Merge branch 'main' into djairo-wrapping

particle-track-and-trace/src/advection/UVGrid.cpp

@@ -8,14 +8,14 @@
 
 using namespace std;
 
-UVGrid::UVGrid() {
-  auto us = readHydrodynamicU();
-  auto vs = readHydrodynamicV();
+UVGrid::UVGrid(string path) {
+  auto us = readHydrodynamicU(path);
+  auto vs = readHydrodynamicV(path);
   if (us.size() != vs.size()) {
     throw domain_error(sizeError2);
   }
 
-  tie(times, lats, lons) = readGrid();
+  tie(times, lats, lons) = readGrid(path);
 
   timeSize = times.size();
   latSize = lats.size();

particle-track-and-trace/src/advection/UVGrid.h

@@ -11,7 +11,12 @@ private:
    */
   std::vector<Vel> uvData;
 public:
-    UVGrid();
+  /**
+   * Constructs the UVGrid.
+   * @param path The data path where the constructor expects to find
+   * the files hydrodynamic_U.h5, hydrodynamic_V.h5, and grid.h5
+   */
+  UVGrid(std::string path);
 
   /**
    * The matrix has shape (timeSize, latSize, lonSize)
@@ -76,7 +81,7 @@ public:
    * 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;
+  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

particle-track-and-trace/src/advection/readdata.cpp

@@ -7,10 +7,10 @@
 using namespace std;
 using namespace netCDF;
 
-template <typename T>
+template<typename T>
 vector<T> getVarVector(const NcVar &var) {
   int length = 1;
-    for (NcDim dim : var.getDims()) {
+  for (NcDim dim: var.getDims()) {
     length *= dim.getSize();
   }
 
@@ -21,27 +21,31 @@ vector<T> getVarVector(const NcVar &var) {
   return vec;
 }
 
-vector<double> readHydrodynamicU() {
+vector<double> readHydrodynamicU(string path) {
   // Vs and Us flipped cause the files are named incorrectly
-    netCDF::NcFile data("../../../../data/hydrodynamic_V.h5", netCDF::NcFile::read);
+  string fileName = "hydrodynamic_V.h5";
 
-    multimap< string, NcVar > vars = data.getVars();
+  netCDF::NcFile data(path + '/' + fileName, netCDF::NcFile::read);
+
+  multimap<string, NcVar> vars = data.getVars();
 
   return getVarVector<double>(vars.find("vo")->second);
 }
 
-vector<double> readHydrodynamicV() {
+vector<double> readHydrodynamicV(string path) {
   // Vs and Us flipped cause the files are named incorrectly
-    netCDF::NcFile data("../../../../data/hydrodynamic_U.h5", netCDF::NcFile::read);
+  string fileName = "hydrodynamic_U.h5";
+  netCDF::NcFile data(path + '/' + fileName, netCDF::NcFile::read);
 
-    multimap< string, NcVar > vars = data.getVars();
+  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();
+tuple<vector<int>, vector<double>, vector<double>> readGrid(string path) {
+  string fileName = "grid.h5";
+  netCDF::NcFile data(path + '/' + fileName, 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);

particle-track-and-trace/src/advection/readdata.h

@@ -5,18 +5,18 @@
  * reads the file hydrodynamic_U.h5
  * @return the data vector of us
  */
-std::vector<double> readHydrodynamicU();
+std::vector<double> readHydrodynamicU(std::string path);
 
 /**
  * reads the file hydrodynamic_V.h5
  * @return the data vector of vs
  */
-std::vector<double> readHydrodynamicV();
+std::vector<double> readHydrodynamicV(std::string path);
 
 /**
  * Reads the file grid.h5
  * @return a tuple of (times, latitude, longitude)
  */
-std::tuple<std::vector<int>, std::vector<double>, std::vector<double>> readGrid();
+std::tuple<std::vector<int>, std::vector<double>, std::vector<double>> readGrid(std::string path);
 
 #endif //READDATA_H

particle-track-and-trace/src/main.cpp

@@ -23,17 +23,18 @@ using namespace std;
 
 int main() {
   cout << "Reading data..." << endl;
-  shared_ptr<UVGrid> uvGrid = make_shared<UVGrid>();
+  string dataPath = "../../../../data";
+  shared_ptr<UVGrid> uvGrid = make_shared<UVGrid>(dataPath);
   auto kernelRK4 = make_unique<RK4AdvectionKernel>(uvGrid);
   auto kernelRK4BoundaryChecked = make_unique<SnapBoundaryConditionKernel>(std::move(kernelRK4), uvGrid);
   cout << "Starting vtk..." << endl;
 
   auto l = new LGlyphLayer(uvGrid, std::move(kernelRK4BoundaryChecked));
-  l->spoofPoints();
+//  l->spoofPoints();
   l->setDt(DT);
 
   unique_ptr<Program> program = make_unique<Program>(DT);
-  program->addLayer(new BackgroundImage("../../../../data/map_661-661.png"));
+  program->addLayer(new BackgroundImage(dataPath + "/map_661-661.png"));
   program->addLayer(new EGlyphLayer(uvGrid));
   program->addLayer(l);