
+        uvData.push_back(Vel(vel));
+    }
+}
+
+const Vel &UVGrid::operator[](size_t timeIndex, size_t latIndex, size_t lonIndex) const {
+    if(timeIndex < 0 or timeIndex >= timeSize
+        or latIndex < 0 or latIndex >= latSize
+        or lonIndex < 0 or lonIndex >= lonSize) {
+        throw std::out_of_range("Index out of bounds");
+    }
+    size_t index = timeIndex * (latSize * lonSize) + latIndex * lonSize + lonIndex;
+    return uvData[index];
+}
+
+double UVGrid::lonStep() const {
+    return lons[1] - lons[0];
+}
+
+double UVGrid::latStep() const {
+    return lats[1] - lats[0];
+}
+
+int UVGrid::timeStep() const {
+    return times[1] - times[0];
+}
+
+void UVGrid::streamSlice(ostream &os, size_t t) {
+    for (int x = 0; x < latSize; x++) {
+        for (int y = 0; y < lonSize; y++) {
+            auto vel = (*this)[t,x,y];
+            os << vel << " ";
+        }
+      os << endl;
+    }
+}

advection/src/UVGrid.h

@@ -0,0 +1,65 @@
+#ifndef ADVECTION_UVGRID_H
+#define ADVECTION_UVGRID_H
+
+#include <vector>
+#include "Vel.h"
+
+class UVGrid {
+private:
+    /**
+     * 1D data vector of all the us and vs
+     */
+    std::vector<Vel> uvData;
+public:
+    UVGrid();
+
+    /**
+     * The matrix has shape (timeSize, latSize, lonSize)
+     */
+    size_t timeSize;
+    size_t latSize;
+    size_t lonSize;
+
+    /**
+     * Assuming grid is a regular grid, gives the longitudinal spacing of grid.
+     * @return longitudinal spacing
+     */
+    double lonStep() const;
+
+    /**
+     * Assuming grid is a regular grid, gives the latitudinal spacing of grid.
+     * @return latitudinal spacing
+     */
+    double latStep() const;
+
+    /**
+     * Assuming grid is a regular grid, gives the time spacing of grid.
+     * @return time spacing
+     */
+    int timeStep() const;
+
+    /**
+     * times, lats, lons are vector of length timeSize, latSize, lonSize respectively.
+     * The maintain the following invariant:
+     * grid[timeIndex,latIndex,lonIndex] gives the u,v at the point with latitude at lats[latIndex],
+     * with longitude at lons[lonIndex], and with time at times[timeIndex].
+     */
+    std::vector<int> times;
+    std::vector<double> lats;
+    std::vector<double> lons;
+
+    /**
+     * The 3D index into the data. The array is sized by [8761][67][116]
+     * @return Velocity at that index
+     */
+    const Vel& operator[](size_t timeIndex, size_t latIndex, size_t lonIndex) const;
+
+    /**
+     * Streams a slice at timeIndex t of the matrix to the outstream given by os
+     * @param os outstream
+     * @param t index with which to slice matrix
+     */
+    void streamSlice(std::ostream &os, size_t t);
+};
+
+#endif //ADVECTION_UVGRID_H

advection/src/Vel.cpp

@@ -0,0 +1,40 @@
+#include "Vel.h"
+#include <stdexcept>
+#include <iomanip>
+
+using namespace std;
+
+Vel::Vel(double u, double v) : u(u), v(v) {}
+
+Vel::Vel(const std::pair<double, double>& p) : u(p.first), v(p.second) {}
+
+Vel& Vel::operator=(const std::pair<double, double>& p) {
+    u = p.first;
+    v = p.second;
+    return *this;
+}
+
+Vel Vel::operator+(const Vel& other) const {
+    return Vel(u + other.u, v + other.v);
+}
+
+Vel& Vel::operator+=(const Vel& other) {
+    u += other.u;
+    v += other.v;
+    return *this;
+}
+
+template<typename Scalar>
+Vel Vel::operator/(Scalar scalar) const {
+    if (scalar == 0) throw std::runtime_error("Division by zero");
+    return Vel(u / scalar, v / scalar);
+}
+
+std::ostream& operator<<(ostream& os, const Vel& vel) {
+    os << "(";
+    os << fixed << setprecision(2) << setw(5) << vel.u;
+    os << ", ";
+    os << fixed << setprecision(2) << setw(5) << vel.v;
+    os << ")";
+    return os;
+}

