Enhance H5 I/O

CMakeLists.txt

@@ -68,44 +68,44 @@ add_subdirectory(tests)
 
 # #######################################################################
 # Installation
-install(
-    TARGETS dx2
-    EXPORT DX2Targets
-    LIBRARY DESTINATION lib
+# install(
+#     TARGETS dx2
+#     EXPORT DX2Targets
+#     LIBRARY DESTINATION lib
 
-    # FILE_SET HEADERS DESTINATION include/dx2
-)
-install(
-    FILES
-    include/dx2/dx2.h
-    DESTINATION include/dx2
-)
+#     # FILE_SET HEADERS DESTINATION include/dx2
+# )
+# install(
+#     FILES
+#     include/dx2/dx2.h
+#     DESTINATION include/dx2
+# )
 
-install(
-    EXPORT DX2Targets
-    FILE DX2Targets.cmake
-    DESTINATION lib/cmake/DX2
-)
+# install(
+#     EXPORT DX2Targets
+#     FILE DX2Targets.cmake
+#     DESTINATION lib/cmake/DX2
+# )
 
-include(CMakePackageConfigHelpers)
-configure_package_config_file(
-    ${CMAKE_CURRENT_SOURCE_DIR}/Config.cmake.in
-    "${CMAKE_CURRENT_BINARY_DIR}/DX2Config.cmake"
-    INSTALL_DESTINATION "lib/cmake/DX2"
-    NO_SET_AND_CHECK_MACRO
-    NO_CHECK_REQUIRED_COMPONENTS_MACRO
-)
-write_basic_package_version_file(
-    "${CMAKE_CURRENT_BINARY_DIR}/DX2ConfigVersion.cmake"
-    VERSION "${DX2_VERSION_MAJOR}.${DX2_VERSION_MINOR}"
-    COMPATIBILITY AnyNewerVersion
-)
-install(
-    FILES
-    ${CMAKE_CURRENT_BINARY_DIR}/DX2Config.cmake
-    ${CMAKE_CURRENT_BINARY_DIR}/DX2ConfigVersion.cmake
-    DESTINATION lib/cmake/DX2
-)
-export(EXPORT DX2Targets
-    FILE "${CMAKE_CURRENT_BINARY_DIR}/DX2Targets.cmake"
-)
+# include(CMakePackageConfigHelpers)
+# configure_package_config_file(
+#     ${CMAKE_CURRENT_SOURCE_DIR}/Config.cmake.in
+#     "${CMAKE_CURRENT_BINARY_DIR}/DX2Config.cmake"
+#     INSTALL_DESTINATION "lib/cmake/DX2"
+#     NO_SET_AND_CHECK_MACRO
+#     NO_CHECK_REQUIRED_COMPONENTS_MACRO
+# )
+# write_basic_package_version_file(
+#     "${CMAKE_CURRENT_BINARY_DIR}/DX2ConfigVersion.cmake"
+#     VERSION "${DX2_VERSION_MAJOR}.${DX2_VERSION_MINOR}"
+#     COMPATIBILITY AnyNewerVersion
+# )
+# install(
+#     FILES
+#     ${CMAKE_CURRENT_BINARY_DIR}/DX2Config.cmake
+#     ${CMAKE_CURRENT_BINARY_DIR}/DX2ConfigVersion.cmake
+#     DESTINATION lib/cmake/DX2
+# )
+# export(EXPORT DX2Targets
+#     FILE "${CMAKE_CURRENT_BINARY_DIR}/DX2Targets.cmake"
+# )

dx2/CMakeLists.txt

@@ -4,7 +4,7 @@ add_library(
 )
 target_link_libraries(
     dx2
-    PRIVATE
+    PUBLIC
     Eigen3::Eigen
     nlohmann_json::nlohmann_json
     hdf5::hdf5
@@ -16,4 +16,3 @@ target_include_directories(
     $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>
     $<INSTALL_INTERFACE:include>
 )
-target_link_libraries(dx2 PUBLIC $<TARGET_NAME_IF_EXISTS:hdf5::hdf5>)

include/dx2/h5/h5read_processed.hpp

@@ -0,0 +1,87 @@
+#pragma once
+
+#include <cassert>
+#include <chrono>
+#include <cstring>
+#include <hdf5.h>
+#include <hdf5_hl.h>
+#include <iostream>
+#include <string>
+#include <vector>
+
+/**
+ * @brief Reads a dataset from an HDF5 file into an std::vector.
+ *
+ * @tparam T The type of data to read (e.g., int, double).
+ * @param filename The path to the HDF5 file.
+ * @param dataset_name The name of the dataset to read.
+ * @return A std::vector containing the data from the dataset.
+ * @throws std::runtime_error If the file, dataset, or datatype cannot be opened
+ * or read.
+ */
+template <typename T>
+std::vector<T> read_array_from_h5_file(const std::string &filename,
+                                       const std::string &dataset_name) {
+  // Start measuring time
+  auto start_time = std::chrono::high_resolution_clock::now();
+
+  // Open the HDF5 file
+  hid_t file = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+  if (file < 0) {
+    throw std::runtime_error("Error: Unable to open file: " + filename);
+  }
+
+  try {
+    // Open the dataset
+    hid_t dataset = H5Dopen(file, dataset_name.c_str(), H5P_DEFAULT);
+    if (dataset < 0) {
+      throw std::runtime_error("Error: Unable to open dataset: " +
+                               dataset_name);
+    }
+
+    try {
+      // Get the datatype and check size
+      hid_t datatype = H5Dget_type(dataset);
+      size_t datatype_size = H5Tget_size(datatype);
+      if (datatype_size != sizeof(T)) {
+        throw std::runtime_error(
+            "Error: Dataset type size does not match expected type size.");
+      }
+
+      // Get the dataspace and the number of elements
+      hid_t dataspace = H5Dget_space(dataset);
+      size_t num_elements = H5Sget_simple_extent_npoints(dataspace);
+
+      // Allocate a vector to hold the data
+      std::vector<T> data_out(num_elements);
+
+      // Read the data into the vector
+      herr_t status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+                              data_out.data());
+      if (status < 0) {
+        throw std::runtime_error("Error: Unable to read dataset: " +
+                                 dataset_name);
+      }
+
+      // Close the dataset and return the data
+      H5Dclose(dataset);
+      H5Fclose(file);
+
+      // Log timing
+      auto end_time = std::chrono::high_resolution_clock::now();
+      double elapsed_time =
+          std::chrono::duration<double>(end_time - start_time).count();
+      std::cout << "READ TIME for " << dataset_name << " : " << elapsed_time
+                << "s" << std::endl;
+
+      return data_out;
+
+    } catch (...) {
+      H5Dclose(dataset); // Ensure dataset is closed in case of failure
+      throw;
+    }
+  } catch (...) {
+    H5Fclose(file); // Ensure file is closed in case of failure
+    throw;
+  }
+}