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Merge pull request #2 from dials/h5_writer
Create a generic H5 writer — along with unit tests — that can take generic data and write it to a file. As well as adding more robust error handling to the reader. - Create new subdirectory `h5` in `include/dx2` to logically group h5 related code. - Create new header file `dx2/h5/h5write.hpp` to define the writer. - Move `h5read_processed` into `dx2/h5` and add error handling. - Create new test file `test/test_write_h5_array.cxx` for validation. - Modify `CMakeLists.txt` to include the new header file, tests and changes to allow this to be included by other projects. There are several changes that we would like to make to the code, mostly involving better file handling and separately compiled implementations. However, this commit serves as a stepping-stone for cross development where its functionality is needed. These improvements will be followed up in future commits.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| #pragma once | ||
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| #include <cassert> | ||
| #include <chrono> | ||
| #include <cstring> | ||
| #include <hdf5.h> | ||
| #include <hdf5_hl.h> | ||
| #include <iostream> | ||
| #include <string> | ||
| #include <vector> | ||
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| /** | ||
| * @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(); | ||
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| // 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); | ||
| } | ||
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| 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); | ||
| } | ||
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| 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."); | ||
| } | ||
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| // Get the dataspace and the number of elements | ||
| hid_t dataspace = H5Dget_space(dataset); | ||
| size_t num_elements = H5Sget_simple_extent_npoints(dataspace); | ||
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| // Allocate a vector to hold the data | ||
| std::vector<T> data_out(num_elements); | ||
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| // 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); | ||
| } | ||
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| // Close the dataset and return the data | ||
| H5Dclose(dataset); | ||
| H5Fclose(file); | ||
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| // 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; | ||
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| return data_out; | ||
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| } catch (...) { | ||
| H5Dclose(dataset); // Ensure dataset is closed in case of failure | ||
| throw; | ||
| } | ||
| } catch (...) { | ||
| H5Fclose(file); // Ensure file is closed in case of failure | ||
| throw; | ||
| } | ||
| } |
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