advection/src/Vel.h

@@ -0,0 +1,44 @@
+#ifndef ADVECTION_VEL_H
+#define ADVECTION_VEL_H
+
+#include <utility>
+#include <stdexcept>
+#include <iostream>
+#include <format>
+
+class Vel {
+public:
+    double u; // Eastward Current Velocity in the Water Column
+    double v; // Northward Current Velocity in the Water Column
+
+    Vel(double u, double v);
+    Vel(const std::pair<double, double>& p);  // Conversion constructor
+    Vel& operator=(const std::pair<double, double>& p);
+
+    // Operator + to add two Vel objects
+    Vel operator+(const Vel& other) const;
+
+    // Operator += to add another Vel object to this object
+    Vel& operator+=(const Vel& other);
+
+    // Operator * to multiply Vel by a scalar, defined as a member template
+    template<typename Scalar>
+    Vel operator*(Scalar scalar) const {
+        return Vel(u * scalar, v * scalar);
+    }
+
+    // Operator / to divide Vel by a scalar, defined as a member template
+    template<typename Scalar>
+    Vel operator/(Scalar scalar) const;
+
+    // Friend declaration for the stream insertion operator
+    friend std::ostream& operator<<(std::ostream& os, const Vel& vel);
+};
+
+// Non-member function for scalar multiplication on the left
+template<typename Scalar>
+Vel operator*(Scalar scalar, const Vel& p) {
+    return Vel(p.u * scalar, p.v * scalar);
+}
+
+#endif //ADVECTION_VEL_H

advection/src/interpolate.cpp

@@ -0,0 +1,47 @@
+#include "interpolate.h"
+
+using namespace std;
+
+Vel bilinearinterpolate(const UVGrid &uvGrid, int time, double lat, double lon) {
+    double latStep = uvGrid.latStep();
+    double lonStep = uvGrid.lonStep();
+    int timeStep = uvGrid.timeStep();
+
+    int latIndex = (lat - uvGrid.lats[0]) / latStep;
+    int lonIndex = (lon - uvGrid.lons[0]) / lonStep;
+    int timeIndex = (time - uvGrid.times[0]) / timeStep;
+
+    double timeRatio = (static_cast<double>(time) - uvGrid.times[timeIndex]) / timeStep;
+    double latRatio = (lat - uvGrid.lats[latIndex]) / latStep;
+    double lonRatio = (lon - uvGrid.lons[lonIndex]) / lonStep;
+
+    Vel point = {0, 0};
+    for (int timeOffset = 0; timeOffset <= 1; timeOffset++) {
+        for (int latOffset = 0; latOffset <= 1; latOffset++) {
+            for (int lonOffset = 0; lonOffset <= 1; lonOffset++) {
+                auto vertex = uvGrid[
+                        timeIndex + 1 < uvGrid.timeSize ? timeIndex + timeOffset : timeIndex,
+                                latIndex + 1 < uvGrid.latSize ? latIndex + latOffset : latIndex,
+                                lonIndex + 1 < uvGrid.lonSize ? lonIndex + lonOffset : lonIndex
+                ];
+
+                double timeRation = (1 - timeOffset) * (1 - timeRatio) + timeOffset * timeRatio;
+                double latRation = (1 - latOffset) * (1 - latRatio) + latOffset * latRatio;
+                double lonRation = (1 - lonOffset) * (1 - lonRatio) + lonOffset * lonRatio;
+                point += timeRation * latRation * lonRation * vertex;
+            }
+        }
+    }
+
+    return point;
+}
+
+vector<Vel> bilinearinterpolation(const UVGrid &uvGrid, vector<tuple<int, double, double>> points) {
+    vector<Vel> result;
+    result.reserve(points.size());
+    for (auto [time, lat, lon]: points) {
+        result.push_back(bilinearinterpolate(uvGrid, time, lat, lon));
+    }
+
+    return result;
+}

