Create basic h5 filewriter

include/h5/h5write.h

@@ -0,0 +1,80 @@
+#ifndef H5WRITE_H
+#define H5WRITE_H
+
+#include <hdf5.h>
+#include <hdf5_hl.h>
+#include <iostream>
+#include <string>
+#include <vector>
+#include <array>
+#include <cstdlib>
+
+// Function to create a group if it does not exist
+hid_t create_or_open_group(hid_t parent, const std::string &group_name) {
+    hid_t group = H5Gopen(parent, group_name.c_str(), H5P_DEFAULT);
+    if (group < 0) {
+        group = H5Gcreate(parent, group_name.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+        if (group < 0) {
+            std::cerr << "Error: Unable to create group " << group_name << std::endl;
+            std::exit(1);
+        }
+    }
+    return group;
+}
+
+// Function to write a 3D vector dataset to an HDF5 file
+void write_xyzobs_to_h5_file(const std::string &filename,
+                             const std::string &group_path,
+                             const std::string &dataset_name,
+                             const std::vector<std::array<double, 3>> &xyz_data) {
+    hid_t file = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
+    if (file < 0) {
+        file = H5Fcreate(filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+        if (file < 0) {
+            std::cerr << "Error: Unable to create or open file " << filename << std::endl;
+            std::exit(1);
+        }
+    }
+
+    // Create or open the hierarchy: /dials/processing/group_0
+    hid_t dials_group = create_or_open_group(file, "dials");
+    hid_t processing_group = create_or_open_group(dials_group, group_path);
+    hid_t group = create_or_open_group(processing_group, "group_0");
+
+    // Create dataspace for 3D vector data
+    hsize_t dims[2] = {xyz_data.size(), 3};  // Number of elements x 3D coordinates
+    hid_t dataspace = H5Screate_simple(2, dims, NULL);
+
+    // Create dataset
+    hid_t dataset = H5Dcreate(group, dataset_name.c_str(), H5T_NATIVE_DOUBLE, dataspace,
+                              H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+    if (dataset < 0) {
+        std::cerr << "Error: Unable to create dataset " << dataset_name << std::endl;
+        std::exit(1);
+    }
+
+    // Flatten 3D vector data for HDF5 storage
+    std::vector<double> flat_data;
+    for (const auto &xyz : xyz_data) {
+        flat_data.insert(flat_data.end(), xyz.begin(), xyz.end());
+    }
+
+    // Write data to dataset
+    herr_t status = H5Dwrite(dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, flat_data.data());
+    if (status < 0) {
+        std::cerr << "Error: Unable to write data to dataset " << dataset_name << std::endl;
+        std::exit(1);
+    }
+
+    // Cleanup
+    H5Dclose(dataset);
+    H5Sclose(dataspace);
+    H5Gclose(group);
+    H5Gclose(processing_group);
+    H5Gclose(dials_group);
+    H5Fclose(file);
+
+    std::cout << "Successfully wrote 3D vector dataset " << dataset_name << " to " << filename << std::endl;
+}
+
+#endif // H5WRITE_H