From 2443d96733c671906450617e82529fcd6d72b510 Mon Sep 17 00:00:00 2001
From: robin <makenenjoy@gmail.com>
Date: Thu, 18 Apr 2024 13:21:53 +0200
Subject: [PATCH] feat: implemented reading hdf5

---
 .gitignore                      |  2 +
 opening-hdf5/.gitignore         |  4 ++
 opening-hdf5/src/CMakeLists.txt | 28 ++++++++++
 opening-hdf5/src/main.cpp       | 99 +++++++++++++++++++++++++++++++++
 4 files changed, 133 insertions(+)
 create mode 100644 .gitignore
 create mode 100644 opening-hdf5/.gitignore
 create mode 100644 opening-hdf5/src/CMakeLists.txt
 create mode 100644 opening-hdf5/src/main.cpp

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..5ca0973
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,2 @@
+.DS_Store
+
diff --git a/opening-hdf5/.gitignore b/opening-hdf5/.gitignore
new file mode 100644
index 0000000..13c6291
--- /dev/null
+++ b/opening-hdf5/.gitignore
@@ -0,0 +1,4 @@
+.DS_Store
+src/.DS_Store
+src/.cache
+src/build
diff --git a/opening-hdf5/src/CMakeLists.txt b/opening-hdf5/src/CMakeLists.txt
new file mode 100644
index 0000000..07d1489
--- /dev/null
+++ b/opening-hdf5/src/CMakeLists.txt
@@ -0,0 +1,28 @@
+cmake_minimum_required (VERSION 3.28)
+project (ReadHDF5)
+
+set(CMAKE_CXX_STANDARD 23)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
+find_package(netCDF REQUIRED)
+
+add_executable(ReadHDF5 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(ReadHDF5 PUBLIC ${netCDF_INCLUDE_DIR})
+
+find_library(NETCDF_LIB NAMES netcdf-cxx4 netcdf_c++4 PATHS ${NETCDFCXX_LIB_DIR} NO_DEFAULT_PATH)
+target_link_libraries(ReadHDF5 ${NETCDF_LIB})
diff --git a/opening-hdf5/src/main.cpp b/opening-hdf5/src/main.cpp
new file mode 100644
index 0000000..1acc55d
--- /dev/null
+++ b/opening-hdf5/src/main.cpp
@@ -0,0 +1,99 @@
+#include <iostream>
+#include <mdspan>
+#include <print>
+#include <stdexcept>
+
+#include <netcdf>
+
+using namespace std;
+using namespace netCDF;
+
+template <typename T>
+void printContentsOfVec(const std::vector<T>& vec) {
+  for (const auto& element : vec) {
+    cout << element << " ";
+  }
+  cout << std::endl;
+}
+
+template <typename T>
+vector<T> getVarVector(NcVar var) {
+  int length = 1;
+  for (NcDim dim : var.getDims()) {
+    length *= dim.getSize();
+  }
+
+  vector<T> vec(length);
+
+  var.getVar(vec.data());
+
+  return vec;
+}
+
+template <typename T>
+using arr3d = std::mdspan<
+                 T,
+                 std::dextents<
+                     std::size_t,
+                     3
+                 >
+               >;
+
+
+template <typename T>
+void print3DMatrixSlice(arr3d<T> arr, int t) {
+  for (int x = 0; x < arr.extent(1); x++) {
+    for (int y = 0; y < arr.extent(2); y++) {
+      print("{} ", arr[t,x,y]);
+    }
+    println("");
+  }
+}
+
+void print3DMatrixSlice(arr3d<double> arr, int t) {
+  for (int x = 0; x < arr.extent(1); x++) {
+    for (int y = 0; y < arr.extent(2); y++) {
+      print("{:>10.4f} ", arr[t,x,y]);
+    }
+    println("");
+  }
+}
+
+/**
+ * Read a 3D matrix from a NetCDF variable.
+ * Reads data into a contiguous 1D data vector.
+ * Returns a pair of the size of the matrix (in the form of an extent) with the data vector.
+ *
+ * Inteded usage of this function involves using the two returned values
+ * to create an mdspan:
+ *
+ * auto arr = mdspan(vec.data(), size);
+ */
+template <typename T>
+pair<vector<T>, std::dextents<std::size_t, 3>> get3DMat(NcVar var) {
+  if(var.getDimCount() != 3) {
+    throw invalid_argument("Variable is not 3D");
+  }
+  int timeLength = var.getDim(0).getSize();
+  int latLength = var.getDim(1).getSize();
+  int longLength = var.getDim(2).getSize();
+  vector<T> vec(timeLength*latLength*longLength);
+  var.getVar(vec.data());
+  auto arr = std::mdspan(vec.data(), timeLength, latLength, longLength);
+
+  return {vec, arr.extents()};
+}
+
+int main () {
+  netCDF::NcFile data("../../../hdf5/hydrodynamic_U.h5", netCDF::NcFile::read);
+
+  multimap< string, NcVar > vars = data.getVars();
+
+  auto [vec, size] = get3DMat<double>(vars.find("uo")->second);
+
+  auto arr = std::mdspan(vec.data(), size);
+
+  print3DMatrixSlice(arr, 100);
+
+  return 0;
+}