advection/src/interpolate.h

@@ -0,0 +1,28 @@
+#ifndef ADVECTION_INTERPOLATE_H
+#define ADVECTION_INTERPOLATE_H
+
+#include <vector>
+
+#include "UVGrid.h"
+
+/**
+ * Bilinearly interpolate the point (time, lat, lon) to produce the interpolated velocity.
+ * Since it is in 3D, this means that it interpolates against 8 points (excluding edges).
+ * As described in https://numerical.recipes/book.html Chapter 3.6
+ * @param uvGrid velocity grid
+ * @param time time of point
+ * @param lat latitude of point
+ * @param lon longitude of point
+ * @return interpolated velocity
+ */
+Vel bilinearinterpolate(const UVGrid &uvGrid, int time, double lat, double lon);
+
+/**
+ * Helper function for bilnearly interpolating a vector of points
+ * @param uvGrid velocity grid
+ * @param points vector of points
+ * @return interpolated velocities
+ */
+std::vector<Vel> bilinearinterpolation(const UVGrid &uvGrid, std::vector<std::tuple<int, double, double>> points);
+
+#endif //ADVECTION_INTERPOLATE_H

advection/src/main.cpp

@@ -0,0 +1,95 @@
+#include <ranges>
+#include <iomanip>
+#include <stdexcept>
+
+#include "interpolate.h"
+#include "Vel.h"
+#include "EulerAdvectionKernel.h"
+#include "RK4AdvectionKernel.h"
+#include "interpolate.h"
+
+#define NotAKernelError "Template parameter T must derive from AdvectionKernel"
+
+using namespace std;
+
+template <typename AdvectionKernelImpl>
+void advectForSomeTime(const UVGrid &uvGrid, const AdvectionKernelImpl &kernel, double latstart, double lonstart, int i, char colour[10]) {
+
+    // Require at compile time that kernel derives from the abstract class AdvectionKernel
+    static_assert(std::is_base_of<AdvectionKernel, AdvectionKernelImpl>::value, NotAKernelError);
+
+    double lat1 = latstart, lon1 = lonstart;
+    for(int time = 0; time <= 31536000.; time += AdvectionKernel::DT) {
+//        cout << setprecision(8) << lat1 << "," << setprecision(8) << lon1 << ",end" << i << "," << colour << endl;
+        try {
+            auto [templat, templon] = kernel.advect(time, lat1, lon1);
+            lat1 = templat;
+            lon1 = templon;
+        } catch (const out_of_range& e) {
+            cerr << "broke out of loop!" << endl;
+            time = 31536001;
+        }
+    }
+    cout << setprecision(8) << latstart << "," << setprecision(8) << lonstart << ",begin" << i << "," << colour << endl;
+    cout << setprecision(8) << lat1 << "," << setprecision(8) << lon1 << ",end" << i << "," << colour << endl;
+}
+
+void testGridIndexing(const UVGrid *uvGrid) {
+    int time = 20000;
+    cout << "=== land === (should all give 0)" << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 53.80956379699079, -1.6496306344654406) << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 55.31428895563707, -2.851581041325997) << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 47.71548983067583, -1.8704054037408626) << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 56.23521060314398, 8.505979324950573) << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 53.135645440244375, 8.505979324950573) << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 56.44761278775708, -4.140629303756164) << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 52.67625153110339, 0.8978569759455872) << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 52.07154079279377, 4.627951041411331) << endl;
+
