Add libhdf5.

Co-authored-by: Mosè Giordano <[email protected]>
Co-authored-by: Will Graham <[email protected]>

.github/workflows/ci.yml

@@ -60,7 +60,7 @@ jobs:
         if: ${{ contains(matrix.os, 'ubuntu') }}
         run: |
           sudo apt-get update
-          sudo apt-get install libfftw3-dev libgomp1 python3
+          sudo apt-get install libfftw3-dev libhdf5-dev libgomp1 python3
 
       # -------------------------------------------------------------------------------
       # Windows
@@ -77,12 +77,14 @@ jobs:
         run: |
           conda install fftw --yes
           echo "FFTWDIR=C:\Miniconda\envs\test\Library" | Out-File -FilePath $Env:GITHUB_ENV -Encoding utf8 -Append
+          conda install hdf5
+          echo "HDF5_DIR=C:\Miniconda\envs\test\Library" | Out-File -FilePath $Env:GITHUB_ENV -Encoding utf8 -Append
 
       # -------------------------------------------------------------------------------
       # MacOS
       - name: Install dependencies for MacOS
         if: ${{ contains(matrix.os, 'macos') }}
-        run: brew install fftw
+        run: brew install fftw hdf5
 
       - name: Fix omp headers not linked on MacOS
         if: ${{ contains(matrix.os, 'macos') }}

README.md

@@ -48,18 +48,19 @@ To compile on a Mac an x86 compiler with libraries for OpenMP are required,
 which can be installed using [brew](https://brew.sh/) with `brew install llvm`
 then (optionally) set the following cmake arguments
 
-```{sh}
--DCMAKE_CXX_COMPILER=/Users/username/.local/homebrew/opt/llvm/bin/clang++
--DOMP_ROOT=/Users/username/.local/homebrew/opt/llvm/
--DCXX_ROOT=/Users/username/.local/homebrew/opt/llvm
-```
-
-On an ARM Mac install the x86 version of brew with
-```bash
-arch -x86_64 zsh
-arch -x86_64 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
-arch -x86_64 /usr/local/bin/brew install llvm
-```
+    ```{sh}
+    -DCMAKE_CXX_COMPILER=/Users/username/.local/homebrew/opt/llvm/bin/clang++
+    -DOMP_ROOT=/Users/username/.local/homebrew/opt/llvm/
+    -DCXX_ROOT=/Users/username/.local/homebrew/opt/llvm
+    -DHDF5_ROOT=/Users/username/.local/homebrew/opt/hdf5
+    ```
+
+    On an ARM Mac install the x86 version of brew with
+    ```bash
+    arch -x86_64 zsh
+    arch -x86_64 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+    arch -x86_64 /usr/local/bin/brew install llvm hdf5
+    ```
 </details>
 
 

tdms/CMakeLists.txt

@@ -1,7 +1,7 @@
 # General setup ---------------------------------------------------------------
 cmake_minimum_required(VERSION 3.21)
 
-project(tdms LANGUAGES CXX)
+project(tdms LANGUAGES CXX C)
 set(CMAKE_CXX_STANDARD 17)
 
 # Allow building with testing, and default to off
@@ -57,6 +57,9 @@ else()
     find_package(OpenMP REQUIRED)
 endif()
 
+# hdf5 ------------------------------------------------------------------------
+find_package(HDF5 REQUIRED COMPONENTS CXX)
+include_directories(${HDF5_INCLUDE_DIR})
 
 # spdlog ----------------------------------------------------------------------
 find_package(spdlog NO_CMAKE_PACKAGE_REGISTRY QUIET)

tdms/cmake/targets.cmake

@@ -9,6 +9,7 @@ function(release_target)
             ${Matlab_MX_LIBRARY}
             ${Matlab_MAT_LIBRARY}
             ${LIBCXX_LIBRARY}
+            ${HDF5_CXX_LIBRARIES}
             OpenMP::OpenMP_CXX
             spdlog::spdlog
             )
@@ -44,6 +45,7 @@ function(test_target)
             ${Matlab_MX_LIBRARY}
             ${Matlab_MAT_LIBRARY}
             ${LIBCXX_LIBRARY}
+            ${HDF5_CXX_LIBRARIES}
             OpenMP::OpenMP_CXX
             spdlog::spdlog
             )

tdms/include/hdf5_io.h

@@ -0,0 +1,9 @@
+/**
+ * @file hdf5_io.h
+ * @brief File I/O using HDF5
+ */
+
+/**
+ * @brief Test of HDF5 I/O
+ */
+void test_hdf5();

tdms/src/hdf5_io.cpp

@@ -0,0 +1,65 @@
+// own include
+#include "hdf5_io.h"
+
+// std
+#include <string>
+
+// external libraries
+#include <H5Cpp.h>
+
+// own headers
+
+
+#define MAX_NAME_LENGTH 32
+const std::string FileName("SimpleCompound.h5");
+const std::string DatasetName("PersonalInformation");
+const std::string member_age("Age");
+const std::string member_sex("Sex");
+const std::string member_name("Name");
+const std::string member_height("Height");
+
+typedef struct {
+    int age;
+    char sex;
+    char name[MAX_NAME_LENGTH];
+    float height;
+} PersonalInformation;
+
+
+
+void test_hdf5() {
+
+    // Data to write
+    PersonalInformation person_list[] = {
+        { 18, 'M', "Mary",  152.0   },
+        { 32, 'F', "Tom",   178.6   },
+        { 29, 'M', "Tarou", 166.6   }
+    };
+    // the length of the data
+    //int length = sizeof(person_list) / sizeof(PersonalInformation);
+    // the array of each length of multidimentional data.
+    hsize_t dim[1];
+    dim[0] = sizeof(person_list) / sizeof(PersonalInformation);
+
+    // the length of dim
+    int rank = sizeof(dim) / sizeof(hsize_t);
+
+    // defining the datatype to pass HDF55
+    H5::CompType mtype(sizeof(PersonalInformation));
+    mtype.insertMember(member_age, HOFFSET(PersonalInformation, age), H5::PredType::NATIVE_INT);
+    mtype.insertMember(member_sex, HOFFSET(PersonalInformation, sex), H5::PredType::C_S1);
+    mtype.insertMember(member_name, HOFFSET(PersonalInformation, name), H5::StrType(H5::PredType::C_S1, MAX_NAME_LENGTH));
+    mtype.insertMember(member_height, HOFFSET(PersonalInformation, height), H5::PredType::NATIVE_FLOAT);
+
+    // preparation of a dataset and a file.
+    H5::DataSpace space(rank, dim);
+    H5::H5File *file = new H5::H5File(FileName, H5F_ACC_TRUNC);
+    H5::DataSet *dataset = new H5::DataSet(file->createDataSet(DatasetName, mtype, space));
+    // Write
+    dataset->write(person_list, mtype);
+
+    delete dataset;
+    delete file;
+    return;
+
+}