+    cout << "=== ocean === (should give not 0)" << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 47.43923166616274, -4.985451481829083) << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 50.68943556852362, -9.306162999561733) << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 53.70606799886677, -4.518347647034465) << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 60.57987114267971, -12.208262973672621) << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 46.532221548197285, -13.408189172582638) << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 50.92725094937812, 1.3975824052375256) << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 51.4028921682209, 2.4059571950925203) << endl;
+    cout << bilinearinterpolate(*uvGrid, time, 53.448445236769004, 0.7996966058017515) << endl;
+//    cout << bilinearinterpolate(*uvGrid, time, ) << endl;
+}
+
+int main() {
+    std::shared_ptr<UVGrid> uvGrid = std::make_shared<UVGrid>();
+
+    uvGrid->streamSlice(cout, 900);
+
+    auto kernelRK4 = RK4AdvectionKernel(uvGrid);
+
+//    You can use https://maps.co/gis/ to visualise these points
+    cout << "======= RK4 Integration =======" << endl;
+    advectForSomeTime(*uvGrid, kernelRK4, 53.53407391652826, 6.274975037862238, 0, "#ADD8E6");
+    advectForSomeTime(*uvGrid, kernelRK4, 53.494053820479365, 5.673454142386921, 1, "#DC143C");
+    advectForSomeTime(*uvGrid, kernelRK4, 53.49321966653616, 5.681867022043919, 2, "#50C878");
+    advectForSomeTime(*uvGrid, kernelRK4, 53.581548701694324, 6.552600066543153, 3, "#FFEA00");
+    advectForSomeTime(*uvGrid, kernelRK4, 53.431446729744124, 5.241592961691523, 4, "#663399");
+    advectForSomeTime(*uvGrid, kernelRK4, 53.27913608324572, 4.82094897884165, 5, "#FFA500");
+    advectForSomeTime(*uvGrid, kernelRK4, 53.18597595482688, 4.767667388308705, 6, "#008080");
+    advectForSomeTime(*uvGrid, kernelRK4, 53.01592078792383, 4.6064205160882, 7, "#FFB6C1");
+    advectForSomeTime(*uvGrid, kernelRK4, 52.72816940158886, 4.5853883152993635, 8, "#36454F"); // on land
+    advectForSomeTime(*uvGrid, kernelRK4, 52.56142091881038, 4.502661662924255, 9, "#1E90FF"); // Dodger Blue
+    advectForSomeTime(*uvGrid, kernelRK4, 52.23202593893584, 4.2825246383181845, 10, "#FFD700"); // Gold
+    advectForSomeTime(*uvGrid, kernelRK4, 52.08062567609582, 4.112864890830927, 11, "#6A5ACD"); // Slate Blue
+    advectForSomeTime(*uvGrid, kernelRK4, 51.89497719759734, 3.8114033568921686, 12, "#20B2AA"); // Light Sea Green
+    advectForSomeTime(*uvGrid, kernelRK4, 51.752848503723634, 3.664177951809339, 13, "#FF69B4"); // Hot Pink
+    advectForSomeTime(*uvGrid, kernelRK4, 51.64595756528835, 3.626319993352851, 14, "#800080"); // Purple
+    advectForSomeTime(*uvGrid, kernelRK4, 51.55140730645238, 3.4326152213887986, 15, "#FF4500"); // Orange Red
+    advectForSomeTime(*uvGrid, kernelRK4, 51.45679776223422, 3.4452813365018384, 16, "#A52A2A"); // Brown
+    advectForSomeTime(*uvGrid, kernelRK4, 51.41444662720727, 3.4648562416765363, 17, "#4682B4"); // Steel Blue
+    advectForSomeTime(*uvGrid, kernelRK4, 51.37421261203866, 3.2449264214689455, 18, "#FF6347"); // Tomato
+    advectForSomeTime(*uvGrid, kernelRK4, 51.29651848898365, 2.9547572241424773, 19, "#008000"); // Green
+    advectForSomeTime(*uvGrid, kernelRK4, 51.19705098468974, 2.7647654914530024, 20, "#B8860B"); // Dark Goldenrod
+    advectForSomeTime(*uvGrid, kernelRK4, 51.114719857442665, 2.577076679365129, 21, "#FFC0CB"); // Pink
+//    advectForSomeTime(*uvGrid, kernelRK4, ,0);
+
+    return 0;
+}

advection/src/readdata.cpp

@@ -0,0 +1,50 @@
+#include <stdexcept>
+
+#include <netcdf>
+
+#include "readdata.h"
+
+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;
+}
+
+vector<double> readHydrodynamicU() {
+    // Vs and Us flipped cause the files are named incorrectly
+    netCDF::NcFile data("../../../../data/hydrodynamic_V.h5", netCDF::NcFile::read);
+
+    multimap< string, NcVar > vars = data.getVars();
+
+    return getVarVector<double>(vars.find("vo")->second);
+}
+
+vector<double> readHydrodynamicV() {
+    // Vs and Us flipped cause the files are named incorrectly
+    netCDF::NcFile data("../../../../data/hydrodynamic_U.h5", netCDF::NcFile::read);
+
+    multimap< string, NcVar > vars = data.getVars();
+
+    return getVarVector<double>(vars.find("uo")->second);
+}
+
+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};
+}

advection/src/readdata.h

@@ -0,0 +1,22 @@
+#ifndef ADVECTION_READDATA_H
+#define ADVECTION_READDATA_H
+
+/**
+ * reads the file hydrodynamic_U.h5
+ * @return the data vector of us
+ */
+std::vector<double> readHydrodynamicU();
+
+/**
+ * reads the file hydrodynamic_V.h5
+ * @return the data vector of vs
+ */
+std::vector<double> readHydrodynamicV();
+
+/**
+ * Reads the file grid.h5
+ * @return a tuple of (times, latitude, longitude)
+ */
+std::tuple<std::vector<int>, std::vector<double>, std::vector<double>> readGrid();
+
+#endif //ADVECTION_READDATA_H

vtk/src/Program.cpp

@@ -38,6 +38,7 @@ void Program::setupTimer() {
   auto callback = vtkSmartPointer<TimerCallbackCommand>::New(this);
   callback->SetClientData(this);
   this->interact->AddObserver(vtkCommand::TimerEvent, callback);
+  this->interact->AddObserver(vtkCommand::KeyPressEvent, callback);
   this->interact->CreateRepeatingTimer(17); // 60 fps == 1000 / 60 == 16.7 ms per frame
 }
 

vtk/src/commands/SpawnPointCallback.cpp

@@ -50,8 +50,7 @@ void SpawnPointCallback::Execute(vtkObject *caller, unsigned long evId, void *ca
     vtkSmartPointer<vtkCellArray> vertices = vtkSmartPointer<vtkCellArray>::New();
     vertices->InsertNextCell(vertex);
     data->SetVerts(vertices);
-//    data->Modified(); // These might be needed im not sure.
-//    ren->GetRenderWindow()->Render();
+    ren->GetRenderWindow()->Render();
 }
 
 

vtk/src/commands/TimerCallbackCommand.cpp

@@ -8,10 +8,16 @@ TimerCallbackCommand::TimerCallbackCommand() : dt(3600), maxTime(3600*24*365), t
 TimerCallbackCommand* TimerCallbackCommand::New(Program *program) {
   TimerCallbackCommand *cb = new TimerCallbackCommand();
   cb->setProgram(program);
+  cb->setPaused(false);
   return cb;
 }
 
 void TimerCallbackCommand::Execute(vtkObject* caller, unsigned long eventId, void* vtkNotUsed(callData)) {
+  auto intr = reinterpret_cast<vtkRenderWindowInteractor *>(caller);
+  
+  if (eventId == vtkCommand::KeyPressEvent and not strcmp("space", intr->GetKeySym())) {
+    this->paused = ! this->paused;
+  } else if (eventId == vtkCommand::TimerEvent and not this->paused) {
   this->time += this->dt;
 
   if (this->time >= this->maxTime) {
@@ -22,7 +28,13 @@ void TimerCallbackCommand::Execute(vtkObject* caller, unsigned long eventId, voi
   this->program->updateData(this->time);
   }
 
+}
 
 void TimerCallbackCommand::setProgram(Program *program) {
   this->program = program;
 }
+
+
+void TimerCallbackCommand::setPaused(const bool val) {
+  this->paused = val;
+}

vtk/src/commands/TimerCallbackCommand.h

@@ -11,11 +11,13 @@ public:
   void Execute(vtkObject* caller, unsigned long eventId, void* vtkNotUsed(callData)) override;
 
   void setProgram(Program *program);
+  void setPaused(const bool val);
 
 private:
   int time;
   int dt;
   int maxTime;
+  bool paused;
   Program *program;
 };